pax_global_header00006660000000000000000000000064144035605260014517gustar00rootroot0000000000000052 comment=05328f2e8e759f2367e32a980a516ba2e9cd9af1 ctffind-4.1.14/000077500000000000000000000000001440356052600132235ustar00rootroot00000000000000ctffind-4.1.14/AUTHORS000066400000000000000000000000531440356052600142710ustar00rootroot00000000000000Alexis Rohou Tim Grant Nikolaus Grigorieff ctffind-4.1.14/COPYING000066400000000000000000000030711440356052600142570ustar00rootroot00000000000000The Janelia Research Campus Software License 1.2 Copyright (c) 2018, Howard Hughes Medical Institute, All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 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then \ $(AWK) 'BEGIN { in_include_block=0} {\ if (/core_headers.h/) { \ printf "#include \"src/core/core_headers.h\"" \ } \ else { \ if (/BEGIN_FOR_STAND_ALONE_CTFFIND/) { \ in_include_block=1 \ } \ if (in_include_block==1) { \ if (/END_FOR_STAND_ALONE_CTFFIND/) { \ in_include_block=0 \ } \ } \ if ( ! /BEGIN_FOR_STAND_ALONE_CTFFIND/) { \ if (in_include_block==1) { print $0 } \ } \ } \ }' $(top_srcdir)/src/core/image.cpp > $(top_srcdir)/image_trim.cpp; \ fi # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: ctffind-4.1.14/NEWS000066400000000000000000000000001440356052600137100ustar00rootroot00000000000000ctffind-4.1.14/README000066400000000000000000000023531440356052600141060ustar00rootroot00000000000000If possible, use the binary executables available from http://grigoriefflab.janelia.org/ctf. For questions or bug reports, please use our online forum: http://grigoriefflab.janelia.org/ctf/forum If you want to build ctffind from source, see below. 1. Check dependencies There are two dependencies: wxWidgets >= 3.0 and either FFTW or Intel's Math Kernel Library (MKL) 1.1 wxWidgets To check that you have wxWidgets installed, do: which wx-config To check you have the correct version of wxWidgets, do: wx-config --version If you have several versions of wxWidgets installed, you may have to do e.g.: wx-config-3.0 --version or: /path/to/wx-config --version and add the following flag to your configure line: --with-wx-config=/path/to/wx-config-3.0 1.2 Intel MKL If it is available on your system, the configure script should detect Intel's MKL and ensure that the program will be linked against it. This is preferred as it gives a significant performance boost. 1.3 FFTW If the MKL is not available, you need to ensure FFTW is installed. 2. 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ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` case "$ALPHA_CPU_TYPE" in "EV4 (21064)") UNAME_MACHINE="alpha" ;; "EV4.5 (21064)") UNAME_MACHINE="alpha" ;; "LCA4 (21066/21068)") UNAME_MACHINE="alpha" ;; "EV5 (21164)") UNAME_MACHINE="alphaev5" ;; "EV5.6 (21164A)") UNAME_MACHINE="alphaev56" ;; "EV5.6 (21164PC)") UNAME_MACHINE="alphapca56" ;; "EV5.7 (21164PC)") UNAME_MACHINE="alphapca57" ;; "EV6 (21264)") UNAME_MACHINE="alphaev6" ;; "EV6.7 (21264A)") UNAME_MACHINE="alphaev67" ;; "EV6.8CB (21264C)") UNAME_MACHINE="alphaev68" ;; "EV6.8AL (21264B)") UNAME_MACHINE="alphaev68" ;; "EV6.8CX (21264D)") UNAME_MACHINE="alphaev68" ;; "EV6.9A (21264/EV69A)") UNAME_MACHINE="alphaev69" ;; "EV7 (21364)") UNAME_MACHINE="alphaev7" ;; "EV7.9 (21364A)") UNAME_MACHINE="alphaev79" ;; esac # A Pn.n version is a patched version. # A Vn.n version is a released version. # A Tn.n version is a released field test version. # A Xn.n version is an unreleased experimental baselevel. # 1.2 uses "1.2" for uname -r. echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` # Reset EXIT trap before exiting to avoid spurious non-zero exit code. exitcode=$? trap '' 0 exit $exitcode ;; Alpha\ *:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # Should we change UNAME_MACHINE based on the output of uname instead # of the specific Alpha model? echo alpha-pc-interix exit ;; 21064:Windows_NT:50:3) echo alpha-dec-winnt3.5 exit ;; Amiga*:UNIX_System_V:4.0:*) echo m68k-unknown-sysv4 exit ;; *:[Aa]miga[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-amigaos exit ;; *:[Mm]orph[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-morphos exit ;; *:OS/390:*:*) echo i370-ibm-openedition exit ;; *:z/VM:*:*) echo s390-ibm-zvmoe exit ;; *:OS400:*:*) echo powerpc-ibm-os400 exit ;; arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) echo arm-acorn-riscix${UNAME_RELEASE} exit ;; arm*:riscos:*:*|arm*:RISCOS:*:*) echo arm-unknown-riscos exit ;; SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) echo hppa1.1-hitachi-hiuxmpp exit ;; Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. if test "`(/bin/universe) 2>/dev/null`" = att ; then echo pyramid-pyramid-sysv3 else echo pyramid-pyramid-bsd fi exit ;; NILE*:*:*:dcosx) echo pyramid-pyramid-svr4 exit ;; DRS?6000:unix:4.0:6*) echo sparc-icl-nx6 exit ;; DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; s390x:SunOS:*:*) echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) echo i386-pc-auroraux${UNAME_RELEASE} exit ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) eval $set_cc_for_build SUN_ARCH="i386" # If there is a compiler, see if it is configured for 64-bit objects. # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. # This test works for both compilers. if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then SUN_ARCH="x86_64" fi fi echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize # SunOS6. Hard to guess exactly what SunOS6 will be like, but # it's likely to be more like Solaris than SunOS4. echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:*:*) case "`/usr/bin/arch -k`" in Series*|S4*) UNAME_RELEASE=`uname -v` ;; esac # Japanese Language versions have a version number like `4.1.3-JL'. echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` exit ;; sun3*:SunOS:*:*) echo m68k-sun-sunos${UNAME_RELEASE} exit ;; sun*:*:4.2BSD:*) UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 case "`/bin/arch`" in sun3) echo m68k-sun-sunos${UNAME_RELEASE} ;; sun4) echo sparc-sun-sunos${UNAME_RELEASE} ;; esac exit ;; aushp:SunOS:*:*) echo sparc-auspex-sunos${UNAME_RELEASE} exit ;; # The situation for MiNT is a little confusing. The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor # > m68000). The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit ;; mips:*:*:UMIPS | mips:*:*:RISCos) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && SYSTEM_NAME=`$dummy $dummyarg` && { echo "$SYSTEM_NAME"; exit; } echo mips-mips-riscos${UNAME_RELEASE} exit ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` then echo "$SYSTEM_NAME" else echo rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit ;; *:AIX:*:[4567]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${IBM_ARCH}-ibm-aix${IBM_REV} exit ;; *:AIX:*:*) echo rs6000-ibm-aix exit ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 esac ;; esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | grep -q __LP64__ then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit ;; 3050*:HI-UX:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } echo unknown-hitachi-hiuxwe2 exit ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; *:UNICOS/mp:*:*) echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) UNAME_PROCESSOR=`/usr/bin/uname -p` case ${UNAME_PROCESSOR} in amd64) echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; *) echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; esac exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; *:MINGW64*:*) echo ${UNAME_MACHINE}-pc-mingw64 exit ;; *:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; i*:MSYS*:*) echo ${UNAME_MACHINE}-pc-msys exit ;; i*:windows32*:*) # uname -m includes "-pc" on this system. echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; *:Interix*:*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; authenticamd | genuineintel | EM64T) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) echo ia64-unknown-interix${UNAME_RELEASE} exit ;; esac ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; 8664:Windows_NT:*) echo x86_64-pc-mks exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. 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EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep -q ld.so.1 if test "$?" = 0 ; then LIBC="gnulibc1" ; fi echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; arc:Linux:*:* | arceb:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then echo ${UNAME_MACHINE}-unknown-linux-${LIBC} else if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_PCS_VFP then echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabi else echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabihf fi fi exit ;; avr32*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; cris:Linux:*:*) echo ${UNAME_MACHINE}-axis-linux-${LIBC} exit ;; crisv32:Linux:*:*) echo ${UNAME_MACHINE}-axis-linux-${LIBC} exit ;; 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tile*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; vax:Linux:*:*) echo ${UNAME_MACHINE}-dec-linux-${LIBC} exit ;; x86_64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; xtensa*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. echo i386-sequent-sysv4 exit ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} exit ;; i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. echo ${UNAME_MACHINE}-pc-os2-emx exit ;; i*86:XTS-300:*:STOP) echo ${UNAME_MACHINE}-unknown-stop exit ;; i*86:atheos:*:*) echo ${UNAME_MACHINE}-unknown-atheos exit ;; i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) echo ${UNAME_MACHINE}-pc-msdosdjgpp exit ;; i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} else echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} fi exit ;; i*86:*:5:[678]*) # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} exit ;; i*86:*:3.2:*) if test -f /usr/options/cb.name; then UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ && UNAME_MACHINE=i586 (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ && UNAME_MACHINE=i686 (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ && UNAME_MACHINE=i686 echo ${UNAME_MACHINE}-pc-sco$UNAME_REL else echo ${UNAME_MACHINE}-pc-sysv32 fi exit ;; pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about # the processor, so we play safe by assuming i586. # Note: whatever this is, it MUST be the same as what config.sub # prints for the "djgpp" host, or else GDB configury will decide that # this is a cross-build. echo i586-pc-msdosdjgpp exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 exit ;; paragon:*:*:*) echo i860-intel-osf1 exit ;; i860:*:4.*:*) # i860-SVR4 if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 else # Add other i860-SVR4 vendors below as they are discovered. echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 fi exit ;; mini*:CTIX:SYS*5:*) # "miniframe" echo m68010-convergent-sysv exit ;; mc68k:UNIX:SYSTEM5:3.51m) echo m68k-convergent-sysv exit ;; M680?0:D-NIX:5.3:*) echo m68k-diab-dnix exit ;; M68*:*:R3V[5678]*:*) test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) OS_REL='' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; NCR*:*:4.2:* | MPRAS*:*:4.2:*) OS_REL='.3' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit ;; mc68030:UNIX_System_V:4.*:*) echo m68k-atari-sysv4 exit ;; TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; BePC:Haiku:*:*) # Haiku running on Intel PC compatible. echo i586-pc-haiku exit ;; x86_64:Haiku:*:*) echo x86_64-unknown-haiku exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit ;; SX-6:SUPER-UX:*:*) echo sx6-nec-superux${UNAME_RELEASE} exit ;; SX-7:SUPER-UX:*:*) echo sx7-nec-superux${UNAME_RELEASE} exit ;; SX-8:SUPER-UX:*:*) echo sx8-nec-superux${UNAME_RELEASE} exit ;; SX-8R:SUPER-UX:*:*) echo sx8r-nec-superux${UNAME_RELEASE} exit ;; Power*:Rhapsody:*:*) echo powerpc-apple-rhapsody${UNAME_RELEASE} exit ;; *:Rhapsody:*:*) echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} exit ;; *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown eval $set_cc_for_build if test "$UNAME_PROCESSOR" = unknown ; then UNAME_PROCESSOR=powerpc fi if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then case $UNAME_PROCESSOR in i386) UNAME_PROCESSOR=x86_64 ;; powerpc) UNAME_PROCESSOR=powerpc64 ;; esac fi fi echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} exit ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) UNAME_PROCESSOR=`uname -p` if test "$UNAME_PROCESSOR" = "x86"; then UNAME_PROCESSOR=i386 UNAME_MACHINE=pc fi echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} exit ;; *:QNX:*:4*) echo i386-pc-qnx exit ;; NEO-?:NONSTOP_KERNEL:*:*) echo neo-tandem-nsk${UNAME_RELEASE} exit ;; NSE-*:NONSTOP_KERNEL:*:*) echo nse-tandem-nsk${UNAME_RELEASE} exit ;; NSR-?:NONSTOP_KERNEL:*:*) echo nsr-tandem-nsk${UNAME_RELEASE} exit ;; *:NonStop-UX:*:*) echo mips-compaq-nonstopux exit ;; BS2000:POSIX*:*:*) echo bs2000-siemens-sysv exit ;; DS/*:UNIX_System_V:*:*) echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} exit ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. if test "$cputype" = "386"; then UNAME_MACHINE=i386 else UNAME_MACHINE="$cputype" fi echo ${UNAME_MACHINE}-unknown-plan9 exit ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit ;; *:ITS:*:*) echo pdp10-unknown-its exit ;; SEI:*:*:SEIUX) echo mips-sei-seiux${UNAME_RELEASE} exit ;; *:DragonFly:*:*) echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` case "${UNAME_MACHINE}" in A*) echo alpha-dec-vms ; exit ;; I*) echo ia64-dec-vms ; exit ;; V*) echo vax-dec-vms ; exit ;; esac ;; *:XENIX:*:SysV) echo i386-pc-xenix exit ;; i*86:skyos:*:*) echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' exit ;; i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; i*86:AROS:*:*) echo ${UNAME_MACHINE}-pc-aros exit ;; x86_64:VMkernel:*:*) echo ${UNAME_MACHINE}-unknown-esx exit ;; esac eval $set_cc_for_build cat >$dummy.c < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, I don't know.... */ printf ("mips-sony-bsd\n"); exit (0); #else #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 "4" #else "" #endif ); exit (0); #endif #endif #if defined (__arm) && defined (__acorn) && defined (__unix) printf ("arm-acorn-riscix\n"); exit (0); #endif #if defined (hp300) && !defined (hpux) printf ("m68k-hp-bsd\n"); exit (0); #endif #if defined (NeXT) #if !defined (__ARCHITECTURE__) #define __ARCHITECTURE__ "m68k" #endif int version; version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; if (version < 4) printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); else printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); exit (0); #endif #if defined (MULTIMAX) || defined (n16) #if defined (UMAXV) printf ("ns32k-encore-sysv\n"); exit (0); #else #if defined (CMU) printf ("ns32k-encore-mach\n"); exit (0); #else printf ("ns32k-encore-bsd\n"); exit (0); #endif #endif #endif #if defined (__386BSD__) printf ("i386-pc-bsd\n"); exit (0); #endif #if defined (sequent) #if defined (i386) printf ("i386-sequent-dynix\n"); exit (0); #endif #if defined (ns32000) printf ("ns32k-sequent-dynix\n"); exit (0); #endif #endif #if defined (_SEQUENT_) struct utsname un; uname(&un); if (strncmp(un.version, "V2", 2) == 0) { printf ("i386-sequent-ptx2\n"); exit (0); } if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ printf ("i386-sequent-ptx1\n"); exit (0); } printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) # if !defined (ultrix) # include # if defined (BSD) # if BSD == 43 printf ("vax-dec-bsd4.3\n"); exit (0); # else # if BSD == 199006 printf ("vax-dec-bsd4.3reno\n"); exit (0); # else printf ("vax-dec-bsd\n"); exit (0); # endif # endif # else printf ("vax-dec-bsd\n"); exit (0); # endif # else printf ("vax-dec-ultrix\n"); exit (0); # endif #endif #if defined (alliant) && defined (i860) printf ("i860-alliant-bsd\n"); exit (0); #endif exit (1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } # Apollos put the system type in the environment. test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } # Convex versions that predate uname can use getsysinfo(1) if [ -x /usr/convex/getsysinfo ] then case `getsysinfo -f cpu_type` in c1*) echo c1-convex-bsd exit ;; c2*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; c34*) echo c34-convex-bsd exit ;; c38*) echo c38-convex-bsd exit ;; c4*) echo c4-convex-bsd exit ;; esac fi cat >&2 < in order to provide the needed information to handle your system. config.guess timestamp = $timestamp uname -m = `(uname -m) 2>/dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` /bin/uname -X = `(/bin/uname -X) 2>/dev/null` hostinfo = `(hostinfo) 2>/dev/null` /bin/universe = `(/bin/universe) 2>/dev/null` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` /bin/arch = `(/bin/arch) 2>/dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` UNAME_MACHINE = ${UNAME_MACHINE} UNAME_RELEASE = ${UNAME_RELEASE} UNAME_SYSTEM = ${UNAME_SYSTEM} UNAME_VERSION = ${UNAME_VERSION} EOF exit 1 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: ctffind-4.1.14/config.sub000077500000000000000000001053151440356052600152130ustar00rootroot00000000000000#! /bin/sh # Configuration validation subroutine script. # Copyright 1992-2013 Free Software Foundation, Inc. timestamp='2013-04-24' # This file 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 3 of the License, or # (at your option) any later version. # # This program 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 program; if not, see . # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that # program. This Exception is an additional permission under section 7 # of the GNU General Public License, version 3 ("GPLv3"). # Please send patches with a ChangeLog entry to config-patches@gnu.org. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # You can get the latest version of this script from: # http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright 1992-2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \ linux-musl* | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \ knetbsd*-gnu* | netbsd*-gnu* | \ kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; android-linux) os=-linux-android basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. We also ### recognize some manufacturers as not being operating systems, so we ### can provide default operating systems below. case $os in -sun*os*) # Prevent following clause from handling this invalid input. ;; -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ -apple | -axis | -knuth | -cray | -microblaze*) os= basic_machine=$1 ;; -bluegene*) os=-cnk ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 ;; -scout) ;; -wrs) os=-vxworks basic_machine=$1 ;; -chorusos*) os=-chorusos basic_machine=$1 ;; -chorusrdb) os=-chorusrdb basic_machine=$1 ;; -hiux*) os=-hiuxwe2 ;; -sco6) os=-sco5v6 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5) os=-sco3.2v5 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5v6*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*178) os=-lynxos178 ;; -lynx*5) os=-lynxos5 ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | aarch64 | aarch64_be \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ | arc | arceb \ | arm | arm[bl]e | arme[lb] | armv[2-8] | armv[3-8][lb] | armv7[arm] \ | avr | avr32 \ | be32 | be64 \ | bfin \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | epiphany \ | fido | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | hexagon \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ | le32 | le64 \ | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ | maxq | mb | microblaze | microblazeel | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ | mips64r5900 | mips64r5900el \ | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mips64vr5900 | mips64vr5900el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipsr5900 | mipsr5900el \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | moxie \ | mt \ | msp430 \ | nds32 | nds32le | nds32be \ | nios | nios2 | nios2eb | nios2el \ | ns16k | ns32k \ | open8 \ | or1k | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle \ | pyramid \ | rl78 | rx \ | score \ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu \ | tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \ | ubicom32 \ | v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \ | we32k \ | x86 | xc16x | xstormy16 | xtensa \ | z8k | z80) basic_machine=$basic_machine-unknown ;; c54x) basic_machine=tic54x-unknown ;; c55x) basic_machine=tic55x-unknown ;; c6x) basic_machine=tic6x-unknown ;; m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip) basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; ms1) basic_machine=mt-unknown ;; strongarm | thumb | xscale) basic_machine=arm-unknown ;; xgate) basic_machine=$basic_machine-unknown os=-none ;; xscaleeb) basic_machine=armeb-unknown ;; xscaleel) basic_machine=armel-unknown ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ | aarch64-* | aarch64_be-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* | arceb-* \ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ | avr-* | avr32-* \ | be32-* | be64-* \ | bfin-* | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* \ | clipper-* | craynv-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | hexagon-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ | le32-* | le64-* \ | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \ | microblaze-* | microblazeel-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ | mips64r5900-* | mips64r5900el-* \ | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mips64vr5900-* | mips64vr5900el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipsr5900-* | mipsr5900el-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | mt-* \ | msp430-* \ | nds32-* | nds32le-* | nds32be-* \ | nios-* | nios2-* | nios2eb-* | nios2el-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | open8-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \ | pyramid-* \ | rl78-* | romp-* | rs6000-* | rx-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \ | tahoe-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ | tile*-* \ | tron-* \ | ubicom32-* \ | v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \ | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) basic_machine=$basic_machine-unknown ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; abacus) basic_machine=abacus-unknown ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amd64) basic_machine=x86_64-pc ;; amd64-*) basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aros) basic_machine=i386-pc os=-aros ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; blackfin) basic_machine=bfin-unknown os=-linux ;; blackfin-*) basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; bluegene*) basic_machine=powerpc-ibm os=-cnk ;; c54x-*) basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'` ;; c55x-*) basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'` ;; c6x-*) basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'` ;; c90) basic_machine=c90-cray os=-unicos ;; cegcc) basic_machine=arm-unknown os=-cegcc ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | j90) basic_machine=j90-cray os=-unicos ;; craynv) basic_machine=craynv-cray os=-unicosmp ;; cr16 | cr16-*) basic_machine=cr16-unknown os=-elf ;; crds | unos) basic_machine=m68k-crds ;; crisv32 | crisv32-* | etraxfs*) basic_machine=crisv32-axis ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; crx) basic_machine=crx-unknown os=-elf ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; decsystem10* | dec10*) basic_machine=pdp10-dec os=-tops10 ;; decsystem20* | dec20*) basic_machine=pdp10-dec os=-tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; dicos) basic_machine=i686-pc os=-dicos ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; i*86v32) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv32 ;; i*86v4*) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv4 ;; i*86v) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv ;; i*86sol2) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-solaris2 ;; i386mach) basic_machine=i386-mach os=-mach ;; i386-vsta | vsta) basic_machine=i386-unknown os=-vsta ;; iris | iris4d) basic_machine=mips-sgi case $os in -irix*) ;; *) os=-irix4 ;; esac ;; isi68 | isi) basic_machine=m68k-isi os=-sysv ;; m68knommu) basic_machine=m68k-unknown os=-linux ;; m68knommu-*) basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; m88k-omron*) basic_machine=m88k-omron ;; magnum | m3230) basic_machine=mips-mips os=-sysv ;; merlin) basic_machine=ns32k-utek os=-sysv ;; microblaze*) basic_machine=microblaze-xilinx ;; mingw64) basic_machine=x86_64-pc os=-mingw64 ;; mingw32) basic_machine=i386-pc os=-mingw32 ;; mingw32ce) basic_machine=arm-unknown os=-mingw32ce ;; miniframe) basic_machine=m68000-convergent ;; *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) basic_machine=m68k-atari os=-mint ;; mips3*-*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` ;; mips3*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown ;; monitor) basic_machine=m68k-rom68k os=-coff ;; morphos) basic_machine=powerpc-unknown os=-morphos ;; msdos) basic_machine=i386-pc os=-msdos ;; ms1-*) basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'` ;; msys) basic_machine=i386-pc os=-msys ;; mvs) basic_machine=i370-ibm os=-mvs ;; nacl) basic_machine=le32-unknown os=-nacl ;; ncr3000) basic_machine=i486-ncr os=-sysv4 ;; netbsd386) basic_machine=i386-unknown os=-netbsd ;; netwinder) basic_machine=armv4l-rebel os=-linux ;; news | news700 | news800 | news900) basic_machine=m68k-sony os=-newsos ;; news1000) basic_machine=m68030-sony os=-newsos ;; news-3600 | risc-news) basic_machine=mips-sony os=-newsos ;; necv70) basic_machine=v70-nec os=-sysv ;; next | m*-next ) basic_machine=m68k-next case $os in -nextstep* ) ;; -ns2*) os=-nextstep2 ;; *) os=-nextstep3 ;; esac ;; nh3000) basic_machine=m68k-harris os=-cxux ;; nh[45]000) basic_machine=m88k-harris os=-cxux ;; nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; neo-tandem) basic_machine=neo-tandem ;; nse-tandem) basic_machine=nse-tandem ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; openrisc | openrisc-*) basic_machine=or32-unknown ;; os400) basic_machine=powerpc-ibm os=-os400 ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; 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" >&6; } if ${lt_cv_prog_gnu_ld+:} false; then : $as_echo_n "(cached) " >&6 else # I'd rather use --version here, but apparently some GNU lds only accept -v. case `$LD -v 2>&1 &5 $as_echo "$lt_cv_prog_gnu_ld" >&6; } with_gnu_ld=$lt_cv_prog_gnu_ld { $as_echo "$as_me:${as_lineno-$LINENO}: checking for BSD- or MS-compatible name lister (nm)" >&5 $as_echo_n "checking for BSD- or MS-compatible name lister (nm)... " >&6; } if ${lt_cv_path_NM+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$NM"; then # Let the user override the test. lt_cv_path_NM="$NM" else lt_nm_to_check="${ac_tool_prefix}nm" if test -n "$ac_tool_prefix" && test "$build" = "$host"; then lt_nm_to_check="$lt_nm_to_check nm" fi for lt_tmp_nm in $lt_nm_to_check; do lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. tmp_nm="$ac_dir/$lt_tmp_nm" if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then # Check to see if the nm accepts a BSD-compat flag. # Adding the `sed 1q' prevents false positives on HP-UX, which says: # nm: unknown option "B" ignored # Tru64's nm complains that /dev/null is an invalid object file case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in */dev/null* | *'Invalid file or object type'*) lt_cv_path_NM="$tmp_nm -B" break ;; *) case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in */dev/null*) lt_cv_path_NM="$tmp_nm -p" break ;; *) lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but continue # so that we can try to find one that supports BSD flags ;; esac ;; esac fi done IFS="$lt_save_ifs" done : ${lt_cv_path_NM=no} fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_path_NM" >&5 $as_echo "$lt_cv_path_NM" >&6; } if test "$lt_cv_path_NM" != "no"; then NM="$lt_cv_path_NM" else # Didn't find any BSD compatible name lister, look for dumpbin. if test -n "$DUMPBIN"; then : # Let the user override the test. else if test -n "$ac_tool_prefix"; then for ac_prog in dumpbin "link -dump" do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_DUMPBIN+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$DUMPBIN"; then ac_cv_prog_DUMPBIN="$DUMPBIN" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_DUMPBIN="$ac_tool_prefix$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DUMPBIN=$ac_cv_prog_DUMPBIN if test -n "$DUMPBIN"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DUMPBIN" >&5 $as_echo "$DUMPBIN" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$DUMPBIN" && break done fi if test -z "$DUMPBIN"; then ac_ct_DUMPBIN=$DUMPBIN for ac_prog in dumpbin "link -dump" do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_DUMPBIN+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DUMPBIN"; then ac_cv_prog_ac_ct_DUMPBIN="$ac_ct_DUMPBIN" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_DUMPBIN="$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DUMPBIN=$ac_cv_prog_ac_ct_DUMPBIN if test -n "$ac_ct_DUMPBIN"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DUMPBIN" >&5 $as_echo "$ac_ct_DUMPBIN" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$ac_ct_DUMPBIN" && break done if test "x$ac_ct_DUMPBIN" = x; then DUMPBIN=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DUMPBIN=$ac_ct_DUMPBIN fi fi case `$DUMPBIN -symbols /dev/null 2>&1 | sed '1q'` in *COFF*) DUMPBIN="$DUMPBIN -symbols" ;; *) DUMPBIN=: ;; esac fi if test "$DUMPBIN" != ":"; then NM="$DUMPBIN" fi fi test -z "$NM" && NM=nm { $as_echo "$as_me:${as_lineno-$LINENO}: checking the name lister ($NM) interface" >&5 $as_echo_n "checking the name lister ($NM) interface... " >&6; } if ${lt_cv_nm_interface+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:$LINENO: $ac_compile\"" >&5) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&5 (eval echo "\"\$as_me:$LINENO: $NM \\\"conftest.$ac_objext\\\"\"" >&5) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&5 (eval echo "\"\$as_me:$LINENO: output\"" >&5) cat conftest.out >&5 if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest* fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_nm_interface" >&5 $as_echo "$lt_cv_nm_interface" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5 $as_echo_n "checking whether ln -s works... 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Even if it were fixed, the result of this # check would be larger than it should be. lt_cv_sys_max_cmd_len=12288; # 12K is about right ;; gnu*) # Under GNU Hurd, this test is not required because there is # no limit to the length of command line arguments. # Libtool will interpret -1 as no limit whatsoever lt_cv_sys_max_cmd_len=-1; ;; cygwin* | mingw* | cegcc*) # On Win9x/ME, this test blows up -- it succeeds, but takes # about 5 minutes as the teststring grows exponentially. # Worse, since 9x/ME are not pre-emptively multitasking, # you end up with a "frozen" computer, even though with patience # the test eventually succeeds (with a max line length of 256k). # Instead, let's just punt: use the minimum linelength reported by # all of the supported platforms: 8192 (on NT/2K/XP). lt_cv_sys_max_cmd_len=8192; ;; mint*) # On MiNT this can take a long time and run out of memory. lt_cv_sys_max_cmd_len=8192; ;; amigaos*) # On AmigaOS with pdksh, this test takes hours, literally. # So we just punt and use a minimum line length of 8192. lt_cv_sys_max_cmd_len=8192; ;; netbsd* | freebsd* | openbsd* | darwin* | dragonfly*) # This has been around since 386BSD, at least. Likely further. if test -x /sbin/sysctl; then lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` elif test -x /usr/sbin/sysctl; then lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` else lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs fi # And add a safety zone lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` ;; interix*) # We know the value 262144 and hardcode it with a safety zone (like BSD) lt_cv_sys_max_cmd_len=196608 ;; os2*) # The test takes a long time on OS/2. lt_cv_sys_max_cmd_len=8192 ;; osf*) # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not # nice to cause kernel panics so lets avoid the loop below. # First set a reasonable default. lt_cv_sys_max_cmd_len=16384 # if test -x /sbin/sysconfig; then case `/sbin/sysconfig -q proc exec_disable_arg_limit` in *1*) lt_cv_sys_max_cmd_len=-1 ;; esac fi ;; sco3.2v5*) lt_cv_sys_max_cmd_len=102400 ;; sysv5* | sco5v6* | sysv4.2uw2*) kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` if test -n "$kargmax"; then lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'` else lt_cv_sys_max_cmd_len=32768 fi ;; *) lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` if test -n "$lt_cv_sys_max_cmd_len"; then lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` else # Make teststring a little bigger before we do anything with it. # a 1K string should be a reasonable start. for i in 1 2 3 4 5 6 7 8 ; do teststring=$teststring$teststring done SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} # If test is not a shell built-in, we'll probably end up computing a # maximum length that is only half of the actual maximum length, but # we can't tell. while { test "X"`env echo "$teststring$teststring" 2>/dev/null` \ = "X$teststring$teststring"; } >/dev/null 2>&1 && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done # Only check the string length outside the loop. lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` teststring= # Add a significant safety factor because C++ compilers can tack on # massive amounts of additional arguments before passing them to the # linker. It appears as though 1/2 is a usable value. lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` fi ;; esac fi if test -n $lt_cv_sys_max_cmd_len ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sys_max_cmd_len" >&5 $as_echo "$lt_cv_sys_max_cmd_len" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: none" >&5 $as_echo "none" >&6; } fi max_cmd_len=$lt_cv_sys_max_cmd_len : ${CP="cp -f"} : ${MV="mv -f"} : ${RM="rm -f"} { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands some XSI constructs" >&5 $as_echo_n "checking whether the shell understands some XSI constructs... 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" >&6; } if ${lt_cv_to_host_file_cmd+:} false; then : $as_echo_n "(cached) " >&6 else case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_w32 ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_cygwin_to_w32 ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_w32 ;; esac ;; *-*-cygwin* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_cygwin ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_noop ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_cygwin ;; esac ;; * ) # unhandled hosts (and "normal" native builds) lt_cv_to_host_file_cmd=func_convert_file_noop ;; esac fi to_host_file_cmd=$lt_cv_to_host_file_cmd { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_to_host_file_cmd" >&5 $as_echo "$lt_cv_to_host_file_cmd" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to convert $build file names to toolchain format" >&5 $as_echo_n "checking how to convert $build file names to toolchain format... 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" >&6; } if ${lt_cv_ld_reload_flag+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_ld_reload_flag='-r' fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_reload_flag" >&5 $as_echo "$lt_cv_ld_reload_flag" >&6; } reload_flag=$lt_cv_ld_reload_flag case $reload_flag in "" | " "*) ;; *) reload_flag=" $reload_flag" ;; esac reload_cmds='$LD$reload_flag -o $output$reload_objs' case $host_os in cygwin* | mingw* | pw32* | cegcc*) if test "$GCC" != yes; then reload_cmds=false fi ;; darwin*) if test "$GCC" = yes; then reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs' else reload_cmds='$LD$reload_flag -o $output$reload_objs' fi ;; esac if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args. set dummy ${ac_tool_prefix}objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OBJDUMP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OBJDUMP"; then ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OBJDUMP=$ac_cv_prog_OBJDUMP if test -n "$OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OBJDUMP" >&5 $as_echo "$OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OBJDUMP"; then ac_ct_OBJDUMP=$OBJDUMP # Extract the first word of "objdump", so it can be a program name with args. set dummy objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OBJDUMP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OBJDUMP"; then ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OBJDUMP="objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP if test -n "$ac_ct_OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5 $as_echo "$ac_ct_OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OBJDUMP" = x; then OBJDUMP="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OBJDUMP=$ac_ct_OBJDUMP fi else OBJDUMP="$ac_cv_prog_OBJDUMP" fi test -z "$OBJDUMP" && OBJDUMP=objdump { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5 $as_echo_n "checking how to recognize dependent libraries... " >&6; } if ${lt_cv_deplibs_check_method+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_deplibs_check_method='unknown' # Need to set the preceding variable on all platforms that support # interlibrary dependencies. # 'none' -- dependencies not supported. # `unknown' -- same as none, but documents that we really don't know. # 'pass_all' -- all dependencies passed with no checks. # 'test_compile' -- check by making test program. # 'file_magic [[regex]]' -- check by looking for files in library path # which responds to the $file_magic_cmd with a given extended regex. # If you have `file' or equivalent on your system and you're not sure # whether `pass_all' will *always* work, you probably want this one. case $host_os in aix[4-9]*) lt_cv_deplibs_check_method=pass_all ;; beos*) lt_cv_deplibs_check_method=pass_all ;; bsdi[45]*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)' lt_cv_file_magic_cmd='/usr/bin/file -L' lt_cv_file_magic_test_file=/shlib/libc.so ;; cygwin*) # func_win32_libid is a shell function defined in ltmain.sh lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' ;; mingw* | pw32*) # Base MSYS/MinGW do not provide the 'file' command needed by # func_win32_libid shell function, so use a weaker test based on 'objdump', # unless we find 'file', for example because we are cross-compiling. # func_win32_libid assumes BSD nm, so disallow it if using MS dumpbin. if ( test "$lt_cv_nm_interface" = "BSD nm" && file / ) >/dev/null 2>&1; then lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' else # Keep this pattern in sync with the one in func_win32_libid. lt_cv_deplibs_check_method='file_magic file format (pei*-i386(.*architecture: i386)?|pe-arm-wince|pe-x86-64)' lt_cv_file_magic_cmd='$OBJDUMP -f' fi ;; cegcc*) # use the weaker test based on 'objdump'. See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; haiku*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF[ -][0-9][0-9])(-bit)?( [LM]SB)? shared object( file)?[, -]* PA-RISC [0-9]\.[0-9]' lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9]\.[0-9]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[3-9]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5 $as_echo "$lt_cv_deplibs_check_method" >&6; } file_magic_glob= want_nocaseglob=no if test "$build" = "$host"; then case $host_os in mingw* | pw32*) if ( shopt | grep nocaseglob ) >/dev/null 2>&1; then want_nocaseglob=yes else file_magic_glob=`echo aAbBcCdDeEfFgGhHiIjJkKlLmMnNoOpPqQrRsStTuUvVwWxXyYzZ | $SED -e "s/\(..\)/s\/[\1]\/[\1]\/g;/g"` fi ;; esac fi file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dlltool", so it can be a program name with args. set dummy ${ac_tool_prefix}dlltool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_DLLTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$DLLTOOL"; then ac_cv_prog_DLLTOOL="$DLLTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_DLLTOOL="${ac_tool_prefix}dlltool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DLLTOOL=$ac_cv_prog_DLLTOOL if test -n "$DLLTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DLLTOOL" >&5 $as_echo "$DLLTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DLLTOOL"; then ac_ct_DLLTOOL=$DLLTOOL # Extract the first word of "dlltool", so it can be a program name with args. set dummy dlltool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_DLLTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DLLTOOL"; then ac_cv_prog_ac_ct_DLLTOOL="$ac_ct_DLLTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_DLLTOOL="dlltool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DLLTOOL=$ac_cv_prog_ac_ct_DLLTOOL if test -n "$ac_ct_DLLTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DLLTOOL" >&5 $as_echo "$ac_ct_DLLTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DLLTOOL" = x; then DLLTOOL="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DLLTOOL=$ac_ct_DLLTOOL fi else DLLTOOL="$ac_cv_prog_DLLTOOL" fi test -z "$DLLTOOL" && DLLTOOL=dlltool { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to associate runtime and link libraries" >&5 $as_echo_n "checking how to associate runtime and link libraries... " >&6; } if ${lt_cv_sharedlib_from_linklib_cmd+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_sharedlib_from_linklib_cmd='unknown' case $host_os in cygwin* | mingw* | pw32* | cegcc*) # two different shell functions defined in ltmain.sh # decide which to use based on capabilities of $DLLTOOL case `$DLLTOOL --help 2>&1` in *--identify-strict*) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib ;; *) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib_fallback ;; esac ;; *) # fallback: assume linklib IS sharedlib lt_cv_sharedlib_from_linklib_cmd="$ECHO" ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sharedlib_from_linklib_cmd" >&5 $as_echo "$lt_cv_sharedlib_from_linklib_cmd" >&6; } sharedlib_from_linklib_cmd=$lt_cv_sharedlib_from_linklib_cmd test -z "$sharedlib_from_linklib_cmd" && sharedlib_from_linklib_cmd=$ECHO if test -n "$ac_tool_prefix"; then for ac_prog in ar do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_AR+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$AR"; then ac_cv_prog_AR="$AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_AR="$ac_tool_prefix$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5 $as_echo "$AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$AR" && break done fi if test -z "$AR"; then ac_ct_AR=$AR for ac_prog in ar do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_AR+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_AR"; then ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_AR="$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5 $as_echo "$ac_ct_AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$ac_ct_AR" && break done if test "x$ac_ct_AR" = x; then AR="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac AR=$ac_ct_AR fi fi : ${AR=ar} : ${AR_FLAGS=cru} { $as_echo "$as_me:${as_lineno-$LINENO}: checking for archiver @FILE support" >&5 $as_echo_n "checking for archiver @FILE support... " >&6; } if ${lt_cv_ar_at_file+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_ar_at_file=no cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : echo conftest.$ac_objext > conftest.lst lt_ar_try='$AR $AR_FLAGS libconftest.a @conftest.lst >&5' { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$lt_ar_try\""; } >&5 (eval $lt_ar_try) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } if test "$ac_status" -eq 0; then # Ensure the archiver fails upon bogus file names. rm -f conftest.$ac_objext libconftest.a { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$lt_ar_try\""; } >&5 (eval $lt_ar_try) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } if test "$ac_status" -ne 0; then lt_cv_ar_at_file=@ fi fi rm -f conftest.* libconftest.a fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ar_at_file" >&5 $as_echo "$lt_cv_ar_at_file" >&6; } if test "x$lt_cv_ar_at_file" = xno; then archiver_list_spec= else archiver_list_spec=$lt_cv_ar_at_file fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_STRIP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_STRIP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_STRIP="strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_STRIP" = x; then STRIP=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac STRIP=$ac_ct_STRIP fi else STRIP="$ac_cv_prog_STRIP" fi test -z "$STRIP" && STRIP=: if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_RANLIB+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 $as_echo "$RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_RANLIB+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_RANLIB="ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 $as_echo "$ac_ct_RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi test -z "$RANLIB" && RANLIB=: # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$tool_oldlib" ;; *) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$tool_oldlib" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$tool_oldlib" fi case $host_os in darwin*) lock_old_archive_extraction=yes ;; *) lock_old_archive_extraction=no ;; esac # If no C compiler was specified, use CC. LTCC=${LTCC-"$CC"} # If no C compiler flags were specified, use CFLAGS. LTCFLAGS=${LTCFLAGS-"$CFLAGS"} # Allow CC to be a program name with arguments. compiler=$CC # Check for command to grab the raw symbol name followed by C symbol from nm. { $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5 $as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } if ${lt_cv_sys_global_symbol_pipe+:} false; then : $as_echo_n "(cached) " >&6 else # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[BCDEGRST]' # Regexp to match symbols that can be accessed directly from C. sympat='\([_A-Za-z][_A-Za-z0-9]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[ABCDGISTW]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris*) symcode='[BDRT]' ;; sco3.2v5*) symcode='[DT]' ;; sysv4.2uw2*) symcode='[DT]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[ABDT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\)[ ]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\)[ ]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK '"\ " {last_section=section; section=\$ 3};"\ " /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi lt_cv_sys_global_symbol_pipe="$lt_cv_sys_global_symbol_pipe | sed '/ __gnu_lto/d'" # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then # Now try to grab the symbols. nlist=conftest.nm if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| "$lt_cv_sys_global_symbol_pipe" \> $nlist\""; } >&5 (eval $NM conftest.$ac_objext \| "$lt_cv_sys_global_symbol_pipe" \> $nlist) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext /* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests. */ #if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE) /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */ # define LT_DLSYM_CONST #elif defined(__osf__) /* This system does not cope well with relocations in const data. */ # define LT_DLSYM_CONST #else # define LT_DLSYM_CONST const #endif #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ LT_DLSYM_CONST struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_globsym_save_LIBS=$LIBS lt_globsym_save_CFLAGS=$CFLAGS LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS=$lt_globsym_save_LIBS CFLAGS=$lt_globsym_save_CFLAGS else echo "cannot find nm_test_func in $nlist" >&5 fi else echo "cannot find nm_test_var in $nlist" >&5 fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 fi else echo "$progname: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done fi if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5 $as_echo "failed" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5 $as_echo "ok" >&6; } fi # Response file support. if test "$lt_cv_nm_interface" = "MS dumpbin"; then nm_file_list_spec='@' elif $NM --help 2>/dev/null | grep '[@]FILE' >/dev/null; then nm_file_list_spec='@' fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sysroot" >&5 $as_echo_n "checking for sysroot... " >&6; } # Check whether --with-sysroot was given. if test "${with_sysroot+set}" = set; then : withval=$with_sysroot; else with_sysroot=no fi lt_sysroot= case ${with_sysroot} in #( yes) if test "$GCC" = yes; then lt_sysroot=`$CC --print-sysroot 2>/dev/null` fi ;; #( /*) lt_sysroot=`echo "$with_sysroot" | sed -e "$sed_quote_subst"` ;; #( no|'') ;; #( *) { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${with_sysroot}" >&5 $as_echo "${with_sysroot}" >&6; } as_fn_error $? "The sysroot must be an absolute path." "$LINENO" 5 ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${lt_sysroot:-no}" >&5 $as_echo "${lt_sysroot:-no}" >&6; } # Check whether --enable-libtool-lock was given. if test "${enable_libtool_lock+set}" = set; then : enableval=$enable_libtool_lock; fi test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes # Some flags need to be propagated to the compiler or linker for good # libtool support. case $host in ia64-*-hpux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.$ac_objext` in *ELF-32*) HPUX_IA64_MODE="32" ;; *ELF-64*) HPUX_IA64_MODE="64" ;; esac fi rm -rf conftest* ;; *-*-irix6*) # Find out which ABI we are using. echo '#line '$LINENO' "configure"' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then if test "$lt_cv_prog_gnu_ld" = yes; then case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -melf32bsmip" ;; *N32*) LD="${LD-ld} -melf32bmipn32" ;; *64-bit*) LD="${LD-ld} -melf64bmip" ;; esac else case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -32" ;; *N32*) LD="${LD-ld} -n32" ;; *64-bit*) LD="${LD-ld} -64" ;; esac fi fi rm -rf conftest* ;; x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ s390*-*linux*|s390*-*tpf*|sparc*-*linux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *32-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_i386_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_i386" ;; ppc64-*linux*|powerpc64-*linux*) LD="${LD-ld} -m elf32ppclinux" ;; s390x-*linux*) LD="${LD-ld} -m elf_s390" ;; sparc64-*linux*) LD="${LD-ld} -m elf32_sparc" ;; esac ;; *64-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_x86_64_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_x86_64" ;; ppc*-*linux*|powerpc*-*linux*) LD="${LD-ld} -m elf64ppc" ;; s390*-*linux*|s390*-*tpf*) LD="${LD-ld} -m elf64_s390" ;; sparc*-*linux*) LD="${LD-ld} -m elf64_sparc" ;; esac ;; esac fi rm -rf conftest* ;; *-*-sco3.2v5*) # On SCO OpenServer 5, we need -belf to get full-featured binaries. SAVE_CFLAGS="$CFLAGS" CFLAGS="$CFLAGS -belf" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5 $as_echo_n "checking whether the C compiler needs -belf... " >&6; } if ${lt_cv_cc_needs_belf+:} false; then : $as_echo_n "(cached) " >&6 else ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_cc_needs_belf=yes else lt_cv_cc_needs_belf=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5 $as_echo "$lt_cv_cc_needs_belf" >&6; } if test x"$lt_cv_cc_needs_belf" != x"yes"; then # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf CFLAGS="$SAVE_CFLAGS" fi ;; *-*solaris*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *64-bit*) case $lt_cv_prog_gnu_ld in yes*) case $host in i?86-*-solaris*) LD="${LD-ld} -m elf_x86_64" ;; sparc*-*-solaris*) LD="${LD-ld} -m elf64_sparc" ;; esac # GNU ld 2.21 introduced _sol2 emulations. Use them if available. if ${LD-ld} -V | grep _sol2 >/dev/null 2>&1; then LD="${LD-ld}_sol2" fi ;; *) if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then LD="${LD-ld} -64" fi ;; esac ;; esac fi rm -rf conftest* ;; esac need_locks="$enable_libtool_lock" if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}mt", so it can be a program name with args. set dummy ${ac_tool_prefix}mt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_MANIFEST_TOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$MANIFEST_TOOL"; then ac_cv_prog_MANIFEST_TOOL="$MANIFEST_TOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_MANIFEST_TOOL="${ac_tool_prefix}mt" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi MANIFEST_TOOL=$ac_cv_prog_MANIFEST_TOOL if test -n "$MANIFEST_TOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MANIFEST_TOOL" >&5 $as_echo "$MANIFEST_TOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_MANIFEST_TOOL"; then ac_ct_MANIFEST_TOOL=$MANIFEST_TOOL # Extract the first word of "mt", so it can be a program name with args. set dummy mt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_MANIFEST_TOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_MANIFEST_TOOL"; then ac_cv_prog_ac_ct_MANIFEST_TOOL="$ac_ct_MANIFEST_TOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_MANIFEST_TOOL="mt" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_MANIFEST_TOOL=$ac_cv_prog_ac_ct_MANIFEST_TOOL if test -n "$ac_ct_MANIFEST_TOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_MANIFEST_TOOL" >&5 $as_echo "$ac_ct_MANIFEST_TOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_MANIFEST_TOOL" = x; then MANIFEST_TOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac MANIFEST_TOOL=$ac_ct_MANIFEST_TOOL fi else MANIFEST_TOOL="$ac_cv_prog_MANIFEST_TOOL" fi test -z "$MANIFEST_TOOL" && MANIFEST_TOOL=mt { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $MANIFEST_TOOL is a manifest tool" >&5 $as_echo_n "checking if $MANIFEST_TOOL is a manifest tool... " >&6; } if ${lt_cv_path_mainfest_tool+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_path_mainfest_tool=no echo "$as_me:$LINENO: $MANIFEST_TOOL '-?'" >&5 $MANIFEST_TOOL '-?' 2>conftest.err > conftest.out cat conftest.err >&5 if $GREP 'Manifest Tool' conftest.out > /dev/null; then lt_cv_path_mainfest_tool=yes fi rm -f conftest* fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_path_mainfest_tool" >&5 $as_echo "$lt_cv_path_mainfest_tool" >&6; } if test "x$lt_cv_path_mainfest_tool" != xyes; then MANIFEST_TOOL=: fi case $host_os in rhapsody* | darwin*) if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_DSYMUTIL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$DSYMUTIL"; then ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DSYMUTIL=$ac_cv_prog_DSYMUTIL if test -n "$DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5 $as_echo "$DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DSYMUTIL"; then ac_ct_DSYMUTIL=$DSYMUTIL # Extract the first word of "dsymutil", so it can be a program name with args. set dummy dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_DSYMUTIL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DSYMUTIL"; then ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL if test -n "$ac_ct_DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5 $as_echo "$ac_ct_DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DSYMUTIL" = x; then DSYMUTIL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DSYMUTIL=$ac_ct_DSYMUTIL fi else DSYMUTIL="$ac_cv_prog_DSYMUTIL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. set dummy ${ac_tool_prefix}nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_NMEDIT+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$NMEDIT"; then ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi NMEDIT=$ac_cv_prog_NMEDIT if test -n "$NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5 $as_echo "$NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_NMEDIT"; then ac_ct_NMEDIT=$NMEDIT # Extract the first word of "nmedit", so it can be a program name with args. set dummy nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_NMEDIT+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_NMEDIT"; then ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_NMEDIT="nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT if test -n "$ac_ct_NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5 $as_echo "$ac_ct_NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_NMEDIT" = x; then NMEDIT=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac NMEDIT=$ac_ct_NMEDIT fi else NMEDIT="$ac_cv_prog_NMEDIT" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. set dummy ${ac_tool_prefix}lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_LIPO+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$LIPO"; then ac_cv_prog_LIPO="$LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_LIPO="${ac_tool_prefix}lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi LIPO=$ac_cv_prog_LIPO if test -n "$LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5 $as_echo "$LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_LIPO"; then ac_ct_LIPO=$LIPO # Extract the first word of "lipo", so it can be a program name with args. set dummy lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_LIPO+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_LIPO"; then ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_LIPO="lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO if test -n "$ac_ct_LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5 $as_echo "$ac_ct_LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_LIPO" = x; then LIPO=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac LIPO=$ac_ct_LIPO fi else LIPO="$ac_cv_prog_LIPO" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. set dummy ${ac_tool_prefix}otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL"; then ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OTOOL="${ac_tool_prefix}otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL=$ac_cv_prog_OTOOL if test -n "$OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5 $as_echo "$OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL"; then ac_ct_OTOOL=$OTOOL # Extract the first word of "otool", so it can be a program name with args. set dummy otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL"; then ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OTOOL="otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL if test -n "$ac_ct_OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5 $as_echo "$ac_ct_OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL" = x; then OTOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL=$ac_ct_OTOOL fi else OTOOL="$ac_cv_prog_OTOOL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args. set dummy ${ac_tool_prefix}otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OTOOL64+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL64"; then ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL64=$ac_cv_prog_OTOOL64 if test -n "$OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5 $as_echo "$OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL64"; then ac_ct_OTOOL64=$OTOOL64 # Extract the first word of "otool64", so it can be a program name with args. set dummy otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OTOOL64+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL64"; then ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OTOOL64="otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64 if test -n "$ac_ct_OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5 $as_echo "$ac_ct_OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL64" = x; then OTOOL64=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL64=$ac_ct_OTOOL64 fi else OTOOL64="$ac_cv_prog_OTOOL64" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5 $as_echo_n "checking for -single_module linker flag... " >&6; } if ${lt_cv_apple_cc_single_mod+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_apple_cc_single_mod=no if test -z "${LT_MULTI_MODULE}"; then # By default we will add the -single_module flag. You can override # by either setting the environment variable LT_MULTI_MODULE # non-empty at configure time, or by adding -multi_module to the # link flags. rm -rf libconftest.dylib* echo "int foo(void){return 1;}" > conftest.c echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c" >&5 $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err _lt_result=$? # If there is a non-empty error log, and "single_module" # appears in it, assume the flag caused a linker warning if test -s conftest.err && $GREP single_module conftest.err; then cat conftest.err >&5 # Otherwise, if the output was created with a 0 exit code from # the compiler, it worked. elif test -f libconftest.dylib && test $_lt_result -eq 0; then lt_cv_apple_cc_single_mod=yes else cat conftest.err >&5 fi rm -rf libconftest.dylib* rm -f conftest.* fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5 $as_echo "$lt_cv_apple_cc_single_mod" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5 $as_echo_n "checking for -exported_symbols_list linker flag... 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Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs=no fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) case `$LD -v 2>&1` in *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*) ld_shlibs=no cat <<_LT_EOF 1>&2 *** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not *** reliably create shared libraries on SCO systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.16.91.0.3 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF ;; *) # For security reasons, it is highly recommended that you always # use absolute paths for naming shared libraries, and exclude the # DT_RUNPATH tag from executables and libraries. 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then lt_cv_aix_libpath_=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$lt_cv_aix_libpath_"; then lt_cv_aix_libpath_="/usr/lib:/lib" fi fi aix_libpath=$lt_cv_aix_libpath_ fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then func_echo_all "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag="-z nodefs" archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an # empty executable. if test "${lt_cv_aix_libpath+set}" = set; 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then # We only use this code for GNU lds that support --whole-archive. whole_archive_flag_spec='${wl}--whole-archive$convenience ${wl}--no-whole-archive' else # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec='$convenience' fi archive_cmds_need_lc=yes # This is similar to how AIX traditionally builds its shared libraries. archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='' ;; m68k) archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes ;; esac ;; bsdi[45]*) export_dynamic_flag_spec=-rdynamic ;; cygwin* | mingw* | pw32* | cegcc*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. case $cc_basename in cl*) # Native MSVC hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported always_export_symbols=yes file_list_spec='@' # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $output_objdir/$soname $libobjs $compiler_flags $deplibs -Wl,-dll~linknames=' archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then sed -n -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' -e '1\\\!p' < $export_symbols > $output_objdir/$soname.exp; else sed -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; fi~ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ linknames=' # The linker will not automatically build a static lib if we build a DLL. # _LT_TAGVAR(old_archive_from_new_cmds, )='true' enable_shared_with_static_runtimes=yes exclude_expsyms='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*' export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1,DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols' # Don't use ranlib old_postinstall_cmds='chmod 644 $oldlib' postlink_cmds='lt_outputfile="@OUTPUT@"~ lt_tool_outputfile="@TOOL_OUTPUT@"~ case $lt_outputfile in *.exe|*.EXE) ;; *) lt_outputfile="$lt_outputfile.exe" lt_tool_outputfile="$lt_tool_outputfile.exe" ;; esac~ if test "$MANIFEST_TOOL" != ":" && test -f "$lt_outputfile.manifest"; then $MANIFEST_TOOL -manifest "$lt_tool_outputfile.manifest" -outputresource:"$lt_tool_outputfile" || exit 1; $RM "$lt_outputfile.manifest"; fi' ;; *) # Assume MSVC wrapper hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $lib $libobjs $compiler_flags `func_echo_all "$deplibs" | $SED '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_from_new_cmds='true' # FIXME: Should let the user specify the lib program. old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' enable_shared_with_static_runtimes=yes ;; esac ;; darwin* | rhapsody*) archive_cmds_need_lc=no hardcode_direct=no hardcode_automatic=yes hardcode_shlibpath_var=unsupported if test "$lt_cv_ld_force_load" = "yes"; then whole_archive_flag_spec='`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`' else whole_archive_flag_spec='' fi link_all_deplibs=yes allow_undefined_flag="$_lt_dar_allow_undefined" case $cc_basename in ifort*) _lt_dar_can_shared=yes ;; *) _lt_dar_can_shared=$GCC ;; esac if test "$_lt_dar_can_shared" = "yes"; then output_verbose_link_cmd=func_echo_all archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" else ld_shlibs=no fi ;; dgux*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-L$libdir' hardcode_shlibpath_var=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2.*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds='$RM $output_objdir/$soname~$CC -shared $pic_flag ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes export_dynamic_flag_spec='${wl}-E' ;; hpux10*) if test "$GCC" = yes && test "$with_gnu_ld" = no; then archive_cmds='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes fi ;; hpux11*) if test "$GCC" = yes && test "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) # Older versions of the 11.00 compiler do not understand -b yet # (HP92453-01 A.11.01.20 doesn't, HP92453-01 B.11.X.35175-35176.GP does) { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $CC understands -b" >&5 $as_echo_n "checking if $CC understands -b... " >&6; } if ${lt_cv_prog_compiler__b+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_prog_compiler__b=no save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -b" echo "$lt_simple_link_test_code" > conftest.$ac_ext if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then # The linker can only warn and ignore the option if not recognized # So say no if there are warnings if test -s conftest.err; then # Append any errors to the config.log. cat conftest.err 1>&5 $ECHO "$_lt_linker_boilerplate" | $SED '/^$/d' > conftest.exp $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 if diff conftest.exp conftest.er2 >/dev/null; then lt_cv_prog_compiler__b=yes fi else lt_cv_prog_compiler__b=yes fi fi $RM -r conftest* LDFLAGS="$save_LDFLAGS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler__b" >&5 $as_echo "$lt_cv_prog_compiler__b" >&6; } if test x"$lt_cv_prog_compiler__b" = xyes; then archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: case $host_cpu in hppa*64*|ia64*) hardcode_direct=no hardcode_shlibpath_var=no ;; *) hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' # Try to use the -exported_symbol ld option, if it does not # work, assume that -exports_file does not work either and # implicitly export all symbols. # This should be the same for all languages, so no per-tag cache variable. { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $host_os linker accepts -exported_symbol" >&5 $as_echo_n "checking whether the $host_os linker accepts -exported_symbol... " >&6; } if ${lt_cv_irix_exported_symbol+:} false; then : $as_echo_n "(cached) " >&6 else save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int foo (void) { return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_irix_exported_symbol=yes else lt_cv_irix_exported_symbol=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_irix_exported_symbol" >&5 $as_echo "$lt_cv_irix_exported_symbol" >&6; } if test "$lt_cv_irix_exported_symbol" = yes; then archive_expsym_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' fi else archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: inherit_rpath=yes link_all_deplibs=yes ;; netbsd*) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; newsos6) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: hardcode_shlibpath_var=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct=yes hardcode_shlibpath_var=no hardcode_direct_absolute=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-R$libdir' ;; *) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs=no fi ;; os2*) hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes allow_undefined_flag=unsupported archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~echo DATA >> $output_objdir/$libname.def~echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $pic_flag $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec='-rpath $libdir' fi archive_cmds_need_lc='no' hardcode_libdir_separator=: ;; solaris*) no_undefined_flag=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds='$CC -shared $pic_flag ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared $pic_flag ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' ;; *) wlarc='${wl}' archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' ;; esac fi hardcode_libdir_flag_spec='-R$libdir' hardcode_shlibpath_var=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. 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then sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" else sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" fi sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; hppa*64*) shrext_cmds='.sl' hardcode_into_libs=yes dynamic_linker="$host_os dld.sl" shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; *) shrext_cmds='.sl' dynamic_linker="$host_os dld.sl" shlibpath_var=SHLIB_PATH shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' ;; esac # HP-UX runs *really* slowly unless shared libraries are mode 555, ... postinstall_cmds='chmod 555 $lib' # or fails outright, so override atomically: install_override_mode=555 ;; interix[3-9]*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux # correct to gnu/linux during the next big refactor else version_type=irix fi ;; esac need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") libsuff=32 shlibsuff=N32 libmagic=N32;; *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") libsuff=64 shlibsuff=64 libmagic=64-bit;; *) libsuff= shlibsuff= libmagic=never-match;; esac ;; esac shlibpath_var=LD_LIBRARY${shlibsuff}_PATH shlibpath_overrides_runpath=no sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" hardcode_into_libs=yes ;; # No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # Some binutils ld are patched to set DT_RUNPATH if ${lt_cv_shlibpath_overrides_runpath+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_shlibpath_overrides_runpath=no save_LDFLAGS=$LDFLAGS save_libdir=$libdir eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\"" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then : lt_cv_shlibpath_overrides_runpath=yes fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS=$save_LDFLAGS libdir=$save_libdir fi shlibpath_overrides_runpath=$lt_cv_shlibpath_overrides_runpath # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes # Add ABI-specific directories to the system library path. sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /lib /usr/lib" # Append ld.so.conf contents to the search path if test -f /etc/ld.so.conf; then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;s/"//g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. Since this was broken with cross compilers, # most powerpc-linux boxes support dynamic linking these days and # people can always --disable-shared, the test was removed, and we # assume the GNU/Linux dynamic linker is in use. dynamic_linker='GNU/Linux ld.so' ;; netbsd*) version_type=sunos need_lib_prefix=no need_version=no if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' dynamic_linker='NetBSD (a.out) ld.so' else library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='NetBSD ld.elf_so' fi shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes ;; newsos6) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes ;; *nto* | *qnx*) version_type=qnx need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='ldqnx.so' ;; openbsd*) version_type=sunos sys_lib_dlsearch_path_spec="/usr/lib" need_lib_prefix=no # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. case $host_os in openbsd3.3 | openbsd3.3.*) need_version=yes ;; *) need_version=no ;; esac library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' shlibpath_var=LD_LIBRARY_PATH if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then case $host_os in openbsd2.[89] | openbsd2.[89].*) shlibpath_overrides_runpath=no ;; *) shlibpath_overrides_runpath=yes ;; esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; sunos4*) version_type=sunos library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes if test "$with_gnu_ld" = yes; then need_lib_prefix=no fi need_version=yes ;; sysv4 | sysv4.3*) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH case $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no runpath_var=LD_RUN_PATH ;; siemens) need_lib_prefix=no ;; motorola) need_lib_prefix=no need_version=no shlibpath_overrides_runpath=no sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' ;; esac ;; sysv4*MP*) if test -d /usr/nec ;then version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' soname_spec='$libname${shared_ext}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) version_type=freebsd-elf need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes if test "$with_gnu_ld" = yes; then sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' else sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' case $host_os in sco3.2v5*) sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" ;; esac fi sys_lib_dlsearch_path_spec='/usr/lib' ;; tpf*) # TPF is a cross-target only. Preferred cross-host = GNU/Linux. version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; uts4*) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH ;; *) dynamic_linker=no ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5 $as_echo "$dynamic_linker" >&6; } test "$dynamic_linker" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" fi if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5 $as_echo_n "checking how to hardcode library paths into programs... " >&6; } hardcode_action= if test -n "$hardcode_libdir_flag_spec" || test -n "$runpath_var" || test "X$hardcode_automatic" = "Xyes" ; then # We can hardcode non-existent directories. if test "$hardcode_direct" != no && # If the only mechanism to avoid hardcoding is shlibpath_var, we # have to relink, otherwise we might link with an installed library # when we should be linking with a yet-to-be-installed one ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no && test "$hardcode_minus_L" != no; then # Linking always hardcodes the temporary library directory. hardcode_action=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. hardcode_action=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. hardcode_action=unsupported fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action" >&5 $as_echo "$hardcode_action" >&6; } if test "$hardcode_action" = relink || test "$inherit_rpath" = yes; then # Fast installation is not supported enable_fast_install=no elif test "$shlibpath_overrides_runpath" = yes || test "$enable_shared" = no; then # Fast installation is not necessary enable_fast_install=needless fi if test "x$enable_dlopen" != xyes; then enable_dlopen=unknown enable_dlopen_self=unknown enable_dlopen_self_static=unknown else lt_cv_dlopen=no lt_cv_dlopen_libs= case $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32* | cegcc*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5 $as_echo_n "checking for dlopen in -ldl... " >&6; } if ${ac_cv_lib_dl_dlopen+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dl_dlopen=yes else ac_cv_lib_dl_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5 $as_echo "$ac_cv_lib_dl_dlopen" >&6; } if test "x$ac_cv_lib_dl_dlopen" = xyes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes fi ;; *) ac_fn_c_check_func "$LINENO" "shl_load" "ac_cv_func_shl_load" if test "x$ac_cv_func_shl_load" = xyes; then : lt_cv_dlopen="shl_load" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shl_load in -ldld" >&5 $as_echo_n "checking for shl_load in -ldld... " >&6; } if ${ac_cv_lib_dld_shl_load+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char shl_load (); int main () { return shl_load (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dld_shl_load=yes else ac_cv_lib_dld_shl_load=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_shl_load" >&5 $as_echo "$ac_cv_lib_dld_shl_load" >&6; } if test "x$ac_cv_lib_dld_shl_load" = xyes; then : lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld" else ac_fn_c_check_func "$LINENO" "dlopen" "ac_cv_func_dlopen" if test "x$ac_cv_func_dlopen" = xyes; then : lt_cv_dlopen="dlopen" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5 $as_echo_n "checking for dlopen in -ldl... " >&6; } if ${ac_cv_lib_dl_dlopen+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dl_dlopen=yes else ac_cv_lib_dl_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5 $as_echo "$ac_cv_lib_dl_dlopen" >&6; } if test "x$ac_cv_lib_dl_dlopen" = xyes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -lsvld" >&5 $as_echo_n "checking for dlopen in -lsvld... " >&6; } if ${ac_cv_lib_svld_dlopen+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lsvld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_svld_dlopen=yes else ac_cv_lib_svld_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_svld_dlopen" >&5 $as_echo "$ac_cv_lib_svld_dlopen" >&6; } if test "x$ac_cv_lib_svld_dlopen" = xyes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dld_link in -ldld" >&5 $as_echo_n "checking for dld_link in -ldld... " >&6; } if ${ac_cv_lib_dld_dld_link+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. 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See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Alexandre Oliva . case $1 in '') echo "$0: No command. Try '$0 --help' for more information." 1>&2 exit 1; ;; -h | --h*) cat <<\EOF Usage: depcomp [--help] [--version] PROGRAM [ARGS] Run PROGRAMS ARGS to compile a file, generating dependencies as side-effects. Environment variables: depmode Dependency tracking mode. source Source file read by 'PROGRAMS ARGS'. object Object file output by 'PROGRAMS ARGS'. DEPDIR directory where to store dependencies. depfile Dependency file to output. tmpdepfile Temporary file to use when outputting dependencies. libtool Whether libtool is used (yes/no). Report bugs to . EOF exit $? ;; -v | --v*) echo "depcomp $scriptversion" exit $? ;; esac # Get the directory component of the given path, and save it in the # global variables '$dir'. Note that this directory component will # be either empty or ending with a '/' character. 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We # parameterize here, but still list the modes in the big case below, # to make depend.m4 easier to write. Note that we *cannot* use a case # here, because this file can only contain one case statement. if test "$depmode" = hp; then # HP compiler uses -M and no extra arg. gccflag=-M depmode=gcc fi if test "$depmode" = dashXmstdout; then # This is just like dashmstdout with a different argument. dashmflag=-xM depmode=dashmstdout fi cygpath_u="cygpath -u -f -" if test "$depmode" = msvcmsys; then # This is just like msvisualcpp but w/o cygpath translation. # Just convert the backslash-escaped backslashes to single forward # slashes to satisfy depend.m4 cygpath_u='sed s,\\\\,/,g' depmode=msvisualcpp fi if test "$depmode" = msvc7msys; then # This is just like msvc7 but w/o cygpath translation. # Just convert the backslash-escaped backslashes to single forward # slashes to satisfy depend.m4 cygpath_u='sed s,\\\\,/,g' depmode=msvc7 fi if test "$depmode" = xlc; then # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information. gccflag=-qmakedep=gcc,-MF depmode=gcc fi case "$depmode" in gcc3) ## gcc 3 implements dependency tracking that does exactly what ## we want. Yay! Note: for some reason libtool 1.4 doesn't like ## it if -MD -MP comes after the -MF stuff. Hmm. ## Unfortunately, FreeBSD c89 acceptance of flags depends upon ## the command line argument order; so add the flags where they ## appear in depend2.am. Note that the slowdown incurred here ## affects only configure: in makefiles, %FASTDEP% shortcuts this. for arg do case $arg in -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;; *) set fnord "$@" "$arg" ;; esac shift # fnord shift # $arg done "$@" stat=$? if test $stat -ne 0; then rm -f "$tmpdepfile" exit $stat fi mv "$tmpdepfile" "$depfile" ;; gcc) ## Note that this doesn't just cater to obsosete pre-3.x GCC compilers. ## but also to in-use compilers like IMB xlc/xlC and the HP C compiler. ## (see the conditional assignment to $gccflag above). ## There are various ways to get dependency output from gcc. Here's ## why we pick this rather obscure method: ## - Don't want to use -MD because we'd like the dependencies to end ## up in a subdir. Having to rename by hand is ugly. ## (We might end up doing this anyway to support other compilers.) ## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like ## -MM, not -M (despite what the docs say). Also, it might not be ## supported by the other compilers which use the 'gcc' depmode. ## - Using -M directly means running the compiler twice (even worse ## than renaming). if test -z "$gccflag"; then gccflag=-MD, fi "$@" -Wp,"$gccflag$tmpdepfile" stat=$? if test $stat -ne 0; then rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" echo "$object : \\" > "$depfile" # The second -e expression handles DOS-style file names with drive # letters. sed -e 's/^[^:]*: / /' \ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" ## This next piece of magic avoids the "deleted header file" problem. ## The problem is that when a header file which appears in a .P file ## is deleted, the dependency causes make to die (because there is ## typically no way to rebuild the header). We avoid this by adding ## dummy dependencies for each header file. Too bad gcc doesn't do ## this for us directly. ## Some versions of gcc put a space before the ':'. On the theory ## that the space means something, we add a space to the output as ## well. hp depmode also adds that space, but also prefixes the VPATH ## to the object. Take care to not repeat it in the output. ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. tr ' ' "$nl" < "$tmpdepfile" \ | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \ | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; hp) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; sgi) if test "$libtool" = yes; then "$@" "-Wp,-MDupdate,$tmpdepfile" else "$@" -MDupdate "$tmpdepfile" fi stat=$? if test $stat -ne 0; then rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files echo "$object : \\" > "$depfile" # Clip off the initial element (the dependent). Don't try to be # clever and replace this with sed code, as IRIX sed won't handle # lines with more than a fixed number of characters (4096 in # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines; # the IRIX cc adds comments like '#:fec' to the end of the # dependency line. tr ' ' "$nl" < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \ | tr "$nl" ' ' >> "$depfile" echo >> "$depfile" # The second pass generates a dummy entry for each header file. tr ' ' "$nl" < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ >> "$depfile" else make_dummy_depfile fi rm -f "$tmpdepfile" ;; xlc) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; aix) # The C for AIX Compiler uses -M and outputs the dependencies # in a .u file. In older versions, this file always lives in the # current directory. Also, the AIX compiler puts '$object:' at the # start of each line; $object doesn't have directory information. # Version 6 uses the directory in both cases. set_dir_from "$object" set_base_from "$object" if test "$libtool" = yes; then tmpdepfile1=$dir$base.u tmpdepfile2=$base.u tmpdepfile3=$dir.libs/$base.u "$@" -Wc,-M else tmpdepfile1=$dir$base.u tmpdepfile2=$dir$base.u tmpdepfile3=$dir$base.u "$@" -M fi stat=$? if test $stat -ne 0; then rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" exit $stat fi for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" do test -f "$tmpdepfile" && break done aix_post_process_depfile ;; tcc) # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26 # FIXME: That version still under development at the moment of writing. # Make that this statement remains true also for stable, released # versions. # It will wrap lines (doesn't matter whether long or short) with a # trailing '\', as in: # # foo.o : \ # foo.c \ # foo.h \ # # It will put a trailing '\' even on the last line, and will use leading # spaces rather than leading tabs (at least since its commit 0394caf7 # "Emit spaces for -MD"). "$@" -MD -MF "$tmpdepfile" stat=$? if test $stat -ne 0; then rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'. # We have to change lines of the first kind to '$object: \'. sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile" # And for each line of the second kind, we have to emit a 'dep.h:' # dummy dependency, to avoid the deleted-header problem. sed -n -e 's|^ *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile" rm -f "$tmpdepfile" ;; ## The order of this option in the case statement is important, since the ## shell code in configure will try each of these formats in the order ## listed in this file. A plain '-MD' option would be understood by many ## compilers, so we must ensure this comes after the gcc and icc options. pgcc) # Portland's C compiler understands '-MD'. # Will always output deps to 'file.d' where file is the root name of the # source file under compilation, even if file resides in a subdirectory. # The object file name does not affect the name of the '.d' file. # pgcc 10.2 will output # foo.o: sub/foo.c sub/foo.h # and will wrap long lines using '\' : # foo.o: sub/foo.c ... \ # sub/foo.h ... \ # ... set_dir_from "$object" # Use the source, not the object, to determine the base name, since # that's sadly what pgcc will do too. set_base_from "$source" tmpdepfile=$base.d # For projects that build the same source file twice into different object # files, the pgcc approach of using the *source* file root name can cause # problems in parallel builds. Use a locking strategy to avoid stomping on # the same $tmpdepfile. lockdir=$base.d-lock trap " echo '$0: caught signal, cleaning up...' >&2 rmdir '$lockdir' exit 1 " 1 2 13 15 numtries=100 i=$numtries while test $i -gt 0; do # mkdir is a portable test-and-set. if mkdir "$lockdir" 2>/dev/null; then # This process acquired the lock. "$@" -MD stat=$? # Release the lock. rmdir "$lockdir" break else # If the lock is being held by a different process, wait # until the winning process is done or we timeout. while test -d "$lockdir" && test $i -gt 0; do sleep 1 i=`expr $i - 1` done fi i=`expr $i - 1` done trap - 1 2 13 15 if test $i -le 0; then echo "$0: failed to acquire lock after $numtries attempts" >&2 echo "$0: check lockdir '$lockdir'" >&2 exit 1 fi if test $stat -ne 0; then rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" # Each line is of the form `foo.o: dependent.h', # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. # Do two passes, one to just change these to # `$object: dependent.h' and one to simply `dependent.h:'. sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" # Some versions of the HPUX 10.20 sed can't process this invocation # correctly. Breaking it into two sed invocations is a workaround. sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \ | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; hp2) # The "hp" stanza above does not work with aCC (C++) and HP's ia64 # compilers, which have integrated preprocessors. The correct option # to use with these is +Maked; it writes dependencies to a file named # 'foo.d', which lands next to the object file, wherever that # happens to be. # Much of this is similar to the tru64 case; see comments there. set_dir_from "$object" set_base_from "$object" if test "$libtool" = yes; then tmpdepfile1=$dir$base.d tmpdepfile2=$dir.libs/$base.d "$@" -Wc,+Maked else tmpdepfile1=$dir$base.d tmpdepfile2=$dir$base.d "$@" +Maked fi stat=$? if test $stat -ne 0; then rm -f "$tmpdepfile1" "$tmpdepfile2" exit $stat fi for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" do test -f "$tmpdepfile" && break done if test -f "$tmpdepfile"; then sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile" # Add 'dependent.h:' lines. sed -ne '2,${ s/^ *// s/ \\*$// s/$/:/ p }' "$tmpdepfile" >> "$depfile" else make_dummy_depfile fi rm -f "$tmpdepfile" "$tmpdepfile2" ;; tru64) # The Tru64 compiler uses -MD to generate dependencies as a side # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'. # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put # dependencies in 'foo.d' instead, so we check for that too. # Subdirectories are respected. set_dir_from "$object" set_base_from "$object" if test "$libtool" = yes; then # Libtool generates 2 separate objects for the 2 libraries. These # two compilations output dependencies in $dir.libs/$base.o.d and # in $dir$base.o.d. We have to check for both files, because # one of the two compilations can be disabled. We should prefer # $dir$base.o.d over $dir.libs/$base.o.d because the latter is # automatically cleaned when .libs/ is deleted, while ignoring # the former would cause a distcleancheck panic. tmpdepfile1=$dir$base.o.d # libtool 1.5 tmpdepfile2=$dir.libs/$base.o.d # Likewise. tmpdepfile3=$dir.libs/$base.d # Compaq CCC V6.2-504 "$@" -Wc,-MD else tmpdepfile1=$dir$base.d tmpdepfile2=$dir$base.d tmpdepfile3=$dir$base.d "$@" -MD fi stat=$? if test $stat -ne 0; then rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" exit $stat fi for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" do test -f "$tmpdepfile" && break done # Same post-processing that is required for AIX mode. aix_post_process_depfile ;; msvc7) if test "$libtool" = yes; then showIncludes=-Wc,-showIncludes else showIncludes=-showIncludes fi "$@" $showIncludes > "$tmpdepfile" stat=$? grep -v '^Note: including file: ' "$tmpdepfile" if test $stat -ne 0; then rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" echo "$object : \\" > "$depfile" # The first sed program below extracts the file names and escapes # backslashes for cygpath. The second sed program outputs the file # name when reading, but also accumulates all include files in the # hold buffer in order to output them again at the end. This only # works with sed implementations that can handle large buffers. sed < "$tmpdepfile" -n ' /^Note: including file: *\(.*\)/ { s//\1/ s/\\/\\\\/g p }' | $cygpath_u | sort -u | sed -n ' s/ /\\ /g s/\(.*\)/'"$tab"'\1 \\/p s/.\(.*\) \\/\1:/ H $ { s/.*/'"$tab"'/ G p }' >> "$depfile" echo >> "$depfile" # make sure the fragment doesn't end with a backslash rm -f "$tmpdepfile" ;; msvc7msys) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; #nosideeffect) # This comment above is used by automake to tell side-effect # dependency tracking mechanisms from slower ones. dashmstdout) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout, regardless of -o. "$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test "X$1" != 'X--mode=compile'; do shift done shift fi # Remove '-o $object'. IFS=" " for arg do case $arg in -o) shift ;; $object) shift ;; *) set fnord "$@" "$arg" shift # fnord shift # $arg ;; esac done test -z "$dashmflag" && dashmflag=-M # Require at least two characters before searching for ':' # in the target name. This is to cope with DOS-style filenames: # a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise. "$@" $dashmflag | sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$tmpdepfile" rm -f "$depfile" cat < "$tmpdepfile" > "$depfile" # Some versions of the HPUX 10.20 sed can't process this sed invocation # correctly. Breaking it into two sed invocations is a workaround. tr ' ' "$nl" < "$tmpdepfile" \ | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \ | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; dashXmstdout) # This case only exists to satisfy depend.m4. It is never actually # run, as this mode is specially recognized in the preamble. exit 1 ;; makedepend) "$@" || exit $? # Remove any Libtool call if test "$libtool" = yes; then while test "X$1" != 'X--mode=compile'; do shift done shift fi # X makedepend shift cleared=no eat=no for arg do case $cleared in no) set ""; shift cleared=yes ;; esac if test $eat = yes; then eat=no continue fi case "$arg" in -D*|-I*) set fnord "$@" "$arg"; shift ;; # Strip any option that makedepend may not understand. Remove # the object too, otherwise makedepend will parse it as a source file. -arch) eat=yes ;; -*|$object) ;; *) set fnord "$@" "$arg"; shift ;; esac done obj_suffix=`echo "$object" | sed 's/^.*\././'` touch "$tmpdepfile" ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" rm -f "$depfile" # makedepend may prepend the VPATH from the source file name to the object. # No need to regex-escape $object, excess matching of '.' is harmless. sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile" # Some versions of the HPUX 10.20 sed can't process the last invocation # correctly. Breaking it into two sed invocations is a workaround. sed '1,2d' "$tmpdepfile" \ | tr ' ' "$nl" \ | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \ | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" "$tmpdepfile".bak ;; cpp) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout. "$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test "X$1" != 'X--mode=compile'; do shift done shift fi # Remove '-o $object'. IFS=" " for arg do case $arg in -o) shift ;; $object) shift ;; *) set fnord "$@" "$arg" shift # fnord shift # $arg ;; esac done "$@" -E \ | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \ | sed '$ s: \\$::' > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" cat < "$tmpdepfile" >> "$depfile" sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; msvisualcpp) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout. "$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test "X$1" != 'X--mode=compile'; do shift done shift fi IFS=" " for arg do case "$arg" in -o) shift ;; $object) shift ;; "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") set fnord "$@" shift shift ;; *) set fnord "$@" "$arg" shift shift ;; esac done "$@" -E 2>/dev/null | sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile" echo "$tab" >> "$depfile" sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" rm -f "$tmpdepfile" ;; msvcmsys) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; none) exec "$@" ;; *) echo "Unknown depmode $depmode" 1>&2 exit 1 ;; esac exit 0 # Local Variables: # mode: shell-script # sh-indentation: 2 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: ctffind-4.1.14/image_trim.cpp000066400000000000000000004015721440356052600160550ustar00rootroot00000000000000#include "src/core/core_headers.h" wxMutex Image::s_mutexProtectingFFTW; void Image::SetupInitialValues() { logical_x_dimension = 0; logical_y_dimension = 0; logical_z_dimension = 0; is_in_real_space = true; object_is_centred_in_box = true; physical_upper_bound_complex_x = 0; physical_upper_bound_complex_y = 0; physical_upper_bound_complex_z = 0; physical_address_of_box_center_x = 0; physical_address_of_box_center_y = 0; physical_address_of_box_center_z = 0; //physical_index_of_first_negative_frequency_x = 0; physical_index_of_first_negative_frequency_y = 0; physical_index_of_first_negative_frequency_z = 0; fourier_voxel_size_x = 0.0; fourier_voxel_size_y = 0.0; fourier_voxel_size_z = 0.0; logical_upper_bound_complex_x = 0; logical_upper_bound_complex_y = 0; logical_upper_bound_complex_z = 0; logical_lower_bound_complex_x = 0; logical_lower_bound_complex_y = 0; logical_lower_bound_complex_z = 0; logical_upper_bound_real_x = 0; logical_upper_bound_real_y = 0; logical_upper_bound_real_z = 0; logical_lower_bound_real_x = 0; logical_lower_bound_real_y = 0; logical_lower_bound_real_z = 0; insert_into_which_reconstruction = 0; real_values = NULL; complex_values = NULL; is_in_memory = false; real_memory_allocated = 0; plan_fwd = NULL; plan_bwd = NULL; planned = false; padding_jump_value = 0; image_memory_should_not_be_deallocated = false; } Image::Image() { SetupInitialValues(); } Image::Image( const Image &other_image) // copy constructor { SetupInitialValues(); MyDebugPrint("Warning: copying an image object"); *this = other_image; } Image::~Image() { Deallocate(); } int Image::ReturnSmallestLogicalDimension() { if (logical_z_dimension == 1) { return std::min(logical_x_dimension, logical_y_dimension); } else { int temp_int; temp_int = std::min(logical_x_dimension, logical_y_dimension); return std::min(temp_int, logical_z_dimension); } } int Image::ReturnLargestLogicalDimension() { if (logical_z_dimension == 1) { return std::max(logical_x_dimension, logical_y_dimension); } else { int temp_int; temp_int = std::max(logical_x_dimension, logical_y_dimension); return std::max(temp_int, logical_z_dimension); } } void Image::MultiplyPixelWise(Image &other_image) { MyDebugAssertTrue(is_in_memory, "Image memory not allocated"); MyDebugAssertTrue(other_image.is_in_memory, "Other image memory not allocated"); int i; long pixel_counter; if (is_in_real_space) { MyDebugAssertTrue(other_image.is_in_real_space,"Other image needs to be in real space"); MyDebugAssertTrue(HasSameDimensionsAs(&other_image),"Images do not have same dimensions"); for (pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] *= other_image.real_values[pixel_counter]; } } else { if (other_image.is_in_real_space) { /* * This image is in Fourier space, the other image in is in real space. * They better be the expected dimensions! */ MyDebugAssertTrue( other_image.logical_x_dimension == logical_x_dimension/2 + 1 && other_image.logical_y_dimension == logical_y_dimension && other_image.logical_z_dimension == logical_z_dimension, "This image is in Fourier space (dimensions = %i,%i,%i), the other is in real space (dimensions = %i,%i,%i), but it does not have expected dimensions", logical_x_dimension,logical_y_dimension,logical_z_dimension,other_image.logical_x_dimension,other_image.logical_y_dimension,other_image.logical_z_dimension); long pixel_counter_this, pixel_counter_other; int i_other,j_other,k_other; pixel_counter_this = 0; pixel_counter_other = 0; for (k_other = 0; k_other < other_image.logical_z_dimension; k_other++) { for (j_other = 0; j_other < other_image.logical_y_dimension; j_other++) { for (i_other = 0; i_other < other_image.logical_x_dimension; i_other++) { complex_values[pixel_counter_this] *= other_image.real_values[pixel_counter_other]; //complex_values[pixel_counter_this] *= 0.5; pixel_counter_other++; pixel_counter_this++; } pixel_counter_other += other_image.padding_jump_value; } } } else { // Both images are in Fourier space MyDebugAssertTrue(HasSameDimensionsAs(&other_image),"Images do not have same dimensions"); // TODO: add MKL implementation (see EulerSearch::Run for a similar example) for (pixel_counter = 0; pixel_counter < real_memory_allocated / 2; pixel_counter++) { complex_values[pixel_counter] *= other_image.complex_values[pixel_counter]; } } } } void Image::CircleMask(float wanted_mask_radius, bool invert) { MyDebugAssertTrue(is_in_real_space,"Image not in real space"); MyDebugAssertTrue(object_is_centred_in_box,"Object not centered in box"); long pixel_counter; int i,j,k; float x,y,z; float distance_from_center_squared; const float wanted_mask_radius_squared = powf(wanted_mask_radius,2); double average_value = 0.0; long number_of_pixels = 0; pixel_counter = 0; for (k = 0; k < logical_z_dimension; k++) { z = powf(k - physical_address_of_box_center_z, 2); for (j = 0; j < logical_y_dimension; j++) { y = powf(j - physical_address_of_box_center_y, 2); for (i = 0; i < logical_x_dimension; i++) { x = powf(i - physical_address_of_box_center_x, 2); distance_from_center_squared = x + y + z; if (abs(distance_from_center_squared-wanted_mask_radius_squared) <= 4.0) { number_of_pixels++; average_value += real_values[pixel_counter]; } pixel_counter++; } pixel_counter += padding_jump_value; } } // Now we know what value to mask with average_value /= float(number_of_pixels); // Let's mask pixel_counter = 0; for (k = 0; k < logical_z_dimension; k++) { z = powf(k - physical_address_of_box_center_z, 2); for (j = 0; j < logical_y_dimension; j++) { y = powf(j - physical_address_of_box_center_y, 2); for (i = 0; i < logical_x_dimension; i++) { x = powf(i - physical_address_of_box_center_x, 2); distance_from_center_squared = x + y + z; if (invert) { if ( distance_from_center_squared <= wanted_mask_radius_squared) { real_values[pixel_counter] = average_value; } } else { if ( distance_from_center_squared > wanted_mask_radius_squared) { real_values[pixel_counter] = average_value; } } pixel_counter++; } pixel_counter += padding_jump_value; } } } /* * Raise cosine-edged mask. The first argument gives the radius of the midpoint of the cosine (where cos = 0.5) */ float Image::CosineMask(float wanted_mask_radius, float wanted_mask_edge, bool invert, bool force_mask_value, float wanted_mask_value) { // MyDebugAssertTrue(! is_in_real_space || object_is_centred_in_box, "Image in real space but not centered"); if (is_in_real_space) { MyDebugAssertTrue(wanted_mask_edge >= 1.0, "Edge width too small"); } else { MyDebugAssertTrue(wanted_mask_edge > 0.0, "Edge width too small"); } int i; int j; int k; int ii; int jj; int kk; long number_of_pixels; float x; float y; float z; long pixel_counter = 0; float distance_from_center; float mask_radius_plus_edge; float distance_from_center_squared; float mask_radius; float mask_radius_squared; float mask_radius_plus_edge_squared; float edge; double pixel_sum; float frequency; float frequency_squared; double mask_volume = 0.0; mask_radius = wanted_mask_radius - wanted_mask_edge * 0.5; if (mask_radius < 0.0) mask_radius = 0.0; mask_radius_plus_edge = mask_radius + wanted_mask_edge; mask_radius_squared = powf(mask_radius, 2); mask_radius_plus_edge_squared = powf(mask_radius_plus_edge, 2); pixel_sum = 0.0; number_of_pixels = 0; if (is_in_real_space && object_is_centred_in_box) { if (force_mask_value) { pixel_sum = wanted_mask_value; } else { for (k = 0; k < logical_z_dimension; k++) { z = powf(k - physical_address_of_box_center_z, 2); for (j = 0; j < logical_y_dimension; j++) { y = powf(j - physical_address_of_box_center_y, 2); for (i = 0; i < logical_x_dimension; i++) { x = powf(i - physical_address_of_box_center_x, 2); distance_from_center_squared = x + y + z; if (distance_from_center_squared >= mask_radius_squared && distance_from_center_squared <= mask_radius_plus_edge_squared) { pixel_sum += real_values[pixel_counter]; number_of_pixels++; } pixel_counter++; } pixel_counter += padding_jump_value; } } MyDebugAssertTrue(number_of_pixels > 0, "Oops, did not find any pixels to average over"); pixel_sum /= number_of_pixels; } pixel_counter = 0.0; for (k = 0; k < logical_z_dimension; k++) { z = powf(k - physical_address_of_box_center_z, 2); for (j = 0; j < logical_y_dimension; j++) { y = powf(j - physical_address_of_box_center_y, 2); for (i = 0; i < logical_x_dimension; i++) { x = powf(i - physical_address_of_box_center_x, 2); distance_from_center_squared = x + y + z; if (distance_from_center_squared >= mask_radius_squared && distance_from_center_squared <= mask_radius_plus_edge_squared) { distance_from_center = sqrtf(distance_from_center_squared); edge = (1.0 + cosf(PI * (distance_from_center - mask_radius) / wanted_mask_edge)) / 2.0; if (invert) { real_values[pixel_counter] = real_values[pixel_counter] * (1.0 - edge) + edge * pixel_sum; mask_volume += powf(1.0 - edge,2); } else { real_values[pixel_counter] = real_values[pixel_counter] * edge + (1.0 - edge) * pixel_sum; mask_volume += powf(edge,2); } } else if (invert) { if (distance_from_center_squared <= mask_radius_squared) { real_values[pixel_counter] = pixel_sum; } else { mask_volume += 1.0; } } else { if (distance_from_center_squared >= mask_radius_plus_edge_squared) { real_values[pixel_counter] = pixel_sum; } else { mask_volume += 1.0; } } pixel_counter++; } pixel_counter += padding_jump_value; } } } else if (is_in_real_space) { if (force_mask_value) { pixel_sum = wanted_mask_value; } else { for (k = 0; k < logical_z_dimension; k++) { kk = k; if (kk >= physical_address_of_box_center_z) kk -= logical_z_dimension; z = powf(kk, 2); for (j = 0; j < logical_y_dimension; j++) { jj = j; if (jj >= physical_address_of_box_center_y) jj -= logical_y_dimension; y = powf(jj, 2); for (i = 0; i < logical_x_dimension; i++) { ii = i; if (ii >= physical_address_of_box_center_x) ii -= logical_x_dimension; x = powf(ii, 2); distance_from_center_squared = x + y + z; if (distance_from_center_squared >= mask_radius_squared && distance_from_center_squared <= mask_radius_plus_edge_squared) { pixel_sum += real_values[pixel_counter]; number_of_pixels++; } pixel_counter++; } pixel_counter += padding_jump_value; } } pixel_sum /= number_of_pixels; } pixel_counter = 0.0; for (k = 0; k < logical_z_dimension; k++) { kk = k; if (kk >= physical_address_of_box_center_z) kk -= logical_z_dimension; z = powf(kk, 2); for (j = 0; j < logical_y_dimension; j++) { jj = j; if (jj >= physical_address_of_box_center_y) jj -= logical_y_dimension; y = powf(jj, 2); for (i = 0; i < logical_x_dimension; i++) { ii = i; if (ii >= physical_address_of_box_center_x) ii -= logical_x_dimension; x = powf(ii, 2); distance_from_center_squared = x + y + z; if (distance_from_center_squared >= mask_radius_squared && distance_from_center_squared <= mask_radius_plus_edge_squared) { distance_from_center = sqrtf(distance_from_center_squared); edge = (1.0 + cosf(PI * (distance_from_center - mask_radius) / wanted_mask_edge)) / 2.0; real_values[pixel_counter] = real_values[pixel_counter] * edge + (1.0 - edge) * pixel_sum; mask_volume += powf(edge,2); } else if (distance_from_center_squared >= mask_radius_plus_edge_squared) real_values[pixel_counter] = pixel_sum; else { mask_volume += 1.0; } pixel_counter++; } pixel_counter += padding_jump_value; } } } else { for (k = 0; k <= physical_upper_bound_complex_z; k++) { z = powf(ReturnFourierLogicalCoordGivenPhysicalCoord_Z(k) * fourier_voxel_size_z, 2); for (j = 0; j <= physical_upper_bound_complex_y; j++) { y = powf(ReturnFourierLogicalCoordGivenPhysicalCoord_Y(j) * fourier_voxel_size_y, 2); for (i = 0; i <= physical_upper_bound_complex_x; i++) { x = powf(i * fourier_voxel_size_x, 2); // compute squared radius, in units of reciprocal pixels frequency_squared = x + y + z; if (frequency_squared >= mask_radius_squared && frequency_squared <= mask_radius_plus_edge_squared) { frequency = sqrtf(frequency_squared); edge = (1.0 + cosf(PI * (frequency - mask_radius) / wanted_mask_edge)) / 2.0; if (invert) { complex_values[pixel_counter] *= (1.0 - edge); } else { complex_values[pixel_counter] *= edge; } } if (invert) { if (frequency_squared <= mask_radius_squared) complex_values[pixel_counter] = 0.0f + I * 0.0f; } else { if (frequency_squared >= mask_radius_plus_edge_squared) complex_values[pixel_counter] = 0.0f + I * 0.0f; } pixel_counter++; } } } } return float(mask_volume); } Image & Image::operator = (const Image &other_image) { *this = &other_image; return *this; } Image & Image::operator = (const Image *other_image) { // Check for self assignment if(this != other_image) { MyDebugAssertTrue(other_image->is_in_memory, "Other image Memory not allocated"); if (is_in_memory == true) { if (logical_x_dimension != other_image->logical_x_dimension || logical_y_dimension != other_image->logical_y_dimension || logical_z_dimension != other_image->logical_z_dimension) { Deallocate(); Allocate(other_image->logical_x_dimension, other_image->logical_y_dimension, other_image->logical_z_dimension, other_image->is_in_real_space); } } else { Allocate(other_image->logical_x_dimension, other_image->logical_y_dimension, other_image->logical_z_dimension, other_image->is_in_real_space); } // by here the memory allocation should be ok.. is_in_real_space = other_image->is_in_real_space; object_is_centred_in_box = other_image->object_is_centred_in_box; for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] = other_image->real_values[pixel_counter]; } } return *this; } //!> \brief Deallocate all the memory. The idea is to keep this safe in the case that something isn't // allocated, so it can always be safely called. I.e. it should check whatever it is deallocating is // in fact allocated. // void Image::Deallocate() { if (is_in_memory == true && image_memory_should_not_be_deallocated == false) { fftwf_free(real_values); is_in_memory = false; } if (planned == true) { wxMutexLocker lock(s_mutexProtectingFFTW); // the mutex will be unlocked when this object is destroyed (when it goes out of scope) MyDebugAssertTrue(lock.IsOk(),"Mute locking failed"); fftwf_destroy_plan(plan_fwd); fftwf_destroy_plan(plan_bwd); planned = false; } } //!> \brief Allocate memory for the Image object. // // If the object is already allocated with correct dimensions, nothing happens. Otherwise, object is deallocated first. void Image::Allocate(int wanted_x_size, int wanted_y_size, int wanted_z_size, bool should_be_in_real_space) { MyDebugAssertTrue(wanted_x_size > 0 && wanted_y_size > 0 && wanted_z_size > 0,"Bad dimensions: %i %i %i\n",wanted_x_size,wanted_y_size,wanted_z_size); // check to see if we need to do anything? if (is_in_memory == true) { is_in_real_space = should_be_in_real_space; if (wanted_x_size == logical_x_dimension && wanted_y_size == logical_y_dimension && wanted_z_size == logical_z_dimension) { // everything is already done.. is_in_real_space = should_be_in_real_space; // wxPrintf("returning\n"); return; } else Deallocate(); } // if we got here we need to do allocation.. SetLogicalDimensions(wanted_x_size, wanted_y_size, wanted_z_size); is_in_real_space = should_be_in_real_space; // first_x_dimension if (IsEven(wanted_x_size) == true) real_memory_allocated = wanted_x_size / 2 + 1; else real_memory_allocated = (wanted_x_size - 1) / 2 + 1; real_memory_allocated *= wanted_y_size * wanted_z_size; // other dimensions real_memory_allocated *= 2; // room for complex real_values = (float *) fftwf_malloc(sizeof(float) * real_memory_allocated); complex_values = (std::complex*) real_values; // Set the complex_values to point at the newly allocated real values; is_in_memory = true; // Update addresses etc.. UpdateLoopingAndAddressing(); // Prepare the plans for FFTW if (planned == false) { wxMutexLocker lock(s_mutexProtectingFFTW); // the mutex will be unlocked when this object is destroyed (when it goes out of scope) MyDebugAssertTrue(lock.IsOk(),"Mute locking failed"); if (logical_z_dimension > 1) { plan_fwd = fftwf_plan_dft_r2c_3d(logical_z_dimension, logical_y_dimension, logical_x_dimension, real_values, reinterpret_cast(complex_values), FFTW_ESTIMATE); plan_bwd = fftwf_plan_dft_c2r_3d(logical_z_dimension, logical_y_dimension, logical_x_dimension, reinterpret_cast(complex_values), real_values, FFTW_ESTIMATE); } else { plan_fwd = fftwf_plan_dft_r2c_2d(logical_y_dimension, logical_x_dimension, real_values, reinterpret_cast(complex_values), FFTW_ESTIMATE); plan_bwd = fftwf_plan_dft_c2r_2d(logical_y_dimension, logical_x_dimension, reinterpret_cast(complex_values), real_values, FFTW_ESTIMATE); } planned = true; } // set the loop junk value.. if (IsEven(logical_x_dimension) == true) padding_jump_value = 2; else padding_jump_value = 1; // number_of_real_space_pixels = long(logical_x_dimension) * long(logical_y_dimension) * long(logical_z_dimension); ft_normalization_factor = 1.0 / sqrtf(float(number_of_real_space_pixels)); } //!> \brief Allocate memory for the Image object. // // Overloaded version of allocate to cover the supplying just 2 dimensions along with the should_be_in_real_space bool. void Image::Allocate(int wanted_x_size, int wanted_y_size, bool should_be_in_real_space) { Allocate(wanted_x_size, wanted_y_size, 1, should_be_in_real_space); } void Image::AllocateAsPointingToSliceIn3D(Image *wanted3d, long wanted_slice) { Deallocate(); is_in_real_space = wanted3d->is_in_real_space; // if we got here we need to do allocation.. SetLogicalDimensions(wanted3d->logical_x_dimension, wanted3d->logical_y_dimension, 1); // we are not actually allocating, we are pointing.. long bytes_in_slice = wanted3d->real_memory_allocated / wanted3d->logical_z_dimension; image_memory_should_not_be_deallocated = true; is_in_memory = true; // kind of a lie real_memory_allocated = bytes_in_slice; // kind of a lie real_values = wanted3d->real_values + (bytes_in_slice * (wanted_slice - 1)); // point to the 3d.. complex_values = (std::complex*) real_values; // Set the complex_values to point at the newly allocated real values; // Update addresses etc.. UpdateLoopingAndAddressing(); // Prepare the plans for FFTW if (planned == false) { wxMutexLocker lock(s_mutexProtectingFFTW); // the mutex will be unlocked when this object is destroyed (when it goes out of scope) MyDebugAssertTrue(lock.IsOk(),"Mute locking failed"); if (logical_z_dimension > 1) { plan_fwd = fftwf_plan_dft_r2c_3d(logical_z_dimension, logical_y_dimension, logical_x_dimension, real_values, reinterpret_cast(complex_values), FFTW_ESTIMATE); plan_bwd = fftwf_plan_dft_c2r_3d(logical_z_dimension, logical_y_dimension, logical_x_dimension, reinterpret_cast(complex_values), real_values, FFTW_ESTIMATE); } else { plan_fwd = fftwf_plan_dft_r2c_2d(logical_y_dimension, logical_x_dimension, real_values, reinterpret_cast(complex_values), FFTW_ESTIMATE); plan_bwd = fftwf_plan_dft_c2r_2d(logical_y_dimension, logical_x_dimension, reinterpret_cast(complex_values), real_values, FFTW_ESTIMATE); } planned = true; } // set the loop jump value.. if (IsEven(logical_x_dimension) == true) padding_jump_value = 2; else padding_jump_value = 1; // number_of_real_space_pixels = long(logical_x_dimension) * long(logical_y_dimension) * long(logical_z_dimension); ft_normalization_factor = 1.0 / sqrtf(float(number_of_real_space_pixels)); } //!> \brief Change the logical dimensions of an image and update all related values void Image::SetLogicalDimensions(int wanted_x_size, int wanted_y_size, int wanted_z_size) { logical_x_dimension = wanted_x_size; logical_y_dimension = wanted_y_size; logical_z_dimension = wanted_z_size; } //!> \brief Update all properties related to looping & addressing in real & Fourier space, given the current logical dimensions. void Image::UpdateLoopingAndAddressing() { physical_upper_bound_complex_x = logical_x_dimension / 2; physical_upper_bound_complex_y = logical_y_dimension - 1; physical_upper_bound_complex_z = logical_z_dimension - 1; UpdatePhysicalAddressOfBoxCenter(); //physical_index_of_first_negative_frequency_x = logical_x_dimension / 2 + 1; if (IsEven(logical_y_dimension) == true) { physical_index_of_first_negative_frequency_y = logical_y_dimension / 2; } else { physical_index_of_first_negative_frequency_y = logical_y_dimension / 2 + 1; } if (IsEven(logical_z_dimension) == true) { physical_index_of_first_negative_frequency_z = logical_z_dimension / 2; } else { physical_index_of_first_negative_frequency_z = logical_z_dimension / 2 + 1; } // Update the Fourier voxel size fourier_voxel_size_x = 1.0 / double(logical_x_dimension); fourier_voxel_size_y = 1.0 / double(logical_y_dimension); fourier_voxel_size_z = 1.0 / double(logical_z_dimension); // Logical bounds if (IsEven(logical_x_dimension) == true) { logical_lower_bound_complex_x = -logical_x_dimension / 2; logical_upper_bound_complex_x = logical_x_dimension / 2; logical_lower_bound_real_x = -logical_x_dimension / 2; logical_upper_bound_real_x = logical_x_dimension / 2 - 1; } else { logical_lower_bound_complex_x = -(logical_x_dimension-1) / 2; logical_upper_bound_complex_x = (logical_x_dimension-1) / 2; logical_lower_bound_real_x = -(logical_x_dimension-1) / 2; logical_upper_bound_real_x = (logical_x_dimension-1) / 2; } if (IsEven(logical_y_dimension) == true) { logical_lower_bound_complex_y = -logical_y_dimension / 2; logical_upper_bound_complex_y = logical_y_dimension / 2 - 1; logical_lower_bound_real_y = -logical_y_dimension / 2; logical_upper_bound_real_y = logical_y_dimension / 2 - 1; } else { logical_lower_bound_complex_y = -(logical_y_dimension-1) / 2; logical_upper_bound_complex_y = (logical_y_dimension-1) / 2; logical_lower_bound_real_y = -(logical_y_dimension-1) / 2; logical_upper_bound_real_y = (logical_y_dimension-1) / 2; } if (IsEven(logical_z_dimension) == true) { logical_lower_bound_complex_z = -logical_z_dimension / 2; logical_upper_bound_complex_z = logical_z_dimension / 2 - 1; logical_lower_bound_real_z = -logical_z_dimension / 2; logical_upper_bound_real_z = logical_z_dimension / 2 - 1; } else { logical_lower_bound_complex_z = -(logical_z_dimension - 1) / 2; logical_upper_bound_complex_z = (logical_z_dimension - 1) / 2; logical_lower_bound_real_z = -(logical_z_dimension - 1) / 2; logical_upper_bound_real_z = (logical_z_dimension - 1) / 2; } } //!> \brief Returns the physical address of the image origin void Image::UpdatePhysicalAddressOfBoxCenter() { /* if (IsEven(logical_x_dimension)) physical_address_of_box_center_x = logical_x_dimension / 2; else physical_address_of_box_center_x = (logical_x_dimension - 1) / 2; if (IsEven(logical_y_dimension)) physical_address_of_box_center_y = logical_y_dimension / 2; else physical_address_of_box_center_y = (logical_y_dimension - 1) / 2; if (IsEven(logical_z_dimension)) physical_address_of_box_center_z = logical_z_dimension / 2; else physical_address_of_box_center_z = (logical_z_dimension - 1) / 2; */ physical_address_of_box_center_x = logical_x_dimension / 2; physical_address_of_box_center_y = logical_y_dimension / 2; physical_address_of_box_center_z = logical_z_dimension / 2; } // Work out whether a given Fourier component has a Hermitian mate which is also described explicitely by the FFTW bool Image::FourierComponentHasExplicitHermitianMate(int physical_index_x, int physical_index_y, int physical_index_z) { bool explicit_mate; explicit_mate = physical_index_x == 0 && ! ( physical_index_y == 0 && physical_index_z == 0); // We assume that the Y dimension is the non-flat one if (IsEven(logical_y_dimension)) { explicit_mate = explicit_mate && physical_index_y != physical_index_of_first_negative_frequency_y-1; } if (logical_z_dimension > 1) { if (IsEven(logical_z_dimension)) { explicit_mate = explicit_mate && physical_index_z != physical_index_of_first_negative_frequency_z - 1; } } return explicit_mate; } // Work out whether a given Fourier component is a (redundant) Hermitian mate which is described explicitely by the FFTW but // shouldn't be counted in statistics as an independent Fourier component bool Image::FourierComponentIsExplicitHermitianMate(int physical_index_x, int physical_index_y, int physical_index_z) { bool explicit_mate = physical_index_x == 0 && (physical_index_y >= physical_index_of_first_negative_frequency_y || physical_index_z >= physical_index_of_first_negative_frequency_z); return explicit_mate; } //!> \brief Apply a forward FT to the Image object. The FT is scaled. // The DC component is at (self%DIM(1)/2+1,self%DIM(2)/2+1,self%DIM(3)/2+1) (assuming even dimensions) or at (1,1,1) by default. // // // For details on FFTW, see http://www.fftw.org/ // A helpful page for understanding the output format: http://www.dsprelated.com/showmessage/102675/1.php // A helpful page to learn about vectorization and FFTW benchmarking: http://www.dsprelated.com/showmessage/76779/1.php // \todo Check this: http://objectmix.com/fortran/371439-ifort-openmp-fftw-problem.html // // // // A note on scaling: by default, we divide by N, the number of pixels. This ensures that after we do an inverse FT (without further scaling), // we will return to our original values. However, it means that while in Fourier space, the amplitudes are too high, by a factor of sqrt(N), // such that, for example, Parserval's theorem is not satisfied. void Image::ForwardFFT(bool should_scale) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Image already in Fourier space"); MyDebugAssertTrue(planned, "FFT's not planned"); fftwf_execute_dft_r2c(plan_fwd, real_values, reinterpret_cast(complex_values)); if (should_scale) { DivideByConstant(float(number_of_real_space_pixels)); } // Set the image type is_in_real_space = false; } void Image::BackwardFFT() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertFalse(is_in_real_space, "Image already in real space"); fftwf_execute_dft_c2r(plan_bwd, reinterpret_cast(complex_values), real_values); // Set the image type is_in_real_space = true; } //!> \brief Divide all voxels by a constant value (this is actually done as a multiplication by the inverse) void Image::DivideByConstant(float constant_to_divide_by) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); float inverse = 1. / constant_to_divide_by; for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] *= inverse; } } void Image::MultiplyAddConstant(float constant_to_multiply_by, float constant_to_add) { for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] = real_values[pixel_counter] * constant_to_multiply_by + constant_to_add; } } void Image::AddMultiplyConstant(float constant_to_add, float constant_to_multiply_by) { for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] = (real_values[pixel_counter] + constant_to_add) * constant_to_multiply_by; } } void Image::AddMultiplyAddConstant(float first_constant_to_add, float constant_to_multiply_by, float second_constant_to_add) { for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] = (real_values[pixel_counter] + first_constant_to_add) * constant_to_multiply_by + second_constant_to_add; } } //!> \brief Multiply all voxels by a constant value //inline void Image::MultiplyByConstant(float constant_to_multiply_by) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] *= constant_to_multiply_by; } } void Image::TakeReciprocalRealValues(float zeros_become) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { if (real_values[pixel_counter] != 0.0) real_values[pixel_counter] = 1.0 / real_values[pixel_counter]; else real_values[pixel_counter] = zeros_become; } } void Image::InvertRealValues() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] = - real_values[pixel_counter]; } } void Image::SquareRealValues() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Must be in real space to square real values"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter ++ ) { real_values[pixel_counter] *= real_values[pixel_counter]; } } void Image::ExponentiateRealValues() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Must be in real space to square real values"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter ++ ) { real_values[pixel_counter] = exp(real_values[pixel_counter]); } } void Image::SquareRootRealValues() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Must be in real space to square real values"); MyDebugAssertFalse(HasNegativeRealValue(),"Image has negative value(s). Cannot compute square root.\n"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter ++ ) { real_values[pixel_counter] = sqrtf(real_values[pixel_counter]); } } bool Image::IsConstant() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { if (real_values[pixel_counter] != real_values[0]) return false; } return true; } bool Image::IsBinary() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Only makes sense for images in real space") long pixel_counter = 0; for ( int k = 0; k < logical_z_dimension; k ++ ) { for ( int j = 0; j < logical_y_dimension; j ++ ) { for ( int i = 0; i < logical_x_dimension; i ++ ) { if (real_values[pixel_counter] != 0 && real_values[pixel_counter] != 1) return false; pixel_counter++; } pixel_counter += padding_jump_value; } } return true; } bool Image::HasNan() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); if (is_in_real_space == true) { long pixel_counter = 0; for ( int k = 0; k < logical_z_dimension; k ++ ) { for ( int j = 0; j < logical_y_dimension; j ++ ) { for ( int i = 0; i < logical_x_dimension; i ++ ) { if (std::isnan(real_values[pixel_counter])) return true; pixel_counter ++; } pixel_counter += padding_jump_value; } } } else { for (long pixel_counter = 0; pixel_counter < real_memory_allocated/2 ; pixel_counter ++) { if (std::isnan(abs(complex_values[pixel_counter]))) return true; } } return false; } bool Image::HasNegativeRealValue() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); long pixel_counter = 0; for ( int k = 0; k < logical_z_dimension; k ++ ) { for ( int j = 0; j < logical_y_dimension; j ++ ) { for ( int i = 0; i < logical_x_dimension; i ++ ) { if (real_values[pixel_counter] < 0.0) return true; pixel_counter ++; } pixel_counter += padding_jump_value; } } return false; } void Image::ReadSlices(ImageFile *input_file, long start_slice, long end_slice) { MyDebugAssertTrue(start_slice <= end_slice, "Start slice larger than end slice!"); MyDebugAssertTrue(start_slice > 0, "Start slice is less than 0, the first slice is 1!"); MyDebugAssertTrue(end_slice <= input_file->ReturnNumberOfSlices(), "End slice is greater than number of slices in the file!"); MyDebugAssertTrue(input_file->IsOpen(), "Image file is not open!"); // check the allocations.. int number_of_slices = (end_slice - start_slice) + 1; if (logical_x_dimension != input_file->ReturnXSize() || logical_y_dimension != input_file->ReturnYSize() || logical_z_dimension != number_of_slices || is_in_memory == false) { Deallocate(); Allocate(input_file->ReturnXSize(), input_file->ReturnYSize(), number_of_slices); } // We should be set up - so read in the correct values. // AT THE MOMENT, WE CAN ONLY READ REAL SPACE IMAGES, SO OVERRIDE THIS!!!!! is_in_real_space = true; object_is_centred_in_box = true; input_file->ReadSlicesFromDisk(start_slice, end_slice, real_values); // we need to respace this to take into account the FFTW padding.. AddFFTWPadding(); } //!> \brief Read a set of slices from disk (FFTW padding is done automatically) void Image::ReadSlices(MRCFile *input_file, long start_slice, long end_slice) { MyDebugAssertTrue(start_slice <= end_slice, "Start slice larger than end slice!"); MyDebugAssertTrue(start_slice > 0, "Start slice is less than 0, the first slice is 1!"); MyDebugAssertTrue(end_slice <= input_file->ReturnNumberOfSlices(), "End slice is greater than number of slices in the file!"); MyDebugAssertTrue(input_file->my_file.is_open(), "MRCFile not open!"); // check the allocations.. int number_of_slices = (end_slice - start_slice) + 1; if (logical_x_dimension != input_file->ReturnXSize() || logical_y_dimension != input_file->ReturnYSize() || logical_z_dimension != number_of_slices || is_in_memory == false) { Deallocate(); Allocate(input_file->ReturnXSize(), input_file->ReturnYSize(), number_of_slices); } // We should be set up - so read in the correct values. // AT THE MOMENT, WE CAN ONLY READ REAL SPACE IMAGES, SO OVERRIDE THIS!!!!! is_in_real_space = true; object_is_centred_in_box = true; input_file->ReadSlicesFromDisk(start_slice, end_slice, real_values); // we need to respace this to take into account the FFTW padding.. AddFFTWPadding(); } //!> \brief Read a set of slices from disk (FFTW padding is done automatically) void Image::ReadSlices(DMFile *input_file, long start_slice, long end_slice) { MyDebugAssertTrue(start_slice <= end_slice, "Start slice larger than end slice!"); MyDebugAssertTrue(start_slice > 0, "Start slice is less than 0, the first slice is 1!"); MyDebugAssertTrue(end_slice <= input_file->ReturnNumberOfSlices(), "End slice is greater than number of slices in the file!"); MyDebugAssertTrue(start_slice == end_slice, "Can only read one slice at a time from DM files. Sorry.") // check the allocations.. int number_of_slices = (end_slice - start_slice) + 1; if (logical_x_dimension != input_file->ReturnXSize() || logical_y_dimension != input_file->ReturnYSize() || logical_z_dimension != number_of_slices || is_in_memory == false) { Deallocate(); Allocate(input_file->ReturnXSize(), input_file->ReturnYSize(), number_of_slices); } // We should be set up - so read in the correct values. // AT THE MOMENT, WE CAN ONLY READ REAL SPACE IMAGES, SO OVERRIDE THIS!!!!! is_in_real_space = true; object_is_centred_in_box = true; input_file->ReadSliceFromDisk(start_slice - 1, real_values); // DM indexes slices starting at 0 // we need to respace this to take into account the FFTW padding.. AddFFTWPadding(); } //!> \brief Write a set of slices from disk (FFTW padding is done automatically) void Image::WriteSlices(MRCFile *input_file, long start_slice, long end_slice) { MyDebugAssertTrue(start_slice <= end_slice, "Start slice larger than end slice!"); MyDebugAssertTrue(input_file->my_file.is_open(), "MRCFile not open!"); // THIS PROBABLY NEEDS ATTENTION.. if (start_slice == 1) // if the start slice is one, we set the header to match the image { input_file->my_header.SetDimensionsImage(logical_x_dimension,logical_y_dimension); if (end_slice > input_file->ReturnNumberOfSlices()) { input_file->my_header.SetNumberOfImages(end_slice); } //input_file->WriteHeader(); input_file->rewrite_header_on_close = true; } else // if the last slice is bigger than the current max number of slices, increase the max number of slices { if (end_slice > input_file->ReturnNumberOfSlices()) { input_file->my_header.SetNumberOfImages(end_slice); } input_file->rewrite_header_on_close = true; } MyDebugAssertTrue(logical_x_dimension == input_file->ReturnXSize() || logical_y_dimension == input_file->ReturnYSize(), "Image dimensions (%i, %i) and file dimensions (%i, %i) differ!", logical_x_dimension, logical_y_dimension, input_file->ReturnXSize(), input_file->ReturnYSize()); // if the image is complex.. make a temp image and transform it.. int number_of_slices = (end_slice - start_slice) + 1; if (is_in_real_space == false) { Image temp_image; temp_image.CopyFrom(this); temp_image.BackwardFFT(); temp_image.RemoveFFTWPadding(); input_file->WriteSlicesToDisk(start_slice, end_slice, temp_image.real_values); } else // real space { RemoveFFTWPadding(); input_file->WriteSlicesToDisk(start_slice, end_slice, real_values); AddFFTWPadding(); // to go back } } void Image::WriteSlicesAndFillHeader(std::string wanted_filename, float wanted_pixel_size) { MRCFile output_file; output_file.OpenFile(wanted_filename, true); WriteSlices(&output_file,1,logical_z_dimension); output_file.SetPixelSize(wanted_pixel_size); EmpiricalDistribution density_distribution; UpdateDistributionOfRealValues(&density_distribution); output_file.SetDensityStatistics(density_distribution.GetMinimum(), density_distribution.GetMaximum(), density_distribution.GetSampleMean(), sqrtf(density_distribution.GetSampleVariance())); output_file.CloseFile(); } void Image::QuickAndDirtyWriteSlices(std::string filename, long first_slice_to_write, long last_slice_to_write, bool overwrite, float pixel_size) { MyDebugAssertTrue(first_slice_to_write >0, "Slice is less than 1, first slice is 1"); MRCFile output_file(filename, overwrite); WriteSlices(&output_file,first_slice_to_write,last_slice_to_write); if (pixel_size <= 0.0f) pixel_size = 1.0; output_file.SetPixelSize(pixel_size); output_file.WriteHeader(); } void Image::QuickAndDirtyWriteSlice(std::string filename, long slice_to_write, bool overwrite, float pixel_size) { MyDebugAssertTrue(slice_to_write >0, "Slice is less than 1, first slice is 1"); MRCFile output_file(filename, overwrite); WriteSlice(&output_file, slice_to_write); if (pixel_size <= 0.0f) pixel_size = 1.0; output_file.SetPixelSize(pixel_size); output_file.WriteHeader(); } void Image::QuickAndDirtyReadSlice(std::string filename, long slice_to_read) { ImageFile image_file(filename); ReadSlice(&image_file,slice_to_read); } //!> \brief Take a contiguous set of values, and add the FFTW padding. void Image::AddFFTWPadding() { MyDebugAssertTrue(is_in_memory, "Image not allocated!"); int x,y,z; long current_write_position = real_memory_allocated - (1 + padding_jump_value); long current_read_position = (long(logical_x_dimension) * long(logical_y_dimension) * long(logical_z_dimension)) - 1; for (z = 0; z < logical_z_dimension; z++) { for (y = 0; y < logical_y_dimension; y++) { for (x = 0; x < logical_x_dimension; x++) { real_values[current_write_position] = real_values[current_read_position]; current_write_position--; current_read_position--; } current_write_position -= padding_jump_value; } } } //!> \brief Take a set of FFTW padded values, and remove the padding. void Image::RemoveFFTWPadding() { MyDebugAssertTrue(is_in_memory, "Image not allocated!"); int x,y,z; long current_write_position = 0; long current_read_position = 0; for (z = 0; z < logical_z_dimension; z++) { for (y = 0; y < logical_y_dimension; y++) { for (x = 0; x < logical_x_dimension; x++) { real_values[current_write_position] = real_values[current_read_position]; current_write_position++; current_read_position++; } current_read_position +=padding_jump_value; } } } void Image::SetToConstant(float wanted_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] = wanted_value; } } void Image::AddConstant(float wanted_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] += wanted_value; } } void Image::SetMaximumValue(float new_maximum_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); for (long address = 0; address < real_memory_allocated; address++) { real_values[address] = std::min(new_maximum_value,real_values[address]); } } void Image::SetMinimumValue(float new_minimum_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); for (long address = 0; address < real_memory_allocated; address++) { real_values[address] = std::max(new_minimum_value,real_values[address]); } } void Image::Binarise(float threshold_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); for (long address = 0; address < real_memory_allocated; address++) { if (real_values[address] >= threshold_value) real_values[address] = 1.0f; else real_values[address] = 0.0f; } } void Image::SetMinimumAndMaximumValues(float new_minimum_value, float new_maximum_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); for (long address = 0; address < real_memory_allocated; address++) { real_values[address] = std::max(std::min(new_maximum_value,real_values[address]),new_minimum_value); } } float Image::ReturnMaximumDiagonalRadius() { if (is_in_real_space) { return sqrt(pow(physical_address_of_box_center_x,2)+pow(physical_address_of_box_center_y,2)+pow(physical_address_of_box_center_z,2)); } else { return sqrt(pow(logical_lower_bound_complex_x * fourier_voxel_size_x , 2) + pow(logical_lower_bound_complex_y * fourier_voxel_size_y , 2) + pow(logical_lower_bound_complex_z * fourier_voxel_size_z , 2) ); } } void Image::GetMinMax(float &min_value, float &max_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Only real space supported"); min_value = FLT_MAX; max_value = -FLT_MAX; int i, j, k; long address = 0; for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { if (real_values[address] < min_value) min_value = real_values[address]; if (real_values[address] > max_value) max_value = real_values[address]; address++; } address += padding_jump_value; } } } float Image::ReturnAverageOfRealValuesOnEdges() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); double sum; long number_of_pixels; int pixel_counter; int line_counter; int plane_counter; long address; sum = 0.0; number_of_pixels = 0; address = 0; if (logical_z_dimension == 1) { // Two-dimensional image // First line for (pixel_counter=0; pixel_counter < logical_x_dimension; pixel_counter++) { sum += real_values[address]; address++; } number_of_pixels += logical_x_dimension; address += padding_jump_value; // Other lines for (line_counter=1; line_counter < logical_y_dimension-1; line_counter++) { sum += real_values[address]; address += logical_x_dimension-1; sum += real_values[address]; address += padding_jump_value + 1; number_of_pixels += 2; } // Last line for (pixel_counter=0; pixel_counter < logical_x_dimension; pixel_counter++) { sum += real_values[address]; address++; } number_of_pixels += logical_x_dimension; } else { // Three-dimensional volume // First plane for (line_counter=0; line_counter < logical_y_dimension; line_counter++) { for (pixel_counter=0; pixel_counter < logical_x_dimension; pixel_counter++) { sum += real_values[address]; address++; } address += padding_jump_value; } number_of_pixels += logical_x_dimension * logical_y_dimension; // Other planes for (plane_counter = 1; plane_counter < logical_z_dimension - 1; plane_counter++) { for (line_counter=0; line_counter< logical_y_dimension; line_counter++) { if (line_counter == 0 || line_counter == logical_y_dimension-1) { // First and last line of that section for (pixel_counter=0; pixel_counter < logical_x_dimension; pixel_counter++) { sum += real_values[address]; address++; } address += padding_jump_value; number_of_pixels += logical_x_dimension; } else { // All other lines (only count first and last pixel) sum += real_values[address]; address += logical_x_dimension-1; sum += real_values[address]; address += padding_jump_value + 1; number_of_pixels += 2; } } } // Last plane for (line_counter=0; line_counter < logical_y_dimension; line_counter++) { for (pixel_counter=0; pixel_counter < logical_x_dimension; pixel_counter++) { sum += real_values[address]; address++; } address += padding_jump_value; } number_of_pixels += logical_x_dimension * logical_y_dimension; } return sum/float(number_of_pixels); } float Image::ReturnAverageOfRealValuesInRing(float wanted_inner_radius,float wanted_outer_radius) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); MyDebugAssertTrue(wanted_outer_radius > wanted_inner_radius,"Radii don't make sense"); double sum = 0.0; long address = 0; long number_of_pixels = 0; int i; int j; int k; float x; float y; float z; float inner_radius_squared; float outer_radius_squared; float distance_from_center_squared; inner_radius_squared = powf(wanted_inner_radius, 2); outer_radius_squared = powf(wanted_outer_radius, 2); number_of_pixels = 0; for (k = 0; k < logical_z_dimension; k++) { z = powf(k - physical_address_of_box_center_z, 2); for (j = 0; j < logical_y_dimension; j++) { y = powf(j - physical_address_of_box_center_y, 2); for (i = 0; i < logical_x_dimension; i++) { x = powf(i - physical_address_of_box_center_x, 2); distance_from_center_squared = x + y + z; if (distance_from_center_squared >= inner_radius_squared && distance_from_center_squared <= outer_radius_squared) { sum += real_values[address]; number_of_pixels++; } address++; } address += padding_jump_value; } } if (number_of_pixels > 0) { return float(sum / number_of_pixels); } else { return 0.0; } } float Image::ReturnAverageOfRealValuesAtRadius(float wanted_mask_radius) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); double sum = 0.0; long address = 0; long number_of_pixels = 0; int i; int j; int k; float x; float y; float z; float mask_radius_squared; float distance_from_center_squared; mask_radius_squared = powf(wanted_mask_radius, 2); number_of_pixels = 0; for (k = 0; k < logical_z_dimension; k++) { z = powf(k - physical_address_of_box_center_z, 2); for (j = 0; j < logical_y_dimension; j++) { y = powf(j - physical_address_of_box_center_y, 2); for (i = 0; i < logical_x_dimension; i++) { x = powf(i - physical_address_of_box_center_x, 2); distance_from_center_squared = x + y + z; if (fabsf(distance_from_center_squared -mask_radius_squared) < 4.0) { sum += real_values[address]; number_of_pixels++; } address++; } address += padding_jump_value; } } if (number_of_pixels > 0) { return float(sum / number_of_pixels); } else { return 0.0; } } // Find the largest voxel value, only considering voxels which are at least a certain distance from the center and from the edge in each dimension float Image::ReturnMaximumValue(float minimum_distance_from_center, float minimum_distance_from_edge) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); int i,j,k; int i_dist_from_center, j_dist_from_center, k_dist_from_center; float maximum_value = - std::numeric_limits::max(); const int last_acceptable_address_x = logical_x_dimension - minimum_distance_from_edge - 1; const int last_acceptable_address_y = logical_y_dimension - minimum_distance_from_edge - 1; const int last_acceptable_address_z = logical_z_dimension - minimum_distance_from_edge - 1; long address = 0; for (k=0;k 1) { k_dist_from_center = abs(k - physical_address_of_box_center_z); if (k_dist_from_center < minimum_distance_from_center || k < minimum_distance_from_edge || k > last_acceptable_address_z) { address += logical_y_dimension * (logical_x_dimension + padding_jump_value); continue; } } for (j=0;j last_acceptable_address_y) { address += logical_x_dimension + padding_jump_value; continue; } for (i=0;i last_acceptable_address_x) { address++; continue; } maximum_value = std::max(maximum_value,real_values[address]); address++; } address += padding_jump_value; } } return maximum_value; } // Find the largest voxel value, only considering voxels which are at least a certain distance from the center and from the edge in each dimension float Image::ReturnMinimumValue(float minimum_distance_from_center, float minimum_distance_from_edge) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); int i,j,k; int i_dist_from_center, j_dist_from_center, k_dist_from_center; float minimum_value = std::numeric_limits::max(); const int last_acceptable_address_x = logical_x_dimension - minimum_distance_from_edge - 1; const int last_acceptable_address_y = logical_y_dimension - minimum_distance_from_edge - 1; const int last_acceptable_address_z = logical_z_dimension - minimum_distance_from_edge - 1; long address = 0; for (k=0;k 1) { k_dist_from_center = abs(k - physical_address_of_box_center_z); if (k_dist_from_center < minimum_distance_from_center || k < minimum_distance_from_edge || k > last_acceptable_address_z) { address += logical_y_dimension * (logical_x_dimension + padding_jump_value); continue; } } for (j=0;j last_acceptable_address_y) { address += logical_x_dimension + padding_jump_value; continue; } for (i=0;i last_acceptable_address_x) { address++; continue; } minimum_value = std::min(minimum_value,real_values[address]); address++; } address += padding_jump_value; } } return minimum_value; } //TODO: consolidate (reduce code duplication) by using an Empirical distribution object float Image::ReturnMedianOfRealValues() { long number_of_voxels = logical_x_dimension * logical_y_dimension * logical_z_dimension; float *buffer_array = new float[number_of_voxels]; float median_value; long address = 0; long buffer_counter = 0; int i; int j; int k; for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { buffer_array[buffer_counter] = real_values[address]; buffer_counter++; address++; } address += padding_jump_value; } } std::sort(buffer_array, buffer_array + number_of_voxels -1); median_value = buffer_array[number_of_voxels / 2]; delete [] buffer_array; return median_value; } //TODO: consolidate (reduce code duplication) by using an Empirical distribution object float Image::ReturnAverageOfRealValues(float wanted_mask_radius, bool invert_mask) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); double sum = 0.0; long address = 0; long number_of_pixels = 0; int i; int j; int k; float x; float y; float z; float mask_radius_squared; float distance_from_center_squared; if (wanted_mask_radius > 0.0) { mask_radius_squared = powf(wanted_mask_radius, 2); number_of_pixels = 0; for (k = 0; k < logical_z_dimension; k++) { z = powf(k - physical_address_of_box_center_z, 2); for (j = 0; j < logical_y_dimension; j++) { y = powf(j - physical_address_of_box_center_y, 2); for (i = 0; i < logical_x_dimension; i++) { x = powf(i - physical_address_of_box_center_x, 2); distance_from_center_squared = x + y + z; if (invert_mask) { if (distance_from_center_squared > mask_radius_squared) { sum += real_values[address]; number_of_pixels++; } } else { if (distance_from_center_squared <= mask_radius_squared) { sum += real_values[address]; number_of_pixels++; } } address++; } address += padding_jump_value; } } if (number_of_pixels > 0) { return float(sum / number_of_pixels); } else { return 0.0; } } else { for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { sum += real_values[address]; address++; } address += padding_jump_value; } } } return float(sum / (long(logical_x_dimension) * long(logical_y_dimension) * long(logical_z_dimension))); } void Image::UpdateDistributionOfRealValues(EmpiricalDistribution *my_distribution, float wanted_mask_radius, bool outside, float wanted_center_x, float wanted_center_y, float wanted_center_z ) { MyDebugAssertTrue(is_in_real_space, "Image must be in real space"); int i; int j; int k; float x; float y; float z; long pixel_counter = 0; float distance_from_center_squared; float mask_radius_squared; float edge; float center_x; float center_y; float center_z; if (wanted_center_x == 0.0 && wanted_center_y == 0.0 && wanted_center_z == 0.0) { center_x = physical_address_of_box_center_x; center_y = physical_address_of_box_center_y; center_z = physical_address_of_box_center_z; } else { center_x = wanted_center_x; center_y = wanted_center_y; center_z = wanted_center_z; } if (wanted_mask_radius > 0.0) { mask_radius_squared = powf(wanted_mask_radius, 2); for (k = 0; k < logical_z_dimension; k++) { z = powf(k - center_z, 2); for (j = 0; j < logical_y_dimension; j++) { y = powf(j - center_y, 2); for (i = 0; i < logical_x_dimension; i++) { x = powf(i - center_x, 2); distance_from_center_squared = x + y + z; if (outside) { if (distance_from_center_squared > mask_radius_squared) { my_distribution->AddSampleValue(real_values[pixel_counter]); } } else { if (distance_from_center_squared <= mask_radius_squared) { my_distribution->AddSampleValue(real_values[pixel_counter]); } } pixel_counter++; } pixel_counter += padding_jump_value; } } } else { for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { my_distribution->AddSampleValue(real_values[pixel_counter]); pixel_counter++; } pixel_counter += padding_jump_value; } } } } EmpiricalDistribution Image::ReturnDistributionOfRealValues(float wanted_mask_radius, bool outside, float wanted_center_x, float wanted_center_y, float wanted_center_z) { MyDebugAssertTrue(is_in_real_space, "Image must be in real space"); EmpiricalDistribution my_distribution; UpdateDistributionOfRealValues(&my_distribution, wanted_mask_radius, outside, wanted_center_x, wanted_center_y, wanted_center_z); return my_distribution; } void Image::ComputeAverageAndSigmaOfValuesInSpectrum(float minimum_radius, float maximum_radius, float &average, float &sigma, int cross_half_width) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); MyDebugAssertTrue(maximum_radius > minimum_radius,"Maximum radius must be greater than minimum radius"); MyDebugAssertTrue(logical_z_dimension == 1, "Meant for images, not volumes"); // Private variables int i, j; float x_sq, y_sq, rad_sq; EmpiricalDistribution my_distribution; const float min_rad_sq = powf(minimum_radius,2); const float max_rad_sq = powf(maximum_radius,2); const float cross_half_width_sq = powf(cross_half_width,2); long address = -1; for (j=0;j min_rad_sq && rad_sq < max_rad_sq) { my_distribution.AddSampleValue(real_values[address]); } } address += padding_jump_value; } average = my_distribution.GetSampleMean(); sigma = sqrtf(my_distribution.GetSampleVariance()); } void Image::ZeroCentralPixel() { if (is_in_real_space == false) { complex_values[0] = 0.0f * I + 0.0f; } else { MyDebugAssertTrue(logical_z_dimension == 1, "Meant for images, not volumes"); int i,j; long address = 0; for (j=0;j 0, "Will not work with lowest frequency for fitting of 0."); // Local variables double cross_product = 0.0; double norm_image = 0.0; double norm_ctf = 0.0; long number_of_values = 0; int i,j; float i_logi, j_logi; float i_logi_sq, j_logi_sq; const float inverse_logical_x_dimension = 1.0 / float(logical_x_dimension); const float inverse_logical_y_dimension = 1.0 / float(logical_y_dimension); float current_spatial_frequency_squared; const float lowest_freq = powf(ctf.GetLowestFrequencyForFitting(),2); const float highest_freq = powf(ctf.GetHighestFrequencyForFitting(),2); long address = 0; float current_azimuth; float current_ctf_value; const int central_cross_half_width = 10; float astigmatism_penalty; // Loop over half of the image (ignore Friedel mates) for (j=0;j physical_address_of_box_center_y + central_cross_half_width) { address = j * (padding_jump_value + 2 * physical_address_of_box_center_x); j_logi = float(j-physical_address_of_box_center_y)*inverse_logical_y_dimension; j_logi_sq = powf(j_logi,2); for (i=0;i < physical_address_of_box_center_x - central_cross_half_width;i++) { i_logi = float(i-physical_address_of_box_center_x)*inverse_logical_x_dimension; i_logi_sq = powf(i_logi,2); // Where are we? current_spatial_frequency_squared = j_logi_sq + i_logi_sq; if (current_spatial_frequency_squared > lowest_freq && current_spatial_frequency_squared < highest_freq) { current_azimuth = atan2f(j_logi,i_logi); current_ctf_value = fabsf(ctf.Evaluate(current_spatial_frequency_squared,current_azimuth)); // accumulate results number_of_values++; cross_product += real_values[address + i] * current_ctf_value; norm_image += pow(real_values[address + i],2); norm_ctf += pow(current_ctf_value,2); } // end of test whether within min,max frequency range } } } // Compute the penalty due to astigmatism if (ctf.GetAstigmatismTolerance() > 0.0) { astigmatism_penalty = powf(ctf.GetAstigmatism(),2) * 0.5 / powf(ctf.GetAstigmatismTolerance(),2) / float(number_of_values); } else { astigmatism_penalty = 0.0; } // The final score return cross_product / sqrt(norm_image * norm_ctf) - astigmatism_penalty; } // DNM: Set up for doing correlations with a CTF by making tables of all the pixels that are included, and their frequencies and azimuths // When called with addresses NULL, it simply returns the number of values needed in the arrays // When called with proper addresses, it fills the array and computes norm_image and image_mean, which are constant void Image::SetupQuickCorrelationWithCTF(CTF ctf, int &number_of_values, double &norm_image, double &image_mean, int *addresses, float *spatial_frequency_squared, float *azimuth) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); MyDebugAssertTrue(logical_z_dimension == 1, "Meant for images, not volumes"); MyDebugAssertTrue(ctf.GetLowestFrequencyForFitting() > 0, "Will not work with lowest frequency for fitting of 0."); // Local variables int i,j; float i_logi, j_logi; float i_logi_sq, j_logi_sq; const float inverse_logical_x_dimension = 1.0 / float(logical_x_dimension); const float inverse_logical_y_dimension = 1.0 / float(logical_y_dimension); float current_spatial_frequency_squared; const float lowest_freq = powf(ctf.GetLowestFrequencyForFitting(),2); const float highest_freq = powf(ctf.GetHighestFrequencyForFitting(),2); int address = 0; float current_azimuth; const int central_cross_half_width = 10; double image_sum = 0.; number_of_values = 0; norm_image = 0; image_mean = 0.; // Loop over half of the image (ignore Friedel mates) for (j=0;j physical_address_of_box_center_y + central_cross_half_width) { address = j * (padding_jump_value + 2 * physical_address_of_box_center_x); j_logi = float(j-physical_address_of_box_center_y)*inverse_logical_y_dimension; j_logi_sq = powf(j_logi,2); for (i=0;i < physical_address_of_box_center_x - central_cross_half_width;i++) { i_logi = float(i-physical_address_of_box_center_x)*inverse_logical_x_dimension; i_logi_sq = powf(i_logi,2); // Where are we? current_spatial_frequency_squared = j_logi_sq + i_logi_sq; if (current_spatial_frequency_squared > lowest_freq && current_spatial_frequency_squared < highest_freq) { current_azimuth = atan2f(j_logi,i_logi); if (addresses) { addresses[number_of_values] = address + i; spatial_frequency_squared[number_of_values] = current_spatial_frequency_squared; azimuth[number_of_values] = current_azimuth; image_sum += real_values[address + i]; } number_of_values++; } // end of test whether within min,max frequency range } } } // Now get sum of squared deviations from mean, more accurate than using raw cross-products if (addresses) { image_mean = image_sum / number_of_values; for (i = 0; i < number_of_values; i++) norm_image += pow(real_values[addresses[i]] - image_mean, 2); } } // DNM: Computes correlation with the current CTF estimate given the pixel indexes, frequency and azimuth values // It is about 30% faster than original and now returns true correlation coefficient float Image::QuickCorrelationWithCTF(CTF ctf, int number_of_values, double norm_image, double image_mean, int *addresses, float *spatial_frequency_squared, float *azimuth) { // Local variables int i,j; double cross_product = 0.0; double norm_ctf = 0.0; double ctf_sum = 0.; float current_ctf_value; float astigmatism_penalty; for (i = 0; i < number_of_values; i++) { j = addresses[i]; current_ctf_value = fabsf(-sin(ctf.PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(spatial_frequency_squared[i], azimuth[i]))); cross_product += real_values[j] * current_ctf_value; norm_ctf += pow(current_ctf_value,2); ctf_sum += current_ctf_value; } // Compute the penalty due to astigmatism if (ctf.GetAstigmatismTolerance() > 0.0) { astigmatism_penalty = powf(ctf.GetAstigmatism(),2) * 0.5 / powf(ctf.GetAstigmatismTolerance(),2) / float(number_of_values); } else { astigmatism_penalty = 0.0; } // The final score: norm_image is already a sum of squared deviations from mean; norm_ctf requires adjustment to give true CC return (cross_product - image_mean * ctf_sum) / sqrt(norm_image * (norm_ctf - ctf_sum * ctf_sum / number_of_values)) - astigmatism_penalty; } void Image::ApplyMirrorAlongY() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); MyDebugAssertTrue(logical_z_dimension == 1, "Meant for images, not volumes"); int i,j; long address = logical_x_dimension + padding_jump_value; int j_dist; float temp_value; for (j = 1; j < physical_address_of_box_center_y; j++) { j_dist = 2 * ( physical_address_of_box_center_y - j ) * (logical_x_dimension + padding_jump_value); for (i = 0; i < logical_x_dimension; i++) { temp_value = real_values[address]; real_values[address] = real_values[address+j_dist]; real_values[address+j_dist] = temp_value; address++; } address += padding_jump_value; } // The column j=0 is undefined, we set it to the average of the values that were there before the mirror operation was applied temp_value = 0; for (i=0 ; i < logical_x_dimension; i++) { temp_value += real_values[i]; } temp_value /= float(logical_x_dimension); for (i=0 ; i < logical_x_dimension; i++) { real_values[i] = temp_value; } } void Image::InvertPixelOrder() { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); MyDebugAssertTrue(logical_z_dimension == 1, "Meant for images, not volumes"); Image buffer_image; buffer_image.Allocate(logical_x_dimension, logical_y_dimension, 1); buffer_image.SetToConstant(-1.0f); int i,j; long start_address = 0; long end_address = real_memory_allocated - 1 - padding_jump_value; for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { buffer_image.real_values[start_address] = real_values[end_address]; start_address++; end_address--; } start_address += padding_jump_value; end_address -=padding_jump_value; } Consume(&buffer_image); } void Image::AddImage(Image *other_image) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(logical_x_dimension == other_image->logical_x_dimension && logical_y_dimension == other_image->logical_y_dimension && logical_z_dimension == other_image->logical_z_dimension, "Image dimensions do not match, Image %d, %d, %d \nImage to be added %d, %d, %d", logical_x_dimension,logical_y_dimension,logical_z_dimension, other_image->logical_x_dimension,other_image->logical_y_dimension,other_image->logical_z_dimension) ; for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] += other_image->real_values[pixel_counter]; } } void Image::SubtractImage(Image *other_image) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(HasSameDimensionsAs(other_image),"Images should have same dimensions, but they don't: %i %i %i %i %i %i",logical_x_dimension,logical_y_dimension,logical_z_dimension,other_image->logical_x_dimension,other_image->logical_y_dimension,other_image->logical_z_dimension); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] -= other_image->real_values[pixel_counter]; } } void Image::SubtractSquaredImage(Image *other_image) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); for (long pixel_counter = 0; pixel_counter < real_memory_allocated; pixel_counter++) { real_values[pixel_counter] -= powf(other_image->real_values[pixel_counter],2); } } int Image::ReturnFourierLogicalCoordGivenPhysicalCoord_X(int physical_index) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(physical_index <= physical_upper_bound_complex_x, "index out of bounds"); //if (physical_index >= physical_index_of_first_negative_frequency_x) if (physical_index > physical_address_of_box_center_x) { return physical_index - logical_x_dimension; } else return physical_index; } int Image::ReturnFourierLogicalCoordGivenPhysicalCoord_Y(int physical_index) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(physical_index <= physical_upper_bound_complex_y, "index out of bounds"); if (physical_index >= physical_index_of_first_negative_frequency_y) { return physical_index - logical_y_dimension; } else return physical_index; } int Image::ReturnFourierLogicalCoordGivenPhysicalCoord_Z(int physical_index) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(physical_index <= physical_upper_bound_complex_z, "index out of bounds"); if (physical_index >= physical_index_of_first_negative_frequency_z) { return physical_index - logical_z_dimension; } else return physical_index; } // \brief Compute the 1D rotational average // The first element will be the value at the center/origin of the image. // It is assumed the X axis of the Curve object has been setup already. It should run from 0.0 to the maximum value // possible, which is approximately sqrt(2)*0.5 in Fourier space or sqrt(2)*0.5*logical_dimension in real space // (to compute this properly, use ReturnMaximumDiagonalRadius * fourier_voxel_size). To use // The Fourier space radius convention in real space, give fractional_radius_in_real_space void Image::Compute1DRotationalAverage(Curve &average, Curve &number_of_values, bool fractional_radius_in_real_space, bool average_real_parts) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(average.number_of_points == number_of_values.number_of_points,"Curves do not have the same number of points"); MyDebugAssertTrue((is_in_real_space && ! average_real_parts) || ! is_in_real_space, "average_real_part not possible for real space image"); int i; int j; int k; float rad; long address; // Initialise average.ZeroYData(); number_of_values.ZeroYData(); address = 0; // if (is_in_real_space && !fractional_radius_in_real_space) { int i_logi,j_logi,k_logi; for (k=0;knumber_of_points > 0, "Curve not setup"); MyDebugAssertTrue(curve_with_average_power->data_x[0] == 0.0, "Curve does not start at x = 0\n"); MyDebugAssertTrue(curve_with_average_power->data_x[curve_with_average_power->number_of_points-1] >= 0.5, "Curve does not go to at least x = 0.5 (it goes to %f)\n",curve_with_average_power->data_x[curve_with_average_power->number_of_points-1]); MyDebugAssertTrue(curve_with_average_power->number_of_points == curve_with_number_of_values->number_of_points, "Curves need to have the same number of points"); MyDebugAssertTrue(curve_with_average_power->data_x[0] == curve_with_number_of_values->data_x[0], "Curves need to have the same starting point"); MyDebugAssertTrue(curve_with_average_power->data_x[curve_with_average_power->number_of_points-1] == curve_with_number_of_values->data_x[curve_with_number_of_values->number_of_points-1], "Curves need to have the same ending point"); int i,j,k; float sq_dist_x, sq_dist_y, sq_dist_z; int counter; long address; float spatial_frequency; int number_of_hermitian_mates = 0; // Make sure the curves are clean curve_with_average_power->ZeroYData(); curve_with_number_of_values->ZeroYData(); // Get amplitudes and sum them into the curve object address = 0; for ( k = 0; k <= physical_upper_bound_complex_z; k ++ ) { sq_dist_z = powf(ReturnFourierLogicalCoordGivenPhysicalCoord_Z(k) * fourier_voxel_size_z,2); for ( j = 0; j <= physical_upper_bound_complex_y; j ++ ) { sq_dist_y = powf(ReturnFourierLogicalCoordGivenPhysicalCoord_Y(j) * fourier_voxel_size_y,2); for ( i = 0; i <= physical_upper_bound_complex_x; i ++ ) { if (FourierComponentIsExplicitHermitianMate(i,j,k)) { number_of_hermitian_mates++; address ++; continue; } else { sq_dist_x = powf(i * fourier_voxel_size_x,2); spatial_frequency = sqrtf(sq_dist_x+sq_dist_y+sq_dist_z); // TODO: this could be made faster by doing both interpolations in one go, so one wouldn't have to work out twice between which points the interpolation will happen curve_with_average_power->AddValueAtXUsingLinearInterpolation(spatial_frequency,real(complex_values[address]) * real(complex_values[address]) + imag(complex_values[address]) * imag(complex_values[address]), true ); curve_with_number_of_values->AddValueAtXUsingLinearInterpolation(spatial_frequency,1.0, true); address ++; } } } } // Do the actual averaging for ( counter = 0; counter < curve_with_average_power->number_of_points; counter ++ ) { if ( curve_with_number_of_values->data_y[counter] > 0.0 ) { curve_with_average_power->data_y[counter] /= curve_with_number_of_values->data_y[counter]; } else { curve_with_average_power->data_y[counter] = 0.0; } } } void Image::ComputeAmplitudeSpectrumFull2D(Image *amplitude_spectrum, bool calculate_phases, float phase_multiplier) { MyDebugAssertTrue(is_in_memory,"Memory not allocated"); MyDebugAssertTrue(amplitude_spectrum->is_in_memory, "Other image memory not allocated"); MyDebugAssertTrue(HasSameDimensionsAs(amplitude_spectrum), "Images do not have same dimensions"); MyDebugAssertFalse(is_in_real_space,"Image not in Fourier space"); int ampl_addr_i; int ampl_addr_j; int image_addr_i; int image_addr_j; int i_mate; int j_mate; long address_in_amplitude_spectrum = 0; long address_in_self; float amplitude; float phase; // Loop over the amplitude spectrum for (ampl_addr_j = 0; ampl_addr_j < amplitude_spectrum->logical_y_dimension; ampl_addr_j++) { for (ampl_addr_i = 0; ampl_addr_i < amplitude_spectrum->logical_x_dimension; ampl_addr_i++) { address_in_self = ReturnFourier1DAddressFromLogicalCoord(ampl_addr_i-amplitude_spectrum->physical_address_of_box_center_x,ampl_addr_j-amplitude_spectrum->physical_address_of_box_center_y,0); amplitude = abs(complex_values[address_in_self]); if (! calculate_phases) { amplitude_spectrum->real_values[address_in_amplitude_spectrum] = amplitude; } else { if (amplitude != 0.0f) { if (ampl_addr_i >= amplitude_spectrum->physical_address_of_box_center_x) phase = std::arg(complex_values[address_in_self]); else phase = std::arg(conj(complex_values[address_in_self])); } else phase = 0.0f; phase *= phase_multiplier; phase = fmodf(phase, 2.0f * (float)PI); if (phase > PI) phase -= 2.0f * PI; if (phase <= -PI) phase += 2.0f * PI; amplitude_spectrum->real_values[address_in_amplitude_spectrum] = phase; } address_in_amplitude_spectrum++; } address_in_amplitude_spectrum += amplitude_spectrum->padding_jump_value; } // Done amplitude_spectrum->is_in_real_space = true; amplitude_spectrum->object_is_centred_in_box = true; } /* * Real-space box convolution meant for 2D amplitude spectra * * This is adapted from the MSMOOTH subroutine from CTFFIND3, with a different wrap-around behaviour. * Also, in this version, we loop over the full 2D, rather than just half - this runs faster because less logic within the loop * DNM rewrote this to be vastly faster */ void Image::SpectrumBoxConvolution(Image *output_image, int box_size, float minimum_radius) { MyDebugAssertTrue(IsEven(box_size) == false,"Box size must be odd"); MyDebugAssertTrue(logical_z_dimension == 1,"Volumes not supported"); MyDebugAssertTrue(output_image->is_in_memory == true,"Output image not allocated"); MyDebugAssertTrue(HasSameDimensionsAs(output_image),"Output image does not have same dimensions as image"); // Variables const int half_box_size = (box_size-1)/2; const int cross_half_width_to_ignore = 1; int i; int i_sq; int ii; int j; int j_sq; int jj; int num_voxels; int m; int l; const float minimum_radius_sq = pow(minimum_radius,2); float radius_sq; const int first_i_to_ignore = physical_address_of_box_center_x - cross_half_width_to_ignore; const int last_i_to_ignore = physical_address_of_box_center_x + cross_half_width_to_ignore; const int first_j_to_ignore = physical_address_of_box_center_y - cross_half_width_to_ignore; const int last_j_to_ignore = physical_address_of_box_center_y + cross_half_width_to_ignore; // Addresses long address_within_output = 0; long address_within_input; // Starting and ending x indexes of one or two loops for each line int *x1start = new int[logical_x_dimension]; int *x1end = new int[logical_x_dimension]; int *x2start = new int[logical_x_dimension]; int *x2end = new int[logical_x_dimension]; int *numInLineSum = new int[logical_x_dimension]; float *lineSums = new float[logical_x_dimension * logical_y_dimension]; float sum; int ybase; // Get the limits for one or two loops for making line sums at each X position for (i = 0; i < logical_x_dimension; i++) { x1start[i] = i - half_box_size; x1end[i] = i + half_box_size; x2start[i] = 0; x2end[i] = -1; // Wrap around left edge if (x1start[i] < 0) { x2start[i] = x1start[i] + logical_x_dimension; x2end[i] = logical_x_dimension - 1; x1start[i] = 0; } // Or wrap around right edge else if (x1end[i] >= logical_x_dimension) { x2end[i] = x1end[i] - logical_x_dimension; x2start[i] = 0; x1end[i] = logical_x_dimension - 1; } // Or handle intersection with the central cross by trimming or splitting into two loops else if (x1start[i] <= last_i_to_ignore && x1end[i] >= first_i_to_ignore) { if (x1start[i] >= first_i_to_ignore) x1start[i] = last_i_to_ignore + 1; else if (x1end[i] <= last_i_to_ignore) x1end[i] = first_i_to_ignore - 1; else { x2end[i] = x1end[i]; x2start[i] = last_i_to_ignore + 1; x1end[i] = first_i_to_ignore - 1; } } numInLineSum[i] = x1end[i] + 1 - x1start[i]; if (x2end[i] >= x2start[i]) numInLineSum[i] += x2end[i] + 1 - x2start[i]; } // Loop over Y positions for line sums for (jj = 0; jj < logical_y_dimension; jj++) { ybase = jj * (logical_x_dimension + padding_jump_value); // Form line sums at each X position for (i = 0; i < logical_x_dimension; i++) { sum = 0.; for (ii = x1start[i]; ii <= x1end[i]; ii++) sum += real_values[ii + ybase]; for (ii = x2start[i]; ii <= x2end[i]; ii++) sum += real_values[ii + ybase]; lineSums[i + jj * logical_x_dimension] = sum; } } // Loop over the output image for (j = 0; j < logical_y_dimension; j++) { j_sq = pow((j - physical_address_of_box_center_y),2); for (i = 0; i < logical_x_dimension; i++) { i_sq = pow((i - physical_address_of_box_center_x),2); radius_sq = float(i_sq+j_sq); if ( radius_sq <= minimum_radius_sq ) { output_image->real_values[address_within_output] = real_values[address_within_output]; } else { output_image->real_values[address_within_output] = 0.0e0; num_voxels = 0; // Loop over the lines to sum at this pixel to get the box sum for ( m = - half_box_size; m <= half_box_size; m++) { jj = j + m; // wrap around if (jj < 0) { jj += logical_y_dimension; } if (jj >= logical_y_dimension) { jj -= logical_y_dimension; } // In central cross? //if ( abs(jj - physical_address_of_box_center_y) <= cross_half_width_to_ignore ) { continue; } if ( jj >= first_j_to_ignore && jj <= last_j_to_ignore) { continue; } output_image->real_values[address_within_output] += lineSums[i + jj * logical_x_dimension]; num_voxels += numInLineSum[i]; } // end of loop over the box if (num_voxels == 0) { // DNM: if it happens, surely that should be from same address not whatever address_within_input was output_image->real_values[address_within_output] = real_values[address_within_output]; } else { output_image->real_values[address_within_output] /= float(num_voxels); } } address_within_output++; } address_within_output += output_image->padding_jump_value; } delete [] x1start; delete [] x1end; delete [] x2start; delete [] x2end; delete [] lineSums; delete [] numInLineSum; } /* void Image::SpectrumBoxConvolution(Image *output_image, int box_size, float minimum_radius) { MyDebugAssertTrue(IsEven(box_size) == false,"Box size must be odd"); MyDebugAssertTrue(logical_z_dimension == 1,"Volumes not supported"); MyDebugAssertTrue(output_image->is_in_memory == true,"Output image not allocated"); MyDebugAssertTrue(HasSameDimensionsAs(output_image),"Output image does not have same dimensions as image"); // Variables int half_box_size = (box_size-1)/2; int cross_half_width_to_ignore = 1; int i; int i_friedel; int i_sq; int ii; int ii_friedel; int ii_sq; int iii; int j; int j_friedel; int j_sq; int jj; int jj_friedel; int jj_sq; int jjj; float radius; int num_voxels; int m; int l; // Addresses long address_within_output = 0; long address_within_input; // Loop over the output image. To save time, we only loop over one half of the image [BUG: actually this is looping over the full image! for (j = 0; j < logical_y_dimension; j++) { j_friedel = 2 * physical_address_of_box_center_y - j; j_sq = powf((j - physical_address_of_box_center_y),2); for (i = 0; i < logical_x_dimension; i++) { i_friedel = 2 * physical_address_of_box_center_x - i; i_sq = powf((i - physical_address_of_box_center_x),2); //address_within_output = ReturnReal1DAddressFromPhysicalCoord(i,j,0); radius = sqrt(float(i_sq+j_sq)); if ( radius <= minimum_radius ) { output_image->real_values[address_within_output] = real_values[address_within_output]; } else { output_image->real_values[address_within_output] = 0.0e0; num_voxels = 0; for ( m = - half_box_size; m <= half_box_size; m++) { jj = j + m; if (jj < 0) { jj += logical_y_dimension; } if (jj >= logical_y_dimension) { jj -= logical_y_dimension; } jj_friedel = 2 * physical_address_of_box_center_y - jj; jj_sq = powf((jj - physical_address_of_box_center_y),2); for ( l = - half_box_size; l <= half_box_size; l++) { ii = i + l; if (ii < 0) { ii += logical_x_dimension; } if (ii >= logical_x_dimension) { ii -= logical_x_dimension; } ii_friedel = 2 * physical_address_of_box_center_x - ii; ii_sq = powf((ii - physical_address_of_box_center_x),2); // Friedel or not? if ( ii > physical_address_of_box_center_x) { iii = ii_friedel; jjj = jj_friedel; if (jjj > logical_y_dimension - 1 || iii > logical_x_dimension - 1) { continue; } } else { iii = ii; jjj = jj; } // In central cross? if ( abs(iii - physical_address_of_box_center_x) <= cross_half_width_to_ignore || abs(jjj - physical_address_of_box_center_y) <= cross_half_width_to_ignore ) { continue; } address_within_input = ReturnReal1DAddressFromPhysicalCoord(iii,jjj,0); if ( iii < logical_x_dimension && jjj < logical_y_dimension ) // it sometimes happens that we end up on Nyquist Friedel mates that we don't have (perhaps this can be fixed) { output_image->real_values[address_within_output] += real_values[address_within_input]; } num_voxels++; // not sure why this is not within the if branch, like the addition itself - is this a bug? } } // end of loop over the box if (num_voxels == 0) { output_image->real_values[address_within_output] = real_values[address_within_input]; } else { output_image->real_values[address_within_output] /= float(num_voxels); } } if (j_friedel < logical_y_dimension && i_friedel < logical_x_dimension) { output_image->real_values[ReturnReal1DAddressFromPhysicalCoord(i_friedel,j_friedel,0)] = output_image->real_values[ReturnReal1DAddressFromPhysicalCoord(i,j,0)]; } address_within_output++; } address_within_output += output_image->padding_jump_value; } // There are a few pixels that are not set by the logical above for (i = physical_address_of_box_center_x + 1; i < logical_x_dimension; i++) { i_friedel = 2 * physical_address_of_box_center_x - i; output_image->real_values[ReturnReal1DAddressFromPhysicalCoord(i,0,0)] = output_image->real_values[ReturnReal1DAddressFromPhysicalCoord(i_friedel,0,0)]; output_image->real_values[ReturnReal1DAddressFromPhysicalCoord(i,logical_y_dimension-1,0)] = output_image->real_values[ReturnReal1DAddressFromPhysicalCoord(i_friedel,logical_y_dimension - 1,0)]; } } */ //#pragma GCC push_options //#pragma GCC optimize ("O0") // Taper edges of image so that there are no sharp discontinuities in real space // This is a re-implementation of the MRC program taperedgek.for (Richard Henderson, 1987) void Image::TaperEdges() { MyDebugAssertTrue(is_in_memory,"Image not in memory"); MyDebugAssertTrue(is_in_real_space,"Image not in real space"); // Private variables const float fraction_averaging = 30.0; const float fraction_tapering = 30.0; const int averaging_strip_width_x = int(logical_x_dimension/fraction_averaging); //100 const int averaging_strip_width_y = int(logical_y_dimension/fraction_averaging); const int averaging_strip_width_z = int(logical_z_dimension/fraction_averaging); const int tapering_strip_width_x = int(logical_x_dimension/fraction_tapering); //500 const int tapering_strip_width_y = int(logical_y_dimension/fraction_tapering); const int tapering_strip_width_z = int(logical_z_dimension/fraction_tapering); const int smoothing_half_width_x = 1; // 1 const int smoothing_half_width_y = 1; const int smoothing_half_width_z = 1; int current_dimension; int number_of_dimensions; int second_dimension; int third_dimension; int logical_current_dimension; int logical_second_dimension; int logical_third_dimension; int current_tapering_strip_width; int i,j,k; int j_shift,k_shift; int jj,kk; int number_of_values_in_running_average; long address; int smoothing_half_width_third_dimension; int smoothing_half_width_second_dimension; // 2D arrays float *average_for_current_edge_start = NULL; float *average_for_current_edge_finish = NULL; float *average_for_current_edge_average = NULL; float *smooth_average_for_current_edge_start = NULL; float *smooth_average_for_current_edge_finish = NULL; // Start work // Check dimensions of image are OK if (logical_x_dimension < 2 * tapering_strip_width_x || logical_y_dimension < 2 * tapering_strip_width_y) { MyPrintWithDetails("X,Y dimensions of input image are too small: %i %i\n", logical_x_dimension,logical_y_dimension); DEBUG_ABORT; } if (logical_z_dimension > 1 && logical_z_dimension < 2 * tapering_strip_width_z) { MyPrintWithDetails("Z dimension is too small: %i\n",logical_z_dimension); DEBUG_ABORT; } if ( logical_z_dimension > 1 ) { number_of_dimensions = 3; } else { number_of_dimensions = 2; } for (current_dimension=1; current_dimension <= number_of_dimensions; current_dimension++) { switch(current_dimension) { case(1): second_dimension = 2; third_dimension = 3; logical_current_dimension = logical_x_dimension; logical_second_dimension = logical_y_dimension; logical_third_dimension = logical_z_dimension; current_tapering_strip_width = tapering_strip_width_x; smoothing_half_width_second_dimension = smoothing_half_width_y; smoothing_half_width_third_dimension = smoothing_half_width_z; break; case(2): second_dimension = 1; third_dimension = 3; logical_current_dimension = logical_y_dimension; logical_second_dimension = logical_x_dimension; logical_third_dimension = logical_z_dimension; current_tapering_strip_width = tapering_strip_width_y; smoothing_half_width_second_dimension = smoothing_half_width_x; smoothing_half_width_third_dimension = smoothing_half_width_z; break; case(3): second_dimension = 1; third_dimension = 2; logical_current_dimension = logical_z_dimension; logical_second_dimension = logical_x_dimension; logical_third_dimension = logical_y_dimension; current_tapering_strip_width = tapering_strip_width_z; smoothing_half_width_second_dimension = smoothing_half_width_x; smoothing_half_width_third_dimension = smoothing_half_width_y; break; } // Allocate memory if (average_for_current_edge_start != NULL) { delete [] average_for_current_edge_start; delete [] average_for_current_edge_finish; delete [] average_for_current_edge_average; delete [] smooth_average_for_current_edge_start; delete [] smooth_average_for_current_edge_finish; } average_for_current_edge_start = new float[logical_second_dimension*logical_third_dimension]; average_for_current_edge_finish = new float[logical_second_dimension*logical_third_dimension]; average_for_current_edge_average = new float[logical_second_dimension*logical_third_dimension]; smooth_average_for_current_edge_start = new float[logical_second_dimension*logical_third_dimension]; smooth_average_for_current_edge_finish = new float[logical_second_dimension*logical_third_dimension]; // Initialise memory for(i=0;i logical_third_dimension) continue; for (j_shift=-smoothing_half_width_second_dimension;j_shift<=smoothing_half_width_second_dimension;j_shift++) { jj = j+j_shift; if (jj<1 || jj > logical_second_dimension) continue; number_of_values_in_running_average++; smooth_average_for_current_edge_start [(j-1)+(k-1)*logical_second_dimension] += average_for_current_edge_start [(jj-1)+(kk-1)*logical_second_dimension]; smooth_average_for_current_edge_finish[(j-1)+(k-1)*logical_second_dimension] += average_for_current_edge_finish[(jj-1)+(kk-1)*logical_second_dimension]; } } // Now we can compute the average smooth_average_for_current_edge_start [(j-1)+(k-1)*logical_second_dimension] /= float(number_of_values_in_running_average); smooth_average_for_current_edge_finish[(j-1)+(k-1)*logical_second_dimension] /= float(number_of_values_in_running_average); } } // Taper the image for (i=1;i<=logical_current_dimension;i++) { if (i<=current_tapering_strip_width) { switch(current_dimension) { case(1): for (k=1;k<=logical_third_dimension;k++) { for (j=1;j<=logical_second_dimension;j++) { real_values[ReturnReal1DAddressFromPhysicalCoord(i-1,j-1,k-1)] -= smooth_average_for_current_edge_start[(j-1)+(k-1)*logical_second_dimension] * float(current_tapering_strip_width-i+1) / float(current_tapering_strip_width); } } break; case(2): for (k=1;k<=logical_third_dimension;k++) { for (j=1;j<=logical_second_dimension;j++) { real_values[ReturnReal1DAddressFromPhysicalCoord(j-1,i-1,k-1)] -= smooth_average_for_current_edge_start[(j-1)+(k-1)*logical_second_dimension] * float(current_tapering_strip_width-i+1) / float(current_tapering_strip_width); } } break; case(3): for (k=1;k<=logical_third_dimension;k++) { for (j=1;j<=logical_second_dimension;j++) { real_values[ReturnReal1DAddressFromPhysicalCoord(j-1,k-1,i-1)] -= smooth_average_for_current_edge_start[(j-1)+(k-1)*logical_second_dimension] * float(current_tapering_strip_width-i+1) / float(current_tapering_strip_width); } } break; } } else if(i >= logical_current_dimension - current_tapering_strip_width+1) { switch(current_dimension) { case(1): for (k=1;k<=logical_third_dimension;k++) { for (j=1;j<=logical_second_dimension;j++) { real_values[ReturnReal1DAddressFromPhysicalCoord(i-1,j-1,k-1)] -= smooth_average_for_current_edge_finish[(j-1)+(k-1)*logical_second_dimension] * float(current_tapering_strip_width+i-logical_current_dimension) / float(current_tapering_strip_width); } } break; case(2): for (k=1;k<=logical_third_dimension;k++) { for (j=1;j<=logical_second_dimension;j++) { real_values[ReturnReal1DAddressFromPhysicalCoord(j-1,i-1,k-1)] -= smooth_average_for_current_edge_finish[(j-1)+(k-1)*logical_second_dimension] * float(current_tapering_strip_width+i-logical_current_dimension) / float(current_tapering_strip_width); } } break; case(3): for (k=1;k<=logical_third_dimension;k++) { for (j=1;j<=logical_second_dimension;j++) { real_values[ReturnReal1DAddressFromPhysicalCoord(j-1,k-1,i-1)] -= smooth_average_for_current_edge_finish[(j-1)+(k-1)*logical_second_dimension] * float(current_tapering_strip_width+i-logical_current_dimension) / float(current_tapering_strip_width); } } break; } } } } // end of loop over dimensions // Cleanup delete [] average_for_current_edge_start; delete []average_for_current_edge_finish; delete [] average_for_current_edge_average; delete [] smooth_average_for_current_edge_start; delete [] smooth_average_for_current_edge_finish; } //#pragma GCC pop_options // An alternative to ClipInto which only works for 2D real space clipping into larger image. Should be faster. void Image::ClipIntoLargerRealSpace2D(Image *other_image, float wanted_padding_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(other_image->is_in_memory, "Other image Memory not allocated"); MyDebugAssertTrue(is_in_real_space,"Image must be in real space"); MyDebugAssertTrue(object_is_centred_in_box, "real space image, not centred in box"); MyDebugAssertTrue(logical_z_dimension == 1,"Image must be 2D"); MyDebugAssertTrue(logical_x_dimension <= other_image->logical_x_dimension && logical_y_dimension <= other_image->logical_y_dimension, "Image must be smaller than other image"); other_image->is_in_real_space = is_in_real_space; other_image->object_is_centred_in_box = object_is_centred_in_box; // Looping variables long address_in_self = 0; long address_in_other = 0; int i; int j; // The address boudaries in the other_image for the input image data // If we are clipping a (2,2) image into a (4,4) image, we should be // copying into addresses 1 to 2 in both directions // If we are clipping a logical dimension of 2 into a dimension of 5, // we are copying into addresses 1 to 2 const int i_lower_bound = other_image->physical_address_of_box_center_x - physical_address_of_box_center_x; const int j_lower_bound = other_image->physical_address_of_box_center_y - physical_address_of_box_center_y; const int i_upper_bound = i_lower_bound + logical_x_dimension - 1; const int j_upper_bound = j_lower_bound + logical_y_dimension - 1; // Loop over the other (larger) image for (j = 0; j < other_image->logical_y_dimension; j++) { // Check whether this line is outside of the original image if (j < j_lower_bound || j > j_upper_bound) { // Fill this line with the padding value for (i = 0; i < other_image->logical_x_dimension; i++) { other_image->real_values[address_in_other] = wanted_padding_value; address_in_other ++; } } else { // This line is within the central region for (i = 0; i < other_image->logical_x_dimension; i++) { if (i < i_lower_bound || i > i_upper_bound) { // We are near the beginning or the end of the line other_image->real_values[address_in_other] = wanted_padding_value; } else { other_image->real_values[address_in_other] = real_values[address_in_self]; address_in_self++; } address_in_other ++; } } // We've reached the end of the line address_in_other += other_image->padding_jump_value; if (j >= j_lower_bound) address_in_self += padding_jump_value; } } // NOTE: THIS METHOD ADDS, it does not replace. void Image::InsertOtherImageAtSpecifiedPosition(Image *other_image, int wanted_x_coord, int wanted_y_coord, int wanted_z_coord, float threshold_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(other_image->is_in_memory, "Other image Memory not allocated"); MyDebugAssertTrue(is_in_real_space == true, "Only real space make sense"); int kk; int k; int kk_logi; int jj; int jj_logi; int j; int ii; int ii_logi; int i; long pixel_counter = 0; for (kk = 0; kk < other_image->logical_z_dimension; kk++) { //kk_logi = kk - other_image->physical_address_of_box_center_z; k = physical_address_of_box_center_z + wanted_z_coord - other_image->physical_address_of_box_center_z + kk; // k=0; for (jj = 0; jj < other_image->logical_y_dimension; jj++) { //jj_logi = jj - other_image->physical_address_of_box_center_y - 1; j = physical_address_of_box_center_y + wanted_y_coord - other_image->physical_address_of_box_center_y + jj; for (ii = 0; ii < other_image->logical_x_dimension; ii++) { //ii_logi = ii - other_image->physical_address_of_box_center_x - 1; i = physical_address_of_box_center_x + wanted_x_coord - other_image->physical_address_of_box_center_x + ii; if (k < 0 || k >= logical_z_dimension || j < 0 || j >= logical_y_dimension || i < 0 || i >= logical_x_dimension) { } else { if (other_image->real_values[pixel_counter] > threshold_value) real_values[ReturnReal1DAddressFromPhysicalCoord(i, j, k)] += other_image->real_values[pixel_counter]; } pixel_counter++; } pixel_counter+=other_image->padding_jump_value; } } } // If you don't want to clip from the center, you can give wanted_coordinate_of_box_center_{x,y,z}. This will define the pixel in the image at which other_image will be centered. (0,0,0) means center of image. void Image::ClipInto(Image *other_image, float wanted_padding_value, bool fill_with_noise, float wanted_noise_sigma, int wanted_coordinate_of_box_center_x, int wanted_coordinate_of_box_center_y, int wanted_coordinate_of_box_center_z) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(other_image->is_in_memory, "Other image Memory not allocated"); MyDebugAssertFalse(is_in_real_space == true && fill_with_noise == true, "Fill with noise, only for fourier space"); MyDebugAssertFalse((! is_in_real_space) && (wanted_coordinate_of_box_center_x != 0 || wanted_coordinate_of_box_center_y != 0 || wanted_coordinate_of_box_center_z != 0), "Cannot clip off-center in Fourier space"); long pixel_counter = 0; int array_address = 0; int temp_logical_x; int temp_logical_y; int temp_logical_z; int kk; int k; int kk_logi; int jj; int jj_logi; int j; int ii; int ii_logi; int i; double junk; // take other following attributes other_image->is_in_real_space = is_in_real_space; other_image->object_is_centred_in_box = object_is_centred_in_box; if (is_in_real_space == true) { MyDebugAssertTrue(object_is_centred_in_box, "real space image, not centred in box"); for (kk = 0; kk < other_image->logical_z_dimension; kk++) { kk_logi = kk - other_image->physical_address_of_box_center_z; k = physical_address_of_box_center_z + wanted_coordinate_of_box_center_z + kk_logi; for (jj = 0; jj < other_image->logical_y_dimension; jj++) { jj_logi = jj - other_image->physical_address_of_box_center_y; j = physical_address_of_box_center_y + wanted_coordinate_of_box_center_y + jj_logi; for (ii = 0; ii < other_image->logical_x_dimension; ii++) { ii_logi = ii - other_image->physical_address_of_box_center_x; i = physical_address_of_box_center_x + wanted_coordinate_of_box_center_x + ii_logi; if (k < 0 || k >= logical_z_dimension || j < 0 || j >= logical_y_dimension || i < 0 || i >= logical_x_dimension) { other_image->real_values[pixel_counter] = wanted_padding_value; } else { other_image->real_values[pixel_counter] = ReturnRealPixelFromPhysicalCoord(i, j, k); } pixel_counter++; } pixel_counter+=other_image->padding_jump_value; } } } else { for (kk = 0; kk <= other_image->physical_upper_bound_complex_z; kk++) { temp_logical_z = other_image->ReturnFourierLogicalCoordGivenPhysicalCoord_Z(kk); //if (temp_logical_z > logical_upper_bound_complex_z || temp_logical_z < logical_lower_bound_complex_z) continue; for (jj = 0; jj <= other_image->physical_upper_bound_complex_y; jj++) { temp_logical_y = other_image->ReturnFourierLogicalCoordGivenPhysicalCoord_Y(jj); //if (temp_logical_y > logical_upper_bound_complex_y || temp_logical_y < logical_lower_bound_complex_y) continue; for (ii = 0; ii <= other_image->physical_upper_bound_complex_x; ii++) { temp_logical_x = ii; //if (temp_logical_x > logical_upper_bound_complex_x || temp_logical_x < logical_lower_bound_complex_x) continue; if (fill_with_noise == false) other_image->complex_values[pixel_counter] = ReturnComplexPixelFromLogicalCoord(temp_logical_x, temp_logical_y, temp_logical_z, wanted_padding_value + I * 0.0f); else { if (temp_logical_x < logical_lower_bound_complex_x || temp_logical_x > logical_upper_bound_complex_x || temp_logical_y < logical_lower_bound_complex_y ||temp_logical_y > logical_upper_bound_complex_y || temp_logical_z < logical_lower_bound_complex_z || temp_logical_z > logical_upper_bound_complex_z) { other_image->complex_values[pixel_counter] = (global_random_number_generator.GetNormalRandom() * wanted_noise_sigma) + (I * global_random_number_generator.GetNormalRandom() * wanted_noise_sigma); } else { other_image->complex_values[pixel_counter] = complex_values[ReturnFourier1DAddressFromLogicalCoord(temp_logical_x,temp_logical_y, temp_logical_z)]; } } pixel_counter++; } } } // When we are clipping into a larger volume in Fourier space, there is a half-plane (vol) or half-line (2D image) at Nyquist for which FFTW // does not explicitly tell us the values. We need to fill them in. if (logical_y_dimension < other_image->logical_y_dimension || logical_z_dimension < other_image->logical_z_dimension) { // For a 2D image if (logical_z_dimension == 1) { jj = physical_index_of_first_negative_frequency_y; for (ii = 0; ii <= physical_upper_bound_complex_x; ii++) { other_image->complex_values[other_image->ReturnFourier1DAddressFromPhysicalCoord(ii,jj,0)] = complex_values[ReturnFourier1DAddressFromPhysicalCoord(ii,jj,0)]; } } // For a 3D volume else { // Deal with the positive Nyquist of the 2nd dimension for (kk_logi = logical_lower_bound_complex_z; kk_logi <= logical_upper_bound_complex_z; kk_logi ++) { jj = physical_index_of_first_negative_frequency_y; jj_logi = logical_lower_bound_complex_y; for (ii = 0; ii <= physical_upper_bound_complex_x; ii++) { other_image->complex_values[other_image->ReturnFourier1DAddressFromLogicalCoord(ii,jj,kk_logi)] = complex_values[ReturnFourier1DAddressFromLogicalCoord(ii,jj_logi,kk_logi)]; } } // Deal with the positive Nyquist in the 3rd dimension kk = physical_index_of_first_negative_frequency_z; int kk_mirror = other_image->logical_z_dimension - physical_index_of_first_negative_frequency_z; //wxPrintf("\nkk = %i; kk_mirror = %i\n",kk,kk_mirror); int jj_mirror; //wxPrintf("Will loop jj from %i to %i\n",1,physical_index_of_first_negative_frequency_y); for (jj = 1; jj <= physical_index_of_first_negative_frequency_y; jj ++ ) { //jj_mirror = other_image->logical_y_dimension - jj; jj_mirror = jj; for (ii = 0; ii <= physical_upper_bound_complex_x; ii++ ) { //wxPrintf("(1) ii = %i; jj = %i; kk = %i; jj_mirror = %i; kk_mirror = %i\n",ii,jj,kk,jj_mirror,kk_mirror); other_image->complex_values[other_image-> ReturnFourier1DAddressFromPhysicalCoord(ii,jj,kk)] = other_image->complex_values[other_image->ReturnFourier1DAddressFromPhysicalCoord(ii,jj_mirror,kk_mirror)]; } } //wxPrintf("Will loop jj from %i to %i\n", other_image->logical_y_dimension - physical_index_of_first_negative_frequency_y, other_image->logical_y_dimension - 1); for (jj = other_image->logical_y_dimension - physical_index_of_first_negative_frequency_y; jj <= other_image->logical_y_dimension - 1; jj ++) { //jj_mirror = other_image->logical_y_dimension - jj; jj_mirror = jj; for (ii = 0; ii <= physical_upper_bound_complex_x; ii++ ) { //wxPrintf("(2) ii = %i; jj = %i; kk = %i; jj_mirror = %i; kk_mirror = %i\n",ii,jj,kk,jj_mirror,kk_mirror); other_image->complex_values[other_image-> ReturnFourier1DAddressFromPhysicalCoord(ii,jj,kk)] = other_image->complex_values[other_image->ReturnFourier1DAddressFromPhysicalCoord(ii,jj_mirror,kk_mirror)]; } } jj = 0; for (ii = 0; ii <= physical_upper_bound_complex_x; ii++) { other_image->complex_values[other_image->ReturnFourier1DAddressFromPhysicalCoord(ii,jj,kk)] = other_image->complex_values[other_image->ReturnFourier1DAddressFromPhysicalCoord(ii,jj,kk_mirror)]; } } } } } // Bilinear interpolation in real space, at point (x,y) where x and y are physical coordinates (i.e. first pixel has x,y = 0,0) void Image::GetRealValueByLinearInterpolationNoBoundsCheckImage(float &x, float &y, float &interpolated_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(logical_z_dimension == 1, "Not for volumes"); MyDebugAssertTrue(is_in_real_space, "Need to be in real space"); const int i_start = int(x); const int j_start = int(y); const float x_dist = x - float(i_start); const float y_dist = y - float(j_start); const float x_dist_m = 1.0 - x_dist; const float y_dist_m = 1.0 - y_dist; const int address_1 = j_start * (logical_x_dimension + padding_jump_value) + i_start; const int address_2 = address_1 + logical_x_dimension + padding_jump_value; MyDebugAssertTrue(address_1+1 <= real_memory_allocated && address_1 >= 0,"Out of bounds, address 1\n"); MyDebugAssertTrue(address_2+1 <= real_memory_allocated && address_2 >= 0,"Out of bounds, address 2\n"); interpolated_value = x_dist_m * y_dist_m * real_values[address_1] + x_dist * y_dist_m * real_values[address_1 + 1] + x_dist_m * y_dist * real_values[address_2] + x_dist * y_dist * real_values[address_2 + 1]; } void Image::Resize(int wanted_x_dimension, int wanted_y_dimension, int wanted_z_dimension, float wanted_padding_value) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(wanted_x_dimension != 0 && wanted_y_dimension != 0 && wanted_z_dimension != 0, "Resize dimension is zero"); if (logical_x_dimension == wanted_x_dimension && logical_y_dimension == wanted_y_dimension && logical_z_dimension == wanted_z_dimension) return; Image temp_image; temp_image.Allocate(wanted_x_dimension, wanted_y_dimension, wanted_z_dimension, is_in_real_space); ClipInto(&temp_image, wanted_padding_value); //CopyFrom(&temp_image); Consume(&temp_image); } void Image::CopyFrom(Image *other_image) { *this = other_image; } void Image::CopyLoopingAndAddressingFrom(Image *other_image) { object_is_centred_in_box = other_image->object_is_centred_in_box; logical_x_dimension = other_image->logical_x_dimension; logical_y_dimension = other_image->logical_y_dimension; logical_z_dimension = other_image->logical_z_dimension; physical_upper_bound_complex_x = other_image->physical_upper_bound_complex_x; physical_upper_bound_complex_y = other_image->physical_upper_bound_complex_y; physical_upper_bound_complex_z = other_image->physical_upper_bound_complex_z; physical_address_of_box_center_x = other_image->physical_address_of_box_center_x; physical_address_of_box_center_y = other_image->physical_address_of_box_center_y; physical_address_of_box_center_z = other_image->physical_address_of_box_center_z; //physical_index_of_first_negative_frequency_x = other_image->physical_index_of_first_negative_frequency_x; physical_index_of_first_negative_frequency_y = other_image->physical_index_of_first_negative_frequency_y; physical_index_of_first_negative_frequency_z = other_image->physical_index_of_first_negative_frequency_z; fourier_voxel_size_x = other_image->fourier_voxel_size_x; fourier_voxel_size_y = other_image->fourier_voxel_size_y; fourier_voxel_size_z = other_image->fourier_voxel_size_z; logical_upper_bound_complex_x = other_image->logical_upper_bound_complex_x; logical_upper_bound_complex_y = other_image->logical_upper_bound_complex_y; logical_upper_bound_complex_z = other_image->logical_upper_bound_complex_z; logical_lower_bound_complex_x = other_image->logical_lower_bound_complex_x; logical_lower_bound_complex_y = other_image->logical_lower_bound_complex_y; logical_lower_bound_complex_z = other_image->logical_lower_bound_complex_z; logical_upper_bound_real_x = other_image->logical_upper_bound_complex_x; logical_upper_bound_real_y = other_image->logical_upper_bound_complex_y; logical_upper_bound_real_z = other_image->logical_upper_bound_complex_z; logical_lower_bound_real_x = other_image->logical_lower_bound_complex_x; logical_lower_bound_real_y = other_image->logical_lower_bound_complex_y; logical_lower_bound_real_z = other_image->logical_lower_bound_complex_z; padding_jump_value = other_image->padding_jump_value; } void Image::Consume(Image *other_image) // copy the parameters then directly steal the memory of another image, leaving it an empty shell { MyDebugAssertTrue(other_image->is_in_memory, "Other image Memory not allocated"); if (is_in_memory == true) { Deallocate(); } is_in_real_space = other_image->is_in_real_space; real_memory_allocated = other_image->real_memory_allocated; CopyLoopingAndAddressingFrom(other_image); real_values = other_image->real_values; complex_values = other_image->complex_values; is_in_memory = other_image->is_in_memory; plan_fwd = other_image->plan_fwd; plan_bwd = other_image->plan_bwd; planned = other_image->planned; other_image->real_values = NULL; other_image->complex_values = NULL; other_image->is_in_memory = false; other_image->plan_fwd = NULL; other_image->plan_bwd = NULL; other_image->planned = false; number_of_real_space_pixels = other_image->number_of_real_space_pixels; ft_normalization_factor = other_image->ft_normalization_factor; } void Image::RealSpaceIntegerShift(int wanted_x_shift, int wanted_y_shift, int wanted_z_shift) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); int i, j, k; long pixel_counter = 0; long shifted_counter; float *buffer = new float[number_of_real_space_pixels]; shifted_counter = - wanted_x_shift - logical_x_dimension * (wanted_y_shift + logical_y_dimension * wanted_z_shift); shifted_counter = remainderf(float(shifted_counter), float(number_of_real_space_pixels)); if (shifted_counter < 0) shifted_counter += number_of_real_space_pixels; for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { buffer[shifted_counter] = real_values[pixel_counter]; pixel_counter++; shifted_counter++; if (shifted_counter >= number_of_real_space_pixels) shifted_counter -= number_of_real_space_pixels; } pixel_counter += padding_jump_value; } } shifted_counter = 0; pixel_counter = 0; for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { real_values[pixel_counter] = buffer[shifted_counter]; pixel_counter++; shifted_counter++; } pixel_counter += padding_jump_value; } } delete [] buffer; } void Image::DilateBinarizedMask(float dilation_radius) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Not in real space"); int i, j, k; int l, m, n, m2, n2; int lim, nlim; long pixel_counter = 0; long shifted_counter = 0; float dilation_radius_squared = powf(dilation_radius, 2); float *buffer = new float[number_of_real_space_pixels]; for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { buffer[shifted_counter] = real_values[pixel_counter]; pixel_counter++; shifted_counter++; } pixel_counter += padding_jump_value; } } lim = myroundint(dilation_radius); if (IsEven(lim)) lim++; nlim = lim; if (logical_z_dimension == 1) nlim = 0; for (n = -nlim; n <= nlim; n += 2) { n2 = n * n; for (m = -lim; m <= lim; m += 2) { m2 = m * m; for (l = -lim; l <= lim; l += 2) { if (l * l + m2 + n2 <= dilation_radius_squared) { shifted_counter = - l - logical_x_dimension * (m + logical_y_dimension * n); shifted_counter = remainderf(float(shifted_counter), float(number_of_real_space_pixels)); if (shifted_counter < 0) shifted_counter += number_of_real_space_pixels; pixel_counter = 0; for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { real_values[pixel_counter] += buffer[shifted_counter]; pixel_counter++; shifted_counter++; if (shifted_counter >= number_of_real_space_pixels) shifted_counter -= number_of_real_space_pixels; } pixel_counter += padding_jump_value; } } } } } } pixel_counter = 0; for (k = 0; k < logical_z_dimension; k++) { for (j = 0; j < logical_y_dimension; j++) { for (i = 0; i < logical_x_dimension; i++) { if (real_values[pixel_counter] != 0.0) real_values[pixel_counter] = 1.0; pixel_counter++; } pixel_counter += padding_jump_value; } } delete [] buffer; } void Image::PhaseShift(float wanted_x_shift, float wanted_y_shift, float wanted_z_shift) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); bool need_to_fft = false; long pixel_counter = 0; int k; int k_logical; int j; int j_logical; int i; float phase_z; float phase_y; float phase_x; std::complex total_phase_shift; if (is_in_real_space == true) { ForwardFFT(); need_to_fft = true; } for (k=0; k <= physical_upper_bound_complex_z; k++) { k_logical = ReturnFourierLogicalCoordGivenPhysicalCoord_Z(k); phase_z = ReturnPhaseFromShift(wanted_z_shift, k_logical, logical_z_dimension); for (j = 0; j <= physical_upper_bound_complex_y; j++) { j_logical = ReturnFourierLogicalCoordGivenPhysicalCoord_Y(j); phase_y = ReturnPhaseFromShift(wanted_y_shift, j_logical, logical_y_dimension); for (i = 0; i <= physical_upper_bound_complex_x; i++) { phase_x = ReturnPhaseFromShift(wanted_x_shift, i, logical_x_dimension); total_phase_shift = Return3DPhaseFromIndividualDimensions(phase_x, phase_y, phase_z); complex_values[pixel_counter] *= total_phase_shift; pixel_counter++; } } } if (need_to_fft == true) BackwardFFT(); } bool Image::HasSameDimensionsAs(Image *other_image) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(other_image->is_in_memory, "Other image Memory not allocated"); if (logical_x_dimension == other_image->logical_x_dimension && logical_y_dimension == other_image->logical_y_dimension && logical_z_dimension == other_image->logical_z_dimension) return true; else return false; } float Image::ReturnLinearInterpolated2D(float &wanted_physical_x_coordinate, float &wanted_physical_y_coordinate) { MyDebugAssertTrue(is_in_memory, "Memory not allocated"); MyDebugAssertTrue(is_in_real_space, "Is in Fourier space"); if(wanted_physical_x_coordinate < 0 || wanted_physical_x_coordinate > logical_x_dimension - 1) return 0.0; if(wanted_physical_y_coordinate < 0 || wanted_physical_y_coordinate > logical_y_dimension - 1) return 0.0; int i; int j; int int_x_coordinate; int int_y_coordinate; int int_x_coordinate1; int int_y_coordinate1; int int_y; float weight_x; float weight_y; float sum = 0.0; int_x_coordinate = int(floorf(wanted_physical_x_coordinate)); int_y_coordinate = int(floorf(wanted_physical_y_coordinate)); int_x_coordinate1 = int_x_coordinate + 1; int_y_coordinate1 = int_y_coordinate + 1; int_x_coordinate1 = std::min(int_x_coordinate1, logical_x_dimension - 1); int_y_coordinate1 = std::min(int_y_coordinate1, logical_y_dimension - 1); for (j = int_y_coordinate; j <= int_y_coordinate1; j++) { weight_y = (1.0 - fabsf(wanted_physical_y_coordinate - j)); int_y = (logical_x_dimension + padding_jump_value) * j; for (i = int_x_coordinate; i <= int_x_coordinate1; i++) { weight_x = (1.0 - fabsf(wanted_physical_x_coordinate - i)); sum += real_values[int_y + i] * weight_x * weight_y; } } return sum; } void Image::CorrectMagnificationDistortion(float distortion_angle, float distortion_major_axis, float distortion_minor_axis) { MyDebugAssertTrue(logical_z_dimension == 1, "Only 2D Images supported"); long pixel_counter = 0; float angle_in_radians = deg_2_rad(distortion_angle); float x_scale_factor = 1.0 / distortion_major_axis; float y_scale_factor = 1.0 / distortion_minor_axis; float average_edge_value = ReturnAverageOfRealValuesOnEdges(); float new_x; float new_y; float final_x; float final_y; int x,y; Image buffer_image; buffer_image.Allocate(logical_x_dimension, logical_y_dimension, logical_z_dimension, is_in_real_space); //buffer_image.CopyFrom(this); for (y = 0; y < logical_y_dimension; y++) { for (x = 0; x < logical_x_dimension; x++) { // first rotation new_x = float(y - physical_address_of_box_center_y) * sinf(-angle_in_radians) + float(x - physical_address_of_box_center_x) * cosf(-angle_in_radians); new_y = float(y - physical_address_of_box_center_y) * cosf(-angle_in_radians) - float(x - physical_address_of_box_center_x) * sinf(-angle_in_radians); // scale factor new_x *= x_scale_factor; new_y *= y_scale_factor; new_x += physical_address_of_box_center_x; new_y += physical_address_of_box_center_y; // rotate back final_x = float(new_y - physical_address_of_box_center_y) * sinf(angle_in_radians) + float(new_x - physical_address_of_box_center_x) * cosf(angle_in_radians); final_y = float(new_y - physical_address_of_box_center_y) * cosf(angle_in_radians) - float(new_x - physical_address_of_box_center_x) * sinf(angle_in_radians); final_x += physical_address_of_box_center_x; final_y += physical_address_of_box_center_y; if (final_x < 0 || final_x > logical_x_dimension - 1 || final_y < 0 || final_y > logical_y_dimension - 1) real_values[pixel_counter] = average_edge_value; else { buffer_image.real_values[pixel_counter] = ReturnLinearInterpolated2D(final_x, final_y); } pixel_counter++; } pixel_counter += padding_jump_value; } Consume(&buffer_image); } ctffind-4.1.14/install-sh000077500000000000000000000332551440356052600152370ustar00rootroot00000000000000#!/bin/sh # install - install a program, script, or datafile scriptversion=2011-11-20.07; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the # following copyright and license. # # Copyright (C) 1994 X Consortium # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to # deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or # sell copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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If nonempty, add APPEND to the result, # otherwise set result to NONDIR_REPLACEMENT. func_dirname () { func_dirname_result=`$ECHO "${1}" | $SED "$dirname"` if test "X$func_dirname_result" = "X${1}"; then func_dirname_result="${3}" else func_dirname_result="$func_dirname_result${2}" fi } # func_dirname may be replaced by extended shell implementation # func_basename file func_basename () { func_basename_result=`$ECHO "${1}" | $SED "$basename"` } # func_basename may be replaced by extended shell implementation # func_dirname_and_basename file append nondir_replacement # perform func_basename and func_dirname in a single function # call: # dirname: Compute the dirname of FILE. If nonempty, # add APPEND to the result, otherwise set result # to NONDIR_REPLACEMENT. # value returned in "$func_dirname_result" # basename: Compute filename of FILE. # value retuned in "$func_basename_result" # Implementation must be kept synchronized with func_dirname # and func_basename. For efficiency, we do not delegate to # those functions but instead duplicate the functionality here. func_dirname_and_basename () { # Extract subdirectory from the argument. func_dirname_result=`$ECHO "${1}" | $SED -e "$dirname"` if test "X$func_dirname_result" = "X${1}"; then func_dirname_result="${3}" else func_dirname_result="$func_dirname_result${2}" fi func_basename_result=`$ECHO "${1}" | $SED -e "$basename"` } # func_dirname_and_basename may be replaced by extended shell implementation # func_stripname prefix suffix name # strip PREFIX and SUFFIX off of NAME. # PREFIX and SUFFIX must not contain globbing or regex special # characters, hashes, percent signs, but SUFFIX may contain a leading # dot (in which case that matches only a dot). # func_strip_suffix prefix name func_stripname () { case ${2} in .*) func_stripname_result=`$ECHO "${3}" | $SED "s%^${1}%%; s%\\\\${2}\$%%"`;; *) func_stripname_result=`$ECHO "${3}" | $SED "s%^${1}%%; s%${2}\$%%"`;; esac } # func_stripname may be replaced by extended shell implementation # These SED scripts presuppose an absolute path with a trailing slash. pathcar='s,^/\([^/]*\).*$,\1,' pathcdr='s,^/[^/]*,,' removedotparts=':dotsl s@/\./@/@g t dotsl s,/\.$,/,' collapseslashes='s@/\{1,\}@/@g' finalslash='s,/*$,/,' # func_normal_abspath PATH # Remove doubled-up and trailing slashes, "." path components, # and cancel out any ".." path components in PATH after making # it an absolute path. # value returned in "$func_normal_abspath_result" func_normal_abspath () { # Start from root dir and reassemble the path. func_normal_abspath_result= func_normal_abspath_tpath=$1 func_normal_abspath_altnamespace= case $func_normal_abspath_tpath in "") # Empty path, that just means $cwd. func_stripname '' '/' "`pwd`" func_normal_abspath_result=$func_stripname_result return ;; # The next three entries are used to spot a run of precisely # two leading slashes without using negated character classes; # we take advantage of case's first-match behaviour. ///*) # Unusual form of absolute path, do nothing. ;; //*) # Not necessarily an ordinary path; POSIX reserves leading '//' # and for example Cygwin uses it to access remote file shares # over CIFS/SMB, so we conserve a leading double slash if found. func_normal_abspath_altnamespace=/ ;; /*) # Absolute path, do nothing. ;; *) # Relative path, prepend $cwd. func_normal_abspath_tpath=`pwd`/$func_normal_abspath_tpath ;; esac # Cancel out all the simple stuff to save iterations. We also want # the path to end with a slash for ease of parsing, so make sure # there is one (and only one) here. func_normal_abspath_tpath=`$ECHO "$func_normal_abspath_tpath" | $SED \ -e "$removedotparts" -e "$collapseslashes" -e "$finalslash"` while :; do # Processed it all yet? if test "$func_normal_abspath_tpath" = / ; then # If we ascended to the root using ".." the result may be empty now. if test -z "$func_normal_abspath_result" ; then func_normal_abspath_result=/ fi break fi func_normal_abspath_tcomponent=`$ECHO "$func_normal_abspath_tpath" | $SED \ -e "$pathcar"` func_normal_abspath_tpath=`$ECHO "$func_normal_abspath_tpath" | $SED \ -e "$pathcdr"` # Figure out what to do with it case $func_normal_abspath_tcomponent in "") # Trailing empty path component, ignore it. ;; ..) # Parent dir; strip last assembled component from result. func_dirname "$func_normal_abspath_result" func_normal_abspath_result=$func_dirname_result ;; *) # Actual path component, append it. func_normal_abspath_result=$func_normal_abspath_result/$func_normal_abspath_tcomponent ;; esac done # Restore leading double-slash if one was found on entry. func_normal_abspath_result=$func_normal_abspath_altnamespace$func_normal_abspath_result } # func_relative_path SRCDIR DSTDIR # generates a relative path from SRCDIR to DSTDIR, with a trailing # slash if non-empty, suitable for immediately appending a filename # without needing to append a separator. # value returned in "$func_relative_path_result" func_relative_path () { func_relative_path_result= func_normal_abspath "$1" func_relative_path_tlibdir=$func_normal_abspath_result func_normal_abspath "$2" func_relative_path_tbindir=$func_normal_abspath_result # Ascend the tree starting from libdir while :; do # check if we have found a prefix of bindir case $func_relative_path_tbindir in $func_relative_path_tlibdir) # found an exact match func_relative_path_tcancelled= break ;; $func_relative_path_tlibdir*) # found a matching prefix func_stripname "$func_relative_path_tlibdir" '' "$func_relative_path_tbindir" func_relative_path_tcancelled=$func_stripname_result if test -z "$func_relative_path_result"; then func_relative_path_result=. fi break ;; *) func_dirname $func_relative_path_tlibdir func_relative_path_tlibdir=${func_dirname_result} if test "x$func_relative_path_tlibdir" = x ; then # Have to descend all the way to the root! func_relative_path_result=../$func_relative_path_result func_relative_path_tcancelled=$func_relative_path_tbindir break fi func_relative_path_result=../$func_relative_path_result ;; esac done # Now calculate path; take care to avoid doubling-up slashes. func_stripname '' '/' "$func_relative_path_result" func_relative_path_result=$func_stripname_result func_stripname '/' '/' "$func_relative_path_tcancelled" if test "x$func_stripname_result" != x ; then func_relative_path_result=${func_relative_path_result}/${func_stripname_result} fi # Normalisation. If bindir is libdir, return empty string, # else relative path ending with a slash; either way, target # file name can be directly appended. if test ! -z "$func_relative_path_result"; then func_stripname './' '' "$func_relative_path_result/" func_relative_path_result=$func_stripname_result fi } # The name of this program: func_dirname_and_basename "$progpath" progname=$func_basename_result # Make sure we have an absolute path for reexecution: case $progpath in [\\/]*|[A-Za-z]:\\*) ;; *[\\/]*) progdir=$func_dirname_result progdir=`cd "$progdir" && pwd` progpath="$progdir/$progname" ;; *) save_IFS="$IFS" IFS=${PATH_SEPARATOR-:} for progdir in $PATH; do IFS="$save_IFS" test -x "$progdir/$progname" && break done IFS="$save_IFS" test -n "$progdir" || progdir=`pwd` progpath="$progdir/$progname" ;; esac # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed="${SED}"' -e 1s/^X//' sed_quote_subst='s/\([`"$\\]\)/\\\1/g' # Same as above, but do not quote variable references. double_quote_subst='s/\(["`\\]\)/\\\1/g' # Sed substitution that turns a string into a regex matching for the # string literally. sed_make_literal_regex='s,[].[^$\\*\/],\\&,g' # Sed substitution that converts a w32 file name or path # which contains forward slashes, into one that contains # (escaped) backslashes. A very naive implementation. lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' # Re-`\' parameter expansions in output of double_quote_subst that were # `\'-ed in input to the same. If an odd number of `\' preceded a '$' # in input to double_quote_subst, that '$' was protected from expansion. # Since each input `\' is now two `\'s, look for any number of runs of # four `\'s followed by two `\'s and then a '$'. `\' that '$'. bs='\\' bs2='\\\\' bs4='\\\\\\\\' dollar='\$' sed_double_backslash="\ s/$bs4/&\\ /g s/^$bs2$dollar/$bs&/ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g s/\n//g" # Standard options: opt_dry_run=false opt_help=false opt_quiet=false opt_verbose=false opt_warning=: # func_echo arg... # Echo program name prefixed message, along with the current mode # name if it has been set yet. func_echo () { $ECHO "$progname: ${opt_mode+$opt_mode: }$*" } # func_verbose arg... # Echo program name prefixed message in verbose mode only. func_verbose () { $opt_verbose && func_echo ${1+"$@"} # A bug in bash halts the script if the last line of a function # fails when set -e is in force, so we need another command to # work around that: : } # func_echo_all arg... # Invoke $ECHO with all args, space-separated. func_echo_all () { $ECHO "$*" } # func_error arg... # Echo program name prefixed message to standard error. func_error () { $ECHO "$progname: ${opt_mode+$opt_mode: }"${1+"$@"} 1>&2 } # func_warning arg... # Echo program name prefixed warning message to standard error. func_warning () { $opt_warning && $ECHO "$progname: ${opt_mode+$opt_mode: }warning: "${1+"$@"} 1>&2 # bash bug again: : } # func_fatal_error arg... # Echo program name prefixed message to standard error, and exit. func_fatal_error () { func_error ${1+"$@"} exit $EXIT_FAILURE } # func_fatal_help arg... # Echo program name prefixed message to standard error, followed by # a help hint, and exit. func_fatal_help () { func_error ${1+"$@"} func_fatal_error "$help" } help="Try \`$progname --help' for more information." ## default # func_grep expression filename # Check whether EXPRESSION matches any line of FILENAME, without output. func_grep () { $GREP "$1" "$2" >/dev/null 2>&1 } # func_mkdir_p directory-path # Make sure the entire path to DIRECTORY-PATH is available. func_mkdir_p () { my_directory_path="$1" my_dir_list= if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then # Protect directory names starting with `-' case $my_directory_path in -*) my_directory_path="./$my_directory_path" ;; esac # While some portion of DIR does not yet exist... while test ! -d "$my_directory_path"; do # ...make a list in topmost first order. Use a colon delimited # list incase some portion of path contains whitespace. my_dir_list="$my_directory_path:$my_dir_list" # If the last portion added has no slash in it, the list is done case $my_directory_path in */*) ;; *) break ;; esac # ...otherwise throw away the child directory and loop my_directory_path=`$ECHO "$my_directory_path" | $SED -e "$dirname"` done my_dir_list=`$ECHO "$my_dir_list" | $SED 's,:*$,,'` save_mkdir_p_IFS="$IFS"; IFS=':' for my_dir in $my_dir_list; do IFS="$save_mkdir_p_IFS" # mkdir can fail with a `File exist' error if two processes # try to create one of the directories concurrently. Don't # stop in that case! $MKDIR "$my_dir" 2>/dev/null || : done IFS="$save_mkdir_p_IFS" # Bail out if we (or some other process) failed to create a directory. test -d "$my_directory_path" || \ func_fatal_error "Failed to create \`$1'" fi } # func_mktempdir [string] # Make a temporary directory that won't clash with other running # libtool processes, and avoids race conditions if possible. If # given, STRING is the basename for that directory. func_mktempdir () { my_template="${TMPDIR-/tmp}/${1-$progname}" if test "$opt_dry_run" = ":"; then # Return a directory name, but don't create it in dry-run mode my_tmpdir="${my_template}-$$" else # If mktemp works, use that first and foremost my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null` if test ! -d "$my_tmpdir"; then # Failing that, at least try and use $RANDOM to avoid a race my_tmpdir="${my_template}-${RANDOM-0}$$" save_mktempdir_umask=`umask` umask 0077 $MKDIR "$my_tmpdir" umask $save_mktempdir_umask fi # If we're not in dry-run mode, bomb out on failure test -d "$my_tmpdir" || \ func_fatal_error "cannot create temporary directory \`$my_tmpdir'" fi $ECHO "$my_tmpdir" } # func_quote_for_eval arg # Aesthetically quote ARG to be evaled later. # This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT # is double-quoted, suitable for a subsequent eval, whereas # FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters # which are still active within double quotes backslashified. func_quote_for_eval () { case $1 in *[\\\`\"\$]*) func_quote_for_eval_unquoted_result=`$ECHO "$1" | $SED "$sed_quote_subst"` ;; *) func_quote_for_eval_unquoted_result="$1" ;; esac case $func_quote_for_eval_unquoted_result in # Double-quote args containing shell metacharacters to delay # word splitting, command substitution and and variable # expansion for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\"" ;; *) func_quote_for_eval_result="$func_quote_for_eval_unquoted_result" esac } # func_quote_for_expand arg # Aesthetically quote ARG to be evaled later; same as above, # but do not quote variable references. func_quote_for_expand () { case $1 in *[\\\`\"]*) my_arg=`$ECHO "$1" | $SED \ -e "$double_quote_subst" -e "$sed_double_backslash"` ;; *) my_arg="$1" ;; esac case $my_arg in # Double-quote args containing shell metacharacters to delay # word splitting and command substitution for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") my_arg="\"$my_arg\"" ;; esac func_quote_for_expand_result="$my_arg" } # func_show_eval cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. func_show_eval () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$my_cmd" my_status=$? if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_show_eval_locale cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. Use the saved locale for evaluation. func_show_eval_locale () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$lt_user_locale $my_cmd" my_status=$? eval "$lt_safe_locale" if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_tr_sh # Turn $1 into a string suitable for a shell variable name. # Result is stored in $func_tr_sh_result. All characters # not in the set a-zA-Z0-9_ are replaced with '_'. Further, # if $1 begins with a digit, a '_' is prepended as well. func_tr_sh () { case $1 in [0-9]* | *[!a-zA-Z0-9_]*) func_tr_sh_result=`$ECHO "$1" | $SED 's/^\([0-9]\)/_\1/; s/[^a-zA-Z0-9_]/_/g'` ;; * ) func_tr_sh_result=$1 ;; esac } # func_version # Echo version message to standard output and exit. func_version () { $opt_debug $SED -n '/(C)/!b go :more /\./!{ N s/\n# / / b more } :go /^# '$PROGRAM' (GNU /,/# warranty; / { s/^# // s/^# *$// s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/ p }' < "$progpath" exit $? } # func_usage # Echo short help message to standard output and exit. func_usage () { $opt_debug $SED -n '/^# Usage:/,/^# *.*--help/ { s/^# // s/^# *$// s/\$progname/'$progname'/ p }' < "$progpath" echo $ECHO "run \`$progname --help | more' for full usage" exit $? } # func_help [NOEXIT] # Echo long help message to standard output and exit, # unless 'noexit' is passed as argument. func_help () { $opt_debug $SED -n '/^# Usage:/,/# Report bugs to/ { :print s/^# // s/^# *$// s*\$progname*'$progname'* s*\$host*'"$host"'* s*\$SHELL*'"$SHELL"'* s*\$LTCC*'"$LTCC"'* s*\$LTCFLAGS*'"$LTCFLAGS"'* s*\$LD*'"$LD"'* s/\$with_gnu_ld/'"$with_gnu_ld"'/ s/\$automake_version/'"`(${AUTOMAKE-automake} --version) 2>/dev/null |$SED 1q`"'/ s/\$autoconf_version/'"`(${AUTOCONF-autoconf} --version) 2>/dev/null |$SED 1q`"'/ p d } /^# .* home page:/b print /^# General help using/b print ' < "$progpath" ret=$? if test -z "$1"; then exit $ret fi } # func_missing_arg argname # Echo program name prefixed message to standard error and set global # exit_cmd. func_missing_arg () { $opt_debug func_error "missing argument for $1." exit_cmd=exit } # func_split_short_opt shortopt # Set func_split_short_opt_name and func_split_short_opt_arg shell # variables after splitting SHORTOPT after the 2nd character. func_split_short_opt () { my_sed_short_opt='1s/^\(..\).*$/\1/;q' my_sed_short_rest='1s/^..\(.*\)$/\1/;q' func_split_short_opt_name=`$ECHO "$1" | $SED "$my_sed_short_opt"` func_split_short_opt_arg=`$ECHO "$1" | $SED "$my_sed_short_rest"` } # func_split_short_opt may be replaced by extended shell implementation # func_split_long_opt longopt # Set func_split_long_opt_name and func_split_long_opt_arg shell # variables after splitting LONGOPT at the `=' sign. func_split_long_opt () { my_sed_long_opt='1s/^\(--[^=]*\)=.*/\1/;q' my_sed_long_arg='1s/^--[^=]*=//' func_split_long_opt_name=`$ECHO "$1" | $SED "$my_sed_long_opt"` func_split_long_opt_arg=`$ECHO "$1" | $SED "$my_sed_long_arg"` } # func_split_long_opt may be replaced by extended shell implementation exit_cmd=: magic="%%%MAGIC variable%%%" magic_exe="%%%MAGIC EXE variable%%%" # Global variables. nonopt= preserve_args= lo2o="s/\\.lo\$/.${objext}/" o2lo="s/\\.${objext}\$/.lo/" extracted_archives= extracted_serial=0 # If this variable is set in any of the actions, the command in it # will be execed at the end. This prevents here-documents from being # left over by shells. exec_cmd= # func_append var value # Append VALUE to the end of shell variable VAR. func_append () { eval "${1}=\$${1}\${2}" } # func_append may be replaced by extended shell implementation # func_append_quoted var value # Quote VALUE and append to the end of shell variable VAR, separated # by a space. func_append_quoted () { func_quote_for_eval "${2}" eval "${1}=\$${1}\\ \$func_quote_for_eval_result" } # func_append_quoted may be replaced by extended shell implementation # func_arith arithmetic-term... func_arith () { func_arith_result=`expr "${@}"` } # func_arith may be replaced by extended shell implementation # func_len string # STRING may not start with a hyphen. func_len () { func_len_result=`expr "${1}" : ".*" 2>/dev/null || echo $max_cmd_len` } # func_len may be replaced by extended shell implementation # func_lo2o object func_lo2o () { func_lo2o_result=`$ECHO "${1}" | $SED "$lo2o"` } # func_lo2o may be replaced by extended shell implementation # func_xform libobj-or-source func_xform () { func_xform_result=`$ECHO "${1}" | $SED 's/\.[^.]*$/.lo/'` } # func_xform may be replaced by extended shell implementation # func_fatal_configuration arg... # Echo program name prefixed message to standard error, followed by # a configuration failure hint, and exit. func_fatal_configuration () { func_error ${1+"$@"} func_error "See the $PACKAGE documentation for more information." func_fatal_error "Fatal configuration error." } # func_config # Display the configuration for all the tags in this script. func_config () { re_begincf='^# ### BEGIN LIBTOOL' re_endcf='^# ### END LIBTOOL' # Default configuration. $SED "1,/$re_begincf CONFIG/d;/$re_endcf CONFIG/,\$d" < "$progpath" # Now print the configurations for the tags. for tagname in $taglist; do $SED -n "/$re_begincf TAG CONFIG: $tagname\$/,/$re_endcf TAG CONFIG: $tagname\$/p" < "$progpath" done exit $? } # func_features # Display the features supported by this script. func_features () { echo "host: $host" if test "$build_libtool_libs" = yes; then echo "enable shared libraries" else echo "disable shared libraries" fi if test "$build_old_libs" = yes; then echo "enable static libraries" else echo "disable static libraries" fi exit $? } # func_enable_tag tagname # Verify that TAGNAME is valid, and either flag an error and exit, or # enable the TAGNAME tag. We also add TAGNAME to the global $taglist # variable here. func_enable_tag () { # Global variable: tagname="$1" re_begincf="^# ### BEGIN LIBTOOL TAG CONFIG: $tagname\$" re_endcf="^# ### END LIBTOOL TAG CONFIG: $tagname\$" sed_extractcf="/$re_begincf/,/$re_endcf/p" # Validate tagname. case $tagname in *[!-_A-Za-z0-9,/]*) func_fatal_error "invalid tag name: $tagname" ;; esac # Don't test for the "default" C tag, as we know it's # there but not specially marked. case $tagname in CC) ;; *) if $GREP "$re_begincf" "$progpath" >/dev/null 2>&1; then taglist="$taglist $tagname" # Evaluate the configuration. Be careful to quote the path # and the sed script, to avoid splitting on whitespace, but # also don't use non-portable quotes within backquotes within # quotes we have to do it in 2 steps: extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"` eval "$extractedcf" else func_error "ignoring unknown tag $tagname" fi ;; esac } # func_check_version_match # Ensure that we are using m4 macros, and libtool script from the same # release of libtool. func_check_version_match () { if test "$package_revision" != "$macro_revision"; then if test "$VERSION" != "$macro_version"; then if test -z "$macro_version"; then cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from an older release. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from $PACKAGE $macro_version. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF fi else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision, $progname: but the definition of this LT_INIT comes from revision $macro_revision. $progname: You should recreate aclocal.m4 with macros from revision $package_revision $progname: of $PACKAGE $VERSION and run autoconf again. _LT_EOF fi exit $EXIT_MISMATCH fi } # Shorthand for --mode=foo, only valid as the first argument case $1 in clean|clea|cle|cl) shift; set dummy --mode clean ${1+"$@"}; shift ;; compile|compil|compi|comp|com|co|c) shift; set dummy --mode compile ${1+"$@"}; shift ;; execute|execut|execu|exec|exe|ex|e) shift; set dummy --mode execute ${1+"$@"}; shift ;; finish|finis|fini|fin|fi|f) shift; set dummy --mode finish ${1+"$@"}; shift ;; install|instal|insta|inst|ins|in|i) shift; set dummy --mode install ${1+"$@"}; shift ;; link|lin|li|l) shift; set dummy --mode link ${1+"$@"}; shift ;; uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u) shift; set dummy --mode uninstall ${1+"$@"}; shift ;; esac # Option defaults: opt_debug=: opt_dry_run=false opt_config=false opt_preserve_dup_deps=false opt_features=false opt_finish=false opt_help=false opt_help_all=false opt_silent=: opt_warning=: opt_verbose=: opt_silent=false opt_verbose=false # Parse options once, thoroughly. This comes as soon as possible in the # script to make things like `--version' happen as quickly as we can. { # this just eases exit handling while test $# -gt 0; do opt="$1" shift case $opt in --debug|-x) opt_debug='set -x' func_echo "enabling shell trace mode" $opt_debug ;; --dry-run|--dryrun|-n) opt_dry_run=: ;; --config) opt_config=: func_config ;; --dlopen|-dlopen) optarg="$1" opt_dlopen="${opt_dlopen+$opt_dlopen }$optarg" shift ;; --preserve-dup-deps) opt_preserve_dup_deps=: ;; --features) opt_features=: func_features ;; --finish) opt_finish=: set dummy --mode finish ${1+"$@"}; shift ;; --help) opt_help=: ;; --help-all) opt_help_all=: opt_help=': help-all' ;; --mode) test $# = 0 && func_missing_arg $opt && break optarg="$1" opt_mode="$optarg" case $optarg in # Valid mode arguments: clean|compile|execute|finish|install|link|relink|uninstall) ;; # Catch anything else as an error *) func_error "invalid argument for $opt" exit_cmd=exit break ;; esac shift ;; --no-silent|--no-quiet) opt_silent=false func_append preserve_args " $opt" ;; --no-warning|--no-warn) opt_warning=false func_append preserve_args " $opt" ;; --no-verbose) opt_verbose=false func_append preserve_args " $opt" ;; --silent|--quiet) opt_silent=: func_append preserve_args " $opt" opt_verbose=false ;; --verbose|-v) opt_verbose=: func_append preserve_args " $opt" opt_silent=false ;; --tag) test $# = 0 && func_missing_arg $opt && break optarg="$1" opt_tag="$optarg" func_append preserve_args " $opt $optarg" func_enable_tag "$optarg" shift ;; -\?|-h) func_usage ;; --help) func_help ;; --version) func_version ;; # Separate optargs to long options: --*=*) func_split_long_opt "$opt" set dummy "$func_split_long_opt_name" "$func_split_long_opt_arg" ${1+"$@"} shift ;; # Separate non-argument short options: -\?*|-h*|-n*|-v*) func_split_short_opt "$opt" set dummy "$func_split_short_opt_name" "-$func_split_short_opt_arg" ${1+"$@"} shift ;; --) break ;; -*) func_fatal_help "unrecognized option \`$opt'" ;; *) set dummy "$opt" ${1+"$@"}; shift; break ;; esac done # Validate options: # save first non-option argument if test "$#" -gt 0; then nonopt="$opt" shift fi # preserve --debug test "$opt_debug" = : || func_append preserve_args " --debug" case $host in *cygwin* | *mingw* | *pw32* | *cegcc*) # don't eliminate duplications in $postdeps and $predeps opt_duplicate_compiler_generated_deps=: ;; *) opt_duplicate_compiler_generated_deps=$opt_preserve_dup_deps ;; esac $opt_help || { # Sanity checks first: func_check_version_match if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then func_fatal_configuration "not configured to build any kind of library" fi # Darwin sucks eval std_shrext=\"$shrext_cmds\" # Only execute mode is allowed to have -dlopen flags. if test -n "$opt_dlopen" && test "$opt_mode" != execute; then func_error "unrecognized option \`-dlopen'" $ECHO "$help" 1>&2 exit $EXIT_FAILURE fi # Change the help message to a mode-specific one. generic_help="$help" help="Try \`$progname --help --mode=$opt_mode' for more information." } # Bail if the options were screwed $exit_cmd $EXIT_FAILURE } ## ----------- ## ## Main. ## ## ----------- ## # func_lalib_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_lalib_p () { test -f "$1" && $SED -e 4q "$1" 2>/dev/null \ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1 } # func_lalib_unsafe_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function implements the same check as func_lalib_p without # resorting to external programs. To this end, it redirects stdin and # closes it afterwards, without saving the original file descriptor. # As a safety measure, use it only where a negative result would be # fatal anyway. Works if `file' does not exist. func_lalib_unsafe_p () { lalib_p=no if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then for lalib_p_l in 1 2 3 4 do read lalib_p_line case "$lalib_p_line" in \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;; esac done exec 0<&5 5<&- fi test "$lalib_p" = yes } # func_ltwrapper_script_p file # True iff FILE is a libtool wrapper script # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_script_p () { func_lalib_p "$1" } # func_ltwrapper_executable_p file # True iff FILE is a libtool wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_executable_p () { func_ltwrapper_exec_suffix= case $1 in *.exe) ;; *) func_ltwrapper_exec_suffix=.exe ;; esac $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1 } # func_ltwrapper_scriptname file # Assumes file is an ltwrapper_executable # uses $file to determine the appropriate filename for a # temporary ltwrapper_script. func_ltwrapper_scriptname () { func_dirname_and_basename "$1" "" "." func_stripname '' '.exe' "$func_basename_result" func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" } # func_ltwrapper_p file # True iff FILE is a libtool wrapper script or wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_p () { func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1" } # func_execute_cmds commands fail_cmd # Execute tilde-delimited COMMANDS. # If FAIL_CMD is given, eval that upon failure. # FAIL_CMD may read-access the current command in variable CMD! func_execute_cmds () { $opt_debug save_ifs=$IFS; IFS='~' for cmd in $1; do IFS=$save_ifs eval cmd=\"$cmd\" func_show_eval "$cmd" "${2-:}" done IFS=$save_ifs } # func_source file # Source FILE, adding directory component if necessary. # Note that it is not necessary on cygwin/mingw to append a dot to # FILE even if both FILE and FILE.exe exist: automatic-append-.exe # behavior happens only for exec(3), not for open(2)! Also, sourcing # `FILE.' does not work on cygwin managed mounts. func_source () { $opt_debug case $1 in */* | *\\*) . "$1" ;; *) . "./$1" ;; esac } # func_resolve_sysroot PATH # Replace a leading = in PATH with a sysroot. Store the result into # func_resolve_sysroot_result func_resolve_sysroot () { func_resolve_sysroot_result=$1 case $func_resolve_sysroot_result in =*) func_stripname '=' '' "$func_resolve_sysroot_result" func_resolve_sysroot_result=$lt_sysroot$func_stripname_result ;; esac } # func_replace_sysroot PATH # If PATH begins with the sysroot, replace it with = and # store the result into func_replace_sysroot_result. func_replace_sysroot () { case "$lt_sysroot:$1" in ?*:"$lt_sysroot"*) func_stripname "$lt_sysroot" '' "$1" func_replace_sysroot_result="=$func_stripname_result" ;; *) # Including no sysroot. func_replace_sysroot_result=$1 ;; esac } # func_infer_tag arg # Infer tagged configuration to use if any are available and # if one wasn't chosen via the "--tag" command line option. # Only attempt this if the compiler in the base compile # command doesn't match the default compiler. # arg is usually of the form 'gcc ...' func_infer_tag () { $opt_debug if test -n "$available_tags" && test -z "$tagname"; then CC_quoted= for arg in $CC; do func_append_quoted CC_quoted "$arg" done CC_expanded=`func_echo_all $CC` CC_quoted_expanded=`func_echo_all $CC_quoted` case $@ in # Blanks in the command may have been stripped by the calling shell, # but not from the CC environment variable when configure was run. " $CC "* | "$CC "* | " $CC_expanded "* | "$CC_expanded "* | \ " $CC_quoted"* | "$CC_quoted "* | " $CC_quoted_expanded "* | "$CC_quoted_expanded "*) ;; # Blanks at the start of $base_compile will cause this to fail # if we don't check for them as well. *) for z in $available_tags; do if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then # Evaluate the configuration. eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`" CC_quoted= for arg in $CC; do # Double-quote args containing other shell metacharacters. func_append_quoted CC_quoted "$arg" done CC_expanded=`func_echo_all $CC` CC_quoted_expanded=`func_echo_all $CC_quoted` case "$@ " in " $CC "* | "$CC "* | " $CC_expanded "* | "$CC_expanded "* | \ " $CC_quoted"* | "$CC_quoted "* | " $CC_quoted_expanded "* | "$CC_quoted_expanded "*) # The compiler in the base compile command matches # the one in the tagged configuration. # Assume this is the tagged configuration we want. tagname=$z break ;; esac fi done # If $tagname still isn't set, then no tagged configuration # was found and let the user know that the "--tag" command # line option must be used. if test -z "$tagname"; then func_echo "unable to infer tagged configuration" func_fatal_error "specify a tag with \`--tag'" # else # func_verbose "using $tagname tagged configuration" fi ;; esac fi } # func_write_libtool_object output_name pic_name nonpic_name # Create a libtool object file (analogous to a ".la" file), # but don't create it if we're doing a dry run. func_write_libtool_object () { write_libobj=${1} if test "$build_libtool_libs" = yes; then write_lobj=\'${2}\' else write_lobj=none fi if test "$build_old_libs" = yes; then write_oldobj=\'${3}\' else write_oldobj=none fi $opt_dry_run || { cat >${write_libobj}T </dev/null` if test "$?" -eq 0 && test -n "${func_convert_core_file_wine_to_w32_tmp}"; then func_convert_core_file_wine_to_w32_result=`$ECHO "$func_convert_core_file_wine_to_w32_tmp" | $SED -e "$lt_sed_naive_backslashify"` else func_convert_core_file_wine_to_w32_result= fi fi } # end: func_convert_core_file_wine_to_w32 # func_convert_core_path_wine_to_w32 ARG # Helper function used by path conversion functions when $build is *nix, and # $host is mingw, cygwin, or some other w32 environment. Relies on a correctly # configured wine environment available, with the winepath program in $build's # $PATH. Assumes ARG has no leading or trailing path separator characters. # # ARG is path to be converted from $build format to win32. # Result is available in $func_convert_core_path_wine_to_w32_result. # Unconvertible file (directory) names in ARG are skipped; if no directory names # are convertible, then the result may be empty. func_convert_core_path_wine_to_w32 () { $opt_debug # unfortunately, winepath doesn't convert paths, only file names func_convert_core_path_wine_to_w32_result="" if test -n "$1"; then oldIFS=$IFS IFS=: for func_convert_core_path_wine_to_w32_f in $1; do IFS=$oldIFS func_convert_core_file_wine_to_w32 "$func_convert_core_path_wine_to_w32_f" if test -n "$func_convert_core_file_wine_to_w32_result" ; then if test -z "$func_convert_core_path_wine_to_w32_result"; then func_convert_core_path_wine_to_w32_result="$func_convert_core_file_wine_to_w32_result" else func_append func_convert_core_path_wine_to_w32_result ";$func_convert_core_file_wine_to_w32_result" fi fi done IFS=$oldIFS fi } # end: func_convert_core_path_wine_to_w32 # func_cygpath ARGS... # Wrapper around calling the cygpath program via LT_CYGPATH. This is used when # when (1) $build is *nix and Cygwin is hosted via a wine environment; or (2) # $build is MSYS and $host is Cygwin, or (3) $build is Cygwin. In case (1) or # (2), returns the Cygwin file name or path in func_cygpath_result (input # file name or path is assumed to be in w32 format, as previously converted # from $build's *nix or MSYS format). In case (3), returns the w32 file name # or path in func_cygpath_result (input file name or path is assumed to be in # Cygwin format). Returns an empty string on error. # # ARGS are passed to cygpath, with the last one being the file name or path to # be converted. # # Specify the absolute *nix (or w32) name to cygpath in the LT_CYGPATH # environment variable; do not put it in $PATH. func_cygpath () { $opt_debug if test -n "$LT_CYGPATH" && test -f "$LT_CYGPATH"; then func_cygpath_result=`$LT_CYGPATH "$@" 2>/dev/null` if test "$?" -ne 0; then # on failure, ensure result is empty func_cygpath_result= fi else func_cygpath_result= func_error "LT_CYGPATH is empty or specifies non-existent file: \`$LT_CYGPATH'" fi } #end: func_cygpath # func_convert_core_msys_to_w32 ARG # Convert file name or path ARG from MSYS format to w32 format. Return # result in func_convert_core_msys_to_w32_result. func_convert_core_msys_to_w32 () { $opt_debug # awkward: cmd appends spaces to result func_convert_core_msys_to_w32_result=`( cmd //c echo "$1" ) 2>/dev/null | $SED -e 's/[ ]*$//' -e "$lt_sed_naive_backslashify"` } #end: func_convert_core_msys_to_w32 # func_convert_file_check ARG1 ARG2 # Verify that ARG1 (a file name in $build format) was converted to $host # format in ARG2. Otherwise, emit an error message, but continue (resetting # func_to_host_file_result to ARG1). func_convert_file_check () { $opt_debug if test -z "$2" && test -n "$1" ; then func_error "Could not determine host file name corresponding to" func_error " \`$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback: func_to_host_file_result="$1" fi } # end func_convert_file_check # func_convert_path_check FROM_PATHSEP TO_PATHSEP FROM_PATH TO_PATH # Verify that FROM_PATH (a path in $build format) was converted to $host # format in TO_PATH. Otherwise, emit an error message, but continue, resetting # func_to_host_file_result to a simplistic fallback value (see below). func_convert_path_check () { $opt_debug if test -z "$4" && test -n "$3"; then func_error "Could not determine the host path corresponding to" func_error " \`$3'" func_error "Continuing, but uninstalled executables may not work." # Fallback. This is a deliberately simplistic "conversion" and # should not be "improved". See libtool.info. if test "x$1" != "x$2"; then lt_replace_pathsep_chars="s|$1|$2|g" func_to_host_path_result=`echo "$3" | $SED -e "$lt_replace_pathsep_chars"` else func_to_host_path_result="$3" fi fi } # end func_convert_path_check # func_convert_path_front_back_pathsep FRONTPAT BACKPAT REPL ORIG # Modifies func_to_host_path_result by prepending REPL if ORIG matches FRONTPAT # and appending REPL if ORIG matches BACKPAT. func_convert_path_front_back_pathsep () { $opt_debug case $4 in $1 ) func_to_host_path_result="$3$func_to_host_path_result" ;; esac case $4 in $2 ) func_append func_to_host_path_result "$3" ;; esac } # end func_convert_path_front_back_pathsep ################################################## # $build to $host FILE NAME CONVERSION FUNCTIONS # ################################################## # invoked via `$to_host_file_cmd ARG' # # In each case, ARG is the path to be converted from $build to $host format. # Result will be available in $func_to_host_file_result. # func_to_host_file ARG # Converts the file name ARG from $build format to $host format. Return result # in func_to_host_file_result. func_to_host_file () { $opt_debug $to_host_file_cmd "$1" } # end func_to_host_file # func_to_tool_file ARG LAZY # converts the file name ARG from $build format to toolchain format. Return # result in func_to_tool_file_result. If the conversion in use is listed # in (the comma separated) LAZY, no conversion takes place. func_to_tool_file () { $opt_debug case ,$2, in *,"$to_tool_file_cmd",*) func_to_tool_file_result=$1 ;; *) $to_tool_file_cmd "$1" func_to_tool_file_result=$func_to_host_file_result ;; esac } # end func_to_tool_file # func_convert_file_noop ARG # Copy ARG to func_to_host_file_result. func_convert_file_noop () { func_to_host_file_result="$1" } # end func_convert_file_noop # func_convert_file_msys_to_w32 ARG # Convert file name ARG from (mingw) MSYS to (mingw) w32 format; automatic # conversion to w32 is not available inside the cwrapper. Returns result in # func_to_host_file_result. func_convert_file_msys_to_w32 () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then func_convert_core_msys_to_w32 "$1" func_to_host_file_result="$func_convert_core_msys_to_w32_result" fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_msys_to_w32 # func_convert_file_cygwin_to_w32 ARG # Convert file name ARG from Cygwin to w32 format. Returns result in # func_to_host_file_result. func_convert_file_cygwin_to_w32 () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then # because $build is cygwin, we call "the" cygpath in $PATH; no need to use # LT_CYGPATH in this case. func_to_host_file_result=`cygpath -m "$1"` fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_cygwin_to_w32 # func_convert_file_nix_to_w32 ARG # Convert file name ARG from *nix to w32 format. Requires a wine environment # and a working winepath. Returns result in func_to_host_file_result. func_convert_file_nix_to_w32 () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then func_convert_core_file_wine_to_w32 "$1" func_to_host_file_result="$func_convert_core_file_wine_to_w32_result" fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_nix_to_w32 # func_convert_file_msys_to_cygwin ARG # Convert file name ARG from MSYS to Cygwin format. Requires LT_CYGPATH set. # Returns result in func_to_host_file_result. func_convert_file_msys_to_cygwin () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then func_convert_core_msys_to_w32 "$1" func_cygpath -u "$func_convert_core_msys_to_w32_result" func_to_host_file_result="$func_cygpath_result" fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_msys_to_cygwin # func_convert_file_nix_to_cygwin ARG # Convert file name ARG from *nix to Cygwin format. Requires Cygwin installed # in a wine environment, working winepath, and LT_CYGPATH set. Returns result # in func_to_host_file_result. func_convert_file_nix_to_cygwin () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then # convert from *nix to w32, then use cygpath to convert from w32 to cygwin. func_convert_core_file_wine_to_w32 "$1" func_cygpath -u "$func_convert_core_file_wine_to_w32_result" func_to_host_file_result="$func_cygpath_result" fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_nix_to_cygwin ############################################# # $build to $host PATH CONVERSION FUNCTIONS # ############################################# # invoked via `$to_host_path_cmd ARG' # # In each case, ARG is the path to be converted from $build to $host format. # The result will be available in $func_to_host_path_result. # # Path separators are also converted from $build format to $host format. If # ARG begins or ends with a path separator character, it is preserved (but # converted to $host format) on output. # # All path conversion functions are named using the following convention: # file name conversion function : func_convert_file_X_to_Y () # path conversion function : func_convert_path_X_to_Y () # where, for any given $build/$host combination the 'X_to_Y' value is the # same. If conversion functions are added for new $build/$host combinations, # the two new functions must follow this pattern, or func_init_to_host_path_cmd # will break. # func_init_to_host_path_cmd # Ensures that function "pointer" variable $to_host_path_cmd is set to the # appropriate value, based on the value of $to_host_file_cmd. to_host_path_cmd= func_init_to_host_path_cmd () { $opt_debug if test -z "$to_host_path_cmd"; then func_stripname 'func_convert_file_' '' "$to_host_file_cmd" to_host_path_cmd="func_convert_path_${func_stripname_result}" fi } # func_to_host_path ARG # Converts the path ARG from $build format to $host format. Return result # in func_to_host_path_result. func_to_host_path () { $opt_debug func_init_to_host_path_cmd $to_host_path_cmd "$1" } # end func_to_host_path # func_convert_path_noop ARG # Copy ARG to func_to_host_path_result. func_convert_path_noop () { func_to_host_path_result="$1" } # end func_convert_path_noop # func_convert_path_msys_to_w32 ARG # Convert path ARG from (mingw) MSYS to (mingw) w32 format; automatic # conversion to w32 is not available inside the cwrapper. Returns result in # func_to_host_path_result. func_convert_path_msys_to_w32 () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # Remove leading and trailing path separator characters from ARG. MSYS # behavior is inconsistent here; cygpath turns them into '.;' and ';.'; # and winepath ignores them completely. func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_convert_core_msys_to_w32 "$func_to_host_path_tmp1" func_to_host_path_result="$func_convert_core_msys_to_w32_result" func_convert_path_check : ";" \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" fi } # end func_convert_path_msys_to_w32 # func_convert_path_cygwin_to_w32 ARG # Convert path ARG from Cygwin to w32 format. Returns result in # func_to_host_file_result. func_convert_path_cygwin_to_w32 () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # See func_convert_path_msys_to_w32: func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_to_host_path_result=`cygpath -m -p "$func_to_host_path_tmp1"` func_convert_path_check : ";" \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" fi } # end func_convert_path_cygwin_to_w32 # func_convert_path_nix_to_w32 ARG # Convert path ARG from *nix to w32 format. Requires a wine environment and # a working winepath. Returns result in func_to_host_file_result. func_convert_path_nix_to_w32 () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # See func_convert_path_msys_to_w32: func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_convert_core_path_wine_to_w32 "$func_to_host_path_tmp1" func_to_host_path_result="$func_convert_core_path_wine_to_w32_result" func_convert_path_check : ";" \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" fi } # end func_convert_path_nix_to_w32 # func_convert_path_msys_to_cygwin ARG # Convert path ARG from MSYS to Cygwin format. Requires LT_CYGPATH set. # Returns result in func_to_host_file_result. func_convert_path_msys_to_cygwin () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # See func_convert_path_msys_to_w32: func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_convert_core_msys_to_w32 "$func_to_host_path_tmp1" func_cygpath -u -p "$func_convert_core_msys_to_w32_result" func_to_host_path_result="$func_cygpath_result" func_convert_path_check : : \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" : "$1" fi } # end func_convert_path_msys_to_cygwin # func_convert_path_nix_to_cygwin ARG # Convert path ARG from *nix to Cygwin format. Requires Cygwin installed in a # a wine environment, working winepath, and LT_CYGPATH set. Returns result in # func_to_host_file_result. func_convert_path_nix_to_cygwin () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # Remove leading and trailing path separator characters from # ARG. msys behavior is inconsistent here, cygpath turns them # into '.;' and ';.', and winepath ignores them completely. func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_convert_core_path_wine_to_w32 "$func_to_host_path_tmp1" func_cygpath -u -p "$func_convert_core_path_wine_to_w32_result" func_to_host_path_result="$func_cygpath_result" func_convert_path_check : : \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" : "$1" fi } # end func_convert_path_nix_to_cygwin # func_mode_compile arg... func_mode_compile () { $opt_debug # Get the compilation command and the source file. base_compile= srcfile="$nonopt" # always keep a non-empty value in "srcfile" suppress_opt=yes suppress_output= arg_mode=normal libobj= later= pie_flag= for arg do case $arg_mode in arg ) # do not "continue". Instead, add this to base_compile lastarg="$arg" arg_mode=normal ;; target ) libobj="$arg" arg_mode=normal continue ;; normal ) # Accept any command-line options. case $arg in -o) test -n "$libobj" && \ func_fatal_error "you cannot specify \`-o' more than once" arg_mode=target continue ;; -pie | -fpie | -fPIE) func_append pie_flag " $arg" continue ;; -shared | -static | -prefer-pic | -prefer-non-pic) func_append later " $arg" continue ;; -no-suppress) suppress_opt=no continue ;; -Xcompiler) arg_mode=arg # the next one goes into the "base_compile" arg list continue # The current "srcfile" will either be retained or ;; # replaced later. I would guess that would be a bug. -Wc,*) func_stripname '-Wc,' '' "$arg" args=$func_stripname_result lastarg= save_ifs="$IFS"; IFS=',' for arg in $args; do IFS="$save_ifs" func_append_quoted lastarg "$arg" done IFS="$save_ifs" func_stripname ' ' '' "$lastarg" lastarg=$func_stripname_result # Add the arguments to base_compile. func_append base_compile " $lastarg" continue ;; *) # Accept the current argument as the source file. # The previous "srcfile" becomes the current argument. # lastarg="$srcfile" srcfile="$arg" ;; esac # case $arg ;; esac # case $arg_mode # Aesthetically quote the previous argument. func_append_quoted base_compile "$lastarg" done # for arg case $arg_mode in arg) func_fatal_error "you must specify an argument for -Xcompile" ;; target) func_fatal_error "you must specify a target with \`-o'" ;; *) # Get the name of the library object. test -z "$libobj" && { func_basename "$srcfile" libobj="$func_basename_result" } ;; esac # Recognize several different file suffixes. # If the user specifies -o file.o, it is replaced with file.lo case $libobj in *.[cCFSifmso] | \ *.ada | *.adb | *.ads | *.asm | \ *.c++ | *.cc | *.ii | *.class | *.cpp | *.cxx | \ *.[fF][09]? | *.for | *.java | *.go | *.obj | *.sx | *.cu | *.cup) func_xform "$libobj" libobj=$func_xform_result ;; esac case $libobj in *.lo) func_lo2o "$libobj"; obj=$func_lo2o_result ;; *) func_fatal_error "cannot determine name of library object from \`$libobj'" ;; esac func_infer_tag $base_compile for arg in $later; do case $arg in -shared) test "$build_libtool_libs" != yes && \ func_fatal_configuration "can not build a shared library" build_old_libs=no continue ;; -static) build_libtool_libs=no build_old_libs=yes continue ;; -prefer-pic) pic_mode=yes continue ;; -prefer-non-pic) pic_mode=no continue ;; esac done func_quote_for_eval "$libobj" test "X$libobj" != "X$func_quote_for_eval_result" \ && $ECHO "X$libobj" | $GREP '[]~#^*{};<>?"'"'"' &()|`$[]' \ && func_warning "libobj name \`$libobj' may not contain shell special characters." func_dirname_and_basename "$obj" "/" "" objname="$func_basename_result" xdir="$func_dirname_result" lobj=${xdir}$objdir/$objname test -z "$base_compile" && \ func_fatal_help "you must specify a compilation command" # Delete any leftover library objects. if test "$build_old_libs" = yes; then removelist="$obj $lobj $libobj ${libobj}T" else removelist="$lobj $libobj ${libobj}T" fi # On Cygwin there's no "real" PIC flag so we must build both object types case $host_os in cygwin* | mingw* | pw32* | os2* | cegcc*) pic_mode=default ;; esac if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then # non-PIC code in shared libraries is not supported pic_mode=default fi # Calculate the filename of the output object if compiler does # not support -o with -c if test "$compiler_c_o" = no; then output_obj=`$ECHO "$srcfile" | $SED 's%^.*/%%; s%\.[^.]*$%%'`.${objext} lockfile="$output_obj.lock" else output_obj= need_locks=no lockfile= fi # Lock this critical section if it is needed # We use this script file to make the link, it avoids creating a new file if test "$need_locks" = yes; then until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do func_echo "Waiting for $lockfile to be removed" sleep 2 done elif test "$need_locks" = warn; then if test -f "$lockfile"; then $ECHO "\ *** ERROR, $lockfile exists and contains: `cat $lockfile 2>/dev/null` This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi func_append removelist " $output_obj" $ECHO "$srcfile" > "$lockfile" fi $opt_dry_run || $RM $removelist func_append removelist " $lockfile" trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15 func_to_tool_file "$srcfile" func_convert_file_msys_to_w32 srcfile=$func_to_tool_file_result func_quote_for_eval "$srcfile" qsrcfile=$func_quote_for_eval_result # Only build a PIC object if we are building libtool libraries. if test "$build_libtool_libs" = yes; then # Without this assignment, base_compile gets emptied. fbsd_hideous_sh_bug=$base_compile if test "$pic_mode" != no; then command="$base_compile $qsrcfile $pic_flag" else # Don't build PIC code command="$base_compile $qsrcfile" fi func_mkdir_p "$xdir$objdir" if test -z "$output_obj"; then # Place PIC objects in $objdir func_append command " -o $lobj" fi func_show_eval_locale "$command" \ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed, then go on to compile the next one if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then func_show_eval '$MV "$output_obj" "$lobj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi # Allow error messages only from the first compilation. if test "$suppress_opt" = yes; then suppress_output=' >/dev/null 2>&1' fi fi # Only build a position-dependent object if we build old libraries. if test "$build_old_libs" = yes; then if test "$pic_mode" != yes; then # Don't build PIC code command="$base_compile $qsrcfile$pie_flag" else command="$base_compile $qsrcfile $pic_flag" fi if test "$compiler_c_o" = yes; then func_append command " -o $obj" fi # Suppress compiler output if we already did a PIC compilation. func_append command "$suppress_output" func_show_eval_locale "$command" \ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then func_show_eval '$MV "$output_obj" "$obj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi fi $opt_dry_run || { func_write_libtool_object "$libobj" "$objdir/$objname" "$objname" # Unlock the critical section if it was locked if test "$need_locks" != no; then removelist=$lockfile $RM "$lockfile" fi } exit $EXIT_SUCCESS } $opt_help || { test "$opt_mode" = compile && func_mode_compile ${1+"$@"} } func_mode_help () { # We need to display help for each of the modes. case $opt_mode in "") # Generic help is extracted from the usage comments # at the start of this file. func_help ;; clean) $ECHO \ "Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE... Remove files from the build directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, object or program, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; compile) $ECHO \ "Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE Compile a source file into a libtool library object. This mode accepts the following additional options: -o OUTPUT-FILE set the output file name to OUTPUT-FILE -no-suppress do not suppress compiler output for multiple passes -prefer-pic try to build PIC objects only -prefer-non-pic try to build non-PIC objects only -shared do not build a \`.o' file suitable for static linking -static only build a \`.o' file suitable for static linking -Wc,FLAG pass FLAG directly to the compiler COMPILE-COMMAND is a command to be used in creating a \`standard' object file from the given SOURCEFILE. The output file name is determined by removing the directory component from SOURCEFILE, then substituting the C source code suffix \`.c' with the library object suffix, \`.lo'." ;; execute) $ECHO \ "Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]... Automatically set library path, then run a program. This mode accepts the following additional options: -dlopen FILE add the directory containing FILE to the library path This mode sets the library path environment variable according to \`-dlopen' flags. If any of the ARGS are libtool executable wrappers, then they are translated into their corresponding uninstalled binary, and any of their required library directories are added to the library path. Then, COMMAND is executed, with ARGS as arguments." ;; finish) $ECHO \ "Usage: $progname [OPTION]... --mode=finish [LIBDIR]... Complete the installation of libtool libraries. Each LIBDIR is a directory that contains libtool libraries. The commands that this mode executes may require superuser privileges. Use the \`--dry-run' option if you just want to see what would be executed." ;; install) $ECHO \ "Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND... Install executables or libraries. INSTALL-COMMAND is the installation command. The first component should be either the \`install' or \`cp' program. The following components of INSTALL-COMMAND are treated specially: -inst-prefix-dir PREFIX-DIR Use PREFIX-DIR as a staging area for installation The rest of the components are interpreted as arguments to that command (only BSD-compatible install options are recognized)." ;; link) $ECHO \ "Usage: $progname [OPTION]... --mode=link LINK-COMMAND... Link object files or libraries together to form another library, or to create an executable program. LINK-COMMAND is a command using the C compiler that you would use to create a program from several object files. The following components of LINK-COMMAND are treated specially: -all-static do not do any dynamic linking at all -avoid-version do not add a version suffix if possible -bindir BINDIR specify path to binaries directory (for systems where libraries must be found in the PATH setting at runtime) -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3) -export-symbols SYMFILE try to export only the symbols listed in SYMFILE -export-symbols-regex REGEX try to export only the symbols matching REGEX -LLIBDIR search LIBDIR for required installed libraries -lNAME OUTPUT-FILE requires the installed library libNAME -module build a library that can dlopened -no-fast-install disable the fast-install mode -no-install link a not-installable executable -no-undefined declare that a library does not refer to external symbols -o OUTPUT-FILE create OUTPUT-FILE from the specified objects -objectlist FILE Use a list of object files found in FILE to specify objects -precious-files-regex REGEX don't remove output files matching REGEX -release RELEASE specify package release information -rpath LIBDIR the created library will eventually be installed in LIBDIR -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries -shared only do dynamic linking of libtool libraries -shrext SUFFIX override the standard shared library file extension -static do not do any dynamic linking of uninstalled libtool libraries -static-libtool-libs do not do any dynamic linking of libtool libraries -version-info CURRENT[:REVISION[:AGE]] specify library version info [each variable defaults to 0] -weak LIBNAME declare that the target provides the LIBNAME interface -Wc,FLAG -Xcompiler FLAG pass linker-specific FLAG directly to the compiler -Wl,FLAG -Xlinker FLAG pass linker-specific FLAG directly to the linker -XCClinker FLAG pass link-specific FLAG to the compiler driver (CC) All other options (arguments beginning with \`-') are ignored. Every other argument is treated as a filename. Files ending in \`.la' are treated as uninstalled libtool libraries, other files are standard or library object files. If the OUTPUT-FILE ends in \`.la', then a libtool library is created, only library objects (\`.lo' files) may be specified, and \`-rpath' is required, except when creating a convenience library. If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created using \`ar' and \`ranlib', or on Windows using \`lib'. If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file is created, otherwise an executable program is created." ;; uninstall) $ECHO \ "Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE... Remove libraries from an installation directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; *) func_fatal_help "invalid operation mode \`$opt_mode'" ;; esac echo $ECHO "Try \`$progname --help' for more information about other modes." } # Now that we've collected a possible --mode arg, show help if necessary if $opt_help; then if test "$opt_help" = :; then func_mode_help else { func_help noexit for opt_mode in compile link execute install finish uninstall clean; do func_mode_help done } | sed -n '1p; 2,$s/^Usage:/ or: /p' { func_help noexit for opt_mode in compile link execute install finish uninstall clean; do echo func_mode_help done } | sed '1d /^When reporting/,/^Report/{ H d } $x /information about other modes/d /more detailed .*MODE/d s/^Usage:.*--mode=\([^ ]*\) .*/Description of \1 mode:/' fi exit $? fi # func_mode_execute arg... func_mode_execute () { $opt_debug # The first argument is the command name. cmd="$nonopt" test -z "$cmd" && \ func_fatal_help "you must specify a COMMAND" # Handle -dlopen flags immediately. for file in $opt_dlopen; do test -f "$file" \ || func_fatal_help "\`$file' is not a file" dir= case $file in *.la) func_resolve_sysroot "$file" file=$func_resolve_sysroot_result # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$lib' is not a valid libtool archive" # Read the libtool library. dlname= library_names= func_source "$file" # Skip this library if it cannot be dlopened. if test -z "$dlname"; then # Warn if it was a shared library. test -n "$library_names" && \ func_warning "\`$file' was not linked with \`-export-dynamic'" continue fi func_dirname "$file" "" "." dir="$func_dirname_result" if test -f "$dir/$objdir/$dlname"; then func_append dir "/$objdir" else if test ! -f "$dir/$dlname"; then func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" fi fi ;; *.lo) # Just add the directory containing the .lo file. func_dirname "$file" "" "." dir="$func_dirname_result" ;; *) func_warning "\`-dlopen' is ignored for non-libtool libraries and objects" continue ;; esac # Get the absolute pathname. absdir=`cd "$dir" && pwd` test -n "$absdir" && dir="$absdir" # Now add the directory to shlibpath_var. if eval "test -z \"\$$shlibpath_var\""; then eval "$shlibpath_var=\"\$dir\"" else eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\"" fi done # This variable tells wrapper scripts just to set shlibpath_var # rather than running their programs. libtool_execute_magic="$magic" # Check if any of the arguments is a wrapper script. args= for file do case $file in -* | *.la | *.lo ) ;; *) # Do a test to see if this is really a libtool program. if func_ltwrapper_script_p "$file"; then func_source "$file" # Transform arg to wrapped name. file="$progdir/$program" elif func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" func_source "$func_ltwrapper_scriptname_result" # Transform arg to wrapped name. file="$progdir/$program" fi ;; esac # Quote arguments (to preserve shell metacharacters). func_append_quoted args "$file" done if test "X$opt_dry_run" = Xfalse; then if test -n "$shlibpath_var"; then # Export the shlibpath_var. eval "export $shlibpath_var" fi # Restore saved environment variables for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES do eval "if test \"\${save_$lt_var+set}\" = set; then $lt_var=\$save_$lt_var; export $lt_var else $lt_unset $lt_var fi" done # Now prepare to actually exec the command. exec_cmd="\$cmd$args" else # Display what would be done. if test -n "$shlibpath_var"; then eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\"" echo "export $shlibpath_var" fi $ECHO "$cmd$args" exit $EXIT_SUCCESS fi } test "$opt_mode" = execute && func_mode_execute ${1+"$@"} # func_mode_finish arg... func_mode_finish () { $opt_debug libs= libdirs= admincmds= for opt in "$nonopt" ${1+"$@"} do if test -d "$opt"; then func_append libdirs " $opt" elif test -f "$opt"; then if func_lalib_unsafe_p "$opt"; then func_append libs " $opt" else func_warning "\`$opt' is not a valid libtool archive" fi else func_fatal_error "invalid argument \`$opt'" fi done if test -n "$libs"; then if test -n "$lt_sysroot"; then sysroot_regex=`$ECHO "$lt_sysroot" | $SED "$sed_make_literal_regex"` sysroot_cmd="s/\([ ']\)$sysroot_regex/\1/g;" else sysroot_cmd= fi # Remove sysroot references if $opt_dry_run; then for lib in $libs; do echo "removing references to $lt_sysroot and \`=' prefixes from $lib" done else tmpdir=`func_mktempdir` for lib in $libs; do sed -e "${sysroot_cmd} s/\([ ']-[LR]\)=/\1/g; s/\([ ']\)=/\1/g" $lib \ > $tmpdir/tmp-la mv -f $tmpdir/tmp-la $lib done ${RM}r "$tmpdir" fi fi if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then for libdir in $libdirs; do if test -n "$finish_cmds"; then # Do each command in the finish commands. func_execute_cmds "$finish_cmds" 'admincmds="$admincmds '"$cmd"'"' fi if test -n "$finish_eval"; then # Do the single finish_eval. eval cmds=\"$finish_eval\" $opt_dry_run || eval "$cmds" || func_append admincmds " $cmds" fi done fi # Exit here if they wanted silent mode. $opt_silent && exit $EXIT_SUCCESS if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then echo "----------------------------------------------------------------------" echo "Libraries have been installed in:" for libdir in $libdirs; do $ECHO " $libdir" done echo echo "If you ever happen to want to link against installed libraries" echo "in a given directory, LIBDIR, you must either use libtool, and" echo "specify the full pathname of the library, or use the \`-LLIBDIR'" echo "flag during linking and do at least one of the following:" if test -n "$shlibpath_var"; then echo " - add LIBDIR to the \`$shlibpath_var' environment variable" echo " during execution" fi if test -n "$runpath_var"; then echo " - add LIBDIR to the \`$runpath_var' environment variable" echo " during linking" fi if test -n "$hardcode_libdir_flag_spec"; then libdir=LIBDIR eval flag=\"$hardcode_libdir_flag_spec\" $ECHO " - use the \`$flag' linker flag" fi if test -n "$admincmds"; then $ECHO " - have your system administrator run these commands:$admincmds" fi if test -f /etc/ld.so.conf; then echo " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" fi echo echo "See any operating system documentation about shared libraries for" case $host in solaris2.[6789]|solaris2.1[0-9]) echo "more information, such as the ld(1), crle(1) and ld.so(8) manual" echo "pages." ;; *) echo "more information, such as the ld(1) and ld.so(8) manual pages." ;; esac echo "----------------------------------------------------------------------" fi exit $EXIT_SUCCESS } test "$opt_mode" = finish && func_mode_finish ${1+"$@"} # func_mode_install arg... func_mode_install () { $opt_debug # There may be an optional sh(1) argument at the beginning of # install_prog (especially on Windows NT). if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh || # Allow the use of GNU shtool's install command. case $nonopt in *shtool*) :;; *) false;; esac; then # Aesthetically quote it. func_quote_for_eval "$nonopt" install_prog="$func_quote_for_eval_result " arg=$1 shift else install_prog= arg=$nonopt fi # The real first argument should be the name of the installation program. # Aesthetically quote it. func_quote_for_eval "$arg" func_append install_prog "$func_quote_for_eval_result" install_shared_prog=$install_prog case " $install_prog " in *[\\\ /]cp\ *) install_cp=: ;; *) install_cp=false ;; esac # We need to accept at least all the BSD install flags. dest= files= opts= prev= install_type= isdir=no stripme= no_mode=: for arg do arg2= if test -n "$dest"; then func_append files " $dest" dest=$arg continue fi case $arg in -d) isdir=yes ;; -f) if $install_cp; then :; else prev=$arg fi ;; -g | -m | -o) prev=$arg ;; -s) stripme=" -s" continue ;; -*) ;; *) # If the previous option needed an argument, then skip it. if test -n "$prev"; then if test "x$prev" = x-m && test -n "$install_override_mode"; then arg2=$install_override_mode no_mode=false fi prev= else dest=$arg continue fi ;; esac # Aesthetically quote the argument. func_quote_for_eval "$arg" func_append install_prog " $func_quote_for_eval_result" if test -n "$arg2"; then func_quote_for_eval "$arg2" fi func_append install_shared_prog " $func_quote_for_eval_result" done test -z "$install_prog" && \ func_fatal_help "you must specify an install program" test -n "$prev" && \ func_fatal_help "the \`$prev' option requires an argument" if test -n "$install_override_mode" && $no_mode; then if $install_cp; then :; else func_quote_for_eval "$install_override_mode" func_append install_shared_prog " -m $func_quote_for_eval_result" fi fi if test -z "$files"; then if test -z "$dest"; then func_fatal_help "no file or destination specified" else func_fatal_help "you must specify a destination" fi fi # Strip any trailing slash from the destination. func_stripname '' '/' "$dest" dest=$func_stripname_result # Check to see that the destination is a directory. test -d "$dest" && isdir=yes if test "$isdir" = yes; then destdir="$dest" destname= else func_dirname_and_basename "$dest" "" "." destdir="$func_dirname_result" destname="$func_basename_result" # Not a directory, so check to see that there is only one file specified. set dummy $files; shift test "$#" -gt 1 && \ func_fatal_help "\`$dest' is not a directory" fi case $destdir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) for file in $files; do case $file in *.lo) ;; *) func_fatal_help "\`$destdir' must be an absolute directory name" ;; esac done ;; esac # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" staticlibs= future_libdirs= current_libdirs= for file in $files; do # Do each installation. case $file in *.$libext) # Do the static libraries later. func_append staticlibs " $file" ;; *.la) func_resolve_sysroot "$file" file=$func_resolve_sysroot_result # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$file' is not a valid libtool archive" library_names= old_library= relink_command= func_source "$file" # Add the libdir to current_libdirs if it is the destination. if test "X$destdir" = "X$libdir"; then case "$current_libdirs " in *" $libdir "*) ;; *) func_append current_libdirs " $libdir" ;; esac else # Note the libdir as a future libdir. case "$future_libdirs " in *" $libdir "*) ;; *) func_append future_libdirs " $libdir" ;; esac fi func_dirname "$file" "/" "" dir="$func_dirname_result" func_append dir "$objdir" if test -n "$relink_command"; then # Determine the prefix the user has applied to our future dir. inst_prefix_dir=`$ECHO "$destdir" | $SED -e "s%$libdir\$%%"` # Don't allow the user to place us outside of our expected # location b/c this prevents finding dependent libraries that # are installed to the same prefix. # At present, this check doesn't affect windows .dll's that # are installed into $libdir/../bin (currently, that works fine) # but it's something to keep an eye on. test "$inst_prefix_dir" = "$destdir" && \ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir" if test -n "$inst_prefix_dir"; then # Stick the inst_prefix_dir data into the link command. relink_command=`$ECHO "$relink_command" | $SED "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` else relink_command=`$ECHO "$relink_command" | $SED "s%@inst_prefix_dir@%%"` fi func_warning "relinking \`$file'" func_show_eval "$relink_command" \ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"' fi # See the names of the shared library. set dummy $library_names; shift if test -n "$1"; then realname="$1" shift srcname="$realname" test -n "$relink_command" && srcname="$realname"T # Install the shared library and build the symlinks. func_show_eval "$install_shared_prog $dir/$srcname $destdir/$realname" \ 'exit $?' tstripme="$stripme" case $host_os in cygwin* | mingw* | pw32* | cegcc*) case $realname in *.dll.a) tstripme="" ;; esac ;; esac if test -n "$tstripme" && test -n "$striplib"; then func_show_eval "$striplib $destdir/$realname" 'exit $?' fi if test "$#" -gt 0; then # Delete the old symlinks, and create new ones. # Try `ln -sf' first, because the `ln' binary might depend on # the symlink we replace! Solaris /bin/ln does not understand -f, # so we also need to try rm && ln -s. for linkname do test "$linkname" != "$realname" \ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })" done fi # Do each command in the postinstall commands. lib="$destdir/$realname" func_execute_cmds "$postinstall_cmds" 'exit $?' fi # Install the pseudo-library for information purposes. func_basename "$file" name="$func_basename_result" instname="$dir/$name"i func_show_eval "$install_prog $instname $destdir/$name" 'exit $?' # Maybe install the static library, too. test -n "$old_library" && func_append staticlibs " $dir/$old_library" ;; *.lo) # Install (i.e. copy) a libtool object. # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # Deduce the name of the destination old-style object file. case $destfile in *.lo) func_lo2o "$destfile" staticdest=$func_lo2o_result ;; *.$objext) staticdest="$destfile" destfile= ;; *) func_fatal_help "cannot copy a libtool object to \`$destfile'" ;; esac # Install the libtool object if requested. test -n "$destfile" && \ func_show_eval "$install_prog $file $destfile" 'exit $?' # Install the old object if enabled. if test "$build_old_libs" = yes; then # Deduce the name of the old-style object file. func_lo2o "$file" staticobj=$func_lo2o_result func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?' fi exit $EXIT_SUCCESS ;; *) # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # If the file is missing, and there is a .exe on the end, strip it # because it is most likely a libtool script we actually want to # install stripped_ext="" case $file in *.exe) if test ! -f "$file"; then func_stripname '' '.exe' "$file" file=$func_stripname_result stripped_ext=".exe" fi ;; esac # Do a test to see if this is really a libtool program. case $host in *cygwin* | *mingw*) if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" wrapper=$func_ltwrapper_scriptname_result else func_stripname '' '.exe' "$file" wrapper=$func_stripname_result fi ;; *) wrapper=$file ;; esac if func_ltwrapper_script_p "$wrapper"; then notinst_deplibs= relink_command= func_source "$wrapper" # Check the variables that should have been set. test -z "$generated_by_libtool_version" && \ func_fatal_error "invalid libtool wrapper script \`$wrapper'" finalize=yes for lib in $notinst_deplibs; do # Check to see that each library is installed. libdir= if test -f "$lib"; then func_source "$lib" fi libfile="$libdir/"`$ECHO "$lib" | $SED 's%^.*/%%g'` ### testsuite: skip nested quoting test if test -n "$libdir" && test ! -f "$libfile"; then func_warning "\`$lib' has not been installed in \`$libdir'" finalize=no fi done relink_command= func_source "$wrapper" outputname= if test "$fast_install" = no && test -n "$relink_command"; then $opt_dry_run || { if test "$finalize" = yes; then tmpdir=`func_mktempdir` func_basename "$file$stripped_ext" file="$func_basename_result" outputname="$tmpdir/$file" # Replace the output file specification. relink_command=`$ECHO "$relink_command" | $SED 's%@OUTPUT@%'"$outputname"'%g'` $opt_silent || { func_quote_for_expand "$relink_command" eval "func_echo $func_quote_for_expand_result" } if eval "$relink_command"; then : else func_error "error: relink \`$file' with the above command before installing it" $opt_dry_run || ${RM}r "$tmpdir" continue fi file="$outputname" else func_warning "cannot relink \`$file'" fi } else # Install the binary that we compiled earlier. file=`$ECHO "$file$stripped_ext" | $SED "s%\([^/]*\)$%$objdir/\1%"` fi fi # remove .exe since cygwin /usr/bin/install will append another # one anyway case $install_prog,$host in */usr/bin/install*,*cygwin*) case $file:$destfile in *.exe:*.exe) # this is ok ;; *.exe:*) destfile=$destfile.exe ;; *:*.exe) func_stripname '' '.exe' "$destfile" destfile=$func_stripname_result ;; esac ;; esac func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?' $opt_dry_run || if test -n "$outputname"; then ${RM}r "$tmpdir" fi ;; esac done for file in $staticlibs; do func_basename "$file" name="$func_basename_result" # Set up the ranlib parameters. oldlib="$destdir/$name" func_to_tool_file "$oldlib" func_convert_file_msys_to_w32 tool_oldlib=$func_to_tool_file_result func_show_eval "$install_prog \$file \$oldlib" 'exit $?' if test -n "$stripme" && test -n "$old_striplib"; then func_show_eval "$old_striplib $tool_oldlib" 'exit $?' fi # Do each command in the postinstall commands. func_execute_cmds "$old_postinstall_cmds" 'exit $?' done test -n "$future_libdirs" && \ func_warning "remember to run \`$progname --finish$future_libdirs'" if test -n "$current_libdirs"; then # Maybe just do a dry run. $opt_dry_run && current_libdirs=" -n$current_libdirs" exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs' else exit $EXIT_SUCCESS fi } test "$opt_mode" = install && func_mode_install ${1+"$@"} # func_generate_dlsyms outputname originator pic_p # Extract symbols from dlprefiles and create ${outputname}S.o with # a dlpreopen symbol table. func_generate_dlsyms () { $opt_debug my_outputname="$1" my_originator="$2" my_pic_p="${3-no}" my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'` my_dlsyms= if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then if test -n "$NM" && test -n "$global_symbol_pipe"; then my_dlsyms="${my_outputname}S.c" else func_error "not configured to extract global symbols from dlpreopened files" fi fi if test -n "$my_dlsyms"; then case $my_dlsyms in "") ;; *.c) # Discover the nlist of each of the dlfiles. nlist="$output_objdir/${my_outputname}.nm" func_show_eval "$RM $nlist ${nlist}S ${nlist}T" # Parse the name list into a source file. func_verbose "creating $output_objdir/$my_dlsyms" $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\ /* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */ /* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */ #ifdef __cplusplus extern \"C\" { #endif #if defined(__GNUC__) && (((__GNUC__ == 4) && (__GNUC_MINOR__ >= 4)) || (__GNUC__ > 4)) #pragma GCC diagnostic ignored \"-Wstrict-prototypes\" #endif /* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests. */ #if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE) /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */ # define LT_DLSYM_CONST #elif defined(__osf__) /* This system does not cope well with relocations in const data. */ # define LT_DLSYM_CONST #else # define LT_DLSYM_CONST const #endif /* External symbol declarations for the compiler. */\ " if test "$dlself" = yes; then func_verbose "generating symbol list for \`$output'" $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist" # Add our own program objects to the symbol list. progfiles=`$ECHO "$objs$old_deplibs" | $SP2NL | $SED "$lo2o" | $NL2SP` for progfile in $progfiles; do func_to_tool_file "$progfile" func_convert_file_msys_to_w32 func_verbose "extracting global C symbols from \`$func_to_tool_file_result'" $opt_dry_run || eval "$NM $func_to_tool_file_result | $global_symbol_pipe >> '$nlist'" done if test -n "$exclude_expsyms"; then $opt_dry_run || { eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi if test -n "$export_symbols_regex"; then $opt_dry_run || { eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi # Prepare the list of exported symbols if test -z "$export_symbols"; then export_symbols="$output_objdir/$outputname.exp" $opt_dry_run || { $RM $export_symbols eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"' case $host in *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"' ;; esac } else $opt_dry_run || { eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"' eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' case $host in *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$nlist" >> "$output_objdir/$outputname.def"' ;; esac } fi fi for dlprefile in $dlprefiles; do func_verbose "extracting global C symbols from \`$dlprefile'" func_basename "$dlprefile" name="$func_basename_result" case $host in *cygwin* | *mingw* | *cegcc* ) # if an import library, we need to obtain dlname if func_win32_import_lib_p "$dlprefile"; then func_tr_sh "$dlprefile" eval "curr_lafile=\$libfile_$func_tr_sh_result" dlprefile_dlbasename="" if test -n "$curr_lafile" && func_lalib_p "$curr_lafile"; then # Use subshell, to avoid clobbering current variable values dlprefile_dlname=`source "$curr_lafile" && echo "$dlname"` if test -n "$dlprefile_dlname" ; then func_basename "$dlprefile_dlname" dlprefile_dlbasename="$func_basename_result" else # no lafile. user explicitly requested -dlpreopen . $sharedlib_from_linklib_cmd "$dlprefile" dlprefile_dlbasename=$sharedlib_from_linklib_result fi fi $opt_dry_run || { if test -n "$dlprefile_dlbasename" ; then eval '$ECHO ": $dlprefile_dlbasename" >> "$nlist"' else func_warning "Could not compute DLL name from $name" eval '$ECHO ": $name " >> "$nlist"' fi func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe | $SED -e '/I __imp/d' -e 's/I __nm_/D /;s/_nm__//' >> '$nlist'" } else # not an import lib $opt_dry_run || { eval '$ECHO ": $name " >> "$nlist"' func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe >> '$nlist'" } fi ;; *) $opt_dry_run || { eval '$ECHO ": $name " >> "$nlist"' func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe >> '$nlist'" } ;; esac done $opt_dry_run || { # Make sure we have at least an empty file. test -f "$nlist" || : > "$nlist" if test -n "$exclude_expsyms"; then $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T $MV "$nlist"T "$nlist" fi # Try sorting and uniquifying the output. if $GREP -v "^: " < "$nlist" | if sort -k 3 /dev/null 2>&1; then sort -k 3 else sort +2 fi | uniq > "$nlist"S; then : else $GREP -v "^: " < "$nlist" > "$nlist"S fi if test -f "$nlist"S; then eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"' else echo '/* NONE */' >> "$output_objdir/$my_dlsyms" fi echo >> "$output_objdir/$my_dlsyms" "\ /* The mapping between symbol names and symbols. */ typedef struct { const char *name; void *address; } lt_dlsymlist; extern LT_DLSYM_CONST lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[]; LT_DLSYM_CONST lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[] = {\ { \"$my_originator\", (void *) 0 }," case $need_lib_prefix in no) eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; *) eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; esac echo >> "$output_objdir/$my_dlsyms" "\ {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt_${my_prefix}_LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif\ " } # !$opt_dry_run pic_flag_for_symtable= case "$compile_command " in *" -static "*) ;; *) case $host in # compiling the symbol table file with pic_flag works around # a FreeBSD bug that causes programs to crash when -lm is # linked before any other PIC object. But we must not use # pic_flag when linking with -static. The problem exists in # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. *-*-freebsd2.*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;; *-*-hpux*) pic_flag_for_symtable=" $pic_flag" ;; *) if test "X$my_pic_p" != Xno; then pic_flag_for_symtable=" $pic_flag" fi ;; esac ;; esac symtab_cflags= for arg in $LTCFLAGS; do case $arg in -pie | -fpie | -fPIE) ;; *) func_append symtab_cflags " $arg" ;; esac done # Now compile the dynamic symbol file. func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?' # Clean up the generated files. func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"' # Transform the symbol file into the correct name. symfileobj="$output_objdir/${my_outputname}S.$objext" case $host in *cygwin* | *mingw* | *cegcc* ) if test -f "$output_objdir/$my_outputname.def"; then compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` else compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$symfileobj%"` fi ;; *) compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$symfileobj%"` ;; esac ;; *) func_fatal_error "unknown suffix for \`$my_dlsyms'" ;; esac else # We keep going just in case the user didn't refer to # lt_preloaded_symbols. The linker will fail if global_symbol_pipe # really was required. # Nullify the symbol file. compile_command=`$ECHO "$compile_command" | $SED "s% @SYMFILE@%%"` finalize_command=`$ECHO "$finalize_command" | $SED "s% @SYMFILE@%%"` fi } # func_win32_libid arg # return the library type of file 'arg' # # Need a lot of goo to handle *both* DLLs and import libs # Has to be a shell function in order to 'eat' the argument # that is supplied when $file_magic_command is called. # Despite the name, also deal with 64 bit binaries. func_win32_libid () { $opt_debug win32_libid_type="unknown" win32_fileres=`file -L $1 2>/dev/null` case $win32_fileres in *ar\ archive\ import\ library*) # definitely import win32_libid_type="x86 archive import" ;; *ar\ archive*) # could be an import, or static # Keep the egrep pattern in sync with the one in _LT_CHECK_MAGIC_METHOD. if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | $EGREP 'file format (pei*-i386(.*architecture: i386)?|pe-arm-wince|pe-x86-64)' >/dev/null; then func_to_tool_file "$1" func_convert_file_msys_to_w32 win32_nmres=`eval $NM -f posix -A \"$func_to_tool_file_result\" | $SED -n -e ' 1,100{ / I /{ s,.*,import, p q } }'` case $win32_nmres in import*) win32_libid_type="x86 archive import";; *) win32_libid_type="x86 archive static";; esac fi ;; *DLL*) win32_libid_type="x86 DLL" ;; *executable*) # but shell scripts are "executable" too... case $win32_fileres in *MS\ Windows\ PE\ Intel*) win32_libid_type="x86 DLL" ;; esac ;; esac $ECHO "$win32_libid_type" } # func_cygming_dll_for_implib ARG # # Platform-specific function to extract the # name of the DLL associated with the specified # import library ARG. # Invoked by eval'ing the libtool variable # $sharedlib_from_linklib_cmd # Result is available in the variable # $sharedlib_from_linklib_result func_cygming_dll_for_implib () { $opt_debug sharedlib_from_linklib_result=`$DLLTOOL --identify-strict --identify "$1"` } # func_cygming_dll_for_implib_fallback_core SECTION_NAME LIBNAMEs # # The is the core of a fallback implementation of a # platform-specific function to extract the name of the # DLL associated with the specified import library LIBNAME. # # SECTION_NAME is either .idata$6 or .idata$7, depending # on the platform and compiler that created the implib. # # Echos the name of the DLL associated with the # specified import library. func_cygming_dll_for_implib_fallback_core () { $opt_debug match_literal=`$ECHO "$1" | $SED "$sed_make_literal_regex"` $OBJDUMP -s --section "$1" "$2" 2>/dev/null | $SED '/^Contents of section '"$match_literal"':/{ # Place marker at beginning of archive member dllname section s/.*/====MARK====/ p d } # These lines can sometimes be longer than 43 characters, but # are always uninteresting /:[ ]*file format pe[i]\{,1\}-/d /^In archive [^:]*:/d # Ensure marker is printed /^====MARK====/p # Remove all lines with less than 43 characters /^.\{43\}/!d # From remaining lines, remove first 43 characters s/^.\{43\}//' | $SED -n ' # Join marker and all lines until next marker into a single line /^====MARK====/ b para H $ b para b :para x s/\n//g # Remove the marker s/^====MARK====// # Remove trailing dots and whitespace s/[\. \t]*$// # Print /./p' | # we now have a list, one entry per line, of the stringified # contents of the appropriate section of all members of the # archive which possess that section. Heuristic: eliminate # all those which have a first or second character that is # a '.' (that is, objdump's representation of an unprintable # character.) This should work for all archives with less than # 0x302f exports -- but will fail for DLLs whose name actually # begins with a literal '.' or a single character followed by # a '.'. # # Of those that remain, print the first one. $SED -e '/^\./d;/^.\./d;q' } # func_cygming_gnu_implib_p ARG # This predicate returns with zero status (TRUE) if # ARG is a GNU/binutils-style import library. Returns # with nonzero status (FALSE) otherwise. func_cygming_gnu_implib_p () { $opt_debug func_to_tool_file "$1" func_convert_file_msys_to_w32 func_cygming_gnu_implib_tmp=`$NM "$func_to_tool_file_result" | eval "$global_symbol_pipe" | $EGREP ' (_head_[A-Za-z0-9_]+_[ad]l*|[A-Za-z0-9_]+_[ad]l*_iname)$'` test -n "$func_cygming_gnu_implib_tmp" } # func_cygming_ms_implib_p ARG # This predicate returns with zero status (TRUE) if # ARG is an MS-style import library. Returns # with nonzero status (FALSE) otherwise. func_cygming_ms_implib_p () { $opt_debug func_to_tool_file "$1" func_convert_file_msys_to_w32 func_cygming_ms_implib_tmp=`$NM "$func_to_tool_file_result" | eval "$global_symbol_pipe" | $GREP '_NULL_IMPORT_DESCRIPTOR'` test -n "$func_cygming_ms_implib_tmp" } # func_cygming_dll_for_implib_fallback ARG # Platform-specific function to extract the # name of the DLL associated with the specified # import library ARG. # # This fallback implementation is for use when $DLLTOOL # does not support the --identify-strict option. # Invoked by eval'ing the libtool variable # $sharedlib_from_linklib_cmd # Result is available in the variable # $sharedlib_from_linklib_result func_cygming_dll_for_implib_fallback () { $opt_debug if func_cygming_gnu_implib_p "$1" ; then # binutils import library sharedlib_from_linklib_result=`func_cygming_dll_for_implib_fallback_core '.idata$7' "$1"` elif func_cygming_ms_implib_p "$1" ; then # ms-generated import library sharedlib_from_linklib_result=`func_cygming_dll_for_implib_fallback_core '.idata$6' "$1"` else # unknown sharedlib_from_linklib_result="" fi } # func_extract_an_archive dir oldlib func_extract_an_archive () { $opt_debug f_ex_an_ar_dir="$1"; shift f_ex_an_ar_oldlib="$1" if test "$lock_old_archive_extraction" = yes; then lockfile=$f_ex_an_ar_oldlib.lock until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do func_echo "Waiting for $lockfile to be removed" sleep 2 done fi func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" \ 'stat=$?; rm -f "$lockfile"; exit $stat' if test "$lock_old_archive_extraction" = yes; then $opt_dry_run || rm -f "$lockfile" fi if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then : else func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib" fi } # func_extract_archives gentop oldlib ... func_extract_archives () { $opt_debug my_gentop="$1"; shift my_oldlibs=${1+"$@"} my_oldobjs="" my_xlib="" my_xabs="" my_xdir="" for my_xlib in $my_oldlibs; do # Extract the objects. case $my_xlib in [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;; *) my_xabs=`pwd`"/$my_xlib" ;; esac func_basename "$my_xlib" my_xlib="$func_basename_result" my_xlib_u=$my_xlib while :; do case " $extracted_archives " in *" $my_xlib_u "*) func_arith $extracted_serial + 1 extracted_serial=$func_arith_result my_xlib_u=lt$extracted_serial-$my_xlib ;; *) break ;; esac done extracted_archives="$extracted_archives $my_xlib_u" my_xdir="$my_gentop/$my_xlib_u" func_mkdir_p "$my_xdir" case $host in *-darwin*) func_verbose "Extracting $my_xabs" # Do not bother doing anything if just a dry run $opt_dry_run || { darwin_orig_dir=`pwd` cd $my_xdir || exit $? darwin_archive=$my_xabs darwin_curdir=`pwd` darwin_base_archive=`basename "$darwin_archive"` darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true` if test -n "$darwin_arches"; then darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'` darwin_arch= func_verbose "$darwin_base_archive has multiple architectures $darwin_arches" for darwin_arch in $darwin_arches ; do func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}" $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}" cd "unfat-$$/${darwin_base_archive}-${darwin_arch}" func_extract_an_archive "`pwd`" "${darwin_base_archive}" cd "$darwin_curdir" $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" done # $darwin_arches ## Okay now we've a bunch of thin objects, gotta fatten them up :) darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u` darwin_file= darwin_files= for darwin_file in $darwin_filelist; do darwin_files=`find unfat-$$ -name $darwin_file -print | sort | $NL2SP` $LIPO -create -output "$darwin_file" $darwin_files done # $darwin_filelist $RM -rf unfat-$$ cd "$darwin_orig_dir" else cd $darwin_orig_dir func_extract_an_archive "$my_xdir" "$my_xabs" fi # $darwin_arches } # !$opt_dry_run ;; *) func_extract_an_archive "$my_xdir" "$my_xabs" ;; esac my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | sort | $NL2SP` done func_extract_archives_result="$my_oldobjs" } # func_emit_wrapper [arg=no] # # Emit a libtool wrapper script on stdout. # Don't directly open a file because we may want to # incorporate the script contents within a cygwin/mingw # wrapper executable. Must ONLY be called from within # func_mode_link because it depends on a number of variables # set therein. # # ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR # variable will take. If 'yes', then the emitted script # will assume that the directory in which it is stored is # the $objdir directory. This is a cygwin/mingw-specific # behavior. func_emit_wrapper () { func_emit_wrapper_arg1=${1-no} $ECHO "\ #! $SHELL # $output - temporary wrapper script for $objdir/$outputname # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # The $output program cannot be directly executed until all the libtool # libraries that it depends on are installed. # # This wrapper script should never be moved out of the build directory. # If it is, it will not operate correctly. # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. sed_quote_subst='$sed_quote_subst' # Be Bourne compatible if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which # is contrary to our usage. Disable this feature. alias -g '\${1+\"\$@\"}'='\"\$@\"' setopt NO_GLOB_SUBST else case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac fi BIN_SH=xpg4; export BIN_SH # for Tru64 DUALCASE=1; export DUALCASE # for MKS sh # The HP-UX ksh and POSIX shell print the target directory to stdout # if CDPATH is set. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH relink_command=\"$relink_command\" # This environment variable determines our operation mode. if test \"\$libtool_install_magic\" = \"$magic\"; then # install mode needs the following variables: generated_by_libtool_version='$macro_version' notinst_deplibs='$notinst_deplibs' else # When we are sourced in execute mode, \$file and \$ECHO are already set. if test \"\$libtool_execute_magic\" != \"$magic\"; then file=\"\$0\"" qECHO=`$ECHO "$ECHO" | $SED "$sed_quote_subst"` $ECHO "\ # A function that is used when there is no print builtin or printf. func_fallback_echo () { eval 'cat <<_LTECHO_EOF \$1 _LTECHO_EOF' } ECHO=\"$qECHO\" fi # Very basic option parsing. These options are (a) specific to # the libtool wrapper, (b) are identical between the wrapper # /script/ and the wrapper /executable/ which is used only on # windows platforms, and (c) all begin with the string "--lt-" # (application programs are unlikely to have options which match # this pattern). # # There are only two supported options: --lt-debug and # --lt-dump-script. There is, deliberately, no --lt-help. # # The first argument to this parsing function should be the # script's $0 value, followed by "$@". lt_option_debug= func_parse_lt_options () { lt_script_arg0=\$0 shift for lt_opt do case \"\$lt_opt\" in --lt-debug) lt_option_debug=1 ;; --lt-dump-script) lt_dump_D=\`\$ECHO \"X\$lt_script_arg0\" | $SED -e 's/^X//' -e 's%/[^/]*$%%'\` test \"X\$lt_dump_D\" = \"X\$lt_script_arg0\" && lt_dump_D=. lt_dump_F=\`\$ECHO \"X\$lt_script_arg0\" | $SED -e 's/^X//' -e 's%^.*/%%'\` cat \"\$lt_dump_D/\$lt_dump_F\" exit 0 ;; --lt-*) \$ECHO \"Unrecognized --lt- option: '\$lt_opt'\" 1>&2 exit 1 ;; esac done # Print the debug banner immediately: if test -n \"\$lt_option_debug\"; then echo \"${outputname}:${output}:\${LINENO}: libtool wrapper (GNU $PACKAGE$TIMESTAMP) $VERSION\" 1>&2 fi } # Used when --lt-debug. Prints its arguments to stdout # (redirection is the responsibility of the caller) func_lt_dump_args () { lt_dump_args_N=1; for lt_arg do \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[\$lt_dump_args_N]: \$lt_arg\" lt_dump_args_N=\`expr \$lt_dump_args_N + 1\` done } # Core function for launching the target application func_exec_program_core () { " case $host in # Backslashes separate directories on plain windows *-*-mingw | *-*-os2* | *-cegcc*) $ECHO "\ if test -n \"\$lt_option_debug\"; then \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[0]: \$progdir\\\\\$program\" 1>&2 func_lt_dump_args \${1+\"\$@\"} 1>&2 fi exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} " ;; *) $ECHO "\ if test -n \"\$lt_option_debug\"; then \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[0]: \$progdir/\$program\" 1>&2 func_lt_dump_args \${1+\"\$@\"} 1>&2 fi exec \"\$progdir/\$program\" \${1+\"\$@\"} " ;; esac $ECHO "\ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 exit 1 } # A function to encapsulate launching the target application # Strips options in the --lt-* namespace from \$@ and # launches target application with the remaining arguments. func_exec_program () { case \" \$* \" in *\\ --lt-*) for lt_wr_arg do case \$lt_wr_arg in --lt-*) ;; *) set x \"\$@\" \"\$lt_wr_arg\"; shift;; esac shift done ;; esac func_exec_program_core \${1+\"\$@\"} } # Parse options func_parse_lt_options \"\$0\" \${1+\"\$@\"} # Find the directory that this script lives in. thisdir=\`\$ECHO \"\$file\" | $SED 's%/[^/]*$%%'\` test \"x\$thisdir\" = \"x\$file\" && thisdir=. # Follow symbolic links until we get to the real thisdir. file=\`ls -ld \"\$file\" | $SED -n 's/.*-> //p'\` while test -n \"\$file\"; do destdir=\`\$ECHO \"\$file\" | $SED 's%/[^/]*\$%%'\` # If there was a directory component, then change thisdir. if test \"x\$destdir\" != \"x\$file\"; then case \"\$destdir\" in [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; *) thisdir=\"\$thisdir/\$destdir\" ;; esac fi file=\`\$ECHO \"\$file\" | $SED 's%^.*/%%'\` file=\`ls -ld \"\$thisdir/\$file\" | $SED -n 's/.*-> //p'\` done # Usually 'no', except on cygwin/mingw when embedded into # the cwrapper. WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_arg1 if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then # special case for '.' if test \"\$thisdir\" = \".\"; then thisdir=\`pwd\` fi # remove .libs from thisdir case \"\$thisdir\" in *[\\\\/]$objdir ) thisdir=\`\$ECHO \"\$thisdir\" | $SED 's%[\\\\/][^\\\\/]*$%%'\` ;; $objdir ) thisdir=. ;; esac fi # Try to get the absolute directory name. absdir=\`cd \"\$thisdir\" && pwd\` test -n \"\$absdir\" && thisdir=\"\$absdir\" " if test "$fast_install" = yes; then $ECHO "\ program=lt-'$outputname'$exeext progdir=\"\$thisdir/$objdir\" if test ! -f \"\$progdir/\$program\" || { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ test \"X\$file\" != \"X\$progdir/\$program\"; }; then file=\"\$\$-\$program\" if test ! -d \"\$progdir\"; then $MKDIR \"\$progdir\" else $RM \"\$progdir/\$file\" fi" $ECHO "\ # relink executable if necessary if test -n \"\$relink_command\"; then if relink_command_output=\`eval \$relink_command 2>&1\`; then : else $ECHO \"\$relink_command_output\" >&2 $RM \"\$progdir/\$file\" exit 1 fi fi $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || { $RM \"\$progdir/\$program\"; $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } $RM \"\$progdir/\$file\" fi" else $ECHO "\ program='$outputname' progdir=\"\$thisdir/$objdir\" " fi $ECHO "\ if test -f \"\$progdir/\$program\"; then" # fixup the dll searchpath if we need to. # # Fix the DLL searchpath if we need to. Do this before prepending # to shlibpath, because on Windows, both are PATH and uninstalled # libraries must come first. if test -n "$dllsearchpath"; then $ECHO "\ # Add the dll search path components to the executable PATH PATH=$dllsearchpath:\$PATH " fi # Export our shlibpath_var if we have one. if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then $ECHO "\ # Add our own library path to $shlibpath_var $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" # Some systems cannot cope with colon-terminated $shlibpath_var # The second colon is a workaround for a bug in BeOS R4 sed $shlibpath_var=\`\$ECHO \"\$$shlibpath_var\" | $SED 's/::*\$//'\` export $shlibpath_var " fi $ECHO "\ if test \"\$libtool_execute_magic\" != \"$magic\"; then # Run the actual program with our arguments. func_exec_program \${1+\"\$@\"} fi else # The program doesn't exist. \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 \$ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 exit 1 fi fi\ " } # func_emit_cwrapperexe_src # emit the source code for a wrapper executable on stdout # Must ONLY be called from within func_mode_link because # it depends on a number of variable set therein. func_emit_cwrapperexe_src () { cat < #include #ifdef _MSC_VER # include # include # include #else # include # include # ifdef __CYGWIN__ # include # endif #endif #include #include #include #include #include #include #include #include /* declarations of non-ANSI functions */ #if defined(__MINGW32__) # ifdef __STRICT_ANSI__ int _putenv (const char *); # endif #elif defined(__CYGWIN__) # ifdef __STRICT_ANSI__ char *realpath (const char *, char *); int putenv (char *); int setenv (const char *, const char *, int); # endif /* #elif defined (other platforms) ... */ #endif /* portability defines, excluding path handling macros */ #if defined(_MSC_VER) # define setmode _setmode # define stat _stat # define chmod _chmod # define getcwd _getcwd # define putenv _putenv # define S_IXUSR _S_IEXEC # ifndef _INTPTR_T_DEFINED # define _INTPTR_T_DEFINED # define intptr_t int # endif #elif defined(__MINGW32__) # define setmode _setmode # define stat _stat # define chmod _chmod # define getcwd _getcwd # define putenv _putenv #elif defined(__CYGWIN__) # define HAVE_SETENV # define FOPEN_WB "wb" /* #elif defined (other platforms) ... */ #endif #if defined(PATH_MAX) # define LT_PATHMAX PATH_MAX #elif defined(MAXPATHLEN) # define LT_PATHMAX MAXPATHLEN #else # define LT_PATHMAX 1024 #endif #ifndef S_IXOTH # define S_IXOTH 0 #endif #ifndef S_IXGRP # define S_IXGRP 0 #endif /* path handling portability macros */ #ifndef DIR_SEPARATOR # define DIR_SEPARATOR '/' # define PATH_SEPARATOR ':' #endif #if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \ defined (__OS2__) # define HAVE_DOS_BASED_FILE_SYSTEM # define FOPEN_WB "wb" # ifndef DIR_SEPARATOR_2 # define DIR_SEPARATOR_2 '\\' # endif # ifndef PATH_SEPARATOR_2 # define PATH_SEPARATOR_2 ';' # endif #endif #ifndef DIR_SEPARATOR_2 # define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR) #else /* DIR_SEPARATOR_2 */ # define IS_DIR_SEPARATOR(ch) \ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2)) #endif /* DIR_SEPARATOR_2 */ #ifndef PATH_SEPARATOR_2 # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR) #else /* PATH_SEPARATOR_2 */ # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2) #endif /* PATH_SEPARATOR_2 */ #ifndef FOPEN_WB # define FOPEN_WB "w" #endif #ifndef _O_BINARY # define _O_BINARY 0 #endif #define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type))) #define XFREE(stale) do { \ if (stale) { free ((void *) stale); stale = 0; } \ } while (0) #if defined(LT_DEBUGWRAPPER) static int lt_debug = 1; #else static int lt_debug = 0; #endif const char *program_name = "libtool-wrapper"; /* in case xstrdup fails */ void *xmalloc (size_t num); char *xstrdup (const char *string); const char *base_name (const char *name); char *find_executable (const char *wrapper); char *chase_symlinks (const char *pathspec); int make_executable (const char *path); int check_executable (const char *path); char *strendzap (char *str, const char *pat); void lt_debugprintf (const char *file, int line, const char *fmt, ...); void lt_fatal (const char *file, int line, const char *message, ...); static const char *nonnull (const char *s); static const char *nonempty (const char *s); void lt_setenv (const char *name, const char *value); char *lt_extend_str (const char *orig_value, const char *add, int to_end); void lt_update_exe_path (const char *name, const char *value); void lt_update_lib_path (const char *name, const char *value); char **prepare_spawn (char **argv); void lt_dump_script (FILE *f); EOF cat <= 0) && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH))) return 1; else return 0; } int make_executable (const char *path) { int rval = 0; struct stat st; lt_debugprintf (__FILE__, __LINE__, "(make_executable): %s\n", nonempty (path)); if ((!path) || (!*path)) return 0; if (stat (path, &st) >= 0) { rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR); } return rval; } /* Searches for the full path of the wrapper. Returns newly allocated full path name if found, NULL otherwise Does not chase symlinks, even on platforms that support them. */ char * find_executable (const char *wrapper) { int has_slash = 0; const char *p; const char *p_next; /* static buffer for getcwd */ char tmp[LT_PATHMAX + 1]; int tmp_len; char *concat_name; lt_debugprintf (__FILE__, __LINE__, "(find_executable): %s\n", nonempty (wrapper)); if ((wrapper == NULL) || (*wrapper == '\0')) return NULL; /* Absolute path? */ #if defined (HAVE_DOS_BASED_FILE_SYSTEM) if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':') { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } else { #endif if (IS_DIR_SEPARATOR (wrapper[0])) { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } #if defined (HAVE_DOS_BASED_FILE_SYSTEM) } #endif for (p = wrapper; *p; p++) if (*p == '/') { has_slash = 1; break; } if (!has_slash) { /* no slashes; search PATH */ const char *path = getenv ("PATH"); if (path != NULL) { for (p = path; *p; p = p_next) { const char *q; size_t p_len; for (q = p; *q; q++) if (IS_PATH_SEPARATOR (*q)) break; p_len = q - p; p_next = (*q == '\0' ? q : q + 1); if (p_len == 0) { /* empty path: current directory */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal (__FILE__, __LINE__, "getcwd failed: %s", nonnull (strerror (errno))); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); } else { concat_name = XMALLOC (char, p_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, p, p_len); concat_name[p_len] = '/'; strcpy (concat_name + p_len + 1, wrapper); } if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } } /* not found in PATH; assume curdir */ } /* Relative path | not found in path: prepend cwd */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal (__FILE__, __LINE__, "getcwd failed: %s", nonnull (strerror (errno))); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); return NULL; } char * chase_symlinks (const char *pathspec) { #ifndef S_ISLNK return xstrdup (pathspec); #else char buf[LT_PATHMAX]; struct stat s; char *tmp_pathspec = xstrdup (pathspec); char *p; int has_symlinks = 0; while (strlen (tmp_pathspec) && !has_symlinks) { lt_debugprintf (__FILE__, __LINE__, "checking path component for symlinks: %s\n", tmp_pathspec); if (lstat (tmp_pathspec, &s) == 0) { if (S_ISLNK (s.st_mode) != 0) { has_symlinks = 1; break; } /* search backwards for last DIR_SEPARATOR */ p = tmp_pathspec + strlen (tmp_pathspec) - 1; while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) p--; if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) { /* no more DIR_SEPARATORS left */ break; } *p = '\0'; } else { lt_fatal (__FILE__, __LINE__, "error accessing file \"%s\": %s", tmp_pathspec, nonnull (strerror (errno))); } } XFREE (tmp_pathspec); if (!has_symlinks) { return xstrdup (pathspec); } tmp_pathspec = realpath (pathspec, buf); if (tmp_pathspec == 0) { lt_fatal (__FILE__, __LINE__, "could not follow symlinks for %s", pathspec); } return xstrdup (tmp_pathspec); #endif } char * strendzap (char *str, const char *pat) { size_t len, patlen; assert (str != NULL); assert (pat != NULL); len = strlen (str); patlen = strlen (pat); if (patlen <= len) { str += len - patlen; if (strcmp (str, pat) == 0) *str = '\0'; } return str; } void lt_debugprintf (const char *file, int line, const char *fmt, ...) { va_list args; if (lt_debug) { (void) fprintf (stderr, "%s:%s:%d: ", program_name, file, line); va_start (args, fmt); (void) vfprintf (stderr, fmt, args); va_end (args); } } static void lt_error_core (int exit_status, const char *file, int line, const char *mode, const char *message, va_list ap) { fprintf (stderr, "%s:%s:%d: %s: ", program_name, file, line, mode); vfprintf (stderr, message, ap); fprintf (stderr, ".\n"); if (exit_status >= 0) exit (exit_status); } void lt_fatal (const char *file, int line, const char *message, ...) { va_list ap; va_start (ap, message); lt_error_core (EXIT_FAILURE, file, line, "FATAL", message, ap); va_end (ap); } static const char * nonnull (const char *s) { return s ? s : "(null)"; } static const char * nonempty (const char *s) { return (s && !*s) ? "(empty)" : nonnull (s); } void lt_setenv (const char *name, const char *value) { lt_debugprintf (__FILE__, __LINE__, "(lt_setenv) setting '%s' to '%s'\n", nonnull (name), nonnull (value)); { #ifdef HAVE_SETENV /* always make a copy, for consistency with !HAVE_SETENV */ char *str = xstrdup (value); setenv (name, str, 1); #else int len = strlen (name) + 1 + strlen (value) + 1; char *str = XMALLOC (char, len); sprintf (str, "%s=%s", name, value); if (putenv (str) != EXIT_SUCCESS) { XFREE (str); } #endif } } char * lt_extend_str (const char *orig_value, const char *add, int to_end) { char *new_value; if (orig_value && *orig_value) { int orig_value_len = strlen (orig_value); int add_len = strlen (add); new_value = XMALLOC (char, add_len + orig_value_len + 1); if (to_end) { strcpy (new_value, orig_value); strcpy (new_value + orig_value_len, add); } else { strcpy (new_value, add); strcpy (new_value + add_len, orig_value); } } else { new_value = xstrdup (add); } return new_value; } void lt_update_exe_path (const char *name, const char *value) { lt_debugprintf (__FILE__, __LINE__, "(lt_update_exe_path) modifying '%s' by prepending '%s'\n", nonnull (name), nonnull (value)); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); /* some systems can't cope with a ':'-terminated path #' */ int len = strlen (new_value); while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1])) { new_value[len-1] = '\0'; } lt_setenv (name, new_value); XFREE (new_value); } } void lt_update_lib_path (const char *name, const char *value) { lt_debugprintf (__FILE__, __LINE__, "(lt_update_lib_path) modifying '%s' by prepending '%s'\n", nonnull (name), nonnull (value)); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); } } EOF case $host_os in mingw*) cat <<"EOF" /* Prepares an argument vector before calling spawn(). Note that spawn() does not by itself call the command interpreter (getenv ("COMSPEC") != NULL ? getenv ("COMSPEC") : ({ OSVERSIONINFO v; v.dwOSVersionInfoSize = sizeof(OSVERSIONINFO); GetVersionEx(&v); v.dwPlatformId == VER_PLATFORM_WIN32_NT; }) ? "cmd.exe" : "command.com"). Instead it simply concatenates the arguments, separated by ' ', and calls CreateProcess(). We must quote the arguments since Win32 CreateProcess() interprets characters like ' ', '\t', '\\', '"' (but not '<' and '>') in a special way: - Space and tab are interpreted as delimiters. They are not treated as delimiters if they are surrounded by double quotes: "...". - Unescaped double quotes are removed from the input. Their only effect is that within double quotes, space and tab are treated like normal characters. - Backslashes not followed by double quotes are not special. - But 2*n+1 backslashes followed by a double quote become n backslashes followed by a double quote (n >= 0): \" -> " \\\" -> \" \\\\\" -> \\" */ #define SHELL_SPECIAL_CHARS "\"\\ \001\002\003\004\005\006\007\010\011\012\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037" #define SHELL_SPACE_CHARS " \001\002\003\004\005\006\007\010\011\012\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037" char ** prepare_spawn (char **argv) { size_t argc; char **new_argv; size_t i; /* Count number of arguments. */ for (argc = 0; argv[argc] != NULL; argc++) ; /* Allocate new argument vector. */ new_argv = XMALLOC (char *, argc + 1); /* Put quoted arguments into the new argument vector. */ for (i = 0; i < argc; i++) { const char *string = argv[i]; if (string[0] == '\0') new_argv[i] = xstrdup ("\"\""); else if (strpbrk (string, SHELL_SPECIAL_CHARS) != NULL) { int quote_around = (strpbrk (string, SHELL_SPACE_CHARS) != NULL); size_t length; unsigned int backslashes; const char *s; char *quoted_string; char *p; length = 0; backslashes = 0; if (quote_around) length++; for (s = string; *s != '\0'; s++) { char c = *s; if (c == '"') length += backslashes + 1; length++; if (c == '\\') backslashes++; else backslashes = 0; } if (quote_around) length += backslashes + 1; quoted_string = XMALLOC (char, length + 1); p = quoted_string; backslashes = 0; if (quote_around) *p++ = '"'; for (s = string; *s != '\0'; s++) { char c = *s; if (c == '"') { unsigned int j; for (j = backslashes + 1; j > 0; j--) *p++ = '\\'; } *p++ = c; if (c == '\\') backslashes++; else backslashes = 0; } if (quote_around) { unsigned int j; for (j = backslashes; j > 0; j--) *p++ = '\\'; *p++ = '"'; } *p = '\0'; new_argv[i] = quoted_string; } else new_argv[i] = (char *) string; } new_argv[argc] = NULL; return new_argv; } EOF ;; esac cat <<"EOF" void lt_dump_script (FILE* f) { EOF func_emit_wrapper yes | $SED -n -e ' s/^\(.\{79\}\)\(..*\)/\1\ \2/ h s/\([\\"]\)/\\\1/g s/$/\\n/ s/\([^\n]*\).*/ fputs ("\1", f);/p g D' cat <<"EOF" } EOF } # end: func_emit_cwrapperexe_src # func_win32_import_lib_p ARG # True if ARG is an import lib, as indicated by $file_magic_cmd func_win32_import_lib_p () { $opt_debug case `eval $file_magic_cmd \"\$1\" 2>/dev/null | $SED -e 10q` in *import*) : ;; *) false ;; esac } # func_mode_link arg... func_mode_link () { $opt_debug case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) # It is impossible to link a dll without this setting, and # we shouldn't force the makefile maintainer to figure out # which system we are compiling for in order to pass an extra # flag for every libtool invocation. # allow_undefined=no # FIXME: Unfortunately, there are problems with the above when trying # to make a dll which has undefined symbols, in which case not # even a static library is built. For now, we need to specify # -no-undefined on the libtool link line when we can be certain # that all symbols are satisfied, otherwise we get a static library. allow_undefined=yes ;; *) allow_undefined=yes ;; esac libtool_args=$nonopt base_compile="$nonopt $@" compile_command=$nonopt finalize_command=$nonopt compile_rpath= finalize_rpath= compile_shlibpath= finalize_shlibpath= convenience= old_convenience= deplibs= old_deplibs= compiler_flags= linker_flags= dllsearchpath= lib_search_path=`pwd` inst_prefix_dir= new_inherited_linker_flags= avoid_version=no bindir= dlfiles= dlprefiles= dlself=no export_dynamic=no export_symbols= export_symbols_regex= generated= libobjs= ltlibs= module=no no_install=no objs= non_pic_objects= precious_files_regex= prefer_static_libs=no preload=no prev= prevarg= release= rpath= xrpath= perm_rpath= temp_rpath= thread_safe=no vinfo= vinfo_number=no weak_libs= single_module="${wl}-single_module" func_infer_tag $base_compile # We need to know -static, to get the right output filenames. for arg do case $arg in -shared) test "$build_libtool_libs" != yes && \ func_fatal_configuration "can not build a shared library" build_old_libs=no break ;; -all-static | -static | -static-libtool-libs) case $arg in -all-static) if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then func_warning "complete static linking is impossible in this configuration" fi if test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; -static) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=built ;; -static-libtool-libs) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; esac build_libtool_libs=no build_old_libs=yes break ;; esac done # See if our shared archives depend on static archives. test -n "$old_archive_from_new_cmds" && build_old_libs=yes # Go through the arguments, transforming them on the way. while test "$#" -gt 0; do arg="$1" shift func_quote_for_eval "$arg" qarg=$func_quote_for_eval_unquoted_result func_append libtool_args " $func_quote_for_eval_result" # If the previous option needs an argument, assign it. if test -n "$prev"; then case $prev in output) func_append compile_command " @OUTPUT@" func_append finalize_command " @OUTPUT@" ;; esac case $prev in bindir) bindir="$arg" prev= continue ;; dlfiles|dlprefiles) if test "$preload" = no; then # Add the symbol object into the linking commands. func_append compile_command " @SYMFILE@" func_append finalize_command " @SYMFILE@" preload=yes fi case $arg in *.la | *.lo) ;; # We handle these cases below. force) if test "$dlself" = no; then dlself=needless export_dynamic=yes fi prev= continue ;; self) if test "$prev" = dlprefiles; then dlself=yes elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then dlself=yes else dlself=needless export_dynamic=yes fi prev= continue ;; *) if test "$prev" = dlfiles; then func_append dlfiles " $arg" else func_append dlprefiles " $arg" fi prev= continue ;; esac ;; expsyms) export_symbols="$arg" test -f "$arg" \ || func_fatal_error "symbol file \`$arg' does not exist" prev= continue ;; expsyms_regex) export_symbols_regex="$arg" prev= continue ;; framework) case $host in *-*-darwin*) case "$deplibs " in *" $qarg.ltframework "*) ;; *) func_append deplibs " $qarg.ltframework" # this is fixed later ;; esac ;; esac prev= continue ;; inst_prefix) inst_prefix_dir="$arg" prev= continue ;; objectlist) if test -f "$arg"; then save_arg=$arg moreargs= for fil in `cat "$save_arg"` do # func_append moreargs " $fil" arg=$fil # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then func_append dlfiles " $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. func_append dlprefiles " $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi done else func_fatal_error "link input file \`$arg' does not exist" fi arg=$save_arg prev= continue ;; precious_regex) precious_files_regex="$arg" prev= continue ;; release) release="-$arg" prev= continue ;; rpath | xrpath) # We need an absolute path. case $arg in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac if test "$prev" = rpath; then case "$rpath " in *" $arg "*) ;; *) func_append rpath " $arg" ;; esac else case "$xrpath " in *" $arg "*) ;; *) func_append xrpath " $arg" ;; esac fi prev= continue ;; shrext) shrext_cmds="$arg" prev= continue ;; weak) func_append weak_libs " $arg" prev= continue ;; xcclinker) func_append linker_flags " $qarg" func_append compiler_flags " $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xcompiler) func_append compiler_flags " $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xlinker) func_append linker_flags " $qarg" func_append compiler_flags " $wl$qarg" prev= func_append compile_command " $wl$qarg" func_append finalize_command " $wl$qarg" continue ;; *) eval "$prev=\"\$arg\"" prev= continue ;; esac fi # test -n "$prev" prevarg="$arg" case $arg in -all-static) if test -n "$link_static_flag"; then # See comment for -static flag below, for more details. func_append compile_command " $link_static_flag" func_append finalize_command " $link_static_flag" fi continue ;; -allow-undefined) # FIXME: remove this flag sometime in the future. func_fatal_error "\`-allow-undefined' must not be used because it is the default" ;; -avoid-version) avoid_version=yes continue ;; -bindir) prev=bindir continue ;; -dlopen) prev=dlfiles continue ;; -dlpreopen) prev=dlprefiles continue ;; -export-dynamic) export_dynamic=yes continue ;; -export-symbols | -export-symbols-regex) if test -n "$export_symbols" || test -n "$export_symbols_regex"; then func_fatal_error "more than one -exported-symbols argument is not allowed" fi if test "X$arg" = "X-export-symbols"; then prev=expsyms else prev=expsyms_regex fi continue ;; -framework) prev=framework continue ;; -inst-prefix-dir) prev=inst_prefix continue ;; # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:* # so, if we see these flags be careful not to treat them like -L -L[A-Z][A-Z]*:*) case $with_gcc/$host in no/*-*-irix* | /*-*-irix*) func_append compile_command " $arg" func_append finalize_command " $arg" ;; esac continue ;; -L*) func_stripname "-L" '' "$arg" if test -z "$func_stripname_result"; then if test "$#" -gt 0; then func_fatal_error "require no space between \`-L' and \`$1'" else func_fatal_error "need path for \`-L' option" fi fi func_resolve_sysroot "$func_stripname_result" dir=$func_resolve_sysroot_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) absdir=`cd "$dir" && pwd` test -z "$absdir" && \ func_fatal_error "cannot determine absolute directory name of \`$dir'" dir="$absdir" ;; esac case "$deplibs " in *" -L$dir "* | *" $arg "*) # Will only happen for absolute or sysroot arguments ;; *) # Preserve sysroot, but never include relative directories case $dir in [\\/]* | [A-Za-z]:[\\/]* | =*) func_append deplibs " $arg" ;; *) func_append deplibs " -L$dir" ;; esac func_append lib_search_path " $dir" ;; esac case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`$ECHO "$dir" | $SED 's*/lib$*/bin*'` case :$dllsearchpath: in *":$dir:"*) ;; ::) dllsearchpath=$dir;; *) func_append dllsearchpath ":$dir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) func_append dllsearchpath ":$testbindir";; esac ;; esac continue ;; -l*) if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc* | *-*-haiku*) # These systems don't actually have a C or math library (as such) continue ;; *-*-os2*) # These systems don't actually have a C library (as such) test "X$arg" = "X-lc" && continue ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. test "X$arg" = "X-lc" && continue ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C and math libraries are in the System framework func_append deplibs " System.ltframework" continue ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype test "X$arg" = "X-lc" && continue ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work test "X$arg" = "X-lc" && continue ;; esac elif test "X$arg" = "X-lc_r"; then case $host in *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc_r directly, use -pthread flag. continue ;; esac fi func_append deplibs " $arg" continue ;; -module) module=yes continue ;; # Tru64 UNIX uses -model [arg] to determine the layout of C++ # classes, name mangling, and exception handling. # Darwin uses the -arch flag to determine output architecture. -model|-arch|-isysroot|--sysroot) func_append compiler_flags " $arg" func_append compile_command " $arg" func_append finalize_command " $arg" prev=xcompiler continue ;; -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe \ |-threads|-fopenmp|-openmp|-mp|-xopenmp|-omp|-qsmp=*) func_append compiler_flags " $arg" func_append compile_command " $arg" func_append finalize_command " $arg" case "$new_inherited_linker_flags " in *" $arg "*) ;; * ) func_append new_inherited_linker_flags " $arg" ;; esac continue ;; -multi_module) single_module="${wl}-multi_module" continue ;; -no-fast-install) fast_install=no continue ;; -no-install) case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*) # The PATH hackery in wrapper scripts is required on Windows # and Darwin in order for the loader to find any dlls it needs. func_warning "\`-no-install' is ignored for $host" func_warning "assuming \`-no-fast-install' instead" fast_install=no ;; *) no_install=yes ;; esac continue ;; -no-undefined) allow_undefined=no continue ;; -objectlist) prev=objectlist continue ;; -o) prev=output ;; -precious-files-regex) prev=precious_regex continue ;; -release) prev=release continue ;; -rpath) prev=rpath continue ;; -R) prev=xrpath continue ;; -R*) func_stripname '-R' '' "$arg" dir=$func_stripname_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; =*) func_stripname '=' '' "$dir" dir=$lt_sysroot$func_stripname_result ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac case "$xrpath " in *" $dir "*) ;; *) func_append xrpath " $dir" ;; esac continue ;; -shared) # The effects of -shared are defined in a previous loop. continue ;; -shrext) prev=shrext continue ;; -static | -static-libtool-libs) # The effects of -static are defined in a previous loop. # We used to do the same as -all-static on platforms that # didn't have a PIC flag, but the assumption that the effects # would be equivalent was wrong. It would break on at least # Digital Unix and AIX. continue ;; -thread-safe) thread_safe=yes continue ;; -version-info) prev=vinfo continue ;; -version-number) prev=vinfo vinfo_number=yes continue ;; -weak) prev=weak continue ;; -Wc,*) func_stripname '-Wc,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" func_append arg " $func_quote_for_eval_result" func_append compiler_flags " $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Wl,*) func_stripname '-Wl,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" func_append arg " $wl$func_quote_for_eval_result" func_append compiler_flags " $wl$func_quote_for_eval_result" func_append linker_flags " $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Xcompiler) prev=xcompiler continue ;; -Xlinker) prev=xlinker continue ;; -XCClinker) prev=xcclinker continue ;; # -msg_* for osf cc -msg_*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; # Flags to be passed through unchanged, with rationale: # -64, -mips[0-9] enable 64-bit mode for the SGI compiler # -r[0-9][0-9]* specify processor for the SGI compiler # -xarch=*, -xtarget=* enable 64-bit mode for the Sun compiler # +DA*, +DD* enable 64-bit mode for the HP compiler # -q* compiler args for the IBM compiler # -m*, -t[45]*, -txscale* architecture-specific flags for GCC # -F/path path to uninstalled frameworks, gcc on darwin # -p, -pg, --coverage, -fprofile-* profiling flags for GCC # @file GCC response files # -tp=* Portland pgcc target processor selection # --sysroot=* for sysroot support # -O*, -flto*, -fwhopr*, -fuse-linker-plugin GCC link-time optimization -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*|-tp=*|--sysroot=*| \ -O*|-flto*|-fwhopr*|-fuse-linker-plugin) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" func_append compile_command " $arg" func_append finalize_command " $arg" func_append compiler_flags " $arg" continue ;; # Some other compiler flag. -* | +*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; *.$objext) # A standard object. func_append objs " $arg" ;; *.lo) # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then func_append dlfiles " $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. func_append dlprefiles " $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi ;; *.$libext) # An archive. func_append deplibs " $arg" func_append old_deplibs " $arg" continue ;; *.la) # A libtool-controlled library. func_resolve_sysroot "$arg" if test "$prev" = dlfiles; then # This library was specified with -dlopen. func_append dlfiles " $func_resolve_sysroot_result" prev= elif test "$prev" = dlprefiles; then # The library was specified with -dlpreopen. func_append dlprefiles " $func_resolve_sysroot_result" prev= else func_append deplibs " $func_resolve_sysroot_result" fi continue ;; # Some other compiler argument. *) # Unknown arguments in both finalize_command and compile_command need # to be aesthetically quoted because they are evaled later. func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; esac # arg # Now actually substitute the argument into the commands. if test -n "$arg"; then func_append compile_command " $arg" func_append finalize_command " $arg" fi done # argument parsing loop test -n "$prev" && \ func_fatal_help "the \`$prevarg' option requires an argument" if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then eval arg=\"$export_dynamic_flag_spec\" func_append compile_command " $arg" func_append finalize_command " $arg" fi oldlibs= # calculate the name of the file, without its directory func_basename "$output" outputname="$func_basename_result" libobjs_save="$libobjs" if test -n "$shlibpath_var"; then # get the directories listed in $shlibpath_var eval shlib_search_path=\`\$ECHO \"\${$shlibpath_var}\" \| \$SED \'s/:/ /g\'\` else shlib_search_path= fi eval sys_lib_search_path=\"$sys_lib_search_path_spec\" eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\" func_dirname "$output" "/" "" output_objdir="$func_dirname_result$objdir" func_to_tool_file "$output_objdir/" tool_output_objdir=$func_to_tool_file_result # Create the object directory. func_mkdir_p "$output_objdir" # Determine the type of output case $output in "") func_fatal_help "you must specify an output file" ;; *.$libext) linkmode=oldlib ;; *.lo | *.$objext) linkmode=obj ;; *.la) linkmode=lib ;; *) linkmode=prog ;; # Anything else should be a program. esac specialdeplibs= libs= # Find all interdependent deplibs by searching for libraries # that are linked more than once (e.g. -la -lb -la) for deplib in $deplibs; do if $opt_preserve_dup_deps ; then case "$libs " in *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi func_append libs " $deplib" done if test "$linkmode" = lib; then libs="$predeps $libs $compiler_lib_search_path $postdeps" # Compute libraries that are listed more than once in $predeps # $postdeps and mark them as special (i.e., whose duplicates are # not to be eliminated). pre_post_deps= if $opt_duplicate_compiler_generated_deps; then for pre_post_dep in $predeps $postdeps; do case "$pre_post_deps " in *" $pre_post_dep "*) func_append specialdeplibs " $pre_post_deps" ;; esac func_append pre_post_deps " $pre_post_dep" done fi pre_post_deps= fi deplibs= newdependency_libs= newlib_search_path= need_relink=no # whether we're linking any uninstalled libtool libraries notinst_deplibs= # not-installed libtool libraries notinst_path= # paths that contain not-installed libtool libraries case $linkmode in lib) passes="conv dlpreopen link" for file in $dlfiles $dlprefiles; do case $file in *.la) ;; *) func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file" ;; esac done ;; prog) compile_deplibs= finalize_deplibs= alldeplibs=no newdlfiles= newdlprefiles= passes="conv scan dlopen dlpreopen link" ;; *) passes="conv" ;; esac for pass in $passes; do # The preopen pass in lib mode reverses $deplibs; put it back here # so that -L comes before libs that need it for instance... if test "$linkmode,$pass" = "lib,link"; then ## FIXME: Find the place where the list is rebuilt in the wrong ## order, and fix it there properly tmp_deplibs= for deplib in $deplibs; do tmp_deplibs="$deplib $tmp_deplibs" done deplibs="$tmp_deplibs" fi if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan"; then libs="$deplibs" deplibs= fi if test "$linkmode" = prog; then case $pass in dlopen) libs="$dlfiles" ;; dlpreopen) libs="$dlprefiles" ;; link) libs="$deplibs %DEPLIBS% $dependency_libs" ;; esac fi if test "$linkmode,$pass" = "lib,dlpreopen"; then # Collect and forward deplibs of preopened libtool libs for lib in $dlprefiles; do # Ignore non-libtool-libs dependency_libs= func_resolve_sysroot "$lib" case $lib in *.la) func_source "$func_resolve_sysroot_result" ;; esac # Collect preopened libtool deplibs, except any this library # has declared as weak libs for deplib in $dependency_libs; do func_basename "$deplib" deplib_base=$func_basename_result case " $weak_libs " in *" $deplib_base "*) ;; *) func_append deplibs " $deplib" ;; esac done done libs="$dlprefiles" fi if test "$pass" = dlopen; then # Collect dlpreopened libraries save_deplibs="$deplibs" deplibs= fi for deplib in $libs; do lib= found=no case $deplib in -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe \ |-threads|-fopenmp|-openmp|-mp|-xopenmp|-omp|-qsmp=*) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else func_append compiler_flags " $deplib" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) func_append new_inherited_linker_flags " $deplib" ;; esac fi fi continue ;; -l*) if test "$linkmode" != lib && test "$linkmode" != prog; then func_warning "\`-l' is ignored for archives/objects" continue fi func_stripname '-l' '' "$deplib" name=$func_stripname_result if test "$linkmode" = lib; then searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path" else searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path" fi for searchdir in $searchdirs; do for search_ext in .la $std_shrext .so .a; do # Search the libtool library lib="$searchdir/lib${name}${search_ext}" if test -f "$lib"; then if test "$search_ext" = ".la"; then found=yes else found=no fi break 2 fi done done if test "$found" != yes; then # deplib doesn't seem to be a libtool library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue else # deplib is a libtool library # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib, # We need to do some special things here, and not later. if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $deplib "*) if func_lalib_p "$lib"; then library_names= old_library= func_source "$lib" for l in $old_library $library_names; do ll="$l" done if test "X$ll" = "X$old_library" ; then # only static version available found=no func_dirname "$lib" "" "." ladir="$func_dirname_result" lib=$ladir/$old_library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue fi fi ;; *) ;; esac fi fi ;; # -l *.ltframework) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) func_append new_inherited_linker_flags " $deplib" ;; esac fi fi continue ;; -L*) case $linkmode in lib) deplibs="$deplib $deplibs" test "$pass" = conv && continue newdependency_libs="$deplib $newdependency_libs" func_stripname '-L' '' "$deplib" func_resolve_sysroot "$func_stripname_result" func_append newlib_search_path " $func_resolve_sysroot_result" ;; prog) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi if test "$pass" = scan; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi func_stripname '-L' '' "$deplib" func_resolve_sysroot "$func_stripname_result" func_append newlib_search_path " $func_resolve_sysroot_result" ;; *) func_warning "\`-L' is ignored for archives/objects" ;; esac # linkmode continue ;; # -L -R*) if test "$pass" = link; then func_stripname '-R' '' "$deplib" func_resolve_sysroot "$func_stripname_result" dir=$func_resolve_sysroot_result # Make sure the xrpath contains only unique directories. case "$xrpath " in *" $dir "*) ;; *) func_append xrpath " $dir" ;; esac fi deplibs="$deplib $deplibs" continue ;; *.la) func_resolve_sysroot "$deplib" lib=$func_resolve_sysroot_result ;; *.$libext) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi case $linkmode in lib) # Linking convenience modules into shared libraries is allowed, # but linking other static libraries is non-portable. case " $dlpreconveniencelibs " in *" $deplib "*) ;; *) valid_a_lib=no case $deplibs_check_method in match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` if eval "\$ECHO \"$deplib\"" 2>/dev/null | $SED 10q \ | $EGREP "$match_pattern_regex" > /dev/null; then valid_a_lib=yes fi ;; pass_all) valid_a_lib=yes ;; esac if test "$valid_a_lib" != yes; then echo $ECHO "*** Warning: Trying to link with static lib archive $deplib." echo "*** I have the capability to make that library automatically link in when" echo "*** you link to this library. But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have" echo "*** because the file extensions .$libext of this argument makes me believe" echo "*** that it is just a static archive that I should not use here." else echo $ECHO "*** Warning: Linking the shared library $output against the" $ECHO "*** static library $deplib is not portable!" deplibs="$deplib $deplibs" fi ;; esac continue ;; prog) if test "$pass" != link; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi continue ;; esac # linkmode ;; # *.$libext *.lo | *.$objext) if test "$pass" = conv; then deplibs="$deplib $deplibs" elif test "$linkmode" = prog; then if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlopen support or we're linking statically, # we need to preload. func_append newdlprefiles " $deplib" compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else func_append newdlfiles " $deplib" fi fi continue ;; %DEPLIBS%) alldeplibs=yes continue ;; esac # case $deplib if test "$found" = yes || test -f "$lib"; then : else func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'" fi # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$lib" \ || func_fatal_error "\`$lib' is not a valid libtool archive" func_dirname "$lib" "" "." ladir="$func_dirname_result" dlname= dlopen= dlpreopen= libdir= library_names= old_library= inherited_linker_flags= # If the library was installed with an old release of libtool, # it will not redefine variables installed, or shouldnotlink installed=yes shouldnotlink=no avoidtemprpath= # Read the .la file func_source "$lib" # Convert "-framework foo" to "foo.ltframework" if test -n "$inherited_linker_flags"; then tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'` for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do case " $new_inherited_linker_flags " in *" $tmp_inherited_linker_flag "*) ;; *) func_append new_inherited_linker_flags " $tmp_inherited_linker_flag";; esac done fi dependency_libs=`$ECHO " $dependency_libs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan" || { test "$linkmode" != prog && test "$linkmode" != lib; }; then test -n "$dlopen" && func_append dlfiles " $dlopen" test -n "$dlpreopen" && func_append dlprefiles " $dlpreopen" fi if test "$pass" = conv; then # Only check for convenience libraries deplibs="$lib $deplibs" if test -z "$libdir"; then if test -z "$old_library"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # It is a libtool convenience library, so add in its objects. func_append convenience " $ladir/$objdir/$old_library" func_append old_convenience " $ladir/$objdir/$old_library" elif test "$linkmode" != prog && test "$linkmode" != lib; then func_fatal_error "\`$lib' is not a convenience library" fi tmp_libs= for deplib in $dependency_libs; do deplibs="$deplib $deplibs" if $opt_preserve_dup_deps ; then case "$tmp_libs " in *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi func_append tmp_libs " $deplib" done continue fi # $pass = conv # Get the name of the library we link against. linklib= if test -n "$old_library" && { test "$prefer_static_libs" = yes || test "$prefer_static_libs,$installed" = "built,no"; }; then linklib=$old_library else for l in $old_library $library_names; do linklib="$l" done fi if test -z "$linklib"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # This library was specified with -dlopen. if test "$pass" = dlopen; then if test -z "$libdir"; then func_fatal_error "cannot -dlopen a convenience library: \`$lib'" fi if test -z "$dlname" || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlname, no dlopen support or we're linking # statically, we need to preload. We also need to preload any # dependent libraries so libltdl's deplib preloader doesn't # bomb out in the load deplibs phase. func_append dlprefiles " $lib $dependency_libs" else func_append newdlfiles " $lib" fi continue fi # $pass = dlopen # We need an absolute path. case $ladir in [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;; *) abs_ladir=`cd "$ladir" && pwd` if test -z "$abs_ladir"; then func_warning "cannot determine absolute directory name of \`$ladir'" func_warning "passing it literally to the linker, although it might fail" abs_ladir="$ladir" fi ;; esac func_basename "$lib" laname="$func_basename_result" # Find the relevant object directory and library name. if test "X$installed" = Xyes; then if test ! -f "$lt_sysroot$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then func_warning "library \`$lib' was moved." dir="$ladir" absdir="$abs_ladir" libdir="$abs_ladir" else dir="$lt_sysroot$libdir" absdir="$lt_sysroot$libdir" fi test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes else if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then dir="$ladir" absdir="$abs_ladir" # Remove this search path later func_append notinst_path " $abs_ladir" else dir="$ladir/$objdir" absdir="$abs_ladir/$objdir" # Remove this search path later func_append notinst_path " $abs_ladir" fi fi # $installed = yes func_stripname 'lib' '.la' "$laname" name=$func_stripname_result # This library was specified with -dlpreopen. if test "$pass" = dlpreopen; then if test -z "$libdir" && test "$linkmode" = prog; then func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'" fi case "$host" in # special handling for platforms with PE-DLLs. *cygwin* | *mingw* | *cegcc* ) # Linker will automatically link against shared library if both # static and shared are present. Therefore, ensure we extract # symbols from the import library if a shared library is present # (otherwise, the dlopen module name will be incorrect). We do # this by putting the import library name into $newdlprefiles. # We recover the dlopen module name by 'saving' the la file # name in a special purpose variable, and (later) extracting the # dlname from the la file. if test -n "$dlname"; then func_tr_sh "$dir/$linklib" eval "libfile_$func_tr_sh_result=\$abs_ladir/\$laname" func_append newdlprefiles " $dir/$linklib" else func_append newdlprefiles " $dir/$old_library" # Keep a list of preopened convenience libraries to check # that they are being used correctly in the link pass. test -z "$libdir" && \ func_append dlpreconveniencelibs " $dir/$old_library" fi ;; * ) # Prefer using a static library (so that no silly _DYNAMIC symbols # are required to link). if test -n "$old_library"; then func_append newdlprefiles " $dir/$old_library" # Keep a list of preopened convenience libraries to check # that they are being used correctly in the link pass. test -z "$libdir" && \ func_append dlpreconveniencelibs " $dir/$old_library" # Otherwise, use the dlname, so that lt_dlopen finds it. elif test -n "$dlname"; then func_append newdlprefiles " $dir/$dlname" else func_append newdlprefiles " $dir/$linklib" fi ;; esac fi # $pass = dlpreopen if test -z "$libdir"; then # Link the convenience library if test "$linkmode" = lib; then deplibs="$dir/$old_library $deplibs" elif test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$dir/$old_library $compile_deplibs" finalize_deplibs="$dir/$old_library $finalize_deplibs" else deplibs="$lib $deplibs" # used for prog,scan pass fi continue fi if test "$linkmode" = prog && test "$pass" != link; then func_append newlib_search_path " $ladir" deplibs="$lib $deplibs" linkalldeplibs=no if test "$link_all_deplibs" != no || test -z "$library_names" || test "$build_libtool_libs" = no; then linkalldeplibs=yes fi tmp_libs= for deplib in $dependency_libs; do case $deplib in -L*) func_stripname '-L' '' "$deplib" func_resolve_sysroot "$func_stripname_result" func_append newlib_search_path " $func_resolve_sysroot_result" ;; esac # Need to link against all dependency_libs? if test "$linkalldeplibs" = yes; then deplibs="$deplib $deplibs" else # Need to hardcode shared library paths # or/and link against static libraries newdependency_libs="$deplib $newdependency_libs" fi if $opt_preserve_dup_deps ; then case "$tmp_libs " in *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi func_append tmp_libs " $deplib" done # for deplib continue fi # $linkmode = prog... if test "$linkmode,$pass" = "prog,link"; then if test -n "$library_names" && { { test "$prefer_static_libs" = no || test "$prefer_static_libs,$installed" = "built,yes"; } || test -z "$old_library"; }; then # We need to hardcode the library path if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then # Make sure the rpath contains only unique directories. case "$temp_rpath:" in *"$absdir:"*) ;; *) func_append temp_rpath "$absdir:" ;; esac fi # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) func_append compile_rpath " $absdir" ;; esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) func_append finalize_rpath " $libdir" ;; esac ;; esac fi # $linkmode,$pass = prog,link... if test "$alldeplibs" = yes && { test "$deplibs_check_method" = pass_all || { test "$build_libtool_libs" = yes && test -n "$library_names"; }; }; then # We only need to search for static libraries continue fi fi link_static=no # Whether the deplib will be linked statically use_static_libs=$prefer_static_libs if test "$use_static_libs" = built && test "$installed" = yes; then use_static_libs=no fi if test -n "$library_names" && { test "$use_static_libs" = no || test -z "$old_library"; }; then case $host in *cygwin* | *mingw* | *cegcc*) # No point in relinking DLLs because paths are not encoded func_append notinst_deplibs " $lib" need_relink=no ;; *) if test "$installed" = no; then func_append notinst_deplibs " $lib" need_relink=yes fi ;; esac # This is a shared library # Warn about portability, can't link against -module's on some # systems (darwin). Don't bleat about dlopened modules though! dlopenmodule="" for dlpremoduletest in $dlprefiles; do if test "X$dlpremoduletest" = "X$lib"; then dlopenmodule="$dlpremoduletest" break fi done if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then echo if test "$linkmode" = prog; then $ECHO "*** Warning: Linking the executable $output against the loadable module" else $ECHO "*** Warning: Linking the shared library $output against the loadable module" fi $ECHO "*** $linklib is not portable!" fi if test "$linkmode" = lib && test "$hardcode_into_libs" = yes; then # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) func_append compile_rpath " $absdir" ;; esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) func_append finalize_rpath " $libdir" ;; esac ;; esac fi if test -n "$old_archive_from_expsyms_cmds"; then # figure out the soname set dummy $library_names shift realname="$1" shift libname=`eval "\\$ECHO \"$libname_spec\""` # use dlname if we got it. it's perfectly good, no? if test -n "$dlname"; then soname="$dlname" elif test -n "$soname_spec"; then # bleh windows case $host in *cygwin* | mingw* | *cegcc*) func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; esac eval soname=\"$soname_spec\" else soname="$realname" fi # Make a new name for the extract_expsyms_cmds to use soroot="$soname" func_basename "$soroot" soname="$func_basename_result" func_stripname 'lib' '.dll' "$soname" newlib=libimp-$func_stripname_result.a # If the library has no export list, then create one now if test -f "$output_objdir/$soname-def"; then : else func_verbose "extracting exported symbol list from \`$soname'" func_execute_cmds "$extract_expsyms_cmds" 'exit $?' fi # Create $newlib if test -f "$output_objdir/$newlib"; then :; else func_verbose "generating import library for \`$soname'" func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?' fi # make sure the library variables are pointing to the new library dir=$output_objdir linklib=$newlib fi # test -n "$old_archive_from_expsyms_cmds" if test "$linkmode" = prog || test "$opt_mode" != relink; then add_shlibpath= add_dir= add= lib_linked=yes case $hardcode_action in immediate | unsupported) if test "$hardcode_direct" = no; then add="$dir/$linklib" case $host in *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;; *-*-sysv4*uw2*) add_dir="-L$dir" ;; *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \ *-*-unixware7*) add_dir="-L$dir" ;; *-*-darwin* ) # if the lib is a (non-dlopened) module then we can not # link against it, someone is ignoring the earlier warnings if /usr/bin/file -L $add 2> /dev/null | $GREP ": [^:]* bundle" >/dev/null ; then if test "X$dlopenmodule" != "X$lib"; then $ECHO "*** Warning: lib $linklib is a module, not a shared library" if test -z "$old_library" ; then echo echo "*** And there doesn't seem to be a static archive available" echo "*** The link will probably fail, sorry" else add="$dir/$old_library" fi elif test -n "$old_library"; then add="$dir/$old_library" fi fi esac elif test "$hardcode_minus_L" = no; then case $host in *-*-sunos*) add_shlibpath="$dir" ;; esac add_dir="-L$dir" add="-l$name" elif test "$hardcode_shlibpath_var" = no; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; relink) if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$dir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$absdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) func_append add_dir " -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; *) lib_linked=no ;; esac if test "$lib_linked" != yes; then func_fatal_configuration "unsupported hardcode properties" fi if test -n "$add_shlibpath"; then case :$compile_shlibpath: in *":$add_shlibpath:"*) ;; *) func_append compile_shlibpath "$add_shlibpath:" ;; esac fi if test "$linkmode" = prog; then test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs" test -n "$add" && compile_deplibs="$add $compile_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" if test "$hardcode_direct" != yes && test "$hardcode_minus_L" != yes && test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) func_append finalize_shlibpath "$libdir:" ;; esac fi fi fi if test "$linkmode" = prog || test "$opt_mode" = relink; then add_shlibpath= add_dir= add= # Finalize command for both is simple: just hardcode it. if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$libdir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$libdir" add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) func_append finalize_shlibpath "$libdir:" ;; esac add="-l$name" elif test "$hardcode_automatic" = yes; then if test -n "$inst_prefix_dir" && test -f "$inst_prefix_dir$libdir/$linklib" ; then add="$inst_prefix_dir$libdir/$linklib" else add="$libdir/$linklib" fi else # We cannot seem to hardcode it, guess we'll fake it. add_dir="-L$libdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) func_append add_dir " -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" fi if test "$linkmode" = prog; then test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs" test -n "$add" && finalize_deplibs="$add $finalize_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" fi fi elif test "$linkmode" = prog; then # Here we assume that one of hardcode_direct or hardcode_minus_L # is not unsupported. This is valid on all known static and # shared platforms. if test "$hardcode_direct" != unsupported; then test -n "$old_library" && linklib="$old_library" compile_deplibs="$dir/$linklib $compile_deplibs" finalize_deplibs="$dir/$linklib $finalize_deplibs" else compile_deplibs="-l$name -L$dir $compile_deplibs" finalize_deplibs="-l$name -L$dir $finalize_deplibs" fi elif test "$build_libtool_libs" = yes; then # Not a shared library if test "$deplibs_check_method" != pass_all; then # We're trying link a shared library against a static one # but the system doesn't support it. # Just print a warning and add the library to dependency_libs so # that the program can be linked against the static library. echo $ECHO "*** Warning: This system can not link to static lib archive $lib." echo "*** I have the capability to make that library automatically link in when" echo "*** you link to this library. But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have." if test "$module" = yes; then echo "*** But as you try to build a module library, libtool will still create " echo "*** a static module, that should work as long as the dlopening application" echo "*** is linked with the -dlopen flag to resolve symbols at runtime." if test -z "$global_symbol_pipe"; then echo echo "*** However, this would only work if libtool was able to extract symbol" echo "*** lists from a program, using \`nm' or equivalent, but libtool could" echo "*** not find such a program. So, this module is probably useless." echo "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi else deplibs="$dir/$old_library $deplibs" link_static=yes fi fi # link shared/static library? if test "$linkmode" = lib; then if test -n "$dependency_libs" && { test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes || test "$link_static" = yes; }; then # Extract -R from dependency_libs temp_deplibs= for libdir in $dependency_libs; do case $libdir in -R*) func_stripname '-R' '' "$libdir" temp_xrpath=$func_stripname_result case " $xrpath " in *" $temp_xrpath "*) ;; *) func_append xrpath " $temp_xrpath";; esac;; *) func_append temp_deplibs " $libdir";; esac done dependency_libs="$temp_deplibs" fi func_append newlib_search_path " $absdir" # Link against this library test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs" # ... and its dependency_libs tmp_libs= for deplib in $dependency_libs; do newdependency_libs="$deplib $newdependency_libs" case $deplib in -L*) func_stripname '-L' '' "$deplib" func_resolve_sysroot "$func_stripname_result";; *) func_resolve_sysroot "$deplib" ;; esac if $opt_preserve_dup_deps ; then case "$tmp_libs " in *" $func_resolve_sysroot_result "*) func_append specialdeplibs " $func_resolve_sysroot_result" ;; esac fi func_append tmp_libs " $func_resolve_sysroot_result" done if test "$link_all_deplibs" != no; then # Add the search paths of all dependency libraries for deplib in $dependency_libs; do path= case $deplib in -L*) path="$deplib" ;; *.la) func_resolve_sysroot "$deplib" deplib=$func_resolve_sysroot_result func_dirname "$deplib" "" "." dir=$func_dirname_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;; *) absdir=`cd "$dir" && pwd` if test -z "$absdir"; then func_warning "cannot determine absolute directory name of \`$dir'" absdir="$dir" fi ;; esac if $GREP "^installed=no" $deplib > /dev/null; then case $host in *-*-darwin*) depdepl= eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib` if test -n "$deplibrary_names" ; then for tmp in $deplibrary_names ; do depdepl=$tmp done if test -f "$absdir/$objdir/$depdepl" ; then depdepl="$absdir/$objdir/$depdepl" darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` if test -z "$darwin_install_name"; then darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` fi func_append compiler_flags " ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" func_append linker_flags " -dylib_file ${darwin_install_name}:${depdepl}" path= fi fi ;; *) path="-L$absdir/$objdir" ;; esac else eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` test -z "$libdir" && \ func_fatal_error "\`$deplib' is not a valid libtool archive" test "$absdir" != "$libdir" && \ func_warning "\`$deplib' seems to be moved" path="-L$absdir" fi ;; esac case " $deplibs " in *" $path "*) ;; *) deplibs="$path $deplibs" ;; esac done fi # link_all_deplibs != no fi # linkmode = lib done # for deplib in $libs if test "$pass" = link; then if test "$linkmode" = "prog"; then compile_deplibs="$new_inherited_linker_flags $compile_deplibs" finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs" else compiler_flags="$compiler_flags "`$ECHO " $new_inherited_linker_flags" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` fi fi dependency_libs="$newdependency_libs" if test "$pass" = dlpreopen; then # Link the dlpreopened libraries before other libraries for deplib in $save_deplibs; do deplibs="$deplib $deplibs" done fi if test "$pass" != dlopen; then if test "$pass" != conv; then # Make sure lib_search_path contains only unique directories. lib_search_path= for dir in $newlib_search_path; do case "$lib_search_path " in *" $dir "*) ;; *) func_append lib_search_path " $dir" ;; esac done newlib_search_path= fi if test "$linkmode,$pass" != "prog,link"; then vars="deplibs" else vars="compile_deplibs finalize_deplibs" fi for var in $vars dependency_libs; do # Add libraries to $var in reverse order eval tmp_libs=\"\$$var\" new_libs= for deplib in $tmp_libs; do # FIXME: Pedantically, this is the right thing to do, so # that some nasty dependency loop isn't accidentally # broken: #new_libs="$deplib $new_libs" # Pragmatically, this seems to cause very few problems in # practice: case $deplib in -L*) new_libs="$deplib $new_libs" ;; -R*) ;; *) # And here is the reason: when a library appears more # than once as an explicit dependence of a library, or # is implicitly linked in more than once by the # compiler, it is considered special, and multiple # occurrences thereof are not removed. Compare this # with having the same library being listed as a # dependency of multiple other libraries: in this case, # we know (pedantically, we assume) the library does not # need to be listed more than once, so we keep only the # last copy. This is not always right, but it is rare # enough that we require users that really mean to play # such unportable linking tricks to link the library # using -Wl,-lname, so that libtool does not consider it # for duplicate removal. case " $specialdeplibs " in *" $deplib "*) new_libs="$deplib $new_libs" ;; *) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$deplib $new_libs" ;; esac ;; esac ;; esac done tmp_libs= for deplib in $new_libs; do case $deplib in -L*) case " $tmp_libs " in *" $deplib "*) ;; *) func_append tmp_libs " $deplib" ;; esac ;; *) func_append tmp_libs " $deplib" ;; esac done eval $var=\"$tmp_libs\" done # for var fi # Last step: remove runtime libs from dependency_libs # (they stay in deplibs) tmp_libs= for i in $dependency_libs ; do case " $predeps $postdeps $compiler_lib_search_path " in *" $i "*) i="" ;; esac if test -n "$i" ; then func_append tmp_libs " $i" fi done dependency_libs=$tmp_libs done # for pass if test "$linkmode" = prog; then dlfiles="$newdlfiles" fi if test "$linkmode" = prog || test "$linkmode" = lib; then dlprefiles="$newdlprefiles" fi case $linkmode in oldlib) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for archives" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for archives" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for archives" test -n "$xrpath" && \ func_warning "\`-R' is ignored for archives" test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for archives" test -n "$release" && \ func_warning "\`-release' is ignored for archives" test -n "$export_symbols$export_symbols_regex" && \ func_warning "\`-export-symbols' is ignored for archives" # Now set the variables for building old libraries. build_libtool_libs=no oldlibs="$output" func_append objs "$old_deplibs" ;; lib) # Make sure we only generate libraries of the form `libNAME.la'. case $outputname in lib*) func_stripname 'lib' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" ;; *) test "$module" = no && \ func_fatal_help "libtool library \`$output' must begin with \`lib'" if test "$need_lib_prefix" != no; then # Add the "lib" prefix for modules if required func_stripname '' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" else func_stripname '' '.la' "$outputname" libname=$func_stripname_result fi ;; esac if test -n "$objs"; then if test "$deplibs_check_method" != pass_all; then func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs" else echo $ECHO "*** Warning: Linking the shared library $output against the non-libtool" $ECHO "*** objects $objs is not portable!" func_append libobjs " $objs" fi fi test "$dlself" != no && \ func_warning "\`-dlopen self' is ignored for libtool libraries" set dummy $rpath shift test "$#" -gt 1 && \ func_warning "ignoring multiple \`-rpath's for a libtool library" install_libdir="$1" oldlibs= if test -z "$rpath"; then if test "$build_libtool_libs" = yes; then # Building a libtool convenience library. # Some compilers have problems with a `.al' extension so # convenience libraries should have the same extension an # archive normally would. oldlibs="$output_objdir/$libname.$libext $oldlibs" build_libtool_libs=convenience build_old_libs=yes fi test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for convenience libraries" test -n "$release" && \ func_warning "\`-release' is ignored for convenience libraries" else # Parse the version information argument. save_ifs="$IFS"; IFS=':' set dummy $vinfo 0 0 0 shift IFS="$save_ifs" test -n "$7" && \ func_fatal_help "too many parameters to \`-version-info'" # convert absolute version numbers to libtool ages # this retains compatibility with .la files and attempts # to make the code below a bit more comprehensible case $vinfo_number in yes) number_major="$1" number_minor="$2" number_revision="$3" # # There are really only two kinds -- those that # use the current revision as the major version # and those that subtract age and use age as # a minor version. But, then there is irix # which has an extra 1 added just for fun # case $version_type in # correct linux to gnu/linux during the next big refactor darwin|linux|osf|windows|none) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_revision" ;; freebsd-aout|freebsd-elf|qnx|sunos) current="$number_major" revision="$number_minor" age="0" ;; irix|nonstopux) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_minor" lt_irix_increment=no ;; esac ;; no) current="$1" revision="$2" age="$3" ;; esac # Check that each of the things are valid numbers. case $current in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "CURRENT \`$current' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $revision in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "REVISION \`$revision' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $age in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "AGE \`$age' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac if test "$age" -gt "$current"; then func_error "AGE \`$age' is greater than the current interface number \`$current'" func_fatal_error "\`$vinfo' is not valid version information" fi # Calculate the version variables. major= versuffix= verstring= case $version_type in none) ;; darwin) # Like Linux, but with the current version available in # verstring for coding it into the library header func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" # Darwin ld doesn't like 0 for these options... func_arith $current + 1 minor_current=$func_arith_result xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision" verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" ;; freebsd-aout) major=".$current" versuffix=".$current.$revision"; ;; freebsd-elf) major=".$current" versuffix=".$current" ;; irix | nonstopux) if test "X$lt_irix_increment" = "Xno"; then func_arith $current - $age else func_arith $current - $age + 1 fi major=$func_arith_result case $version_type in nonstopux) verstring_prefix=nonstopux ;; *) verstring_prefix=sgi ;; esac verstring="$verstring_prefix$major.$revision" # Add in all the interfaces that we are compatible with. loop=$revision while test "$loop" -ne 0; do func_arith $revision - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring_prefix$major.$iface:$verstring" done # Before this point, $major must not contain `.'. major=.$major versuffix="$major.$revision" ;; linux) # correct to gnu/linux during the next big refactor func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" ;; osf) func_arith $current - $age major=.$func_arith_result versuffix=".$current.$age.$revision" verstring="$current.$age.$revision" # Add in all the interfaces that we are compatible with. loop=$age while test "$loop" -ne 0; do func_arith $current - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring:${iface}.0" done # Make executables depend on our current version. func_append verstring ":${current}.0" ;; qnx) major=".$current" versuffix=".$current" ;; sunos) major=".$current" versuffix=".$current.$revision" ;; windows) # Use '-' rather than '.', since we only want one # extension on DOS 8.3 filesystems. func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; *) func_fatal_configuration "unknown library version type \`$version_type'" ;; esac # Clear the version info if we defaulted, and they specified a release. if test -z "$vinfo" && test -n "$release"; then major= case $version_type in darwin) # we can't check for "0.0" in archive_cmds due to quoting # problems, so we reset it completely verstring= ;; *) verstring="0.0" ;; esac if test "$need_version" = no; then versuffix= else versuffix=".0.0" fi fi # Remove version info from name if versioning should be avoided if test "$avoid_version" = yes && test "$need_version" = no; then major= versuffix= verstring="" fi # Check to see if the archive will have undefined symbols. if test "$allow_undefined" = yes; then if test "$allow_undefined_flag" = unsupported; then func_warning "undefined symbols not allowed in $host shared libraries" build_libtool_libs=no build_old_libs=yes fi else # Don't allow undefined symbols. allow_undefined_flag="$no_undefined_flag" fi fi func_generate_dlsyms "$libname" "$libname" "yes" func_append libobjs " $symfileobj" test "X$libobjs" = "X " && libobjs= if test "$opt_mode" != relink; then # Remove our outputs, but don't remove object files since they # may have been created when compiling PIC objects. removelist= tempremovelist=`$ECHO "$output_objdir/*"` for p in $tempremovelist; do case $p in *.$objext | *.gcno) ;; $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*) if test "X$precious_files_regex" != "X"; then if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1 then continue fi fi func_append removelist " $p" ;; *) ;; esac done test -n "$removelist" && \ func_show_eval "${RM}r \$removelist" fi # Now set the variables for building old libraries. if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then func_append oldlibs " $output_objdir/$libname.$libext" # Transform .lo files to .o files. oldobjs="$objs "`$ECHO "$libobjs" | $SP2NL | $SED "/\.${libext}$/d; $lo2o" | $NL2SP` fi # Eliminate all temporary directories. #for path in $notinst_path; do # lib_search_path=`$ECHO "$lib_search_path " | $SED "s% $path % %g"` # deplibs=`$ECHO "$deplibs " | $SED "s% -L$path % %g"` # dependency_libs=`$ECHO "$dependency_libs " | $SED "s% -L$path % %g"` #done if test -n "$xrpath"; then # If the user specified any rpath flags, then add them. temp_xrpath= for libdir in $xrpath; do func_replace_sysroot "$libdir" func_append temp_xrpath " -R$func_replace_sysroot_result" case "$finalize_rpath " in *" $libdir "*) ;; *) func_append finalize_rpath " $libdir" ;; esac done if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then dependency_libs="$temp_xrpath $dependency_libs" fi fi # Make sure dlfiles contains only unique files that won't be dlpreopened old_dlfiles="$dlfiles" dlfiles= for lib in $old_dlfiles; do case " $dlprefiles $dlfiles " in *" $lib "*) ;; *) func_append dlfiles " $lib" ;; esac done # Make sure dlprefiles contains only unique files old_dlprefiles="$dlprefiles" dlprefiles= for lib in $old_dlprefiles; do case "$dlprefiles " in *" $lib "*) ;; *) func_append dlprefiles " $lib" ;; esac done if test "$build_libtool_libs" = yes; then if test -n "$rpath"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc* | *-*-haiku*) # these systems don't actually have a c library (as such)! ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C library is in the System framework func_append deplibs " System.ltframework" ;; *-*-netbsd*) # Don't link with libc until the a.out ld.so is fixed. ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work ;; *) # Add libc to deplibs on all other systems if necessary. if test "$build_libtool_need_lc" = "yes"; then func_append deplibs " -lc" fi ;; esac fi # Transform deplibs into only deplibs that can be linked in shared. name_save=$name libname_save=$libname release_save=$release versuffix_save=$versuffix major_save=$major # I'm not sure if I'm treating the release correctly. I think # release should show up in the -l (ie -lgmp5) so we don't want to # add it in twice. Is that correct? release="" versuffix="" major="" newdeplibs= droppeddeps=no case $deplibs_check_method in pass_all) # Don't check for shared/static. Everything works. # This might be a little naive. We might want to check # whether the library exists or not. But this is on # osf3 & osf4 and I'm not really sure... Just # implementing what was already the behavior. newdeplibs=$deplibs ;; test_compile) # This code stresses the "libraries are programs" paradigm to its # limits. Maybe even breaks it. We compile a program, linking it # against the deplibs as a proxy for the library. Then we can check # whether they linked in statically or dynamically with ldd. $opt_dry_run || $RM conftest.c cat > conftest.c </dev/null` $nocaseglob else potential_libs=`ls $i/$libnameglob[.-]* 2>/dev/null` fi for potent_lib in $potential_libs; do # Follow soft links. if ls -lLd "$potent_lib" 2>/dev/null | $GREP " -> " >/dev/null; then continue fi # The statement above tries to avoid entering an # endless loop below, in case of cyclic links. # We might still enter an endless loop, since a link # loop can be closed while we follow links, # but so what? potlib="$potent_lib" while test -h "$potlib" 2>/dev/null; do potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'` case $potliblink in [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";; *) potlib=`$ECHO "$potlib" | $SED 's,[^/]*$,,'`"$potliblink";; esac done if eval $file_magic_cmd \"\$potlib\" 2>/dev/null | $SED -e 10q | $EGREP "$file_magic_regex" > /dev/null; then func_append newdeplibs " $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes echo $ECHO "*** Warning: linker path does not have real file for library $a_deplib." echo "*** I have the capability to make that library automatically link in when" echo "*** you link to this library. But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have" echo "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for file magic test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a file magic. 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But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have" echo "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a regex pattern. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. func_append newdeplibs " $a_deplib" ;; esac done # Gone through all deplibs. ;; none | unknown | *) newdeplibs="" tmp_deplibs=`$ECHO " $deplibs" | $SED 's/ -lc$//; s/ -[LR][^ ]*//g'` if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then for i in $predeps $postdeps ; do # can't use Xsed below, because $i might contain '/' tmp_deplibs=`$ECHO " $tmp_deplibs" | $SED "s,$i,,"` done fi case $tmp_deplibs in *[!\ \ ]*) echo if test "X$deplibs_check_method" = "Xnone"; then echo "*** Warning: inter-library dependencies are not supported in this platform." else echo "*** Warning: inter-library dependencies are not known to be supported." fi echo "*** All declared inter-library dependencies are being dropped." droppeddeps=yes ;; esac ;; esac versuffix=$versuffix_save major=$major_save release=$release_save libname=$libname_save name=$name_save case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library with the System framework newdeplibs=`$ECHO " $newdeplibs" | $SED 's/ -lc / System.ltframework /'` ;; esac if test "$droppeddeps" = yes; then if test "$module" = yes; then echo echo "*** Warning: libtool could not satisfy all declared inter-library" $ECHO "*** dependencies of module $libname. Therefore, libtool will create" echo "*** a static module, that should work as long as the dlopening" echo "*** application is linked with the -dlopen flag." if test -z "$global_symbol_pipe"; then echo echo "*** However, this would only work if libtool was able to extract symbol" echo "*** lists from a program, using \`nm' or equivalent, but libtool could" echo "*** not find such a program. So, this module is probably useless." echo "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi else echo "*** The inter-library dependencies that have been dropped here will be" echo "*** automatically added whenever a program is linked with this library" echo "*** or is declared to -dlopen it." if test "$allow_undefined" = no; then echo echo "*** Since this library must not contain undefined symbols," echo "*** because either the platform does not support them or" echo "*** it was explicitly requested with -no-undefined," echo "*** libtool will only create a static version of it." if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi fi fi # Done checking deplibs! deplibs=$newdeplibs fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" case $host in *-*-darwin*) newdeplibs=`$ECHO " $newdeplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` deplibs=`$ECHO " $deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $deplibs " in *" -L$path/$objdir "*) func_append new_libs " -L$path/$objdir" ;; esac ;; esac done for deplib in $deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) func_append new_libs " $deplib" ;; esac ;; *) func_append new_libs " $deplib" ;; esac done deplibs="$new_libs" # All the library-specific variables (install_libdir is set above). library_names= old_library= dlname= # Test again, we may have decided not to build it any more if test "$build_libtool_libs" = yes; then # Remove ${wl} instances when linking with ld. # FIXME: should test the right _cmds variable. case $archive_cmds in *\$LD\ *) wl= ;; esac if test "$hardcode_into_libs" = yes; then # Hardcode the library paths hardcode_libdirs= dep_rpath= rpath="$finalize_rpath" test "$opt_mode" != relink && rpath="$compile_rpath$rpath" for libdir in $rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then func_replace_sysroot "$libdir" libdir=$func_replace_sysroot_result if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" func_append dep_rpath " $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) func_append perm_rpath " $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval "dep_rpath=\"$hardcode_libdir_flag_spec\"" fi if test -n "$runpath_var" && test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do func_append rpath "$dir:" done eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var" fi test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs" fi shlibpath="$finalize_shlibpath" test "$opt_mode" != relink && shlibpath="$compile_shlibpath$shlibpath" if test -n "$shlibpath"; then eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var" fi # Get the real and link names of the library. eval shared_ext=\"$shrext_cmds\" eval library_names=\"$library_names_spec\" set dummy $library_names shift realname="$1" shift if test -n "$soname_spec"; then eval soname=\"$soname_spec\" else soname="$realname" fi if test -z "$dlname"; then dlname=$soname fi lib="$output_objdir/$realname" linknames= for link do func_append linknames " $link" done # Use standard objects if they are pic test -z "$pic_flag" && libobjs=`$ECHO "$libobjs" | $SP2NL | $SED "$lo2o" | $NL2SP` test "X$libobjs" = "X " && libobjs= delfiles= if test -n "$export_symbols" && test -n "$include_expsyms"; then $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp" export_symbols="$output_objdir/$libname.uexp" func_append delfiles " $export_symbols" fi orig_export_symbols= case $host_os in cygwin* | mingw* | cegcc*) if test -n "$export_symbols" && test -z "$export_symbols_regex"; then # exporting using user supplied symfile if test "x`$SED 1q $export_symbols`" != xEXPORTS; then # and it's NOT already a .def file. Must figure out # which of the given symbols are data symbols and tag # them as such. So, trigger use of export_symbols_cmds. # export_symbols gets reassigned inside the "prepare # the list of exported symbols" if statement, so the # include_expsyms logic still works. orig_export_symbols="$export_symbols" export_symbols= always_export_symbols=yes fi fi ;; esac # Prepare the list of exported symbols if test -z "$export_symbols"; then if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols cmds=$export_symbols_cmds save_ifs="$IFS"; IFS='~' for cmd1 in $cmds; do IFS="$save_ifs" # Take the normal branch if the nm_file_list_spec branch # doesn't work or if tool conversion is not needed. case $nm_file_list_spec~$to_tool_file_cmd in *~func_convert_file_noop | *~func_convert_file_msys_to_w32 | ~*) try_normal_branch=yes eval cmd=\"$cmd1\" func_len " $cmd" len=$func_len_result ;; *) try_normal_branch=no ;; esac if test "$try_normal_branch" = yes \ && { test "$len" -lt "$max_cmd_len" \ || test "$max_cmd_len" -le -1; } then func_show_eval "$cmd" 'exit $?' skipped_export=false elif test -n "$nm_file_list_spec"; then func_basename "$output" output_la=$func_basename_result save_libobjs=$libobjs save_output=$output output=${output_objdir}/${output_la}.nm func_to_tool_file "$output" libobjs=$nm_file_list_spec$func_to_tool_file_result func_append delfiles " $output" func_verbose "creating $NM input file list: $output" for obj in $save_libobjs; do func_to_tool_file "$obj" $ECHO "$func_to_tool_file_result" done > "$output" eval cmd=\"$cmd1\" func_show_eval "$cmd" 'exit $?' output=$save_output libobjs=$save_libobjs skipped_export=false else # The command line is too long to execute in one step. func_verbose "using reloadable object file for export list..." skipped_export=: # Break out early, otherwise skipped_export may be # set to false by a later but shorter cmd. break fi done IFS="$save_ifs" if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi fi if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "$include_expsyms" | $SP2NL >> "$tmp_export_symbols"' fi if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter func_append delfiles " $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi tmp_deplibs= for test_deplib in $deplibs; do case " $convenience " in *" $test_deplib "*) ;; *) func_append tmp_deplibs " $test_deplib" ;; esac done deplibs="$tmp_deplibs" if test -n "$convenience"; then if test -n "$whole_archive_flag_spec" && test "$compiler_needs_object" = yes && test -z "$libobjs"; then # extract the archives, so we have objects to list. # TODO: could optimize this to just extract one archive. whole_archive_flag_spec= fi if test -n "$whole_archive_flag_spec"; then save_libobjs=$libobjs eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= else gentop="$output_objdir/${outputname}x" func_append generated " $gentop" func_extract_archives $gentop $convenience func_append libobjs " $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi fi if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then eval flag=\"$thread_safe_flag_spec\" func_append linker_flags " $flag" fi # Make a backup of the uninstalled library when relinking if test "$opt_mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $? fi # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then eval test_cmds=\"$module_expsym_cmds\" cmds=$module_expsym_cmds else eval test_cmds=\"$module_cmds\" cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then eval test_cmds=\"$archive_expsym_cmds\" cmds=$archive_expsym_cmds else eval test_cmds=\"$archive_cmds\" cmds=$archive_cmds fi fi if test "X$skipped_export" != "X:" && func_len " $test_cmds" && len=$func_len_result && test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then : else # The command line is too long to link in one step, link piecewise # or, if using GNU ld and skipped_export is not :, use a linker # script. # Save the value of $output and $libobjs because we want to # use them later. If we have whole_archive_flag_spec, we # want to use save_libobjs as it was before # whole_archive_flag_spec was expanded, because we can't # assume the linker understands whole_archive_flag_spec. # This may have to be revisited, in case too many # convenience libraries get linked in and end up exceeding # the spec. if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then save_libobjs=$libobjs fi save_output=$output func_basename "$output" output_la=$func_basename_result # Clear the reloadable object creation command queue and # initialize k to one. test_cmds= concat_cmds= objlist= last_robj= k=1 if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then output=${output_objdir}/${output_la}.lnkscript func_verbose "creating GNU ld script: $output" echo 'INPUT (' > $output for obj in $save_libobjs do func_to_tool_file "$obj" $ECHO "$func_to_tool_file_result" >> $output done echo ')' >> $output func_append delfiles " $output" func_to_tool_file "$output" output=$func_to_tool_file_result elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then output=${output_objdir}/${output_la}.lnk func_verbose "creating linker input file list: $output" : > $output set x $save_libobjs shift firstobj= if test "$compiler_needs_object" = yes; then firstobj="$1 " shift fi for obj do func_to_tool_file "$obj" $ECHO "$func_to_tool_file_result" >> $output done func_append delfiles " $output" func_to_tool_file "$output" output=$firstobj\"$file_list_spec$func_to_tool_file_result\" else if test -n "$save_libobjs"; then func_verbose "creating reloadable object files..." output=$output_objdir/$output_la-${k}.$objext eval test_cmds=\"$reload_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 # Loop over the list of objects to be linked. for obj in $save_libobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result if test "X$objlist" = X || test "$len" -lt "$max_cmd_len"; then func_append objlist " $obj" else # The command $test_cmds is almost too long, add a # command to the queue. if test "$k" -eq 1 ; then # The first file doesn't have a previous command to add. reload_objs=$objlist eval concat_cmds=\"$reload_cmds\" else # All subsequent reloadable object files will link in # the last one created. reload_objs="$objlist $last_robj" eval concat_cmds=\"\$concat_cmds~$reload_cmds~\$RM $last_robj\" fi last_robj=$output_objdir/$output_la-${k}.$objext func_arith $k + 1 k=$func_arith_result output=$output_objdir/$output_la-${k}.$objext objlist=" $obj" func_len " $last_robj" func_arith $len0 + $func_len_result len=$func_arith_result fi done # Handle the remaining objects by creating one last # reloadable object file. All subsequent reloadable object # files will link in the last one created. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ reload_objs="$objlist $last_robj" eval concat_cmds=\"\${concat_cmds}$reload_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\" fi func_append delfiles " $output" else output= fi if ${skipped_export-false}; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols libobjs=$output # Append the command to create the export file. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\" fi fi test -n "$save_libobjs" && func_verbose "creating a temporary reloadable object file: $output" # Loop through the commands generated above and execute them. save_ifs="$IFS"; IFS='~' for cmd in $concat_cmds; do IFS="$save_ifs" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$opt_mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" if test -n "$export_symbols_regex" && ${skipped_export-false}; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi if ${skipped_export-false}; then if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "$include_expsyms" | $SP2NL >> "$tmp_export_symbols"' fi if test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter func_append delfiles " $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi fi libobjs=$output # Restore the value of output. output=$save_output if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= fi # Expand the library linking commands again to reset the # value of $libobjs for piecewise linking. # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then cmds=$module_expsym_cmds else cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then cmds=$archive_expsym_cmds else cmds=$archive_cmds fi fi fi if test -n "$delfiles"; then # Append the command to remove temporary files to $cmds. eval cmds=\"\$cmds~\$RM $delfiles\" fi # Add any objects from preloaded convenience libraries if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" func_append generated " $gentop" func_extract_archives $gentop $dlprefiles func_append libobjs " $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$opt_mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" # Restore the uninstalled library and exit if test "$opt_mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $? if test -n "$convenience"; then if test -z "$whole_archive_flag_spec"; then func_show_eval '${RM}r "$gentop"' fi fi exit $EXIT_SUCCESS fi # Create links to the real library. for linkname in $linknames; do if test "$realname" != "$linkname"; then func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?' fi done # If -module or -export-dynamic was specified, set the dlname. if test "$module" = yes || test "$export_dynamic" = yes; then # On all known operating systems, these are identical. dlname="$soname" fi fi ;; obj) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for objects" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for objects" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for objects" test -n "$xrpath" && \ func_warning "\`-R' is ignored for objects" test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for objects" test -n "$release" && \ func_warning "\`-release' is ignored for objects" case $output in *.lo) test -n "$objs$old_deplibs" && \ func_fatal_error "cannot build library object \`$output' from non-libtool objects" libobj=$output func_lo2o "$libobj" obj=$func_lo2o_result ;; *) libobj= obj="$output" ;; esac # Delete the old objects. $opt_dry_run || $RM $obj $libobj # Objects from convenience libraries. This assumes # single-version convenience libraries. Whenever we create # different ones for PIC/non-PIC, this we'll have to duplicate # the extraction. reload_conv_objs= gentop= # reload_cmds runs $LD directly, so let us get rid of # -Wl from whole_archive_flag_spec and hope we can get by with # turning comma into space.. wl= if test -n "$convenience"; then if test -n "$whole_archive_flag_spec"; then eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\" reload_conv_objs=$reload_objs\ `$ECHO "$tmp_whole_archive_flags" | $SED 's|,| |g'` else gentop="$output_objdir/${obj}x" func_append generated " $gentop" func_extract_archives $gentop $convenience reload_conv_objs="$reload_objs $func_extract_archives_result" fi fi # If we're not building shared, we need to use non_pic_objs test "$build_libtool_libs" != yes && libobjs="$non_pic_objects" # Create the old-style object. reload_objs="$objs$old_deplibs "`$ECHO "$libobjs" | $SP2NL | $SED "/\.${libext}$/d; /\.lib$/d; $lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test output="$obj" func_execute_cmds "$reload_cmds" 'exit $?' # Exit if we aren't doing a library object file. if test -z "$libobj"; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS fi if test "$build_libtool_libs" != yes; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi # Create an invalid libtool object if no PIC, so that we don't # accidentally link it into a program. # $show "echo timestamp > $libobj" # $opt_dry_run || eval "echo timestamp > $libobj" || exit $? exit $EXIT_SUCCESS fi if test -n "$pic_flag" || test "$pic_mode" != default; then # Only do commands if we really have different PIC objects. reload_objs="$libobjs $reload_conv_objs" output="$libobj" func_execute_cmds "$reload_cmds" 'exit $?' fi if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS ;; prog) case $host in *cygwin*) func_stripname '' '.exe' "$output" output=$func_stripname_result.exe;; esac test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for programs" test -n "$release" && \ func_warning "\`-release' is ignored for programs" test "$preload" = yes \ && test "$dlopen_support" = unknown \ && test "$dlopen_self" = unknown \ && test "$dlopen_self_static" = unknown && \ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support." case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library is the System framework compile_deplibs=`$ECHO " $compile_deplibs" | $SED 's/ -lc / System.ltframework /'` finalize_deplibs=`$ECHO " $finalize_deplibs" | $SED 's/ -lc / System.ltframework /'` ;; esac case $host in *-*-darwin*) # Don't allow lazy linking, it breaks C++ global constructors # But is supposedly fixed on 10.4 or later (yay!). if test "$tagname" = CXX ; then case ${MACOSX_DEPLOYMENT_TARGET-10.0} in 10.[0123]) func_append compile_command " ${wl}-bind_at_load" func_append finalize_command " ${wl}-bind_at_load" ;; esac fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" compile_deplibs=`$ECHO " $compile_deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` finalize_deplibs=`$ECHO " $finalize_deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $compile_deplibs " in *" -L$path/$objdir "*) func_append new_libs " -L$path/$objdir" ;; esac ;; esac done for deplib in $compile_deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) func_append new_libs " $deplib" ;; esac ;; *) func_append new_libs " $deplib" ;; esac done compile_deplibs="$new_libs" func_append compile_command " $compile_deplibs" func_append finalize_command " $finalize_deplibs" if test -n "$rpath$xrpath"; then # If the user specified any rpath flags, then add them. for libdir in $rpath $xrpath; do # This is the magic to use -rpath. case "$finalize_rpath " in *" $libdir "*) ;; *) func_append finalize_rpath " $libdir" ;; esac done fi # Now hardcode the library paths rpath= hardcode_libdirs= for libdir in $compile_rpath $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" func_append rpath " $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) func_append perm_rpath " $libdir" ;; esac fi case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$libdir:"*) ;; ::) dllsearchpath=$libdir;; *) func_append dllsearchpath ":$libdir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) func_append dllsearchpath ":$testbindir";; esac ;; esac done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi compile_rpath="$rpath" rpath= hardcode_libdirs= for libdir in $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" func_append rpath " $flag" fi elif test -n "$runpath_var"; then case "$finalize_perm_rpath " in *" $libdir "*) ;; *) func_append finalize_perm_rpath " $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi finalize_rpath="$rpath" if test -n "$libobjs" && test "$build_old_libs" = yes; then # Transform all the library objects into standard objects. compile_command=`$ECHO "$compile_command" | $SP2NL | $SED "$lo2o" | $NL2SP` finalize_command=`$ECHO "$finalize_command" | $SP2NL | $SED "$lo2o" | $NL2SP` fi func_generate_dlsyms "$outputname" "@PROGRAM@" "no" # template prelinking step if test -n "$prelink_cmds"; then func_execute_cmds "$prelink_cmds" 'exit $?' fi wrappers_required=yes case $host in *cegcc* | *mingw32ce*) # Disable wrappers for cegcc and mingw32ce hosts, we are cross compiling anyway. wrappers_required=no ;; *cygwin* | *mingw* ) if test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; *) if test "$need_relink" = no || test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; esac if test "$wrappers_required" = no; then # Replace the output file specification. compile_command=`$ECHO "$compile_command" | $SED 's%@OUTPUT@%'"$output"'%g'` link_command="$compile_command$compile_rpath" # We have no uninstalled library dependencies, so finalize right now. exit_status=0 func_show_eval "$link_command" 'exit_status=$?' if test -n "$postlink_cmds"; then func_to_tool_file "$output" postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` func_execute_cmds "$postlink_cmds" 'exit $?' fi # Delete the generated files. if test -f "$output_objdir/${outputname}S.${objext}"; then func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"' fi exit $exit_status fi if test -n "$compile_shlibpath$finalize_shlibpath"; then compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command" fi if test -n "$finalize_shlibpath"; then finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command" fi compile_var= finalize_var= if test -n "$runpath_var"; then if test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do func_append rpath "$dir:" done compile_var="$runpath_var=\"$rpath\$$runpath_var\" " fi if test -n "$finalize_perm_rpath"; then # We should set the runpath_var. rpath= for dir in $finalize_perm_rpath; do func_append rpath "$dir:" done finalize_var="$runpath_var=\"$rpath\$$runpath_var\" " fi fi if test "$no_install" = yes; then # We don't need to create a wrapper script. link_command="$compile_var$compile_command$compile_rpath" # Replace the output file specification. link_command=`$ECHO "$link_command" | $SED 's%@OUTPUT@%'"$output"'%g'` # Delete the old output file. $opt_dry_run || $RM $output # Link the executable and exit func_show_eval "$link_command" 'exit $?' if test -n "$postlink_cmds"; then func_to_tool_file "$output" postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` func_execute_cmds "$postlink_cmds" 'exit $?' fi exit $EXIT_SUCCESS fi if test "$hardcode_action" = relink; then # Fast installation is not supported link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" func_warning "this platform does not like uninstalled shared libraries" func_warning "\`$output' will be relinked during installation" else if test "$fast_install" != no; then link_command="$finalize_var$compile_command$finalize_rpath" if test "$fast_install" = yes; then relink_command=`$ECHO "$compile_var$compile_command$compile_rpath" | $SED 's%@OUTPUT@%\$progdir/\$file%g'` else # fast_install is set to needless relink_command= fi else link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" fi fi # Replace the output file specification. link_command=`$ECHO "$link_command" | $SED 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` # Delete the old output files. $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname func_show_eval "$link_command" 'exit $?' if test -n "$postlink_cmds"; then func_to_tool_file "$output_objdir/$outputname" postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` func_execute_cmds "$postlink_cmds" 'exit $?' fi # Now create the wrapper script. func_verbose "creating $output" # Quote the relink command for shipping. if test -n "$relink_command"; then # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" fi done relink_command="(cd `pwd`; $relink_command)" relink_command=`$ECHO "$relink_command" | $SED "$sed_quote_subst"` fi # Only actually do things if not in dry run mode. $opt_dry_run || { # win32 will think the script is a binary if it has # a .exe suffix, so we strip it off here. case $output in *.exe) func_stripname '' '.exe' "$output" output=$func_stripname_result ;; esac # test for cygwin because mv fails w/o .exe extensions case $host in *cygwin*) exeext=.exe func_stripname '' '.exe' "$outputname" outputname=$func_stripname_result ;; *) exeext= ;; esac case $host in *cygwin* | *mingw* ) func_dirname_and_basename "$output" "" "." output_name=$func_basename_result output_path=$func_dirname_result cwrappersource="$output_path/$objdir/lt-$output_name.c" cwrapper="$output_path/$output_name.exe" $RM $cwrappersource $cwrapper trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15 func_emit_cwrapperexe_src > $cwrappersource # The wrapper executable is built using the $host compiler, # because it contains $host paths and files. 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then eval exec "$exec_cmd" exit $EXIT_FAILURE fi exit $exit_status # The TAGs below are defined such that we never get into a situation # in which we disable both kinds of libraries. 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See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with GNU Libtool; see the file COPYING. If not, a copy # can be downloaded from http://www.gnu.org/licenses/gpl.html, or # obtained by writing to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. ]) # serial 57 LT_INIT # LT_PREREQ(VERSION) # ------------------ # Complain and exit if this libtool version is less that VERSION. m4_defun([LT_PREREQ], [m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1, [m4_default([$3], [m4_fatal([Libtool version $1 or higher is required], 63)])], [$2])]) # _LT_CHECK_BUILDDIR # ------------------ # Complain if the absolute build directory name contains unusual characters m4_defun([_LT_CHECK_BUILDDIR], [case `pwd` in *\ * | *\ *) AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;; esac ]) # LT_INIT([OPTIONS]) # ------------------ AC_DEFUN([LT_INIT], [AC_PREREQ([2.58])dnl We use AC_INCLUDES_DEFAULT AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl AC_BEFORE([$0], [LT_LANG])dnl AC_BEFORE([$0], [LT_OUTPUT])dnl AC_BEFORE([$0], [LTDL_INIT])dnl m4_require([_LT_CHECK_BUILDDIR])dnl dnl Autoconf doesn't catch unexpanded LT_ macros by default: m4_pattern_forbid([^_?LT_[A-Z_]+$])dnl m4_pattern_allow([^(_LT_EOF|LT_DLGLOBAL|LT_DLLAZY_OR_NOW|LT_MULTI_MODULE)$])dnl dnl aclocal doesn't pull ltoptions.m4, ltsugar.m4, or ltversion.m4 dnl unless we require an AC_DEFUNed macro: AC_REQUIRE([LTOPTIONS_VERSION])dnl AC_REQUIRE([LTSUGAR_VERSION])dnl AC_REQUIRE([LTVERSION_VERSION])dnl AC_REQUIRE([LTOBSOLETE_VERSION])dnl m4_require([_LT_PROG_LTMAIN])dnl _LT_SHELL_INIT([SHELL=${CONFIG_SHELL-/bin/sh}]) dnl Parse OPTIONS _LT_SET_OPTIONS([$0], [$1]) # This can be used to rebuild libtool when needed LIBTOOL_DEPS="$ltmain" # Always use our own libtool. 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#endif int fnord () { return 42; } int main () { void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW); int status = $lt_dlunknown; if (self) { if (dlsym (self,"fnord")) status = $lt_dlno_uscore; else { if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore; else puts (dlerror ()); } /* dlclose (self); */ } else puts (dlerror ()); return status; }] _LT_EOF if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null lt_status=$? case x$lt_status in x$lt_dlno_uscore) $1 ;; x$lt_dlneed_uscore) $2 ;; x$lt_dlunknown|x*) $3 ;; esac else : # compilation failed $3 fi fi rm -fr conftest* ])# _LT_TRY_DLOPEN_SELF # LT_SYS_DLOPEN_SELF # ------------------ AC_DEFUN([LT_SYS_DLOPEN_SELF], [m4_require([_LT_HEADER_DLFCN])dnl if test "x$enable_dlopen" != xyes; then enable_dlopen=unknown enable_dlopen_self=unknown enable_dlopen_self_static=unknown else lt_cv_dlopen=no lt_cv_dlopen_libs= case $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; 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esac # HP-UX runs *really* slowly unless shared libraries are mode 555, ... postinstall_cmds='chmod 555 $lib' # or fails outright, so override atomically: install_override_mode=555 ;; interix[[3-9]]*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux # correct to gnu/linux during the next big refactor else version_type=irix fi ;; esac need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") libsuff=32 shlibsuff=N32 libmagic=N32;; *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") libsuff=64 shlibsuff=64 libmagic=64-bit;; *) libsuff= shlibsuff= libmagic=never-match;; esac ;; esac shlibpath_var=LD_LIBRARY${shlibsuff}_PATH shlibpath_overrides_runpath=no sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" hardcode_into_libs=yes ;; # No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # Some binutils ld are patched to set DT_RUNPATH AC_CACHE_VAL([lt_cv_shlibpath_overrides_runpath], [lt_cv_shlibpath_overrides_runpath=no save_LDFLAGS=$LDFLAGS save_libdir=$libdir eval "libdir=/foo; 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esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; 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hppa*64*) [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF[ -][0-9][0-9])(-bit)?( [LM]SB)? shared object( file)?[, -]* PA-RISC [0-9]\.[0-9]'] lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]]\.[[0-9]]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[[3-9]]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac ]) file_magic_glob= want_nocaseglob=no if test "$build" = "$host"; then case $host_os in mingw* | pw32*) if ( shopt | grep nocaseglob ) >/dev/null 2>&1; then want_nocaseglob=yes else file_magic_glob=`echo aAbBcCdDeEfFgGhHiIjJkKlLmMnNoOpPqQrRsStTuUvVwWxXyYzZ | $SED -e "s/\(..\)/s\/[[\1]]\/[[\1]]\/g;/g"` fi ;; esac fi file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown _LT_DECL([], [deplibs_check_method], [1], [Method to check whether dependent libraries are shared objects]) _LT_DECL([], [file_magic_cmd], [1], [Command to use when deplibs_check_method = "file_magic"]) _LT_DECL([], [file_magic_glob], [1], [How to find potential files when deplibs_check_method = "file_magic"]) _LT_DECL([], [want_nocaseglob], [1], [Find potential files using nocaseglob when deplibs_check_method = "file_magic"]) ])# _LT_CHECK_MAGIC_METHOD # LT_PATH_NM # ---------- # find the pathname to a BSD- or MS-compatible name lister AC_DEFUN([LT_PATH_NM], [AC_REQUIRE([AC_PROG_CC])dnl AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM, [if test -n "$NM"; then # Let the user override the test. lt_cv_path_NM="$NM" else lt_nm_to_check="${ac_tool_prefix}nm" if test -n "$ac_tool_prefix" && test "$build" = "$host"; then lt_nm_to_check="$lt_nm_to_check nm" fi for lt_tmp_nm in $lt_nm_to_check; do lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. tmp_nm="$ac_dir/$lt_tmp_nm" if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then # Check to see if the nm accepts a BSD-compat flag. # Adding the `sed 1q' prevents false positives on HP-UX, which says: # nm: unknown option "B" ignored # Tru64's nm complains that /dev/null is an invalid object file case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in */dev/null* | *'Invalid file or object type'*) lt_cv_path_NM="$tmp_nm -B" break ;; *) case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in */dev/null*) lt_cv_path_NM="$tmp_nm -p" break ;; *) lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but continue # so that we can try to find one that supports BSD flags ;; esac ;; esac fi done IFS="$lt_save_ifs" done : ${lt_cv_path_NM=no} fi]) if test "$lt_cv_path_NM" != "no"; then NM="$lt_cv_path_NM" else # Didn't find any BSD compatible name lister, look for dumpbin. if test -n "$DUMPBIN"; then : # Let the user override the test. else AC_CHECK_TOOLS(DUMPBIN, [dumpbin "link -dump"], :) case `$DUMPBIN -symbols /dev/null 2>&1 | sed '1q'` in *COFF*) DUMPBIN="$DUMPBIN -symbols" ;; *) DUMPBIN=: ;; esac fi AC_SUBST([DUMPBIN]) if test "$DUMPBIN" != ":"; then NM="$DUMPBIN" fi fi test -z "$NM" && NM=nm AC_SUBST([NM]) _LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface], [lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:$LINENO: $ac_compile\"" >&AS_MESSAGE_LOG_FD) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:$LINENO: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:$LINENO: output\"" >&AS_MESSAGE_LOG_FD) cat conftest.out >&AS_MESSAGE_LOG_FD if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest*]) ])# LT_PATH_NM # Old names: AU_ALIAS([AM_PROG_NM], [LT_PATH_NM]) AU_ALIAS([AC_PROG_NM], [LT_PATH_NM]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_PROG_NM], []) dnl AC_DEFUN([AC_PROG_NM], []) # _LT_CHECK_SHAREDLIB_FROM_LINKLIB # -------------------------------- # how to determine the name of the shared library # associated with a specific link library. # -- PORTME fill in with the dynamic library characteristics m4_defun([_LT_CHECK_SHAREDLIB_FROM_LINKLIB], [m4_require([_LT_DECL_EGREP]) m4_require([_LT_DECL_OBJDUMP]) m4_require([_LT_DECL_DLLTOOL]) AC_CACHE_CHECK([how to associate runtime and link libraries], lt_cv_sharedlib_from_linklib_cmd, [lt_cv_sharedlib_from_linklib_cmd='unknown' case $host_os in cygwin* | mingw* | pw32* | cegcc*) # two different shell functions defined in ltmain.sh # decide which to use based on capabilities of $DLLTOOL case `$DLLTOOL --help 2>&1` in *--identify-strict*) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib ;; *) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib_fallback ;; esac ;; *) # fallback: assume linklib IS sharedlib lt_cv_sharedlib_from_linklib_cmd="$ECHO" ;; esac ]) sharedlib_from_linklib_cmd=$lt_cv_sharedlib_from_linklib_cmd test -z "$sharedlib_from_linklib_cmd" && sharedlib_from_linklib_cmd=$ECHO _LT_DECL([], [sharedlib_from_linklib_cmd], [1], [Command to associate shared and link libraries]) ])# _LT_CHECK_SHAREDLIB_FROM_LINKLIB # _LT_PATH_MANIFEST_TOOL # ---------------------- # locate the manifest tool m4_defun([_LT_PATH_MANIFEST_TOOL], [AC_CHECK_TOOL(MANIFEST_TOOL, mt, :) test -z "$MANIFEST_TOOL" && MANIFEST_TOOL=mt AC_CACHE_CHECK([if $MANIFEST_TOOL is a manifest tool], [lt_cv_path_mainfest_tool], [lt_cv_path_mainfest_tool=no echo "$as_me:$LINENO: $MANIFEST_TOOL '-?'" >&AS_MESSAGE_LOG_FD $MANIFEST_TOOL '-?' 2>conftest.err > conftest.out cat conftest.err >&AS_MESSAGE_LOG_FD if $GREP 'Manifest Tool' conftest.out > /dev/null; then lt_cv_path_mainfest_tool=yes fi rm -f conftest*]) if test "x$lt_cv_path_mainfest_tool" != xyes; then MANIFEST_TOOL=: fi _LT_DECL([], [MANIFEST_TOOL], [1], [Manifest tool])dnl ])# _LT_PATH_MANIFEST_TOOL # LT_LIB_M # -------- # check for math library AC_DEFUN([LT_LIB_M], [AC_REQUIRE([AC_CANONICAL_HOST])dnl LIBM= case $host in *-*-beos* | *-*-cegcc* | *-*-cygwin* | *-*-haiku* | *-*-pw32* | *-*-darwin*) # These system don't have libm, or don't need it ;; *-ncr-sysv4.3*) AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw") AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm") ;; *) AC_CHECK_LIB(m, cos, LIBM="-lm") ;; esac AC_SUBST([LIBM]) ])# LT_LIB_M # Old name: AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_CHECK_LIBM], []) # _LT_COMPILER_NO_RTTI([TAGNAME]) # ------------------------------- m4_defun([_LT_COMPILER_NO_RTTI], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= if test "$GCC" = yes; then case $cc_basename in nvcc*) _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -Xcompiler -fno-builtin' ;; *) _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' ;; esac _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions], lt_cv_prog_compiler_rtti_exceptions, [-fno-rtti -fno-exceptions], [], [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"]) fi _LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1], [Compiler flag to turn off builtin functions]) ])# _LT_COMPILER_NO_RTTI # _LT_CMD_GLOBAL_SYMBOLS # ---------------------- m4_defun([_LT_CMD_GLOBAL_SYMBOLS], [AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([AC_PROG_AWK])dnl AC_REQUIRE([LT_PATH_NM])dnl AC_REQUIRE([LT_PATH_LD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_TAG_COMPILER])dnl # Check for command to grab the raw symbol name followed by C symbol from nm. AC_MSG_CHECKING([command to parse $NM output from $compiler object]) AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe], [ # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[[BCDEGRST]]' # Regexp to match symbols that can be accessed directly from C. sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[[BCDT]]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[[ABCDGISTW]]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[[ABCDEGRST]]' fi ;; irix* | nonstopux*) symcode='[[BCDEGRST]]' ;; osf*) symcode='[[BCDEGQRST]]' ;; solaris*) symcode='[[BDRT]]' ;; sco3.2v5*) symcode='[[DT]]' ;; sysv4.2uw2*) symcode='[[DT]]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[[ABDT]]' ;; sysv4) symcode='[[DFNSTU]]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[[ABCDGIRSTW]]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\)[[ ]]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\)[[ ]]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK ['"\ " {last_section=section; section=\$ 3};"\ " /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx]" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi lt_cv_sys_global_symbol_pipe="$lt_cv_sys_global_symbol_pipe | sed '/ __gnu_lto/d'" # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if AC_TRY_EVAL(ac_compile); then # Now try to grab the symbols. nlist=conftest.nm if AC_TRY_EVAL(NM conftest.$ac_objext \| "$lt_cv_sys_global_symbol_pipe" \> $nlist) && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext /* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests. */ #if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE) /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */ # define LT@&t@_DLSYM_CONST #elif defined(__osf__) /* This system does not cope well with relocations in const data. */ # define LT@&t@_DLSYM_CONST #else # define LT@&t@_DLSYM_CONST const #endif #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ LT@&t@_DLSYM_CONST struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[[]] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_globsym_save_LIBS=$LIBS lt_globsym_save_CFLAGS=$CFLAGS LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS=$lt_globsym_save_LIBS CFLAGS=$lt_globsym_save_CFLAGS else echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD fi else echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done ]) if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then AC_MSG_RESULT(failed) else AC_MSG_RESULT(ok) fi # Response file support. if test "$lt_cv_nm_interface" = "MS dumpbin"; then nm_file_list_spec='@' elif $NM --help 2>/dev/null | grep '[[@]]FILE' >/dev/null; then nm_file_list_spec='@' fi _LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1], [Take the output of nm and produce a listing of raw symbols and C names]) _LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1], [Transform the output of nm in a proper C declaration]) _LT_DECL([global_symbol_to_c_name_address], [lt_cv_sys_global_symbol_to_c_name_address], [1], [Transform the output of nm in a C name address pair]) _LT_DECL([global_symbol_to_c_name_address_lib_prefix], [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1], [Transform the output of nm in a C name address pair when lib prefix is needed]) _LT_DECL([], [nm_file_list_spec], [1], [Specify filename containing input files for $NM]) ]) # _LT_CMD_GLOBAL_SYMBOLS # _LT_COMPILER_PIC([TAGNAME]) # --------------------------- m4_defun([_LT_COMPILER_PIC], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_wl, $1)= _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)= m4_if([$1], [CXX], [ # C++ specific cases for pic, static, wl, etc. if test "$GXX" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | os2* | pw32* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; *djgpp*) # DJGPP does not support shared libraries at all _LT_TAGVAR(lt_prog_compiler_pic, $1)= ;; haiku*) # PIC is the default for Haiku. # The "-static" flag exists, but is broken. _LT_TAGVAR(lt_prog_compiler_static, $1)= ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else case $host_os in aix[[4-9]]*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; chorus*) case $cc_basename in cxch68*) # Green Hills C++ Compiler # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" ;; esac ;; mingw* | cygwin* | os2* | pw32* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; dgux*) case $cc_basename in ec++*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; ghcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; freebsd* | dragonfly*) # FreeBSD uses GNU C++ ;; hpux9* | hpux10* | hpux11*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' if test "$host_cpu" != ia64; then _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' fi ;; aCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac ;; *) ;; esac ;; interix*) # This is c89, which is MS Visual C++ (no shared libs) # Anyone wants to do a port? ;; irix5* | irix6* | nonstopux*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' # CC pic flag -KPIC is the default. ;; *) ;; esac ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in KCC*) # KAI C++ Compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; ecpc* ) # old Intel C++ for x86_64 which still supported -KPIC. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; icpc* ) # Intel C++, used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; pgCC* | pgcpp*) # Portland Group C++ compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; cxx*) # Compaq C++ # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xlc* | xlC* | bgxl[[cC]]* | mpixl[[cC]]*) # IBM XL 8.0, 9.0 on PPC and BlueGene _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C++ 5.9 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; esac ;; esac ;; lynxos*) ;; m88k*) ;; mvs*) case $cc_basename in cxx*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall' ;; *) ;; esac ;; netbsd*) ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; osf3* | osf4* | osf5*) case $cc_basename in KCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' ;; RCC*) # Rational C++ 2.4.1 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; cxx*) # Digital/Compaq C++ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; *) ;; esac ;; psos*) ;; solaris*) case $cc_basename in CC* | sunCC*) # Sun C++ 4.2, 5.x and Centerline C++ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; gcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' ;; *) ;; esac ;; sunos4*) case $cc_basename in CC*) # Sun C++ 4.x _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; lcc*) # Lucid _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; esac ;; tandem*) case $cc_basename in NCC*) # NonStop-UX NCC 3.20 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; *) ;; esac ;; vxworks*) ;; *) _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; esac fi ], [ if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; haiku*) # PIC is the default for Haiku. # The "-static" flag exists, but is broken. _LT_TAGVAR(lt_prog_compiler_static, $1)= ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; msdosdjgpp*) # Just because we use GCC doesn't mean we suddenly get shared libraries # on systems that don't support them. _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no enable_shared=no ;; *nto* | *qnx*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac case $cc_basename in nvcc*) # Cuda Compiler Driver 2.2 _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Xlinker ' if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then _LT_TAGVAR(lt_prog_compiler_pic, $1)="-Xcompiler $_LT_TAGVAR(lt_prog_compiler_pic, $1)" fi ;; esac else # PORTME Check for flag to pass linker flags through the system compiler. case $host_os in aix*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; hpux9* | hpux10* | hpux11*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but # not for PA HP-UX. case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac # Is there a better lt_prog_compiler_static that works with the bundled CC? _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' ;; irix5* | irix6* | nonstopux*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC (with -KPIC) is the default. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in # old Intel for x86_64 which still supported -KPIC. ecc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; # icc used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. icc* | ifort*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; # Lahey Fortran 8.1. lf95*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared' _LT_TAGVAR(lt_prog_compiler_static, $1)='--static' ;; nagfor*) # NAG Fortran compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,-Wl,,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; pgcc* | pgf77* | pgf90* | pgf95* | pgfortran*) # Portland Group compilers (*not* the Pentium gcc compiler, # which looks to be a dead project) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; ccc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # All Alpha code is PIC. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xl* | bgxl* | bgf* | mpixl*) # IBM XL C 8.0/Fortran 10.1, 11.1 on PPC and BlueGene _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ Ceres\ Fortran* | *Sun*Fortran*\ [[1-7]].* | *Sun*Fortran*\ 8.[[0-3]]*) # Sun Fortran 8.3 passes all unrecognized flags to the linker _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='' ;; *Sun\ F* | *Sun*Fortran*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; *Sun\ C*) # Sun C 5.9 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' ;; *Intel*\ [[CF]]*Compiler*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; *Portland\ Group*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; esac ;; esac ;; newsos6) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; *nto* | *qnx*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; osf3* | osf4* | osf5*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # All OSF/1 code is PIC. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; rdos*) _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; solaris*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' case $cc_basename in f77* | f90* | f95* | sunf77* | sunf90* | sunf95*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ';; *) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,';; esac ;; sunos4*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; sysv4 | sysv4.2uw2* | sysv4.3*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; sysv4*MP*) if test -d /usr/nec ;then _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Kconform_pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; unicos*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; uts4*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; *) _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; esac fi ]) case $host_os in # For platforms which do not support PIC, -DPIC is meaningless: *djgpp*) _LT_TAGVAR(lt_prog_compiler_pic, $1)= ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)="$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t@m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])" ;; esac AC_CACHE_CHECK([for $compiler option to produce PIC], [_LT_TAGVAR(lt_cv_prog_compiler_pic, $1)], [_LT_TAGVAR(lt_cv_prog_compiler_pic, $1)=$_LT_TAGVAR(lt_prog_compiler_pic, $1)]) _LT_TAGVAR(lt_prog_compiler_pic, $1)=$_LT_TAGVAR(lt_cv_prog_compiler_pic, $1) # # Check to make sure the PIC flag actually works. # if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then _LT_COMPILER_OPTION([if $compiler PIC flag $_LT_TAGVAR(lt_prog_compiler_pic, $1) works], [_LT_TAGVAR(lt_cv_prog_compiler_pic_works, $1)], [$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t@m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])], [], [case $_LT_TAGVAR(lt_prog_compiler_pic, $1) in "" | " "*) ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)=" $_LT_TAGVAR(lt_prog_compiler_pic, $1)" ;; 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osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*' _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $pic_flag $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' else _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*' _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir' fi _LT_TAGVAR(archive_cmds_need_lc, $1)='no' _LT_TAGVAR(hardcode_libdir_separator, $1)=: ;; solaris*) _LT_TAGVAR(no_undefined_flag, $1)=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared $pic_flag ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' ;; *) wlarc='${wl}' _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; 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GCC discards it without `$wl', # but is careful enough not to reorder. # Supported since Solaris 2.6 (maybe 2.5.1?) if test "$GCC" = yes; then _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' else _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract' fi ;; esac _LT_TAGVAR(link_all_deplibs, $1)=yes ;; sunos4*) if test "x$host_vendor" = xsequent; then # Use $CC to link under sequent, because it throws in some extra .o # files that make .init and .fini sections work. _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' else _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' fi _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; sysv4) case $host_vendor in sni) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_direct, $1)=yes # is this really true??? ;; siemens) ## LD is ld it makes a PLAMLIB ## CC just makes a GrossModule. _LT_TAGVAR(archive_cmds, $1)='$LD -G -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(reload_cmds, $1)='$CC -r -o $output$reload_objs' _LT_TAGVAR(hardcode_direct, $1)=no ;; motorola) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_direct, $1)=no #Motorola manual says yes, but my tests say they lie ;; esac runpath_var='LD_RUN_PATH' _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; sysv4.3*) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_shlibpath_var, $1)=no _LT_TAGVAR(export_dynamic_flag_spec, $1)='-Bexport' ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_shlibpath_var, $1)=no runpath_var=LD_RUN_PATH hardcode_runpath_var=yes _LT_TAGVAR(ld_shlibs, $1)=yes fi ;; sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*) _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text' _LT_TAGVAR(archive_cmds_need_lc, $1)=no _LT_TAGVAR(hardcode_shlibpath_var, $1)=no runpath_var='LD_RUN_PATH' if test "$GCC" = yes; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' else _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' fi ;; sysv5* | sco3.2v5* | sco5v6*) # Note: We can NOT use -z defs as we might desire, because we do not # link with -lc, and that would cause any symbols used from libc to # always be unresolved, which means just about no library would # ever link correctly. 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(KAI) C++ Compiler # KCC will only create a shared library if the output file # ends with ".so" (or ".sl" for HP-UX), so rename the library # to its proper name (with version) after linking. _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib' _LT_TAGVAR(archive_expsym_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib' # Commands to make compiler produce verbose output that lists # what "hidden" libraries, object files and flags are used when # linking a shared library. # # There doesn't appear to be a way to prevent this compiler from # explicitly linking system object files so we need to strip them # from the output so that they don't get included in the library # dependencies. output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; 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|| _lt_function_replace_fail=: else # Save a `func_append' function call even when '+=' is not available sed -e 's%func_append \([[a-zA-Z_]]\{1,\}\) "%\1="$\1%g' $cfgfile > $cfgfile.tmp \ && mv -f "$cfgfile.tmp" "$cfgfile" \ || (rm -f "$cfgfile" && cp "$cfgfile.tmp" "$cfgfile" && rm -f "$cfgfile.tmp") test 0 -eq $? || _lt_function_replace_fail=: fi if test x"$_lt_function_replace_fail" = x":"; then AC_MSG_WARN([Unable to substitute extended shell functions in $ofile]) fi ]) # _LT_PATH_CONVERSION_FUNCTIONS # ----------------------------- # Determine which file name conversion functions should be used by # func_to_host_file (and, implicitly, by func_to_host_path). These are needed # for certain cross-compile configurations and native mingw. m4_defun([_LT_PATH_CONVERSION_FUNCTIONS], [AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_CANONICAL_BUILD])dnl AC_MSG_CHECKING([how to convert $build file names to $host format]) AC_CACHE_VAL(lt_cv_to_host_file_cmd, [case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_w32 ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_cygwin_to_w32 ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_w32 ;; esac ;; *-*-cygwin* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_cygwin ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_noop ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_cygwin ;; esac ;; * ) # unhandled hosts (and "normal" native builds) lt_cv_to_host_file_cmd=func_convert_file_noop ;; esac ]) to_host_file_cmd=$lt_cv_to_host_file_cmd AC_MSG_RESULT([$lt_cv_to_host_file_cmd]) _LT_DECL([to_host_file_cmd], [lt_cv_to_host_file_cmd], [0], [convert $build file names to $host format])dnl AC_MSG_CHECKING([how to convert $build file names to toolchain format]) AC_CACHE_VAL(lt_cv_to_tool_file_cmd, [#assume ordinary cross tools, or native build. lt_cv_to_tool_file_cmd=func_convert_file_noop case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_tool_file_cmd=func_convert_file_msys_to_w32 ;; esac ;; esac ]) to_tool_file_cmd=$lt_cv_to_tool_file_cmd AC_MSG_RESULT([$lt_cv_to_tool_file_cmd]) _LT_DECL([to_tool_file_cmd], [lt_cv_to_tool_file_cmd], [0], [convert $build files to toolchain format])dnl ])# _LT_PATH_CONVERSION_FUNCTIONS ctffind-4.1.14/m4/ltoptions.m4000066400000000000000000000300731440356052600160430ustar00rootroot00000000000000# Helper functions for option handling. -*- Autoconf -*- # # Copyright (C) 2004, 2005, 2007, 2008, 2009 Free Software Foundation, # Inc. # Written by Gary V. Vaughan, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 7 ltoptions.m4 # This is to help aclocal find these macros, as it can't see m4_define. AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])]) # _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME) # ------------------------------------------ m4_define([_LT_MANGLE_OPTION], [[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])]) # _LT_SET_OPTION(MACRO-NAME, OPTION-NAME) # --------------------------------------- # Set option OPTION-NAME for macro MACRO-NAME, and if there is a # matching handler defined, dispatch to it. Other OPTION-NAMEs are # saved as a flag. m4_define([_LT_SET_OPTION], [m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]), _LT_MANGLE_DEFUN([$1], [$2]), [m4_warning([Unknown $1 option `$2'])])[]dnl ]) # _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET]) # ------------------------------------------------------------ # Execute IF-SET if OPTION is set, IF-NOT-SET otherwise. m4_define([_LT_IF_OPTION], [m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])]) # _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET) # ------------------------------------------------------- # Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME # are set. m4_define([_LT_UNLESS_OPTIONS], [m4_foreach([_LT_Option], m4_split(m4_normalize([$2])), [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option), [m4_define([$0_found])])])[]dnl m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3 ])[]dnl ]) # _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST) # ---------------------------------------- # OPTION-LIST is a space-separated list of Libtool options associated # with MACRO-NAME. If any OPTION has a matching handler declared with # LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about # the unknown option and exit. m4_defun([_LT_SET_OPTIONS], [# Set options m4_foreach([_LT_Option], m4_split(m4_normalize([$2])), [_LT_SET_OPTION([$1], _LT_Option)]) m4_if([$1],[LT_INIT],[ dnl dnl Simply set some default values (i.e off) if boolean options were not dnl specified: _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no ]) _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no ]) dnl dnl If no reference was made to various pairs of opposing options, then dnl we run the default mode handler for the pair. For example, if neither dnl `shared' nor `disable-shared' was passed, we enable building of shared dnl archives by default: _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED]) _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC]) _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC]) _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install], [_LT_ENABLE_FAST_INSTALL]) ]) ])# _LT_SET_OPTIONS ## --------------------------------- ## ## Macros to handle LT_INIT options. ## ## --------------------------------- ## # _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME) # ----------------------------------------- m4_define([_LT_MANGLE_DEFUN], [[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])]) # LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE) # ----------------------------------------------- m4_define([LT_OPTION_DEFINE], [m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl ])# LT_OPTION_DEFINE # dlopen # ------ LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes ]) AU_DEFUN([AC_LIBTOOL_DLOPEN], [_LT_SET_OPTION([LT_INIT], [dlopen]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `dlopen' option into LT_INIT's first parameter.]) ]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], []) # win32-dll # --------- # Declare package support for building win32 dll's. LT_OPTION_DEFINE([LT_INIT], [win32-dll], [enable_win32_dll=yes case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-cegcc*) AC_CHECK_TOOL(AS, as, false) AC_CHECK_TOOL(DLLTOOL, dlltool, false) AC_CHECK_TOOL(OBJDUMP, objdump, false) ;; esac test -z "$AS" && AS=as _LT_DECL([], [AS], [1], [Assembler program])dnl test -z "$DLLTOOL" && DLLTOOL=dlltool _LT_DECL([], [DLLTOOL], [1], [DLL creation program])dnl test -z "$OBJDUMP" && OBJDUMP=objdump _LT_DECL([], [OBJDUMP], [1], [Object dumper program])dnl ])# win32-dll AU_DEFUN([AC_LIBTOOL_WIN32_DLL], [AC_REQUIRE([AC_CANONICAL_HOST])dnl _LT_SET_OPTION([LT_INIT], [win32-dll]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `win32-dll' option into LT_INIT's first parameter.]) ]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], []) # _LT_ENABLE_SHARED([DEFAULT]) # ---------------------------- # implement the --enable-shared flag, and supports the `shared' and # `disable-shared' LT_INIT options. # DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. m4_define([_LT_ENABLE_SHARED], [m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl AC_ARG_ENABLE([shared], [AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@], [build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])], [p=${PACKAGE-default} case $enableval in yes) enable_shared=yes ;; no) enable_shared=no ;; *) enable_shared=no # Look at the argument we got. We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for pkg in $enableval; do IFS="$lt_save_ifs" if test "X$pkg" = "X$p"; then enable_shared=yes fi done IFS="$lt_save_ifs" ;; esac], [enable_shared=]_LT_ENABLE_SHARED_DEFAULT) _LT_DECL([build_libtool_libs], [enable_shared], [0], [Whether or not to build shared libraries]) ])# _LT_ENABLE_SHARED LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])]) LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])]) # Old names: AC_DEFUN([AC_ENABLE_SHARED], [_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared]) ]) AC_DEFUN([AC_DISABLE_SHARED], [_LT_SET_OPTION([LT_INIT], [disable-shared]) ]) AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)]) AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_ENABLE_SHARED], []) dnl AC_DEFUN([AM_DISABLE_SHARED], []) # _LT_ENABLE_STATIC([DEFAULT]) # ---------------------------- # implement the --enable-static flag, and support the `static' and # `disable-static' LT_INIT options. # DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. m4_define([_LT_ENABLE_STATIC], [m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl AC_ARG_ENABLE([static], [AS_HELP_STRING([--enable-static@<:@=PKGS@:>@], [build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])], [p=${PACKAGE-default} case $enableval in yes) enable_static=yes ;; no) enable_static=no ;; *) enable_static=no # Look at the argument we got. We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for pkg in $enableval; do IFS="$lt_save_ifs" if test "X$pkg" = "X$p"; then enable_static=yes fi done IFS="$lt_save_ifs" ;; esac], [enable_static=]_LT_ENABLE_STATIC_DEFAULT) _LT_DECL([build_old_libs], [enable_static], [0], [Whether or not to build static libraries]) ])# _LT_ENABLE_STATIC LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])]) LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])]) # Old names: AC_DEFUN([AC_ENABLE_STATIC], [_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static]) ]) AC_DEFUN([AC_DISABLE_STATIC], [_LT_SET_OPTION([LT_INIT], [disable-static]) ]) AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)]) AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_ENABLE_STATIC], []) dnl AC_DEFUN([AM_DISABLE_STATIC], []) # _LT_ENABLE_FAST_INSTALL([DEFAULT]) # ---------------------------------- # implement the --enable-fast-install flag, and support the `fast-install' # and `disable-fast-install' LT_INIT options. # DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. m4_define([_LT_ENABLE_FAST_INSTALL], [m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl AC_ARG_ENABLE([fast-install], [AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@], [optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])], [p=${PACKAGE-default} case $enableval in yes) enable_fast_install=yes ;; no) enable_fast_install=no ;; *) enable_fast_install=no # Look at the argument we got. We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for pkg in $enableval; do IFS="$lt_save_ifs" if test "X$pkg" = "X$p"; then enable_fast_install=yes fi done IFS="$lt_save_ifs" ;; esac], [enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT) _LT_DECL([fast_install], [enable_fast_install], [0], [Whether or not to optimize for fast installation])dnl ])# _LT_ENABLE_FAST_INSTALL LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])]) LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])]) # Old names: AU_DEFUN([AC_ENABLE_FAST_INSTALL], [_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `fast-install' option into LT_INIT's first parameter.]) ]) AU_DEFUN([AC_DISABLE_FAST_INSTALL], [_LT_SET_OPTION([LT_INIT], [disable-fast-install]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `disable-fast-install' option into LT_INIT's first parameter.]) ]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], []) dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], []) # _LT_WITH_PIC([MODE]) # -------------------- # implement the --with-pic flag, and support the `pic-only' and `no-pic' # LT_INIT options. # MODE is either `yes' or `no'. If omitted, it defaults to `both'. m4_define([_LT_WITH_PIC], [AC_ARG_WITH([pic], [AS_HELP_STRING([--with-pic@<:@=PKGS@:>@], [try to use only PIC/non-PIC objects @<:@default=use both@:>@])], [lt_p=${PACKAGE-default} case $withval in yes|no) pic_mode=$withval ;; *) pic_mode=default # Look at the argument we got. We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for lt_pkg in $withval; do IFS="$lt_save_ifs" if test "X$lt_pkg" = "X$lt_p"; then pic_mode=yes fi done IFS="$lt_save_ifs" ;; esac], [pic_mode=default]) test -z "$pic_mode" && pic_mode=m4_default([$1], [default]) _LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl ])# _LT_WITH_PIC LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])]) LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])]) # Old name: AU_DEFUN([AC_LIBTOOL_PICMODE], [_LT_SET_OPTION([LT_INIT], [pic-only]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `pic-only' option into LT_INIT's first parameter.]) ]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_PICMODE], []) ## ----------------- ## ## LTDL_INIT Options ## ## ----------------- ## m4_define([_LTDL_MODE], []) LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive], [m4_define([_LTDL_MODE], [nonrecursive])]) LT_OPTION_DEFINE([LTDL_INIT], [recursive], [m4_define([_LTDL_MODE], [recursive])]) LT_OPTION_DEFINE([LTDL_INIT], [subproject], [m4_define([_LTDL_MODE], [subproject])]) m4_define([_LTDL_TYPE], []) LT_OPTION_DEFINE([LTDL_INIT], [installable], [m4_define([_LTDL_TYPE], [installable])]) LT_OPTION_DEFINE([LTDL_INIT], [convenience], [m4_define([_LTDL_TYPE], [convenience])]) ctffind-4.1.14/m4/ltsugar.m4000066400000000000000000000104241440356052600154670ustar00rootroot00000000000000# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*- # # Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc. # Written by Gary V. Vaughan, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 6 ltsugar.m4 # This is to help aclocal find these macros, as it can't see m4_define. AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])]) # lt_join(SEP, ARG1, [ARG2...]) # ----------------------------- # Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their # associated separator. # Needed until we can rely on m4_join from Autoconf 2.62, since all earlier # versions in m4sugar had bugs. m4_define([lt_join], [m4_if([$#], [1], [], [$#], [2], [[$2]], [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])]) m4_define([_lt_join], [m4_if([$#$2], [2], [], [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])]) # lt_car(LIST) # lt_cdr(LIST) # ------------ # Manipulate m4 lists. # These macros are necessary as long as will still need to support # Autoconf-2.59 which quotes differently. m4_define([lt_car], [[$1]]) m4_define([lt_cdr], [m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])], [$#], 1, [], [m4_dquote(m4_shift($@))])]) m4_define([lt_unquote], $1) # lt_append(MACRO-NAME, STRING, [SEPARATOR]) # ------------------------------------------ # Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'. # Note that neither SEPARATOR nor STRING are expanded; they are appended # to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked). # No SEPARATOR is output if MACRO-NAME was previously undefined (different # than defined and empty). # # This macro is needed until we can rely on Autoconf 2.62, since earlier # versions of m4sugar mistakenly expanded SEPARATOR but not STRING. m4_define([lt_append], [m4_define([$1], m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])]) # lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...]) # ---------------------------------------------------------- # Produce a SEP delimited list of all paired combinations of elements of # PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list # has the form PREFIXmINFIXSUFFIXn. # Needed until we can rely on m4_combine added in Autoconf 2.62. m4_define([lt_combine], [m4_if(m4_eval([$# > 3]), [1], [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl [[m4_foreach([_Lt_prefix], [$2], [m4_foreach([_Lt_suffix], ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[, [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])]) # lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ]) # ----------------------------------------------------------------------- # Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited # by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ. m4_define([lt_if_append_uniq], [m4_ifdef([$1], [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1], [lt_append([$1], [$2], [$3])$4], [$5])], [lt_append([$1], [$2], [$3])$4])]) # lt_dict_add(DICT, KEY, VALUE) # ----------------------------- m4_define([lt_dict_add], [m4_define([$1($2)], [$3])]) # lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE) # -------------------------------------------- m4_define([lt_dict_add_subkey], [m4_define([$1($2:$3)], [$4])]) # lt_dict_fetch(DICT, KEY, [SUBKEY]) # ---------------------------------- m4_define([lt_dict_fetch], [m4_ifval([$3], m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]), m4_ifdef([$1($2)], [m4_defn([$1($2)])]))]) # lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE]) # ----------------------------------------------------------------- m4_define([lt_if_dict_fetch], [m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4], [$5], [$6])]) # lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...]) # -------------------------------------------------------------- m4_define([lt_dict_filter], [m4_if([$5], [], [], [lt_join(m4_quote(m4_default([$4], [[, ]])), lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]), [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl ]) ctffind-4.1.14/m4/ltversion.m4000066400000000000000000000012621440356052600160330ustar00rootroot00000000000000# ltversion.m4 -- version numbers -*- Autoconf -*- # # Copyright (C) 2004 Free Software Foundation, Inc. # Written by Scott James Remnant, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # @configure_input@ # serial 3337 ltversion.m4 # This file is part of GNU Libtool m4_define([LT_PACKAGE_VERSION], [2.4.2]) m4_define([LT_PACKAGE_REVISION], [1.3337]) AC_DEFUN([LTVERSION_VERSION], [macro_version='2.4.2' macro_revision='1.3337' _LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?]) _LT_DECL(, macro_revision, 0) ]) ctffind-4.1.14/m4/lt~obsolete.m4000066400000000000000000000137561440356052600163730ustar00rootroot00000000000000# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*- # # Copyright (C) 2004, 2005, 2007, 2009 Free Software Foundation, Inc. # Written by Scott James Remnant, 2004. # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 5 lt~obsolete.m4 # These exist entirely to fool aclocal when bootstrapping libtool. # # In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN) # which have later been changed to m4_define as they aren't part of the # exported API, or moved to Autoconf or Automake where they belong. # # The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN # in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us # using a macro with the same name in our local m4/libtool.m4 it'll # pull the old libtool.m4 in (it doesn't see our shiny new m4_define # and doesn't know about Autoconf macros at all.) # # So we provide this file, which has a silly filename so it's always # included after everything else. This provides aclocal with the # AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything # because those macros already exist, or will be overwritten later. # We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6. # # Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here. # Yes, that means every name once taken will need to remain here until # we give up compatibility with versions before 1.7, at which point # we need to keep only those names which we still refer to. # This is to help aclocal find these macros, as it can't see m4_define. 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All rights reserved. # Use is subject to Janelia Farm Research Campus Software Copyright 1.1 # license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html ) # # Last modification: Tapu Shaik, April 2018 # Alexis Rohou, Dec 2018 (adding score to plot) # Parse arguments if [ $# -ne 1 ] then echo "Usage: `basename $0` output_from_ctffind_avrot.txt" exit 65 fi input_fn=$1 output_fn=${1%%.???}.pdf #input_summary_fn=$(ls ${1%%_avrot.???}.${1##*.}) input_summary_fn="${1%%_avrot.???}.${1##*.}" # Check whether gnuplot is available if ! hash gnuplot 2>/dev/null; then echo "Gnuplot was not found on your system. Please make sure it is installed." exit -1 fi # Check whether gnuplot >= 4.6 is available gnuplot_version=$( gnuplot --version | awk '{print $2}' ) compare_result=$( echo "$gnuplot_version >= 4.6" | bc ) if [ $compare_result -le 0 ]; then echo "This script requires gnuplot version >= 4.6, but you have version $gnuplot_version" exit -1 fi # Define a neat function function transpose_ignore_comments { gawk ' { if ($1 ~ /^#/) { print $0 } else { for (i=1; i<=NF; i++) { a[NR,i] = $i } } } NF>p { p = NF } END { for(j=1; j<=p; j++) { str=a[1,j] for(i=2; i<=NR; i++){ str=str" "a[i,j]; } print str } }' $1 } # CTFFind outputs data in lines, but gnuplot wants things in columns transpose_ignore_comments $input_fn > /tmp/tmp.txt # Let's grab useful values pixel_size=$(gawk 'match($0,/Pixel size: ([0-9.]*)/,a) {print a[1]}' $input_fn) number_of_micrographs=$(gawk 'match($0,/Number of micrographs: ([0-9]*)/,a) {print a[1]}' $input_fn) mic_name=$(grep "Input file:" $input_fn | awk 'BEGIN {FS="Input file: "} {print $2}' | cut -d " " -f1 | sed 's/_/\\\_/g') lines_per_micrograph=6 if [ -f $input_summary_fn ]; then # Let's grab values from the summary file i=0 while read -a myArray do if [[ ${myArray[0]} != \#* ]]; then df_one[++i]=${myArray[1]} df_two[i]=${myArray[2]} angast[i]=${myArray[3]} pshift[i]=${myArray[4]} score[i]=${myArray[5]} maxres[i]=${myArray[6]} fi done < $input_summary_fn else df_one[0]="0" df_two[0]="0" angast[0]="0" pshift[0]="0" score[0]="0" maxres[0]="0" fi # Run Gnuplot gnuplot > /dev/null 2>&1 < temp.txt set border linewidth 1.5 if (strstrt(GPVAL_TERMINALS, 'pdfcairo') > 0) { set terminal pdfcairo size 10.0cm,4.0cm enhanced font 'Arial,9' set output '$output_fn' } else { set terminal postscript size 10,4 enhanced font 'Arial,14' set output '${output_fn%%.pdf}.ps' } # color definitions set style line 1 lc rgb '#0060ad' lt 1 lw 2 pt 7 # --- blue set style line 2 lc rgb 'red' lt 1 lw 1 pt 7 fill transparent solid 0.5 # --- red set style line 3 lc rgb 'orange' lt 3 lw 1 pt 7 # --- orange set style line 4 lc rgb 'light-blue' lt 1 lw 2 pt 7 # --- light blue set style line 5 lc rgb 'green' lt 1 lw 2 pt 7 set style line 6 lc rgb 'gray' lt 1 lw 2 pt 7 set xlabel 'Spatial frequency(1/Å)' set ylabel 'Amplitude (or cross-correlation)' set yrange [-0.1:1.1] set key outside defocus_1_values="${df_one[*]}" defocus_2_values="${df_two[*]}" angast_values="${angast[*]}" pshift_values="${pshift[*]}" score_values="${score[*]}" maxres_values="${maxres[*]}" do for [current_micrograph=1:$number_of_micrographs] { def_1=sprintf('%.0f Å',word(defocus_1_values,current_micrograph)+0) def_2=sprintf('%.0f Å',word(defocus_2_values,current_micrograph)+0) angast=sprintf('%.1f °',word(angast_values,current_micrograph)+0) pshift=sprintf('%.2f rad',word(pshift_values,current_micrograph)+0) score=sprintf('%.3f',word(score_values,current_micrograph)+0) maxres=sprintf('%.2f Å',word(maxres_values,current_micrograph)+0) # set title 'Micrograph '.current_micrograph." of $number_of_micrographs\n{/*0.5 Defocus 1: ".def_1.' | Defocus 2: '.def_2.' | Azimuth: '.angast.' | Phase shift: '.pshift.' | Score: '.score.'}' set title '$mic_name, '.current_micrograph." of $number_of_micrographs micrographs\n{/*0.5 Defocus 1: ".def_1.' | Defocus 2: '.def_2.' | Azimuth: '.angast.' | Phase shift: '.pshift.' | Score: '.score.' | MaxRes: '.maxres.'}' plot '/tmp/tmp.txt' using (\$1):(column(4+(current_micrograph-1)*$lines_per_micrograph)) w lines ls 3 title 'CTF fit', \ '' using (\$1):(column(5+(current_micrograph-1)*$lines_per_micrograph)) w lines ls 1 title 'Quality of fit', \ '' using (\$1):(column(3+(current_micrograph-1)*$lines_per_micrograph)) w lines ls 5 title 'Amplitude spectrum' } EOF # Convert the postscript file to a pdf file if needed if [ -f ${output_fn%%.pdf}.ps ]; then ps2pdf ${output_fn%%.pdf}.ps $output_fn fi # Fix the title of the PDF file if hash pdftk 2>/dev/null; then echo "InfoKey: Title" > /tmp/pdftemp.txt echo "InfoValue: $1" >> /tmp/pdftemp.txt mv ${output_fn} /tmp/tmp.pdf pdftk /tmp/tmp.pdf update_info /tmp/pdftemp.txt output $output_fn elif hash exiftool 2>/dev/null; then exiftool -Title="$1" ${output_fn} else echo "Neither pdftk nor exiftool were found on your system. Please install one of them to get improved metadata in your output PDF file." fi # Make a PNG version #convert -density 300 -flatten ${output_fn} ${output_fn%%.pdf}.png # Let the user know where to find results echo " " echo "Generated plots of 1D profiles and fits: ${output_fn}" echo " " ctffind-4.1.14/src/000077500000000000000000000000001440356052600140125ustar00rootroot00000000000000ctffind-4.1.14/src/core/000077500000000000000000000000001440356052600147425ustar00rootroot00000000000000ctffind-4.1.14/src/core/abstract_image_file.cpp000066400000000000000000000003141440356052600214100ustar00rootroot00000000000000#include "core_headers.h" AbstractImageFile::AbstractImageFile() { } AbstractImageFile::AbstractImageFile(std::string wanted_filename, bool overwrite) { } AbstractImageFile::~AbstractImageFile() { } ctffind-4.1.14/src/core/abstract_image_file.h000066400000000000000000000016541440356052600210650ustar00rootroot00000000000000class AbstractImageFile { public: wxFileName filename; AbstractImageFile(); AbstractImageFile(std::string filename, bool overwrite = false); ~AbstractImageFile(); virtual int ReturnXSize() = 0; virtual int ReturnYSize() = 0; virtual int ReturnZSize() = 0; virtual int ReturnNumberOfSlices() = 0; virtual float ReturnPixelSize() = 0; virtual bool IsOpen() = 0; virtual bool OpenFile(std::string filename, bool overwrite = false, bool wait_for_file_to_exist = false) = 0; // Return true if everything about the file looks OK virtual void CloseFile() = 0; virtual void ReadSliceFromDisk(int slice_number, float *output_array) = 0; virtual void ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array) = 0; virtual void WriteSliceToDisk(int slice_number, float *input_array) = 0; virtual void WriteSlicesToDisk(int start_slice, int end_slice, float *input_array) = 0; virtual void PrintInfo() = 0; }; ctffind-4.1.14/src/core/angles_and_shifts.h000066400000000000000000000022111440356052600205620ustar00rootroot00000000000000/* \brief AnglesAndShifts class (particle Euler angles and shifts) */ class AnglesAndShifts { public: RotationMatrix euler_matrix; AnglesAndShifts(); AnglesAndShifts(float wanted_euler_phi, float wanted_euler_theta, float wanted_euler_psi, float wanted_shift_x = 0.0, float wanted_shift_y = 0.0); // constructor with size // ~AnglesAndShifts(); // destructor void GenerateEulerMatrices(float wanted_euler_phi, float wanted_euler_theta, float wanted_euler_psi); void GenerateRotationMatrix2D(float wanted_rotation_angle_in_degrees); void Init(float wanted_euler_phi_in_degrees, float wanted_euler_theta_in_degrees, float wanted_euler_psi_in_degrees, float wanted_shift_x, float wanted_shift_y); inline float ReturnPhiAngle() {return euler_phi;}; inline float ReturnThetaAngle() {return euler_theta;}; inline float ReturnPsiAngle() {return euler_psi;}; inline float ReturnShiftX() {return shift_x;}; inline float ReturnShiftY() {return shift_y;}; private: float euler_phi; // in degrees float euler_theta; // in degrees float euler_psi; // in degrees float shift_x; // in Angstrom float shift_y; // in Angstrom }; ctffind-4.1.14/src/core/angular_distribution_histogram.h000066400000000000000000000030631440356052600234220ustar00rootroot00000000000000class AngularDistributionHistogram { public: wxArrayFloat histogram_data; wxArrayFloat phi_boundaries; wxArrayFloat theta_boundaries; int number_of_theta_steps; int number_of_phi_steps; AngularDistributionHistogram(); ~AngularDistributionHistogram(); void AddPosition(float theta, float phi); float GetHistogramValue(float theta, float phi); void Init(int wanted_number_of_theta_steps, int wanted_number_of_phi_steps); void GetMinMaxValues(float &min_value, float &max_value); void GetDistributionStatistics(float &min_value, float &max_value, float &average_value, float &std_dev); void PrintToTerminal(); void Clear(); inline int ReturnThetaBin(float theta) { //MyDebugAssertTrue(theta >= 0.0f && theta <= 90.0f, "Theta out of range here") int theta_bin; for (theta_bin = 0; theta_bin < theta_boundaries.GetCount(); theta_bin++) { if (theta < theta_boundaries[theta_bin]) { return theta_bin; } } // if we get here must be last bin.. return theta_boundaries.GetCount(); } inline int ReturnPhiBin(float phi) { //MyDebugAssertTrue(phi >= 0.0f && phi <= 360.0f, "Phi out of range here") //put it in the range of 0-360; while (phi < 0.0f) phi+=360.0f; while (phi > 360.f) phi-=360.0f; int phi_bin; for (phi_bin = 0; phi_bin < phi_boundaries.GetCount(); phi_bin++) { if (phi < phi_boundaries[phi_bin]) { return phi_bin; } } // if we got here, must be last bin.. return phi_boundaries.GetCount(); } }; WX_DECLARE_OBJARRAY(AngularDistributionHistogram, ArrayofAngularDistributionHistograms); ctffind-4.1.14/src/core/asset_group.h000066400000000000000000000023271440356052600174520ustar00rootroot00000000000000class AssetGroup { long number_allocated; public: AssetGroup(); AssetGroup( const AssetGroup &obj); // copy contructor ~AssetGroup(); int id; long *members; long number_of_members; wxString name; bool can_be_picked; // Used by FindParticlesPanel to keep track of whether all images within the group are ready to be picked void SetName(wxString wanted_name); void AddMember(long number_to_add); void RemoveMember(long number_to_remove); void RemoveAll(); void CopyFrom(AssetGroup *other_group); long FindMember(long member_to_find); AssetGroup & operator = (const AssetGroup &t); AssetGroup & operator = (const AssetGroup *t); }; class AssetGroupList { long number_allocated; public: AssetGroupList(); ~AssetGroupList(); long number_of_groups; AssetGroup *groups; long ReturnNumberOfGroups(); void AddGroup(wxString name); void AddGroup(AssetGroup *group_to_add); void RemoveGroup(long number_to_remove); void AddMemberToGroup(long wanted_group_number, long member_to_add); long ReturnGroupMember(long wanted_group_number, long wanted_member); void RemoveAssetFromExtraGroups(long wanted_asset); void ShiftMembersDueToAssetRemoval(long number_to_shift_after); void RemoveAll(); }; ctffind-4.1.14/src/core/assets.h000066400000000000000000000151331440356052600164200ustar00rootroot00000000000000#ifndef __ASSETS_H__ #define __ASSETS_H__ class Asset { public : int asset_id; int parent_id; wxFileName filename; bool is_valid; wxString asset_name; Asset(); ~Asset(); // pure virtual wxString ReturnFullPathString(); wxString ReturnShortNameString(); }; class MovieAsset : public Asset { public: MovieAsset(); MovieAsset(wxString wanted_filename); ~MovieAsset(); int position_in_stack; int x_size; int y_size; int number_of_frames; double pixel_size; double microscope_voltage; double spherical_aberration; double dose_per_frame; double total_dose; wxString gain_filename; double output_binning_factor; // If this is a super-resolution movie, but we never intend to use the "super resolution" part of the spectrum, this factor should be > 1 bool correct_mag_distortion; double mag_distortion_angle; double mag_distortion_major_scale; double mag_distortion_minor_scale; bool protein_is_white; void Update(wxString wanted_filename); //void Recheck_if_valid(); void CopyFrom(Asset *other_asset); //long FindMember(long member_to_find); }; class ImageAsset : public Asset { public: ImageAsset(); ImageAsset(wxString wanted_filename); ~ImageAsset(); int position_in_stack; int alignment_id; int ctf_estimation_id; int x_size; int y_size; double pixel_size; double microscope_voltage; double spherical_aberration; bool protein_is_white; void Update(wxString wanted_filename); void CopyFrom(Asset *other_asset); }; class ParticlePositionAsset : public Asset { public: ParticlePositionAsset(); ParticlePositionAsset(const float &wanted_x_in_angstroms, const float &wanted_y_in_angstroms); ~ParticlePositionAsset(); void Reset(); int picking_id; int pick_job_id; int parent_template_id; double x_position; double y_position; double peak_height; double template_phi; double template_theta; double template_psi; void CopyFrom(Asset *other_asset); }; WX_DECLARE_OBJARRAY(ParticlePositionAsset, ArrayOfParticlePositionAssets); class VolumeAsset : public Asset { public: VolumeAsset(); VolumeAsset(wxString wanted_filename); ~VolumeAsset(); long reconstruction_job_id; int x_size; int y_size; int z_size; double pixel_size; void Update(wxString wanted_filename); void CopyFrom(Asset *other_asset); }; /* class ClassesAsset : public Asset { public: ClassesAsset(); ~ClassesAsset(); long classification_job_id; long refinement_package_id; void CopyFrom(Asset *other_asset); };*/ class AssetList { protected : long number_allocated; public : AssetList(); ~AssetList(); long number_of_assets; Asset *assets; virtual void AddAsset(Asset *asset_to_add) = 0; virtual void RemoveAsset(long number_to_remove) = 0; virtual void RemoveAll() = 0; // virtual long FindFile(wxFileName file_to_find) = 0; virtual void CheckMemory() = 0; virtual Asset * ReturnAssetPointer(long wanted_asset) = 0; virtual MovieAsset * ReturnMovieAssetPointer(long wanted_asset); virtual ImageAsset * ReturnImageAssetPointer(long wanted_asset); virtual ParticlePositionAsset * ReturnParticlePositionAssetPointer(long wanted_asset); virtual VolumeAsset* ReturnVolumeAssetPointer(long wanted_asset); virtual int ReturnAssetID(long wanted_asset) = 0; virtual long ReturnParentAssetID(long wanted_asset) = 0; virtual wxString ReturnAssetName(long wanted_asset) = 0; virtual int ReturnArrayPositionFromID(int wanted_id, int last_found_position = 0) = 0; virtual int ReturnArrayPositionFromParentID(int wanted_id) = 0; virtual wxString ReturnAssetFullFilename(long wanted_asst) = 0; long ReturnNumberOfAssets() {return number_of_assets;} }; class MovieAssetList : public AssetList { public: MovieAssetList(); ~MovieAssetList(); Asset * ReturnAssetPointer(long wanted_asset); MovieAsset * ReturnMovieAssetPointer(long wanted_asset); int ReturnAssetID(long wanted_asset); long ReturnParentAssetID(long wanted_asset); wxString ReturnAssetName(long wanted_asset); int ReturnArrayPositionFromID(int wanted_id, int last_found_position = 0 ); int ReturnArrayPositionFromParentID(int wanted_id); wxString ReturnAssetFullFilename(long wanted_asst); void AddAsset(Asset *asset_to_add); void RemoveAsset(long number_to_remove); void RemoveAll(); long FindFile(wxFileName file_to_find, bool also_check_vs_shortname = false, long max_asset_number_to_check = -1); void CheckMemory(); }; class ImageAssetList : public AssetList { public: ImageAssetList(); ~ImageAssetList(); Asset * ReturnAssetPointer(long wanted_asset); ImageAsset * ReturnImageAssetPointer(long wanted_asset); int ReturnAssetID(long wanted_asset); long ReturnParentAssetID(long wanted_asset); wxString ReturnAssetName(long wanted_asset); int ReturnArrayPositionFromID(int wanted_id, int last_found_position = 0 ); int ReturnArrayPositionFromParentID(int wanted_id); wxString ReturnAssetFullFilename(long wanted_asst); void AddAsset(Asset *asset_to_add); void RemoveAsset(long number_to_remove); void RemoveAll(); long FindFile(wxFileName file_to_find, bool also_check_vs_shortname = false, long max_asset_number_to_check = -1); void CheckMemory(); }; class ParticlePositionAssetList : public AssetList { public: ParticlePositionAssetList(); ~ParticlePositionAssetList(); Asset * ReturnAssetPointer(long wanted_asset); ParticlePositionAsset * ReturnParticlePositionAssetPointer(long wanted_asset); int ReturnAssetID(long wanted_asset); long ReturnParentAssetID(long wanted_asset); wxString ReturnAssetName(long wanted_asset) {return wxEmptyString;}; wxString ReturnAssetFullFilename(long wanted_asst) {return wxEmptyString;}; int ReturnArrayPositionFromID(int wanted_id, int last_found_position = 0 ); int ReturnArrayPositionFromParentID(int wanted_id); void AddAsset(Asset *asset_to_add); void RemoveAsset(long number_to_remove); void RemoveAssetsWithGivenParentImageID(long parent_image_id); void RemoveAll(); void CheckMemory(); }; class VolumeAssetList : public AssetList { public: VolumeAssetList(); ~VolumeAssetList(); Asset * ReturnAssetPointer(long wanted_asset); VolumeAsset * ReturnVolumeAssetPointer(long wanted_asset); int ReturnAssetID(long wanted_asset); long ReturnParentAssetID(long wanted_asset); wxString ReturnAssetName(long wanted_asset); int ReturnArrayPositionFromID(int wanted_id, int last_found_position = 0 ); int ReturnArrayPositionFromParentID(int wanted_id); wxString ReturnAssetFullFilename(long wanted_asst); void AddAsset(Asset *asset_to_add); void RemoveAsset(long number_to_remove); void RemoveAll(); long FindFile(wxFileName file_to_find, bool also_check_vs_shortname = false, long max_asset_number_to_check = -1); void CheckMemory(); }; #endif ctffind-4.1.14/src/core/basic_star_file_reader.h000066400000000000000000000040111440356052600215420ustar00rootroot00000000000000class StarFileParameters { public : int position_in_stack; float phi; float theta; float psi; float x_shift; float y_shift; float defocus1; float defocus2; float defocus_angle; float phase_shift; StarFileParameters(); }; WX_DECLARE_OBJARRAY(StarFileParameters, ArrayofStarFileParameters); class BasicStarFileReader { int current_position_in_stack; int current_column; int phi_column; int theta_column; int psi_column; int xshift_column; int yshift_column; int defocus1_column; int defocus2_column; int defocus_angle_column; int phase_shift_column; public: wxString filename; // wxFileInputStream *input_file_stream; // wxTextInputStream *input_text_stream; wxTextFile *input_file; ArrayofStarFileParameters cached_parameters; BasicStarFileReader(); ~BasicStarFileReader(); BasicStarFileReader(wxString wanted_filename); void Open(wxString wanted_filename); void Close(); bool ReadFile(wxString wanted_filename, wxString *error_string = NULL); bool ExtractParametersFromLine(wxString &wanted_line, wxString *error_string = NULL); inline int ReturnPositionInStack(int line_number) { return cached_parameters[line_number].position_in_stack;} inline float ReturnPhi(int line_number) { return cached_parameters[line_number].phi;} inline float ReturnTheta(int line_number) { return cached_parameters[line_number].theta;} inline float ReturnPsi(int line_number) { return cached_parameters[line_number].psi;} inline float ReturnXShift(int line_number) { return cached_parameters[line_number].x_shift;} inline float ReturnYShift(int line_number) { return cached_parameters[line_number].y_shift;} inline float ReturnDefocus1(int line_number) { return cached_parameters[line_number].defocus1;} inline float ReturnDefocus2(int line_number) { return cached_parameters[line_number].defocus2;} inline float ReturnDefocusAngle(int line_number) { return cached_parameters[line_number].defocus_angle;} inline float ReturnPhaseShift(int line_number) { return cached_parameters[line_number].phase_shift;} }; ctffind-4.1.14/src/core/brute_force_search.cpp000066400000000000000000000253361440356052600213030ustar00rootroot00000000000000#include "core_headers.h" BruteForceSearch::BruteForceSearch() { // Nothing to do until Init is called number_of_dimensions = 0; is_in_memory = false; target_function = NULL; parameters = NULL; starting_value = NULL; best_value = NULL; half_range = NULL; step_size = NULL; dimension_at_max = NULL; best_score = std::numeric_limits::max(); num_iterations = 0; minimise_at_every_step = false; print_progress_bar = false; } BruteForceSearch::~BruteForceSearch() { // if (is_in_memory) { delete [] starting_value; delete [] best_value; delete [] half_range; delete [] step_size; delete [] dimension_at_max; is_in_memory = false; } } void BruteForceSearch::Init(float (*function_to_minimize)(void* parameters, float []), void *wanted_parameters, int num_dim, float wanted_starting_value[], float wanted_half_range[], float wanted_step_size[], bool should_minimise_at_every_step, bool should_print_progress_bar, int wanted_desired_num_threads ) { MyDebugAssertFalse(is_in_memory,"Brute force search object is already setup"); MyDebugAssertTrue(num_dim > 0,"Bad number of dimensions: %i",num_dim); MyDebugAssertTrue(num_dim <= 16,"Recent versions of BruteForceSearch (with threading) may not work with more than 16 dimensions"); // Local variables float *current_values = new float[num_dim]; bool search_done; // Allocate memory number_of_dimensions = num_dim; starting_value = new float[number_of_dimensions]; best_value = new float[number_of_dimensions]; half_range = new float[number_of_dimensions]; step_size = new float[number_of_dimensions]; dimension_at_max = new bool[number_of_dimensions]; is_in_memory = true; // Copy starting values, half range and step size over; initialise for (int dim_counter=0; dim_counter < number_of_dimensions; dim_counter++) { starting_value[dim_counter] = wanted_starting_value[dim_counter]; half_range[dim_counter] = wanted_half_range[dim_counter]; step_size[dim_counter] = wanted_step_size[dim_counter]; dimension_at_max[dim_counter] = false; current_values[dim_counter] = - std::numeric_limits::max(); } // minimise_at_every_step = should_minimise_at_every_step; // Work out how many iterations the exhaustive search will take // we will start at lowest value for each dimension, then go in step sizes, until we get to upper limit. // we will also do extra iterations for the starting value and the upper limit num_iterations = 0; while (true) { IncrementCurrentValues(current_values,search_done); if (search_done) { break; } num_iterations++; } // target_function = function_to_minimize; parameters = wanted_parameters; print_progress_bar = should_print_progress_bar; desired_num_threads = wanted_desired_num_threads; delete [] current_values; } float BruteForceSearch::GetBestValue(int index) { MyDebugAssertTrue(index < number_of_dimensions,"Index %i does not exist (number of dimensions = %i",index,number_of_dimensions); return best_value[index]; } // In the BF loop, this should be called before the scoring function. Before the BF loop, set all values in current_values to -huge void BruteForceSearch::IncrementCurrentValues(float *current_values, bool &search_is_now_completed) { MyDebugAssertTrue(is_in_memory,"Brute force search object not allocated"); int i; int j; // do the increment search_is_now_completed = true; for (i=0;i 0) { for (j=0;j= starting_value[i] + half_range[i]) { current_values[i] = starting_value[i] + half_range[i]; dimension_at_max[i] = true; if (i == number_of_dimensions - 1 ) { search_is_now_completed = true; } } break; } } // end of loop over dimensions for (i=0;i::max(); dimension_at_max[i] = false; } // DNM: Go through the search steps and save the values to be set at each step for (current_iteration=0; current_iteration < num_iterations; current_iteration++) { IncrementCurrentValues(current_values,search_completed); MyDebugAssertFalse(search_completed,"Failed sanity check"); for (i = 0; i < number_of_dimensions; i++) { all_values[number_of_dimensions * current_iteration + i] = current_values[i]; } } // The accuracy for the local minimization if (minimise_at_every_step) for (i=0;i 1 && ! minimise_at_every_step) { wxPrintf("\nRunning brute-force search with %i OpenMP threads\n",numThreads); } if ( print_progress_bar ) { my_progress_bar = new ProgressBar(num_iterations); } // start the brute-force search iterations // DNM the minimizer did not work right with threads, so just run it normally if (minimise_at_every_step) { for (current_iteration=0; current_iteration < num_iterations; current_iteration++) { // what values for the parameters should we try now? // DNM: switch to getting from the list //IncrementCurrentValues(current_values,search_completed); for (i = 0; i < number_of_dimensions; i++) current_values[i] = all_values[number_of_dimensions * current_iteration + i]; ConjugateGradient local_minimizer; for (i=0; iUpdate(num_iterations_completed); } } } else { #pragma omp parallel for default(none) num_threads(numThreads) shared( all_values, all_local_best_values, all_scores,numThreads,num_iterations_completed,my_progress_bar) private(current_iteration, current_values, current_values_for_local_minimization, i, accuracy_for_local_minimization) for (current_iteration=0; current_iteration < num_iterations; current_iteration++) { // Grab the next values to be tried for (i = 0; i < number_of_dimensions; i++) { current_values[i] = all_values[number_of_dimensions * current_iteration + i]; } // Try the current parameters by calling the scoring function all_scores[current_iteration] = target_function(parameters,current_values); // Progress if (print_progress_bar) { #pragma omp atomic num_iterations_completed++; my_progress_bar->Update(num_iterations_completed); } } } if (print_progress_bar) { delete my_progress_bar; } // DNM: Loop through the iterations again and look for the best result for (current_iteration=0; current_iteration < num_iterations; current_iteration++) { for (i = 0; i < number_of_dimensions; i++) { current_values[i] = all_values[number_of_dimensions * current_iteration + i]; } current_score = all_scores[current_iteration]; // Print debug /*wxPrintf("(BF dbg, it %04i) Values: ",current_iteration); for (i=0;iItem(line_number).position_in_stack;} inline int ReturnImageIsActive(int line_number) { return cached_parameters->Item(line_number).image_is_active;} inline float ReturnPhi(int line_number) { return cached_parameters->Item(line_number).phi;} inline float ReturnTheta(int line_number) { return cached_parameters->Item(line_number).theta;} inline float ReturnPsi(int line_number) { return cached_parameters->Item(line_number).psi;} inline float ReturnXShift(int line_number) { return cached_parameters->Item(line_number).x_shift;} inline float ReturnYShift(int line_number) { return cached_parameters->Item(line_number).y_shift;} inline float ReturnDefocus1(int line_number) { return cached_parameters->Item(line_number).defocus_1;} inline float ReturnDefocus2(int line_number) { return cached_parameters->Item(line_number).defocus_2;} inline float ReturnDefocusAngle(int line_number) { return cached_parameters->Item(line_number).defocus_angle;} inline float ReturnPhaseShift(int line_number) { return cached_parameters->Item(line_number).phase_shift;} inline int ReturnLogP(int line_number) { return cached_parameters->Item(line_number).logp;} inline float ReturnSigma(int line_number) { return cached_parameters->Item(line_number).sigma;} inline float ReturnScore(int line_number) { return cached_parameters->Item(line_number).score;} inline float ReturnScoreChange(int line_number) { return cached_parameters->Item(line_number).score_change;} inline float ReturnPixelSize(int line_number) { return cached_parameters->Item(line_number).pixel_size;} inline float ReturnMicroscopekV(int line_number) { return cached_parameters->Item(line_number).microscope_voltage_kv;} inline float ReturnMicroscopeCs(int line_number) { return cached_parameters->Item(line_number).microscope_spherical_aberration_mm;} inline float ReturnBeamTiltX(int line_number) { return cached_parameters->Item(line_number).beam_tilt_x;} inline float ReturnBeamTiltY(int line_number) { return cached_parameters->Item(line_number).beam_tilt_y;} }; ctffind-4.1.14/src/core/classification.h000066400000000000000000000032061440356052600201070ustar00rootroot00000000000000class ClassificationResult { public: ClassificationResult(); ~ClassificationResult(); long position_in_stack; float psi; float xshift; float yshift; int best_class; float sigma; float logp; }; WX_DECLARE_OBJARRAY(ClassificationResult, ArrayofClassificationResults); class Classification { public : Classification(); ~Classification(); long classification_id; long refinement_package_asset_id; wxString name; wxString class_average_file; bool classification_was_imported_or_generated; wxDateTime datetime_of_run; long starting_classification_id; long number_of_particles; int number_of_classes; float low_resolution_limit; float high_resolution_limit; float mask_radius; float angular_search_step; float search_range_x; float search_range_y; float smoothing_factor; bool exclude_blank_edges; bool auto_percent_used; float percent_used; void SizeAndFillWithEmpty(long number_of_particles); ArrayofClassificationResults classification_results; wxString WriteFrealignParameterFiles(wxString base_filename, RefinementPackage *parent_refinement_package); }; WX_DECLARE_OBJARRAY(Classification, ArrayofClassifications); class ShortClassificationInfo { public : ShortClassificationInfo(); long classification_id; long refinement_package_asset_id; wxString name; wxString class_average_file; long number_of_particles; int number_of_classes; float high_resolution_limit; ShortClassificationInfo & operator = (const Classification &other_classification); ShortClassificationInfo & operator = (const Classification *other_classification); }; WX_DECLARE_OBJARRAY(ShortClassificationInfo, ArrayofShortClassificationInfos); ctffind-4.1.14/src/core/classification_selection.h000066400000000000000000000006001440356052600221470ustar00rootroot00000000000000class ClassificationSelection { public: ClassificationSelection(); ~ClassificationSelection(); long selection_id; wxString name; wxDateTime creation_date; long refinement_package_asset_id; long classification_id; int number_of_classes; int number_of_selections; wxArrayLong selections; }; WX_DECLARE_OBJARRAY(ClassificationSelection, ArrayofClassificationSelections); ctffind-4.1.14/src/core/conjugate_gradient.cpp000066400000000000000000000032451440356052600213060ustar00rootroot00000000000000#include "core_headers.h" ConjugateGradient::ConjugateGradient() { is_in_memory = false; n = 0; num_function_calls = 0; best_values = NULL; e = NULL; escale = 0; best_score = std::numeric_limits::max(); target_function = NULL; parameters = NULL; } ConjugateGradient::~ConjugateGradient() { if (is_in_memory) { delete [] best_values; delete [] e; is_in_memory = false; } } float ConjugateGradient::Init(float (*function_to_minimize)(void* parameters, float []), void *parameters_to_pass, int num_dim, float starting_value[], float accuracy[] ) { MyDebugAssertTrue(num_dim > 0,"Initializing conjugate gradient with zero dimensions"); // Copy pointers to the target function and the needed parameters target_function = function_to_minimize; parameters = parameters_to_pass; if (is_in_memory) { delete [] best_values; delete [] e; is_in_memory = false; } // Allocate memory n = num_dim; best_values = new float[n]; e = new float[n]; is_in_memory = true; // Initialise values escale = 100.0; num_function_calls = 0; for (int dim_counter=0; dim_counter < n; dim_counter++) { best_values[dim_counter] = starting_value[dim_counter]; e[dim_counter] = accuracy[dim_counter]; } // Call the target function to find out our starting score best_score = target_function(parameters,starting_value); // MyDebugPrint("Starting score = %f\n",best_score); return best_score; } float ConjugateGradient::Run() { int iprint = 0; int icon = 1; int maxit = 50; int va04_success = 0; va04_success = va04a_(&n,e,&escale,&num_function_calls,target_function,parameters,&best_score,&iprint,&icon,&maxit,best_values); return best_score; } ctffind-4.1.14/src/core/conjugate_gradient.h000066400000000000000000000023551440356052600207540ustar00rootroot00000000000000class ConjugateGradient { // private: bool is_in_memory; int n; // Number of parameters to refine int num_function_calls; // Number of calls to the scoring function float *best_values; // Final best parameters determined by conjugate gradient minimization float *e; // Recalculated accuracy for subroutine va04 float escale; // Anticipated change in the parameters during conjugate gradient minimization float best_score; // Final best score // float (*target_function)(void* parameters, float []); void *parameters; public: // Constructors & destructors ConjugateGradient(); ~ConjugateGradient(); // Methods float Init(float (*function_to_minimize)(void* parameters, float []), void *parameters, int num_dim, float starting_value[], float accuracy[] ); float Run(); inline float GetBestValue(int index) { return best_values[index]; }; inline float GetBestScore() { return best_score; }; inline float *GetPointerToBestValues() { return best_values; }; }; extern "C" { int va04a_(int *n, float *e, float *escale, int *self_num_function_calls__, float (*self_target_function) (void* parameters, float[]), void *self_parameter_ptr__, float *self_best_score__, int *iprint, int *icon, int *maxit, float *x); } ctffind-4.1.14/src/core/core_headers.h000066400000000000000000000047221440356052600175430ustar00rootroot00000000000000typedef struct Peak { float x; float y; float z; float value; long physical_address_within_image; } Peak; typedef struct Kernel2D { int pixel_index[4]; float pixel_weight[4]; } Kernel2D; typedef struct CurvePoint { int index_m; int index_n; float value_m; float value_n; } CurvePoint; #include #include #include #include #include #include #include #include #include #include const std::complex I(0.0,1.0); #include #include #include #include #include #include #include "sqlite/sqlite3.h" #include #include #include #include #include #include #include #include #include #include #include #include "cistem_parameters.h" #include "cistem_star_file_reader.h" #include "defines.h" #include "assets.h" #include "asset_group.h" #include "socket_codes.h" #include "userinput.h" #include "functions.h" #include "randomnumbergenerator.h" #include "tiff/tiffio.h" #include "abstract_image_file.h" #include "mrc_header.h" #include "mrc_file.h" #include "dm_file.h" #include "tiff_file.h" #include "image_file.h" #include "matrix.h" #include "symmetry_matrix.h" #include "ctf.h" #include "curve.h" #include "angles_and_shifts.h" #include "parameter_constraints.h" #include "empirical_distribution.h" #include "image.h" #include "resolution_statistics.h" #include "reconstructed_volume.h" #include "particle.h" #include "reconstruct_3d.h" #include "electron_dose.h" #include "run_profiles.h" #include "angular_distribution_histogram.h" #include "refinement_package.h" #include "refinement.h" #include "classification.h" #include "classification_selection.h" #include "database.h" #include "project.h" #include "job_packager.h" #include "job_tracker.h" #include "numeric_text_file.h" #include "progressbar.h" #include "downhill_simplex.h" #include "brute_force_search.h" #include "conjugate_gradient.h" #include "euler_search.h" #include "frealign_parameter_file.h" #include "basic_star_file_reader.h" #include "particle_finder.h" #include "myapp.h" #include "rle3d.h" #include "local_resolution_estimator.h" #ifdef EXPERIMENTAL #include "pdb.h" #include "water.h" #endif #ifdef MKL #include #endif extern RandomNumberGenerator global_random_number_generator; ctffind-4.1.14/src/core/ctf.cpp000066400000000000000000000523101440356052600162230ustar00rootroot00000000000000#include "core_headers.h" CTF::CTF() { spherical_aberration = 0; wavelength = 0; amplitude_contrast = 0; defocus_1 = 0; defocus_2 = 0; defocus_half_range = 0; astigmatism_azimuth = 0; additional_phase_shift = 0; beam_tilt_x = 0; beam_tilt_y = 0; beam_tilt = 0; beam_tilt_azimuth = 0; particle_shift_x = 0; particle_shift_y = 0; particle_shift = 0; particle_shift_azimuth = 0; // Fitting parameters lowest_frequency_for_fitting = 0; highest_frequency_for_fitting = 0; astigmatism_tolerance = 0; // precomputed_amplitude_contrast_term = 0; squared_wavelength = 0; cubed_wavelength = 0; } CTF::CTF( float wanted_acceleration_voltage, // keV float wanted_spherical_aberration, // mm float wanted_amplitude_contrast, float wanted_defocus_1_in_angstroms, // A float wanted_defocus_2_in_angstroms, // A float wanted_astigmatism_azimuth, // degrees float wanted_lowest_frequency_for_fitting, // 1/A float wanted_highest_frequency_for_fitting, // 1/A float wanted_astigmatism_tolerance, // A. Set to negative to indicate no restraint on astigmatism. float pixel_size, // A float wanted_additional_phase_shift_in_radians, // rad float wanted_beam_tilt_x_in_radians, // rad float wanted_beam_tilt_y_in_radians, // rad float wanted_particle_shift_x_in_angstroms, // A float wanted_particle_shift_y_in_angstroms) // A { Init(wanted_acceleration_voltage,wanted_spherical_aberration,wanted_amplitude_contrast,wanted_defocus_1_in_angstroms,wanted_defocus_2_in_angstroms,wanted_astigmatism_azimuth,wanted_lowest_frequency_for_fitting,wanted_highest_frequency_for_fitting,wanted_astigmatism_tolerance,pixel_size,wanted_additional_phase_shift_in_radians,wanted_beam_tilt_x_in_radians,wanted_beam_tilt_y_in_radians,wanted_particle_shift_x_in_angstroms,wanted_particle_shift_y_in_angstroms); } CTF::CTF( float wanted_acceleration_voltage, // keV float wanted_spherical_aberration, // mm float wanted_amplitude_contrast, float wanted_defocus_1_in_angstroms, // A float wanted_defocus_2_in_angstroms, // A float wanted_astigmatism_azimuth, // degrees float pixel_size, // A float wanted_additional_phase_shift_in_radians, // rad float wanted_beam_tilt_x_in_radians, // rad float wanted_beam_tilt_y_in_radians, // rad float wanted_particle_shift_x_in_angstroms, // A float wanted_particle_shift_y_in_angstroms) // A { Init(wanted_acceleration_voltage,wanted_spherical_aberration,wanted_amplitude_contrast,wanted_defocus_1_in_angstroms,wanted_defocus_2_in_angstroms,wanted_astigmatism_azimuth,0.0,1.0/(2.0*pixel_size),-10.0,pixel_size,wanted_additional_phase_shift_in_radians,wanted_beam_tilt_x_in_radians,wanted_beam_tilt_y_in_radians,wanted_particle_shift_x_in_angstroms,wanted_particle_shift_y_in_angstroms); } CTF::~CTF() { // Nothing to do } void CTF::Init( float wanted_acceleration_voltage_in_kV, // keV float wanted_spherical_aberration_in_mm, // mm float wanted_amplitude_contrast, float wanted_defocus_1_in_angstroms, // A float wanted_defocus_2_in_angstroms, // A float wanted_astigmatism_azimuth_in_degrees, // degrees float pixel_size_in_angstroms, // A float wanted_additional_phase_shift_in_radians) // rad { Init(wanted_acceleration_voltage_in_kV,wanted_spherical_aberration_in_mm,wanted_amplitude_contrast,wanted_defocus_1_in_angstroms,wanted_defocus_2_in_angstroms,wanted_astigmatism_azimuth_in_degrees,0.0,1.0/(2.0*pixel_size_in_angstroms),-10.0,pixel_size_in_angstroms,wanted_additional_phase_shift_in_radians,0.0f,0.0f,0.0f,0.0f); } // Initialise a CTF object void CTF::Init( float wanted_acceleration_voltage_in_kV, // keV float wanted_spherical_aberration_in_mm, // mm float wanted_amplitude_contrast, float wanted_defocus_1_in_angstroms, // A float wanted_defocus_2_in_angstroms, //A float wanted_astigmatism_azimuth_in_degrees, // degrees float wanted_lowest_frequency_for_fitting_in_reciprocal_angstroms, // 1/A float wanted_highest_frequency_for_fitting_in_reciprocal_angstroms, // 1/A float wanted_astigmatism_tolerance_in_angstroms, // A. Set to negative to indicate no restraint on astigmatism. float pixel_size_in_angstroms, // A float wanted_additional_phase_shift_in_radians, // rad float wanted_beam_tilt_x_in_radians, // rad float wanted_beam_tilt_y_in_radians, // rad float wanted_particle_shift_x_in_angstroms, // A float wanted_particle_shift_y_in_angstroms) // A { wavelength = WavelengthGivenAccelerationVoltage(wanted_acceleration_voltage_in_kV) / pixel_size_in_angstroms; squared_wavelength = powf(wavelength,2); cubed_wavelength = powf(wavelength,3); spherical_aberration = wanted_spherical_aberration_in_mm * 10000000.0 / pixel_size_in_angstroms; amplitude_contrast = wanted_amplitude_contrast; defocus_1 = wanted_defocus_1_in_angstroms / pixel_size_in_angstroms; defocus_2 = wanted_defocus_2_in_angstroms / pixel_size_in_angstroms; astigmatism_azimuth = wanted_astigmatism_azimuth_in_degrees / 180.0 * PI; additional_phase_shift = wanted_additional_phase_shift_in_radians; lowest_frequency_for_fitting = wanted_lowest_frequency_for_fitting_in_reciprocal_angstroms * pixel_size_in_angstroms; highest_frequency_for_fitting = wanted_highest_frequency_for_fitting_in_reciprocal_angstroms * pixel_size_in_angstroms; astigmatism_tolerance = wanted_astigmatism_tolerance_in_angstroms / pixel_size_in_angstroms; // gcc catches the zero division somehow, but intel returns a nan. Needed for handling the real and complex terms of the CTF separately. if (fabs(amplitude_contrast - 1.0) < 1e-3) precomputed_amplitude_contrast_term = PI / 2.0f; else precomputed_amplitude_contrast_term = atanf(amplitude_contrast/sqrtf(1.0 - powf(amplitude_contrast, 2))); beam_tilt_x = wanted_beam_tilt_x_in_radians; beam_tilt_y = wanted_beam_tilt_y_in_radians; beam_tilt = sqrtf(powf(beam_tilt_x, 2) + powf(beam_tilt_y, 2)); if ( beam_tilt_x == 0.0f && beam_tilt_y == 0.0f ) { beam_tilt_azimuth = 0.0f; } else { beam_tilt_azimuth = atan2f(beam_tilt_y,beam_tilt_x); } particle_shift_x = wanted_particle_shift_x_in_angstroms / pixel_size_in_angstroms; particle_shift_y = wanted_particle_shift_y_in_angstroms / pixel_size_in_angstroms; particle_shift = sqrtf(powf(particle_shift_x, 2) + powf(particle_shift_y, 2)); if ( particle_shift_x == 0.0f && particle_shift_y == 0.0f ) { particle_shift_azimuth = 0.0f; } else { particle_shift_azimuth = atan2f(particle_shift_y,particle_shift_x); } } /* * Eqn 11 of Rohou & Grigorieff, modified by corrigendum of October 2018 */ int CTF::ReturnNumberOfExtremaBeforeSquaredSpatialFrequency(float squared_spatial_frequency, float azimuth) { int number_of_extrema = 0; int number_of_extrema_before_chi_extremum = 0; float sq_sf_of_chi_extremum = ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenAzimuth(azimuth); if (squared_spatial_frequency <= sq_sf_of_chi_extremum) { number_of_extrema = floor( 1.0 / PI * PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(squared_spatial_frequency,azimuth) + 0.5); } else { number_of_extrema_before_chi_extremum = floor( 1.0 / PI * PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(sq_sf_of_chi_extremum,azimuth) + 0.5); number_of_extrema = floor( 1.0 / PI * PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(squared_spatial_frequency,azimuth) + 0.5); number_of_extrema = number_of_extrema_before_chi_extremum + abs(number_of_extrema - number_of_extrema_before_chi_extremum); } number_of_extrema = abs(number_of_extrema); MyDebugAssertTrue(number_of_extrema >= 0,"Bad number of extrema: %i (%i rounded from %f, phase shift = %f)\n",number_of_extrema, int(floor( 1.0 / PI * PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(squared_spatial_frequency,azimuth) + 0.5)), 1.0 / PI * PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(squared_spatial_frequency,azimuth) + 0.5, PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(squared_spatial_frequency,azimuth)); return number_of_extrema; } /* * Compute the frequency of the Nth zero of the CTF. */ float CTF::ReturnSquaredSpatialFrequencyOfAZero(int which_zero, float azimuth, bool inaccurate_is_ok) { /* * The method used below (ReturnSquaredSpatialFrequencyGivenPhaseShiftAndAzimuth) makes assumptions which mean it will * only return the correct spatial frequency for the CTF zeroes between the origin and the frequency at which * the phase aberration peaks. */ float phase_shift; float defocus = DefocusGivenAzimuth(azimuth); if (defocus > 0.0) { phase_shift = which_zero * PI; } else { phase_shift = -1.0 * which_zero * PI; } if (! inaccurate_is_ok) { MyDebugAssertTrue(phase_shift <= ReturnPhaseAberrationMaximum(),"Oops, this method only works for the first few zeroes"); } return ReturnSquaredSpatialFrequencyGivenPhaseShiftAndAzimuth(phase_shift,azimuth); } /* * Return the maximum phase aberration anywhere on the spectrum */ float CTF::ReturnPhaseAberrationMaximum() { return std::max(ReturnPhaseAberrationMaximumGivenDefocus(defocus_1),ReturnPhaseAberrationMaximumGivenDefocus(defocus_2)); } float CTF::ReturnPhaseAberrationMaximumGivenDefocus(float defocus) { return PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(defocus),defocus); } /* * Return the squared spatial frequency at which the phase aberration function reaches its extremum */ float CTF::ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenAzimuth(float azimuth) { return ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(DefocusGivenAzimuth(azimuth)); } /* * Return the squared spatial frequency at which the phase aberration function reaches its extremum */ float CTF::ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(float defocus) { if (defocus <= 0.0) { /* * When the defocus value is negative (i.e. we are overfocus), the phase aberration * quadratic decreases from sf 0.0 onwards. Mathematically, the parabola peaks in * the negative squared spatial frequency. But there's no such thing as a negative squared * sf. */ return 0.0; } else if (spherical_aberration == 0.0) { return 9999.999; } else { return defocus / (squared_wavelength * spherical_aberration) ; } } /* * Return the squared spatial frequency at which a given phase aberration is obtained. Note that this will return only one of the * spatial frequencies, whereas the phase aberration function is a quadratic polynomial function of the squared * spatial frequency, which means that a given phase shift can be achieved at two spatial frequencies. * * Also, this function is written assuming underfocus and positive spherical aberration * * TODO: take into account multiple solutions */ float CTF::ReturnSquaredSpatialFrequencyGivenPhaseShiftAndAzimuth(float phase_shift, float azimuth) { const float a = -0.5 * PI * cubed_wavelength * spherical_aberration; const float b = PI * wavelength * DefocusGivenAzimuth(azimuth); const float c = additional_phase_shift + precomputed_amplitude_contrast_term; const float det = powf(b,2.0) - 4.0 * a * (c-phase_shift); if (spherical_aberration == 0.0) { return (phase_shift - c) / b; } else { MyDebugAssertTrue(a != 0.0,"Bad values for either cubed wavelength (%f) or spherical aberration (%f) (a = %f)\n",cubed_wavelength,spherical_aberration,a); if (det < 0.0) { //MyPrintWithDetails("Ooops, negative determinant\n"); //DEBUG_ABORT; return 0.0; } else { const float solution_one = ( -b + sqrtf(det)) / (2.0 * a); const float solution_two = ( -b - sqrtf(det)) / (2.0 * a); if ( solution_one > 0 && solution_two > 0 ) { if (solution_one <= solution_two) { return solution_one; } else { return solution_two; } } else if ( solution_one > 0 ) { return solution_one; } else if ( solution_two > 0 ) return solution_two; else { #ifdef DEBUG MyPrintWithDetails("Ooops, did not find solutions to the phase aberration equation\n"); DEBUG_ABORT; #else return 0.0; #endif } } } } // Set the defocus and astigmatism angle, given in pixels and radians void CTF::SetDefocus(float wanted_defocus_1_pixels, float wanted_defocus_2_pixels, float wanted_astigmatism_angle_radians) { defocus_1 = wanted_defocus_1_pixels; defocus_2 = wanted_defocus_2_pixels; astigmatism_azimuth = wanted_astigmatism_angle_radians; } // Set the additional phase shift, given in radians void CTF::SetAdditionalPhaseShift(float wanted_additional_phase_shift_radians) { additional_phase_shift = fmodf(wanted_additional_phase_shift_radians,(float)PI); } // Set the beam tilt, given in radians void CTF::SetBeamTilt(float wanted_beam_tilt_x_in_radians, float wanted_beam_tilt_y_in_radians, float wanted_particle_shift_x_in_pixels, float wanted_particle_shift_y_in_pixels) { beam_tilt_x = wanted_beam_tilt_x_in_radians; beam_tilt_y = wanted_beam_tilt_y_in_radians; beam_tilt = sqrtf(powf(beam_tilt_x, 2) + powf(beam_tilt_y, 2)); if ( beam_tilt_x == 0.0f && beam_tilt_y == 0.0f ) { beam_tilt_azimuth = 0.0f; } else { beam_tilt_azimuth = atan2f(beam_tilt_y,beam_tilt_x); } particle_shift_x = wanted_particle_shift_x_in_pixels; particle_shift_y = wanted_particle_shift_y_in_pixels; particle_shift = sqrtf(powf(particle_shift_x, 2) + powf(particle_shift_y, 2)); if ( particle_shift_x == 0.0f && particle_shift_y == 0.0f ) { particle_shift_azimuth = 0.0f; } else { particle_shift_azimuth = atan2f(particle_shift_y,particle_shift_x); } } // Set the highest frequency used for fitting void CTF::SetHighestFrequencyForFitting(float wanted_highest_frequency_in_reciprocal_pixels) { highest_frequency_for_fitting = wanted_highest_frequency_in_reciprocal_pixels; } // Return the value of the CTF at the given squared spatial frequency and azimuth std::complex CTF::EvaluateComplex(float squared_spatial_frequency, float azimuth) { float phase_aberration = PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(squared_spatial_frequency,azimuth); return - sinf( phase_aberration ) - I * cosf( phase_aberration ); // Frealign code: // CTF=CMPLX(WGH1*SCHI-WGH2*CCHI,-WGH1*CCHI-WGH2*SCHI) // wxPrintf("cistem real = %g\n", -sinf(chi + pre)); // wxPrintf("frealign real= %g\n", sqrtf(1.0 - powf(amplitude_contrast, 2)) * sinf(-chi) - amplitude_contrast * cosf(-chi)); // wxPrintf("cistem comp = %g\n", -cosf(chi + pre)); // wxPrintf("frealign comp= %g\n", -sqrtf(1.0 - powf(amplitude_contrast, 2)) * cosf(-chi) - amplitude_contrast * sinf(-chi)); } // Return the value of the CTF at the given squared spatial frequency and azimuth float CTF::Evaluate(float squared_spatial_frequency, float azimuth) { return -sinf( PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(squared_spatial_frequency,azimuth) ); } /* returns the argument (radians) to the sine and cosine terms of the ctf We follow the convention that underfocusing the objective lens gives rise to a positive phase shift of scattered electrons, whereas the spherical aberration gives a negative phase shift of scattered electrons. Note that there is an additional (precomputed) term so that the CTF can then be computed by simply taking the sine of the returned phase shift. */ float CTF::PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(float squared_spatial_frequency, float defocus) { return PIf * wavelength * squared_spatial_frequency * ( defocus - 0.5f * squared_wavelength * squared_spatial_frequency * spherical_aberration) + additional_phase_shift + precomputed_amplitude_contrast_term; } float CTF::PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(float squared_spatial_frequency, float azimuth) { return PIf * wavelength * squared_spatial_frequency * ( DefocusGivenAzimuth(azimuth) - 0.5f * squared_wavelength * squared_spatial_frequency * spherical_aberration) + additional_phase_shift + precomputed_amplitude_contrast_term; } std::complex CTF::EvaluateBeamTiltPhaseShift(float squared_spatial_frequency, float azimuth) { MyDebugAssertTrue(squared_spatial_frequency >= 0.0f,"Bad squared spatial frequency: %f", squared_spatial_frequency); // Save some time if no beam tilt if (beam_tilt == 0.0f && particle_shift == 0.0f) { return 1.0f + I * 0.0f; } else { float phase_shift = PhaseShiftGivenBeamTiltAndShift(squared_spatial_frequency, BeamTiltGivenAzimuth(azimuth), ParticleShiftGivenAzimuth(azimuth)); // wxPrintf("p1 = %g\n", phase_shift); // phase_shift = fmodf(phase_shift, 2.0f * (float)PI); // if (phase_shift > PI) phase_shift -= 2.0f * PI; // if (phase_shift <= -PI) phase_shift += 2.0f * PI; // wxPrintf("p2 = %g\n", phase_shift); // phase_shift = rad_2_deg(phase_shift); // return phase_shift + I * 0.0f; return cosf( phase_shift ) + I * sinf( phase_shift ); } } // Return the phase shift generated by beam tilt float CTF::PhaseShiftGivenBeamTiltAndShift(float squared_spatial_frequency, float beam_tilt, float particle_shift) { float spatial_frequency = sqrtf(squared_spatial_frequency); float phase_shift = 2.0f * PI * spherical_aberration * squared_wavelength * squared_spatial_frequency * spatial_frequency * beam_tilt; phase_shift -= 2.0f * PI * spatial_frequency * particle_shift; phase_shift = fmodf(phase_shift, 2.0f * (float)PI); if (phase_shift > PI) phase_shift -= 2.0f * PI; if (phase_shift <= -PI) phase_shift += 2.0f * PI; return phase_shift; } // Return the effective defocus at the azimuth of interest float CTF::DefocusGivenAzimuth(float azimuth) { return 0.5f * ( defocus_1 + defocus_2 + cosf( 2.0f * (azimuth - astigmatism_azimuth )) * (defocus_1 - defocus_2)); } // Return the effective beam tilt at the azimuth of interest float CTF::BeamTiltGivenAzimuth(float azimuth) { return beam_tilt * cosf( azimuth - beam_tilt_azimuth ); } // Return the effective beam tilt at the azimuth of interest float CTF::ParticleShiftGivenAzimuth(float azimuth) { return particle_shift * cosf( azimuth - particle_shift_azimuth); } // Given acceleration voltage in keV, return the electron wavelength in Angstroms float CTF::WavelengthGivenAccelerationVoltage( float acceleration_voltage ) { return 12.26f / sqrtf(1000.0f * acceleration_voltage + 0.9784f * powf(1000.0f * acceleration_voltage,2)/powf(10.0f,6)); } // Compare two CTF objects and return true if they are within a specified defocus tolerance bool CTF::IsAlmostEqualTo(CTF *wanted_ctf, float delta_defocus) { float delta; if (fabsf(this->spherical_aberration - wanted_ctf->spherical_aberration) > 0.01) return false; if (fabsf(this->wavelength - wanted_ctf->wavelength) > 0.0001) return false; if (fabsf(this->amplitude_contrast - wanted_ctf->amplitude_contrast) > 0.0001) return false; if (fabsf(this->defocus_1 - wanted_ctf->defocus_1) > delta_defocus) return false; if (fabsf(this->defocus_2 - wanted_ctf->defocus_2) > delta_defocus) return false; if (fabsf(this->beam_tilt_x - wanted_ctf->beam_tilt_x) > 0.00001) return false; if (fabsf(this->beam_tilt_y - wanted_ctf->beam_tilt_y) > 0.00001) return false; if (fabsf(this->particle_shift_x - wanted_ctf->particle_shift_x) > 0.001) return false; if (fabsf(this->particle_shift_y - wanted_ctf->particle_shift_y) > 0.001) return false; delta = fabsf(this->additional_phase_shift - wanted_ctf->additional_phase_shift); delta = fmodf(delta, 2.0f * (float)PI); // 0.0277 = 5/180 (5 deg tolerance) if (delta > 0.0277) return false; delta = fabsf(this->astigmatism_azimuth - wanted_ctf->astigmatism_azimuth); delta = fmodf(delta, (float)PI); // 0.0277 = 5/180 (5 deg tolerance) if (delta > 0.0277) return false; return true; } bool CTF::BeamTiltIsAlmostEqualTo(CTF *wanted_ctf, float delta_beam_tilt) { if (fabsf(this->beam_tilt_x - wanted_ctf->beam_tilt_x) > delta_beam_tilt) return false; if (fabsf(this->beam_tilt_y - wanted_ctf->beam_tilt_y) > delta_beam_tilt) return false; return true; } void CTF::CopyFrom(CTF other_ctf) { spherical_aberration = other_ctf.spherical_aberration; wavelength = other_ctf.wavelength; amplitude_contrast = other_ctf.amplitude_contrast; defocus_1 = other_ctf.defocus_1; defocus_2 = other_ctf.defocus_2; defocus_half_range = other_ctf.defocus_half_range; astigmatism_azimuth = other_ctf.astigmatism_azimuth; additional_phase_shift = other_ctf.additional_phase_shift; // Fitting parameters lowest_frequency_for_fitting = other_ctf.lowest_frequency_for_fitting; highest_frequency_for_fitting = other_ctf.highest_frequency_for_fitting; astigmatism_tolerance = other_ctf.astigmatism_tolerance; // precomputed_amplitude_contrast_term = other_ctf.precomputed_amplitude_contrast_term; squared_wavelength = other_ctf.squared_wavelength; cubed_wavelength = other_ctf.cubed_wavelength; } // Enforce the convention that df1 > df2 and -90 < angast < 90 void CTF::EnforceConvention() { float defocus_tmp; if ( defocus_1 < defocus_2 ) { defocus_tmp = defocus_2; defocus_2 = defocus_1; defocus_1 = defocus_tmp; astigmatism_azimuth += PIf*0.5f; } astigmatism_azimuth -= PIf * roundf(astigmatism_azimuth/PIf); } void CTF::ChangePixelSize(float old_pixel_size, float new_pixel_size) { float scale = old_pixel_size/new_pixel_size; spherical_aberration *= scale; wavelength *= scale; amplitude_contrast *= scale; defocus_1 *= scale; defocus_2 *= scale; defocus_half_range *= scale; // Fitting parameters lowest_frequency_for_fitting /= scale; highest_frequency_for_fitting /= scale; astigmatism_tolerance *= scale; // squared_wavelength = powf(wavelength,2); cubed_wavelength = powf(wavelength,3); } ctffind-4.1.14/src/core/ctf.h000066400000000000000000000137271440356052600157010ustar00rootroot00000000000000class CTF { private: float spherical_aberration; float wavelength; float amplitude_contrast; float defocus_1; float defocus_2; float defocus_half_range; float astigmatism_azimuth; float additional_phase_shift; float beam_tilt_x; // rad float beam_tilt_y; // rad float beam_tilt; // rad float beam_tilt_azimuth; // rad float particle_shift_x; // pixels float particle_shift_y; // pixels float particle_shift; // A float particle_shift_azimuth; // rad // Fitting parameters float lowest_frequency_for_fitting; float highest_frequency_for_fitting; float astigmatism_tolerance; // Precomputed terms to make evaluations faster float precomputed_amplitude_contrast_term; float squared_wavelength; float cubed_wavelength; public: // Constructors, destructors CTF(); CTF( float acceleration_voltage, float spherical_aberration, float amplitude_contrast, float defocus_1, float defocus_2, float astigmatism_azimuth, float lowest_frequency_for_fitting, float highest_frequency_for_fitting, float astigmatism_tolerance, float pixel_size, float additional_phase_shift, float beam_tilt_x = 0.0f, float beam_tilt_y = 0.0f, float particle_shift_x = 0.0f, float particle_shift_y = 0.0f); CTF( float wanted_acceleration_voltage, // keV float wanted_spherical_aberration, // mm float wanted_amplitude_contrast, float wanted_defocus_1_in_angstroms, // A float wanted_defocus_2_in_angstroms, // A float wanted_astigmatism_azimuth, // degrees float pixel_size, // A float wanted_additional_phase_shift_in_radians, // rad float wanted_beam_tilt_x_in_radians = 0.0f, // rad float wanted_beam_tilt_y_in_radians = 0.0f, // rad float wanted_particle_shift_x_in_angstroms = 0.0f, // A float wanted_particle_shift_y_in_angstroms = 0.0f); // A ~CTF(); void Init( float wanted_acceleration_voltage_in_kV, // keV float wanted_spherical_aberration_in_mm, // mm float wanted_amplitude_contrast, float wanted_defocus_1_in_angstroms, // A float wanted_defocus_2_in_angstroms, //A float wanted_astigmatism_azimuth_in_degrees, // degrees float wanted_lowest_frequency_for_fitting_in_reciprocal_angstroms, // 1/A float wanted_highest_frequency_for_fitting_in_reciprocal_angstroms, // 1/A float wanted_astigmatism_tolerance_in_angstroms, // A. Set to negative to indicate no restraint on astigmatism. float pixel_size_in_angstroms, // A float wanted_additional_phase_shift_in_radians, //rad float wanted_beam_tilt_x_in_radians = 0.0f, // rad float wanted_beam_tilt_y_in_radians = 0.0f, // rad float wanted_particle_shift_x_in_angstroms = 0.0f, // A float wanted_particle_shift_y_in_angstroms = 0.0f); // A void Init( float wanted_acceleration_voltage_in_kV, // keV float wanted_spherical_aberration_in_mm, // mm float wanted_amplitude_contrast, float wanted_defocus_1_in_angstroms, // A float wanted_defocus_2_in_angstroms, //A float wanted_astigmatism_azimuth_in_degrees, // degrees float pixel_size_in_angstroms, // A float wanted_additional_phase_shift_in_radians); //rad void SetDefocus(float wanted_defocus_1_pixels, float wanted_defocus_2_pixels, float wanted_astigmatism_angle_radians); void SetAdditionalPhaseShift(float wanted_additional_phase_shift_radians); void SetBeamTilt(float wanted_beam_tilt_x_in_radians, float wanted_beam_tilt_y_in_radians, float wanted_particle_shift_x_in_pixels = 0.0f, float wanted_particle_shift_y_in_pixels = 0.0f); void SetHighestFrequencyForFitting(float wanted_highest_frequency_in_reciprocal_pixels); // std::complex EvaluateComplex(float squared_spatial_frequency, float azimuth); float Evaluate(float squared_spatial_frequency, float azimuth); float PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(float squared_spatial_frequency, float azimuth); std::complex EvaluateBeamTiltPhaseShift(float squared_spatial_frequency, float azimuth); float PhaseShiftGivenBeamTiltAndShift(float squared_spatial_frequency, float beam_tilt, float particle_shift = 0.0f); float PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(float squared_spatial_frequency, float defocus); float DefocusGivenAzimuth(float azimuth); float BeamTiltGivenAzimuth(float azimuth); float ParticleShiftGivenAzimuth(float azimuth); float WavelengthGivenAccelerationVoltage(float acceleration_voltage); inline float GetLowestFrequencyForFitting() { return lowest_frequency_for_fitting; }; inline float GetHighestFrequencyForFitting() { return highest_frequency_for_fitting; }; inline float GetAstigmatismTolerance() { return astigmatism_tolerance; }; inline float GetAstigmatism(){ return defocus_1 - defocus_2; }; bool IsAlmostEqualTo(CTF *wanted_ctf, float delta_defocus = 100.0f); bool BeamTiltIsAlmostEqualTo(CTF *wanted_ctf, float delta_beam_tilt = 0.00001f); void EnforceConvention(); void PrintInfo(); void CopyFrom(CTF other_ctf); void ChangePixelSize(float old_pixel_size, float new_pixel_size); inline float GetDefocus1() { return defocus_1; }; inline float GetDefocus2() { return defocus_2; }; inline float GetBeamTiltX() { return beam_tilt_x; }; inline float GetBeamTiltY() { return beam_tilt_y; }; inline float GetSphericalAberration(){return spherical_aberration;}; inline float GetAstigmatismAzimuth() { return astigmatism_azimuth; }; inline float GetAdditionalPhaseShift() { return additional_phase_shift; }; inline float GetWavelength() { return wavelength; }; int ReturnNumberOfExtremaBeforeSquaredSpatialFrequency(float squared_spatial_frequency, float azimuth); float ReturnSquaredSpatialFrequencyGivenPhaseShiftAndAzimuth(float phase_shift, float azimuth); float ReturnSquaredSpatialFrequencyOfAZero(int which_zero, float azimuth, bool inaccurate_is_ok = false); float ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenAzimuth(float azimuth); float ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(float defocus); float ReturnPhaseAberrationMaximum(); float ReturnPhaseAberrationMaximumGivenDefocus(float defocus); }; ctffind-4.1.14/src/core/curve.cpp000066400000000000000000001140521440356052600165750ustar00rootroot00000000000000#include "core_headers.h" #include // this is a magic incantation which must be done! WX_DEFINE_OBJARRAY(ArrayofCurves); void LS_POLY(float *x_data, float *y_data, int number_of_points, int order_of_polynomial, float *output_smoothed_curve, float *output_coefficients); Curve::Curve() { have_polynomial = false; have_savitzky_golay = false; number_of_points = 0; allocated_space_for_points = 100; data_x = new float[100]; data_y = new float[100]; polynomial_fit = NULL; // allocate on fit.. savitzky_golay_fit = NULL; savitzky_golay_coefficients = NULL; polynomial_order = 0; polynomial_coefficients = NULL; savitzky_golay_polynomial_order = 0; savitzky_golay_window_size = 0; index_of_last_point_used = 0; } Curve::Curve( const Curve &other_curve) // copy constructor { MyDebugPrint("Warning: copying a curve object"); have_polynomial = false; have_savitzky_golay = false; number_of_points = 0; allocated_space_for_points = 100; data_x = new float[100]; data_y = new float[100]; polynomial_fit = NULL; // allocate on fit.. savitzky_golay_fit = NULL; savitzky_golay_coefficients = NULL; polynomial_order = 0; polynomial_coefficients = NULL; savitzky_golay_polynomial_order = 0; savitzky_golay_window_size = 0; index_of_last_point_used = 0; *this = other_curve; //DEBUG_ABORT; } Curve::~Curve() { delete [] data_x; delete [] data_y; if (have_polynomial == true) { delete [] polynomial_fit; delete [] polynomial_coefficients; polynomial_fit = NULL; have_polynomial = false; } if (have_savitzky_golay == true) { delete [] savitzky_golay_fit; savitzky_golay_fit = NULL; DeleteSavitzkyGolayCoefficients(); have_savitzky_golay = false; } } void Curve::DeleteSavitzkyGolayCoefficients() { MyDebugAssertTrue(savitzky_golay_coefficients != NULL, "Oops trying to deallocate coefficients when they are not allocated\n"); for (int pixel_counter = 0; pixel_counter < number_of_points; pixel_counter ++ ) { if (savitzky_golay_coefficients[pixel_counter] != NULL) { delete [] savitzky_golay_coefficients[pixel_counter]; } } delete [] savitzky_golay_coefficients; savitzky_golay_coefficients = NULL; } void Curve::AllocateSavitzkyGolayCoefficients() { MyDebugAssertTrue(savitzky_golay_coefficients == NULL,"Oops, trying to allocate coffecients when they are already allocated\n"); MyDebugAssertTrue(savitzky_golay_polynomial_order > 0, "Oops, looks like the SG polynomial order was not set properly\n"); savitzky_golay_coefficients = new float*[number_of_points]; int counter; for (int pixel_counter = 0; pixel_counter < number_of_points; pixel_counter ++ ) { savitzky_golay_coefficients[pixel_counter] = new float[savitzky_golay_polynomial_order + 1]; // Initialise for (counter = 0; counter < savitzky_golay_polynomial_order + 1; counter ++) { savitzky_golay_coefficients[pixel_counter][counter] = 0.0; } } } Curve & Curve::operator = (const Curve *other_curve) { // Check for self assignment if(this != other_curve) { int counter; if (number_of_points != other_curve->number_of_points) { delete [] data_x; delete [] data_y; allocated_space_for_points = other_curve->allocated_space_for_points; data_x = new float[allocated_space_for_points]; data_y = new float[allocated_space_for_points]; polynomial_order = other_curve->polynomial_order; savitzky_golay_polynomial_order = other_curve->savitzky_golay_polynomial_order; if (have_polynomial == true) { delete [] polynomial_fit; delete [] polynomial_coefficients; } if (have_savitzky_golay == true) { delete [] savitzky_golay_fit; DeleteSavitzkyGolayCoefficients(); } if (other_curve->have_polynomial == true) { polynomial_fit = new float[number_of_points]; polynomial_coefficients = new float[polynomial_order]; } if (other_curve->have_savitzky_golay == true) { savitzky_golay_fit = new float[number_of_points]; AllocateSavitzkyGolayCoefficients(); } } else { polynomial_order = other_curve->polynomial_order; savitzky_golay_polynomial_order = other_curve->savitzky_golay_polynomial_order; if (have_polynomial != other_curve->have_polynomial) { if (have_polynomial == true) { delete [] polynomial_coefficients; delete [] polynomial_fit; } else { polynomial_fit = new float[number_of_points]; polynomial_coefficients = new float[polynomial_order]; } } if (have_savitzky_golay != other_curve->have_savitzky_golay) { if (have_savitzky_golay == true) { delete [] savitzky_golay_fit; DeleteSavitzkyGolayCoefficients(); } else { savitzky_golay_fit = new float[number_of_points]; AllocateSavitzkyGolayCoefficients(); } } } number_of_points = other_curve->number_of_points; have_polynomial = other_curve->have_polynomial; have_savitzky_golay = other_curve->have_savitzky_golay; savitzky_golay_polynomial_order = other_curve->savitzky_golay_polynomial_order; savitzky_golay_window_size = other_curve->savitzky_golay_window_size; index_of_last_point_used = other_curve->index_of_last_point_used; for (counter = 0; counter < number_of_points; counter++) { data_x[counter] = other_curve->data_x[counter]; data_y[counter] = other_curve->data_y[counter]; } if (have_polynomial == true) { for (counter = 0; counter < number_of_points; counter++) { polynomial_fit[counter] = other_curve->polynomial_fit[counter]; } for (counter = 0; counter < polynomial_order; counter++) { polynomial_coefficients[counter] = other_curve->polynomial_coefficients[counter]; } } if (have_savitzky_golay == true) { for (counter = 0; counter < number_of_points; counter++) { savitzky_golay_fit[counter] = other_curve->savitzky_golay_fit[counter]; for (int degree = 0; degree <= savitzky_golay_polynomial_order; degree++) { savitzky_golay_coefficients[counter][degree] = other_curve->savitzky_golay_coefficients[counter][degree]; } } } } return *this; } Curve & Curve::operator = (const Curve &other_curve) { *this = &other_curve; return *this; } void Curve::SetupXAxis(const float lower_bound, const float upper_bound, const int wanted_number_of_points) { MyDebugAssertFalse(isnan(lower_bound),"Lower bound is NaN"); MyDebugAssertFalse(isnan(upper_bound),"Lower bound is NaN"); MyDebugAssertTrue(wanted_number_of_points > 1,"Bad number of points"); ClearData(); AllocateMemory(wanted_number_of_points); for ( int counter = 0; counter < wanted_number_of_points; counter++ ) { AddPoint(counter * (upper_bound - lower_bound)/float(wanted_number_of_points-1) + lower_bound, 0.0); } } void Curve::ZeroYData() { for (int counter = 0; counter < number_of_points; counter++) { data_y[counter] = 0; } } void Curve::SetYToConstant(float wanted_constant) { MyDebugAssertTrue(number_of_points > 0, "No points to set"); for (int counter = 0; counter < number_of_points; counter++) { data_y[counter] = wanted_constant; } } void Curve::AddWith(Curve *other_curve) { MyDebugAssertTrue(number_of_points > 0, "No points to interpolate"); MyDebugAssertTrue(number_of_points == other_curve->number_of_points, "Different number of points"); for (int counter = 0; counter < number_of_points; counter++) { data_y[counter] += other_curve->data_y[counter]; } } void Curve::DivideBy(Curve *other_curve) { MyDebugAssertTrue(number_of_points > 0, "No points to interpolate"); MyDebugAssertTrue(number_of_points == other_curve->number_of_points, "Different number of points"); for (int counter = 0; counter < number_of_points; counter++) { if (other_curve->data_y[counter] != 0.0) data_y[counter] /= other_curve->data_y[counter]; } } float Curve::ReturnAverageValue() { MyDebugAssertTrue(number_of_points > 0, "No points to average"); float sum = 0.0f; for (int counter = 0; counter < number_of_points; counter++) { sum += data_y[counter]; } return sum / float(number_of_points); } void Curve::ZeroAfterIndex(int index) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); if (index + 1 <= number_of_points) { for (int counter = index + 1; counter < number_of_points; counter++) { data_y[counter] = 0.0; } } } void Curve::FlattenBeforeIndex(int index) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); if (index > number_of_points) index = number_of_points; for (int counter = 0; counter < index; counter++) { data_y[counter] = data_y[index]; } } void Curve::ResampleCurve(Curve *input_curve, int wanted_number_of_points) { MyDebugAssertTrue(input_curve->number_of_points > 0, "Input curve is empty"); MyDebugAssertTrue(wanted_number_of_points > 1, "wanted_number_of_points is smaller than 2"); Curve temp_curve; float i_x; for (int i = 0; i < wanted_number_of_points; i++) { i_x = float(i * input_curve->number_of_points) / float(wanted_number_of_points) * (1.0 - 1.0 / float(wanted_number_of_points - 1)); temp_curve.AddPoint(i_x, input_curve->ReturnLinearInterpolationFromI(i_x)); } CopyFrom(&temp_curve); } float Curve::ReturnLinearInterpolationFromI(float wanted_i) { MyDebugAssertTrue(number_of_points > 0, "No points to interpolate"); MyDebugAssertTrue(wanted_i <= number_of_points - 1, "Index too high"); MyDebugAssertTrue(wanted_i >= 0, "Index too low"); int i = int(wanted_i); float distance_below = wanted_i - i; float distance_above = 1.0 - distance_below; float distance; if (distance_below == 0.0) return data_y[i]; if (distance_above == 0.0) return data_y[i + 1]; return (1.0 - distance_above) * data_y[i + 1] + (1.0 - distance_below) * data_y[i]; } float Curve::ReturnLinearInterpolationFromX(float wanted_x) { MyDebugAssertTrue(number_of_points > 0, "No points to interpolate"); MyDebugAssertTrue(wanted_x >= data_x[0] - (data_x[number_of_points-1]-data_x[0])*0.01 && wanted_x <= data_x[number_of_points-1] + (data_x[number_of_points-1]-data_x[0])*0.01, "Wanted X (%f) falls outside of range (%f to %f)\n",wanted_x, data_x[0],data_x[number_of_points-1]); float value_to_return = 0.0; const int index_of_previous_bin = ReturnIndexOfNearestPreviousBin(wanted_x); if (index_of_previous_bin == number_of_points-1) { value_to_return = data_y[number_of_points-1]; } else { float distance = (wanted_x - data_x[index_of_previous_bin])/(data_x[index_of_previous_bin+1] - data_x[index_of_previous_bin]); value_to_return += data_y[index_of_previous_bin] * (1.0 - distance); value_to_return += data_y[index_of_previous_bin+1] * distance; } return value_to_return; } void Curve::ComputeMaximumValueAndMode(float &maximum_value, float &mode) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); maximum_value = - FLT_MAX; for ( int counter = 0; counter < number_of_points; counter ++ ) { if (data_y[counter] > maximum_value) { maximum_value = data_y[counter]; mode = data_x[counter]; } } } // This is meant to be used to measure, e.g., the full-width at half-maximum of a histogram // stored as a curve float Curve::ReturnFullWidthAtGivenValue(const float &wanted_value) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); int first_bin_above_value = -1; int last_bin_above_value = -1; for ( int counter = 0; counter < number_of_points; counter ++ ) { if (first_bin_above_value == -1 && data_y[counter] > wanted_value) first_bin_above_value = counter; if (last_bin_above_value == -1 && first_bin_above_value != -1 && data_y[counter] < wanted_value) last_bin_above_value = counter - 1; } MyDebugAssertTrue(first_bin_above_value != -1,"Could not find first bin above value"); MyDebugAssertTrue(last_bin_above_value != -1,"Could not find last bin above value"); return data_x[last_bin_above_value + 1] - data_x[first_bin_above_value]; } float Curve::ReturnMaximumValue() { float maximum_value, mode; ComputeMaximumValueAndMode(maximum_value,mode); return maximum_value; } float Curve::ReturnMode() { float maximum_value, mode; ComputeMaximumValueAndMode(maximum_value,mode); return mode; } // Scale the Y values so that the peak is at 1.0 (assumes all Y values >=0) void Curve::NormalizeMaximumValue() { #ifdef DEBUG for ( int counter = 0; counter < number_of_points; counter ++ ) { if (data_y[counter] < 0.0) MyDebugAssertTrue(false,"This routine assumes all Y values are positive, but value %i is %f\n",counter,data_y[counter]); } #endif const float maximum_value = ReturnMaximumValue(); if (maximum_value > 0.0) { float factor = 1.0 / maximum_value; for ( int counter = 0; counter < number_of_points; counter ++ ) { data_y[counter] *= factor; } } } // Replace Y values with their log, base 10 void Curve::Logarithm() { #ifdef DEBUG for ( int counter = 0; counter < number_of_points; counter ++ ) { if (data_y[counter] < 0.0) MyDebugAssertTrue(false,"This routine assumes all Y values are positive, but value %i is %f\n",counter,data_y[counter]); } #endif for ( int counter = 0; counter < number_of_points; counter ++ ) { data_y[counter] = log10(data_y[counter]); } } void Curve::SquareRoot() { #ifdef DEBUG for ( int counter = 0; counter < number_of_points; counter ++ ) { if (data_y[counter] < 0.0) MyDebugAssertTrue(false,"This routine assumes all Y values are positive, but value %i is %f\n",counter,data_y[counter]); } #endif for (int counter = 0; counter < number_of_points; counter ++ ) { data_y[counter] = sqrtf(data_y[counter]); } } CurvePoint Curve::ReturnValueAtXUsingLinearInterpolation(float wanted_x, float value_to_add, bool assume_linear_x) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); MyDebugAssertTrue(wanted_x >= data_x[0] - (data_x[number_of_points-1]-data_x[0])*0.01 && wanted_x <= data_x[number_of_points-1] + (data_x[number_of_points-1]-data_x[0])*0.01, "Wanted X (%f) falls outside of range (%f to %f)\n",wanted_x, data_x[0],data_x[number_of_points-1]); int index_of_previous_bin; CurvePoint return_value; if (assume_linear_x) { index_of_previous_bin = int((wanted_x - data_x[0]) / (data_x[1] - data_x[0])); } else { index_of_previous_bin = ReturnIndexOfNearestPreviousBin(wanted_x); } MyDebugAssertTrue(index_of_previous_bin >= 0 && index_of_previous_bin < number_of_points,"Oops. Bad index_of_previous_bin: %i\n",index_of_previous_bin); if (index_of_previous_bin == number_of_points - 1) { return_value.index_m = index_of_previous_bin; return_value.index_n = index_of_previous_bin; return_value.value_m = value_to_add; return_value.value_n = 0.0; } else { float distance = (wanted_x - data_x[index_of_previous_bin]) / (data_x[index_of_previous_bin + 1] - data_x[index_of_previous_bin]); return_value.index_m = index_of_previous_bin; return_value.index_n = index_of_previous_bin + 1; return_value.value_m = value_to_add * (1.0 - distance); return_value.value_n = value_to_add * distance; } return return_value; } // If it the data_x values form a linear axies (i.e. they are regularly spaced), give assume_linear_x true. void Curve::AddValueAtXUsingLinearInterpolation(float wanted_x, float value_to_add, bool assume_linear_x) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); MyDebugAssertTrue(wanted_x >= data_x[0] - (data_x[number_of_points-1]-data_x[0])*0.01 && wanted_x <= data_x[number_of_points-1] + (data_x[number_of_points-1]-data_x[0])*0.01, "Wanted X (%f) falls outside of range (%f to %f)\n",wanted_x, data_x[0],data_x[number_of_points-1]); CurvePoint return_value; return_value = ReturnValueAtXUsingLinearInterpolation(wanted_x, value_to_add, assume_linear_x); data_y[return_value.index_m] += return_value.value_m; data_y[return_value.index_n] += return_value.value_n; } void Curve::AddValueAtXUsingNearestNeighborInterpolation(float wanted_x, float value_to_add) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); MyDebugAssertTrue(wanted_x >= data_x[0] - (data_x[number_of_points-1]-data_x[0])*0.01 && wanted_x <= data_x[number_of_points-1] + (data_x[number_of_points-1]-data_x[0])*0.01, "Wanted X (%f) falls outside of range (%f to %f)\n",wanted_x, data_x[0],data_x[number_of_points-1]); data_y[ReturnIndexOfNearestPointFromX(wanted_x)] += value_to_add; } void Curve::PrintToStandardOut() { for (int i = 0; i < number_of_points; i++) { wxPrintf("%f %f\n",data_x[i],data_y[i]); } } void Curve::WriteToFile(wxString output_file, wxString header_line) { MyDebugAssertTrue(number_of_points > 0, "Curve is empty"); float temp_float[2]; NumericTextFile output_curve_file(output_file, OPEN_TO_WRITE, 2); output_curve_file.WriteCommentLine(header_line); for (int i = 0; i < number_of_points; i++) { temp_float[0] = data_x[i]; temp_float[1] = data_y[i]; output_curve_file.WriteLine(temp_float); } } void Curve::WriteToFile(wxString output_file) { WriteToFile(output_file,"C X Y"); } void Curve::CopyDataFromArrays(double *x_series, double *y_series, int wanted_number_of_points) { ClearData(); for (int counter=0; counter < wanted_number_of_points; counter++) { AddPoint(float(x_series[counter]),float(y_series[counter])); } } void Curve::CopyYValuesFromArray(double *y_series, int wanted_number_of_points) { ClearData(); for (int counter=0; counter < wanted_number_of_points; counter++) { AddPoint(float(counter),float(y_series[counter])); } } void Curve::CopyFrom(Curve *other_curve) { *this = other_curve; } void Curve::GetXMinMax(float &min_value, float &max_value) { min_value = FLT_MAX; max_value = -FLT_MAX; for (int point_counter = 0; point_counter < number_of_points; point_counter++) { min_value = std::min(min_value, data_x[point_counter]); max_value = std::max(max_value, data_x[point_counter]); } } void Curve::GetYMinMax(float &min_value, float &max_value) { min_value = FLT_MAX; max_value = -FLT_MAX; for (int point_counter = 0; point_counter < number_of_points; point_counter++) { min_value = std::min(min_value, data_y[point_counter]); max_value = std::max(max_value, data_y[point_counter]); } } void Curve::CheckMemory() { if (number_of_points >= allocated_space_for_points) { // reallocate.. if (allocated_space_for_points < 10000) allocated_space_for_points *= 2; else allocated_space_for_points += 10000; float *x_buffer = new float[allocated_space_for_points]; float *y_buffer = new float[allocated_space_for_points]; for (long counter = 0; counter < number_of_points; counter++) { x_buffer[counter] = data_x[counter]; y_buffer[counter] = data_y[counter]; } delete [] data_x; delete [] data_y; data_x = x_buffer; data_y = y_buffer; } } void Curve::AllocateMemory(int wanted_number_of_points) { delete [] data_x; delete [] data_y; allocated_space_for_points = wanted_number_of_points; data_x = new float[allocated_space_for_points]; data_y = new float[allocated_space_for_points]; number_of_points = 0; } void Curve::AddPoint(float x_value, float y_value) { // check memory CheckMemory(); // add the point data_x[number_of_points] = x_value; data_y[number_of_points] = y_value; number_of_points++; } void Curve::ClearData() { number_of_points = 0; if (have_polynomial == true) { delete [] polynomial_fit; delete [] polynomial_coefficients; have_polynomial = false; } if (have_savitzky_golay == true) { delete [] savitzky_golay_fit; have_savitzky_golay = false; } } void Curve::MultiplyByConstant(float constant_to_multiply_by) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); for (int counter = 0; counter < number_of_points; counter ++ ) { data_y[counter] *= constant_to_multiply_by; } } // It is assumed that the X axis has spatial frequencies in reciprocal pixels (0.5 is Nyquist) void Curve::ApplyCTF(CTF ctf_to_apply, float azimuth_in_radians) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); for (int counter = 0; counter < number_of_points; counter ++ ) { data_y[counter] *= ctf_to_apply.Evaluate(powf(data_x[counter],2),azimuth_in_radians); } } void Curve::ApplyCosineMask(float wanted_x_of_cosine_start, float wanted_cosine_width_in_x, bool undo) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); float current_x; float edge; for (int counter = 0; counter < number_of_points; counter ++ ) { current_x = data_x[counter]; if (current_x >= wanted_x_of_cosine_start && current_x <= wanted_x_of_cosine_start + wanted_cosine_width_in_x) { edge = (1.0 + cosf(PI * (current_x - wanted_x_of_cosine_start) / wanted_cosine_width_in_x)) / 2.0; if (undo) { //MyDebugAssertFalse(edge == 0.0,"Raised cosine should not be 0.0"); if (edge > 0.0) data_y[counter] /= edge; } else { data_y[counter] *= edge; } } else if (current_x > wanted_x_of_cosine_start + wanted_cosine_width_in_x) { data_y[counter] = 0.0; } } } float Curve::ReturnSavitzkyGolayInterpolationFromX( float wanted_x ) { //MyDebugAssertTrue(wanted_x >= data_x[0] && wanted_x <= data_x[number_of_points],"Wanted x (%f) outside of range (%f to %f)\n",wanted_x,data_x[0],data_x[number_of_points]); // Find the nearest data point to the wanted_x int index_of_nearest_point = ReturnIndexOfNearestPointFromX( wanted_x ); // Evaluate the polynomial defined at the nearest point. // TODO: use a better algorithm to evaluate the poynomial, e.g. Horner, see Numerical Recipes double y = savitzky_golay_coefficients[index_of_nearest_point][0]; for (int order = 1; order <= savitzky_golay_polynomial_order; order++) { y += pow(wanted_x,order) * savitzky_golay_coefficients[index_of_nearest_point][order]; } return float(y); } int Curve::ReturnIndexOfNearestPointFromX( float wanted_x ) { //MyDebugAssertTrue(wanted_x >= data_x[0] && wanted_x <= data_x[number_of_points],"Wanted x (%f) outside of range (%f to %f)\n",wanted_x,data_x[0],data_x[number_of_points]); int index_of_nearest_point = 0; int counter = 0; float distance_to_current_point = wanted_x - data_x[counter]; float distance_to_nearest_point = distance_to_current_point; for (counter = 1; counter < number_of_points; counter ++) { distance_to_current_point = wanted_x - data_x[counter]; if (fabs(distance_to_current_point) <= fabs(distance_to_nearest_point)) { distance_to_nearest_point = distance_to_current_point; index_of_nearest_point = counter; } else { break; } } return index_of_nearest_point; } //TODO: write a quicker version of this int Curve::ReturnIndexOfNearestPreviousBin(float wanted_x) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); MyDebugAssertTrue(wanted_x >= data_x[0] - (data_x[number_of_points-1]-data_x[0])*0.01 && wanted_x <= data_x[number_of_points-1] + (data_x[number_of_points-1]-data_x[0])*0.01, "Wanted X (%f) falls outside of range (%f to %f)\n",wanted_x, data_x[0],data_x[number_of_points-1]); for (int counter = index_of_last_point_used; counter < number_of_points; counter++) { if (wanted_x >=data_x[counter] && wanted_x < data_x[counter+1]) { index_of_last_point_used = counter; return counter; } } for (int counter = index_of_last_point_used-1; counter >=0; counter--) { if (wanted_x >=data_x[counter] && wanted_x < data_x[counter+1]) { index_of_last_point_used = counter; return counter; } } if (wanted_x < data_x[0]) { index_of_last_point_used = 0; return 0; } else if (wanted_x >= data_x[number_of_points-1]) { index_of_last_point_used = number_of_points - 1; return number_of_points - 1; } // Should never get here MyDebugAssertTrue(false,"Oops, programming error\n"); return 0; } void Curve::FitSavitzkyGolayToData(int wanted_window_size, int wanted_polynomial_order) { // make sure the window size is odd MyDebugAssertTrue(IsOdd(wanted_window_size) == true, "Window must be odd!") MyDebugAssertTrue(wanted_window_size < number_of_points, "Window size is larger than the number of points!"); MyDebugAssertTrue(wanted_polynomial_order < wanted_window_size, "polynomial order is larger than the window size!"); int pixel_counter; int polynomial_counter; int end_start; int half_pixel = wanted_window_size / 2; float *fit_array_x = new float[wanted_window_size]; float *fit_array_y = new float[wanted_window_size]; float *output_fit_array = new float[wanted_window_size]; //float *coefficients = new float[wanted_polynomial_order+1]; // Remember the polymomal order and the window size savitzky_golay_polynomial_order = wanted_polynomial_order; savitzky_golay_window_size = wanted_window_size; // Allocate array of coefficient arrays, to be kept in memory for later use (e.g. for interpolation) if (savitzky_golay_coefficients != NULL) { DeleteSavitzkyGolayCoefficients(); } // Allocate memory for smooth y values if (have_savitzky_golay == true) { delete [] savitzky_golay_fit; } AllocateSavitzkyGolayCoefficients(); savitzky_golay_fit = new float[number_of_points]; have_savitzky_golay = true; // loop over all the points.. for (pixel_counter = 0; pixel_counter < number_of_points - 2 * half_pixel; pixel_counter++ ) { // for this pixel, extract the window, fit the polynomial, and copy the average into the output array for (polynomial_counter = 0; polynomial_counter < wanted_window_size; polynomial_counter++) { fit_array_x[polynomial_counter] = data_x[pixel_counter + polynomial_counter]; fit_array_y[polynomial_counter] = data_y[pixel_counter + polynomial_counter]; } // fit a polynomial to this data.. LS_POLY(fit_array_x, fit_array_y, wanted_window_size, wanted_polynomial_order, output_fit_array, savitzky_golay_coefficients[half_pixel + pixel_counter]); // take the middle pixel, and put it into the output array.. savitzky_golay_fit[half_pixel + pixel_counter] = output_fit_array[half_pixel]; } // now we need to take care of the ends - first the start.. // DNM: Need to take actual points beyond the end of the fitted points in the middle for (polynomial_counter = 0; polynomial_counter < wanted_window_size; polynomial_counter++) { fit_array_x[polynomial_counter] = data_x[polynomial_counter]; if (polynomial_counter < half_pixel || polynomial_counter >= number_of_points - half_pixel) fit_array_y[polynomial_counter] = data_y[polynomial_counter]; else fit_array_y[polynomial_counter] = savitzky_golay_fit[polynomial_counter]; } // fit a polynomial to this data.. LS_POLY(fit_array_x, fit_array_y, wanted_window_size, wanted_polynomial_order, output_fit_array, savitzky_golay_coefficients[half_pixel - 1]); // copy the required data back.. for (pixel_counter = 0; pixel_counter < half_pixel - 1; pixel_counter++) { for (polynomial_counter = 0; polynomial_counter <= savitzky_golay_polynomial_order; polynomial_counter ++) { savitzky_golay_coefficients[pixel_counter][polynomial_counter] = savitzky_golay_coefficients[half_pixel - 1][polynomial_counter]; } } for (polynomial_counter = 0; polynomial_counter < half_pixel; polynomial_counter++) { //savitzky_golay_coefficients[polynomial_counter] = savitzky_golay_coefficients[half_pixel - 1]; savitzky_golay_fit[polynomial_counter] = output_fit_array[polynomial_counter]; } // now the end.. end_start = number_of_points - wanted_window_size; pixel_counter = 0; for (polynomial_counter = end_start; polynomial_counter < number_of_points; polynomial_counter++) { fit_array_x[pixel_counter] = data_x[polynomial_counter]; if (pixel_counter > half_pixel) fit_array_y[pixel_counter] = data_y[polynomial_counter]; else fit_array_y[pixel_counter] = savitzky_golay_fit[polynomial_counter]; pixel_counter++; } // fit a polynomial to this data.. LS_POLY(fit_array_x, fit_array_y, wanted_window_size, wanted_polynomial_order, output_fit_array, savitzky_golay_coefficients[number_of_points - half_pixel]); // copy the required data back.. for (pixel_counter = number_of_points - half_pixel + 1; pixel_counter < number_of_points - 1; pixel_counter++) { for (polynomial_counter = 0; polynomial_counter <= savitzky_golay_polynomial_order; polynomial_counter ++) { savitzky_golay_coefficients[pixel_counter][polynomial_counter] = savitzky_golay_coefficients[number_of_points - half_pixel][polynomial_counter]; } } pixel_counter = half_pixel + 1; for (polynomial_counter = number_of_points - half_pixel; polynomial_counter < number_of_points; polynomial_counter++) { //savitzky_golay_coefficients[polynomial_counter] = savitzky_golay_coefficients[number_of_points - half_pixel]; savitzky_golay_fit[polynomial_counter] = output_fit_array[pixel_counter]; pixel_counter++; } delete [] fit_array_x; delete [] fit_array_y; delete [] output_fit_array; } void Curve::FitPolynomialToData(int wanted_polynomial_order) { if (have_polynomial == true) { delete [] polynomial_coefficients; delete [] polynomial_fit; } polynomial_fit = new float[number_of_points]; polynomial_order = wanted_polynomial_order; polynomial_coefficients = new float[polynomial_order]; have_polynomial = true; LS_POLY(data_x, data_y, number_of_points, polynomial_order, polynomial_fit, polynomial_coefficients); // weird old code to do the fit } void Curve::Reciprocal() { #ifdef DEBUG for ( int counter = 0; counter < number_of_points; counter ++ ) { if (data_y[counter] < 0.0) MyDebugAssertTrue(false,"This routine assumes all Y values are positive, but value %i is %f\n",counter,data_y[counter]); } #endif for (int counter = 0; counter < number_of_points; counter ++ ) { if (data_y[counter] != 0.0) data_y[counter] = 1.0 / data_y[counter]; } } void Curve::DivideBy(Curve &other_curve) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); MyDebugAssertTrue(number_of_points == other_curve.number_of_points, "Number of points in curves not equal"); for (int counter = 0; counter < number_of_points; counter ++ ) { if (other_curve.data_y[counter] != 0.0) data_y[counter] = data_y[counter] / other_curve.data_y[counter]; } } void Curve::MultiplyBy(Curve &other_curve) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); MyDebugAssertTrue(number_of_points == other_curve.number_of_points, "Number of points in curves not equal"); for (int counter = 0; counter < number_of_points; counter ++ ) { data_y[counter] = data_y[counter] * other_curve.data_y[counter]; } } void Curve::MultiplyXByConstant(float constant_to_multiply_by) { MyDebugAssertTrue(number_of_points > 0, "No points in curve"); for (int counter = 0; counter < number_of_points; counter ++ ) { data_x[counter] *= constant_to_multiply_by; } } /*************************************************** * Program to demonstrate least squares * * polynomial fitting subroutine * * ------------------------------------------------ * * Reference: BASIC Scientific Subroutines, Vol. II * * By F.R. Ruckdeschel, BYTE/McGRAWW-HILL, 1981 [1].* * * * C++ version by J-P Moreau, Paris * * (www.jpmoreau.fr) * * ------------------------------------------------ * typedef double TAB[SIZE+1]; int i,l,m,n; double dd,e1,vv; TAB x,y,v,a,b,c,d,c2,e,f; /**************************************************************** * LEAST SQUARES POLYNOMIAL FITTING SUBROUTINE * * ------------------------------------------------------------- * * This program least squares fits a polynomial to input data. * * forsythe orthogonal polynomials are used in the fitting. * * The number of data points is n. * * The data is input to the subroutine in x[i], y[i] pairs. * * The coefficients are returned in c[i], * * the smoothed data is returned in v[i], * * the order of the fit is specified by m. * * The standard deviation of the fit is returned in d. * * There are two options available by use of the parameter e: * * 1. if e = 0, the fit is to order m, * * 2. if e > 0, the order of fit increases towards m, but will * * stop if the relative standard deviation does not decrease * * by more than e between successive fits. * * The order of the fit then obtained is l. * ****************************************************************/ /* void Curve::LS_POLY() { double a[polynomial_order + 2];// double b[polynomial_order + 2];// double c[polynomial_order + 3]; double c2[polynomial_order + 2]; double f[polynomial_order + 2];// double v[number_of_points + 1]; double d[number_of_points + 1]; double e[number_of_points + 1];// double x[number_of_points + 1]; double y[number_of_points + 1]; int l;// int n = number_of_points;// int m = polynomial_order;// double e1 = 0.0;// double dd; double vv; //Labels: e10,e15,e20,e30,e50,fin; int i; int l2; int n1; // double a1;// double a2; double b1; double b2; double c1;// double d1;// double f1;// double f2; double v1; // double v2; double w;// l = 0; n1 = m + 1; v1 = 1e7; for (i = 0; i < number_of_points; i++) { x[i + 1] = data_x[i]; wxPrintf("Before %i = %f\n", i, data_y[i]); y[i + 1] = data_y[i]; } // Initialize the arrays for (i = 1; i < n1+1; i++) { a[i] = 0; b[i] = 0; f[i] = 0; }; for (i = 1; i < n+1; i++) { v[i] = 0; d[i] = 0; } d1 = sqrt(n); w = d1; for (i = 1; i < n+1; i++) { e[i] = 1 / w; } f1 = d1; a1 = 0; for (i = 1; i < n+1; i++) { a1 = a1 + x[i] * e[i] * e[i]; } c1 = 0; for (i = 1; i < n+1; i++) { c1 = c1 + y[i] * e[i]; } b[1] = 1 / f1; f[1] = b[1] * c1; for (i = 1; i < n+1; i++) { v[i] = v[i] + e[i] * c1; } m = 1; e10: // Save latest results for (i = 1; i < l+1; i++) c2[i] = c[i]; l2 = l; v2 = v1; f2 = f1; a2 = a1; f1 = 0; for (i = 1; i < n+1; i++) { b1 = e[i]; e[i] = (x[i] - a2) * e[i] - f2 * d[i]; d[i] = b1; f1 = f1 + e[i] * e[i]; } f1 = sqrt(f1); for (i = 1; i < n+1; i++) e[i] = e[i] / f1; a1 = 0; for (i = 1; i < n+1; i++) a1 = a1 + x[i] * e[i] * e[i]; c1 = 0; for (i = 1; i < n+1; i++) c1 = c1 + e[i] * y[i]; m = m + 1; i = 0; e15: l = m - i; b2 = b[l]; d1 = 0; if (l > 1) d1 = b[l - 1]; d1 = d1 - a2 * b[l] - f2 * a[l]; b[l] = d1 / f1; a[l] = b2; i = i + 1; if (i != m) goto e15; for (i = 1; i < n+1; i++) v[i] = v[i] + e[i] * c1; for (i = 1; i < n1+1; i++) { f[i] = f[i] + b[i] * c1; c[i] = f[i]; } vv = 0; for (i = 1; i < n+1; i++) vv = vv + (v[i] - y[i]) * (v[i] - y[i]); //Note the division is by the number of degrees of freedom vv = sqrt(vv / (n - l - 1)); l = m; if (e1 == 0) goto e20; //Test for minimal improvement if (fabs(v1 - vv) / vv < e1) goto e50; //if error is larger, quit if (e1 * vv > e1 * v1) goto e50; v1 = vv; e20: if (m == n1) goto e30; goto e10; e30: //Shift the c[i] down, so c(0) is the constant term for (i = 1; i < l+1; i++) c[i - 1] = c[i]; c[l] = 0; //l is the order of the polynomial fitted l = l - 1; dd = vv; goto fin; e50: // Aborted sequence, recover last values l = l2; vv = v2; for (i = 1; i < l+1; i++) c[i] = c2[i]; goto e30; fin: ; for (i = 0; i < number_of_points; i++) { polynomial_fit[i] = v[i + 1]; wxPrintf("After %i = %f\n", i, polynomial_fit[i]); } for (i = 0; i < polynomial_order; i++) { polynomial_coefficients[i] = c[i + 1]; } } */ void LS_POLY(float *x_data, float *y_data, int number_of_points, int order_of_polynomial, float *output_smoothed_curve, float *output_coefficients) { double a[order_of_polynomial + 2]; double b[order_of_polynomial + 2]; double c[order_of_polynomial + 3]; double c2[order_of_polynomial + 2]; double f[order_of_polynomial + 2]; double v[number_of_points + 1]; double d[number_of_points + 1]; double e[number_of_points + 1]; double x[number_of_points + 1]; double y[number_of_points + 1]; int l;// int n = number_of_points; int m = order_of_polynomial; double e1 = 0.0;// double dd; double vv; //Labels: e10,e15,e20,e30,e50,fin; int i; int l2; int n1; double a1; double a2; double b1; double b2; double c1; double d1; double f1; double f2; double v1; double v2; double w; l = 0; n1 = m + 1; v1 = 1e7; for (i = 0; i < number_of_points; i++) { x[i + 1] = x_data[i]; y[i + 1] = y_data[i]; //wxPrintf("Before %i = %f\n", i, y_data[i]); } // Initialize the arrays for (i = 1; i < n1+1; i++) { a[i] = 0; b[i] = 0; f[i] = 0; }; for (i = 1; i < n+1; i++) { v[i] = 0; d[i] = 0; } d1 = sqrt(n); w = d1; for (i = 1; i < n+1; i++) { e[i] = 1 / w; } f1 = d1; a1 = 0; for (i = 1; i < n+1; i++) { a1 = a1 + x[i] * e[i] * e[i]; } c1 = 0; for (i = 1; i < n+1; i++) { c1 = c1 + y[i] * e[i]; } b[1] = 1 / f1; f[1] = b[1] * c1; for (i = 1; i < n+1; i++) { v[i] = v[i] + e[i] * c1; } m = 1; e10: // Save latest results for (i = 1; i < l+1; i++) c2[i] = c[i]; l2 = l; v2 = v1; f2 = f1; a2 = a1; f1 = 0; for (i = 1; i < n+1; i++) { b1 = e[i]; e[i] = (x[i] - a2) * e[i] - f2 * d[i]; d[i] = b1; f1 = f1 + e[i] * e[i]; } f1 = sqrt(f1); for (i = 1; i < n+1; i++) e[i] = e[i] / f1; a1 = 0; for (i = 1; i < n+1; i++) a1 = a1 + x[i] * e[i] * e[i]; c1 = 0; for (i = 1; i < n+1; i++) c1 = c1 + e[i] * y[i]; m = m + 1; i = 0; e15: l = m - i; b2 = b[l]; d1 = 0; if (l > 1) d1 = b[l - 1]; d1 = d1 - a2 * b[l] - f2 * a[l]; b[l] = d1 / f1; a[l] = b2; i = i + 1; if (i != m) goto e15; for (i = 1; i < n+1; i++) v[i] = v[i] + e[i] * c1; for (i = 1; i < n1+1; i++) { f[i] = f[i] + b[i] * c1; c[i] = f[i]; } vv = 0; for (i = 1; i < n+1; i++) vv = vv + (v[i] - y[i]) * (v[i] - y[i]); //Note the division is by the number of degrees of freedom vv = sqrt(vv / (n - l - 1)); l = m; if (e1 == 0) goto e20; //Test for minimal improvement if (fabs(v1 - vv) / vv < e1) goto e50; //if error is larger, quit if (e1 * vv > e1 * v1) goto e50; v1 = vv; e20: if (m == n1) goto e30; goto e10; e30: //Shift the c[i] down, so c(0) is the constant term for (i = 1; i < l+1; i++) c[i - 1] = c[i]; c[l] = 0; //l is the order of the polynomial fitted l = l - 1; dd = vv; goto fin; e50: // Aborted sequence, recover last values l = l2; vv = v2; for (i = 1; i < l+1; i++) c[i] = c2[i]; goto e30; fin: ; for (i = 0; i < number_of_points; i++) { output_smoothed_curve[i] = v[i + 1]; // output_smoothed_curve[i] = y[i + 1]; //wxPrintf("After %i = %f\n", i, output_smoothed_curve[i]); } // coefficient 0: constant // coefficient 1: linear // coefficient 2: square // coefficient 3: cube // ... for (i = 0; i <= order_of_polynomial; i++) { output_coefficients[i] = c[i]; } } ctffind-4.1.14/src/core/curve.h000066400000000000000000000061731440356052600162460ustar00rootroot00000000000000 class Curve { private: public: bool have_polynomial = false; bool have_savitzky_golay = false; int number_of_points = 0; int allocated_space_for_points = 0; float *data_x = NULL; float *data_y = NULL; float *polynomial_fit = NULL; float *savitzky_golay_fit = NULL; int savitzky_golay_window_size = 0; int savitzky_golay_polynomial_order = 0; float **savitzky_golay_coefficients = NULL; int polynomial_order = 0; float *polynomial_coefficients = 0; // Constructors, destructors Curve(); ~Curve(); Curve( const Curve &other_curve); Curve & operator = (const Curve &other_curve); Curve & operator = (const Curve *other_curve); void ResampleCurve(Curve *input_curve, int wanted_number_of_points); float ReturnLinearInterpolationFromI(float wanted_i); float ReturnLinearInterpolationFromX(float wanted_x); CurvePoint ReturnValueAtXUsingLinearInterpolation(float wanted_x, float value_to_add, bool assume_linear_x); void AddValueAtXUsingLinearInterpolation(float wanted_x, float value_to_add, bool assume_linear_x); void AddValueAtXUsingNearestNeighborInterpolation(float wanted_x, float value_to_add); int ReturnIndexOfNearestPreviousBin(float wanted_x); void PrintToStandardOut(); void WriteToFile(wxString output_filename); void WriteToFile(wxString output_filename,wxString header_line); void CopyFrom(Curve *other_curve); void CopyDataFromArrays( double *x_series, double *y_series, const int wanted_number_of_points); void CopyYValuesFromArray( double *y_series, const int wanted_number_of_points); void ClearData(); void MultiplyByConstant(float constant_to_multiply_by); void MultiplyXByConstant(float constant_to_multiply_by); void AddPoint(float x_value, float y_value); void FitPolynomialToData(int wanted_polynomial_order = 6); void FitSavitzkyGolayToData(int wanted_window_size, int wanted_polynomial_order); float ReturnSavitzkyGolayInterpolationFromX( float wanted_x ); int ReturnIndexOfNearestPointFromX( float wanted_x ); void DeleteSavitzkyGolayCoefficients(); void AllocateSavitzkyGolayCoefficients(); void CheckMemory(); void AllocateMemory(int wanted_number_of_points); void AddWith(Curve *other_curve); void DivideBy(Curve *other_curve); void SetupXAxis(const float lower_bound, const float upper_bound, const int wanted_number_of_points); float ReturnMaximumValue(); float ReturnMode(); void ComputeMaximumValueAndMode(float &maximum_value, float &mode); float ReturnFullWidthAtGivenValue(const float &wanted_value); void NormalizeMaximumValue(); void Logarithm(); void ZeroYData(); void ApplyCTF(CTF ctf_to_apply, float azimuth_in_radians = 0.0); void SquareRoot(); void Reciprocal(); void DivideBy(Curve &other_curve); void MultiplyBy(Curve &other_curve); void ZeroAfterIndex(int index); void FlattenBeforeIndex(int index); float ReturnAverageValue(); void ApplyCosineMask(float wanted_x_of_cosine_start, float wanted_cosine_width_in_x, bool undo = false); void GetXMinMax(float &min_value, float &max_value); void GetYMinMax(float &min_value, float &max_value); void SetYToConstant(float wanted_constant); private: int index_of_last_point_used; }; WX_DECLARE_OBJARRAY(Curve, ArrayofCurves); ctffind-4.1.14/src/core/database.h000066400000000000000000000525331440356052600166670ustar00rootroot00000000000000class Database { bool is_open; bool in_batch_insert; bool in_batch_select; int number_of_active_transactions; sqlite3_stmt *batch_statement; bool should_do_local_commit; // used for functions to decide whether to do a commit themselves, or to leave it for someone else to commit. if already in a begin, it won't do begin commit. public : sqlite3 *sqlite_database; int last_return_code; wxFileName database_file; Database(); ~Database(); void Close(bool remove_lock = true); wxString ReturnFilename() {return database_file.GetFullPath();}; bool CreateNewDatabase(wxFileName database_file); bool Open(wxFileName file_to_open, bool disable_locking = false); inline void Begin() { if (number_of_active_transactions == 0) ExecuteSQL("BEGIN IMMEDIATE;");// we can start, otherwise, we are already in begin commit number_of_active_transactions++; // MyPrintWithDetails("\nBegin %i\n", number_of_active_transactions); } inline void Commit() { number_of_active_transactions--; if (number_of_active_transactions == 0) ExecuteSQL("COMMIT;"); //MyPrintWithDetails("\nCommit %i\n", number_of_active_transactions); } bool CreateTable(const char *table_name, const char *column_format, ...); bool DeleteTable(const char *table_name); bool AddColumnToTable(wxString table_name, wxString column_name, wxString column_format, wxString default_value); //bool DeleteTable(const char *table_name); bool InsertOrReplace(const char *table_name, const char *column_format, ...); bool GetMasterSettings(wxFileName &project_directory, wxString &project_name, int &imported_integer_version, double &total_cpu_hours, int &total_jobs_run); bool SetProjectStatistics(double &total_cpu_hours, int &total_jobs_run); bool CreateAllTables(); void BeginBatchInsert(const char *table_name, int number_of_columns, ...); void AddToBatchInsert(const char *column_format, ...); void EndBatchInsert(); bool BeginBatchSelect(const char *select_command); bool GetFromBatchSelect(const char *column_format, ...); void EndBatchSelect(); int ExecuteSQL(const char *command); int Prepare(wxString select_command, sqlite3_stmt **current_statement); int Step(sqlite3_stmt *current_statement); int Finalize(sqlite3_stmt *current_statement); void CheckBindCode(int return_code); int ReturnSingleIntFromSelectCommand(wxString select_command); long ReturnSingleLongFromSelectCommand(wxString select_command); double ReturnSingleDoubleFromSelectCommand(wxString select_command); wxArrayLong ReturnLongArrayFromSelectCommand(wxString select_command); wxArrayString ReturnStringArrayFromSelectCommand(wxString select_command); bool DoesTableExist(wxString table_name); bool DoesColumnExist(wxString table_name, wxString column_name); void ReturnProcessLockInfo(long &active_process_id, wxString &active_hostname); void SetProcessLockInfo(long &active_process_id, wxString &active_hostname); long ReturnRefinementIDGivenReconstructionID(long reconstruction_id); // Get various id numbers and counts long ReturnHighestRefinementID(); long ReturnHighestStartupID(); long ReturnHighestReconstructionID(); long ReturnHighestClassificationID(); int ReturnHighestAlignmentID(); int ReturnHighestAlignmentJobID(); int ReturnHighestFindCTFID(); int ReturnHighestFindCTFJobID(); int ReturnHighestPickingID(); int ReturnHighestPickingJobID(); int ReturnHighestParticlePositionID(); long ReturnHighestClassumSelectionID(); int ReturnNumberOfPreviousMovieAlignmentsByAssetID(int wanted_asset_id); int ReturnNumberOfPreviousCTFEstimationsByAssetID(int wanted_asset_id); int ReturnNumberOfPreviousParticlePicksByAssetID(int wanted_asset_id); int ReturnNumberOfAlignmentJobs(); int ReturnNumberOfCTFEstimationJobs(); int ReturnNumberOfPickingJobs(); int ReturnNumberOfImageAssetsWithCTFEstimates(); void GetUniqueAlignmentIDs(int *alignment_job_ids, int number_of_alignmnet_jobs); void GetUniqueCTFEstimationIDs(int *ctf_estimation_job_ids, int number_of_ctf_estimation_jobs); void GetUniquePickingJobIDs(int *picking_job_ids, int number_of_picking_jobs); void GetUniqueIDsOfImagesWithCTFEstimations(int *image_ids, int &number_of_image_ids); void GetMovieImportDefaults(float &voltage, float &spherical_aberration, float &pixel_size, float &exposure_per_frame, bool &movies_are_gain_corrected, wxString &gain_reference_filename, bool &resample_movies, float &desired_pixel_size, bool &correct_mag_distortion, float &mag_distortion_angle, float &mag_distortion_major_scale, float &mag_distortion_minor_scale, bool &protein_is_white); void GetImageImportDefaults(float &voltage, float &spherical_aberration, float &pixel_size, bool &protein_is_white); void GetActiveDefocusValuesByImageID(long wanted_image_id, float &defocus_1, float &defocus_2, float &defocus_angle, float &phase_shift, float&litude_contrast); void AddRefinementPackageAsset(RefinementPackage *asset_to_add); wxArrayLong Return2DClassMembers(long wanted_classifiction_id, int wanted_class); //Convenience insertion functions.. //void AddSingleMovieAsset(int movie_asset_id, wxString filename, int position_in_stack, int x_size, int y_size, int number_of_frames, double voltage, double pixel_size, double dose_per_frame, double spherical_aberration); bool AddOrReplaceRunProfile(RunProfile *profile_to_add); bool DeleteRunProfile(int wanted_id); void BeginMovieAssetInsert(); void AddNextMovieAsset(int movie_asset_id, wxString name, wxString filename, int position_in_stack, int x_size, int y_size, int number_of_frames, double voltage, double pixel_size, double dose_per_frame, double spherical_aberration, wxString gain_filename, double output_binning_factor, int correct_mag_distortion, float mag_distortion_angle, float mag_distortion_major_scale, float mag_distortion_minor_scale, int protein_is_white); void EndMovieAssetInsert(); void BeginImageAssetInsert(); void AddNextImageAsset(int image_asset_id, wxString name, wxString filename, int position_in_stack, int parent_movie_id, int alignment_id, int ctf_estimation_id, int x_size, int y_size, double voltage, double pixel_size, double spherical_aberration, int protein_is_white); void EndImageAssetInsert() {EndBatchInsert();}; void BeginVolumeAssetInsert(); void AddNextVolumeAsset(int image_asset_id, wxString name, wxString filename, int reconstruction_job_id, double pixel_size, int x_size, int y_size, int z_size); void EndVolumeAssetInsert() {EndBatchInsert();}; void BeginParticlePositionAssetInsert(); //void AddNextParticlePositionAsset(int particle_position_asset_id, int parent_image_asset_id, int pick_job_id, double x_position, double y_position); void AddNextParticlePositionAsset(const ParticlePositionAsset *asset); void EndParticlePositionAssetInsert() {EndBatchInsert();}; /* void BeginAbInitioParticlePositionAssetInsert(); void AddNextAbInitioParticlePositionAsset(int particle_position_asset_id, int parent_image_asset_id, int pick_job_id, double x_position, double y_position, double peak_height); void EndAbInitioParticlePositionAssetInsert() {EndBatchInsert();}; */ // Table creation wrappers.. bool CreateProcessLockTable() {return CreateTable("PROCESS_LOCK", "plt", "NUMBER", "ACTIVE_PROCESS", "ACTIVE_HOST");}; bool CreateParticlePickingListTable() {return CreateTable("PARTICLE_PICKING_LIST", "piiiirrrriiiii", "PICKING_ID", "DATETIME_OF_RUN", "PICKING_JOB_ID", "PARENT_IMAGE_ASSET_ID", "PICKING_ALGORITHM","CHARACTERISTIC_RADIUS", "MAXIMUM_RADIUS","THRESHOLD_PEAK_HEIGHT","HIGHEST_RESOLUTION_USED_IN_PICKING","MIN_DIST_FROM_EDGES","AVOID_HIGH_VARIANCE","AVOID_HIGH_LOW_MEAN","NUM_BACKGROUND_BOXES","MANUAL_EDIT");}; bool CreateParticlePositionAssetTable() {return CreateTable("PARTICLE_POSITION_ASSETS", "piiirrrirrr", "PARTICLE_POSITION_ASSET_ID", "PARENT_IMAGE_ASSET_ID", "PICKING_ID", "PICK_JOB_ID", "X_POSITION", "Y_POSITION","PEAK_HEIGHT","TEMPLATE_ASSET_ID","TEMPLATE_PSI","TEMPLATE_THETA","TEMPLATE_PHI");}; bool CreateParticlePositionGroupListTable() {return CreateTable("PARTICLE_POSITION_GROUP_LIST", "pti", "GROUP_ID", "GROUP_NAME", "LIST_ID" );}; bool CreateParticlePickingResultsTable(const int &picking_job_id) {return CreateTable(wxString::Format("PARTICLE_PICKING_RESULTS_%i",picking_job_id),"piirrrirrr","POSITION_ID","PICKING_ID","PARENT_IMAGE_ASSET_ID","X_POSITION", "Y_POSITION","PEAK_HEIGHT","TEMPLATE_ASSET_ID","TEMPLATE_PSI","TEMPLATE_THETA","TEMPLATE_PHI");}; bool CreateImageAssetTable() {return CreateTable("IMAGE_ASSETS", "pttiiiiiirrri", "IMAGE_ASSET_ID", "NAME", "FILENAME", "POSITION_IN_STACK", "PARENT_MOVIE_ID", "ALIGNMENT_ID", "CTF_ESTIMATION_ID", "X_SIZE", "Y_SIZE", "PIXEL_SIZE", "VOLTAGE", "SPHERICAL_ABERRATION","PROTEIN_IS_WHITE");}; bool CreateMovieAssetTable() {return CreateTable("MOVIE_ASSETS", "pttiiiirrrrtrirrri", "MOVIE_ASSET_ID", "NAME", "FILENAME", "POSITION_IN_STACK", "X_SIZE", "Y_SIZE", "NUMBER_OF_FRAMES", "VOLTAGE", "PIXEL_SIZE", "DOSE_PER_FRAME", "SPHERICAL_ABERRATION", "GAIN_FILENAME","OUTPUT_BINNING_FACTOR", "CORRECT_MAG_DISTORTION", "MAG_DISTORTION_ANGLE", "MAG_DISTORTION_MAJOR_SCALE", "MAG_DISTORTION_MINOR_SCALE","PROTEIN_IS_WHITE");}; bool CreateVolumeAssetTable() {return CreateTable("VOLUME_ASSETS", "pttiriii", "VOLUME_ASSET_ID", "NAME", "FILENAME", "RECONSTRUCTION_JOB_ID", "PIXEL_SIZE", "X_SIZE", "Y_SIZE", "Z_SIZE");}; bool CreateVolumeGroupListTable() {return CreateTable("VOLUME_GROUP_LIST", "pti", "GROUP_ID", "GROUP_NAME", "LIST_ID" );}; bool CreateRefinementPackageAssetTable() {return CreateTable("REFINEMENT_PACKAGE_ASSETS", "pttitrriiii", "REFINEMENT_PACKAGE_ASSET_ID", "NAME", "STACK_FILENAME", "STACK_BOX_SIZE", "SYMMETRY", "MOLECULAR_WEIGHT", "PARTICLE_SIZE","NUMBER_OF_CLASSES", "NUMBER_OF_REFINEMENTS", "LAST_REFINEMENT_ID", "STACK_HAS_WHITE_PROTEIN");}; bool CreateRefinementPackageContainedParticlesTable(const long refinement_package_asset_id) {return CreateTable(wxString::Format("REFINEMENT_PACKAGE_CONTAINED_PARTICLES_%li", refinement_package_asset_id), "piirrrrrrrrrr", "ORIGINAL_PARTICLE_POSITION_ASSET_ID", "PARENT_IMAGE_ASSET_ID", "POSITION_IN_STACK", "X_POSITION", "Y_POSITION", "PIXEL_SIZE", "DEFOCUS_1", "DEFOCUS_2", "DEFOCUS_ANGLE", "PHASE_SHIFT", "SPHERICAL_ABERRATION", "MICROSCOPE_VOLTAGE", "AMPLITUDE_CONTRAST");}; bool CreateRefinementPackageCurrent3DReferencesTable(const long refinement_package_asset_id) {return CreateTable(wxString::Format("REFINEMENT_PACKAGE_CURRENT_REFERENCES_%li", refinement_package_asset_id), "pi", "CLASS_NUMBER", "VOLUME_ASSET_ID");}; bool CreateRefinementPackageRefinementsList(const long refinement_package_asset_id) {return CreateTable(wxString::Format("REFINEMENT_PACKAGE_REFINEMENTS_LIST_%li", refinement_package_asset_id), "pl", "REFINEMENT_NUMBER", "REFINEMENT_ID");}; bool CreateRefinementPackageClassificationsList(const long refinement_package_asset_id) {return CreateTable(wxString::Format("REFINEMENT_PACKAGE_CLASSIFICATIONS_LIST_%li", refinement_package_asset_id), "pl", "CLASSIFICATION_NUMBER", "CLASSIFICATION_ID");}; bool CreateRefinementListTable() {return CreateTable("REFINEMENT_LIST", "Pltillllirr", "REFINEMENT_ID", "REFINEMENT_PACKAGE_ASSET_ID", "NAME", "RESOLUTION_STATISTICS_ARE_GENERATED", "DATETIME_OF_RUN", "STARTING_REFINEMENT_ID", "NUMBER_OF_PARTICLES", "NUMBER_OF_CLASSES", "RESOLUTION_STATISTICS_BOX_SIZE", "RESOLUTION_STATISTICS_PIXEL_SIZE", "PERCENT_USED");}; bool CreateRefinementDetailsTable(const long refinement_id) {return CreateTable(wxString::Format("REFINEMENT_DETAILS_%li", refinement_id), "plrrrrrrirrrrirrrrirrrrlliiilrrir", "CLASS_NUMBER", "REFERENCE_VOLUME_ASSET_ID", "LOW_RESOLUTION_LIMIT", "HIGH_RESOLUTION_LIMIT", "MASK_RADIUS", "SIGNED_CC_RESOLUTION_LIMIT", "GLOBAL_RESOLUTION_LIMIT", "GLOBAL_MASK_RADIUS", "NUMBER_RESULTS_TO_REFINE", "ANGULAR_SEARCH_STEP", "SEARCH_RANGE_X", "SEARCH_RANGE_Y", "CLASSIFICATION_RESOLUTION_LIMIT", "SHOULD_FOCUS_CLASSIFY", "SPHERE_X_COORD", "SPHERE_Y_COORD", "SPHERE_Z_COORD", "SPHERE_RADIUS", "SHOULD_REFINE_CTF", "DEFOCUS_SEARCH_RANGE", "DEFOCUS_SEARCH_STEP", "AVERAGE_OCCUPANCY", "ESTIMATED_RESOLUTION", "RECONSTRUCTED_VOLUME_ASSET_ID", "RECONSTRUCTION_ID", "SHOULD_AUTOMASK", "SHOULD_REFINE_INPUT_PARAMS", "SHOULD_USE_SUPPLIED_MASK", "MASK_ASSET_ID", "MASK_EDGE_WIDTH", "OUTSIDE_MASK_WEIGHT", "SHOULD_LOWPASS_OUTSIDE_MASK", "MASK_FILTER_RESOLUTION");}; bool CreateRefinementResultTable(const long refinement_id, const int class_number) {return CreateTable(wxString::Format("REFINEMENT_RESULT_%li_%i", refinement_id, class_number), "Prrrrrrrrrrrrri", "POSITION_IN_STACK", "PSI", "THETA", "PHI", "XSHIFT", "YSHIFT", "DEFOCUS1", "DEFOCUS2", "DEFOCUS_ANGLE", "PHASE_SHIFT", "OCCUPANCY", "LOGP", "SIGMA", "SCORE", "IMAGE_IS_ACTIVE");}; bool CreateRefinementResolutionStatisticsTable(const long refinement_id, int class_number) {return CreateTable(wxString::Format("REFINEMENT_RESOLUTION_STATISTICS_%li_%i", refinement_id, class_number), "prrrrr", "SHELL", "RESOLUTION", "FSC", "PART_FSC", "PART_SSNR", "REC_SSNR");}; bool CreateRefinementAngularDistributionTable(const long refinement_id, const int class_number) { return CreateTable(wxString::Format("REFINEMENT_ANGULAR_DISTRIBUTION_%li_%i", refinement_id, class_number), "pr", "BIN_NUMBER", "NUMBER_IN_BIN");} bool CreateClassificationListTable() {return CreateTable("CLASSIFICATION_LIST", "Plttilllirrrrrrriir", "CLASSIFICATION_ID", "REFINEMENT_PACKAGE_ASSET_ID", "NAME", "CLASS_AVERAGE_FILE", "REFINEMENT_WAS_IMPORTED_OR_GENERATED", "DATETIME_OF_RUN", "STARTING_CLASSIFICATION_ID", "NUMBER_OF_PARTICLES", "NUMBER_OF_CLASSES", "LOW_RESOLUTION_LIMIT", "HIGH_RESOLUTION_LIMIT", "MASK_RADIUS", "ANGULAR_SEARCH_STEP", "SEARCH_RANGE_X", "SEARCH_RANGE_Y", "SMOOTHING_FACTOR", "EXCLUDE_BLANK_EDGES", "AUTO_PERCENT_USED", "PERCENT_USED" ); }; bool CreateClassificationResultTable(const long classification_id) {return CreateTable(wxString::Format("CLASSIFICATION_RESULT_%li", classification_id), "Prrrirr", "POSITION_IN_STACK", "PSI", "XSHIFT", "YSHIFT", "BEST_CLASS", "SIGMA", "LOGP");}; bool CreateClassificationSelectionListTable() {return CreateTable("CLASSIFICATION_SELECTION_LIST", "Ptlllii", "SELECTION_ID", "SELECTION_NAME", "CREATION_DATE", "REFINEMENT_PACKAGE_ID", "CLASSIFICATION_ID", "NUMBER_OF_CLASSES", "NUMBER_OF_SELECTIONS");}; bool CreateClassificationSelectionTable(const long selection_id) {return CreateTable(wxString::Format("CLASSIFICATION_SELECTION_%li", selection_id), "pl", "SELECTION_NUMBER", "CLASS_AVERAGE_NUMBER");}; bool CreateMovieImportDefaultsTable() {return CreateTable("MOVIE_IMPORT_DEFAULTS", "prrrritirirrri", "NUMBER", "VOLTAGE", "SPHERICAL_ABERRATION", "PIXEL_SIZE", "EXPOSURE_PER_FRAME", "MOVIES_ARE_GAIN_CORRECTED", "GAIN_REFERENCE_FILENAME", "RESAMPLE_MOVIES", "DESIRED_PIXEL_SIZE", "CORRECT_MAG_DISTORTION", "MAG_DISTORTION_ANGLE", "MAG_DISTORTION_MAJOR_SCALE", "MAG_DISTORTION_MINOR_SCALE", "PROTEIN_IS_WHITE" );}; bool CreateImageImportDefaultsTable() {return CreateTable("IMAGE_IMPORT_DEFAULTS", "prrri", "NUMBER", "VOLTAGE", "SPHERICAL_ABERRATION", "PIXEL_SIZE", "PROTEIN_IS_WHITE");}; bool CreateStartupListTable() { return CreateTable("STARTUP_LIST", "Pltiirriirrrir", "STARTUP_ID", "REFINEMENT_PACKAGE_ASSET_ID", "NAME", "NUMBER_OF_STARTS", "NUMBER_OF_CYCLES", "INITIAL_RES_LIMIT", "FINAL_RES_LIMIT", "AUTO_MASK", "AUTO_PERCENT_USED", "INITIAL_PERCENT_USED", "FINAL_PERCENT_USED", "MASK_RADIUS", "APPLY_LIKELIHOOD_BLURRING", "SMOOTHING_FACTOR");}; bool CreateStartupResultTable(const long startup_id) {return CreateTable(wxString::Format("STARTUP_RESULT_%li", startup_id), "pl", "CLASS_NUMBER", "VOLUME_ASSET_ID");}; bool CreateReconstructionListTable() { return CreateTable("RECONSTRUCTION_LIST", "Plltrrrriiiiril", "RECONSTRUCTION_ID", "REFINEMENT_PACKAGE_ID", "REFINEMENT_ID", "NAME", "INNER_MASK_RADIUS", "OUTER_MASK_RADIUS", "RESOLUTION_LIMIT", "SCORE_WEIGHT_CONVERSION", "SHOULD_ADJUST_SCORES", "SHOULD_CROP_IMAGES", "SHOULD_SAVE_HALF_MAPS", "SHOULD_LIKELIHOOD_BLUR", "SMOOTHING_FACTOR", "CLASS_NUMBER", "VOLUME_ASSET_ID");} void DoVacuum() {ExecuteSQL("VACUUM");} // Convenience select functions... void BeginAllMovieAssetsSelect(); MovieAsset GetNextMovieAsset(); void EndAllMovieAssetsSelect(){EndBatchSelect();}; void BeginAllMovieGroupsSelect(); AssetGroup GetNextMovieGroup(); void EndAllMovieGroupsSelect(){EndBatchSelect();}; void BeginAllImageAssetsSelect(); ImageAsset GetNextImageAsset(); void EndAllImageAssetsSelect(){EndBatchSelect();}; void BeginAllImageGroupsSelect(); AssetGroup GetNextImageGroup(); void EndAllImageGroupsSelect(){EndBatchSelect();}; void BeginAllParticlePositionAssetsSelect(); ParticlePositionAsset GetNextParticlePositionAsset(); ParticlePositionAsset GetNextParticlePositionAssetFromResults(); void EndAllParticlePositionAssetsSelect() {EndBatchSelect();}; void BeginAllParticlePositionGroupsSelect(); AssetGroup GetNextParticlePositionGroup(); void EndAllParticlePositionGroupsSelect(){EndBatchSelect();}; void BeginAllVolumeAssetsSelect(); VolumeAsset GetNextVolumeAsset(); void EndAllVolumeAssetsSelect() {EndBatchSelect();}; void BeginAllVolumeGroupsSelect(); AssetGroup GetNextVolumeGroup(); void EndAllVolumeGroupsSelect(){EndBatchSelect();}; void BeginAllRunProfilesSelect(); RunProfile GetNextRunProfile(); void EndAllRunProfilesSelect(){EndBatchSelect();}; void BeginAllRefinementPackagesSelect(); RefinementPackage* GetNextRefinementPackage(); void EndAllRefinementPackagesSelect() {EndBatchSelect();}; void AddStartupJob(long startup_job_id, long refinement_package_asset_id, wxString name, int number_of_starts, int number_of_cycles, float initial_res_limit, float final_res_limit, bool auto_mask, bool auto_percent_used, float initial_percent_used, float final_percent_used, float mask_radius, bool apply_blurring, float smoothing_factor, wxArrayLong result_volume_ids); void AddReconstructionJob(long reconstruction_id, long refinement_package_asset_id, long refinement_id, wxString name, float inner_mask_radius, float outer_mask_radius, float resolution_limit, float score_weight_conversion, bool should_adjust_score, bool should_crop_images, bool should_save_half_maps, bool should_likelihood_blur, float smoothing_factor, int class_number, long volume_asset_id); void GetReconstructionJob(long wanted_reconstruction_id, long &refinement_package_asset_id, long &refinement_id, wxString &name, float &inner_mask_radius, float &outer_mask_radius, float &resolution_limit, float &score_weight_conversion, bool &should_adjust_score, bool &should_crop_images, bool &should_save_half_maps, bool &should_likelihood_blur, float &smoothing_factor, int &class_number, long &volume_asset_id); // Convenience CTF parameter function void GetCTFParameters( const int &ctf_estimation_id, double &acceleration_voltage, double &spherical_aberration, double &litude_constrast, double &defocus_1, double &defocus_2, double &defocus_angle, double &additional_phase_shift, double &iciness ); void AddCTFIcinessColumnIfNecessary(); // Particle position asset management void RemoveParticlePositionsWithGivenParentImageIDFromGroup( const int &group_number_following_gui_convention, const int &parent_image_asset_id); void RemoveParticlePositionAssetsPickedFromImagesAlsoPickedByGivenPickingJobID( const int &picking_job_id); void RemoveParticlePositionAssetsPickedFromImageWithGivenID( const int &parent_image_asset_id ); void CopyParticleAssetsFromResultsTable(const int &picking_job_id, const int &parent_image_asset_id); void AddArrayOfParticlePositionAssetsToResultsTable(const int &picking_job_id, ArrayOfParticlePositionAssets *array_of_assets); void AddArrayOfParticlePositionAssetsToAssetsTable(ArrayOfParticlePositionAssets *array_of_assets); ArrayOfParticlePositionAssets ReturnArrayOfParticlePositionAssetsFromResultsTable(const int &picking_job_id, const int &parent_image_asset_id); ArrayOfParticlePositionAssets ReturnArrayOfParticlePositionAssetsFromAssetsTable(const int &parent_image_asset_id); // Particle picking results management void RemoveParticlePositionsFromResultsList(const int &picking_job_id, const int &parent_image_asset_id); int ReturnPickingIDGivenPickingJobIDAndParentImageID(const int & picking_job_id, const int &parent_image_asset_id); void SetManualEditForPickingID(const int &picking_id, const bool wanted_manual_edit); void AddRefinement(Refinement *refinement_to_add); void UpdateRefinementResolutionStatistics(Refinement *refinement_to_update); void AddRefinementAngularDistribution(AngularDistributionHistogram &histogram_to_add, long refinement_id, int class_number); void GetRefinementAngularDistributionHistogramData(long wanted_refinement_id, int wanted_class_number, AngularDistributionHistogram &histogram_to_fill); Refinement *GetRefinementByID(long wanted_refinement_id, bool include_particle_info = true); void AddClassification(Classification *classification_to_add); Classification *GetClassificationByID(long wanted_classification_id); void AddClassificationSelection(ClassificationSelection *classification_selection_to_add); //ClassificationSelection *GetClassificationSelectionByID(long wanted_selection_id); }; class BeginCommitLocker // just call begin in the contructor, and commit in the destructor, if it hasn't already been called. { Database *active_database; bool already_sent_commit; public: BeginCommitLocker(Database *wanted_database); ~BeginCommitLocker(); void Commit(); }; ctffind-4.1.14/src/core/defines.h000066400000000000000000000040351440356052600165320ustar00rootroot00000000000000#define INTEGER_DATABASE_VERSION 1 #define CISTEM_VERSION_TEXT "1.0.2-beta" #define START_PORT 3000 #define END_PORT 5000 // Define PI constants #define PI 3.14159265359 #define PIf 3.14159265359f #define ANSI_COLOR_RED "\x1b[31m" #define ANSI_COLOR_GREEN "\x1b[32m" #define ANSI_COLOR_YELLOW "\x1b[33m" #define ANSI_COLOR_BLUE "\x1b[34m" #define ANSI_COLOR_MAGENTA "\x1b[35m" #define ANSI_COLOR_CYAN "\x1b[36m" #define ANSI_COLOR_RESET "\x1b[0m" #define ANSI_UNDERLINE "\e[4m" #define ANSI_UNDERLINE_OFF "\e[24m" #define ANSI_BLINK_SLOW "\x1b[5m" #define ANSI_BLINK_OFF "\x1b[25m" #define SCALED_IMAGE_SIZE 1200 #define CheckSuccess(bool_to_check) if (bool_to_check == false) {return false;}; #define MyPrintWithDetails(...) {wxPrintf(__VA_ARGS__); wxPrintf("From %s:%i\n%s\n", __FILE__,__LINE__,__PRETTY_FUNCTION__);} #define MyPrintfGreen(...) {wxPrintf(ANSI_COLOR_GREEN); wxPrintf(__VA_ARGS__); wxPrintf(ANSI_COLOR_RESET);} #define MyPrintfCyan(...) {wxPrintf(ANSI_COLOR_CYAN); wxPrintf(__VA_ARGS__); wxPrintf(ANSI_COLOR_RESET);} #define MyPrintfRed(...) {wxPrintf(ANSI_COLOR_RED); wxPrintf(__VA_ARGS__); wxPrintf(ANSI_COLOR_RESET);} #ifdef DEBUG #define MyDebugPrintWithDetails(...) {wxPrintf(__VA_ARGS__); wxPrintf("From %s:%i\n%s\n", __FILE__,__LINE__,__PRETTY_FUNCTION__);} #define MyDebugPrint(...) {wxPrintf(__VA_ARGS__); wxPrintf("\n");} #define MyDebugAssertTrue(cond, msg, ...) {if ((cond) != true) { wxPrintf("\n" msg, ##__VA_ARGS__); wxPrintf("\nFailed Assert at %s:%i\n%s\n", __FILE__,__LINE__,__PRETTY_FUNCTION__); DEBUG_ABORT;}} #define MyDebugAssertFalse(cond, msg, ...) {if ((cond) == true) { wxPrintf("\n" msg, ##__VA_ARGS__); wxPrintf("\nFailed Assert at %s:%i\n%s\n", __FILE__,__LINE__,__PRETTY_FUNCTION__); DEBUG_ABORT;}} #define DEBUG_ABORT abort(); #else #define MyDebugPrintWithDetails(...) #define MyDebugPrint(...) #define MyDebugAssertTrue(cond, msg, ...) #define MyDebugAssertFalse(cond, msg, ...) #define DEBUG_ABORT exit(-1); #endif WX_DECLARE_OBJARRAY(float, wxArrayFloat); WX_DECLARE_OBJARRAY(bool, wxArrayBool); ctffind-4.1.14/src/core/dm_file.cpp000066400000000000000000000537001440356052600170520ustar00rootroot00000000000000/* \brief Object to handle Gatan's Digital Micrograph files * * Adapted from Bernard Heynman's Bsoft * */ #include "core_headers.h" #include #include DMFile::DMFile() { version = 0; show = 0; level = 0; sb = 0; endianness = 1; ss = 1; keep = 0; } DMFile::DMFile(std::string wanted_filename, bool overwrite) { version = 0; show = 0; level = 0; sb = 0; endianness = 1; keep = 0; OpenFile(wanted_filename); } DMFile::DMFile(wxString wanted_filename) { version = 0; show = 0; level = 0; sb = 0; endianness = 1; keep = 0; OpenFile(wanted_filename.ToStdString()); } DMFile::~DMFile() { CloseFile(); true; } bool DMFile::OpenFile(std::string wanted_filename, bool overwrite, bool wait_for_file_to_exist) { MyDebugAssertFalse(overwrite,"Overwriting is not supported for DM files"); MyDebugAssertFalse(wait_for_file_to_exist,"Waiting for file to exist not supported for DM files"); unsigned char *fake_pointer; readDM(wxString(wanted_filename), fake_pointer, false); filename = wxString(wanted_filename); pixel_size = 1.0; //TODO: figure out where the pixel size is (if anywhere) // TODO: return false if something is fishy about this file return true; } void DMFile::CloseFile() { filename = ""; } bool DMFile::IsOpen(){ return filename != ""; } void DMFile::ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array) { MyDebugAssertTrue(start_slice==end_slice, "Can only read single slice at a time from DM files. Sorry"); ReadSliceFromDisk(start_slice,output_array); } // Wanted_slice should be numbered from 0. It's assumed output_array is already allocated to correct dimensions void DMFile::ReadSliceFromDisk(int wanted_slice, float *output_array) { MyDebugAssertTrue(wanted_slice == 0, "Bad start_slice: %i.\n", wanted_slice); MyDebugAssertTrue(wanted_slice < n,"Can't read slice %i. There are only %i.\n",wanted_slice,n); unsigned char *p; // Allocate a temporary array to hold data from disk p = new unsigned char[alloc_size()]; // Read data from disk readDM(filename,p,true,wanted_slice); // Apply mirror operation to achieve the same data layout as IMOD's dm2mrc long counter = 0; long mirror_address = 0; int i,j; for (j=0; j < int(sizeY()); j++) { mirror_address = (sizeY() - 1 - j) * sizeX(); for (i=0; i < int(sizeX()); i++) { output_array[counter] = reinterpret_cast < float * > (p)[mirror_address]; counter++; mirror_address++; } } delete [] p; } /** @brief Reading a Digital Micrograph image file format. @param *p the image structure. @param readdata flag to activate reading of image data. @param img_select image selection in multi-image file (-1 = all images). @return int error code (<0 means failure). A 2D/3D image format used with CCD cameras in electron microscopy. File format extensions: .dm, .DM Two types: Fixed format (new) and the Macintosh format (old) Fixed format: Header size: 24 bytes (fixed). Byte order determination: An endian flag: Must be 65535 or swap everything Data types: many. Macintosh format: Hermitian Header size: 8 bytes (fixed). Byte order determination: Big-endian Data types: many. **/ int DMFile::readDM(wxString wanted_filename, unsigned char *p, bool readdata, int img_select) { std::ifstream* fimg = new std::ifstream(wanted_filename); if ( fimg->fail() ) return -1; // Read a small block at the beginning to see if it is the fixed or tagged format char buf[1024]; fimg->read(buf, 4); if ( fimg->fail() ) return -2; version = *((int *) buf); if ( version > 100 ) version = buf[3]; if ( show == 1 ) MyDebugPrint("Magic number = %i\n",version); fimg->seekg(0, std::ios::beg); switch ( version ) { case 0: readFixedDMHeader(fimg, p, readdata); break; case 3: case 4: readTagGroupWithVersion(fimg, p, readdata, img_select); break; default: MyDebugAssertFalse(true,"Digital Micrograph format version %i not supported!\n",version); wxPrintf("Digital Micrograph format version %i not supported!\n",version); abort; } fimg->close(); delete fimg; return 0; } int DMFile::readFixedDMHeader(std::ifstream* fimg, unsigned char* p, bool readdata) { DMhead* header = new DMhead; DMMachead* macheader = (DMMachead *) header; // if ( fread( header, sizeof(DMhead), 1, fimg ) < 1 ) return -2; fimg->read((char *)header, sizeof(DMhead)); if ( fimg->fail() ) return -2; if ( show ) MyDebugPrint("DEBUG readFixedDMHeader: macheader= %i width = %i height = %i\n", macheader, macheader->width, macheader->height); data_offset(8); if ( ( macheader->width < 1 ) || ( macheader->height < 1 ) ) { macheader = (DMMachead *) ((char*)header + 6); data_offset(data_offset() + 6); } if ( show ) MyDebugPrint("DEBUG readFixedDMHeader: macheader= %i width = %i height = %i\n", macheader, macheader->width, macheader->height); // Determine header type int i, fixed(1), sb(0); /* if ( macheader->width == 0 && macheader->height == -1 ) { fixed = 1; sb = 0; } else if ( macheader->width == -1 && macheader->height == 0 ) { fixed = 1; sb = 1; } else if ( systype(0) >= LittleIEEE ) sb = 1; */ // Swap bytes if necessary unsigned char* b = (unsigned char *) header; if ( sb ) { if ( fixed ) { if ( show ) MyDebugPrint("Warning: Swapping header byte order for 4-byte types\n"); for ( i=0; i<24; i+=4 ) swapbytes(b+i, 4); } else { b = (unsigned char *) macheader; if ( show ) MyDebugPrint("Warning: Swapping header byte order for 2-byte types\n"); for ( i=0; i<8; i+=2 ) swapbytes(b+i, 2); } } // Map the parameters images(1); channels(1); compound_type(TSimple); if ( fixed ) { size(header->xSize, header->ySize, header->zSize); data_offset(24); datatype_from_dm3_type(header->type); } else { size(macheader->width, macheader->height, 1); switch( macheader->type ) { case 6 : data_type(UCharacter); break; case 14 : data_type(UCharacter); break; case 9 : data_type(SCharacter); break; case 10 : data_type(UShort); break; case 1 : data_type(Short); break; case 7 : data_type(Integer); break; case 2 : data_type(Float); break; case 3 : data_type(Float); compound_type(TComplex); channels(2); break; case 13 : data_type(Double); compound_type(TComplex); channels(2); break; default : data_type(UCharacter); } } //p->image = new Bsub_image[p->images()]; delete header; if ( readdata ) { MyDebugPrintWithDetails("About to read %li bytes\n",long(alloc_size())); fimg->read((char *)p, alloc_size()); if ( fimg->fail() ) return -3; if ( sb ) swapbytes(alloc_size(), p, data_type_size()); } fimg->close(); return sb; } /* Main DM3/4 file database: Arrangement: The file header (TagGroupWithVersion) contains 4 items: Version: 1-4 (4 byte) Size of contained data (TagGroupData): v1-v3 (4 byte), v4 (8 byte) Endianness: 0,1 (4 byte) Content (TagGroupData) Important image information: Main block: "ImageList" May contain more than one image, usually a small display version followed by the real data Important elements: Pixel size (nm): ImageData/Calibrations/Dimension/Scale Data element type: ImageData/DataType Image size: ImageData/Dimensions Data element size: ImageData/PixelDepth Camera pixel size (um): ImageTags/Acquisition/Device/CCD/Pixel Size (um) Dose rate: ImageTags/Calibration/Dose rate/Calibration Magnification: ImageTags/Microscope Info/Actual Magnification Acceleration voltage: ImageTags/Microscope Info/Voltage */ int DMFile::readTagGroupWithVersion(std::ifstream* fimg, unsigned char* p, bool readdata, int img_select) { //if ( verbose & VERB_DEBUG_DM ) show = 2; keep = level = 0; size_t file_length(0), val(0); char buf[1024]; fimg->read(buf, 4); if ( fimg->fail() ) return -2; version = *((int *) buf); if ( version > 100 ) { sb = 1; version = buf[3]; } file_length = dm_read_integer(fimg, sizeof(size_t)); // File length file_length += 16; endianness = dm_read_integer(fimg, sizeof(unsigned int)); // Endianness if ( show == 1 ) { if ( sb ) std::cout << "Warning: Swapping header bytes" << endl; std::cout << "Version: " << version << endl; std::cout << "File length: " << file_length << endl; std::cout << "Endianness: " << endianness << endl; } /* if ( file_length <= 16 ) { std::cout << "Error: file length = " << file_length << endl; return error_show("File length specifier incorrect!\n", __FILE__, __LINE__); } */ MyDebugAssertTrue(file_length > 16,"Error: file length specifier incorrect. File length = %i\n",file_length); if ( show == 2 ) { std::cout << "" << endl; std::cout << "" << endl; std::cout << "" << endl; } // Set up default parameters size(1, 1, 1); images(1); channels(1); readTagGroupData(fimg, 0, p, readdata); val = dm_read_integer(fimg, sizeof(unsigned int)); // 500 val = dm_read_integer(fimg, sizeof(unsigned int)); // Label size if ( val ) { fimg->read(buf, val); if ( show == 2 ) std::cout << "<" << buf << "/>" << endl; } if ( show == 1 ) std::cout << endl; if ( show == 2 ) std::cout << "" << endl; if ( img_select >= 0 ) { data_offset(data_offset()+img_select*sizeX()*sizeY()*sizeZ()*channels()*data_type_size()); images(1); } /* if ( !p->image ) { if ( images() < 1 ) images(1); p->image = new Bsub_image[p->images()]; } */ if ( show_scale() != 1 ) { sampling(samplingX()/show_scale(), samplingY()/show_scale(), 1); show_scale(1); } if ( readdata ) { //MyDebugPrintWithDetails("About to read %li bytes\n",long(alloc_size())); fimg->seekg(data_offset(), std::ios_base::beg); //p->data_alloc(); //fimg->read((char *)p->data_pointer(), p->alloc_size()); fimg->read((char *)p, alloc_size()); } return version; } // TagGroupData contains 3 items // Sorted flag: 0,1; v3-v4 (1 byte) // Open flag: 0,1; v3-v4 (1 byte) // Number of records (TagEntry/TagSubGroup): v3 (4 byte), v4 (8 byte) // Content (TagGroupData) int DMFile::readTagGroupData(std::ifstream* fimg, int dim_flag, unsigned char* p, bool readdata) { unsigned char sorted, open; size_t i, ntag(0); int notag(0); *fimg >> sorted; *fimg >> open; ntag = dm_read_integer(fimg, sizeof(size_t)); // Number of tags if ( show == 1 ) std::cout << "\tntag=" << ntag; if ( show == 2 ) { for ( i=0; i" << endl; } for ( i=0; i" << endl; } return 0; } /* Image data is assigned to the data pointer based on the keep flag Associated properties are also kept */ int DMFile::readTag(std::ifstream* fimg, int dim_flag, unsigned char* p, bool readdata, int& notag) { unsigned char t, tag[128]; unsigned short len; size_t i, j, k, data_size(0); size_t nnum, size(0), nstr, narr, nel, dt, dtarr[128], dtlen; // Change in v4 double val, arr[256]; char buf[1024]; level++; // Common part of TagSubGroup and TagEntry records // Selector (1 byte): TagSubGroup=20, TagEntry=21 // Length of label (2 bytes) // Label *fimg >> t; len = dm_read_integer(fimg, sizeof(unsigned short)); // cout << "\tlen=" << len << endl; if ( len > 128 ) { std::cout << "\tlen=" << len << endl; std::cerr << "Error: tag length too long!" << endl; DEBUG_ABORT; } if ( len ) { fimg->read((char *)tag, len); tag[len] = 0; tag_convert(tag); notag = 0; } else { snprintf((char *)tag, 128, "%d", notag); notag++; } if ( show == 1 ) { std::cout << endl; for ( i=0; i" << tag << "" << endl; } if ( version == 4 ) { // Changed in v4 size = dm_read_integer(fimg, sizeof(size_t)); // Size of data type & data if ( show == 1 ) std::cout << "\tsize=" << size; } if ( t == 20 ) { // TagSubGroup record if ( strcmp((char *)tag, "Dimensions") == 0 ) dim_flag = 1; readTagGroupData(fimg, dim_flag, p, readdata); } else if ( t == 21 ) { // TagEntry record fimg->read((char *)buf, 4); // String = "%%%%" buf[4] = 0; nnum = dm_read_integer(fimg, sizeof(size_t)); // Number of integers in array if ( show == 1 ) std::cout << "\t" << std::setw(4) << buf << "\tnnum=" << nnum; for ( i=0; i" << endl; } level++; for ( k=0; k" << endl; } } else if ( dt == 18 ) { // String fimg->read((char *)buf, dtarr[1]); if ( show == 1 ) std::cout << "\tstrlen=" << dtarr[1]; if ( show == 2 ) { for ( i=0; i" << buf << "" << endl; } } else if ( dt == 20 ) { // Data array if ( dtarr[1] == 15 ) narr = dtarr[3]; else narr = 1; nel = dtarr[nnum-1]; // Number of elements if ( show == 1 ) std::cout << "\tarr=" << narr << "x" << nel; if ( show == 2 ) { for ( i=0; i" << endl; } level++; if ( dtarr[1] == 15 ) { // Struct if ( show == 1 ) std::cout << "\tstruct=" << narr << "x" << nel; if ( show == 2 ) { for ( i=0; i" << endl; } level++; for ( i=0; i" << endl; } } else { narr = 1; dtlen = dm3_type_length(dtarr[1]); data_size = nel*dtlen; // The big image data block is not printed for the plist format if ( strcmp((char *)tag, "Data") == 0 && nel > 1e6 ) { keep = 1; if ( show == 1 ) std::cout << "\tdata_size=" << data_size; // if ( readdata ) { // p->data_alloc(data_size); // fimg->read((char *)p->data_pointer(), data_size); // } else { // fimg->seekg(data_size, ios_base::cur); // } data_offset(fimg->tellg()); fimg->seekg(data_size, std::ios_base::cur); } else { for ( i=0; iread((char *)buf, dtlen); // Element value } } } level--; if ( show == 2 ) { for ( i=0; i" << endl; } } else { std::cerr << "Error: Data type " << dt << " not defined!" << endl; } if ( keep && strcmp((char *)tag, "ImageData") == 0 ) keep = 0; if ( keep ) { if ( strcmp((char *)tag, "DataType") == 0 ) { datatype_from_dm3_type((DMDataType)val); if ( show == 1 ) std::cout << "\tdatatype=" << data_type() << "\tcompoundtype=" << compound_type() << "\tc=" << channels() << "\tval=" << val; } if ( strcmp((char *)tag, "Minimum Value (counts)") == 0 ) { minimum(val); } if ( strcmp((char *)tag, "Maximum Value (counts)") == 0 ) { maximum(val); } if ( dim_flag == 1 ) { sizeX((size_t) val); dim_flag = 2; } else if ( dim_flag == 2 ) { sizeY((size_t) val); dim_flag = 3; } else if ( dim_flag == 3 ) { images((size_t) val); dim_flag = 0; if ( show == 1 ) std::cout << "\tx=" << sizeX() << "\ty=" << sizeY() << "\tn=" << images(); } if ( strcmp((char *)tag, "PixelDepth") == 0 ) { if ( show == 1 ) std::cout << "\t" << tag << "=" << val << endl; } if ( strcmp((char *)tag, "Pixel Size (um)") == 0 ) { sampling(arr[0], arr[1], 1); if ( show == 1 ) std::cout << "\t" << tag << "=" << samplingX() << samplingY() << samplingZ() << endl; // cout << tab << tag << "=" << p->sampling() << endl; } if ( strcmp((char *)tag, "Actual Magnification") == 0 ) { show_scale(val/1e4); if ( show == 1 ) std::cout << "\t" << tag << "=" << val << endl; // cout << tab << tag << "=" << val << endl; } if ( strcmp((char *)tag, "Pixel Upsampling") == 0 ) { if ( show == 1 ) std::cout << "\t" << "\t" << "=" << arr[0] << "x" << arr[1] << endl; } if ( strcmp((char *)tag, "SourceSize_Pixels") == 0 ) { if ( show == 1 ) std::cout << "\t" << "\t" << "=" << arr[0] << "x" << arr[1] << endl; } // if ( strcmp(tag, "ImageIndex") == 0 ) { // if ( show == 1 ) cout << tab << tag << "=" << val << endl; // } if ( strstr((char *)tag, "Emission") ) { if ( show == 1 ) { std::cout << "\t" << tag << "=" << val << endl; for ( i=0; iread(buf, dtlen); if ( sb - endianness ) swapbytes((unsigned char *)buf, dtlen); switch ( dm3_type ) { case 2: ivalue = *((short *) buf); break; case 3: ivalue = *((int *) buf); break; case 4: ivalue = *((unsigned short *) buf); break; case 5: ivalue = *((unsigned int *) buf); break; case 6: dvalue = *((float *) buf); break; case 7: dvalue = *((double *) buf); break; case 8: ivalue = *buf; break; case 9: ivalue = *buf; break; case 10: ivalue = *buf; break; case 11: ivalue = *((long *) buf); break; case 12: ivalue = *((unsigned long *) buf); break; default: std::cerr << "Error: Data type " << dm3_type << " not defined!" << endl; } if ( !dvalue ) dvalue = ivalue; if ( show == 1 ) std::cout << "\t" << dvalue; if ( show == 2 ) { for ( i=0; i" << dvalue << "" << endl; else std::cout << "" << ivalue << "" << endl; } return dvalue; } int DMFile::dm3_type_length(int dm3_type) { int dtlen = 0; switch ( dm3_type ) { case 2: dtlen = 2; break; case 3: dtlen = 4; break; case 4: dtlen = 2; break; case 5: dtlen = 4; break; case 6: dtlen = 4; break; case 7: dtlen = 8; break; case 8: dtlen = 1; break; case 9: dtlen = 1; break; case 10: dtlen = 1; break; case 11: dtlen = 8; break; case 12: dtlen = 8; break; default: std::cerr << "Error: Data type " << dm3_type << " length not defined!" << endl; } return dtlen; } unsigned long DMFile::dm_read_integer(std::ifstream* fimg, long len) { unsigned short sval(0); unsigned int ival(0); unsigned long lval(0); char buf[1024]; if ( version < 4 && len > 4 ) len = 4; fimg->read(buf, len); if ( sb ) swapbytes((unsigned char *)buf, len); switch ( len ) { case 2: sval = *((unsigned short *) buf); lval = sval; break; case 4: ival = *((unsigned int *) buf); lval = ival; break; case 8: lval = *((unsigned long *) buf); break; default: lval = *buf; } return lval; } int DMFile::tag_convert(unsigned char* tag) { for ( ; *tag; tag++ ) if ( *tag > 127 ) *tag -= 64; return 0; } DataType DMFile::datatype_from_dm3_type(DMDataType dm3_type) { if ( show ) MyDebugPrint("\tDMDataType= %i\n",dm3_type); compound_type(TSimple); channels(1); DataType datatype = Unknown_Type; switch( dm3_type ) { case BINARY_DATA : datatype = UCharacter; break; case UNSIGNED_INT8_DATA : datatype = UCharacter; break; case SIGNED_INT8_DATA : datatype = SCharacter; break; case RGB_DATA : case RGB_UINT8_DATA : datatype = UCharacter; channels(3); compound_type(TRGB); break; case OS_RGBA_UINT8_DATA : datatype = UCharacter; channels(4); compound_type(TRGBA); break; case UNSIGNED_INT16_DATA : datatype = UShort; break; case RGB_UINT16_DATA : datatype = UShort; channels(3); compound_type(TRGB); break; case RGBA_UINT16_DATA : datatype = UShort; channels(4); compound_type(TRGBA); break; case SIGNED_INT16_DATA : datatype = Short; break; case UNSIGNED_INT32_DATA : datatype = UInteger; break; case SIGNED_INT32_DATA : datatype = Integer; break; case REAL4_DATA : datatype = Float; break; case RGBA_FLOAT32_DATA : datatype = Float; channels(4); compound_type(TRGBA); break; case REAL8_DATA : datatype = Double; break; case RGB_FLOAT64_DATA : datatype = Double; channels(3); compound_type(TRGB); break; case RGBA_FLOAT64_DATA : datatype = Double; channels(4); compound_type(TRGBA); break; case COMPLEX8_DATA : datatype = Float; compound_type(TComplex); break; case COMPLEX16_DATA : datatype = Double; compound_type(TComplex); break; default : datatype = UCharacter; } data_type(datatype); if ( compound_type() == TComplex ) channels(2); return datatype; } /** @brief Returns the size of the datatype in bytes. @return size_t data type size. The Bit type returns 1. **/ size_t DMFile::data_type_size() { size_t typesize(0); switch ( datatype ) { case Bit: case UCharacter: case SCharacter: typesize = sizeof(char); break; case UShort: case Short:typesize = sizeof(short); break; case UInteger: case Integer: typesize = sizeof(int); break; case ULong: case Long: typesize = sizeof(long); break; case Float: typesize = sizeof(float); break; case Double: typesize = sizeof(double); break; default: typesize = 0; } return typesize; } ctffind-4.1.14/src/core/dm_file.h000066400000000000000000000203471440356052600165200ustar00rootroot00000000000000/* \brief Object to handle Gatan's Digital Micrograph files * * Adapted from Bernard Heynman's Bsoft * */ void swapbytes(unsigned char* v, size_t n); void swapbytes(size_t size, unsigned char* v, size_t n); /** @enum CompoundType @brief Compound data type specifier. This determines what compound data type is used in an image. **/ enum CompoundType { TSimple = 0, // Single value data type TComplex = 1, // 2-value complex type TVector3 = 3, // 3-value vector type TView = 4, // 4-value view type TRGB = 10, // Red-green-blue interleaved TRGBA = 11, // Red-green-blue-alpha interleaved TCMYK = 12, // Cyan-magenta-yellow-black interleaved TMulti = 99 // Arbitrary number of channels } ; enum DMDataType { NULL_DATA, SIGNED_INT16_DATA, REAL4_DATA, COMPLEX8_DATA, OBSELETE_DATA, // 4 PACKED_DATA, UNSIGNED_INT8_DATA, SIGNED_INT32_DATA, RGB_DATA, // 8 SIGNED_INT8_DATA, UNSIGNED_INT16_DATA, UNSIGNED_INT32_DATA, REAL8_DATA, // 12 COMPLEX16_DATA, BINARY_DATA, RGBA_FLOAT32_DATA, RGB_UINT16_DATA , // 16 RGB_FLOAT64_DATA, RGBA_FLOAT64_DATA, RGBA_UINT16_DATA, // 19 RGB_UINT8_DATA , RGBA_UINT8_DATA, LAST_DATA, OS_RGBA_UINT8_DATA // 23 } ; #ifndef _datatype_ /** @enum DataType @brief Base data type specifier. This determines what simple data type is used in an image. **/ enum DataType { Unknown_Type = 0, // Undefined data type Bit = 1, // Bit/binary type UCharacter = 2, // Unsigned character or byte type SCharacter = 3, // Signed character UShort = 4, // Unsigned integer (2-byte) Short = 5, // Signed integer (2-byte) UInteger = 6, // Unsigned integer (4-byte) Integer = 7, // Signed integer (4-byte) ULong = 8, // Unsigned integer (4 or 8 byte, depending on system) Long = 9, // Signed integer (4 or 8 byte, depending on system) Float = 10, // Floating point (4-byte) Double = 11, // Double precision floating point (8-byte) } ; #define _datatype_ #endif class DMFile : public AbstractImageFile { private: wxString filename; int version; int show; int level; int sb; int endianness; int keep; size_t offset; // Data offset size_t n; // Number of images size_t c; // Number of channels CompoundType compoundtype; // Compound data type size_t x, y, z; // Dimensions, xyz DataType datatype; // Base data type size_t px, py, pz; // Page dimensions double ux, uy, uz; // Voxel units (angstrom/pixel edge) double ss; // Display scale double min, max; // Limits float pixel_size; int readFixedDMHeader(std::ifstream* fimg, unsigned char* p, bool readdata = true); int readTagGroupWithVersion(std::ifstream* fimg, unsigned char* p, bool readdata = true, int img_select = -1); DataType datatype_from_dm3_type(DMDataType dm3_type); unsigned long dm_read_integer(std::ifstream* fimg, long len); int readTagGroupData(std::ifstream* fimg, int dim_flag, unsigned char* p, bool readdata); int readTag(std::ifstream* fimg, int dim_flag, unsigned char* p, bool readdata, int& notag); double dm3_value(std::ifstream* fimg, int dm3_type); int dm3_type_length(int dm3_type); int tag_convert(unsigned char* tag); size_t data_offset() { return offset; } void data_offset(size_t doff) { offset = doff; } size_t images() { return n; } void images(size_t nn) { n = nn; } size_t channels() { return c; } void channels(size_t cc) { c = cc; } CompoundType compound_type() { return compoundtype; } void compound_type(CompoundType ct) { compoundtype = ct; } void size(size_t nx, size_t ny, size_t nz) { x=nx; y=ny; z=nz; } void sizeX(size_t nx) { x = nx; } void sizeY(size_t ny) { y = ny; } void sizeZ(size_t nz) { z = nz; } void sampling(double s) { if (x > 1) ux = s; if (y > 1) uy = s; if (z > 1) uz = s; //check_sampling(); } void sampling(double sx, double sy, double sz) { ux = sx; uy = sy; uz = sz; //check_sampling(); } double samplingX() { return ux; }; double samplingY() { return uy; }; double samplingZ() { return uz; }; double show_scale() { return ss; } void show_scale(double scale) { ss = scale; } DataType data_type() { return datatype; } void data_type(DataType dt) { datatype = dt; } // Data allocation and assignment size_t alloc_size() { MyDebugAssertFalse(datatype == Bit, "Bit datatype not supported yet. px not set - need to understand Bsoft better to implement this properly. Sorry.\n"); return (datatype == Bit) ? (px / 8) * y * z * n : c * x * y * z * n * data_type_size(); } double minimum() { return min; } double maximum() { return max; } void minimum(double d) { min = d; } void maximum(double d) { max = d; } public: // Constructors, destructors DMFile(); DMFile(wxString wanted_filename); DMFile(std::string filename, bool overwrite = false); ~DMFile(); // int ReturnXSize() { return x; }; int ReturnYSize() { return y; }; int ReturnZSize() { return z; }; int ReturnNumberOfSlices() { return z; }; inline float ReturnPixelSize() { return pixel_size; }; bool IsOpen(); bool OpenFile(std::string filename, bool overwrite = false, bool wait_for_file_to_exist = false); void CloseFile(); void ReadSliceFromDisk(int wanted_slice, float *output_array); void ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array); void WriteSliceToDisk(int slice_number, float *input_array) { wxPrintf("WriteSliceToDisk not yet implemented for DM files\n"); DEBUG_ABORT; }; void WriteSlicesToDisk(int start_slice, int end_slice, float *input_array) { wxPrintf("WriteSlicesToDisk not yet implemented for DM files\n"); DEBUG_ABORT; }; void PrintInfo() { wxPrintf("PrintInfo not yet implemented for DM files\n"); DEBUG_ABORT; }; private: // int readDM(wxString wanted_filename, unsigned char *p, bool readdata = true, int img_select = -1); // size_t sizeX() const { return x; } size_t sizeY() const { return y; } size_t sizeZ() const { return z; } size_t data_type_size(); }; struct DMhead { // file header for DM Fixed Format Specification unsigned int endian; // if not 0x0000FFFF then byte swap (including next 5 parameters). int xSize; int ySize; int zSize; int depth; // data type size in bytes - may be determined by data atype below DMDataType type; // An enumerated value } ; struct DMMachead { // file header for old DM Macintosh Format Specification short width; short height; short bytes_per_pixel; short type; } ; /* The header information is stored in four short integers (16 bits each). Each integer is stored with the high byte first (Motorola or 'big-endian' format). The image data is stored row by row as a continuous stream of data (i.e. no line feeds, carriage returns, or end of file control characters are present in the file). The amount of storage space that each pixel in the image occupies depends on the data type. The header and the image data are stored in the binary format (not in the ASCII format). The format for the small header image file is described below. Field Position Length Width of image 0 2 bytes (integer) Height of image 2 2 bytes (integer) Bytes per pixel 4 2 bytes (integer) Encoded data type6 2 bytes (integer) Image data 8 Width * height * bytes per pixel The encoding of the data type (at position 6) is shown below. Value Data Type 1 2 byte signed integer 2 Floating point IEEE standard 754 3 8 byte complex floating point (real, imaginary) 5 Packed complex 6 1 byte unsigned integer 7 4 byte signed integer 8 4 byte RGB 9 1 byte signed integer 10 2 byte unsigned integer 11 4 byte unsigned integer 12 8 byte double 13 16 byte complex double (real, imaginary) 14 1 byte binary data */ struct DM3head { // All 3 fields must be big-endian int version; // 2/3/4 int file_length; // Actually file length - 16 = size of root tag directory int endianness; // 0=big, 1=little char sorted; // Flag for sorted tag (1) char open; // Flag for open tag (1) int ntag; // Number of tags } ; struct DM4head { // All 3 fields must be big-endian int version; // 2/3/4 unsigned long file_length; // Actually file length - 16 = size of root tag directory int endianness; // 0=big, 1=little char sorted; // Flag for sorted tag (1) char open; // Flag for open tag (1) int ntag; // Number of tags } ; ctffind-4.1.14/src/core/downhill_simplex.cpp000066400000000000000000000172661440356052600210430ustar00rootroot00000000000000#include "core_headers.h" DownhillSimplex::DownhillSimplex() { // assume one dimension number_of_dimensions = 1; tolerance = 1.0e-5; Setup(); } DownhillSimplex::DownhillSimplex(long set_number_of_dimensions) { number_of_dimensions = set_number_of_dimensions; tolerance = 1.0e-5; Setup(); } DownhillSimplex::~DownhillSimplex() { delete[] minimised_values; free_dmatrix(initial_values, 1, number_of_dimensions + 2, 1, number_of_dimensions + 1); } void DownhillSimplex::Setup() { minimised_values = new double[number_of_dimensions + 2]; initial_values=dmatrix(1, number_of_dimensions + 2, 1, number_of_dimensions + 1); } void DownhillSimplex::amoeba(double **p, double y[], long ndim, double ftol, double funk(double []), long *nfunk) { long i,ihi,ilo,inhi,j,mpts=ndim+1; double rtol,sum,swap,ysave,ytry,*psum; psum=dvector(1,ndim); *nfunk=0; for (j=1;j<=ndim;j++) { for (sum=0.0,i=1;i<=mpts;i++) sum += p[i][j]; psum[j]=sum; } for (;;) { ilo=1; ihi = y[1]>y[2] ? (inhi=2,1) : (inhi=1,2); for (i=1;i<=mpts;i++) { if (y[i] <= y[ilo]) ilo=i; if (y[i] > y[ihi]) { inhi=ihi; ihi=i; } else if (y[i] > y[inhi] && i != ihi) inhi=i; } rtol=2.0*fabs(y[ihi]-y[ilo])/(fabs(y[ihi])+fabs(y[ilo])+1.0e-10); if (rtol < ftol) { {swap=y[1];y[1]=y[ilo];y[ilo]=swap;} for (i=1;i<=ndim;i++) {swap=p[1][i];p[1][i]=p[ilo][i];p[ilo][i]=swap;} break; } *nfunk +=2; ytry=amotry(p,y,psum,ndim,funk,ihi,-1.0); if (ytry<=y[ilo]) ytry=amotry(p,y,psum,ndim,funk,ihi,2.0);/////////////////// else if (ytry >= y[inhi]) { ysave=y[ihi]; ytry=amotry(p,y,psum,ndim,funk,ihi,0.5); if (ytry >= ysave) { for (i=1;i<=mpts;i++) { if (i != ilo) { for (j=1;j<=ndim;j++) p[i][j]=psum[j]=0.5*(p[i][j]+p[ilo][j]); y[i]=funk(psum); } } *nfunk += ndim; for (j=1;j<=ndim;j++) { for (sum=0.0,i=1;i<=mpts;i++) sum += p[i][j]; psum[j]=sum; } } } else --(*nfunk); } free_dvector(psum,1,ndim); } void DownhillSimplex::amoeba(double **p, double y[], long ndim, double ftol, void *pt2Object, double (*callback)(void* pt2Object, double []), long *nfunk) { long i,ihi,ilo,inhi,j,mpts=ndim+1; double rtol,sum,swap,ysave,ytry,*psum; psum=dvector(1,ndim); *nfunk=0; for (j=1;j<=ndim;j++) { for (sum=0.0,i=1;i<=mpts;i++) sum += p[i][j]; psum[j]=sum; } for (;;) { ilo=1; ihi = y[1]>y[2] ? (inhi=2,1) : (inhi=1,2); for (i=1;i<=mpts;i++) { if (y[i] <= y[ilo]) ilo=i; if (y[i] > y[ihi]) { inhi=ihi; ihi=i; } else if (y[i] > y[inhi] && i != ihi) inhi=i; } rtol=2.0*fabs(y[ihi]-y[ilo])/(fabs(y[ihi])+fabs(y[ilo])+1.0e-10); if (rtol < ftol) { {swap=y[1];y[1]=y[ilo];y[ilo]=swap;} for (i=1;i<=ndim;i++) {swap=p[1][i];p[1][i]=p[ilo][i];p[ilo][i]=swap;} break; } *nfunk +=2; ytry=amotry(p,y,psum,ndim,pt2Object,callback,ihi,-1.0); if (ytry<=y[ilo]) ytry=amotry(p,y,psum,ndim,pt2Object,callback,ihi,2.0);/////////////////// else if (ytry >= y[inhi]) { ysave=y[ihi]; ytry=amotry(p,y,psum,ndim,pt2Object,callback,ihi,0.5); if (ytry >= ysave) { for (i=1;i<=mpts;i++) { if (i != ilo) { for (j=1;j<=ndim;j++) p[i][j]=psum[j]=0.5*(p[i][j]+p[ilo][j]); y[i]=callback(pt2Object,psum); } } *nfunk += ndim; for (j=1;j<=ndim;j++) { for (sum=0.0,i=1;i<=mpts;i++) sum += p[i][j]; psum[j]=sum; } } } else --(*nfunk); } free_dvector(psum,1,ndim); } double DownhillSimplex::amotry(double **p,double y[], double psum[], long ndim, double funk(double []), long ihi, double fac) { long j; double fac1,fac2,ytry,*ptry; ptry=dvector(1,ndim); fac1=(1.0-fac)/ndim; fac2=fac1-fac; for (j=1;j<=ndim;j++) ptry[j]=psum[j]*fac1-p[ihi][j]*fac2; ytry=funk(ptry); if (ytry < y[ihi]) { y[ihi]=ytry; for (j=1;j<=ndim;j++) { psum[j] +=ptry[j]-p[ihi][j]; p[ihi][j]=ptry[j]; } } free_dvector(ptry,1,ndim); //prlongf("f=%lf,",ytry); return ytry; } double DownhillSimplex::amotry(double **p,double y[], double psum[], long ndim, void *pt2Object, double (*callback)(void* pt2Object, double []), long ihi, double fac) { long j; double fac1,fac2,ytry,*ptry; ptry=dvector(1,ndim); fac1=(1.0-fac)/ndim; fac2=fac1-fac; for (j=1;j<=ndim;j++) ptry[j]=psum[j]*fac1-p[ihi][j]*fac2; ytry=callback(pt2Object,ptry); if (ytry < y[ihi]) { y[ihi]=ytry; for (j=1;j<=ndim;j++) { psum[j] +=ptry[j]-p[ihi][j]; p[ihi][j]=ptry[j]; } } free_dvector(ptry,1,ndim); //prlongf("f=%lf,",ytry); return ytry; } void DownhillSimplex::minimise_function(double function_to_min(double [])) { long nfunk = 0; // hold the number of evaluations y = dvector(1, number_of_dimensions + 2); p = dmatrix(1, number_of_dimensions + 2, 1, number_of_dimensions +1); // fill p... blank minimised values for(long i=1; i<= number_of_dimensions+1 ; i++) { for (long i2 = 1; i2 <= number_of_dimensions +1; i2++) { p[i][i2] = initial_values[i][i2]; } minimised_values[i] = 0; } // evaluate the starting values... for(long i=1; i<= number_of_dimensions+1 ; i++) { y[i] = function_to_min(p[i]); } // do the minimisation amoeba(p, y, number_of_dimensions, tolerance, function_to_min, &nfunk); // do another (should be cheap) amoeba(p, y, number_of_dimensions, tolerance, function_to_min, &nfunk); // return the best values (middle of the simplex) for(long i=1; i<= number_of_dimensions; i++) { minimised_values[i] = p[1][i]; } } void DownhillSimplex::minimise_function(void *pt2Object, double (*callback)(void* pt2Object, double [])) { long nfunk = 0; // hold the number of evaluations y = dvector(1, number_of_dimensions + 2); p = dmatrix(1, number_of_dimensions + 2, 1, number_of_dimensions +1); // fill p... blank minimised values for(long i=1; i<= number_of_dimensions+1 ; i++) { for (long i2 = 1; i2 <= number_of_dimensions +1; i2++) { p[i][i2] = initial_values[i][i2]; } minimised_values[i] = 0; } // evaluate the starting values... for(long i=1; i<= number_of_dimensions+1 ; i++) { y[i] = callback(pt2Object, p[i]); } // do the minimisation amoeba(p, y, number_of_dimensions, tolerance, pt2Object, callback, &nfunk); // do another (should be cheap) amoeba(p, y, number_of_dimensions, tolerance, pt2Object, callback, &nfunk); // return the best values (middle of the simplex) for(long i=1; i<= number_of_dimensions; i++) { minimised_values[i] = p[1][i]; } } double *DownhillSimplex::dvector(long nl,long nh) { double *v; v=(double *)malloc((unsigned) (nh-nl+1)*sizeof(double)); if (!v) { MyPrintWithDetails("Allocation failure in dvector()\n"); DEBUG_ABORT; } return v-nl; } double **DownhillSimplex::dmatrix(long nrl, long nrh, long ncl, long nch) { long i; double **m; m=(double **) malloc((unsigned) (nrh-nrl+1)*sizeof(double*)); if (!m) { MyPrintWithDetails("Allocation failure in dmatrix()\n"); DEBUG_ABORT; } m -= nrl; for(i=nrl;i<=nrh;i++) { m[i]=(double *) malloc((unsigned) (nch-ncl+1)*sizeof(double)); if (!m[i]) { MyPrintWithDetails("Allocation failure in dmatrix()\n"); DEBUG_ABORT; } m[i] -= ncl; } return m; } void DownhillSimplex::free_dvector(double *v, long nl, long nh) { free((char*) (v+nl)); } void DownhillSimplex::free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch) { long i; for(i=nrh;i>=nrl;i--) free((char*) (m[i]+ncl)); free((char*) (m+nrl)); } ctffind-4.1.14/src/core/downhill_simplex.h000066400000000000000000000062401440356052600204760ustar00rootroot00000000000000// // DownhillSimplex // // Timothy Grant // // 20061007 // // // Downhill simplex function minimisation, this is all stolen from // numerical recipes. you have to set the initial_values, call // minimise function, and the minimised result will be placed in // minimised values // // TO USE // // You must have a setup DownhillSimplex object, either by constructing // with the number of required dimensions (default is 1), or by setting // the number of dimensions and then calling setup. // // You must then input your starting values, they are set to 0 as default. // There are number_of_dimensions squared starting values, or polongs on // the simplex. for example if you have 3 dimensions x, y, z // // initial_values[0][0] = first x // initial_values[0][1] = first y // initial_values[0][2] = first z // // initial_values[1][0] = second x // initial_values[1][1] = second y // initial_values[1][2] = second z // // and so on, and so on. When these are set, you can call the // minimise function routine, in which you must specify the function // to minimise. You setup this function yourself, and it must take // a double[number_of_dimensions] input (the values currently being // evaluated) and return a double (the result of the evaluation). // // The function will hopefully return the values in minimised_values // that lead to the minimum value. (This is a minimization, if you // are looking for a maximum, return 1 / your result // // class DownhillSimplex { /////////////////////////////////////////////////////////////////////////////// // Private stuff, these are the functions stolen from NR, they don't // // need to be called directly. // /////////////////////////////////////////////////////////////////////////////// void amoeba(double **p, double y[], long ndim, double ftol, double funk(double []), long *nfunk); void amoeba(double **p, double y[], long ndim, double ftol, void *pt2Object, double (*callback)(void* pt2Object, double []), long *nfunk); double amotry(double **p,double y[], double psum[], long ndim, double funk(double []), long ihi, double fac); double amotry(double **p,double y[], double psum[], long ndim, void *pt2Object, double (*callback)(void* pt2Object, double []), long ihi, double fac); double *dvector(long nl, long nh); double **dmatrix(long nrl, long nrh, long ncl, long nch); void free_dvector(double *v, long nl, long nh); void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch); double **p; // input values double *y; // evaluated results public: double **initial_values; double *minimised_values; long number_of_dimensions; double tolerance; // Constructors DownhillSimplex(); DownhillSimplex(long set_number_of_dimensions); // Destructors ~DownhillSimplex(); // Functions void Setup(); void minimise_function(double function_to_min(double [])); void minimise_function(void *pt2Object, double (*callback)(void* pt2Object, double [])); }; ctffind-4.1.14/src/core/electron_dose.h000066400000000000000000000016661440356052600177510ustar00rootroot00000000000000class ElectronDose { private: public: float acceleration_voltage; float critical_dose_a; float critical_dose_b; float critical_dose_c; float voltage_scaling_factor; float pixel_size; ElectronDose(); ElectronDose(float wanted_acceleration_voltage, float wanted_pixel_size); void Init(float wanted_acceleration_voltage, float wanted_pixel_size); float ReturnCriticalDose(float spatial_frequency); float ReturnDoseFilter(float dose_at_end_of_frame, float critical_dose); void CalculateDoseFilterAs1DArray(Image *ref_image, float *filter_array, float dose_start, float dose_finish); }; inline float ElectronDose::ReturnCriticalDose(float spatial_frequency) { return (critical_dose_a * pow(spatial_frequency, critical_dose_b) + critical_dose_c) * voltage_scaling_factor; } inline float ElectronDose::ReturnDoseFilter(float dose_at_end_of_frame, float critical_dose) { return exp((-0.5 * dose_at_end_of_frame) / critical_dose); } ctffind-4.1.14/src/core/empirical_distribution.cpp000066400000000000000000000034511440356052600222150ustar00rootroot00000000000000#include "core_headers.h" // Initialise an empirical distribution EmpiricalDistribution::EmpiricalDistribution() { Reset(); } EmpiricalDistribution::~EmpiricalDistribution() { // Here, would deallocate sample_values array } void EmpiricalDistribution::Reset() { sum_of_samples = 0.0; sum_of_squared_samples = 0.0; number_of_samples = 0; minimum = std::numeric_limits::max(); maximum = - std::numeric_limits::max(); is_constant = true; last_added_value = 0.0; } void EmpiricalDistribution::AddSampleValue(float sample_value) { sum_of_samples += sample_value; sum_of_squared_samples += pow(sample_value,2); number_of_samples++; minimum = std::min(minimum,sample_value); maximum = std::max(maximum,sample_value); if (number_of_samples == 1) { is_constant = true; } else { is_constant = is_constant && last_added_value == sample_value; } last_added_value = sample_value; } bool EmpiricalDistribution::IsConstant() { return is_constant; } float EmpiricalDistribution::GetSampleSumOfSquares() { return sum_of_squared_samples; } long EmpiricalDistribution::GetNumberOfSamples() { return number_of_samples; } float EmpiricalDistribution::GetSampleSum() { return sum_of_samples; } float EmpiricalDistribution::GetSampleMean() { if (number_of_samples > 0) { return sum_of_samples / float(number_of_samples); } else { return 0.0; } } float EmpiricalDistribution::GetSampleVariance() { if (number_of_samples > 0) { return (sum_of_squared_samples / float(number_of_samples)) - pow(sum_of_samples/float(number_of_samples),2); } else { return 0.0; } } float EmpiricalDistribution::GetUnbiasedEstimateOfPopulationVariance() { if (number_of_samples > 0) { return GetSampleVariance() * float(number_of_samples) / float(number_of_samples-1); } else { return 0.0; } } ctffind-4.1.14/src/core/empirical_distribution.h000066400000000000000000000012531440356052600216600ustar00rootroot00000000000000class EmpiricalDistribution { private: double sum_of_samples; double sum_of_squared_samples; long number_of_samples; float minimum; float maximum; bool is_constant; float last_added_value; public: // Constructors, destructors EmpiricalDistribution(); ~EmpiricalDistribution(); void AddSampleValue(float sample_value); long GetNumberOfSamples(); float GetSampleSum(); float GetSampleMean(); float GetSampleVariance(); float GetSampleSumOfSquares(); float GetUnbiasedEstimateOfPopulationVariance(); inline float GetMinimum() {return minimum;}; inline float GetMaximum() {return maximum;}; bool IsConstant(); void PopulateHistogram(); void Reset(); }; ctffind-4.1.14/src/core/euler_search.h000066400000000000000000000035611440356052600175610ustar00rootroot00000000000000class EulerSearch { // Brute-force search to find matching projections public: int number_of_search_dimensions; int refine_top_N; int number_of_search_positions; int best_parameters_to_keep; float angular_step_size; float max_search_x; float max_search_y; float phi_max; float phi_start; float theta_max; float theta_start; float psi_max; float psi_step; float psi_start; float **list_of_search_parameters; float **list_of_best_parameters; // Kernel2D **kernel_index; // float *best_values; // float best_score; float resolution_limit; bool *parameter_map; bool test_mirror; wxString symmetry_symbol; // Constructors & destructors EulerSearch(); ~EulerSearch(); // Methods void Init(float wanted_resolution_limit, bool *wanted_parameter_map, int wanted_parameters_to_keep); void InitGrid(wxString wanted_symmetry_symbol, float angular_step_size, float wanted_phi_start, float wanted_theta_start, float wanted_psi_max, float wanted_psi_step, float wanted_psi_start, float wanted_resolution_limit, bool *parameter_map, int wanted_parameters_to_keep); void InitRandom(wxString wanted_symmetry_symbol, float wanted_psi_step, int wanted_number_of_search_positions, float wanted_resolution_limit, bool *wanted_parameter_map, int wanted_parameters_to_keep); void Run(Particle &particle, Image &input_3d, float *starting_values, Image *projections); void CalculateGridSearchPositions(bool random_start_angle = true); void CalculateRandomSearchPositions(); void SetSymmetryLimits(); // void RotateFourier2DFromIndex(Image &image_to_rotate, Image &rotated_image, Kernel2D &kernel_index); // void RotateFourier2DIndex(Image &image_to_rotate, Kernel2D &kernel_index, AnglesAndShifts &rotation_angle, float resolution_limit = 1.0, float padding_factor = 1.0); Kernel2D ReturnLinearInterpolatedFourierKernel2D(Image &image_to_rotate, float &x, float &y); }; ctffind-4.1.14/src/core/f2c.h000066400000000000000000000111061440356052600155640ustar00rootroot00000000000000/* f2c.h -- Standard Fortran to C header file */ /** barf [ba:rf] 2. "He suggested using FORTRAN, and everybody barfed." - From The Shogakukan DICTIONARY OF NEW ENGLISH (Second edition) */ #ifndef F2C_INCLUDE #define F2C_INCLUDE typedef int integer; typedef unsigned int uinteger; typedef char *address; typedef short int shortint; typedef float real; typedef double doublereal; typedef struct { real r, i; } complex; typedef struct { doublereal r, i; } doublecomplex; typedef long int logical; typedef short int shortlogical; typedef char logical1; typedef char integer1; #ifdef INTEGER_STAR_8 /* Adjust for integer*8. */ typedef long long longint; /* system-dependent */ typedef unsigned long long ulongint; /* system-dependent */ #define qbit_clear(a,b) ((a) & ~((ulongint)1 << (b))) #define qbit_set(a,b) ((a) | ((ulongint)1 << (b))) #endif #define TRUE_ (1) #define FALSE_ (0) /* Extern is for use with -E */ #ifndef Extern #define Extern extern #endif /* I/O stuff */ #ifdef f2c_i2 /* for -i2 */ typedef short flag; typedef short ftnlen; typedef short ftnint; #else typedef long int flag; typedef long int ftnlen; typedef long int ftnint; #endif /*external read, write*/ typedef struct { flag cierr; ftnint ciunit; flag ciend; char *cifmt; ftnint cirec; } cilist; /*internal read, write*/ typedef struct { flag icierr; char *iciunit; flag iciend; char *icifmt; ftnint icirlen; ftnint icirnum; } icilist; /*open*/ typedef struct { flag oerr; ftnint ounit; char *ofnm; ftnlen ofnmlen; char *osta; char *oacc; char *ofm; ftnint orl; char *oblnk; } olist; /*close*/ typedef struct { flag cerr; ftnint cunit; char *csta; } cllist; /*rewind, backspace, endfile*/ typedef struct { flag aerr; ftnint aunit; } alist; /* inquire */ typedef struct { flag inerr; ftnint inunit; char *infile; ftnlen infilen; ftnint *inex; /*parameters in standard's order*/ ftnint *inopen; ftnint *innum; ftnint *innamed; char *inname; ftnlen innamlen; char *inacc; ftnlen inacclen; char *inseq; ftnlen inseqlen; char *indir; ftnlen indirlen; char *infmt; ftnlen infmtlen; char *inform; ftnint informlen; char *inunf; ftnlen inunflen; ftnint *inrecl; ftnint *innrec; char *inblank; ftnlen inblanklen; } inlist; #define VOID void union Multitype { /* for multiple entry points */ integer1 g; shortint h; integer i; /* longint j; */ real r; doublereal d; complex c; doublecomplex z; }; typedef union Multitype Multitype; /*typedef long int Long;*/ /* No longer used; formerly in Namelist */ struct Vardesc { /* for Namelist */ char *name; char *addr; ftnlen *dims; int type; }; typedef struct Vardesc Vardesc; struct Namelist { char *name; Vardesc **vars; int nvars; }; typedef struct Namelist Namelist; #define abs(x) ((x) >= 0 ? (x) : -(x)) #define dabs(x) (doublereal)abs(x) #define min(a,b) ((a) <= (b) ? (a) : (b)) #define max(a,b) ((a) >= (b) ? (a) : (b)) #define dmin(a,b) (doublereal)min(a,b) #define dmax(a,b) (doublereal)max(a,b) #define bit_test(a,b) ((a) >> (b) & 1) #define bit_clear(a,b) ((a) & ~((uinteger)1 << (b))) #define bit_set(a,b) ((a) | ((uinteger)1 << (b))) /* procedure parameter types for -A and -C++ */ #define F2C_proc_par_types 1 #ifdef __cplusplus typedef int /* Unknown procedure type */ (*U_fp)(...); typedef shortint (*J_fp)(...); typedef integer (*I_fp)(...); typedef real (*R_fp)(...); typedef doublereal (*D_fp)(...), (*E_fp)(...); typedef /* Complex */ VOID (*C_fp)(...); typedef /* Double Complex */ VOID (*Z_fp)(...); typedef logical (*L_fp)(...); typedef shortlogical (*K_fp)(...); typedef /* Character */ VOID (*H_fp)(...); typedef /* Subroutine */ int (*S_fp)(...); #else typedef int /* Unknown procedure type */ (*U_fp)(); typedef shortint (*J_fp)(); typedef integer (*I_fp)(); typedef real (*R_fp)(); typedef doublereal (*D_fp)(), (*E_fp)(); typedef /* Complex */ VOID (*C_fp)(); typedef /* Double Complex */ VOID (*Z_fp)(); typedef logical (*L_fp)(); typedef shortlogical (*K_fp)(); typedef /* Character */ VOID (*H_fp)(); typedef /* Subroutine */ int (*S_fp)(); #endif /* E_fp is for real functions when -R is not specified */ typedef VOID C_f; /* complex function */ typedef VOID H_f; /* character function */ typedef VOID Z_f; /* double complex function */ typedef doublereal E_f; /* real function with -R not specified */ /* undef any lower-case symbols that your C compiler predefines, e.g.: */ #ifndef Skip_f2c_Undefs #undef cray #undef gcos #undef mc68010 #undef mc68020 #undef mips #undef pdp11 #undef sgi #undef sparc #undef sun #undef sun2 #undef sun3 #undef sun4 #undef u370 #undef u3b #undef u3b2 #undef u3b5 #undef unix #undef vax #endif #endif ctffind-4.1.14/src/core/frealign_parameter_file.h000066400000000000000000000040751440356052600217470ustar00rootroot00000000000000/* \brief FrealignParameterFile class */ class FrealignParameterFile { public: FILE *parameter_file; wxString filename; int access_type; int records_per_line; int number_of_lines; int current_line; float *parameter_cache; float average_defocus; float defocus_coeff_a; float defocus_coeff_b; FrealignParameterFile(); ~FrealignParameterFile(); FrealignParameterFile(wxString wanted_filename, int wanted_access_type, int wanted_records_per_line = 17); void Open(wxString wanted_filename, int wanted_access_type, int wanted_records_per_line = 17); void Close(); void WriteCommentLine(wxString comment_string); void WriteLine(float *parameters, bool comment = false); int ReadFile(bool exclude_negative_film_numbers = false, int particles_in_stack = -1); void ReadLine(float *parameters, int wanted_line_number = -1); float ReadParameter(int wanted_line_number, int wanted_index); void UpdateParameter(int wanted_line_number, int wanted_index, float wanted_value); void Rewind(); float ReturnMin(int wanted_index, bool exclude_negative_film_numbers = false); float ReturnMax(int wanted_index, bool exclude_negative_film_numbers = false); double ReturnAverage(int wanted_index, bool exclude_negative_film_numbers = false); void RemoveOutliers(int wanted_index, float wanted_standard_deviation, bool exclude_negative_film_numbers = false, bool reciprocal_square = false); float ReturnThreshold(float wanted_percentage, bool exclude_negative_film_numbers = false); void CalculateDefocusDependence(bool exclude_negative_film_numbers = false); void AdjustScores(bool exclude_negative_film_numbers = false); float ReturnScoreAdjustment(float defocus); void ReduceAngles(); float ReturnDistributionMax(int wanted_index, int selector = 0, bool exclude_negative_film_numbers = false); float ReturnDistributionSigma(int wanted_index, float distribution_max, int selector = 0, bool exclude_negative_film_numbers = false); void SetParameters(int wanted_index, float wanted_value, float wanted_sigma = 0.0, int selector = 0, bool exclude_negative_film_numbers = false); }; ctffind-4.1.14/src/core/functions.cpp000066400000000000000000000705221440356052600174640ustar00rootroot00000000000000#include "core_headers.h" // for ip address #include #include #include #include #include #include /** @brief Swaps bytes. @param *v a pointer to the bytes. @param n number of bytes to swap. Byte swapping is done in place. **/ void swapbytes(unsigned char* v, size_t n) { unsigned char t; size_t i; for ( i=0, n--; i file_byte_size) { fclose(input); return false; } if (x_size < 1 || y_size < 1 || number_of_images < 1) { fclose(input); return false; } } fclose(input); return true; } // Assumption is that turning off of events etc has been done, and that // all other considerations have done. void SendwxStringToSocket(wxString *string_to_send, wxSocketBase *socket) { wxCharBuffer buffer = string_to_send->mb_str(); int length_of_string = buffer.length(); unsigned char *char_pointer; // send the length of the string, followed by the string char_pointer = (unsigned char*)&length_of_string; WriteToSocket(socket, char_pointer, 4, true); WriteToSocket(socket, buffer.data(), length_of_string, true); } // This is here as when the binned resolution is too close to the refinement resolution or reconstruction // resolution (could be 1 or other or both), then it seems to cause some problems - e.g. in Proteasome. // I'm going to add a 1.3 factor here, but this can be changed. // // My plan is to use this function all the places it is calculated in the code, so that changing it here will change // it everywhere. int ReturnSafeBinnedBoxSize(int original_box_size, float bin_factor) { //return (original_box_size / bin_factor) * 1.3f; return myroundint(float(original_box_size) / bin_factor); } wxString ReceivewxStringFromSocket(wxSocketBase *socket) { int length_of_string; unsigned char *char_pointer; // receive the length of the string, followed by the string char_pointer = (unsigned char*)&length_of_string; ReadFromSocket(socket, char_pointer, 4, true); // setup a temp array to receive the string into. unsigned char *transfer_buffer = new unsigned char[length_of_string + 1]; // + 1 for the terminating null character; ReadFromSocket(socket, transfer_buffer, length_of_string, true); // add the null transfer_buffer[length_of_string] = 0; // make a wxstring from this buffer.. wxString temp_string(transfer_buffer); // delete the buffer delete [] transfer_buffer; return temp_string; } wxArrayString ReturnIPAddress() { struct ifaddrs * ifAddrStruct=NULL; struct ifaddrs * ifa=NULL; void * tmpAddrPtr=NULL; char addressBuffer[INET_ADDRSTRLEN + 1]; wxString ip_address; wxArrayString all_ip_addresses; for (int counter = 0; counter <= INET_ADDRSTRLEN; counter++) { addressBuffer[counter] = 0; } getifaddrs(&ifAddrStruct); for (ifa = ifAddrStruct; ifa != NULL; ifa = ifa->ifa_next) { if (!ifa->ifa_addr) { continue; } if (ifa->ifa_addr->sa_family == AF_INET) { // check it is IP4 // is a valid IP4 Address tmpAddrPtr=&((struct sockaddr_in *)ifa->ifa_addr)->sin_addr; inet_ntop(AF_INET, tmpAddrPtr, addressBuffer, INET_ADDRSTRLEN); ip_address = addressBuffer; ip_address.Trim(); ip_address.Trim(false); if (ip_address.Find("127.0.0.1") == wxNOT_FOUND) all_ip_addresses.Add(ip_address); //if (memcmp(addressBuffer, "127.0.0.1", INET_ADDRSTRLEN) != 0) ip_address = addressBuffer; //if (memcmp(addressBuffer, "127.0.0.1", INET_ADDRSTRLEN) != 0) all_ip_addresses.Add(addressBuffer); } } all_ip_addresses.Add("127.0.0.1"); /* wxPrintf("There are %li ip addresses\n", all_ip_addresses.GetCount()); for (int counter = 0; counter < all_ip_addresses.GetCount(); counter++) { wxPrintf("%i = %s\n", counter, all_ip_addresses.Item(counter)); }*/ if (ifAddrStruct!=NULL) freeifaddrs(ifAddrStruct); return all_ip_addresses; } wxString ReturnIPAddressFromSocket(wxSocketBase *socket) { wxString ip_address; wxIPV4address my_address; socket->GetLocal(my_address); ip_address = my_address.IPAddress(); // is this 127.0.0.1 - in which case it may cause trouble.. /* if (ip_address == "127.0.0.1") { ip_address = ""; //ip_address = ReturnIPAddress(); // last chance to get a non loopback address }*/ return ip_address; } /* * * String manipulations * */ std::string FilenameReplaceExtension(std::string filename, std::string new_extension) { return filename.substr(0,filename.find_last_of('.')+1)+new_extension; } std::string FilenameAddSuffix(std::string filename, std::string suffix_to_add) { return filename.substr(0,filename.find_last_of('.')) + suffix_to_add + filename.substr(filename.find_last_of('.'), filename.length() - 1); } int ReturnClosestFactorizedUpper(int wanted_int, int largest_factor, bool enforce_even) { int number; int remainder = wanted_int; int factor; int temp_int; if (enforce_even) { temp_int = wanted_int; if (! IsEven(temp_int)) temp_int++; for (number = temp_int; number < 10000 * wanted_int; number += 2) { remainder = number; for (factor = 2; (factor <= largest_factor) && (remainder != 1); factor++) { temp_int = remainder % factor; while (temp_int == 0) { remainder /= factor; temp_int = remainder % factor; } } if (remainder == 1) break; } } else { for (number = wanted_int; number < 10000 * wanted_int; number++) { remainder = number; for (factor = 2; (factor <= largest_factor) && (remainder != 1); factor++) { temp_int = remainder % factor; while (temp_int == 0) { remainder /= factor; temp_int = remainder % factor; } } if (remainder == 1) break; } } return number; } int ReturnClosestFactorizedLower(int wanted_int, int largest_factor, bool enforce_even) { int number; int remainder = wanted_int; int factor; int temp_int; if (enforce_even) { temp_int = wanted_int; if (! IsEven(temp_int)) temp_int--; for (number = temp_int; number >= 2; number -= 2) { remainder = number; for (factor = 2; (factor <= largest_factor) && (remainder != 1); factor++) { temp_int = remainder % factor; while (temp_int == 0) { remainder /= factor; temp_int = remainder % factor; } } if (remainder == 1) break; } } else { for (number = wanted_int; number >= 1; number--) { remainder = number; for (factor = 2; (factor <= largest_factor) && (remainder != 1); factor++) { temp_int = remainder % factor; while (temp_int == 0) { remainder /= factor; temp_int = remainder % factor; } } if (remainder == 1) break; } } return number; } float CalculateAngularStep(float required_resolution, float radius_in_angstroms) { return 360.0 * required_resolution / PI / radius_in_angstroms; } void Allocate2DFloatArray(float **&array, int dim1, int dim2) { array = new float* [dim1]; // dynamic array of pointers to float for (int i = 0; i < dim1; ++i) { array[i] = new float[dim2]; // each i-th pointer is now pointing to dynamic array (size number_of_positions) of actual float values } } void Deallocate2DFloatArray(float **&array, int dim1) { for (int i = 0; i < dim1; ++i) { delete [] array[i]; // each i-th pointer must be deleted first } delete [] array; // now delete pointer array } long ReturnFileSizeInBytes(wxString filename) { long size; std::ifstream filesize(filename, std::ifstream::ate | std::ifstream::binary); size = filesize.tellg(); filesize.close(); return size; } void CheckSocketForError(wxSocketBase *socket_to_check) { if (socket_to_check->Error() == true) { wxPrintf("Socket Error : "); switch(socket_to_check->LastError()) { case wxSOCKET_NOERROR : wxPrintf("No Error!\n"); break; case wxSOCKET_INVOP : wxPrintf("Invalid Operation.\n"); break; case wxSOCKET_IOERR : wxPrintf("Input/Output error.\n"); break; case wxSOCKET_INVADDR : wxPrintf("Invalid address passed to wxSocket.\n"); break; case wxSOCKET_INVSOCK : wxPrintf("Invalid socket (uninitialized).\n"); break; case wxSOCKET_NOHOST : wxPrintf("No corresponding host.\n"); break; case wxSOCKET_INVPORT : wxPrintf("Invalid port.\n"); break; case wxSOCKET_WOULDBLOCK : wxPrintf("The socket is non-blocking and the operation would block.\n"); break; case wxSOCKET_TIMEDOUT : wxPrintf("The timeout for this operation expired.\n"); break; case wxSOCKET_MEMERR : wxPrintf("Memory exhausted.\n"); break; // you can have any number of case statements. default : wxPrintf("unknown.\n"); } } } wxString ReturnSocketErrorText(wxSocketBase *socket_to_check) { if (socket_to_check->Error() == true) { switch(socket_to_check->LastError()) { case wxSOCKET_NOERROR : return "No Error!"; break; case wxSOCKET_INVOP : return "Invalid Operation."; break; case wxSOCKET_IOERR : return "Input/Output error"; break; case wxSOCKET_INVADDR : return "Invalid address passed to wxSocket."; break; case wxSOCKET_INVSOCK : return "Invalid socket (uninitialized)."; break; case wxSOCKET_NOHOST : return "No corresponding host."; break; case wxSOCKET_INVPORT : return "Invalid port."; break; case wxSOCKET_WOULDBLOCK : return ("The socket is non-blocking and the operation would block"); break; case wxSOCKET_TIMEDOUT : return "The timeout for this operation expired."; break; case wxSOCKET_MEMERR : return "Memory exhausted."; break; // you can have any number of case statements. default : return("Unknown error."); } } else return "Error, not set."; } float ReturnSumOfLogP(float logp1, float logp2, float log_range = 20.0) { float logp; if (logp2 < logp1 - log_range) { logp = logp1; } else if (logp1 < logp2 - log_range) { logp = logp2; } else { logp = logp1 + log(double(1.0) + exp(double(logp2) - double(logp1))); } return logp; } float ReturnMagDistortionCorrectedPixelSize(float original_pixel_size, float major_axis_scale, float minor_axis_scale) { float average_scale = (major_axis_scale + minor_axis_scale) / 2.0; return original_pixel_size / average_scale; } void SplitFileIntoDirectoryAndFile(wxString &input_file, wxString &output_directory, wxString &output_file) { wxFileName current_filename = input_file; wxArrayString directories = current_filename.GetDirs(); output_directory = "/"; for (int directory_counter = 0; directory_counter < directories.GetCount(); directory_counter++) { output_directory += directories.Item(directory_counter); output_directory += "/"; } output_file = current_filename.GetFullName(); } int ReturnNumberofAsymmetricUnits(wxString symmetry) { wxString current_symmetry_string = symmetry; wxChar symmetry_type; long symmetry_number; current_symmetry_string = current_symmetry_string.Trim(); current_symmetry_string = current_symmetry_string.Trim(false); MyDebugAssertTrue(current_symmetry_string.Length() > 0, "symmetry string is blank"); symmetry_type = current_symmetry_string.Capitalize()[0]; if (current_symmetry_string.Length() == 1) { symmetry_number = 0; } else { if (! current_symmetry_string.Mid(1).ToLong(&symmetry_number)) { MyPrintWithDetails("Error: Invalid n after symmetry symbol: %s\n", current_symmetry_string.Mid(1)); DEBUG_ABORT; } } if (symmetry_type == 'C') { return int(symmetry_number); } else if (symmetry_type == 'D') { return int(symmetry_number * 2); } else if (symmetry_type == 'T') { return 12; } else if (symmetry_type == 'O') { return 24; } else if (symmetry_type == 'I') { return 60; } // shouldn't get here return 1; } // Return a vector with the rank of the elements of the input array std::vector rankSort(const float* v_temp, const size_t size) { std::vector > v_sort(size); for (size_t i = 0U; i < size; ++i) { v_sort[i] = std::make_pair(v_temp[i], i); } sort(v_sort.begin(), v_sort.end()); std::pair rank; std::vector result(size); for (size_t i = 0U; i < size; ++i) { if (v_sort[i].first != rank.first) { rank = std::make_pair(v_sort[i].first, i); } result[v_sort[i].second] = rank.second; } return result; } std::vector rankSort(const std::vector& v_temp) { std::vector > v_sort(v_temp.size()); for (size_t i = 0U; i < v_sort.size(); ++i) { v_sort[i] = std::make_pair(v_temp[i], i); } sort(v_sort.begin(), v_sort.end()); std::pair rank; std::vector result(v_temp.size()); for (size_t i = 0U; i < v_sort.size(); ++i) { if (v_sort[i].first != rank.first) { rank = std::make_pair(v_sort[i].first, i); } result[v_sort[i].second] = rank.second; } return result; } wxString StringFromSocketCode(unsigned char *socket_input_buffer) { if (memcmp(socket_input_buffer, socket_please_identify, SOCKET_CODE_SIZE) == 0) { return "socket_please_identify"; } if (memcmp(socket_input_buffer, socket_identification, SOCKET_CODE_SIZE) == 0) { return "socket_identification"; } if (memcmp(socket_input_buffer, socket_you_are_connected, SOCKET_CODE_SIZE) == 0) { return "socket_you_are_connected"; } if (memcmp(socket_input_buffer, socket_send_job_details, SOCKET_CODE_SIZE) == 0) { return "socket_send_job_details"; } if (memcmp(socket_input_buffer, socket_ready_to_send_job_package, SOCKET_CODE_SIZE) == 0) { return "socket_ready_to_send_job_package"; } if (memcmp(socket_input_buffer, socket_send_job_package, SOCKET_CODE_SIZE) == 0) { return "socket_send_job_package"; } if (memcmp(socket_input_buffer, socket_you_are_the_master, SOCKET_CODE_SIZE) == 0) { return "socket_you_are_the_master"; } if (memcmp(socket_input_buffer, socket_you_are_a_slave, SOCKET_CODE_SIZE) == 0) { return "socket_you_are_a_slave"; } if (memcmp(socket_input_buffer, socket_send_next_job, SOCKET_CODE_SIZE) == 0) { return "socket_send_next_job"; } if (memcmp(socket_input_buffer, socket_time_to_die, SOCKET_CODE_SIZE) == 0) { return "socket_time_to_die"; } if (memcmp(socket_input_buffer, socket_ready_to_send_single_job, SOCKET_CODE_SIZE) == 0) { return "socket_ready_to_send_single_job"; } if (memcmp(socket_input_buffer, socket_send_single_job, SOCKET_CODE_SIZE) == 0) { return "socket_send_single_job"; } if (memcmp(socket_input_buffer, socket_i_have_an_error, SOCKET_CODE_SIZE) == 0) { return "socket_i_have_an_error"; } if (memcmp(socket_input_buffer, socket_i_have_info, SOCKET_CODE_SIZE) == 0) { return "socket_i_have_info"; } if (memcmp(socket_input_buffer, socket_job_finished, SOCKET_CODE_SIZE) == 0) { return "socket_job_finished"; } if (memcmp(socket_input_buffer, socket_number_of_connections, SOCKET_CODE_SIZE) == 0) { return "socket_number_of_connections"; } if (memcmp(socket_input_buffer, socket_all_jobs_finished, SOCKET_CODE_SIZE) == 0) { return "socket_all_jobs_finished"; } if (memcmp(socket_input_buffer, socket_job_result, SOCKET_CODE_SIZE) == 0) { return "socket_job_result"; } if (memcmp(socket_input_buffer, socket_job_result_queue, SOCKET_CODE_SIZE) == 0) { return "socket_job_result_queue"; } if (memcmp(socket_input_buffer, socket_result_with_image_to_write, SOCKET_CODE_SIZE) == 0) { return "socket_result_with_image_to_write"; } return "socket code not recognized"; } // this was provided by David Mastronarde /*! * Returns 1 if the size [nx], [ny] matches a size that the SerialEMCCD plugin to * DigitalMicrograph would save as 4-bit data packed into a byte mode file for * super-resolution frames from a K2 camera. The sizes tested are 3838x7420, 3710x7676, * 3840x7424, and 3712x7680. */ int sizeCanBe4BitK2SuperRes(int nx, int ny) { int allowedX[2] = {7676, 7680}; int allowedY[2] = {7420, 7424}; int numTest = sizeof(allowedX) / sizeof(int); int ind; for (ind = 0; ind < numTest; ind++) if ((nx == allowedX[ind] / 2 && ny == allowedY[ind]) || (nx == allowedY[ind] / 2 && ny == allowedX[ind])) return 1; return 0; } // Headers for time and processor count #ifdef _OPENMP #include #endif #ifdef _WIN32 #include typedef BOOL (WINAPI *LPFN_GLPI)(PSYSTEM_LOGICAL_PROCESSOR_INFORMATION, PDWORD); #else #include #endif #ifdef __APPLE__ #include #endif #define B3DMIN(a,b) ((a) < (b) ? (a) : (b)) #define B3DMAX(a,b) ((a) > (b) ? (a) : (b)) #define B3DCLAMP(a,b,c) a = B3DMAX((b), B3DMIN((c), (a))) #define CPUINFO_LINE 80 #define MAX_CPU_SOCKETS 64 static int fgetline(FILE *fp, char s[], int limit) { int c, i, length; if (fp == NULL){ return(-1); } if (limit < 3){ return(-1); } for (i=0; ( ((c = getc(fp)) != EOF) && (i < (limit-1)) && (c != '\n') ); i++) s[i]=c; // 1/25/12: Take off a return too! if (i > 0 && s[i-1] == '\r') i--; // A \n or EOF on the first character leaves i at 0, so there is nothing // special to be handled about i being 1, 9/18/09 s[i]='\0'; length = i; if (c == EOF) return (-1 * (length + 2)); else return (length); } /*! * Returns the number of physical processor cores in [physical] and the number of logical * processors in [logical]. The return value is 1 if valid information could not be * obtained for both items. It uses sysctlbyname on Mac, GetLogicalProcessorInformation * on Windows, and /proc/cpuinfo on Linux. */ static int numCoresAndLogicalProcs(int *physical, int *logical) { int processorCoreCount = 0; int logicalProcessorCount = 0; #ifdef __APPLE__ int temp = 0; size_t lenPhys = sizeof(int); #elif defined(_WIN32) LPFN_GLPI glpi; PSYSTEM_LOGICAL_PROCESSOR_INFORMATION buffer = NULL; PSYSTEM_LOGICAL_PROCESSOR_INFORMATION ptr = NULL; DWORD returnLength = 0; DWORD byteOffset = 0; DWORD numBits = sizeof(ULONG_PTR) * 8; ULONG_PTR bitTest; DWORD i; #else FILE *fp; unsigned char socketFlags[MAX_CPU_SOCKETS]; char linebuf[CPUINFO_LINE]; int err, len, curID, curCores; char *colon; #endif #ifdef __APPLE__ if (!sysctlbyname("hw.physicalcpu" , &temp, &lenPhys, NULL, 0)) processorCoreCount = temp; lenPhys = 4; if (!sysctlbyname("hw.logicalcpu" , &temp, &lenPhys, NULL, 0)) logicalProcessorCount = temp; #elif defined(_WIN32) /* This is adapted from https://msdn.microsoft.com/en-us/library/ms683194 On systems with more than 64 logical processors, the GetLogicalProcessorInformation function retrieves logical processor information about processors in the processor group to which the calling thread is currently assigned. Use the GetLogicalProcessorInformationEx function to retrieve information about processors in all processor groups on the system. (Windows 7/Server 2008 or above). */ glpi = (LPFN_GLPI)GetProcAddress(GetModuleHandle(TEXT("kernel32")), "GetLogicalProcessorInformation"); if (glpi) { if (!glpi(buffer, &returnLength) && GetLastError() == ERROR_INSUFFICIENT_BUFFER && returnLength > 0) { buffer = (PSYSTEM_LOGICAL_PROCESSOR_INFORMATION)malloc(returnLength); if (buffer) { if (glpi(buffer, &returnLength)) { ptr = buffer; while (byteOffset + sizeof(SYSTEM_LOGICAL_PROCESSOR_INFORMATION) <= returnLength) { if (ptr->Relationship == RelationProcessorCore) { processorCoreCount++; bitTest = (ULONG_PTR)1; for (i = 0; i < numBits; i++) { if (ptr->ProcessorMask & bitTest) logicalProcessorCount++; bitTest *= 2; } } byteOffset += sizeof(SYSTEM_LOGICAL_PROCESSOR_INFORMATION); ptr++; } free(buffer); } } } } #else /* Linux: look at /proc/cpuinfo */ fp = fopen("/proc/cpuinfo", "r"); if (fp) { curID = -1; curCores = -1; memset(socketFlags, 0, MAX_CPU_SOCKETS); while (1) { err = 0; len = fgetline(fp, linebuf, CPUINFO_LINE); if (!len) continue; if (len == -2) break; err = 1; if (len == -1) break; /* Look for a "physical id :" and a "cpu cores :" in either order */ if (strstr(linebuf, "physical id")) { /* Error if already got a physical id without cpu cores */ if (curID >= 0) break; colon = strchr(linebuf, ':'); if (colon) curID = atoi(colon+1); /* Error if no colon or ID out of range */ if (!colon || curID < 0 || curID >= MAX_CPU_SOCKETS) break; } if (strstr(linebuf, "cpu cores")) { /* Error if already got a cpu cores without physical id */ if (curCores >= 0) break; colon = strchr(linebuf, ':'); if (colon) curCores = atoi(colon+1); /* Error if no colon or core count illegal */ if (!colon || curCores <= 0) break; } /* If have both ID and core count, add one logical processor and the number of cores the first time this ID is seen to the core count; set ID flag and reset the tow numbers */ if (curID >= 0 && curCores > 0) { logicalProcessorCount++; if (!socketFlags[curID]) processorCoreCount += curCores; socketFlags[curID] = 1; curID = -1; curCores = -1; } err = 0; if (len < 0) break; } if (err) processorCoreCount *= -1; fclose(fp); } #endif *physical = processorCoreCount; *logical = logicalProcessorCount; return (processorCoreCount <= 0 || logicalProcessorCount < 0) ? 1 : 0; } /* * Warn the user if the number of threads they are asking for seems * excessive. * If OpenMP is not available, reset the number of threads to 1. */ int CheckNumberOfThreads(int number_of_threads) { #ifdef _OPENMP int number_logical_cores; int number_physical_cores; int num_threads_from_environment; // Work out number of cores numCoresAndLogicalProcs(&number_physical_cores,&number_logical_cores); if (number_of_threads > number_logical_cores && number_logical_cores > 0) { wxPrintf("\nWarning: you are using %i threads, which is more than %i, the number of logical cores. This could be inefficient.\n\n",number_of_threads,number_logical_cores); } else if (number_of_threads > number_physical_cores && number_physical_cores > 0) { wxPrintf("\nWarning: you are using %i threads, which is more than %i, the number of phyiscal cores. This could be inefficient.\n\n",number_of_threads,number_physical_cores); } return number_of_threads; #else wxPrintf("OpenMP is not available - will not use parallel threads.\n\n"); return 1; #endif } /* * Get an appropriately limited number of threads * This routine was written by David Mastronarde for IMOD, with the logic being * that the user would suggest a number of threads, but that suggestion would * be curtailed by actual core numbers and OpenMP environment variables. */ int ReturnAppropriateNumberOfThreads(int optimalThreads) { int numThreads = optimalThreads; int physicalProcs = 0; int logicalProcessorCount = 0; int processorCoreCount = 0; #ifdef _OPENMP static int limThreads = -1; static int numProcs = -1; static int forceThreads = -1; static int ompNumProcs = -1; char *ompNum; /* One-time determination of number of physical and logical cores */ if (numProcs < 0) { ompNumProcs = numProcs = omp_get_num_procs(); /* if there are legal numbers and the logical count is the OMP number, set the physical processor count */ if (!numCoresAndLogicalProcs(&processorCoreCount, &logicalProcessorCount) && processorCoreCount > 0 && logicalProcessorCount == numProcs) physicalProcs = processorCoreCount; if (getenv("IMOD_REPORT_CORES")) wxPrintf("core count = %d logical processors = %d OMP num = %d => physical " "processors = %d\n", processorCoreCount, logicalProcessorCount, numProcs, physicalProcs); fflush(stdout); if (physicalProcs > 0) numProcs = B3DMIN(numProcs, physicalProcs); } /* Limit by number of real cores */ numThreads = B3DMAX(1, B3DMIN(numProcs, numThreads)); /* One-time determination of the limit set by OMP_NUM_THREADS */ if (limThreads < 0) { ompNum = getenv("OMP_NUM_THREADS"); if (ompNum) limThreads = atoi(ompNum); limThreads = B3DMAX(0, limThreads); } /* Limit to number set by OMP_NUM_THREADS and to number of real cores */ if (limThreads > 0) numThreads = B3DMIN(limThreads, numThreads); /* One-time determination of whether user wants to force a number of threads */ if (forceThreads < 0) { forceThreads = 0; ompNum = getenv("IMOD_FORCE_OMP_THREADS"); if (ompNum) { if (!strcmp(ompNum, "ALL_CORES")) { if (numProcs > 0) forceThreads = numProcs; } else if (!strcmp(ompNum, "ALL_HYPER")) { if (ompNumProcs > 0) forceThreads = ompNumProcs; } else { forceThreads = atoi(ompNum); forceThreads = B3DMAX(0, forceThreads); } } } /* Force the number if set */ if (forceThreads > 0) numThreads = forceThreads; if (getenv("IMOD_REPORT_CORES")) wxPrintf("numProcs %d limThreads %d numThreads %d\n", numProcs, limThreads, numThreads); fflush(stdout); #else numThreads = 1; #endif return numThreads; } /*! * Returns the thread number of the current thread, numbered from 0 */ int ReturnThreadNumberOfCurrentThread() { #ifdef _OPENMP return omp_get_thread_num(); #else return 0; #endif } // Inverse error function and complementary inverse error function // https://stackoverflow.com/questions/27229371/inverse-error-function-in-c double cisTEM_erfinv(double x) { double tt1, tt2, lnx, sgn; sgn = (x < 0) ? -1.0 : 1.0; x = (1 - x)*(1 + x); // x = 1 - x*x; lnx = log(x); tt1 = 2/(PI*0.147) + 0.5 * lnx; tt2 = 1/(0.147) * lnx; return(sgn*sqrt(-tt1 + sqrt(tt1*tt1 - tt2))); } double cisTEM_erfcinv(double x) { return cisTEM_erfinv(1.0 - x); } ctffind-4.1.14/src/core/functions.h000066400000000000000000000234371440356052600171340ustar00rootroot00000000000000 void swapbytes(unsigned char* v, size_t n); void swapbytes(size_t size, unsigned char* v, size_t n); bool GetMRCDetails(const char *filename, int &x_size, int &y_size, int &number_of_images); inline void ZeroBoolArray(bool *array_to_zero, int size_of_array) { for (int counter = 0; counter < size_of_array; counter++) { array_to_zero[counter] = false; } } int sizeCanBe4BitK2SuperRes(int nx, int ny); // provided by David Mastronarde inline void ZeroIntArray(int *array_to_zero, int size_of_array) { for (int counter = 0; counter < size_of_array; counter++) { array_to_zero[counter] = 0; } } inline void ZeroLongArray(long *array_to_zero, int size_of_array) { for (int counter = 0; counter < size_of_array; counter++) { array_to_zero[counter] = 0; } } inline void ZeroFloatArray(float *array_to_zero, int size_of_array) { for (int counter = 0; counter < size_of_array; counter++) { array_to_zero[counter] = 0.0; } } int ReturnSafeBinnedBoxSize(int original_box_size, float bin_factor); float ReturnMagDistortionCorrectedPixelSize(float original_pixel_size, float major_axis_scale, float minor_axis_scale); wxString ReturnSocketErrorText(wxSocketBase *socket_to_check); inline void WriteToSocket ( wxSocketBase *socket, const void * buffer, wxUint32 nbytes, bool die_on_error = false) { bool should_abort = false; if (socket != NULL) { if (socket->IsOk() == true && socket->IsConnected() == true) { #ifdef DEBUG // socket->SetFlags(wxSOCKET_WAITALL | wxSOCKET_BLOCK); //if (socket->GetFlags() != (wxSOCKET_WAITALL) && socket->GetFlags() != (wxSOCKET_WAITALL | wxSOCKET_BLOCK)) {MyPrintWithDetails("Wait all flag not set!"); should_abort = true;} if (socket->GetFlags() != (wxSOCKET_WAITALL | wxSOCKET_BLOCK)) {MyPrintWithDetails("Wait all / block flag not set!"); should_abort = true;} #endif //socket->SetTimeout(60); socket->WaitForWrite(); socket->Write(buffer, nbytes); int number_of_retries = 0; while (socket->LastWriteCount() == 0 && number_of_retries < 10) { wxMilliSleep(100); socket->WaitForWrite(); socket->Write(buffer, nbytes); number_of_retries++; } if (socket->LastWriteCount() != nbytes) {MyDebugPrintWithDetails("Socket didn't write all bytes! (%u / %u) with %i retries ", socket->LastWriteCount(), nbytes, number_of_retries); should_abort = true;} if (socket->Error() == true) {MyDebugPrintWithDetails("Socket has an error (%s) ", ReturnSocketErrorText(socket)); should_abort = true;} if (should_abort == true) { #ifdef DEBUG wxIPV4address peer_address; socket->GetPeer(peer_address); wxPrintf("Failed socket is connected to : %s, (%s)\n", peer_address.Hostname(), peer_address.IPAddress()); socket->Destroy(); socket = NULL; wxFAIL; DEBUG_ABORT; #else exit(-1); #endif } } else { if (die_on_error == true) DEBUG_ABORT; } } } inline void ReadFromSocket ( wxSocketBase *socket, void * buffer, wxUint32 nbytes, bool die_on_error = false) { bool should_abort = false; if (socket != NULL) { if (socket->IsOk() == true && socket->IsConnected() == true) { #ifdef DEBUG // socket->SetFlags(wxSOCKET_WAITALL | wxSOCKET_BLOCK); //if (socket->GetFlags() != (wxSOCKET_WAITALL) && socket->GetFlags() != (wxSOCKET_WAITALL | wxSOCKET_BLOCK)) {MyPrintWithDetails("Wait all flag not set!"); should_abort = true;} if (socket->GetFlags() != (wxSOCKET_WAITALL | wxSOCKET_BLOCK)) {MyPrintWithDetails("Wait all / block flag not set!"); should_abort = true;} #endif //socket->SetTimeout(60); socket->WaitForRead(); socket->Read(buffer, nbytes); int number_of_retries = 0; while (socket->LastReadCount() == 0 && number_of_retries < 10) { wxMilliSleep(100); socket->WaitForRead(); socket->Read(buffer, nbytes); number_of_retries++; } if (socket->LastReadCount() != nbytes) {MyDebugPrintWithDetails("Socket didn't read all bytes! (%u / %u) with %i retries ", socket->LastReadCount(), nbytes, number_of_retries); should_abort = true;} if (socket->Error() == true) {MyDebugPrintWithDetails("Socket has an error (%s) ", ReturnSocketErrorText(socket)); should_abort = true;} if (should_abort == true) { #ifdef DEBUG wxIPV4address peer_address; socket->GetPeer(peer_address); wxPrintf("Failed socket is connected to : %s, (%s)\n", peer_address.Hostname(), peer_address.IPAddress()); socket->Destroy(); socket = NULL; wxFAIL; DEBUG_ABORT; #else exit(-1); #endif } } else { if (die_on_error == true) DEBUG_ABORT; } } } inline void ZeroDoubleArray(double *array_to_zero, int size_of_array) { for (int counter = 0; counter < size_of_array; counter++) { array_to_zero[counter] = 0.0; } } inline bool IsEven(int number_to_check) { if ( number_to_check % 2== 0 ) return true; else return false; } inline bool DoesFileExist(wxString filename) { std::ifstream file_to_check (filename.c_str()); if(file_to_check.is_open()) return true; return false; } inline bool DoesFileExistWithWait(wxString filename, int max_wait_time_in_seconds) { if ( ! DoesFileExist(filename) ) { for (int wait_counter = 0; wait_counter < max_wait_time_in_seconds; wait_counter ++) { wxSleep(1); if (DoesFileExist(filename)) break; } } return DoesFileExist(filename); } inline float rad_2_deg(float radians) { return radians / (PI / 180.); } inline float deg_2_rad(float degrees) { return degrees * PI / 180.; } inline float sinc(float radians) { if (radians == 0.0) return 1.0; if (radians >= 0.01) return sinf(radians) / radians; float temp_float = radians * radians; return 1.0 - temp_float / 6.0 + temp_float * temp_float / 120.0; } inline double myround(double a) { if (a > 0) return double(long(a + 0.5)); else return double(long(a - 0.5)); } inline float myround(float a) { if (a > 0) return float(int(a + 0.5)); else return float(int(a - 0.5)); } inline int myroundint(double a) { if (a > 0) return int(a + 0.5); else return int(a - 0.5); } inline int myroundint(float a) { if (a > 0) return int(a + 0.5); else return int(a - 0.5); } inline bool IsOdd(int number) { if ((number & 1) == 0) return false; else return true; } wxArrayString ReturnIPAddress(); wxString ReturnIPAddressFromSocket(wxSocketBase *socket); void SendwxStringToSocket(wxString *string_to_send, wxSocketBase *socket); wxString ReceivewxStringFromSocket(wxSocketBase *socket); inline float ReturnPhaseFromShift(float real_space_shift, float distance_from_origin, float dimension_size) { return real_space_shift * distance_from_origin * 2.0 * PI / dimension_size; } inline std::complex Return3DPhaseFromIndividualDimensions( float phase_x, float phase_y, float phase_z) { float temp_phase = -phase_x-phase_y-phase_z; return cosf(temp_phase) + sinf(temp_phase) * I; } inline bool DoublesAreAlmostTheSame(double a, double b) { return (fabs(a-b) < 0.000001); } inline bool FloatsAreAlmostTheSame(float a, float b) { return (fabs(a-b) < 0.0001); } inline bool InputIsATerminal() { return isatty(fileno(stdin)); }; inline bool OutputIsAtTerminal() { return isatty(fileno(stdout)); } float CalculateAngularStep(float required_resolution, float radius_in_angstroms); int ReturnClosestFactorizedUpper(int wanted_int, int largest_factor, bool enforce_even = false); int ReturnClosestFactorizedLower(int wanted_int, int largest_factor, bool enforce_even = false); /* * * String manipulations * */ std::string FilenameReplaceExtension(std::string filename, std::string new_extension); std::string FilenameAddSuffix(std::string filename, std::string suffix_to_add); void SplitFileIntoDirectoryAndFile(wxString &input_file, wxString &output_directory, wxString &output_file); void Allocate2DFloatArray(float **&array, int dim1, int dim2); void Deallocate2DFloatArray(float **&array, int dim1); void CheckSocketForError(wxSocketBase *socket_to_check); inline wxString BoolToYesNo(bool b) { return b ? "Yes" : "No"; } long ReturnFileSizeInBytes(wxString filename); inline float kDa_to_Angstrom3(float kilo_daltons) { return kilo_daltons * 1000.0 / 0.81; } inline bool IsAValidSymmetry(wxString *string_to_check) { long junk; wxString buffer_string = *string_to_check; buffer_string.Trim(); buffer_string.Trim(false); if (string_to_check->StartsWith("C") == false && string_to_check->StartsWith("c") == false && string_to_check->StartsWith("D") == false && string_to_check->StartsWith("d") == false && string_to_check->StartsWith("I") == false && string_to_check->StartsWith("i") == false && string_to_check->StartsWith("O") == false && string_to_check->StartsWith("o") == false && string_to_check->StartsWith("T") == false && string_to_check->StartsWith("t") == false) return false; if (buffer_string.Mid(1).IsEmpty() == true && (buffer_string.StartsWith("I") == true || buffer_string.StartsWith("i") == true || buffer_string.StartsWith("T") == true || buffer_string.StartsWith("t") == true || buffer_string.StartsWith("O") == true || buffer_string.StartsWith("o") == true )) return true; return string_to_check->Mid(1).ToLong(&junk); } float ReturnSumOfLogP(float logp1, float logp2, float log_range); int ReturnNumberofAsymmetricUnits(wxString symmetry); inline float ConvertProjectionXYToThetaInDegrees(float x, float y) // assumes that max x,y is 1 { return rad_2_deg(asin(sqrtf(powf(x,2) + powf(y,2)))); } inline float ConvertXYToPhiInDegrees(float x, float y) { if (x == 0 && y==0) return 0; else return rad_2_deg(atan2f(y, x)); } std::vector rankSort(const float* v_temp, const size_t size); std::vector rankSort(const std::vector& v_temp); wxString StringFromSocketCode(unsigned char *socket_input_buffer); int CheckNumberOfThreads(int number_of_threads); // From David Mastronarde int ReturnAppropriateNumberOfThreads(int optimalThreads); int ReturnThreadNumberOfCurrentThread(); double cisTEM_erfinv(double x); double cisTEM_erfcinv(double x); ctffind-4.1.14/src/core/globals.cpp000066400000000000000000000003471440356052600170750ustar00rootroot00000000000000#include "core_headers.h" RandomNumberGenerator global_random_number_generator(-1); #include // this is a magic incantation which must be done! WX_DEFINE_OBJARRAY(wxArrayFloat); WX_DEFINE_OBJARRAY(wxArrayBool); ctffind-4.1.14/src/core/image.h000066400000000000000000000667521440356052600162150ustar00rootroot00000000000000/* \brief Image class (derived from Fortran images module) for information on actual data management / addressing see the image_data_array class.. */ class ReconstructedVolume; class EulerSearch; class ResolutionStatistics; class RotationMatrix; class Image { public: int logical_x_dimension; // !< Logical (X) dimensions of the image., Note that this does not necessarily correspond to memory allocation dimensions (ie physical dimensions). int logical_y_dimension; // !< Logical (Y) dimensions of the image., Note that this does not necessarily correspond to memory allocation dimensions (ie physical dimensions). int logical_z_dimension; // !< Logical (Z) dimensions of the image., Note that this does not necessarily correspond to memory allocation dimensions (ie physical dimensions). bool is_in_real_space; // !< Whether the image is in real or Fourier space bool object_is_centred_in_box; //!< Whether the object or region of interest is near the center of the box (as opposed to near the corners and wrapped around). This refers to real space and is meaningless in Fourier space. int physical_upper_bound_complex_x; // !< In each dimension, the upper bound of the complex image's physical addresses int physical_upper_bound_complex_y; // !< In each dimension, the upper bound of the complex image's physical addresses int physical_upper_bound_complex_z; // !< In each dimension, the upper bound of the complex image's physical addresses int physical_address_of_box_center_x; // !< In each dimension, the address of the pixel at the origin int physical_address_of_box_center_y; // !< In each dimension, the address of the pixel at the origin int physical_address_of_box_center_z; // !< In each dimension, the address of the pixel at the origin //int physical_index_of_first_negative_frequency_x; // !< In each dimension, the physical index of the first pixel which stores negative frequencies int physical_index_of_first_negative_frequency_y; // !< In each dimension, the physical index of the first pixel which stores negative frequencies int physical_index_of_first_negative_frequency_z; // !< In each dimension, the physical index of the first pixel which stores negative frequencies float fourier_voxel_size_x; // !< Distance from Fourier voxel to Fourier voxel, expressed in reciprocal pixels float fourier_voxel_size_y; // !< Distance from Fourier voxel to Fourier voxel, expressed in reciprocal pixels float fourier_voxel_size_z; // !< Distance from Fourier voxel to Fourier voxel, expressed in reciprocal pixels int logical_upper_bound_complex_x; // !< In each dimension, the upper bound of the complex image's logical addresses int logical_upper_bound_complex_y; // !< In each dimension, the upper bound of the complex image's logical addresses int logical_upper_bound_complex_z; // !< In each dimension, the upper bound of the complex image's logical addresses int logical_lower_bound_complex_x; // !< In each dimension, the lower bound of the complex image's logical addresses int logical_lower_bound_complex_y; // !< In each dimension, the lower bound of the complex image's logical addresses int logical_lower_bound_complex_z; // !< In each dimension, the lower bound of the complex image's logical addresses int logical_upper_bound_real_x; // !< In each dimension, the upper bound of the real image's logical addresses int logical_upper_bound_real_y; // !< In each dimension, the upper bound of the real image's logical addresses int logical_upper_bound_real_z; // !< In each dimension, the upper bound of the real image's logical addresses int logical_lower_bound_real_x; // !< In each dimension, the lower bound of the real image's logical addresses int logical_lower_bound_real_y; // !< In each dimension, the lower bound of the real image's logical addresses int logical_lower_bound_real_z; // !< In each dimension, the lower bound of the real image's logical addresses long real_memory_allocated; // !< Number of floats allocated in real space; int padding_jump_value; // !< The FFTW padding value, if odd this is 2, if even it is 1. It is used in loops etc over real space. int insert_into_which_reconstruction; // !< Determines which reconstruction the image will be inserted into (for FSC calculation). long number_of_real_space_pixels; // !< Total number of pixels in real space float ft_normalization_factor; // !< Normalization factor for the Fourier transform (1/sqrt(N), where N is the number of pixels in real space) // Arrays to hold voxel values float *real_values; // !< Real array to hold values for REAL images. std::complex *complex_values; // !< Complex array to hold values for COMP images. bool is_in_memory; // !< Whether image values are in-memory, in other words whether the image has memory space allocated to its data array. Default = .FALSE. // FFTW-specfic fftwf_plan plan_fwd; // !< FFTW plan for the image (fwd) fftwf_plan plan_bwd; // !< FFTW plan for the image (bwd) bool planned; // !< Whether the plan has been setup by/for FFTW bool image_memory_should_not_be_deallocated; // !< Don't deallocate the memory, generally should only be used when doing something funky with the pointers static wxMutex s_mutexProtectingFFTW; // Methods Image(); Image( const Image &other_image); // copy constructor ~Image(); Image & operator = (const Image &t); Image & operator = (const Image *t); void SetupInitialValues(); void Allocate(int wanted_x_size, int wanted_y_size, int wanted_z_size = 1, bool is_in_real_space = true); void Allocate(int wanted_x_size, int wanted_y_size, bool is_in_real_space = true); void AllocateAsPointingToSliceIn3D(Image *wanted3d, long wanted_slice); void Deallocate(); int ReturnSmallestLogicalDimension(); int ReturnLargestLogicalDimension(); void SampleFFT(Image &sampled_image, int sample_rate); float ReturnSumOfSquares(float wanted_mask_radius = 0.0, float wanted_center_x = 0.0, float wanted_center_y = 0.0, float wanted_center_z = 0.0, bool invert_mask = false); float ReturnSumOfRealValues(); float ReturnSigmaNoise(); float ReturnSigmaNoise(Image &matching_projection, float mask_radius = 0.0); float ReturnImageScale(Image &matching_projection, float mask_radius = 0.0); float ReturnCorrelationCoefficientUnnormalized(Image &other_image, float wanted_mask_radius = 0.0); float ReturnPixelWiseProduct(Image &other_image); float GetWeightedCorrelationWithImage(Image &projection_image, int *bins, float signed_CC_limit); void PhaseFlipPixelWise(Image &other_image); void MultiplyPixelWiseReal(Image &other_image, bool absolute = false); void MultiplyPixelWise(Image &other_image); void ConjugateMultiplyPixelWise(Image &other_image); void ComputeFSCVectorized(Image *other_image, Image *work_this_image_squared, Image *work_other_image_squared, Image *work_cross_product_image, int number_of_shells, int *shell_number, float *computed_fsc, double *work_sum_of_squares, double *work_sum_of_other_squares, double *work_sum_of_cross_products); void ComputeFSC(Image *other_image, int number_of_shells, int *shell_number, float *computed_fsc, double *work_sum_of_squares, double *work_sum_of_other_squares, double *work_sum_of_cross_products); void DividePixelWise(Image &other_image); void AddGaussianNoise(float wanted_sigma_value = 1.0); long ZeroFloat(float wanted_mask_radius = 0.0, bool outsize = false); long ZeroFloatAndNormalize(float wanted_sigma_value = 1.0, float wanted_mask_radius = 0.0, bool outside = false); long Normalize(float wanted_sigma_value = 1.0, float wanted_mask_radius = 0.0, bool outside = false); void NormalizeSumOfSquares(); void ZeroFloatOutside(float wanted_mask_radius, bool invert_mask = false); void ReplaceOutliersWithMean(float maximum_n_sigmas); float ReturnVarianceOfRealValues(float wanted_mask_radius = 0.0, float wanted_center_x = 0.0, float wanted_center_y = 0.0, float wanted_center_z = 0.0, bool invert_mask = false); EmpiricalDistribution ReturnDistributionOfRealValues(float wanted_mask_radius = 0.0, bool outside = false, float wanted_center_x = 0.0, float wanted_center_y = 0.0, float wanted_center_z = 0.0); void UpdateDistributionOfRealValues(EmpiricalDistribution *distribution_to_update, float wanted_mask_radius = 0.0, bool outside = false, float wanted_center_x = 0.0, float wanted_center_y = 0.0, float wanted_center_z = 0.0); void ApplySqrtNFilter(); void Whiten(float resolution_limit = 1.0, Curve *whitening_filter = NULL); void OptimalFilterBySNRImage(Image &SNR_image, int include_reference_weighting = 1); void MultiplyByWeightsCurve(Curve &weights, float scale_factor = 1.0); void WeightBySSNR(Image &ctf_image, float molecular_mass_kDa, float pixel_size, Curve &SSNR, Image &projection_image, bool weight_particle_image, bool weight_projection_image); void OptimalFilterSSNR(Curve &SSNR); void OptimalFilterFSC(Curve &FSC); void OptimalFilterWarp(CTF ctf, float pixel_size_in_angstroms, float ssnr_falloff_fudge_factor = 1.0, float ssnr_scale_fudge_factor = 1.0); //float Correct3D(float wanted_mask_radius = 0.0); float CorrectSinc(float wanted_mask_radius = 0.0, float padding_factor = 1.0, bool force_background_value = false, float wanted_mask_value = 0.0); void MirrorXFourier2D(Image &mirrored_image); void MirrorYFourier2D(Image &mirrored_image); void RotateQuadrants(Image &rotated_image, int quad_i); void Rotate3DByRotationMatrixAndOrApplySymmetry(RotationMatrix &wanted_matrix, float wanted_max_radius_in_pixels = 0.0, wxString wanted_symmetry="C1"); // use identiy matrix to just impose sym void Rotate3DByRotationMatrixAndOrApplySymmetryThenShift(RotationMatrix &wanted_matrix, float wanted_x_shift, float wanted_y_shift, float wanted_z_shift, float wanted_max_radius_in_pixels = 0.0, wxString wanted_symmetry = "C1"); // like above but with shift void Rotate3DThenShiftThenApplySymmetry(RotationMatrix &wanted_matrix, float wanted_x_shift, float wanted_y_shift, float wanted_z_shift, float wanted_max_radius_in_pixels = 0.0, wxString wanted_symmetry = "C1"); void GenerateReferenceProjections(Image *projections, EulerSearch ¶meters, float resolution); void RotateFourier2DGenerateIndex(Kernel2D **&kernel_index, float psi_max, float psi_step, float psi_start, bool invert_angle = false); void RotateFourier2DDeleteIndex(Kernel2D **&kernel_index, float psi_max, float psi_step); void RotateFourier2DFromIndex(Image &rotated_image, Kernel2D *kernel_index); void RotateFourier2DIndex(Kernel2D *kernel_index, AnglesAndShifts &rotation_angle, float resolution_limit = 1.0, float padding_factor = 1.0); Kernel2D ReturnLinearInterpolatedFourierKernel2D(float &x, float &y); void RotateFourier2D(Image &rotated_image, AnglesAndShifts &rotation_angle, float resolution_limit_in_reciprocal_pixels = 1.0, bool use_nearest_neighbor = false); void Rotate2D(Image &rotated_image, AnglesAndShifts &rotation_angle, float mask_radius_in_pixels = 0.0); void Rotate2DSample(Image &rotated_image, AnglesAndShifts &rotation_angle, float mask_radius_in_pixels = 0.0); float ReturnLinearInterpolated2D(float &wanted_physical_x_coordinate, float &wanted_physical_y_coordinate); float ReturnNearest2D(float &wanted_physical_x_coordinate, float &wanted_physical_y_coordinate); void ExtractSlice(Image &image_to_extract, AnglesAndShifts &angles_and_shifts_of_image, float resolution_limit = 1.0, bool apply_resolution_limit = true); void ExtractSliceByRotMatrix(Image &image_to_extract, RotationMatrix &wanted_matrix, float resolution_limit = 1.0, bool apply_resolution_limit = true); std::complex ReturnNearestFourier2D(float &x, float &y); std::complex ReturnLinearInterpolatedFourier2D(float &x, float &y); std::complex ReturnLinearInterpolatedFourier(float &x, float &y, float &z); void AddByLinearInterpolationReal(float &wanted_x_coordinate, float &wanted_y_coordinate, float &wanted_z_coordinate, float &wanted_value); void AddByLinearInterpolationFourier2D(float &wanted_x_coordinate, float &wanted_y_coordinate, std::complex &wanted_value); float CosineRingMask(float wanted_inner_radius, float wanted_outer_radius, float wanted_mask_edge); float CosineMask(float wanted_mask_radius, float wanted_mask_edge, bool invert = false, bool force_mask_value = false, float wanted_mask_value = 0.0); void GaussianLowPassFilter(float sigma); void GaussianHighPassFilter(float sigma); void ApplyLocalResolutionFilter(Image &local_resolution_map, float pixel_size, int wanted_number_of_levels); void CircleMask(float wanted_mask_radius, bool invert = false); void CircleMaskWithValue(float wanted_mask_radius, float wanted_mask_value, bool invert = false); void SquareMaskWithValue(float wanted_mask_dim, float wanted_mask_value, bool invert = false, int wanted_center_x = 0, int wanted_center_y = 0, int wanted_center_z = 0); void TriangleMask(float wanted_triangle_half_base_length); void CalculateCTFImage(CTF &ctf_of_image, bool calculate_complex_ctf = false); void CalculateBeamTiltImage(CTF &ctf_of_image, bool output_phase_shifts = false); bool ContainsBlankEdges(float mask_radius = 0.0); void CorrectMagnificationDistortion(float distortion_angle, float distortion_major_axis, float distortion_minor_axis); float ApplyMask(Image &mask_file, float cosine_edge_width, float weight_outside_mask, float low_pass_filter_outside, float filter_cosine_edge_width, float outside_mask_value = 0.0, bool use_outside_mask_value = false); Peak CenterOfMass(float threshold = 0.0, bool apply_threshold = false); Peak StandardDeviationOfMass(float threshold = 0.0, bool apply_threshold = false, bool invert_densities = false); float ReturnAverageOfMaxN(int number_of_pixels_to_average = 100, float mask_radius = 0.0); void AddSlices(Image &sum_of_slices, int first_slice = 0, int last_slice = 0, bool calculate_average = false); inline long ReturnVolumeInRealSpace() { return number_of_real_space_pixels; }; inline long ReturnReal1DAddressFromPhysicalCoord(int wanted_x, int wanted_y, int wanted_z) { MyDebugAssertTrue(wanted_x >= 0 && wanted_x < logical_x_dimension && wanted_y >= 0 && wanted_y < logical_y_dimension && wanted_z >= 0 && wanted_z < logical_z_dimension, "Requested pixel (%i, %i, %i) is outside range (%i-%i, %i-%i, %i-%i)", wanted_x, wanted_y, wanted_z,0,logical_x_dimension-1,0,logical_y_dimension-1,0,logical_z_dimension-1); return ((long(logical_x_dimension + padding_jump_value) * long(logical_y_dimension)) * long(wanted_z)) + (long(logical_x_dimension + padding_jump_value) * long(wanted_y)) + long(wanted_x); }; inline float ReturnRealPixelFromPhysicalCoord(int wanted_x, int wanted_y, int wanted_z) { MyDebugAssertTrue(is_in_real_space == true, "Requested real pixel, but image is in Fourier space"); return real_values[ReturnReal1DAddressFromPhysicalCoord(wanted_x, wanted_y, wanted_z)]; }; inline long ReturnFourier1DAddressFromPhysicalCoord(int wanted_x, int wanted_y, int wanted_z) { MyDebugAssertTrue(wanted_x >= 0 && wanted_x <= physical_address_of_box_center_x && wanted_y >= 0 && wanted_y <= physical_upper_bound_complex_y && wanted_z >= 0 && wanted_z <= physical_upper_bound_complex_z, "Address (%i %i %i) out of bounds (%i to %i; %i to %i; %i to %i)!",wanted_x,wanted_y,wanted_z,0,physical_upper_bound_complex_x,0,physical_upper_bound_complex_y,0,physical_upper_bound_complex_z ); return ((long(physical_upper_bound_complex_x + 1) * long(physical_upper_bound_complex_y + 1)) * wanted_z) + (long(physical_upper_bound_complex_x + 1) * wanted_y) + wanted_x; }; inline long ReturnFourier1DAddressFromLogicalCoord(int wanted_x, int wanted_y, int wanted_z) { MyDebugAssertTrue(wanted_x >= logical_lower_bound_complex_x && wanted_x <=logical_upper_bound_complex_x && wanted_y >= logical_lower_bound_complex_y && wanted_y <= logical_upper_bound_complex_y && wanted_z >= logical_lower_bound_complex_z && wanted_z <= logical_upper_bound_complex_z, "Logical coordinates (%i, %i, %i) are out of bounds (%i to %i ; %i to %i; %i to %i)\n", wanted_x, wanted_y, wanted_z, logical_lower_bound_complex_x, logical_upper_bound_complex_x, logical_lower_bound_complex_y, logical_upper_bound_complex_y, logical_lower_bound_complex_z, logical_upper_bound_complex_z) int physical_x_address; int physical_y_address; int physical_z_address; if (wanted_x >= 0) { physical_x_address = wanted_x; if (wanted_y >= 0) { physical_y_address = wanted_y; } else { physical_y_address = logical_y_dimension + wanted_y; } if (wanted_z >= 0) { physical_z_address = wanted_z; } else { physical_z_address = logical_z_dimension + wanted_z; } } else { physical_x_address = -wanted_x; if (wanted_y > 0) { physical_y_address = logical_y_dimension - wanted_y; } else { physical_y_address = -wanted_y; } if (wanted_z > 0) { physical_z_address = logical_z_dimension - wanted_z; } else { physical_z_address = -wanted_z; } } return ReturnFourier1DAddressFromPhysicalCoord(physical_x_address, physical_y_address, physical_z_address); }; std::complex ReturnComplexPixelFromLogicalCoord(int wanted_x, int wanted_y, int wanted_z, std::complex out_of_bounds_value) { if (wanted_x < logical_lower_bound_complex_x || wanted_x > logical_upper_bound_complex_x || wanted_y < logical_lower_bound_complex_y ||wanted_y > logical_upper_bound_complex_y || wanted_z < logical_lower_bound_complex_z || wanted_z > logical_upper_bound_complex_z) { return out_of_bounds_value; } else return complex_values[ReturnFourier1DAddressFromLogicalCoord(wanted_x, wanted_y, wanted_z)]; }; bool HasSameDimensionsAs(Image *other_image); inline bool IsCubic() { return (logical_x_dimension == logical_y_dimension && logical_x_dimension == logical_z_dimension); } inline bool IsSquare() { MyDebugAssertTrue(logical_z_dimension == 1, "Image is three-dimensional"); return (logical_x_dimension == logical_y_dimension); } bool IsBinary(); void SetLogicalDimensions(int wanted_x_size, int wanted_y_size, int wanted_z_size = 1); void UpdateLoopingAndAddressing(); void UpdatePhysicalAddressOfBoxCenter(); int ReturnFourierLogicalCoordGivenPhysicalCoord_X(int physical_index); int ReturnFourierLogicalCoordGivenPhysicalCoord_Y(int physical_index); int ReturnFourierLogicalCoordGivenPhysicalCoord_Z(int physical_index); float ReturnMaximumDiagonalRadius(); bool FourierComponentHasExplicitHermitianMate(int physical_index_x, int physical_index_y, int physical_index_z); bool FourierComponentIsExplicitHermitianMate(int physical_index_x, int physical_index_y, int physical_index_z); inline void NormalizeFT() { MultiplyByConstant(ft_normalization_factor); } inline void NormalizeFTAndInvertRealValues() { MultiplyByConstant(-ft_normalization_factor); } void DivideByConstant(float constant_to_divide_by); void MultiplyByConstant(float constant_to_multiply_by); void InvertRealValues(); void TakeReciprocalRealValues(float zeros_become = 0.0); void AddConstant(float constant_to_add); void MultiplyAddConstant(float constant_to_multiply_by, float constant_to_add); void AddMultiplyConstant(float constant_to_add, float constant_to_multiply_by); void AddMultiplyAddConstant(float first_constant_to_add, float constant_to_multiply_by, float second_constant_to_add); void SquareRealValues(); void SquareRootRealValues(); void ExponentiateRealValues(); long ReturnNumberofNonZeroPixels(); void ForwardFFT(bool should_scale = true); void BackwardFFT(); void AddFFTWPadding(); void RemoveFFTWPadding(); inline void ReadSlice(MRCFile *input_file, long slice_to_read) { MyDebugAssertTrue(slice_to_read > 0, "Start slice is 0, the first slice is 1!"); MyDebugAssertTrue(slice_to_read <= input_file->ReturnNumberOfSlices(), "End slice (%li) is greater than number of slices in the file! (%i)", slice_to_read, input_file->ReturnNumberOfSlices());ReadSlices(input_file, slice_to_read, slice_to_read);}; //!> \brief Read a a slice from disk..(this just calls ReadSlices) inline void ReadSlice(DMFile *input_file, long slice_to_read) { MyDebugAssertTrue(slice_to_read > 0, "Start slice is 0, the first slice is 1!"); MyDebugAssertTrue(slice_to_read <= input_file->ReturnNumberOfSlices(), "End slice (%li) is greater than number of slices in the file! (%i)", slice_to_read, input_file->ReturnNumberOfSlices());ReadSlices(input_file, slice_to_read, slice_to_read);}; //!> \brief Read a a slice from disk..(this just calls ReadSlices) inline void ReadSlice(ImageFile *input_file, long slice_to_read) { MyDebugAssertTrue(slice_to_read > 0, "Start slice is 0, the first slice is 1!"); MyDebugAssertTrue(slice_to_read <= input_file->ReturnNumberOfSlices(), "End slice (%li) is greater than number of slices in the file! (%i)", slice_to_read, input_file->ReturnNumberOfSlices());ReadSlices(input_file, slice_to_read, slice_to_read);}; //!> \brief Read a a slice from disk..(this just calls ReadSlices) void ReadSlices(MRCFile *input_file, long start_slice, long end_slice); void ReadSlices(DMFile *input_file, long start_slice, long end_slice); void ReadSlices(ImageFile *input_file, long start_slice, long end_slice); inline void WriteSlice(MRCFile *input_file, long slice_to_write) { MyDebugAssertTrue(slice_to_write > 0, "Start slice is 0, the first slice is 1!"); WriteSlices(input_file, slice_to_write, slice_to_write);} void WriteSlices(MRCFile *input_file, long start_slice, long end_slice); void WriteSlicesAndFillHeader(std::string wanted_filename, float wanted_pixel_size); void QuickAndDirtyWriteSlices(std::string filename, long first_slice_to_write, long last_slice_to_write, bool overwrite = false, float pixel_size = 0.0f); void QuickAndDirtyWriteSlice(std::string filename, long slice_to_write, bool overwrite = false, float pixel_size = 0.0f); void QuickAndDirtyReadSlice(std::string filename, long slice_to_read); bool IsConstant(); bool HasNan(); bool HasNegativeRealValue(); void SetToConstant(float wanted_value); void ClipIntoLargerRealSpace2D(Image *other_image, float wanted_padding_value = 0); void ClipInto(Image *other_image, float wanted_padding_value = 0.0, bool fill_with_noise = false, float wanted_noise_sigma = 1.0,int wanted_coordinate_of_box_center_x=0, int wanted_coordinate_of_box_center_y=0, int wanted_coordinate_of_box_center_z=0); void InsertOtherImageAtSpecifiedPosition(Image *other_image, int wanted_x_coord, int wanted_y_coord, int wanted_z_coord, float threshold_value = -FLT_MAX); void Resize(int wanted_x_dimension, int wanted_y_dimension, int wanted_z_dimension, float wanted_padding_value = 0); void CopyFrom(Image *other_image); void CopyLoopingAndAddressingFrom(Image *other_image); void Consume(Image *other_image); void RealSpaceIntegerShift(int wanted_x_shift, int wanted_y_shift, int wanted_z_shift = 0); void DilateBinarizedMask(float dilation_radius); void PhaseShift(float wanted_x_shift, float wanted_y_shift, float wanted_z_shift = 0.0); void AddImage(Image *other_image); void SubtractImage(Image *other_image); void SubtractSquaredImage(Image *other_image); void ApplyBFactor(float bfactor); void ApplyBFactorAndWhiten(Curve &power_spectrum, float bfactor_low, float bfactor_high, float bfactor_res_limit); void CalculateDerivative(float direction_in_x = 0.0f, float direction_in_y = 0.0f, float direction_in_z = 0.0f); void SharpenMap(float pixel_size, float resolution_limit, bool invert_hand = false, float inner_mask_radius = 0.0f, float outer_mask_radius = 100.0f, float start_res_for_whitening = 8.0f, float additional_bfactor_low = 0.0f, float additional_bfactor_high = 0.0f, float filter_edge = 20.0f, Image *input_mask = NULL, ResolutionStatistics *resolution_statistics = NULL, float statistics_scale_factor = 1.0f, Curve *original_log_plot = NULL, Curve *sharpened_log_plot = NULL); void InvertHandedness(); void ApplyCTFPhaseFlip(CTF ctf_to_apply); void ApplyCTF(CTF ctf_to_apply, bool absolute = false, bool apply_beam_tilt = false); void ApplyCurveFilter(Curve *filter_to_apply, float resolution_limit = 1.0); void MaskCentralCross(int vertical_half_width = 1, int horizontal_half_width = 1); void ZeroCentralPixel(); void CalculateCrossCorrelationImageWith(Image *other_image); void SwapRealSpaceQuadrants(); void ComputeAmplitudeSpectrumFull2D(Image *other_image, bool calculate_phases = false, float phase_multiplier = 1.0f); void ComputeAmplitudeSpectrum(Image *other_image, bool signed_values = false); void ComputeHistogramOfRealValuesCurve(Curve *histogram_curve); void Compute1DPowerSpectrumCurve(Curve *curve_with_average_power, Curve *curve_with_number_of_values); void Compute1DRotationalAverage(Curve &average, Curve &number_of_values, bool fractional_radius_in_real_space = false, bool average_real_parts = false); void ComputeSpatialFrequencyAtEveryVoxel(); void AverageRadially(); void ComputeLocalMeanAndVarianceMaps(Image *local_mean_map, Image *local_variance_map, Image *mask, long number_of_pixels_within_mask); void SpectrumBoxConvolution(Image *output_image, int box_size, float minimum_radius); void TaperEdges(); float ReturnAverageOfRealValues(float wanted_mask_radius = 0.0, bool invert_mask = false); float ReturnMedianOfRealValues(); float ReturnAverageOfRealValuesOnEdges(); float ReturnAverageOfRealValuesAtRadius(float wanted_mask_radius); float ReturnAverageOfRealValuesInRing(float wanted_inner_radius,float wanted_outer_radius); float ReturnSigmaOfFourierValuesOnEdges(); float ReturnSigmaOfFourierValuesOnEdgesAndCorners(); float ReturnMaximumValue(float minimum_distance_from_center = 0.0, float minimum_distance_from_edge = 0.0); float ReturnMinimumValue(float minimum_distance_from_center = 0.0, float minimum_distance_from_edge = 0.0); void SetMaximumValue(float new_maximum_value); void SetMinimumValue(float new_minimum_value); void SetMinimumAndMaximumValues( float new_minimum_value, float new_maximum_value); void Binarise(float threshold_value); void ComputeAverageAndSigmaOfValuesInSpectrum(float minimum_radius, float maximum_radius, float &average, float &sigma, int cross_half_width = 2); void SetMaximumValueOnCentralCross(float maximum_value); void ApplyMirrorAlongY(); void InvertPixelOrder(); void GetMinMax(float &min_value, float &max_value); void RandomisePhases(float wanted_radius_in_reciprocal_pixels); float GetCorrelationWithCTF(CTF ctf); void SetupQuickCorrelationWithCTF(CTF ctf, int &number_of_values, double &norm_image, double &image_mean, int *addresses, float *spatial_frequency_squared, float *azimuth); float QuickCorrelationWithCTF(CTF ctf, int number_of_values, double norm_image, double image_mean, int *addresses, float *spatial_frequency_squared, float *azimuth); float ReturnIcinessOfSpectrum(float pixel_size_in_Angstroms); // Interpolation void GetRealValueByLinearInterpolationNoBoundsCheckImage(float &x, float &y, float &interpolated_value); Peak FindPeakAtOriginFast2D(int max_pix_x, int max_pix_y); Peak FindPeakWithIntegerCoordinates(float wanted_min_radius = 0.0, float wanted_max_radius = FLT_MAX, int wanted_min_distance_from_edges = 0); Peak FindPeakWithParabolaFit(float wanted_min_radius = 0.0, float wanted_max_radius = FLT_MAX); void SubSampleWithNoisyResampling(Image *first_sampled_image, Image *second_sampled_image); void SubSampleMask(Image *first_sampled_image, Image *second_sampled_image); // Test patterns void Sine1D(int number_of_periods); // for displaying void CreateOrthogonalProjectionsImage(Image *image_to_create, bool include_projections = true, float scale_factor = 1.0f, float mask_radius_in_pixels = 0.0f); }; ctffind-4.1.14/src/core/image_file.cpp000066400000000000000000000117011440356052600175270ustar00rootroot00000000000000#include "core_headers.h" ImageFile::ImageFile() { filename = wxFileName(""); file_type = UNSUPPORTED_FILE_TYPE; file_type_string = "Unsupported file type"; } ImageFile::ImageFile(std::string wanted_filename, bool overwrite) { OpenFile(wanted_filename,overwrite); } ImageFile::~ImageFile() { CloseFile(); } void ImageFile::SetFileTypeFromExtension() { wxString ext = filename.GetExt(); if (ext.IsSameAs("tif") || ext.IsSameAs("tiff")) { file_type = TIFF_FILE; file_type_string = "TIFF"; } else if (ext.IsSameAs("mrc") || ext.IsSameAs("mrcs") || ext.IsSameAs("ccp4")) { file_type = MRC_FILE; file_type_string = "MRC"; } else if (ext.IsSameAs("dm3") || ext.IsSameAs("dm4") || ext.IsSameAs("dm")) { file_type = DM_FILE; file_type_string = "DM"; } else { file_type = UNSUPPORTED_FILE_TYPE; file_type_string = "Unsupported file type"; } } bool ImageFile::OpenFile(std::string wanted_filename, bool overwrite, bool wait_for_file_to_exist) { bool file_seems_ok = false; filename = wanted_filename; SetFileTypeFromExtension(); switch(file_type) { case TIFF_FILE: file_seems_ok = tiff_file.OpenFile(wanted_filename, overwrite, wait_for_file_to_exist); break; case MRC_FILE: file_seems_ok = mrc_file.OpenFile(wanted_filename, overwrite, wait_for_file_to_exist); break; case DM_FILE: file_seems_ok = dm_file.OpenFile(wanted_filename, overwrite, wait_for_file_to_exist); break; default: MyPrintWithDetails("Unsupported file type\n"); MyDebugAssertTrue(false,"Unsupported file type: %s\n",filename.GetFullPath().ToStdString()); abort; break; } return file_seems_ok; } void ImageFile::CloseFile() { switch(file_type) { case TIFF_FILE: tiff_file.CloseFile(); break; case MRC_FILE: mrc_file.CloseFile(); break; case DM_FILE: dm_file.CloseFile(); break; } } void ImageFile::ReadSliceFromDisk(int slice_number, float *output_array) { ReadSlicesFromDisk(slice_number,slice_number,output_array); } void ImageFile::ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array) { switch(file_type) { case TIFF_FILE: tiff_file.ReadSlicesFromDisk(start_slice, end_slice, output_array); break; case MRC_FILE: mrc_file.ReadSlicesFromDisk(start_slice, end_slice, output_array); break; case DM_FILE: dm_file.ReadSlicesFromDisk(start_slice-1, end_slice-1, output_array); break; default: MyPrintWithDetails("Unsupported file type\n"); abort; break; } } void ImageFile::WriteSliceToDisk(int slice_number, float *input_array) { WriteSlicesToDisk(slice_number, slice_number, input_array); } void ImageFile::WriteSlicesToDisk(int start_slice, int end_slice, float *input_array) { switch(file_type) { case TIFF_FILE: tiff_file.WriteSlicesToDisk(start_slice, end_slice, input_array); break; case MRC_FILE: mrc_file.WriteSlicesToDisk(start_slice, end_slice, input_array); break; case DM_FILE: dm_file.WriteSlicesToDisk(start_slice, end_slice, input_array); break; default: MyPrintWithDetails("Unsupported file type\n"); abort; break; } } int ImageFile::ReturnXSize() { switch(file_type) { case TIFF_FILE: return tiff_file.ReturnXSize(); break; case MRC_FILE: return mrc_file.ReturnXSize(); break; case DM_FILE: return dm_file.ReturnXSize(); break; default: MyPrintWithDetails("Unsupported file type\n"); abort; break; } } int ImageFile::ReturnYSize() { switch(file_type) { case TIFF_FILE: return tiff_file.ReturnYSize(); break; case MRC_FILE: return mrc_file.ReturnYSize(); break; case DM_FILE: return dm_file.ReturnYSize(); break; default: MyPrintWithDetails("Unsupported file type\n"); abort; break; } } int ImageFile::ReturnZSize() { switch(file_type) { case TIFF_FILE: return tiff_file.ReturnZSize(); break; case MRC_FILE: return mrc_file.ReturnZSize(); break; case DM_FILE: return dm_file.ReturnZSize(); break; default: MyPrintWithDetails("Unsupported file type\n"); abort; break; } } int ImageFile::ReturnNumberOfSlices() { switch(file_type) { case TIFF_FILE: return tiff_file.ReturnNumberOfSlices(); break; case MRC_FILE: return mrc_file.ReturnNumberOfSlices(); break; case DM_FILE: return dm_file.ReturnNumberOfSlices(); break; default: MyPrintWithDetails("Unsupported file type\n"); abort; break; } } float ImageFile::ReturnPixelSize() { switch(file_type) { case TIFF_FILE: return tiff_file.ReturnPixelSize(); break; case MRC_FILE: return mrc_file.ReturnPixelSize(); break; case DM_FILE: return dm_file.ReturnPixelSize(); break; default: MyPrintWithDetails("Unsupported file type\n"); abort; break; } } bool ImageFile::IsOpen() { switch(file_type) { case TIFF_FILE: return tiff_file.IsOpen(); break; case MRC_FILE: return mrc_file.IsOpen(); break; case DM_FILE: return dm_file.IsOpen(); default: MyPrintWithDetails("Unsupported file type\n"); abort; break; } } void ImageFile::PrintInfo() { wxPrintf("File name: %s\n",filename.GetFullName()); wxPrintf("File type: %s\n",file_type_string); wxPrintf("Dimensions: X = %i Y = %i Z = %i\n",ReturnXSize(),ReturnYSize(),ReturnZSize()); wxPrintf("Number of slices: %i\n",ReturnNumberOfSlices()); } ctffind-4.1.14/src/core/image_file.h000066400000000000000000000021261440356052600171750ustar00rootroot00000000000000/* * Provide a common interface to interact with all the different * files we support (MRC, DM, TIF, etc.) */ enum supported_file_types { MRC_FILE, TIFF_FILE, DM_FILE, UNSUPPORTED_FILE_TYPE }; class ImageFile : public AbstractImageFile { private: // These are the actual file objects doing the work MRCFile mrc_file; TiffFile tiff_file; DMFile dm_file; int file_type; wxString file_type_string; void SetFileTypeFromExtension(); public: ImageFile(); ImageFile(std::string wanted_filename, bool overwrite = false); ~ImageFile(); int ReturnXSize(); int ReturnYSize(); int ReturnZSize(); int ReturnNumberOfSlices(); float ReturnPixelSize(); bool IsOpen(); bool OpenFile(std::string wanted_filename, bool overwrite, bool wait_for_file_to_exist = false); void CloseFile(); void ReadSliceFromDisk(int slice_number, float *output_array); void ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array); void WriteSliceToDisk(int slice_number, float *input_array); void WriteSlicesToDisk(int start_slice, int end_slice, float *input_array); void PrintInfo(); }; ctffind-4.1.14/src/core/job_packager.cpp000066400000000000000000001265261440356052600200710ustar00rootroot00000000000000#include "core_headers.h" void JobPackage::SendJobPackage(wxSocketBase *socket) // package the whole object into a single char stream which can be decoded at the other end.. { SETUP_SOCKET_CODES long counter; long job_counter; long argument_counter; long byte_counter; long command_counter; int length_of_string; int number_of_arguments; int temp_int; int temp_job_number; float temp_float; std::string temp_string; unsigned char* char_pointer; // first work out how long the character array needs to be.. long transfer_size = ReturnEncodedByteTransferSize(); // allocate a character array for the jobs.. unsigned char *transfer_buffer = new unsigned char[transfer_size]; // fill the buffer, first number of jobs char_pointer = (unsigned char*)&number_of_jobs; transfer_buffer[0] = char_pointer[0]; transfer_buffer[1] = char_pointer[1]; transfer_buffer[2] = char_pointer[2]; transfer_buffer[3] = char_pointer[3]; /////////////////////////////////////// // RUN PROFILE ////////////////////////////////////// // number_of_run_commands char_pointer = (unsigned char*)& my_profile.number_of_run_commands; transfer_buffer[4] = char_pointer[0]; transfer_buffer[5] = char_pointer[1]; transfer_buffer[6] = char_pointer[2]; transfer_buffer[7] = char_pointer[3]; // executable name temp_int = my_profile.executable_name.Length(); char_pointer = (unsigned char*)& temp_int; transfer_buffer[8] = char_pointer[0]; transfer_buffer[9] = char_pointer[1]; transfer_buffer[10] = char_pointer[2]; transfer_buffer[11] = char_pointer[3]; byte_counter = 12; for (counter = 0; counter < my_profile.executable_name.Length(); counter++) { transfer_buffer[byte_counter] = my_profile.executable_name.GetChar(counter); byte_counter++; } // gui_address temp_int = my_profile.gui_address.Length(); char_pointer = (unsigned char*)& temp_int; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; for (counter = 0; counter < my_profile.gui_address.Length(); counter++) { transfer_buffer[byte_counter] = my_profile.gui_address.GetChar(counter); byte_counter++; } // controller_address temp_int = my_profile.controller_address.Length(); char_pointer = (unsigned char*)& temp_int; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; for (counter = 0; counter < my_profile.controller_address.Length(); counter++) { transfer_buffer[byte_counter] = my_profile.controller_address.GetChar(counter); byte_counter++; } // now add each run_command for (command_counter = 0; command_counter < my_profile.number_of_run_commands; command_counter++) { length_of_string = my_profile.run_commands[command_counter].command_to_run.Length(); char_pointer = (unsigned char*)&length_of_string; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; // now the contents of the command.. for (counter = 0; counter < length_of_string; counter++) { transfer_buffer[byte_counter] = static_cast (my_profile.run_commands[command_counter].command_to_run[counter]); byte_counter++; } // number of copies.. char_pointer = (unsigned char*) &my_profile.run_commands[command_counter].number_of_copies; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; // delay time in ms.. char_pointer = (unsigned char*) &my_profile.run_commands[command_counter].delay_time_in_ms; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; } // now append all the job info.. /////////////////// // END RUN PROFILE ////////////////////// for (job_counter = 0; job_counter < number_of_jobs; job_counter++) { // job_number for this job char_pointer = (unsigned char*)&jobs[job_counter].job_number; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; // add number of arguments for this job char_pointer = (unsigned char*)&jobs[job_counter].number_of_arguments; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; // for this job we loop over all arguments for (argument_counter = 0; argument_counter < jobs[job_counter].number_of_arguments; argument_counter++) { // ok, what is this argument.. if (jobs[job_counter].arguments[argument_counter].type_of_argument == INTEGER) { // set the descriptor byte transfer_buffer[byte_counter] = INTEGER; byte_counter++; // set the value of the integer.. temp_int = jobs[job_counter].arguments[argument_counter].ReturnIntegerArgument(); char_pointer = (unsigned char*)&temp_int; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; } else if (jobs[job_counter].arguments[argument_counter].type_of_argument == FLOAT) { // set the descriptor byte transfer_buffer[byte_counter] = FLOAT; byte_counter++; // set the value of the float.. temp_float = jobs[job_counter].arguments[argument_counter].ReturnFloatArgument(); char_pointer = (unsigned char*)&temp_float; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; } else if (jobs[job_counter].arguments[argument_counter].type_of_argument == BOOL) { // set the descriptor byte transfer_buffer[byte_counter] = BOOL; byte_counter++; // set the value of the bool.. transfer_buffer[byte_counter] = (unsigned char) jobs[job_counter].arguments[argument_counter].ReturnBoolArgument(); byte_counter++; } else if (jobs[job_counter].arguments[argument_counter].type_of_argument == TEXT) { // set the descriptor byte transfer_buffer[byte_counter] = TEXT; byte_counter++; // add the length of the string.. temp_string = jobs[job_counter].arguments[argument_counter].ReturnStringArgument(); length_of_string = temp_string.length(); char_pointer = (unsigned char*)&length_of_string; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; // now add the contents of the string.. for (counter = 0; counter < length_of_string; counter++) { transfer_buffer[byte_counter] = temp_string[counter]; byte_counter++; } } else { MyPrintWithDetails("Unknown Argument Type!"); DEBUG_ABORT; } } } // now we should everything encoded, so send the information to the socket.. // disable events on the socket.. //socket->SetNotify(wxSOCKET_LOST_FLAG); // inform what we want to do.. WriteToSocket(socket, socket_ready_to_send_job_package, SOCKET_CODE_SIZE, true); // we should get a message saying the socket is ready to receive the data.. ReadFromSocket(socket, &socket_input_buffer, SOCKET_CODE_SIZE, true); // check it is ok.. if (memcmp(socket_input_buffer, socket_send_job_package, SOCKET_CODE_SIZE) == 0) // send it.. { // first - send how many bytes it is.. char_pointer = (unsigned char*)&transfer_size; WriteToSocket(socket, char_pointer, 8, true); // now send the whole buffer.. MyDebugPrint("doing socket write"); WriteToSocket(socket, transfer_buffer, transfer_size, true); } else { MyPrintWithDetails("Oops, didn't understand the reply!"); DEBUG_ABORT; } // restore socket events.. //socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); delete [] transfer_buffer; } void JobPackage::ReceiveJobPackage(wxSocketBase *socket) { SETUP_SOCKET_CODES long counter; long command_counter; long job_counter; long argument_counter; long byte_counter; long transfer_size; int wanted_number_of_jobs; int wanted_number_of_processes; int number_of_run_commands; int number_of_copies; int delay_in_ms; std::string wanted_command_to_run; int length_of_string; int number_of_arguments; int temp_job_number; int temp_int; float temp_float; std::string temp_string; unsigned char* char_pointer; RunProfile temp_run_profile; wxString temp_wxstring; wxString executable_name; wxString gui_address; wxString controller_address; // disable events on the socket.. // socket->SetNotify(wxSOCKET_LOST_FLAG); // socket->SetFlags(wxSOCKET_BLOCK); // Send a message saying we are ready to receive the package WriteToSocket(socket, socket_send_job_package, SOCKET_CODE_SIZE, true); char_pointer = (unsigned char*)&transfer_size; // receive how many bytes we need for the buffer.. ReadFromSocket(socket, char_pointer, 8, true); MyDebugPrint("Package is %li bytes long", transfer_size); // allocate an array.. unsigned char *transfer_buffer = new unsigned char[transfer_size]; // now receive the package.. ReadFromSocket(socket, transfer_buffer, transfer_size, true); wxPrintf("We read %u bytes\n", socket->LastReadCount()); //MyDebugPrint("Received package, decoding job..."); // restore socket events.. // socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); // now we need to decode the buffer // number of jobs char_pointer = (unsigned char*)&wanted_number_of_jobs; char_pointer[0] = transfer_buffer[0]; char_pointer[1] = transfer_buffer[1]; char_pointer[2] = transfer_buffer[2]; char_pointer[3] = transfer_buffer[3]; //MyDebugPrint("There are %i jobs", wanted_number_of_jobs); // number of run commands char_pointer = (unsigned char*)&number_of_run_commands; char_pointer[0] = transfer_buffer[4]; char_pointer[1] = transfer_buffer[5]; char_pointer[2] = transfer_buffer[6]; char_pointer[3] = transfer_buffer[7]; //MyDebugPrint("There are %i commands", number_of_run_commands); // executable name char_pointer = (unsigned char*)& temp_int; char_pointer[0] = transfer_buffer[8]; char_pointer[1] = transfer_buffer[9]; char_pointer[2] = transfer_buffer[10]; char_pointer[3] = transfer_buffer[11]; byte_counter = 12; executable_name = ""; for (counter = 0; counter < temp_int; counter++) { executable_name += transfer_buffer[byte_counter]; byte_counter++; } // gui address char_pointer = (unsigned char*)& temp_int; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; gui_address = ""; for (counter = 0; counter < temp_int; counter++) { gui_address += transfer_buffer[byte_counter]; byte_counter++; } // controller address char_pointer = (unsigned char*)& temp_int; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; controller_address = ""; for (counter = 0; counter < temp_int; counter++) { controller_address += transfer_buffer[byte_counter]; byte_counter++; } // each run command for (command_counter = 0; command_counter < number_of_run_commands; command_counter++) { char_pointer = (unsigned char*)&length_of_string; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; temp_wxstring = ""; // now the contents of the command.. for (counter = 0; counter < length_of_string; counter++) { temp_wxstring += transfer_buffer[byte_counter]; byte_counter++; } // number of copies.. char_pointer = (unsigned char*)&number_of_copies; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // delay_in_ms.. char_pointer = (unsigned char*)&delay_in_ms; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // add the command. temp_run_profile.AddCommand(temp_wxstring, number_of_copies, delay_in_ms); } // now we need to loop over all the jobs.. temp_run_profile.gui_address = gui_address; temp_run_profile.controller_address = controller_address; Reset(temp_run_profile, executable_name, wanted_number_of_jobs); for (job_counter = 0; job_counter < number_of_jobs; job_counter++) { char_pointer = (unsigned char*)&temp_job_number; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // How many arguments are there for this job char_pointer = (unsigned char*)&temp_int; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // reset the job.. jobs[job_counter].Reset(temp_int); jobs[job_counter].job_number = temp_job_number; // for this job we loop over all arguments for (argument_counter = 0; argument_counter < jobs[job_counter].number_of_arguments; argument_counter++) { // ok, what is this argument.. jobs[job_counter].arguments[argument_counter].type_of_argument = int(transfer_buffer[byte_counter]); byte_counter++; if (jobs[job_counter].arguments[argument_counter].type_of_argument == INTEGER) { // read the value of the integer.. char_pointer = (unsigned char*)&temp_int; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // allocate memory jobs[job_counter].arguments[argument_counter].integer_argument = new int; jobs[job_counter].arguments[argument_counter].integer_argument[0] = temp_int; } else if (jobs[job_counter].arguments[argument_counter].type_of_argument == FLOAT) { // read the value of the float.. char_pointer = (unsigned char*)&temp_float; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // allocate memory jobs[job_counter].arguments[argument_counter].float_argument = new float; jobs[job_counter].arguments[argument_counter].float_argument[0] = temp_float; } else if (jobs[job_counter].arguments[argument_counter].type_of_argument == BOOL) { // read the value of the bool.. // allocate memory jobs[job_counter].arguments[argument_counter].bool_argument = new bool; jobs[job_counter].arguments[argument_counter].bool_argument[0] = bool(transfer_buffer[byte_counter]); byte_counter++; } else if (jobs[job_counter].arguments[argument_counter].type_of_argument == TEXT) { // read length of command string char_pointer = (unsigned char*)&length_of_string; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // allocate memory jobs[job_counter].arguments[argument_counter].string_argument = new std::string; jobs[job_counter].arguments[argument_counter].string_argument[0].clear(); // fill the string.. for (counter = 0; counter < length_of_string; counter++) { jobs[job_counter].arguments[argument_counter].string_argument[0] += transfer_buffer[byte_counter]; byte_counter++; } } else { MyPrintWithDetails("Unknown Argument Type!"); DEBUG_ABORT; } } } MyDebugPrint("Job Decoded"); // delete the buffer delete [] transfer_buffer; } long JobPackage::ReturnEncodedByteTransferSize() { long byte_size = 0; long counter; // size of the profile.. byte_size += 8; // number_of_jobs and number_of_run_commands // executable name byte_size += 4; // length of string byte_size += my_profile.executable_name.Length(); // gui_address byte_size += 4; byte_size += my_profile.gui_address.Length(); // controller address byte_size += 4; byte_size += my_profile.controller_address.Length(); for (counter = 0; counter < my_profile.number_of_run_commands; counter++) { byte_size += 4; // length_of_current_command; byte_size += my_profile.run_commands[counter].command_to_run.Length(); // actual text; byte_size += 4; // number_of_copies; byte_size += 4; // delay time in ms } for (counter = 0; counter < number_of_jobs; counter++) { byte_size += jobs[counter].ReturnEncodedByteTransferSize(); } return byte_size; } JobPackage::JobPackage(RunProfile wanted_profile, wxString wanted_executable_name, int wanted_number_of_jobs) { Reset(wanted_profile, wanted_executable_name, wanted_number_of_jobs); } JobPackage::JobPackage() { number_of_jobs = 0; number_of_added_jobs = 0; // memory allocation.. if (number_of_jobs > 0) { if (number_of_jobs == 1) jobs = new RunJob; else jobs = new RunJob[number_of_jobs]; } } JobPackage::~JobPackage() { if (number_of_jobs > 0) { if (number_of_jobs == 1) delete jobs; else delete [] jobs; } } void JobPackage::Reset(RunProfile wanted_profile, wxString wanted_executable_name,int wanted_number_of_jobs) { if (number_of_jobs > 0) { if (number_of_jobs == 1) delete jobs; else delete [] jobs; } number_of_jobs = wanted_number_of_jobs; number_of_added_jobs = 0; // memory allocation.. if (number_of_jobs == 1) jobs = new RunJob; else jobs = new RunJob[number_of_jobs]; my_profile = wanted_profile; my_profile.executable_name = wanted_executable_name; //my_profile.SubstituteExecutableName(wanted_executable_name); } void JobPackage::AddJob(const char *format, ...) { MyDebugAssertTrue(number_of_added_jobs < number_of_jobs, "number of jobs exceeded!"); va_list args; va_start(args, format); jobs[number_of_added_jobs].job_number = number_of_added_jobs; jobs[number_of_added_jobs].SetArguments(format, args); va_end(args); number_of_added_jobs++; } int JobPackage::ReturnNumberOfJobsRemaining() { int number_remaining = 0; for (long counter = 0; counter < number_of_jobs; counter++) { if (jobs[counter].has_been_run == false) number_remaining++; } return number_remaining; } RunJob::RunJob() { job_number = -1; has_been_run = false; number_of_arguments = 0; arguments = NULL; } RunJob::~RunJob() { Deallocate(); } void RunJob::SendJob(wxSocketBase *socket) { SETUP_SOCKET_CODES long counter; long argument_counter; long byte_counter = 0; int length_of_string; int temp_int; float temp_float; std::string temp_string; unsigned char* char_pointer; long transfer_size = ReturnEncodedByteTransferSize(); // allocate a character array for the jobs.. unsigned char *transfer_buffer = new unsigned char[transfer_size]; // job_number char_pointer = (unsigned char*)&job_number; transfer_buffer[0] = char_pointer[0]; transfer_buffer[1] = char_pointer[1]; transfer_buffer[2] = char_pointer[2]; transfer_buffer[3] = char_pointer[3]; // number of arguments.. char_pointer = (unsigned char*)&number_of_arguments; transfer_buffer[4] = char_pointer[0]; transfer_buffer[5] = char_pointer[1]; transfer_buffer[6] = char_pointer[2]; transfer_buffer[7] = char_pointer[3]; byte_counter = 8; for (argument_counter = 0; argument_counter < number_of_arguments; argument_counter++) { // ok, what is this argument.. if (arguments[argument_counter].type_of_argument == INTEGER) { // set the descriptor byte transfer_buffer[byte_counter] = INTEGER; byte_counter++; // set the value of the integer.. temp_int = arguments[argument_counter].ReturnIntegerArgument(); char_pointer = (unsigned char*)&temp_int; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; } else if (arguments[argument_counter].type_of_argument == FLOAT) { // set the descriptor byte transfer_buffer[byte_counter] = FLOAT; byte_counter++; // set the value of the float.. temp_float = arguments[argument_counter].ReturnFloatArgument(); char_pointer = (unsigned char*)&temp_float; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; } else if (arguments[argument_counter].type_of_argument == BOOL) { // set the descriptor byte transfer_buffer[byte_counter] = BOOL; byte_counter++; // set the value of the bool.. transfer_buffer[byte_counter] = (unsigned char) arguments[argument_counter].ReturnBoolArgument(); byte_counter++; } else if (arguments[argument_counter].type_of_argument == TEXT) { // set the descriptor byte transfer_buffer[byte_counter] = TEXT; byte_counter++; // add the length of the string.. temp_string = arguments[argument_counter].ReturnStringArgument(); length_of_string = temp_string.length(); char_pointer = (unsigned char*)&length_of_string; transfer_buffer[byte_counter] = char_pointer[0]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[1]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[2]; byte_counter++; transfer_buffer[byte_counter] = char_pointer[3]; byte_counter++; // now add the contents of the string.. for (counter = 0; counter < length_of_string; counter++) { transfer_buffer[byte_counter] = temp_string[counter]; byte_counter++; } } else { MyPrintWithDetails("Unrecognized argument!"); DEBUG_ABORT; } } // now we should everything encoded, so send the information to the socket.. // disable events on the socket.. // socket->SetNotify(wxSOCKET_LOST_FLAG); // inform what we want to do.. WriteToSocket(socket, socket_ready_to_send_single_job, SOCKET_CODE_SIZE, true); // we should get a message saying the socket is ready to receive the data.. // ReadFromSocket(socket, &socket_input_buffer, SOCKET_CODE_SIZE); // check it is ok.. //if (memcmp(socket_input_buffer, socket_send_single_job, SOCKET_CODE_SIZE) == 0) // send it.. //{ // first - send how many bytes it is.. char_pointer = (unsigned char*)&transfer_size; WriteToSocket(socket, char_pointer, 8, true); // now send the whole buffer.. WriteToSocket(socket, transfer_buffer, transfer_size, true); // } // else // { // MyPrintWithDetails("Oops, didn't understand the reply!"); // DEBUG_ABORT; // } // restore socket events.. // socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); delete [] transfer_buffer; } void RunJob::RecieveJob(wxSocketBase *socket) { SETUP_SOCKET_CODES long counter; long argument_counter; long byte_counter; long transfer_size; int length_of_string; int number_of_arguments; int temp_int; int temp_job_number; float temp_float; std::string temp_string; unsigned char* char_pointer; // disable events on the socket.. // socket->SetNotify(wxSOCKET_LOST_FLAG); // Send a message saying we are ready to receive the package //WriteToSocket(socket, socket_send_single_job, SOCKET_CODE_SIZE); char_pointer = (unsigned char*)&transfer_size; // receive how many bytes we need for the buffer.. ReadFromSocket(socket, char_pointer, 8, true); // allocate an array.. unsigned char *transfer_buffer = new unsigned char[transfer_size]; // now receive the package.. ReadFromSocket(socket, transfer_buffer, transfer_size, true); // restore socket events.. // socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); // now we need to decode the buffer byte_counter = 0; // job id char_pointer = (unsigned char*)&temp_job_number; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // How many arguments are there for this job char_pointer = (unsigned char*)&number_of_arguments; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // reset the job.. Reset(number_of_arguments); job_number = temp_job_number; // for this job we loop over all arguments for (argument_counter = 0; argument_counter < number_of_arguments; argument_counter++) { // ok, what is this argument.. arguments[argument_counter].type_of_argument = int(transfer_buffer[byte_counter]); byte_counter++; if (arguments[argument_counter].type_of_argument == INTEGER) { // read the value of the integer.. char_pointer = (unsigned char*)&temp_int; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // allocate memory arguments[argument_counter].integer_argument = new int; arguments[argument_counter].integer_argument[0] = temp_int; } else if (arguments[argument_counter].type_of_argument == FLOAT) { // read the value of the float.. char_pointer = (unsigned char*)&temp_float; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // allocate memory arguments[argument_counter].float_argument = new float; arguments[argument_counter].float_argument[0] = temp_float; } else if (arguments[argument_counter].type_of_argument == BOOL) { // read the value of the bool.. // allocate memory arguments[argument_counter].bool_argument = new bool; arguments[argument_counter].bool_argument[0] = bool(transfer_buffer[byte_counter]); byte_counter++; } else if (arguments[argument_counter].type_of_argument == TEXT) { // read length of command string char_pointer = (unsigned char*)&length_of_string; char_pointer[0] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[1] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[2] = transfer_buffer[byte_counter]; byte_counter++; char_pointer[3] = transfer_buffer[byte_counter]; byte_counter++; // allocate memory arguments[argument_counter].string_argument = new std::string; arguments[argument_counter].string_argument[0].clear(); // fill the string.. for (counter = 0; counter < length_of_string; counter++) { arguments[argument_counter].string_argument[0] += transfer_buffer[byte_counter]; byte_counter++; } } else { MyDebugPrint("Unknown Argument!!"); DEBUG_ABORT; } } // delete the buffer delete [] transfer_buffer; } void RunJob::Deallocate() { if (number_of_arguments > 0) { if (number_of_arguments == 1) delete arguments; else delete [] arguments; } } void RunJob::ManualSetArguments(const char *format, ...) { va_list args; va_start(args, format); SetArguments(format, args); va_end(args); } void RunJob::SetArguments(const char *format, va_list args) { Deallocate(); // work out the number of arguments number_of_arguments = strlen(format); // allocate space if (number_of_arguments == 1) arguments = new RunArgument; else arguments = new RunArgument[number_of_arguments]; // fill the arguments.. long counter = 0; while (*format!= '\0') { if (*format == 't' || *format == 's') // argument is text.. { arguments[counter].SetStringArgument(va_arg(args, const char *)); } else if (*format == 'f') // float { arguments[counter].SetFloatArgument(va_arg(args, double)); } else if (*format == 'i') // integer { arguments[counter].SetIntArgument(va_arg(args, int)); } else if (*format == 'b') // bool { arguments[counter].SetBoolArgument(va_arg(args, int)); } else { MyPrintWithDetails("Error: Unknown format character!\n"); } counter++; ++format; } } void RunJob::Reset(int wanted_number_of_arguments) { Deallocate(); number_of_arguments = wanted_number_of_arguments; if (number_of_arguments == 1) arguments = new RunArgument; else arguments = new RunArgument[number_of_arguments]; job_number = -1; has_been_run = false; } void RunJob::PrintAllArguments() { wxPrintf("\n\n"); for (int counter = 0; counter < number_of_arguments; counter++) { if (arguments[counter].type_of_argument == TEXT) { wxPrintf("Argument %3i is a string : %s\n", counter, arguments[counter].ReturnStringArgument()); } else if (arguments[counter].type_of_argument == INTEGER) { wxPrintf("Argument %3i is an integer : %i\n", counter, arguments[counter].ReturnIntegerArgument()); } else if (arguments[counter].type_of_argument == FLOAT) { wxPrintf("Argument %3i is a float : %f\n", counter, arguments[counter].ReturnFloatArgument()); } else if (arguments[counter].type_of_argument == BOOL) { wxPrintf("Argument %3i is a bool : ", counter); if (arguments[counter].ReturnBoolArgument() == true) wxPrintf("TRUE\n"); else wxPrintf("FALSE\n"); } } } long RunJob::ReturnEncodedByteTransferSize() { long byte_size = 0; long counter; for (counter = 0; counter < number_of_arguments; counter++) { byte_size += arguments[counter].ReturnEncodedByteTransferSize(); } return byte_size + 8; // argument bytes, + 4 bytes for the number of arguments + 4 bytes for job_number } RunArgument::RunArgument() { is_allocated = false; type_of_argument = NONE; string_argument = NULL; integer_argument = NULL; float_argument = NULL; bool_argument = NULL; } RunArgument::~RunArgument() { if (is_allocated == true) Deallocate(); } void RunArgument::Deallocate() { if (type_of_argument == TEXT) delete string_argument; else if (type_of_argument == INTEGER) delete integer_argument; else if (type_of_argument == FLOAT) delete float_argument; else if (type_of_argument == BOOL) delete bool_argument; is_allocated = false; } long RunArgument::ReturnEncodedByteTransferSize() { MyDebugAssertTrue(type_of_argument != NONE, "Can't calculate size of a nothing argument!!"); if (type_of_argument == TEXT) return string_argument->length() + 4 + 1; // descriptor byte + length of string (4 bytes) + 1 byte per character else if (type_of_argument == BOOL) return 2; // descriptor bytes + bool bytes else return 5; // descriptor byte + 4 data bytes } void RunArgument::SetStringArgument(const char *wanted_text) { if (is_allocated == true) Deallocate(); type_of_argument = TEXT; string_argument = new std::string; string_argument[0] = wanted_text; is_allocated = true; } void RunArgument::SetIntArgument(int wanted_argument) { if (is_allocated == true) Deallocate(); type_of_argument = INTEGER; integer_argument = new int; integer_argument[0] = wanted_argument; is_allocated = true; } void RunArgument::SetFloatArgument(float wanted_argument) { if (is_allocated == true) Deallocate(); type_of_argument = FLOAT; float_argument = new float; float_argument[0] = wanted_argument; is_allocated = true; } void RunArgument::SetBoolArgument(bool wanted_argument) { if (is_allocated == true) Deallocate(); type_of_argument = BOOL; bool_argument = new bool; bool_argument[0] = wanted_argument; is_allocated = true; } #include // this is a magic incantation which must be done! WX_DEFINE_OBJARRAY(ArrayofJobResults); WX_DEFINE_OBJARRAY(ArrayofJobPackages); JobResult::JobResult() { job_number = -1; result_size = 0; result_data = NULL; } JobResult::JobResult(int wanted_result_size, float *wanted_result_data) { SetResult(wanted_result_size, wanted_result_data); } JobResult::~JobResult() { if (result_size != 0 && result_data != NULL) { delete [] result_data; } } JobResult::JobResult( const JobResult &obj) // copy contructor { result_size = 0; result_data = NULL; job_number = obj.job_number; SetResult(obj.result_size, obj.result_data); } JobResult & JobResult::operator = (const JobResult *other_result) { // Check for self assignment if(this != other_result) { job_number = other_result->job_number; SetResult(other_result->result_size, other_result->result_data); } return *this; } JobResult & JobResult::operator = (const JobResult &other_result) { *this = &other_result; return *this; } void JobResult::SetResult(int wanted_result_size, float *wanted_result_data) { if (result_size != 0 || result_data != NULL) { delete [] result_data; } result_size = wanted_result_size; if (wanted_result_size > 0) { result_data = new float[result_size]; for (int counter = 0; counter < result_size; counter++) { result_data[counter] = wanted_result_data[counter]; } } else { result_data = NULL; } } void JobResult::SendToSocket(wxSocketBase *wanted_socket) { char job_number_and_result_size[8]; unsigned char *byte_pointer; byte_pointer = (unsigned char*) &job_number; job_number_and_result_size[0] = byte_pointer[0]; job_number_and_result_size[1] = byte_pointer[1]; job_number_and_result_size[2] = byte_pointer[2]; job_number_and_result_size[3] = byte_pointer[3]; byte_pointer = (unsigned char*) &result_size; job_number_and_result_size[4] = byte_pointer[0]; job_number_and_result_size[5] = byte_pointer[1]; job_number_and_result_size[6] = byte_pointer[2]; job_number_and_result_size[7] = byte_pointer[3]; WriteToSocket(wanted_socket, &job_number_and_result_size, 8, true); if (result_size > 0) { WriteToSocket(wanted_socket, result_data, result_size * 4, true); } } void JobResult::ReceiveFromSocket(wxSocketBase *wanted_socket) { char job_number_and_result_size[8]; int new_result_size; unsigned char *byte_pointer; ReadFromSocket(wanted_socket, job_number_and_result_size, 8, true); byte_pointer = (unsigned char*) &job_number; byte_pointer[0] = job_number_and_result_size[0]; byte_pointer[1] = job_number_and_result_size[1]; byte_pointer[2] = job_number_and_result_size[2]; byte_pointer[3] = job_number_and_result_size[3]; byte_pointer = (unsigned char*) &new_result_size; byte_pointer[0] = job_number_and_result_size[4]; byte_pointer[1] = job_number_and_result_size[5]; byte_pointer[2] = job_number_and_result_size[6]; byte_pointer[3] = job_number_and_result_size[7]; if (new_result_size != result_size) { if (result_size != 0 && result_data != NULL) { delete [] result_data; } result_size = new_result_size; if (result_size == 0) { result_data = NULL; } else result_data = new float[new_result_size]; } if (result_size > 0) { ReadFromSocket(wanted_socket, result_data, result_size*4, true); } } void ReceiveResultQueueFromSocket(wxSocketBase *socket, ArrayofJobResults &my_array) { int total_number_of_bytes; int number_of_jobs; int job_counter; int job_number; int result_size; int byte_counter; unsigned char *byte_pointer; int result_byte_counter; JobResult temp_result; // clear the array my_array.Clear(); // recieve the total number of bytes.. ReadFromSocket(socket, &total_number_of_bytes, 4, true); //wxPrintf("(Recieve) Total Size is %i bytes\n", total_number_of_bytes); // make the array.. unsigned char *buffer_array = new unsigned char[total_number_of_bytes]; // receieve ReadFromSocket(socket, buffer_array, total_number_of_bytes, true); byte_pointer = (unsigned char*) &number_of_jobs; byte_pointer[0] = buffer_array[0]; byte_pointer[1] = buffer_array[1]; byte_pointer[2] = buffer_array[2]; byte_pointer[3] = buffer_array[3]; byte_counter = 4; for (job_counter = 0; job_counter < number_of_jobs; job_counter++) { byte_pointer = (unsigned char*) &job_number; byte_pointer[0] = buffer_array[byte_counter]; byte_counter++; byte_pointer[1] = buffer_array[byte_counter]; byte_counter++; byte_pointer[2] = buffer_array[byte_counter]; byte_counter++; byte_pointer[3] = buffer_array[byte_counter]; byte_counter++; byte_pointer = (unsigned char*) &result_size; byte_pointer[0] = buffer_array[byte_counter]; byte_counter++; byte_pointer[1] = buffer_array[byte_counter]; byte_counter++; byte_pointer[2] = buffer_array[byte_counter]; byte_counter++; byte_pointer[3] = buffer_array[byte_counter]; byte_counter++; temp_result.job_number = job_number; if (temp_result.result_size != result_size) { if (temp_result.result_size != 0 && temp_result.result_data != NULL) { delete [] temp_result.result_data; } temp_result.result_size = result_size; if (result_size == 0) { temp_result.result_data = NULL; } else temp_result.result_data = new float[result_size]; } for (result_byte_counter = 0; result_byte_counter < result_size; result_byte_counter++) { byte_pointer = (unsigned char*) &temp_result.result_data[result_byte_counter]; if (byte_counter >= total_number_of_bytes) wxPrintf("byte_counter = %i/%i\n", byte_counter, total_number_of_bytes); byte_pointer[0] = buffer_array[byte_counter]; byte_counter++; byte_pointer[1] = buffer_array[byte_counter]; byte_counter++; byte_pointer[2] = buffer_array[byte_counter]; byte_counter++; byte_pointer[3] = buffer_array[byte_counter]; byte_counter++; } // add it to the array. my_array.Add(temp_result); } delete [] buffer_array; } void SendResultQueueToSocket(wxSocketBase *socket, ArrayofJobResults &my_array) { int total_number_of_bytes = 4; // number of results int number_of_jobs = my_array.GetCount(); unsigned char *byte_pointer; int byte_counter = 0; int job_counter; int result_byte_counter; //wxPrintf("there are %i jobs\n", number_of_jobs); for (job_counter = 0; job_counter < number_of_jobs; job_counter++) { total_number_of_bytes += 8; // job_number, result_size total_number_of_bytes += my_array.Item(job_counter).result_size * 4; // actual result // wxPrintf("result size for job %i = %i\n", job_counter, my_array.Item(job_counter).result_size); } //wxPrintf("(Write) Total Size is %i bytes\n", total_number_of_bytes); unsigned char *buffer_array = new unsigned char[total_number_of_bytes]; byte_pointer = (unsigned char*) &number_of_jobs; buffer_array[0] = byte_pointer[0]; buffer_array[1] = byte_pointer[1]; buffer_array[2] = byte_pointer[2]; buffer_array[3] = byte_pointer[3]; byte_counter = 4; for (job_counter = 0; job_counter < number_of_jobs; job_counter++) { byte_pointer = (unsigned char*) &my_array.Item(job_counter).job_number; buffer_array[byte_counter] = byte_pointer[0]; byte_counter++; buffer_array[byte_counter] = byte_pointer[1]; byte_counter++; buffer_array[byte_counter] = byte_pointer[2]; byte_counter++; buffer_array[byte_counter] = byte_pointer[3]; byte_counter++; byte_pointer = (unsigned char*) &my_array.Item(job_counter).result_size; buffer_array[byte_counter] = byte_pointer[0]; byte_counter++; buffer_array[byte_counter] = byte_pointer[1]; byte_counter++; buffer_array[byte_counter] = byte_pointer[2]; byte_counter++; buffer_array[byte_counter] = byte_pointer[3]; byte_counter++; for (result_byte_counter = 0; result_byte_counter < my_array.Item(job_counter).result_size; result_byte_counter++) { byte_pointer = (unsigned char*) &my_array.Item(job_counter).result_data[result_byte_counter]; // wxPrintf("byte_counter = %i\n", byte_counter); buffer_array[byte_counter] = byte_pointer[0]; byte_counter++; buffer_array[byte_counter] = byte_pointer[1]; byte_counter++; buffer_array[byte_counter] = byte_pointer[2]; byte_counter++; buffer_array[byte_counter] = byte_pointer[3]; byte_counter++; } } // send the number of bytes WriteToSocket(socket, &total_number_of_bytes, 4, true); // send the array.. WriteToSocket(socket, buffer_array, total_number_of_bytes, true); delete [] buffer_array; } ctffind-4.1.14/src/core/job_packager.h000066400000000000000000000067711440356052600175350ustar00rootroot00000000000000#define NONE 0 #define TEXT 1 #define INTEGER 2 #define FLOAT 3 #define BOOL 4 // we need a header to describe how to decode the stream. - which i'm about to make up off the top of my head.. SENDER AND RECEIVER MUST HAVE THE SAME ENDIANESS // 4 bytes = number_of_jobs (int) // 4 bytes = number_of_processes (int) // 4 bytes = length_of_command_string (int) // n bytes = command_string (chars) // then we loop over each job.. of which there are (1st 4 bytes) // 4 bytes = number_of_arguments; // 1 byte = type of argument; // (on of following depending on type of argument :-) // 4 bytes - int // 4 bytes - float // 4 bytes - length of text (int) followed by n bytes where n is length of string // 1 byte - bool (0 or 1) class RunArgument { public : bool is_allocated; int type_of_argument; std::string *string_argument; int *integer_argument; float *float_argument; bool *bool_argument; RunArgument(); ~RunArgument(); void Deallocate(); void SetStringArgument(const char *wanted_text); void SetIntArgument(int wanted_argument); void SetFloatArgument(float wanted_argument); void SetBoolArgument(bool wanted_argument); inline std::string ReturnStringArgument() {MyDebugAssertTrue(type_of_argument == TEXT, "Returning wrong type!"); return string_argument[0];} inline int ReturnIntegerArgument() {MyDebugAssertTrue(type_of_argument == INTEGER, "Returning wrong type!"); return integer_argument[0];} inline float ReturnFloatArgument() {MyDebugAssertTrue(type_of_argument == FLOAT, "Returning wrong type!"); return float_argument[0];} inline bool ReturnBoolArgument() {MyDebugAssertTrue(type_of_argument == BOOL, "Returning wrong type!"); return bool_argument[0];} long ReturnEncodedByteTransferSize(); }; class RunJob { public: int job_number; int number_of_arguments; bool has_been_run; RunArgument *arguments; RunJob(); ~RunJob(); void Reset(int wanted_number_of_arguments); void Deallocate(); void SetArguments(const char *format, va_list args); void ManualSetArguments(const char *format, ...); long ReturnEncodedByteTransferSize(); void SendJob(wxSocketBase *socket); void RecieveJob(wxSocketBase *socket); void PrintAllArguments(); }; class JobPackage { public : int number_of_jobs; int number_of_added_jobs; RunProfile my_profile; RunJob *jobs; JobPackage(RunProfile wanted_profile, wxString wanted_executable_name, int wanted_number_of_jobs); JobPackage(); ~JobPackage(); void Reset(RunProfile wanted_profile, wxString wanted_executable_name, int wanted_number_of_jobs); void AddJob(const char *format, ...); void SendJobPackage(wxSocketBase *socket); void ReceiveJobPackage(wxSocketBase *socket); long ReturnEncodedByteTransferSize(); int ReturnNumberOfJobsRemaining(); }; WX_DECLARE_OBJARRAY(JobPackage, ArrayofJobPackages); class JobResult { public: int job_number; int result_size; float *result_data; JobResult(); JobResult(int wanted_result_size, float *wanted_result_data); JobResult( const JobResult &obj); // copy contructor ~JobResult(); JobResult & operator = (const JobResult &other_result); JobResult & operator = (const JobResult *other_result); void SetResult(int wanted_result_size, float *wanted_result_data); void SendToSocket(wxSocketBase *wanted_socket); void ReceiveFromSocket(wxSocketBase *wanted_socket); }; WX_DECLARE_OBJARRAY(JobResult, ArrayofJobResults); void ReceiveResultQueueFromSocket(wxSocketBase *socket, ArrayofJobResults &my_array); void SendResultQueueToSocket(wxSocketBase *socket, ArrayofJobResults &my_array); ctffind-4.1.14/src/core/job_tracker.cpp000066400000000000000000000100461440356052600177340ustar00rootroot00000000000000#include "core_headers.h" JobTracker::JobTracker() { total_number_of_jobs = 0; total_running_processes = 0; total_number_of_finished_jobs = 0; time_of_last_remaining_time_call = 0; start_time = 0; last_update_time = 0; last_update_time_total_running_processes = 0; last_update_seconds_per_job_per_process = 0; time_remaining.hours = 99; time_remaining.minutes = 99; time_remaining.seconds = 99; old_time_remaining.hours = -1; old_time_remaining.minutes = -1; old_time_remaining.seconds = -1; old_percent_complete = -1; } JobTracker::~JobTracker() { } void JobTracker::StartTracking(int wanted_total_number_of_jobs) { total_number_of_jobs = wanted_total_number_of_jobs; total_running_processes = 0; total_number_of_finished_jobs = 0; start_time = time(NULL); last_update_time = start_time; last_update_seconds_per_job_per_process = -1; last_update_time_total_running_processes = 0; time_remaining.hours = 99; time_remaining.minutes = 99; time_remaining.seconds = 99; old_time_remaining.hours = -1; old_time_remaining.minutes = -1; old_time_remaining.seconds = -1; } void JobTracker::AddConnection() { total_running_processes++; } void JobTracker::MarkJobFinished() { long current_time = time(NULL); long seconds_per_job_per_process_since_last_update; long time_since_last_update = current_time - last_update_time; long total_time = current_time - start_time; float naive_time_per_process = (float(total_time) / float(total_number_of_finished_jobs)); /* if (last_update_time_total_running_processes == 0) { // this is the first job, and provides us with an estimate for how long one job takes.. last_update_seconds_per_job_per_process = time_since_last_update; } else { seconds_per_job_per_process_since_last_update = float(time_since_last_update) / float(last_update_time_total_running_processes); last_update_seconds_per_job_per_process *= float(total_number_of_finished_jobs); last_update_seconds_per_job_per_process += float(seconds_per_job_per_process_since_last_update); last_update_seconds_per_job_per_process /= float(total_number_of_finished_jobs + 1); } //wxPrintf("Job finished new process time = %f seconds\nnaive time = %f seconds\n", last_update_seconds_per_job_per_process, naive_time_per_process); total_number_of_finished_jobs++; last_update_time_total_running_processes = total_running_processes; if (naive_time_per_process < last_update_seconds_per_job_per_process) last_update_seconds_per_job_per_process = naive_time_per_process;*/ total_number_of_finished_jobs++; last_update_seconds_per_job_per_process = naive_time_per_process; } TimeRemaining JobTracker::ReturnRemainingTime() { long current_time = time(NULL); if (current_time - time_of_last_remaining_time_call >= 1) { long seconds_remaining = (total_number_of_jobs - total_number_of_finished_jobs) * last_update_seconds_per_job_per_process; if (seconds_remaining > 3600) time_remaining.hours = seconds_remaining / 3600; else time_remaining.hours = 0; if (seconds_remaining > 60) time_remaining.minutes = (seconds_remaining / 60) - (time_remaining.hours * 60); else time_remaining.minutes = 0; time_remaining.seconds = seconds_remaining - ((time_remaining.hours * 60 + time_remaining.minutes) * 60); time_of_last_remaining_time_call = current_time; } //wxPrintf("Per process = %f, Returning %ih:%im:%is\n", last_update_seconds_per_job_per_process, time_remaining.hours, time_remaining.minutes, time_remaining.seconds); return time_remaining; } bool JobTracker::ShouldUpdate() { TimeRemaining new_time_remaining = ReturnRemainingTime(); int new_percentage_complete = ReturnPercentCompleted(); bool should_update = false; if (old_percent_complete != new_percentage_complete) { old_percent_complete = new_percentage_complete; should_update = true; } if (new_time_remaining.hours != old_time_remaining.hours || new_time_remaining.minutes != old_time_remaining.minutes || new_time_remaining.seconds != old_time_remaining.seconds) { old_time_remaining = new_time_remaining; should_update = true; } return should_update; } ctffind-4.1.14/src/core/job_tracker.h000066400000000000000000000016661440356052600174110ustar00rootroot00000000000000typedef struct TimeRemaining { int hours; int minutes; int seconds; } TimeRemaining; class JobTracker { public : int total_number_of_jobs; int total_running_processes; int total_number_of_finished_jobs; int last_update_time_total_running_processes; long start_time; long last_update_time; float last_update_seconds_per_job_per_process; long time_of_last_remaining_time_call; int old_percent_complete; TimeRemaining old_time_remaining; TimeRemaining time_remaining; JobTracker(); ~JobTracker(); void StartTracking(int wanted_total_number_of_jobs); void AddConnection(); void MarkJobFinished(); TimeRemaining ReturnRemainingTime(); inline int ReturnPercentCompleted() {return int(myround((float(total_number_of_finished_jobs) / float(total_number_of_jobs)) * 100.0)); wxPrintf("Returning %i%\n", int(myround((float(total_number_of_finished_jobs) / float(total_number_of_jobs)) * 100.0)));}; bool ShouldUpdate(); }; ctffind-4.1.14/src/core/local_resolution_estimator.h000066400000000000000000000065701440356052600225670ustar00rootroot00000000000000// Compute local resolution estimates class LocalResolutionEstimator { public: LocalResolutionEstimator(); ~LocalResolutionEstimator(); void SetAllUserParameters( Image *wanted_input_volume_one, Image *wanted_input_volume_two, Image *wanted_mask_volume, int wanted_first_slice, int wanted_last_slice, int wanted_sampling_step, float input_pixel_size_in_Angstroms, int wanted_box_size, float wanted_threshold_snr, // snr treshold. 0.334 gives the 0.143 criterion float wanted_threshold_confidence_n_sigma, // confidence - number of sigmas above estimate we want to be bool wanted_use_fixed_fsc_threshold, float wanted_fixed_fsc_threshold, wxString wanted_symmetry_symbol, bool wanted_whiten_half_maps, int wanted_padding_factor ); void EstimateLocalResolution(Image *local_resolution_volume); private: // Parameters from the user int box_size; int number_of_fsc_shells; float pixel_size_in_Angstroms; float highest_resolution_expected_in_Angstroms; float maximum_radius_in_Angstroms; Image *input_volume_one; Image *input_volume_two; Image *input_volume_mask; // don't bother calculating local resolution outside the mask int first_slice; // don't calculate resolution before first slice (xy plane) of the volume int last_slice; bool use_fixed_fsc_threshold; float fixed_fsc_threshold; float threshold_confidence_n_sigma; // confidence - number of sigmas above estimate we want to be float threshold_snr; // snr treshold. 0.334 gives the 0.143 criterion float resolution_value_before_first_shell; //40.0;// float resolution_value_where_wont_estimate; bool whiten_half_maps; int padding_factor; // Internal Image box_one_no_padding; Image box_two_no_padding; Image box_one; Image box_two; int *shell_number_lut; // a look-up table: for each voxel in the local_volumes, remember what fsc shell we're in bool shell_number_lut_is_allocated; int sampling_step; // we don't necessarily need to estimate the resolution at every voxel int symmetry_redundancy; // Private methods void AllocateShellNumberLUT(); void DeallocateShellNumberLUT(); void PopulateShellNumberLUT(); void CountIndependentVoxelsPerShell(float number_of_independent_voxels[], float wanted_scaling_factor); void ComputeFSCThresholdBasedOnUnbiasedSNREstimator(float number_of_independent_voxels[], float fsc_threshold[] ); void ComputeLocalFSCAndCompareToThreshold(float fsc_threshold[], Image *local_resolution_volume, Image box_mask); void AllocateLocalVolumes(); void DeallocateLocalVolumes(); void SetInputVolumes(Image *wanted_input_volume_one, Image *wanted_input_volume_two, Image *wanted_mask_volume); inline void SetPixelSize(float wanted_pixel_size_in_Angstroms) {pixel_size_in_Angstroms = wanted_pixel_size_in_Angstroms;}; inline void SetBoxSize(int wanted_box_size) {box_size = wanted_box_size;}; float ReturnResolutionOfIntersectionBetweenFSCAndThreshold(float resolution_one, float resolution_two, float fsc_one, float fsc_two, float threshold_one, float threshold_two); // The key equations float SigmaZSquaredAuto(float number_of_independent_voxels); float SigmaZSquared(float rho, float number_of_independent_voxels); float RhoThreshold(float snr_threshold_halfmaps, float number_of_sigmas, float number_of_independent_voxels, int number_of_iterations = 2); }; ctffind-4.1.14/src/core/matrix.cpp000066400000000000000000000454271440356052600167660ustar00rootroot00000000000000#include "core_headers.h" // these are needed for the simple rotation matrix creation, which uses very optimized code from an old game programming library i wrote when i was about 12, // think i got it from a book i had about game programming in c.. it's probably slower than what the compiler would do these days. #define AL_PI 3.14159265358979323846 #define _AL_SINCOS(x, s, c) __asm__ ("fsincos" : "=t" (c), "=u" (s) : "0" (x)) #define FLOATSINCOS(x, s, c) _AL_SINCOS((x) * AL_PI / 128.0, s ,c) #define MAKE_ROTATION_f(x, y, z) \ float sin_x, cos_x; \ float sin_y, cos_y; \ float sin_z, cos_z; \ float sinx_siny, cosx_siny; \ \ FLOATSINCOS(x, sin_x, cos_x); \ FLOATSINCOS(y, sin_y, cos_y); \ FLOATSINCOS(z, sin_z, cos_z); \ \ sinx_siny = sin_x * sin_y; \ cosx_siny = cos_x * sin_y; #define R00_f (cos_y * cos_z) #define R10_f ((sinx_siny * cos_z) - (cos_x * sin_z)) #define R20_f ((cosx_siny * cos_z) + (sin_x * sin_z)) #define R01_f (cos_y * sin_z) #define R11_f ((sinx_siny * sin_z) + (cos_x * cos_z)) #define R21_f ((cosx_siny * sin_z) - (sin_x * cos_z)) #define R02_f (-sin_y) #define R12_f (sin_x * cos_y) #define R22_f (cos_x * cos_y) RotationMatrix::RotationMatrix() { SetToConstant(0.0); } RotationMatrix RotationMatrix::operator + (const RotationMatrix &other) { RotationMatrix temp_matrix; temp_matrix.m[0][0] = this->m[0][0] + other.m[0][0]; temp_matrix.m[0][1] = this->m[0][1] + other.m[0][1]; temp_matrix.m[0][2] = this->m[0][2] + other.m[0][2]; temp_matrix.m[1][0] = this->m[1][0] + other.m[1][0]; temp_matrix.m[1][1] = this->m[1][1] + other.m[1][1]; temp_matrix.m[1][2] = this->m[1][2] + other.m[1][2]; temp_matrix.m[2][0] = this->m[2][0] + other.m[2][0]; temp_matrix.m[2][1] = this->m[2][1] + other.m[2][1]; temp_matrix.m[2][2] = this->m[2][2] + other.m[2][2]; return temp_matrix; } RotationMatrix RotationMatrix::operator - (const RotationMatrix &other) { RotationMatrix temp_matrix; temp_matrix.m[0][0] = this->m[0][0] - other.m[0][0]; temp_matrix.m[0][1] = this->m[0][1] - other.m[0][1]; temp_matrix.m[0][2] = this->m[0][2] - other.m[0][2]; temp_matrix.m[1][0] = this->m[1][0] - other.m[1][0]; temp_matrix.m[1][1] = this->m[1][1] - other.m[1][1]; temp_matrix.m[1][2] = this->m[1][2] - other.m[1][2]; temp_matrix.m[2][0] = this->m[2][0] - other.m[2][0]; temp_matrix.m[2][1] = this->m[2][1] - other.m[2][1]; temp_matrix.m[2][2] = this->m[2][2] - other.m[2][2]; return temp_matrix; } RotationMatrix RotationMatrix::operator * (const RotationMatrix &other) { RotationMatrix temp_matrix; temp_matrix.m[0][0] = this->m[0][0] * other.m[0][0] + this->m[0][1] * other.m[1][0] + this->m[0][2] * other.m[2][0]; temp_matrix.m[0][1] = this->m[0][0] * other.m[0][1] + this->m[0][1] * other.m[1][1] + this->m[0][2] * other.m[2][1]; temp_matrix.m[0][2] = this->m[0][0] * other.m[0][2] + this->m[0][1] * other.m[1][2] + this->m[0][2] * other.m[2][2]; temp_matrix.m[1][0] = this->m[1][0] * other.m[0][0] + this->m[1][1] * other.m[1][0] + this->m[1][2] * other.m[2][0]; temp_matrix.m[1][1] = this->m[1][0] * other.m[0][1] + this->m[1][1] * other.m[1][1] + this->m[1][2] * other.m[2][1]; temp_matrix.m[1][2] = this->m[1][0] * other.m[0][2] + this->m[1][1] * other.m[1][2] + this->m[1][2] * other.m[2][2]; temp_matrix.m[2][0] = this->m[2][0] * other.m[0][0] + this->m[2][1] * other.m[1][0] + this->m[2][2] * other.m[2][0]; temp_matrix.m[2][1] = this->m[2][0] * other.m[0][1] + this->m[2][1] * other.m[1][1] + this->m[2][2] * other.m[2][1]; temp_matrix.m[2][2] = this->m[2][0] * other.m[0][2] + this->m[2][1] * other.m[1][2] + this->m[2][2] * other.m[2][2]; return temp_matrix; } RotationMatrix &RotationMatrix::operator = (const RotationMatrix &other) // &other contains the address of the other matrix { *this = &other; return *this; } RotationMatrix &RotationMatrix::operator = (const RotationMatrix *other) // *other is a pointer to the other matrix { // Check for self assignment if (this != other) { this->m[0][0] = other->m[0][0]; this->m[0][1] = other->m[0][1]; this->m[0][2] = other->m[0][2]; this->m[1][0] = other->m[1][0]; this->m[1][1] = other->m[1][1]; this->m[1][2] = other->m[1][2]; this->m[2][0] = other->m[2][0]; this->m[2][1] = other->m[2][1]; this->m[2][2] = other->m[2][2]; } return *this; } RotationMatrix &RotationMatrix::operator += (const RotationMatrix &other) { *this += &other; return *this; } RotationMatrix &RotationMatrix::operator += (const RotationMatrix *other) { this->m[0][0] += other->m[0][0]; this->m[0][1] += other->m[0][1]; this->m[0][2] += other->m[0][2]; this->m[1][0] += other->m[1][0]; this->m[1][1] += other->m[1][1]; this->m[1][2] += other->m[1][2]; this->m[2][0] += other->m[2][0]; this->m[2][1] += other->m[2][1]; this->m[2][2] += other->m[2][2]; return *this; } RotationMatrix &RotationMatrix::operator -= (const RotationMatrix &other) { *this -= &other; return *this; } RotationMatrix &RotationMatrix::operator -= (const RotationMatrix *other) { this->m[0][0] -= other->m[0][0]; this->m[0][1] -= other->m[0][1]; this->m[0][2] -= other->m[0][2]; this->m[1][0] -= other->m[1][0]; this->m[1][1] -= other->m[1][1]; this->m[1][2] -= other->m[1][2]; this->m[2][0] -= other->m[2][0]; this->m[2][1] -= other->m[2][1]; this->m[2][2] -= other->m[2][2]; return *this; } RotationMatrix &RotationMatrix::operator *= (const RotationMatrix &other) { *this *= &other; return *this; } RotationMatrix &RotationMatrix::operator *= (const RotationMatrix *other) { RotationMatrix temp_matrix; temp_matrix = *this * *other; *this = temp_matrix; return *this; } RotationMatrix RotationMatrix::ReturnTransposed() { RotationMatrix temp_matrix; temp_matrix.m[0][0] = this->m[0][0]; temp_matrix.m[0][1] = this->m[1][0]; temp_matrix.m[0][2] = this->m[2][0]; temp_matrix.m[1][0] = this->m[0][1]; temp_matrix.m[1][1] = this->m[1][1]; temp_matrix.m[1][2] = this->m[2][1]; temp_matrix.m[2][0] = this->m[0][2]; temp_matrix.m[2][1] = this->m[1][2]; temp_matrix.m[2][2] = this->m[2][2]; return temp_matrix; } void RotationMatrix::SetToIdentity() { this->m[0][0] = 1.0; this->m[1][0] = 0.0; this->m[2][0] = 0.0; this->m[0][1] = 0.0; this->m[1][1] = 1.0; this->m[2][1] = 0.0; this->m[0][2] = 0.0; this->m[1][2] = 0.0; this->m[2][2] = 1.0; } void RotationMatrix::SetToRotation(float input_x, float input_y, float input_z) { float x = (256.0 / 360.0) * input_x; float y = (256.0 / 360.0) * input_y; float z = (256.0 / 360.0) * input_z; MAKE_ROTATION_f(x, y, z); /* m->v[0][0] = R00_f; m->v[0][1] = R01_f; m->v[0][2] = R02_f; m->v[1][0] = R10_f; m->v[1][1] = R11_f; m->v[1][2] = R12_f; m->v[2][0] = R20_f; m->v[2][1] = R21_f; m->v[2][2] = R22_f; m->t[0] = m->t[1] = m->t[2] = 0;*/ this->m[0][0] = R00_f; this->m[1][0] = R01_f; this->m[2][0] = R02_f; this->m[0][1] = R10_f; this->m[1][1] = R11_f; this->m[2][1] = R12_f; this->m[0][2] = R20_f; this->m[1][2] = R21_f; this->m[2][2] = R22_f; } void RotationMatrix::ConvertToValidEulerAngles(float &output_phi_in_degrees, float &output_theta_in_degrees, float &output_psi_in_degrees) { // taken from Richard Henderson's ROT2EUL function. float cos_theta; float sin_theta; float cos_phi; float sin_phi; float cos_psi; float sin_psi; // first get cos(theta),theta and sin(theta) cos_theta = std::max(-1.0f, std::min(1.0f, m[2][2])); sin_theta = sqrtf(std::max(0.0f, 1-powf(m[2][2], 2))); output_theta_in_degrees = rad_2_deg(acosf(cos_theta)); //for theta not equal to 0 or 180, PHI, PSI are unique if (fabsf(fabsf(cos_theta) - 1.0f) > 0.00001) { cos_phi = m[0][2] / sin_theta; sin_phi = m[1][2] / sin_theta; cos_phi = std::max(-1.0f, std::min(1.0f, cos_phi)); output_phi_in_degrees = acosf(cos_phi); if (sin_phi < 0.0f) output_phi_in_degrees = -output_phi_in_degrees; output_phi_in_degrees = rad_2_deg(output_phi_in_degrees); cos_psi = -m[2][0] / sin_theta; sin_psi = m[2][1] / sin_theta; cos_psi = std::max(-1.0f, std::min(1.0f, cos_psi)); output_psi_in_degrees = acosf(cos_psi); if (sin_psi < 0.0f) output_psi_in_degrees = -output_psi_in_degrees; output_psi_in_degrees = rad_2_deg(output_psi_in_degrees); } else { // for THETA=0/180, PHI and PSI can have an infinite number of values, only // [PSI-PHI] is defined, so PHI can be set to zero without restriction output_phi_in_degrees = 0.0f; cos_psi = m[0][0]; sin_psi = m[1][0]; cos_psi = std::max(-1.0f, std::min(1.0f, cos_psi)); output_psi_in_degrees = acosf(cos_psi); if (sin_psi <= 0.0f) output_psi_in_degrees = -output_psi_in_degrees; output_psi_in_degrees = rad_2_deg(output_psi_in_degrees); } // check we are close to original rotation matrix, if not refine.. RotationMatrix test_matrix; test_matrix.SetToEulerRotation(output_phi_in_degrees, output_theta_in_degrees, output_psi_in_degrees); bool should_throw_error = false; if (fabsf(test_matrix.m[0][0] - this->m[0][0]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[1][0] - this->m[1][0]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[2][0] - this->m[2][0]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[0][1] - this->m[0][1]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[1][1] - this->m[1][1]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[2][1] - this->m[2][1]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[0][2] - this->m[0][2]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[1][2] - this->m[1][2]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[2][2] - this->m[2][2]) > 0.001) should_throw_error = true; if (should_throw_error == true) // the matrix is not right, this is probably an edge case, the theta will be close to right, but the phi can have significant error - lets brute force around the found solution to refine it! (note this "improves" on a nobel prize winners work :) ) { //wxPrintf("\nFound Angles before refinement= (%.2f, %.2f, %.2f)\n\n", output_phi_in_degrees, output_theta_in_degrees, output_psi_in_degrees); /*wxPrintf("Found Matrix before refinement :- \n\n%+.4f\t%+.4f\t%+.4f\n", test_matrix.m[0][0], test_matrix.m[1][0], test_matrix.m[2][0]); wxPrintf("%+.4f\t%+.4f\t%+.4f\n", test_matrix.m[0][1], test_matrix.m[1][1], test_matrix.m[2][1]); wxPrintf("%+.4f\t%+.4f\t%+.4f\n", test_matrix.m[0][2], test_matrix.m[1][2], test_matrix.m[2][2]);*/ float old_best_phi = output_phi_in_degrees; float old_best_theta = output_theta_in_degrees; float old_best_psi = output_psi_in_degrees; float current_difference; float best_difference = FLT_MAX; float current_phi; float current_theta; float current_psi; float best_phi; float best_theta; float best_psi; for (current_phi = old_best_phi - 1.0f; current_phi < old_best_phi + 1.0f; current_phi += 1.0f) { for (current_theta = old_best_theta - 1.0f; current_theta < old_best_theta + 1.0f; current_theta += 1.0f) { for (current_psi = old_best_psi - 90.0f; current_psi < old_best_psi + 90.0f; current_psi += 5.0f) { test_matrix.SetToEulerRotation(current_phi, current_theta, current_psi); current_difference = 0.0f; current_difference += fabsf(test_matrix.m[0][0] - this->m[0][0]); current_difference += fabsf(test_matrix.m[1][0] - this->m[1][0]); current_difference += fabsf(test_matrix.m[2][0] - this->m[2][0]); current_difference += fabsf(test_matrix.m[0][1] - this->m[0][1]); current_difference += fabsf(test_matrix.m[1][1] - this->m[1][1]); current_difference += fabsf(test_matrix.m[2][1] - this->m[2][1]); current_difference += fabsf(test_matrix.m[0][2] - this->m[0][2]); current_difference += fabsf(test_matrix.m[1][2] - this->m[1][2]); current_difference += fabsf(test_matrix.m[2][2] - this->m[2][2]); if (current_difference < best_difference) { best_difference = current_difference; best_phi = current_phi; best_theta = current_theta; best_psi = current_psi; } } } } old_best_phi = best_phi; old_best_theta = best_theta; old_best_psi = best_psi; for (current_phi = best_phi - 1.0f; current_phi < old_best_phi + 1.0f; current_phi += 0.1f) { for (current_theta = best_theta - 1.0f; current_theta < old_best_theta + 1.0f; current_theta += 0.1f) { for (current_psi = best_psi - 5.0f; current_psi < old_best_psi + 5.0f; current_psi += 0.1f) { test_matrix.SetToEulerRotation(current_phi, current_theta, current_psi); current_difference = 0.0f; current_difference += fabsf(test_matrix.m[0][0] - this->m[0][0]); current_difference += fabsf(test_matrix.m[1][0] - this->m[1][0]); current_difference += fabsf(test_matrix.m[2][0] - this->m[2][0]); current_difference += fabsf(test_matrix.m[0][1] - this->m[0][1]); current_difference += fabsf(test_matrix.m[1][1] - this->m[1][1]); current_difference += fabsf(test_matrix.m[2][1] - this->m[2][1]); current_difference += fabsf(test_matrix.m[0][2] - this->m[0][2]); current_difference += fabsf(test_matrix.m[1][2] - this->m[1][2]); current_difference += fabsf(test_matrix.m[2][2] - this->m[2][2]); if (current_difference < best_difference) { best_difference = current_difference; best_phi = current_phi; best_theta = current_theta; best_psi = current_psi; } } } } old_best_phi = best_phi; old_best_theta = best_theta; old_best_psi = best_psi; for (current_phi = best_phi - 0.1f; current_phi < old_best_phi + 0.1f; current_phi += 0.01f) { for (current_theta = best_theta - 0.1f; current_theta < old_best_theta + 0.1f; current_theta += 0.01f) { for (current_psi = best_psi - 0.1f; current_psi < old_best_psi + 0.1f; current_psi += 0.01f) { test_matrix.SetToEulerRotation(current_phi, current_theta, current_psi); current_difference = 0.0f; current_difference += fabsf(test_matrix.m[0][0] - this->m[0][0]); current_difference += fabsf(test_matrix.m[1][0] - this->m[1][0]); current_difference += fabsf(test_matrix.m[2][0] - this->m[2][0]); current_difference += fabsf(test_matrix.m[0][1] - this->m[0][1]); current_difference += fabsf(test_matrix.m[1][1] - this->m[1][1]); current_difference += fabsf(test_matrix.m[2][1] - this->m[2][1]); current_difference += fabsf(test_matrix.m[0][2] - this->m[0][2]); current_difference += fabsf(test_matrix.m[1][2] - this->m[1][2]); current_difference += fabsf(test_matrix.m[2][2] - this->m[2][2]); if (current_difference < best_difference) { best_difference = current_difference; best_phi = current_phi; best_theta = current_theta; best_psi = current_psi; } } } } output_phi_in_degrees = best_phi; output_theta_in_degrees = best_theta; output_psi_in_degrees = best_psi; //wxPrintf("\nFound Angles = (%.2f, %.2f, %.2f)\n\n", output_phi_in_degrees, output_theta_in_degrees, output_psi_in_degrees); } // if in debug mode do a final check /*#ifdef DEBUG test_matrix.SetToEulerRotation(output_phi_in_degrees, output_theta_in_degrees, output_psi_in_degrees); should_throw_error = false; if (fabsf(test_matrix.m[0][0] - this->m[0][0]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[1][0] - this->m[1][0]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[2][0] - this->m[2][0]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[0][1] - this->m[0][1]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[1][1] - this->m[1][1]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[2][1] - this->m[2][1]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[0][2] - this->m[0][2]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[1][2] - this->m[1][2]) > 0.001) should_throw_error = true; if (fabsf(test_matrix.m[2][2] - this->m[2][2]) > 0.001) should_throw_error = true; if (should_throw_error == true) { MyPrintWithDetails("Rotation Matrix to Euler angles conversion failed\n"); wxPrintf("\nFound Angles = (%.2f, %.2f, %.2f)\n\n", output_phi_in_degrees, output_theta_in_degrees, output_psi_in_degrees); wxPrintf("Matrix :- \n\n%+.4f\t%+.4f\t%+.4f\n", m[0][0], m[1][0], m[2][0]); wxPrintf("%+.4f\t%+.4f\t%+.4f\n", m[0][1], m[1][1], m[2][1]); wxPrintf("%+.4f\t%+.4f\t%+.4f\n\n", m[0][2], m[1][2], m[2][2]); wxPrintf("cos_theta values = %.2f\n", fabsf(fabsf(cos_theta) - 1.0f)); wxPrintf("Found Matrix :- \n\n%+.4f\t%+.4f\t%+.4f\n", test_matrix.m[0][0], test_matrix.m[1][0], test_matrix.m[2][0]); wxPrintf("%+.4f\t%+.4f\t%+.4f\n", test_matrix.m[0][1], test_matrix.m[1][1], test_matrix.m[2][1]); wxPrintf("%+.4f\t%+.4f\t%+.4f\n", test_matrix.m[0][2], test_matrix.m[1][2], test_matrix.m[2][2]); wxPrintf("Difference :- \n\n%+.4f\t%+.4f\t%+.4f\n", fabsf(m[0][0] - test_matrix.m[0][0]), fabsf(m[1][0] - test_matrix.m[1][0]), fabsf(m[2][0] - test_matrix.m[2][0])); wxPrintf("%+.4f\t%+.4f\t%+.4f\n", fabsf(m[0][1] - test_matrix.m[0][1]), fabsf(m[1][1] - test_matrix.m[1][1]), fabsf(m[2][1] - test_matrix.m[2][1])); wxPrintf("%+.4f\t%+.4f\t%+.4f\n\n", fabsf(m[0][2] - test_matrix.m[0][2]), fabsf(m[1][2] - test_matrix.m[1][2]), fabsf(m[2][2] - test_matrix.m[2][2])); DEBUG_ABORT; } #endif*/ } void RotationMatrix::SetToEulerRotation(float wanted_euler_phi_in_degrees, float wanted_euler_theta_in_degrees, float wanted_euler_psi_in_degrees) { float cos_phi; float sin_phi; float cos_theta; float sin_theta; float cos_psi; float sin_psi; cos_phi = cosf(deg_2_rad(wanted_euler_phi_in_degrees)); sin_phi = sinf(deg_2_rad(wanted_euler_phi_in_degrees)); cos_theta = cosf(deg_2_rad(wanted_euler_theta_in_degrees)); sin_theta = sinf(deg_2_rad(wanted_euler_theta_in_degrees)); cos_psi = cosf(deg_2_rad(wanted_euler_psi_in_degrees)); sin_psi = sinf(deg_2_rad(wanted_euler_psi_in_degrees)); m[0][0] = cos_phi * cos_theta * cos_psi - sin_phi * sin_psi; m[1][0] = sin_phi * cos_theta * cos_psi + cos_phi * sin_psi; m[2][0] = -sin_theta * cos_psi; m[0][1] = -cos_phi * cos_theta * sin_psi - sin_phi * cos_psi; m[1][1] = -sin_phi * cos_theta * sin_psi + cos_phi * cos_psi; m[2][1] = sin_theta * sin_psi; m[0][2] = sin_theta * cos_phi; m[1][2] = sin_theta * sin_phi; m[2][2] = cos_theta; }void ConvertToValidEulerAngles(float &output_phi, float &output_theta, float &output_psi); void RotationMatrix::SetToConstant(float constant) { this->m[0][0] = constant; this->m[1][0] = constant; this->m[2][0] = constant; this->m[0][1] = constant; this->m[1][1] = constant; this->m[2][1] = constant; this->m[0][2] = constant; this->m[1][2] = constant; this->m[2][2] = constant; } void RotationMatrix::SetToValues(float m00, float m10, float m20, float m01, float m11, float m21, float m02, float m12, float m22) { this->m[0][0] = m00; this->m[1][0] = m10; this->m[2][0] = m20; this->m[0][1] = m01; this->m[1][1] = m11; this->m[2][1] = m21; this->m[0][2] = m02; this->m[1][2] = m12; this->m[2][2] = m22; } ctffind-4.1.14/src/core/matrix.h000066400000000000000000000041631440356052600164230ustar00rootroot00000000000000/* \brief RotationMatrix class */ class RotationMatrix { public: float m[3][3]; /* 3D rotation matrix*/ RotationMatrix(); // ~RotationMatrix(); RotationMatrix operator + (const RotationMatrix &other); RotationMatrix operator - (const RotationMatrix &other); RotationMatrix operator * (const RotationMatrix &other); RotationMatrix &operator = (const RotationMatrix &other); RotationMatrix &operator = (const RotationMatrix *other); RotationMatrix &operator += (const RotationMatrix &other); RotationMatrix &operator += (const RotationMatrix *other); RotationMatrix &operator -= (const RotationMatrix &other); RotationMatrix &operator -= (const RotationMatrix *other); RotationMatrix &operator *= (const RotationMatrix &other); RotationMatrix &operator *= (const RotationMatrix *other); RotationMatrix ReturnTransposed(); void SetToIdentity(); void SetToConstant(float constant); void SetToRotation(float input_x, float input_y, float input_z); void SetToEulerRotation(float wanted_euler_phi_in_degrees, float wanted_euler_theta_in_degrees, float wanted_euler_psi_in_degrees); void ConvertToValidEulerAngles(float &output_phi_in_degrees, float &output_theta_in_degrees, float &output_psi_in_degrees); void SetToValues(float m00, float m10, float m20, float m01, float m11, float m21, float m02, float m12, float m22); inline void RotateCoords(float &input_x_coord, float &input_y_coord, float &input_z_coord, float &output_x_coord, float &output_y_coord, float &output_z_coord) { output_x_coord = this->m[0][0] * input_x_coord + this->m[0][1] * input_y_coord + this->m[0][2] * input_z_coord; output_y_coord = this->m[1][0] * input_x_coord + this->m[1][1] * input_y_coord + this->m[1][2] * input_z_coord; output_z_coord = this->m[2][0] * input_x_coord + this->m[2][1] * input_y_coord + this->m[2][2] * input_z_coord; }; inline void RotateCoords2D(float &input_x_coord, float &input_y_coord, float &output_x_coord, float &output_y_coord) { output_x_coord = this->m[0][0] * input_x_coord + this->m[0][1] * input_y_coord; output_y_coord = this->m[1][0] * input_x_coord + this->m[1][1] * input_y_coord; }; }; ctffind-4.1.14/src/core/mrc_file.cpp000066400000000000000000000277161440356052600172430ustar00rootroot00000000000000#include "core_headers.h" MRCFile::MRCFile() { rewrite_header_on_close = false; } MRCFile::MRCFile(std::string filename, bool overwrite) { rewrite_header_on_close = false; OpenFile(filename, overwrite); } MRCFile::MRCFile(std::string filename, bool overwrite,bool wait_for_file_to_exist) { rewrite_header_on_close = false; OpenFile(filename, overwrite,wait_for_file_to_exist); } MRCFile::~MRCFile() { CloseFile(); } void MRCFile::CloseFile() { if (my_file.is_open()) { if (rewrite_header_on_close == true) WriteHeader(); my_file.close(); } } bool MRCFile::OpenFile(std::string wanted_filename, bool overwrite, bool wait_for_file_to_exist) { // MyDebugAssertFalse(my_file.is_open(), "File Already Open: %s",wanted_filename); CloseFile(); bool file_already_exists; if (wait_for_file_to_exist) { file_already_exists = DoesFileExistWithWait(wanted_filename, max_number_of_seconds_to_wait_for_file_to_exist); } else { file_already_exists = DoesFileExist(wanted_filename); } // if overwrite is specified, then we delete the file nomatter what.. // if it isn't, then we need to know if the file already exists.. if (overwrite == true) file_already_exists = false; // Now open it, truncating to 0 if it doesn't already exist, or we specified overwrite if (file_already_exists == true) { my_file.open(wanted_filename.c_str(), std::ios::in | std::ios::out | std::ios::binary); if (my_file.is_open() == false) { // Try without connecting the out (i.e. read only) my_file.open(wanted_filename.c_str(), std::ios::in | std::ios::binary); // If it still didn't work, we're buggered if (my_file.is_open() == false) { MyPrintWithDetails("Opening of file %s failed!! - Exiting..\n\n", wanted_filename.c_str()); DEBUG_ABORT; } } // read the header if (file_already_exists == true) my_header.ReadHeader(&my_file); } else { my_file.open(wanted_filename.c_str(), std::ios::in | std::ios::out | std::ios::trunc | std::ios::binary); if (my_file.is_open() == false) { MyPrintWithDetails("Opening of file %s failed!! - Exiting..\n\n", wanted_filename.c_str()); DEBUG_ABORT; } // Blank the header, it'll have to be written with the correct values later.. my_header.BlankHeader(); } rewrite_header_on_close = false; filename = wanted_filename; // TODO: return false is something is wrong about this file return true; } void MRCFile::PrintInfo() { wxPrintf("\nSummary information for file %s\n",filename); my_header.PrintInfo(); wxPrintf("\n"); } float MRCFile::ReturnPixelSize() { return my_header.ReturnPixelSize(); } void MRCFile::SetPixelSize(float wanted_pixel_size) { my_header.SetPixelSize(wanted_pixel_size); } void MRCFile::ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array) { MyDebugAssertTrue(my_file.is_open(), "File not open!"); MyDebugAssertTrue(start_slice <= ReturnNumberOfSlices(), "Start slice number larger than total slices!"); MyDebugAssertTrue(end_slice <= ReturnNumberOfSlices(), "end slice number larger than total slices!"); MyDebugAssertTrue(start_slice <= end_slice, "Start slice larger than end slice!"); //MyDebugAssertTrue(my_header.ReturnMachineStamp() == my_header.ReturnLocalMachineStamp(), "Byteswapping not yet supported"); //wxPrintf("mchst from headers: %i, local mchst: %i\n",my_header.ReturnMachineStamp(), my_header.ReturnLocalMachineStamp()); // calculate and seek to the start byte.. long records_to_read; long bytes_per_slice; long image_offset; long current_position; long seek_position; if (my_header.Mode() == 101) { records_to_read = long(my_header.ReturnDimensionX()) * long(my_header.ReturnDimensionY()) * (long(end_slice - start_slice) + 1); if (IsOdd(my_header.ReturnDimensionX()) == true) { bytes_per_slice = ((long(my_header.ReturnDimensionX()) - 1) / 2) + 1; bytes_per_slice *= long(my_header.ReturnDimensionY()); } else { bytes_per_slice = long(my_header.ReturnDimensionX()) / 2; bytes_per_slice *= long(my_header.ReturnDimensionY()); } image_offset = (start_slice - 1) * bytes_per_slice; current_position = my_file.tellg(); seek_position = 1024 + image_offset + my_header.SymmetryDataBytes(); } else { // check for mastronarde 4-bit hack. if (my_header.ReturnIfThisIsInMastronarde4BitHackFormat() == true) { records_to_read = long(my_header.ReturnDimensionX()) * long(my_header.ReturnDimensionY()) * (long(end_slice - start_slice) + 1); records_to_read /= 2; bytes_per_slice = long(my_header.ReturnDimensionX()) * long(my_header.ReturnDimensionY()) * long(my_header.BytesPerPixel()); image_offset = long(start_slice - 1) * bytes_per_slice; } else { records_to_read = long(my_header.ReturnDimensionX()) * long(my_header.ReturnDimensionY()) * (long(end_slice - start_slice) + 1); bytes_per_slice = long(my_header.ReturnDimensionX()) * long(my_header.ReturnDimensionY()) * long(my_header.BytesPerPixel()); image_offset = long(start_slice - 1) * bytes_per_slice; } current_position = my_file.tellg(); seek_position = 1024 + image_offset + my_header.SymmetryDataBytes(); } if (current_position != seek_position) my_file.seekg(seek_position); // we need a temp array for non float formats.. switch ( my_header.Mode() ) { // 1-byte integer case 0: { long output_counter = 0; uint8 low_4bits; uint8 hi_4bits; char *temp_char_array = new char [records_to_read]; my_file.read(temp_char_array, records_to_read); for (long counter = 0; counter < records_to_read; counter++) { if (my_header.ReturnIfThisIsInMastronarde4BitHackFormat() == true) { low_4bits = temp_char_array[counter] & 0x0F; hi_4bits = (temp_char_array[counter]>>4) & 0x0F; output_array[output_counter] = float(low_4bits); output_counter ++; output_array[output_counter] = float(hi_4bits); output_counter ++; } else { output_array[counter] = float(temp_char_array[counter]); } } delete [] temp_char_array; } break; // 2-byte integer case 1: { short *temp_short_array = new short [records_to_read]; my_file.read((char*)temp_short_array, records_to_read * 2); for (long counter = 0; counter < records_to_read; counter++) { output_array[counter] = float(temp_short_array[counter]); } delete [] temp_short_array; } break; // 4-byte real case 2: my_file.read((char*)output_array, records_to_read * 4); break; // unsigned 2-byte integers case 6: { unsigned short int *temp_int_array = new unsigned short int [records_to_read]; my_file.read((char*)temp_int_array, records_to_read * 2); for (long counter = 0; counter < records_to_read; counter++) { output_array[counter] = float(temp_int_array[counter]); } delete [] temp_int_array; } break; // 101.. 4-bit integer.. case 101: { // horrible format.. each byte is two pixels, if x is odd then the last one is padded. // so recalculate the number of bytes to read long input_array_position = 0; long output_array_position = 0; int x_pos = 0; long actual_bytes_to_read = ((end_slice - start_slice) + 1) * bytes_per_slice; uint8 hi_4bits; uint8 low_4bits; char *temp_char_array = new char [actual_bytes_to_read]; my_file.read(temp_char_array, actual_bytes_to_read); // now we have to convert.. for (long counter = 0; counter < actual_bytes_to_read; counter++) { low_4bits = temp_char_array[input_array_position] & 0x0F; hi_4bits = (temp_char_array[input_array_position]>>4) & 0x0F; //wxPrintf("\n\ninput = %i, low = %i, high = %i\n\n", int(temp_char_array[input_array_position]), int(low_4bits), int(hi_4bits)); input_array_position++; x_pos++; if (x_pos == my_header.ReturnDimensionX() && IsOdd(my_header.ReturnDimensionX()) == true) { x_pos = 0; output_array[output_array_position] = float(low_4bits); output_array_position++; } else { output_array[output_array_position] = float(low_4bits); output_array_position++; output_array[output_array_position] = float(hi_4bits); output_array_position++; } } delete [] temp_char_array; } break; default: { MyPrintfRed("Error: mode %i MRC files not currently supported\n",my_header.Mode()); DEBUG_ABORT; } break; } { /* * Deal with the cases where the data are not indexed like this: * - fastest = column (map_c = 1) * - medium = row (map_r = 2) * - slow = section (map_s = 3) */ long counter; long counter_in_file; long number_of_voxels = my_header.ReturnDimensionX()*my_header.ReturnDimensionY()*my_header.ReturnDimensionZ(); // int col_index; int row_index; int sec_index; if (my_header.ReturnMapC() == 1 && my_header.ReturnMapR() == 2 && my_header.ReturnMapS() == 3) { // Nothing to do, this is how cisTEM expects the data to be laid out } else if (my_header.ReturnMapS() == 1 && my_header.ReturnMapC() ==3) { // Allocate a temp array and copy data over float * temp_array; temp_array = new float[number_of_voxels]; for (counter = 0; counter < number_of_voxels; counter ++ ) {temp_array[counter] = output_array[counter];} // Loop over output array and copy voxel values over one by one counter = 0; for (sec_index=0; sec_index < my_header.ReturnDimensionZ(); sec_index++) //z { for (row_index=0; row_index < my_header.ReturnDimensionY(); row_index++) //y { for (col_index=0; col_index < my_header.ReturnDimensionX(); col_index++) //x { // compute address of voxel in the file counter_in_file = sec_index + my_header.ReturnDimensionZ() * row_index + my_header.ReturnDimensionZ()*my_header.ReturnDimensionY() * col_index; MyDebugAssertTrue(counter_in_file >= 0 && counter_in_file < number_of_voxels,"Oops bad counter_in_file = %li\n",counter_in_file); MyDebugAssertTrue(counter >= 0 && counter < number_of_voxels,"Oops bad counter = %li\n",counter); output_array[counter] = temp_array[counter_in_file]; counter++; } } } // Deallocate temp array delete [] temp_array; } else { wxPrintf("Ooops, strange ordering of data in MRC file not yet supported"); abort(); } } } void MRCFile::WriteSlicesToDisk(int start_slice, int end_slice, float *input_array) { MyDebugAssertTrue(my_file.is_open(), "File not open!"); MyDebugAssertTrue(start_slice <= end_slice, "Start slice larger than end slice!"); MyDebugAssertTrue(start_slice <= ReturnNumberOfSlices(), "Start slice number larger than total slices!"); MyDebugAssertTrue(end_slice <= ReturnNumberOfSlices(), "end slice number larger than total slices!"); // calculate and seek to the start byte.. long records_to_read = long(my_header.ReturnDimensionX()) * long(my_header.ReturnDimensionY()) * long((end_slice - start_slice) + 1); long bytes_per_slice = long(my_header.ReturnDimensionX()) * long(my_header.ReturnDimensionY()) * long(my_header.BytesPerPixel()); long image_offset = long(start_slice - 1) * bytes_per_slice; long current_position = my_file.tellg(); long seek_position = 1024 + image_offset + long(my_header.SymmetryDataBytes()); if (current_position != seek_position) my_file.seekg(seek_position); // we need a temp array for non float formats.. switch ( my_header.Mode() ) { case 0: { char *temp_char_array = new char [records_to_read]; for (long counter = 0; counter < records_to_read; counter++) { temp_char_array[counter] = char(input_array[counter]); } my_file.write(temp_char_array, records_to_read); delete [] temp_char_array; } break; case 1: { short *temp_short_array = new short [records_to_read]; for (long counter = 0; counter < records_to_read; counter++) { temp_short_array[counter] = short(input_array[counter]); } my_file.write((char*)temp_short_array, records_to_read * 2); delete [] temp_short_array; } break; case 2: my_file.write((char*)input_array, records_to_read * 4); break; default: { MyPrintfRed("Error: mode %i MRC files not currently supported\n",my_header.Mode()); DEBUG_ABORT; } break; } } ctffind-4.1.14/src/core/mrc_file.h000066400000000000000000000034721440356052600167010ustar00rootroot00000000000000// \brief Object for manipulating MRC Files.. // class MRCFile : public AbstractImageFile { public: std::fstream my_file; MRCHeader my_header; wxString filename; bool rewrite_header_on_close; int max_number_of_seconds_to_wait_for_file_to_exist; MRCFile(); MRCFile(std::string filename, bool overwrite = false); MRCFile(std::string filename, bool overwrite, bool wait_for_file_to_exist); ~MRCFile(); inline int ReturnXSize() {MyDebugAssertTrue(my_file.is_open(), "File not open!"); return my_header.ReturnDimensionX();}; inline int ReturnYSize() {MyDebugAssertTrue(my_file.is_open(), "File not open!"); return my_header.ReturnDimensionY();}; inline int ReturnZSize() {MyDebugAssertTrue(my_file.is_open(), "File not open!"); return my_header.ReturnDimensionZ();}; inline int ReturnNumberOfSlices() {MyDebugAssertTrue(my_file.is_open(), "File not open!"); return my_header.ReturnDimensionZ();}; inline bool IsOpen() {return my_file.is_open();} bool OpenFile(std::string filename, bool overwrite, bool wait_for_file_to_exist = false); void CloseFile(); inline void ReadSliceFromDisk(int slice_number, float *output_array) {ReadSlicesFromDisk(slice_number, slice_number, output_array);} void ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array); inline void WriteSliceToDisk(int slice_number, float *input_array) {WriteSlicesToDisk(slice_number, slice_number, input_array);} void WriteSlicesToDisk(int start_slice, int end_slice, float *input_array); inline void WriteHeader() {my_header.WriteHeader(&my_file);}; void PrintInfo(); float ReturnPixelSize(); void SetPixelSize(float wanted_pixel_size); inline void SetDensityStatistics( float wanted_min, float wanted_max, float wanted_mean, float wanted_rms ){my_header.SetDensityStatistics(wanted_min, wanted_max, wanted_mean, wanted_rms);} }; ctffind-4.1.14/src/core/mrc_header.cpp000066400000000000000000000206641440356052600175470ustar00rootroot00000000000000#include "core_headers.h" //!> \brief Default contructor - just calls init to setup the pointers. // MRCHeader::MRCHeader() { buffer = new char[1024]; InitPointers(); this_is_in_mastronarde_4bit_hack_format = false; } //!> \brief Default destructor - deallocate the memory; // MRCHeader::~MRCHeader() { delete [] buffer; } void MRCHeader::PrintInfo() { char *current_label = new char[81]; int char_counter; // Work out pixel size float pixel_size[3]; if (cell_a_x[0] == 0.0) { pixel_size[0] = 0.0; } else { pixel_size[0] = cell_a_x[0] / mx[0]; } if (cell_a_y[0] == 0.0) { pixel_size[1] = 0.0; } else { pixel_size[1] = cell_a_y[0] / my[0]; } if (cell_a_z[0] == 0.0) { pixel_size[2] = 0.0; } else { pixel_size[2] = cell_a_z[0] / mz[0]; } // Start printing wxPrintf("Number of columns, rows, sections: %i, %i, %i\n",nx[0],ny[0],nz[0]); wxPrintf("MRC data mode: %i\n",mode[0]); wxPrintf("Bit depth: %i\n",int(bytes_per_pixel * 8)); wxPrintf("Pixel size: %0.3f %0.3f %0.3f\n",pixel_size[0],pixel_size[1],pixel_size[2]); wxPrintf("Column index: %i; Row index: %i; Section index: %i\n",map_c[0],map_r[0],map_s[0]); wxPrintf("Bytes in symmetry header: %i\n",symmetry_data_bytes[0]); for (int label_counter=0; label_counter < number_of_labels_used[0]; label_counter++) { for (char_counter=0;char_counter < 80; char_counter++) { current_label[char_counter] = labels[label_counter*80+char_counter]; } current_label[80] = 0; wxPrintf("Label %i : %s\n",label_counter+1,current_label); } delete [] current_label; } float MRCHeader::ReturnPixelSize() { if (cell_a_x[0] == 0.0) { return 0.0; } else { return cell_a_x[0] / mx[0]; } } // Make sure to call this after the volume / image dimensions have been set void MRCHeader::SetPixelSize(float wanted_pixel_size) { cell_a_x[0] = wanted_pixel_size * mx[0]; cell_a_y[0] = wanted_pixel_size * my[0]; cell_a_z[0] = wanted_pixel_size * mz[0]; } void MRCHeader::SetDimensionsImage(int wanted_x_dim, int wanted_y_dim) { nx[0] = wanted_x_dim; ny[0] = wanted_y_dim; nxstart[0] = 0; nystart[0] = 0; nzstart[0] = 0; mx[0] = wanted_x_dim; my[0] = wanted_y_dim; space_group_number[0] = 1; // Contravening MRC2014 definition, which indicate we should set this to 0 when dealing with (stacks of) 2D images } void MRCHeader::SetNumberOfImages(int wanted_number_of_images) { nz[0] = wanted_number_of_images; mz[0] = wanted_number_of_images; } void MRCHeader::SetDimensionsVolume(int wanted_x_dim, int wanted_y_dim, int wanted_z_dim) { nx[0] = wanted_x_dim; ny[0] = wanted_y_dim; nz[0] = wanted_z_dim; nxstart[0] = 0; nystart[0] = 0; nzstart[0] = 0; mx[0] = wanted_x_dim; my[0] = wanted_y_dim; mz[0] = wanted_z_dim; space_group_number[0] = 1; } void MRCHeader::SetDensityStatistics( float wanted_min, float wanted_max, float wanted_mean, float wanted_rms ) { dmin[0] = wanted_min; dmax[0] = wanted_max; dmean[0] = wanted_mean; rms[0] = wanted_rms; } void MRCHeader::ResetLabels() { labels[0] = '*'; labels[1] = '*'; labels[2] = ' '; labels[3] = 'G'; labels[4] = 'u'; labels[5] = 'i'; labels[6] = 'X'; labels[7] = ' '; labels[8] = '*'; labels[9] = '*'; for (int counter = 10; counter < 800; counter++) { labels[counter] = ' '; } number_of_labels_used[0] = 1; } void MRCHeader::ResetOrigin() { origin_x[0] = 0; origin_y[0] = 0; origin_z[0] = 0; } void MRCHeader::SetOrigin(float wanted_x, float wanted_y, float wanted_z) { origin_x[0] = wanted_x; origin_y[0] = wanted_y; origin_z[0] = wanted_z; } //!> \brief Setup the pointers so that they point to the correct place in the buffer // void MRCHeader::InitPointers() { nx = (int*) &buffer[0]; ny = (int*) &buffer[4]; nz = (int*) &buffer[8]; mode = (int*) &buffer[12]; nxstart = (int*) &buffer[16]; nystart = (int*) &buffer[20]; nzstart = (int*) &buffer[24]; mx = (int*) &buffer[28]; my = (int*) &buffer[32]; mz = (int*) &buffer[36]; cell_a_x = (float*) &buffer[40]; cell_a_y = (float*) &buffer[44]; cell_a_z = (float*) &buffer[48]; cell_b_x = (float*) &buffer[52]; cell_b_y = (float*) &buffer[56]; cell_b_z = (float*) &buffer[60]; map_c = (int*) &buffer[64]; map_r = (int*) &buffer[68]; map_s = (int*) &buffer[72]; dmin = (float*) &buffer[76]; dmax = (float*) &buffer[80]; dmean = (float*) &buffer[84]; space_group_number = (int*) &buffer[88]; symmetry_data_bytes = (int*) &buffer[92]; extra = (int*) &buffer[96]; origin_x = (float*) &buffer[196]; origin_y = (float*) &buffer[200]; origin_z = (float*) &buffer[204]; map = (char*) &buffer[208]; machine_stamp = (int*) &buffer[212]; rms = (float*) &buffer[216]; number_of_labels_used = (int*) &buffer[220]; labels = (char*) &buffer[224]; } void MRCHeader::ReadHeader(std::fstream *MRCFile) { MyDebugAssertTrue(MRCFile->is_open(), "File not open!"); // Read the first 1024 bytes into buffer, the pointers should then all be set.. MRCFile->seekg(0); MRCFile->read (buffer, 1024); // work out some extra details.. switch ( mode[0] ) { case 0: bytes_per_pixel = 1; pixel_data_are_signed = true; // Note that MRC mode 0 is sometimes signed, sometimes not signed. TODO: sort this out by checking the imodStamp header pixel_data_are_of_type = MRCByte; pixel_data_are_complex = false; // need to check for 4-bit.. if (sizeCanBe4BitK2SuperRes(nx[0], ny[0]) == 1) // this is David Mastronarde's 4-bit hack { nx[0] *= 2; this_is_in_mastronarde_4bit_hack_format = true; bytes_per_pixel = 0.5; } else { this_is_in_mastronarde_4bit_hack_format = false; } break; case 1: bytes_per_pixel = 2; pixel_data_are_signed = true; pixel_data_are_of_type = Float; pixel_data_are_complex = false; break; case 2: bytes_per_pixel = 4; pixel_data_are_signed = true; pixel_data_are_of_type = MRCByte; pixel_data_are_complex = false; break; case 3: bytes_per_pixel = 2; pixel_data_are_signed = true; pixel_data_are_of_type = MRCInteger; pixel_data_are_complex = true; break; case 4: bytes_per_pixel = 4; pixel_data_are_signed = true; pixel_data_are_of_type = MRCFloat; pixel_data_are_complex = true; break; case 5: bytes_per_pixel = 1; pixel_data_are_signed = false; pixel_data_are_of_type = MRCByte; pixel_data_are_complex = false; break; case 6: bytes_per_pixel = 2; pixel_data_are_signed = false; pixel_data_are_of_type = MRCInteger; pixel_data_are_complex = false; break; case 101 : bytes_per_pixel = 0.5; pixel_data_are_signed = false; pixel_data_are_of_type = MRC4Bit; pixel_data_are_complex = false; break; default: { MyPrintfRed("Error: mode %i MRC files not currently supported\n",mode[0]); DEBUG_ABORT; } break; } } void MRCHeader::WriteHeader(std::fstream *MRCFile) { MyDebugAssertTrue(MRCFile->is_open(), "File not open!"); // Write the first 1024 bytes from buffer. MRCFile->seekg(0); MRCFile->write (buffer, 1024); } void MRCHeader::BlankHeader() { long counter; nx[0] = 0; ny[0] = 0; nz[0] = 0; mode[0] = 2; // always for now nxstart[0] = 0; nystart[0] = 0; nzstart[0] = 0; mx[0] = 1; my[0] = 1; mz[0] = 1; cell_a_x[0] = 1.0; cell_a_y[0] = 1.0; cell_a_z[0] = 1.0; cell_b_x[0] = 90.0; cell_b_y[0] = 90.0; cell_b_z[0] = 90.0; map_c[0] = 1; map_r[0] = 2; map_s[0] = 3; dmin[0] = 0.0; dmax[0] = 0.0; dmean[0] = 0.0; space_group_number[0] = 1; // assume we'll treat stacks of images as volumes symmetry_data_bytes[0] = 0; for (counter = 0; counter < 25; counter++) { extra[counter] = 0; } origin_x[0] = 0; origin_y[0] = 0; origin_z[0] = 0; map[0] = 'M'; map[1] = 'A'; map[2] = 'P'; map[3] = ' '; SetLocalMachineStamp(); rms[0] = 0; number_of_labels_used[0]= 1; ResetLabels(); bytes_per_pixel = 4; } void MRCHeader::SetLocalMachineStamp() { int i = 858927408; char *first_byte = (char*)&i; if (first_byte[0] == '0') { buffer[212] = 68; buffer[213] = 65; buffer[214] = 0; buffer[215] = 0; } else if (first_byte[0] == '3') { buffer[212] = 17; buffer[213] = 17; buffer[214] = 0; buffer[215] = 0; } else { buffer[212] = 34; buffer[213] = 33; buffer[214] = 0; buffer[215] = 0; } } ctffind-4.1.14/src/core/mrc_header.h000066400000000000000000000131721440356052600172100ustar00rootroot00000000000000/* \brief Object for manipulating MRC headers.. // MRC format from http://www2.mrc-lmb.cam.ac.uk/image2000.html Map/Image Header Format Length = 1024 bytes, organized as 56 LONG words followed by space for 10 80 byte text labels. 1 NX number of columns (fastest changing in map) 2 NY number of rows 3 NZ number of sections (slowest changing in map) 4 MODE data type : 0 image : signed 8-bit bytes range -128 to 127 (actually UNSIGNED) x 1 image : 16-bit halfwords 2 image : 32-bit reals 3 transform : complex 16-bit integers 4 transform : complex 32-bit reals 5 NXSTART number of first column in map (Default = 0) 6 NYSTART number of first row in map 7 NZSTART number of first section in map 8 MX number of intervals along X 9 MY number of intervals along Y 10 MZ number of intervals along Z 11-13 CELLA cell dimensions in angstroms 14-16 CELLB cell angles in degrees 17 MAPC axis corresp to cols (1,2,3 for X,Y,Z) 18 MAPR axis corresp to rows (1,2,3 for X,Y,Z) 19 MAPS axis corresp to sections (1,2,3 for X,Y,Z) 20 DMIN minimum density value 21 DMAX maximum density value 22 DMEAN mean density value 23 ISPG space group number 0 or 1 (default=0) 24 NSYMBT number of bytes used for symmetry data (0 or 80) 25-49 EXTRA extra space used for anything - 0 by default 50-52 ORIGIN origin in X,Y,Z used for transforms 53 MAP character string 'MAP ' to identify file type 54 MACHST machine stamp 55 RMS rms deviation of map from mean density 56 NLABL number of labels being used 57-256 LABEL(20,10) 10 80-character text labels Symmetry records follow - if any - stored as text as in International Tables, operators separated by and grouped into 'lines' of 80 characters (ie. symmetry operators do not cross the ends of the 80-character 'lines' and the 'lines' do not terminate in a ). Data records follow. */ // enum MRCDataTypes { MRCByte, MRCInteger, MRCFloat, MRC4Bit }; class MRCHeader { char *buffer; // !< The true byte data // The following are all pointers and just point to the relevant area of the buffer.. int *nx; // !< number of columns (fastest changing in map) int *ny; // !< number of rows int *nz; // !< NZ number of sections (slowest changing in map) int *mode; // !< MODE (data type) 0 = signed 8-bit bytes range -128 to 127 (actually UNSIGNED), 1 = 16-bit halfwords, 2 = 32-bit reals, 3 = complex 16-bit integers, 4 = complex 32-bit reals int *nxstart; // !< number of first column in map (Default = 0) int *nystart; // !< number of first row in map int *nzstart; // !< number of first section in map int *mx; // !< number of intervals along X int *my; // !< number of intervals along Y int *mz; // !< number of intervals along Z float *cell_a_x; // !< cell dimensions in angstroms (X) float *cell_a_y; // !< cell dimensions in angstroms (Y) float *cell_a_z; // !< cell dimensions in angstroms (Z) float *cell_b_x; // !< cell angles in degrees (X) float *cell_b_y; // !< cell angles in degrees (Y) float *cell_b_z; // !< cell angles in degrees (Z) int *map_c; // !< axis corresp to cols (1,2,3 for X,Y,Z) int *map_r; // !< axis corresp to rows (1,2,3 for X,Y,Z) int *map_s; // !< axis corresp to sections (1,2,3 for X,Y,Z) float *dmin; // !< minimum density value float *dmax; // !< maximum density value float *dmean; // !< mean density value int *space_group_number; // !< space group number 0 or 1 (default=0) int *symmetry_data_bytes; // !< number of bytes used for symmetry data (0 or 80) int *extra; // !< extra space used for anything - 0 by default (100 bytes) float *origin_x; // !< origin in X used for transforms float *origin_y; // !< origin in Y used for transforms float *origin_z; // !< origin in Z used for transforms char *map; // !< character string 'MAP ' to identify file type int *machine_stamp; // !< machine stamp float *rms; // !< rms deviation of map from mean density int *number_of_labels_used; // !< number of labels being used char *labels; // !< Labels. 10 80-character text labels // some extra info.. float bytes_per_pixel; bool pixel_data_are_signed; int pixel_data_are_of_type; bool pixel_data_are_complex; bool this_is_in_mastronarde_4bit_hack_format; public: // methods MRCHeader(); ~MRCHeader(); void InitPointers(); void ReadHeader(std::fstream *MRCFile); void WriteHeader(std::fstream *MRCFile); void BlankHeader(); void ResetLabels(); void ResetOrigin(); void SetLocalMachineStamp(); void PrintInfo(); inline int ReturnDimensionX() {return nx[0];}; inline int ReturnDimensionY() {return ny[0];}; inline int ReturnDimensionZ() {return nz[0];}; inline int ReturnMapC() {return map_c[0];}; inline int ReturnMapR() {return map_r[0];}; inline int ReturnMapS() {return map_s[0];}; inline bool ReturnIfThisIsInMastronarde4BitHackFormat() {return this_is_in_mastronarde_4bit_hack_format;} float ReturnPixelSize(); void SetPixelSize(float wanted_pixel_size); void SetDimensionsImage(int wanted_x_dim, int wanted_y_dim); void SetDimensionsVolume(int wanted_x_dim, int wanted_y_dim, int wanted_z_dim); void SetNumberOfImages(int wanted_number_of_images); void SetNumberOfVolumes(int wanted_number_of_volumes); void SetDensityStatistics( float wanted_min, float wanted_max, float wanted_mean, float wanted_rms ); void SetOrigin( float wanted_x, float wanted_y, float wanted_z ); inline float BytesPerPixel() { return bytes_per_pixel; }; inline int Mode() { return mode[0];}; inline int SymmetryDataBytes() { return symmetry_data_bytes[0];}; }; ctffind-4.1.14/src/core/myapp.cpp000066400000000000000000001345671440356052600166140ustar00rootroot00000000000000 #include "core_headers.h" SETUP_SOCKET_CODES wxDEFINE_EVENT(wxEVT_COMMAND_MYTHREAD_COMPLETED, wxThreadEvent); wxDEFINE_EVENT(wxEVT_COMMAND_MYTHREAD_ENDING, wxThreadEvent); wxDEFINE_EVENT(wxEVT_COMMAND_MYTHREAD_SEND_IMAGE_RESULT, wxThreadEvent); wxDEFINE_EVENT(wxEVT_COMMAND_MYTHREAD_SENDERROR, wxThreadEvent); wxDEFINE_EVENT(wxEVT_COMMAND_MYTHREAD_SENDINFO, wxThreadEvent); wxDEFINE_EVENT(wxEVT_COMMAND_MYTHREAD_INTERMEDIATE_RESULT_AVAILABLE, wxThreadEvent); wxDEFINE_EVENT(wxEVT_COMMAND_MYTHREAD_SEND_PROGRAM_DEFINED_RESULT, ReturnProgramDefinedResultEvent); #define THREAD_START_NEXT_JOB 0 #define THREAD_DIE 1 #define THREAD_SLEEP 2 bool MyApp::OnInit() { long counter; int parse_status; int number_of_arguments; thread_next_action = THREAD_SLEEP; number_of_dispatched_jobs = 0; number_of_finished_jobs = 0; number_of_connected_slaves = 0; connection_timer = NULL; zombie_timer = NULL; queue_timer = NULL; queue_timer_set = false; currently_running_a_job = false; time_of_last_queue_send = 0; number_of_results_sent = 0; total_milliseconds_spent_on_threads = 0; ProgramSpecificInit(); wxString current_address; wxArrayString possible_controller_addresses; wxIPV4address junk_address; // Bind the thread events Bind(wxEVT_COMMAND_MYTHREAD_COMPLETED, &MyApp::OnThreadComplete, this); // Called when DoCalculation finishes Bind(wxEVT_COMMAND_MYTHREAD_SENDERROR, &MyApp::OnThreadSendError, this); Bind(wxEVT_COMMAND_MYTHREAD_SENDINFO, &MyApp::OnThreadSendInfo, this); Bind(wxEVT_COMMAND_MYTHREAD_ENDING, &MyApp::OnThreadEnding, this); // When thread is about to die Bind(wxEVT_COMMAND_MYTHREAD_INTERMEDIATE_RESULT_AVAILABLE, &MyApp::OnThreadIntermediateResultAvailable, this); Bind(wxEVT_COMMAND_MYTHREAD_SEND_IMAGE_RESULT, &MyApp::OnThreadSendImageResult, this); Bind(wxEVT_COMMAND_MYTHREAD_SEND_PROGRAM_DEFINED_RESULT, &MyApp::OnThreadSendProgramDefinedResult, this); // Connect to the controller program.. // set up the parameters for passing the gui address.. command_line_parser.SetCmdLine(argc,argv); command_line_parser.AddParam("controller_address",wxCMD_LINE_VAL_STRING, wxCMD_LINE_PARAM_OPTIONAL); command_line_parser.AddParam("controller_port",wxCMD_LINE_VAL_NUMBER, wxCMD_LINE_PARAM_OPTIONAL); command_line_parser.AddParam("job_code",wxCMD_LINE_VAL_STRING, wxCMD_LINE_PARAM_OPTIONAL); // Let the app add options AddCommandLineOptions(); //wxPrintf("\n"); parse_status = command_line_parser.Parse(true); number_of_arguments = command_line_parser.GetParamCount(); if (parse_status != 0) { wxPrintf("\n\n"); return false; } // if we have no arguments run interactively.. if we have 3 continue as though we have network info, else error.. if (number_of_arguments == 0) { is_running_locally = true; DoInteractiveUserInput(); stopwatch.Start(); DoCalculation(); total_milliseconds_spent_on_threads += stopwatch.Time(); fftwf_cleanup(); // this is needed to stop valgrind reporting memory leaks.. exit(0); } else if (number_of_arguments != 3) { command_line_parser.Usage(); wxPrintf("\n\n"); return false; } is_running_locally = false; // get the address and port of the job controller (should be command line options). wxStringTokenizer controller_ip_address_tokens(command_line_parser.GetParam(0),","); while(controller_ip_address_tokens.HasMoreTokens() == true) { current_address = controller_ip_address_tokens.GetNextToken(); possible_controller_addresses.Add(current_address); if (junk_address.Hostname(current_address) == false) { MyDebugPrint(" Error: Address (%s) - not recognized as an IP or hostname\n\n", current_address); exit(-1); }; } if (command_line_parser.GetParam(1).ToLong(&controller_port) == false) { MyPrintWithDetails(" Error: Port (%s) - not recognized as a port\n\n", command_line_parser.GetParam(1)); exit(-1); } if (command_line_parser.GetParam(2).Len() != SOCKET_CODE_SIZE) { { MyPrintWithDetails(" Error: Code (%s) - is the incorrect length (%li instead of %i)\n\n", command_line_parser.GetParam(2), command_line_parser.GetParam(2).Len(), SOCKET_CODE_SIZE); exit(-1); } } // copy over job code. for (counter = 0; counter < SOCKET_CODE_SIZE; counter++) { job_code[counter] = command_line_parser.GetParam(2).GetChar(counter); } // initialise sockets.. wxSocketBase::Initialize(); // Attempt to connect to the controller.. active_controller_address.Service(controller_port); is_connected = false; //MyDebugPrint("\n JOB : Trying to connect to %s:%i (timeout = 30 sec) ...\n", controller_address.IPAddress(), controller_address.Service()); controller_socket = new wxSocketClient(); controller_socket->SetFlags(wxSOCKET_WAITALL | wxSOCKET_BLOCK ); // Setup the event handler and subscribe to most events Bind(wxEVT_SOCKET,wxSocketEventHandler( MyApp::OnOriginalSocketEvent), this, SOCKET_ID ); controller_socket->SetEventHandler(*this, SOCKET_ID); controller_socket->SetNotify(wxSOCKET_INPUT_FLAG |wxSOCKET_LOST_FLAG); controller_socket->Notify(true); //wxSleep(2); for (counter = 0; counter < possible_controller_addresses.GetCount(); counter++) { active_controller_address.Hostname(possible_controller_addresses.Item(counter)); controller_socket->Connect(active_controller_address, false); controller_socket->WaitOnConnect(4); if (controller_socket->IsConnected() == false) { controller_socket->Close(); //wxPrintf("Connection Failed.\n\n"); } else { break; } } controller_socket->SetFlags(wxSOCKET_WAITALL | wxSOCKET_BLOCK ); if (controller_socket->IsConnected() == false || controller_socket->IsOk() == false) { controller_socket->Close(); MyDebugPrint(" JOB : Failed ! Unable to connect\n"); return false; } // we are apparently connected, but this can be a lie as a certain number of connections appear to just be accepted by the operating // system - if the port if valid. So if we don't get any events from this socket within 10 seconds, we are going to try again... number_of_failed_connections = 0; i_am_a_zombie = true; Bind(wxEVT_TIMER, wxTimerEventHandler( MyApp::OnZombieTimer ), this, 1); zombie_timer = new wxTimer(this, 1); zombie_timer->StartOnce(10000); // go into the event loop return true; } // Placeholder (to be overridden) function to add options to the command line void MyApp::AddCommandLineOptions( ) { return; } void MyApp::OnOriginalSocketEvent(wxSocketEvent &event) { wxSocketBase *sock = event.GetSocket(); MyDebugAssertTrue(sock == controller_socket, "Original Socket event from Non controller socket??"); sock->SetFlags(wxSOCKET_WAITALL | wxSOCKET_BLOCK); // if we got here, we have actual communication, and therefore we are not a zombie.. i_am_a_zombie = false; if (zombie_timer != NULL) { delete zombie_timer; zombie_timer = NULL; } // Now we process the event switch(event.GetSocketEvent()) { case wxSOCKET_INPUT: { // We disable input events, so that the test doesn't trigger // wxSocketEvent again. sock->SetNotify(wxSOCKET_LOST_FLAG); ReadFromSocket(sock, &socket_input_buffer, SOCKET_CODE_SIZE); if (memcmp(socket_input_buffer, socket_please_identify, SOCKET_CODE_SIZE) == 0) // identification { // send the job identification to complete the connection WriteToSocket(sock, job_code, SOCKET_CODE_SIZE); // Enable input events again sock->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } else if (memcmp(socket_input_buffer, socket_you_are_the_master, SOCKET_CODE_SIZE) == 0) // we are the master.. so setup job control and prepare to receive connections { //MyDebugPrint("JOB : I am the master"); i_am_the_master = true; // we need to start a server so that the slaves can connect.. SetupServer(); // I have to send my ip address to the controller.. my_ip_address = ReturnIPAddressFromSocket(sock); SendwxStringToSocket(&my_ip_address, sock); SendwxStringToSocket(&my_port_string, sock); // ok, now get the job details from the conduit controller WriteToSocket(sock, socket_send_job_details, SOCKET_CODE_SIZE); // it should now send a conformation code followed by the package.. // sock->WaitForRead(10); // if (sock->IsData() == true) //{ ReadFromSocket(sock, &socket_input_buffer, SOCKET_CODE_SIZE); // is this correct? if ((memcmp(socket_input_buffer, socket_ready_to_send_job_package, SOCKET_CODE_SIZE) != 0) ) { MyDebugPrintWithDetails("JOB Master : Oops unidentified message!"); sock->Destroy(); sock = NULL; ExitMainLoop(); return; } else { // receive the job details.. my_job_package.ReceiveJobPackage(sock); //MyDebugPrint("JOB Master : Job Package Received"); // allocate space for socket pointers.. number_of_connected_slaves = 0; slave_sockets = new wxSocketBase*[my_job_package.my_profile.ReturnTotalJobs()]; for (int counter = 0; counter < my_job_package.my_profile.ReturnTotalJobs(); counter++) { slave_sockets[counter] = NULL; } } // } //else //{ // MyDebugPrintWithDetails(" JOB MASTER : ...Read Timeout waiting for job package \n\n"); // // time out - close the connection // sock->Destroy(); // sock = NULL; // ExitMainLoop(); // return; //} // Setup a timer for any straggling connections.. Bind(wxEVT_TIMER, wxTimerEventHandler( MyApp::OnConnectionTimer ), this, 0); connection_timer = new wxTimer(this, 0); connection_timer->Start(5000); // Enable input events again sock->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); // redirect socket events appropriately Unbind(wxEVT_SOCKET,wxSocketEventHandler( MyApp::OnOriginalSocketEvent), this, SOCKET_ID ); Bind(wxEVT_SOCKET, wxSocketEventHandler( MyApp::OnControllerSocketEvent), this, SOCKET_ID ); // queue timer event Bind(wxEVT_TIMER, wxTimerEventHandler( MyApp::OnQueueTimer ), this, 2); } else if (memcmp(socket_input_buffer, socket_you_are_a_slave, SOCKET_CODE_SIZE) == 0) // i'm a slave.. who is the master { long received_port; i_am_the_master = false; // get the master_ip_address; master_ip_address = ReceivewxStringFromSocket(sock); master_port_string = ReceivewxStringFromSocket(sock); master_port_string.ToLong(&received_port); master_port = (short int) received_port; // now we drop the connection, and connect to our new master.. Unbind(wxEVT_SOCKET,wxSocketEventHandler( MyApp::OnOriginalSocketEvent), this, SOCKET_ID ); sock->Destroy(); Bind(wxEVT_SOCKET, wxSocketEventHandler( MyApp::OnMasterSocketEvent), this, SOCKET_ID ); // connect to the new master.. controller_socket = new wxSocketClient(); controller_socket->SetFlags(wxSOCKET_WAITALL | wxSOCKET_BLOCK ); active_controller_address.Hostname(master_ip_address); active_controller_address.Service(master_port); // Setup the event handler and subscribe to most events controller_socket->SetEventHandler(*this, SOCKET_ID); controller_socket->SetNotify(wxSOCKET_INPUT_FLAG |wxSOCKET_LOST_FLAG); controller_socket->Notify(true); controller_socket->Connect(active_controller_address, false); controller_socket->WaitOnConnect(10); controller_socket->SetFlags( wxSOCKET_WAITALL | wxSOCKET_BLOCK ); if (controller_socket->IsConnected() == false) { controller_socket->Close(); MyDebugPrint("JOB : Failed ! Unable to connect\n"); } // Start the worker thread.. stopwatch.Start(); work_thread = new CalculateThread(this, GetMaxJobWaitTimeInSeconds()); if ( work_thread->Run() != wxTHREAD_NO_ERROR ) { MyPrintWithDetails("Can't create the thread!"); delete work_thread; work_thread = NULL; ExitMainLoop(); } // we are apparently connected, but this can be a lie = a certain number of connections appear to just be accepted by the operating // system - if the port if valid. So if we don't get any events from this socket with 30 seconds, we are going to assume something // went wrong and die... i_am_a_zombie = true; Bind(wxEVT_TIMER, wxTimerEventHandler( MyApp::OnZombieTimer ), this, 1); zombie_timer = new wxTimer(this, 1); zombie_timer->Start(120000, true); } else { MyDebugPrintWithDetails("Unknown Message!") ExitMainLoop(); return; } break; } case wxSOCKET_LOST: { wxPrintf("JOB : Socket Disconnected!!\n"); sock->Destroy(); ExitMainLoop(); return; break; } default: ; } } void MyApp::OnControllerSocketEvent(wxSocketEvent &event) { //SETUP_SOCKET_CODES wxString s = _("JOB MASTER : OnControllerSocketEvent: "); wxSocketBase *sock = event.GetSocket(); sock->SetFlags(wxSOCKET_WAITALL | wxSOCKET_BLOCK); MyDebugAssertTrue(sock == controller_socket, "Controller Socket event from Non Controller socket??"); // First, print a message switch(event.GetSocketEvent()) { case wxSOCKET_INPUT : s.Append(_("wxSOCKET_INPUT\n")); break; case wxSOCKET_LOST : s.Append(_("wxSOCKET_LOST\n")); break; default : s.Append(_("Unexpected event !\n")); break; } //m_text->AppendText(s); //MyDebugPrint(s); // Now we process the event switch(event.GetSocketEvent()) { case wxSOCKET_INPUT: { // We disable input events, so that the test doesn't trigger // wxSocketEvent again. sock->SetNotify(wxSOCKET_LOST_FLAG); ReadFromSocket(sock, &socket_input_buffer, SOCKET_CODE_SIZE); /* if (memcmp(socket_input_buffer, socket_ready_to_send_job_package, SOCKET_CODE_SIZE) == 0) // we are connected to the relevant gui panel. { //SPACER DELETE }*/ if (memcmp(socket_input_buffer, socket_time_to_die, SOCKET_CODE_SIZE) == 0) // we are connected to the relevant gui panel. { // tell any connected slaves to die. then exit.. for (int counter = 0; counter < number_of_connected_slaves; counter++) { if (slave_sockets[counter] != NULL) { long milliseconds_spent_on_slave_thread = 0; slave_sockets[counter]->SetNotify(false); WriteToSocket(slave_sockets[counter], socket_time_to_die, SOCKET_CODE_SIZE); ReadFromSocket(slave_sockets[counter], &milliseconds_spent_on_slave_thread, sizeof(long)); MyDebugAssertTrue(milliseconds_spent_on_slave_thread > 0,"Oops. Negative milliseconds spent on slave thread: %li\n",milliseconds_spent_on_slave_thread); total_milliseconds_spent_on_threads += milliseconds_spent_on_slave_thread; slave_sockets[counter]->Destroy(); slave_sockets[counter] = NULL; } } sock->Destroy(); ExitMainLoop(); exit(0); return; } // Enable input events again. sock->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); break; } case wxSOCKET_LOST: { wxPrintf("JOB CONTROL : Socket Disconnected!!\n"); sock->Destroy(); // tell the slaves to die.. for (int counter = 0; counter < number_of_connected_slaves; counter++) { if (slave_sockets[counter] != NULL) { long milliseconds_spent_on_slave_thread = 0; slave_sockets[counter]->SetNotify(false); WriteToSocket(slave_sockets[counter], socket_time_to_die, SOCKET_CODE_SIZE); ReadFromSocket(slave_sockets[counter], &milliseconds_spent_on_slave_thread, sizeof(long)); MyDebugAssertTrue(milliseconds_spent_on_slave_thread > 0,"Oops. Negative milliseconds spent on slave thread: %li\n",milliseconds_spent_on_slave_thread); total_milliseconds_spent_on_threads += milliseconds_spent_on_slave_thread; slave_sockets[counter]->Destroy(); slave_sockets[counter] = NULL; } } ExitMainLoop(); exit(0); return; break; } default: ; } } void MyApp::SendNextJobTo(wxSocketBase *socket) { //SETUP_SOCKET_CODES // if we haven't dispatched all jobs yet, then send it, otherwise tell the slave to die.. if (number_of_dispatched_jobs < my_job_package.number_of_jobs) { my_job_package.jobs[number_of_dispatched_jobs].SendJob(socket); number_of_dispatched_jobs++; } else { WriteToSocket(socket, socket_time_to_die, SOCKET_CODE_SIZE); // Receive timing for that slave before its thread dies long milliseconds_spent_on_slave_thread = 0; ReadFromSocket(socket, &milliseconds_spent_on_slave_thread, sizeof(long)); MyDebugAssertTrue(milliseconds_spent_on_slave_thread > 0,"Oops. Negative milliseconds spent on slave thread: %li\n",milliseconds_spent_on_slave_thread); total_milliseconds_spent_on_threads += milliseconds_spent_on_slave_thread; socket->Destroy(); socket = NULL; } } void MyApp::SendJobFinished(int job_number) { MyDebugAssertTrue(i_am_the_master == true, "SendJobFinished called by a slave!"); controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_job_finished, SOCKET_CODE_SIZE); // send the job number of the current job.. WriteToSocket(controller_socket, &job_number, 4); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } void MyApp::SendJobResult(JobResult *result) { MyDebugAssertTrue(i_am_the_master == true, "SendJobResult called by a slave!"); controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_job_result, SOCKET_CODE_SIZE); result->SendToSocket(controller_socket); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } void MyApp::SendJobResultQueue(ArrayofJobResults &queue_to_send) { MyDebugAssertTrue(i_am_the_master == true, "SendJobResultQueue called by a slave!"); controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_job_result_queue, SOCKET_CODE_SIZE); SendResultQueueToSocket(controller_socket, queue_to_send); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } void MyApp::MasterSendIntenalQueue() { // wxPrintf("(Master) Sending internal queue of %li jobs (%i), sending on to controller\n", job_queue.GetCount(), job_queue.Item(0).job_number); SendJobResultQueue(job_queue); job_queue.Clear(); time_of_last_queue_send = time(NULL); //wxPrintf("(Master) Queue sent\n"); } void MyApp::SendAllJobsFinished() { MyDebugAssertTrue(i_am_the_master == true, "SendAllJobsFinished called by a slave!"); // we will send all jobs finished - but first we need to ensure we have sent any results in the result queue // wait for 5 seconds to give slaves times to send in their last jobs.. wxSleep(1); Yield(); if (job_queue.GetCount() != 0) MasterSendIntenalQueue(); controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_all_jobs_finished, SOCKET_CODE_SIZE); WriteToSocket(controller_socket, &total_milliseconds_spent_on_threads, sizeof(long)); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } // This is when running on the master. It handles events on the socket connected to the slaves void MyApp::OnSlaveSocketEvent(wxSocketEvent &event) { wxString s = _("JOB MASTER: OnSlaveSocketEvent: "); wxSocketBase *sock = event.GetSocket(); sock->SetFlags( wxSOCKET_WAITALL | wxSOCKET_BLOCK); float *result; // First, print a message /* switch(event.GetSocketEvent()) { case wxSOCKET_INPUT : s.Append(_("wxSOCKET_INPUT\n")); break; case wxSOCKET_LOST : s.Append(_("wxSOCKET_LOST\n")); break; default : s.Append(_("Unexpected event !\n")); break; }*/ //MyDebugPrint(s); // Now we process the event switch(event.GetSocketEvent()) { case wxSOCKET_INPUT: { // We disable input events, so that the test doesn't trigger // wxSocketEvent again. sock->SetNotify(wxSOCKET_LOST_FLAG); ReadFromSocket(sock, &socket_input_buffer, SOCKET_CODE_SIZE); if (memcmp(socket_input_buffer, socket_send_next_job, SOCKET_CODE_SIZE) == 0) // identification { // MyDebugPrint("JOB MASTER : SEND NEXT JOB"); // if there is a result to send on, get it.. JobResult temp_result; temp_result.ReceiveFromSocket(sock); // Send the next job SendNextJobTo(sock); // Send info that the job has finished, and if necessary the result.. if (temp_result.job_number != -1) { if (temp_result.result_size > 0) { SendJobResult(&temp_result); } else // just say job finished.. { SendJobFinished(temp_result.job_number); } number_of_finished_jobs++; my_job_package.jobs[temp_result.job_number].has_been_run = true; if (number_of_finished_jobs == my_job_package.number_of_jobs) { SendAllJobsFinished(); //wxPrintf("Sending all jobs finished (%li / %i)\n", number_of_finished_jobs, my_job_package.number_of_jobs); if (my_job_package.ReturnNumberOfJobsRemaining() != 0) { SocketSendError("All jobs should be finished, but job package is not empty."); } // time to die! controller_socket->Destroy(); ExitMainLoop(); return; } } if (sock == NULL) return; } else if (memcmp(socket_input_buffer, socket_i_have_an_error, SOCKET_CODE_SIZE) == 0) // identification { // got an error message.. //MyDebugPrint("JOB MASTER : Error Message"); wxString error_message; error_message = ReceivewxStringFromSocket(sock); // send the error message up the chain.. SocketSendError(error_message); } else if (memcmp(socket_input_buffer, socket_i_have_info, SOCKET_CODE_SIZE) == 0) // identification { // got an error message.. //MyDebugPrint("JOB MASTER : Error Message"); wxString info_message; info_message = ReceivewxStringFromSocket(sock); // send the error message up the chain.. SocketSendInfo(info_message); } else if (memcmp(socket_input_buffer, socket_job_result, SOCKET_CODE_SIZE) == 0) // identification { JobResult temp_result; temp_result.ReceiveFromSocket(sock); // wxPrintf("Sending int. Job Master (%f)\n", temp_result.result_data[0]); SendJobResult(&temp_result); } else if (memcmp(socket_input_buffer, socket_job_result_queue, SOCKET_CODE_SIZE) == 0) // identification { ArrayofJobResults temp_array; //wxPrintf("(Master) Receieved socket_job_result_queue - receiving queue from slave\n"); ReceiveResultQueueFromSocket(sock, temp_array); // copy these results to our own result queue for (int counter = 0; counter < temp_array.GetCount(); counter++) { job_queue.Add(temp_array.Item(counter)); } if (queue_timer_set == false) { queue_timer_set = true; queue_timer = new wxTimer(this, 2); queue_timer->StartOnce(1000); } } else if (memcmp(socket_input_buffer, socket_result_with_image_to_write, SOCKET_CODE_SIZE) == 0) // identification { Image image_to_write; int details[3]; ReadFromSocket(sock, details, sizeof(int) * 3); image_to_write.Allocate(details[0], details[1], 1); int position_in_stack = details[2]; ReadFromSocket(sock, image_to_write.real_values, image_to_write.real_memory_allocated * sizeof(float)); wxString filename_to_write; filename_to_write = ReceivewxStringFromSocket(sock); if (master_output_file.IsOpen() == false || master_output_file.filename != filename_to_write) { master_output_file.OpenFile(filename_to_write.ToStdString(), true); image_to_write.WriteSlice(&master_output_file, 1); // to setup the file.. } image_to_write.WriteSlice(&master_output_file, position_in_stack); float temp_float; temp_float = position_in_stack; JobResult job_to_queue; job_to_queue.SetResult(1, &temp_float); job_queue.Add(job_to_queue); if (queue_timer_set == false) { queue_timer_set = true; queue_timer = new wxTimer(this, 2); queue_timer->StartOnce(1000); } } else if (memcmp(socket_input_buffer, socket_program_defined_result, SOCKET_CODE_SIZE) == 0) // identification { float *data_array; int details[3]; ReadFromSocket(sock, details, sizeof(int) * 3); data_array = new float[details[0]]; int result_number = details[1]; int number_of_expected_results = details[2]; ReadFromSocket(sock, data_array, details[0] * sizeof(float)); MasterHandleProgramDefinedResult(data_array, details[0], result_number, number_of_expected_results); delete [] data_array; } /* else if (memcmp(socket_input_buffer, socket_send_timing_for_thread, SOCKET_CODE_SIZE) == 0) // identification { long milliseconds_spent_on_slave_thread; ReadFromSocket(sock, &milliseconds_spent_on_slave_thread, sizeof(long)); total_milliseconds_spent_on_threads += milliseconds_spent_on_slave_thread; wxPrintf("master received this timing: %ld\n",milliseconds_spent_on_slave_thread); } */ // Enable input events again. sock->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); break; } case wxSOCKET_LOST: { if (number_of_dispatched_jobs < my_job_package.number_of_jobs) { SocketSendError("Error: A slave has disconnected before all jobs are finished."); } //wxPrintf("JOB Master : a slave socket Disconnected!!\n"); if (sock != NULL) sock->Destroy(); //ExitMainLoop(); //DEBUG_ABORT; break; } default: ; } } void MyApp::SetupServer() { wxIPV4address my_address; wxIPV4address buffer_address; //MyDebugPrint("Setting up Server..."); for (short int current_port = START_PORT; current_port <= END_PORT; current_port++) { if (current_port == END_PORT) { wxPrintf("JOB MASTER : Could not find a valid port !\n\n"); ExitMainLoop(); return; } my_port = current_port; my_address.Service(my_port); socket_server = new wxSocketServer(my_address); socket_server->SetFlags( wxSOCKET_WAITALL | wxSOCKET_BLOCK ); if ( socket_server->Ok()) { // setup events for the socket server.. socket_server->SetEventHandler(*this, SERVER_ID); socket_server->SetNotify(wxSOCKET_CONNECTION_FLAG); socket_server->Notify(true); Bind(wxEVT_SOCKET, wxSocketEventHandler( MyApp::OnServerEvent), this, SERVER_ID); my_port_string = wxString::Format("%hi", my_port); /* buffer_address.Hostname(wxGetFullHostName()); // hopefully get my ip my_ip_address = buffer_address.IPAddress(); */ break; } else socket_server->Destroy(); } } void MyApp::OnConnectionTimer(wxTimerEvent& event) { CheckForConnections(); } void MyApp::OnZombieTimer(wxTimerEvent& event) { if (i_am_a_zombie == true) { number_of_failed_connections++; if (number_of_failed_connections >= 5) ExitMainLoop(); controller_socket->Close(); controller_socket->Connect(active_controller_address, false); controller_socket->WaitOnConnect(120); if (controller_socket->IsConnected() == false) { controller_socket->Close(); //wxPrintf("Connection Failed.\n\n"); } controller_socket->SetFlags(wxSOCKET_WAITALL | wxSOCKET_BLOCK ); if (controller_socket->IsConnected() == false || controller_socket->IsOk() == false) { controller_socket->Close(); MyDebugPrint(" JOB : Failed ! Unable to connect\n"); ExitMainLoop(); } // once again, we are parently connected, but this can be a lie as a certain number of connections appear to just be accepted by the operating // system - if the port if valid. So if we don't get any events from this socket within 10 seconds, we are going to try again... zombie_timer = new wxTimer(this, 1); zombie_timer->StartOnce(10000); } } void MyApp::OnQueueTimer(wxTimerEvent& event) { //wxPrintf("Queue timer fired\n"); if (job_queue.GetCount() > 0) { // wxPrintf("sending from timer\n"); MasterSendIntenalQueue(); } queue_timer_set = false; delete queue_timer; } void MyApp::OnServerEvent(wxSocketEvent& event) // this should only be called by the master { MyDebugAssertTrue(i_am_the_master == true, "Server event called by non master!"); CheckForConnections(); } void MyApp::CheckForConnections() { // SETUP_SOCKET_CODES wxSocketBase *sock = NULL; while (1==1) { sock = socket_server->Accept(false); if (sock == NULL) break; sock->SetFlags( wxSOCKET_WAITALL | wxSOCKET_BLOCK ); sock->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(sock, socket_please_identify, SOCKET_CODE_SIZE); // sock->WaitForRead(5); // if (sock->IsData() == true) // { ReadFromSocket(sock, &socket_input_buffer, SOCKET_CODE_SIZE); // does this correspond to our job code? if ((memcmp(socket_input_buffer, job_code, SOCKET_CODE_SIZE) != 0) ) { SocketSendError("Received Unknown Job ID (leftover process from a cancelled job?)- Closing Connection"); // incorrect identification - close the connection.. sock->Destroy(); sock = NULL; } else { // A slave has connected Unbind(wxEVT_SOCKET,wxSocketEventHandler( MyApp::OnOriginalSocketEvent), this, SOCKET_ID ); Bind(wxEVT_SOCKET, wxSocketEventHandler( MyApp::OnSlaveSocketEvent), this, SOCKET_ID ); // we need to setup events of this socket.. sock->SetEventHandler(*this, SOCKET_ID); sock->SetNotify(wxSOCKET_INPUT_FLAG |wxSOCKET_LOST_FLAG); sock->Notify(true); slave_sockets[number_of_connected_slaves] = sock; number_of_connected_slaves++; //SocketSendInfo(wxString::Format("slave slaves connected = %li", number_of_connected_slaves)); // tell it is is connected.. WriteToSocket(sock, socket_you_are_connected, SOCKET_CODE_SIZE); // if we have them all we can delete the timer.. int number_of_commands_to_run; if (my_job_package.number_of_jobs + 1 < my_job_package.my_profile.ReturnTotalJobs()) number_of_commands_to_run = my_job_package.number_of_jobs + 1; else number_of_commands_to_run = my_job_package.my_profile.ReturnTotalJobs(); if (number_of_connected_slaves == number_of_commands_to_run - 1) { connection_timer->Stop(); Unbind(wxEVT_TIMER, wxTimerEventHandler( MyApp::OnConnectionTimer ), this); delete connection_timer; SocketSendInfo("All slaves have re-connected to the master."); } } // } //else //{ // SocketSendError("JOB MASTER : ...Read Timeout waiting for job ID"); // // time out - close the connection // sock->Destroy(); // sock = NULL; // } } } void MyApp::OnMasterSocketEvent(wxSocketEvent& event) { //SETUP_SOCKET_CODES wxString s = _("JOB : OnMasterSocketEvent: "); wxSocketBase *sock = event.GetSocket(); sock->SetFlags( wxSOCKET_WAITALL | wxSOCKET_BLOCK ); MyDebugAssertTrue(sock == controller_socket, "Master Socket event from Non controller socket??"); // First, print a message switch(event.GetSocketEvent()) { case wxSOCKET_INPUT : s.Append(_("wxSOCKET_INPUT\n")); break; case wxSOCKET_LOST : s.Append(_("wxSOCKET_LOST\n")); break; default : s.Append(_("Unexpected event !\n")); break; } //MyDebugPrint(s); // if we got here, we are not a zombie.. i_am_a_zombie = false; if (zombie_timer != NULL) { delete zombie_timer; zombie_timer = NULL; } // Now we process the event switch(event.GetSocketEvent()) { case wxSOCKET_INPUT: { // We disable input events, so that the test doesn't trigger // wxSocketEvent again. sock->SetNotify(wxSOCKET_LOST_FLAG); ReadFromSocket(sock, &socket_input_buffer, SOCKET_CODE_SIZE, true); if (memcmp(socket_input_buffer, socket_please_identify, SOCKET_CODE_SIZE) == 0) // identification { // send the job identification to complete the connection //MyDebugPrint("JOB SLAVE : Sending Identification") WriteToSocket(sock, job_code, SOCKET_CODE_SIZE, true); } else if (memcmp(socket_input_buffer, socket_you_are_connected, SOCKET_CODE_SIZE) == 0) // identification { // we are connected, request the first job.. is_connected = true; //MyDebugPrint("JOB SLAVE : Requesting job"); WriteToSocket(sock, socket_send_next_job, SOCKET_CODE_SIZE, true); JobResult temp_result; // dummy result for the initial request - not reallt very nice temp_result.job_number = -1; temp_result.result_size = 0; temp_result.SendToSocket(sock); } else if (memcmp(socket_input_buffer, socket_ready_to_send_single_job, SOCKET_CODE_SIZE) == 0) // identification { // are we currently running a job? MyDebugAssertTrue(currently_running_a_job == false, "Received a new job, when already running a job!"); // recieve job // MyDebugPrint("JOB SLAVE : About to receive new job") my_current_job.RecieveJob(sock); // run a thread for this job.. //MyDebugPrint("JOB SLAVE : New Job, starting thread") //MyDebugAssertTrue(work_thread == NULL, "Running a new thread, but old thread is not NULL"); wxMutexLocker *lock = new wxMutexLocker(job_lock); if (lock->IsOk() == true) { MyDebugAssertFalse(thread_next_action = THREAD_START_NEXT_JOB, "Thread action is already start job"); thread_next_action = THREAD_START_NEXT_JOB; } else { SocketSendError("Job Lock Error!"); MyPrintWithDetails("Can't get job lock!"); } delete lock; /* work_thread = new CalculateThread(this); if ( work_thread->Run() != wxTHREAD_NO_ERROR ) { MyPrintWithDetails("Can't create the thread!"); delete work_thread; work_thread = NULL; ExitMainLoop(); return; }*/ //MyDebugPrint("JOB SLAVE : Started Thread"); } else if (memcmp(socket_input_buffer, socket_time_to_die, SOCKET_CODE_SIZE) == 0) // identification { // Timing stuff here long milliseconds_spent_by_thread = stopwatch.Time(); controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, &milliseconds_spent_by_thread, sizeof(long), true); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); // time to die! wxMutexLocker *lock = new wxMutexLocker(job_lock); if (lock->IsOk() == true) { thread_next_action = THREAD_DIE; } else { SocketSendError("Job Lock Error!"); MyPrintWithDetails("Can't get job lock!"); } delete lock; // give the thread some time to die.. wxSleep(5); // process thread events in case it has done something Yield(); //(wxEVT_CATEGORY_THREAD); // finish sock->Destroy(); if (work_thread != NULL) work_thread->Kill(); ExitMainLoop(); exit(0); return; } // Enable input events again. sock->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); break; } case wxSOCKET_LOST: { wxPrintf("JOB : Master Socket Disconnected!!\n"); wxMutexLocker *lock = new wxMutexLocker(job_lock); if (lock->IsOk() == true) { thread_next_action = THREAD_DIE; } else { SocketSendError("Job Lock Error!"); MyPrintWithDetails("Can't get job lock!"); } delete lock; // give the thread some time to die.. wxSleep(5); // process thread events in case it has done something Yield(); //(wxEVT_CATEGORY_THREAD); // finish sock->Destroy(); if (work_thread != NULL) work_thread->Kill(); ExitMainLoop(); exit(0); return; break; } default: ; } } void MyApp::OnThreadComplete(wxThreadEvent& my_event) { //SETUP_SOCKET_CODES // The compute thread is finished.. get the next job // thread should be dead, or nearly dead.. //work_thread = NULL; SendAllResultsFromResultQueue(); // get the next job.. controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_send_next_job, SOCKET_CODE_SIZE, true); // if there is a result - send it to the gui.. my_result.job_number = my_current_job.job_number; my_result.SendToSocket(controller_socket); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); // clear the results queue.. } void MyApp::OnThreadEnding(wxThreadEvent& my_event) { SendAllResultsFromResultQueue(); work_thread = NULL; } void MyApp::OnThreadSendError(wxThreadEvent& my_event) { SocketSendError(my_event.GetString()); //MyDebugPrint("ThreadSendError"); } void MyApp::OnThreadSendInfo(wxThreadEvent& my_event) { SocketSendInfo(my_event.GetString()); //MyDebugPrint("ThreadSendError"); } void MyApp::OnThreadIntermediateResultAvailable(wxThreadEvent& my_event) { // wxPrintf("MyApp::Received result available event..\n"); SendAllResultsFromResultQueue(); } void MyApp::OnThreadSendImageResult(wxThreadEvent& my_event) { MyDebugAssertTrue(i_am_the_master == false, "OnThreadSendImageResult called by master!"); Image image_to_send; image_to_send = my_event.GetPayload(); int position_in_stack = my_event.GetInt(); wxString filename_to_write = my_event.GetString(); int details[3]; details[0] = image_to_send.logical_x_dimension; details[1] = image_to_send.logical_y_dimension; details[2] = position_in_stack; controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_result_with_image_to_write, SOCKET_CODE_SIZE, true); WriteToSocket(controller_socket, details, sizeof(int) * 3, true); WriteToSocket(controller_socket, image_to_send.real_values, image_to_send.real_memory_allocated * sizeof(float), true); SendwxStringToSocket(&filename_to_write, controller_socket); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } void MyApp::OnThreadSendProgramDefinedResult(ReturnProgramDefinedResultEvent& my_event) { MyDebugAssertTrue(i_am_the_master == false, "OnThreadSendImageResult called by master!"); float *array_to_send = my_event.GetResultData(); long size_of_array = my_event.GetSizeOfResultData(); int number_of_expected_results = my_event.GetNumberOfExpectedResults(); int result_number = my_event.GetResultNumber(); int details[3]; details[0] = size_of_array; details[1] = result_number; details[2] = number_of_expected_results; controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_program_defined_result, SOCKET_CODE_SIZE, true); WriteToSocket(controller_socket, details, sizeof(int) * 3, true); WriteToSocket(controller_socket, array_to_send, size_of_array * sizeof(float), true); delete [] array_to_send; controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } void MyApp::SendAllResultsFromResultQueue() { // have we sent results within the last second? if so wait 1s ArrayofJobResults my_queue_array; // we want to pop off all the jobs, and send them in one big lump.. while (1==1) { JobResult *popped_job = PopJobFromResultQueue(); if (popped_job == NULL) { break; } else { my_queue_array.Add(*popped_job); delete popped_job; } } // ok, send them all.. if (my_queue_array.GetCount() > 0) { if (time(NULL) - time_of_last_queue_send < 1) { wxSleep(1); } SendIntermediateResultQueue(my_queue_array); time_of_last_queue_send = time(NULL); } } void MyApp::SendIntermediateResultQueue(ArrayofJobResults &queue_to_send) { MyDebugAssertTrue(i_am_the_master == false, "SendIntermediateResultQueue called by master!"); if (queue_to_send.GetCount() > 0) { controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_job_result_queue, SOCKET_CODE_SIZE, true); SendResultQueueToSocket(controller_socket, queue_to_send); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } } void MyApp::SocketSendError(wxString error_to_send) { // send the error message flag if (is_running_locally == false) { controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_i_have_an_error, SOCKET_CODE_SIZE); SendwxStringToSocket(&error_to_send, controller_socket); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } } void MyApp::SocketSendInfo(wxString info_to_send) { // send the info message flag if (is_running_locally == false) { controller_socket->SetNotify(wxSOCKET_LOST_FLAG); WriteToSocket(controller_socket, socket_i_have_info, SOCKET_CODE_SIZE); SendwxStringToSocket(&info_to_send, controller_socket); controller_socket->SetNotify(wxSOCKET_LOST_FLAG | wxSOCKET_INPUT_FLAG); } } void MyApp::SendError(wxString error_to_send) { if (is_running_locally == true) { wxPrintf("\nError : %s\n", error_to_send); } else if (work_thread != NULL) { work_thread->QueueError(error_to_send); } else { SocketSendError("SendError with null work thread!"); } } void MyApp::SendErrorAndCrash(wxString error_to_send) { SendError(error_to_send); if (!is_running_locally) wxSleep(2); // wait for the main thread to actually send the error DEBUG_ABORT; } void MyApp::SendInfo(wxString info_to_send) { if (is_running_locally == true) { wxPrintf("\nInfo : %s\n", info_to_send); } else if (work_thread != NULL) { work_thread->QueueInfo(info_to_send); } else { SocketSendError("SendInfo with null work thread!"); } } void MyApp::AddJobToResultQueue(JobResult * result_to_add) { // wxPrintf("Adding Job to result Queue\n"); wxMutexLocker *lock = new wxMutexLocker(job_lock); if (lock->IsOk() == true) job_queue.Add(result_to_add); else { SocketSendError("Job Lock Error!"); MyPrintWithDetails("Can't get job lock!"); } delete lock; if (work_thread != NULL) { // wxPrintf("MyApp::Marking Intermediate Result Available...\n"); work_thread->MarkIntermediateResultAvailable(); } else { wxPrintf("Work thread is NULL!\n"); } } void MyApp::SendProcessedImageResult(Image *image_to_send, int position_in_stack, wxString filename_to_save) { if (work_thread != NULL) { work_thread->SendProcessedImageResult(image_to_send, position_in_stack, filename_to_save); } else { wxPrintf("Work thread is NULL!\n"); } } void MyApp::SendProgramDefinedResultToMaster(float *array_to_send, long size_of_array, int result_number, int number_of_expected_results) { if (work_thread != NULL) { work_thread->SendProgramDefinedResultToMaster(array_to_send, size_of_array, result_number, number_of_expected_results); } else { wxPrintf("Work thread is NULL!\n"); } } JobResult * MyApp::PopJobFromResultQueue() { JobResult *popped_job = NULL; wxMutexLocker *lock = new wxMutexLocker(job_lock); if (lock->IsOk() == true) { if (job_queue.GetCount() > 0) { popped_job = job_queue.Detach(0); } } else { SocketSendError("Job Lock Error!"); MyPrintWithDetails("Can't get job lock!"); } delete lock; return popped_job; } // Main execution in this thread.. wxThread::ExitCode CalculateThread::Entry() { int thread_action_copy; long millis_sleeping = 0; while (1==1) { wxMutexLocker *lock = new wxMutexLocker(main_thread_pointer->job_lock); if (lock->IsOk() == true) { thread_action_copy = main_thread_pointer->thread_next_action; } else { QueueError("Job Lock Error!"); } if (main_thread_pointer->thread_next_action == THREAD_START_NEXT_JOB) { main_thread_pointer->thread_next_action = THREAD_SLEEP; millis_sleeping = 0; } delete lock; if (thread_action_copy == THREAD_START_NEXT_JOB) { bool success = main_thread_pointer->DoCalculation(); // This should be overrided per app.. wxThreadEvent *my_thread_event = new wxThreadEvent(wxEVT_COMMAND_MYTHREAD_COMPLETED); if (success == true) my_thread_event->SetInt(1); else my_thread_event->SetInt(0); wxQueueEvent(main_thread_pointer, my_thread_event); } else if (thread_action_copy == THREAD_SLEEP) { wxMilliSleep(100); millis_sleeping += 100; if (millis_sleeping > job_wait_time * 1000) { // we have been waiting for 10 seconds, something probably went wrong - so die. wxPrintf("Calculation thread has been waiting for something to do for %f.2 seconds - going to finish\n", job_wait_time); QueueError(wxString::Format("Calculation thread has been waiting for something to do for %f.2 seconds - going to finish", job_wait_time)); break; } } else if (thread_action_copy == THREAD_DIE) break; } wxThreadEvent *my_thread_event = new wxThreadEvent(wxEVT_COMMAND_MYTHREAD_ENDING); wxQueueEvent(main_thread_pointer, my_thread_event); fftwf_cleanup(); // this is needed to stop valgrind reporting memory leaks.. return (wxThread::ExitCode)0; // success } void CalculateThread::QueueError(wxString error_to_queue) { wxThreadEvent *test_event = new wxThreadEvent(wxEVT_COMMAND_MYTHREAD_SENDERROR); test_event->SetString(error_to_queue); wxQueueEvent(main_thread_pointer, test_event); } void CalculateThread::QueueInfo(wxString info_to_queue) { wxThreadEvent *test_event = new wxThreadEvent(wxEVT_COMMAND_MYTHREAD_SENDINFO); test_event->SetString(info_to_queue); wxQueueEvent(main_thread_pointer, test_event); } void CalculateThread::MarkIntermediateResultAvailable() { wxThreadEvent *test_event = new wxThreadEvent(wxEVT_COMMAND_MYTHREAD_INTERMEDIATE_RESULT_AVAILABLE); wxQueueEvent(main_thread_pointer, test_event); //wxPrintf("CalculateThread::Queueing Result Available Event..\n"); } void CalculateThread::SendProcessedImageResult(Image *image_to_send, int position_in_stack, wxString filename_to_save) { wxThreadEvent *test_event = new wxThreadEvent(wxEVT_COMMAND_MYTHREAD_SEND_IMAGE_RESULT); test_event->SetInt(position_in_stack); test_event->SetString(filename_to_save); test_event->SetPayload(*image_to_send); wxQueueEvent(main_thread_pointer, test_event); } void CalculateThread::SendProgramDefinedResultToMaster(float *array_to_send, long size_of_array, int result_number, int number_of_expected_results) { ReturnProgramDefinedResultEvent *test_event = new ReturnProgramDefinedResultEvent(wxEVT_COMMAND_MYTHREAD_SEND_PROGRAM_DEFINED_RESULT); test_event->SetResultData(array_to_send); test_event->SetSizeOfResultData(size_of_array); test_event->SetResultNumber(result_number); test_event->SetNumberOfExpectedResults(number_of_expected_results); wxQueueEvent(main_thread_pointer, test_event); } CalculateThread::~CalculateThread() { //wxCriticalSectionLocker enter(m_pHandler->m_pThreadCS); // the thread is being destroyed; make sure not to leave dangling pointers around wxMutexLocker *lock = new wxMutexLocker(main_thread_pointer->job_lock); if (lock->IsOk() == true) { main_thread_pointer->work_thread = NULL; } else { QueueError("Job Lock Error!"); } delete lock; main_thread_pointer = NULL; } ctffind-4.1.14/src/core/myapp.h000066400000000000000000000146231440356052600162470ustar00rootroot00000000000000#define SERVER_ID 100 #define SOCKET_ID 101 class ReturnProgramDefinedResultEvent; wxDECLARE_EVENT(RETURN_PROGRAM_DEFINED_RESULT_EVT, ReturnProgramDefinedResultEvent); class ReturnProgramDefinedResultEvent: public wxThreadEvent { public: ReturnProgramDefinedResultEvent(wxEventType commandType = RETURN_PROGRAM_DEFINED_RESULT_EVT, int id = 0) : wxThreadEvent(commandType, id) { } // You *must* copy here the data to be transported ReturnProgramDefinedResultEvent(const ReturnProgramDefinedResultEvent& event) : wxThreadEvent(event) { this->SetResultData(event.GetResultData()); this->SetSizeOfResultData(event.GetSizeOfResultData()); this->SetResultNumber(event.GetResultNumber()); this->SetNumberOfExpectedResults(event.GetNumberOfExpectedResults()); } // Required for sending with wxPostEvent() wxEvent* Clone() const { return new ReturnProgramDefinedResultEvent(*this); } float* GetResultData() const {return m_pointer_to_result_data;} long GetSizeOfResultData() const {return m_size_of_result_data;} int GetResultNumber() const{return m_result_number;} int GetNumberOfExpectedResults() const{return m_number_of_expected_results;} void SetResultData(float *result) {m_pointer_to_result_data = result;} void SetSizeOfResultData(long size) {m_size_of_result_data = size;} void SetResultNumber(int result_number) {m_result_number = result_number;} void SetNumberOfExpectedResults(int number_of_expected_results) {m_number_of_expected_results = number_of_expected_results;} private: float *m_pointer_to_result_data; long m_size_of_result_data; int m_result_number; int m_number_of_expected_results; }; class MyApp; // So CalculateThread class knows about it // The workhorse / calculation thread class CalculateThread : public wxThread { public: CalculateThread(MyApp *handler, float wanted_job_wait_time) : wxThread(wxTHREAD_DETACHED) { main_thread_pointer = handler; job_wait_time = wanted_job_wait_time;} ~CalculateThread(); MyApp *main_thread_pointer; float job_wait_time; void QueueError(wxString error_to_queue); void QueueInfo(wxString info_to_queue); void MarkIntermediateResultAvailable(); void SendProcessedImageResult(Image *image_to_send, int position_in_stack, wxString filename_to_save); void SendProgramDefinedResultToMaster(float *result_to_send, long size_of_result, int result_number, int number_of_expected_results); protected: virtual ExitCode Entry(); long time_sleeping; }; // The console APP class.. should just deal with events.. class MyApp : public wxAppConsole { wxTimer *connection_timer; wxTimer *zombie_timer; wxTimer *queue_timer; bool i_am_a_zombie; bool queue_timer_set; bool running_image_writer_thread; int number_of_failed_connections; void CheckForConnections(); void OnConnectionTimer(wxTimerEvent& event); void OnZombieTimer(wxTimerEvent& event); void OnQueueTimer(wxTimerEvent& event); virtual float GetMaxJobWaitTimeInSeconds() {return 30.0f;} wxStopWatch stopwatch; long total_milliseconds_spent_on_threads; MRCFile master_output_file; public: bool OnInit(); virtual void ProgramSpecificInit() {}; // array for sending back the results - this may be better off being made into an object.. JobResult my_result; ArrayofJobResults job_queue; // socket stuff wxSocketClient *controller_socket; bool is_connected; bool currently_running_a_job; wxIPV4address active_controller_address; long controller_port; unsigned char job_code[SOCKET_CODE_SIZE]; short int my_port; wxString my_ip_address; wxString my_port_string; bool is_running_locally; wxSocketServer *socket_server; bool i_am_the_master; int number_of_results_sent; JobPackage my_job_package; RunJob my_current_job; RunJob global_job_parameters; wxString master_ip_address; wxString master_port_string; short int master_port; long number_of_connected_slaves; // for the master... long number_of_dispatched_jobs; long number_of_finished_jobs; wxSocketBase **slave_sockets; // POINTER TO POINTER.. wxCmdLineParser command_line_parser; virtual bool DoCalculation() = 0; virtual void DoInteractiveUserInput() {wxPrintf("\n Error: This program cannot be run interactively..\n\n"); exit(0);} virtual void AddCommandLineOptions(); void SendError(wxString error_message); void SendErrorAndCrash(wxString error_message); void SendInfo(wxString error_message); void SendIntermediateResultQueue(ArrayofJobResults &queue_to_send); CalculateThread *work_thread; wxMutex job_lock; int thread_next_action; long time_of_last_queue_send; void AddJobToResultQueue(JobResult *); JobResult * PopJobFromResultQueue(); void SendAllResultsFromResultQueue(); void SendProcessedImageResult(Image *image_to_send, int position_in_stack, wxString filename_to_save); void SendProgramDefinedResultToMaster(float *result_to_send, long size_of_result, int result_number, int number_of_expected_results); // can override MasterHandleSpecialResult to do something with this private: void SendJobFinished(int job_number); void SendJobResult(JobResult *result); void SendJobResultQueue(ArrayofJobResults &queue_to_send); void MasterSendIntenalQueue(); void SendAllJobsFinished(); virtual void MasterHandleProgramDefinedResult(float *result_array, long array_size, int result_number, int number_of_expected_results){wxPrintf("warning parent MasterHandleProgramDefinedResult called, you should probably be overriding this!\n");} // can use this for program specific results by overiding in combination with SendSpecialResultForMaster in the program void SocketSendError(wxString error_message); void SocketSendInfo(wxString info_message); void SetupServer(); void SendNextJobTo(wxSocketBase *socket); void OnOriginalSocketEvent(wxSocketEvent& event); void OnMasterSocketEvent(wxSocketEvent& event); void OnSlaveSocketEvent(wxSocketEvent& event); void OnControllerSocketEvent(wxSocketEvent& event); void OnServerEvent(wxSocketEvent& event); void OnThreadComplete(wxThreadEvent& my_event); void OnThreadEnding(wxThreadEvent& my_event); void OnThreadSendError(wxThreadEvent& my_event); void OnThreadSendInfo(wxThreadEvent& my_event); void OnThreadIntermediateResultAvailable(wxThreadEvent& my_event); void OnThreadSendImageResult(wxThreadEvent& my_event); void OnThreadSendProgramDefinedResult(ReturnProgramDefinedResultEvent& my_event); }; ctffind-4.1.14/src/core/numeric_text_file.cpp000066400000000000000000000156301440356052600211600ustar00rootroot00000000000000#include "core_headers.h" NumericTextFile::NumericTextFile() { MyPrintWithDetails("NumericTextfile has been declared with no filename.\n"); DEBUG_ABORT; } NumericTextFile::NumericTextFile(wxString Filename, long wanted_access_type, long wanted_records_per_line) { input_file_stream = NULL; input_text_stream = NULL; output_file_stream = NULL; output_text_stream = NULL; Open(Filename, wanted_access_type, wanted_records_per_line); } NumericTextFile::~NumericTextFile() { Close(); } void NumericTextFile::Open(wxString Filename, long wanted_access_type, long wanted_records_per_line) { access_type = wanted_access_type; records_per_line = wanted_records_per_line; text_filename = Filename; if (access_type == OPEN_TO_READ) { if (input_file_stream != NULL) { if (input_file_stream->GetFile()->IsOpened() == true) { MyPrintWithDetails("File already Open\n"); DEBUG_ABORT; } } } else if (access_type == OPEN_TO_WRITE) { records_per_line = wanted_records_per_line; if (records_per_line <= 0) { MyPrintWithDetails("NumericTextFile asked to OPEN_TO_WRITE, but with erroneous records per line\n"); DEBUG_ABORT; } if (output_file_stream != NULL) { if (output_file_stream->GetFile()->IsOpened() == true) { MyPrintWithDetails("File already Open\n"); DEBUG_ABORT; } } } else { MyPrintWithDetails("Unknown access type!\n"); DEBUG_ABORT; } Init(); } void NumericTextFile::Close() { if (input_text_stream != NULL) delete input_text_stream; if (output_text_stream != NULL) delete output_text_stream; if (output_file_stream != NULL) { if (output_file_stream->GetFile()->IsOpened() == true) output_file_stream->GetFile()->Close(); delete output_file_stream; } if (input_file_stream != NULL) { if (input_file_stream->GetFile()->IsOpened() == true) input_file_stream->GetFile()->Close(); delete input_file_stream; } input_file_stream = NULL; input_text_stream = NULL; output_file_stream = NULL; output_text_stream = NULL; } void NumericTextFile::Init() { if (access_type == OPEN_TO_READ) { wxString current_line; wxString token; double temp_double; int current_records_per_line; int old_records_per_line = -1; input_file_stream = new wxFileInputStream(text_filename); input_text_stream = new wxTextInputStream(*input_file_stream); if (input_file_stream->IsOk() == false) { MyPrintWithDetails("Attempt to access %s for reading failed\n",text_filename); DEBUG_ABORT; } // work out the records per line and how many lines number_of_lines = 0; while (input_file_stream->Eof() == false) { current_line = input_text_stream->ReadLine(); current_line.Trim(false); if (current_line.StartsWith("#") != true && current_line.StartsWith("C") != true && current_line.Length() > 0) { number_of_lines++; wxStringTokenizer tokenizer(current_line); current_records_per_line = 0; while ( tokenizer.HasMoreTokens() ) { token = tokenizer.GetNextToken(); if (token.ToDouble(&temp_double) == false) { MyPrintWithDetails("Failed on the following record : %s\n", token); DEBUG_ABORT; } else { current_records_per_line++; } } // we want to check records_per_line for consistency.. if (old_records_per_line != -1) { if (old_records_per_line != current_records_per_line) { MyPrintWithDetails("Different records per line found"); DEBUG_ABORT; } } old_records_per_line = current_records_per_line; } } records_per_line = current_records_per_line; // rewind the file.. Rewind(); } else if (access_type == OPEN_TO_WRITE) { // check if the file exists.. if (DoesFileExist(text_filename) == true) { if (wxRemoveFile(text_filename) == false) { MyDebugPrintWithDetails("Cannot remove already existing text file"); } } output_file_stream = new wxFileOutputStream(text_filename); output_text_stream = new wxTextOutputStream(*output_file_stream); } } void NumericTextFile::Rewind() { if (access_type == OPEN_TO_READ) { delete input_file_stream; delete input_text_stream; input_file_stream = new wxFileInputStream(text_filename); input_text_stream = new wxTextInputStream(*input_file_stream); } else output_file_stream->GetFile()->Seek(0); } void NumericTextFile::Flush() { if (access_type == OPEN_TO_READ) input_file_stream->GetFile()->Flush(); else output_file_stream->GetFile()->Flush(); } void NumericTextFile::ReadLine(float *data_array) { if (access_type != OPEN_TO_READ) { MyPrintWithDetails("Attempt to read from %s however access type is not READ\n",text_filename); DEBUG_ABORT; } wxString current_line; wxString token; double temp_double; while(input_file_stream->Eof() == false) { current_line = input_text_stream->ReadLine(); current_line.Trim(false); if (current_line.StartsWith("C") == false && current_line.StartsWith("#") == false && current_line.Length() != 0) break; } wxStringTokenizer tokenizer(current_line); for (int counter = 0; counter < records_per_line; counter++ ) { token = tokenizer.GetNextToken(); if (token.ToDouble(&temp_double) == false) { MyPrintWithDetails("Failed on the following record : %s\nFrom Line : %s\n", token.ToUTF8().data(), current_line.ToUTF8().data()); DEBUG_ABORT; } else { data_array[counter] = temp_double; } } } void NumericTextFile::WriteLine(float *data_array) { if (access_type != OPEN_TO_WRITE) { MyPrintWithDetails("Attempt to read from %s however access type is not WRITE\n",text_filename); DEBUG_ABORT; } for (int counter = 0; counter < records_per_line; counter++ ) { // output_text_stream->WriteDouble(data_array[counter]); output_text_stream->WriteString(wxString::Format("%14.5f",data_array[counter])); if (counter != records_per_line - 1) output_text_stream->WriteString(" "); } output_text_stream->WriteString("\n"); } void NumericTextFile::WriteLine(double *data_array) { if (access_type != OPEN_TO_WRITE) { MyPrintWithDetails("Attempt to read from %s however access type is not WRITE\n",text_filename); DEBUG_ABORT; } for (int counter = 0; counter < records_per_line; counter++ ) { output_text_stream->WriteDouble(data_array[counter]); if (counter != records_per_line - 1) output_text_stream->WriteString(" "); } output_text_stream->WriteString("\n"); } void NumericTextFile::WriteCommentLine(const char * format, ...) { va_list args; va_start(args, format); wxString comment_string; wxString buffer; comment_string.PrintfV(format, args); buffer = comment_string; buffer.Trim(false); if (buffer.StartsWith("#") == false && buffer.StartsWith("C") == false) { comment_string = "# " + comment_string; } output_text_stream->WriteString(comment_string); if (comment_string.EndsWith("\n") == false) output_text_stream->WriteString("\n"); va_end(args); } wxString NumericTextFile::ReturnFilename() { return text_filename; } ctffind-4.1.14/src/core/numeric_text_file.h000066400000000000000000000020531440356052600206200ustar00rootroot00000000000000#define OPEN_TO_READ 0 #define OPEN_TO_WRITE 1 #define OPEN_TO_APPEND 2 class NumericTextFile { private: void Init(); wxString text_filename; long access_type; wxFileInputStream *input_file_stream; wxTextInputStream *input_text_stream; wxFileOutputStream *output_file_stream; wxTextOutputStream *output_text_stream; public: // Constructors NumericTextFile(); NumericTextFile(wxString Filename, long wanted_access_type, long wanted_records_per_line = 1); ~NumericTextFile(); // data int number_of_lines; int records_per_line; // Methods void Open(wxString Filename, long wanted_access_type, long wanted_records_per_line = 1); void Close(); void Rewind(); void Flush(); wxString ReturnFilename(); void ReadLine(float *data_array); void WriteLine(float *data_array); void WriteLine(double *data_array); void WriteCommentLine(const char * format, ...); }; ctffind-4.1.14/src/core/parameter_constraints.h000066400000000000000000000052661440356052600215330ustar00rootroot00000000000000/* \brief AnglesAndShifts class (particle Euler angles and shifts) */ class ParameterConstraints { public: ParameterConstraints(); // ~ParameterConstraints(); // destructor void InitPhi(float wanted_phi_average, float wanted_phi_variance, float wanted_phi_noise_variance); void InitTheta(float wanted_theta_average, float wanted_theta_variance, float wanted_theta_noise_variance); void InitPsi(float wanted_psi_average, float wanted_psi_variance, float wanted_psi_noise_variance); void InitShiftX(float wanted_shift_x_average, float wanted_shift_x_variance, float wanted_shift_x_noise_variance); void InitShiftY(float wanted_shift_y_average, float wanted_shift_y_variance, float wanted_shift_y_noise_variance); inline float ReturnPhiAngleLogP(float phi) {return - powf(phi - phi_average,2) / 2.0 / phi_variance;}; inline float ReturnThetaAngleLogP(float theta) {return - powf(theta - theta_average,2) / 2.0 / theta_variance;}; inline float ReturnPsiAngleLogP(float psi) {return - powf(psi - psi_average,2) / 2.0 / psi_variance;}; inline float ReturnShiftXLogP(float shift_x) {return - powf(shift_x - shift_x_average,2) / 2.0 / shift_x_variance;}; inline float ReturnShiftYLogP(float shift_y) {return - powf(shift_y - shift_y_average,2) / 2.0 / shift_y_variance;}; inline float ReturnPhiAnglePenalty(float phi) {return - phi_noise_variance * ReturnPhiAngleLogP(phi);}; inline float ReturnThetaAnglePenalty(float theta) {return - theta_noise_variance * ReturnThetaAngleLogP(theta);}; inline float ReturnPsiAnglePenalty(float psi) {return - psi_noise_variance * ReturnPsiAngleLogP(psi);}; inline float ReturnShiftXPenalty(float shift_x) {return - shift_x_noise_variance * ReturnShiftXLogP(shift_x);}; inline float ReturnShiftYPenalty(float shift_y) {return - shift_y_noise_variance * ReturnShiftYLogP(shift_y);}; // inline void SetAverageShiftX(float wanted_shift_x_average) {shift_x_average = wanted_shift_x_average;}; // inline void SetAverageShiftY(float wanted_shift_y_average) {shift_y_average = wanted_shift_y_average;}; //private: float phi_average; // in degrees float phi_variance; // in degrees float phi_noise_variance; // in density units float theta_average; // in degrees float theta_variance; // in degrees float theta_noise_variance; // in density units float psi_average; // in degrees float psi_variance; // in degrees float psi_noise_variance; // in density units float shift_x_average; // in Angstrom float shift_x_variance; // in Angstrom float shift_x_noise_variance; // in density units float shift_y_average; // in Angstrom float shift_y_variance; // in Angstrom float shift_y_noise_variance; // in density units }; ctffind-4.1.14/src/core/particle.h000066400000000000000000000147421440356052600167260ustar00rootroot00000000000000/* \brief ReconstructedVolume class */ class ReconstructedVolume; class Particle { public: int origin_micrograph; float origin_x_coordinate; // Particle X coordinate in micrograph, in A float origin_y_coordinate; // Particle Y coordinate in micrograph, in A int location_in_stack; // Starts with 0 float pixel_size; // In A float sigma_signal; float sigma_noise; float snr; float logp; // Log likelihood; float particle_occupancy; // Particle occupancy within a class float particle_score; AnglesAndShifts alignment_parameters; RotationMatrix *euler_matrix; /* float phi_average; // In deg float theta_average; // In deg float psi_average; // In deg float shift_x_average; // In A float shift_y_average; // In A float phi_variance; // In deg^2 float theta_variance; // In deg^2 float psi_variance; // In deg^2 float shift_x_variance; // In A^2 float shift_y_variance; // In A^2 */ float scaled_noise_variance; ParameterConstraints parameter_constraints; CTF ctf_parameters; CTF current_ctf; bool ctf_is_initialized; Image *ctf_image; bool ctf_image_calculated; Image *beamtilt_image; bool beamtilt_image_calculated; Image *particle_image; bool includes_reference_ssnr_weighting; bool is_normalized; float normalized_sigma; bool is_phase_flipped; bool is_masked; float mask_radius; // In A float mask_falloff; // In A float mask_volume; // In pixels float molecular_mass_kDa; // In kilo Daltons bool is_filtered; float filter_radius_low; // In 1/pixel float filter_radius_high; // In 1/pixel float filter_falloff; // In 1/pixel float filter_volume; // In reciprocal pixels, including the half of the transform not stored by the FFT float signed_CC_limit; // In 1/pixel, 0.0 = use max resolution bool is_ssnr_filtered; bool is_centered_in_box; int shift_counter; bool insert_even; int number_of_parameters; float target_phase_error; float *temp_float; float *current_parameters; float *parameter_average; float *parameter_variance; bool *parameter_map; bool *constraints_used; int number_of_search_dimensions; int *bin_index; float mask_center_2d_x; float mask_center_2d_y; float mask_center_2d_z; float mask_radius_2d; bool apply_2D_masking; bool no_ctf_weighting; bool complex_ctf; Particle(); Particle(int wanted_logical_x_dimension, int wanted_logical_y_dimension); ~Particle(); void Init(); void AllocateImage(int wanted_logical_x_dimension, int wanted_logical_y_dimension); void AllocateCTFImage(int wanted_logical_x_dimension, int wanted_logical_y_dimension); void Allocate(int wanted_logical_x_dimension, int wanted_logical_y_dimension); void Deallocate(); void ResetImageFlags(); void PhaseShift(); void PhaseShiftInverse(); void Whiten(float resolution_limit = 0.49); void ForwardFFT(); void BackwardFFT(); void CosineMask(bool invert = false, bool force_mask_value = false, float wanted_mask_value = 0.0); void CenterInBox(); void CenterInCorner(); void InitCTF(float voltage_kV, float spherical_aberration_mm, float amplitude_contrast, float defocus_1, float defocus_2, float astigmatism_angle, float phase_shift, float beam_tilt_x = 0.0f, float beam_tilt_y = 0.0f, float particle_shift_x = 0.0f, float particle_shift_y = 0.0f); void SetDefocus(float defocus_1, float defocus_2, float astigmatism_angle, float phase_shift); void SetBeamTilt(float beam_tilt_x, float beam_tilt_y, float particle_shift_x = 0.0f, float particle_shift_y = 0.0f); void InitCTFImage(float voltage_kV, float spherical_aberration_mm, float amplitude_contrast, float defocus_1, float defocus_2, float astigmatism_angle, float phase_shift, float beam_tilt_x = 0.0f, float beam_tilt_y = 0.0f, float particle_shift_x = 0.0f, float particle_shift_y = 0.0f, bool calculate_complex_ctf = false); void PhaseFlipImage(); void CTFMultiplyImage(); void BeamTiltMultiplyImage(); void SetIndexForWeightedCorrelation(bool limit_resolution = true); void WeightBySSNR(Curve &SSNR, int include_reference_weighting = 1, bool no_ctf = false); void WeightBySSNR(Curve &SSNR, Image &projection_image, bool weight_particle_image = true, bool weight_projection_image = true); void CalculateProjection(Image &projection_image, ReconstructedVolume &input_3d); void GetParameters(float *output_parameters); void SetParameters(float *wanted_parameters, bool initialize_scores = false); void SetAlignmentParameters(float wanted_euler_phi, float wanted_euler_theta, float wanted_euler_psi, float wanted_shift_x = 0.0, float wanted_shift_y = 0.0); void SetParameterStatistics(float *wanted_averages, float *wanted_variances); void SetParameterConstraints(float wanted_noise_variance); float ReturnParameterPenalty(float *parameters); float ReturnParameterLogP(float *parameters); int MapParameterAccuracy(float *accuracies); int MapParametersFromExternal(float *input_parameters, float *mapped_parameters); int MapParameters(float *mapped_parameters); int UnmapParametersToExternal(float *output_parameters, float *mapped_parameters); int UnmapParameters(float *mapped_parameters); void FindBeamTilt(Image &sum_of_phase_differences, CTF &input_ctf, float pixel_size, Image &phase_error_output, Image &beamtilt_output, Image &difference_image, float &beamtilt_x, float &beamtilt_y, float &particle_shift_x, float &particle_shift_y, float phase_multiplier = 20.0f, bool progress_bar = false); float ReturnLogLikelihood(Image &input_image, Image &padded_unbinned_image, CTF &input_ctf, ReconstructedVolume &input_3d, ResolutionStatistics &statistics, float classification_resolution_limit, Image *phase_difference = NULL); void CalculateMaskedLogLikelihood(Image &projection_image, ReconstructedVolume &input_3d, float classification_resolution_limit); float MLBlur(Image *input_classes_cache, float var_X, Image &cropped_input_image, Image *rotation_cache, Image &blurred_image, int current_class, int number_of_rotations, float psi_step, float psi_start, float smoothing_factor, float &max_log_particle, int best_class, float best_psi, Image &best_correlation_map, bool calculate_correlation_map_only = false, bool uncrop = true, bool apply_ctf_to_classes = true, Image *image_to_blur = NULL, Image *diff_image_to_blur = NULL); void EstimateSigmaNoise(); }; ctffind-4.1.14/src/core/particle_finder.h000066400000000000000000000152601440356052600202510ustar00rootroot00000000000000// Facilitate automatic particle finding in micrographs class ParticleFinder { public: ParticleFinder(); ~ParticleFinder(); ArrayOfParticlePositionAssets ReturnArrayOfParticlePositionAssets(); void DoItAll(); void RedoWithNewMaximumRadius(); void RedoWithNewTypicalRadius(); void RedoWithNewMinimumPeakHeight(); void RedoWithNewHighestResolution(); void RedoWithNewMinimumDistanceFromEdges(); void RedoWithNewAvoidLowVarianceAreas(); void RedoWithNewAvoidHighVarianceAreas(); void RedoWithNewLowVarianceThreshold(); void RedoWithNewHighVarianceThreshold(); void RedoWithNewAvoidAbnormalLocalMeanAreas(); void RedoWithNewNumberOfBackgroundBoxes(); void RedoWithNewAlgorithmToFindBackground(); wxString ReturnMicrographFilename() { return micrograph_filename; }; CTF ReturnMicrographCTFWithPickingPixelSize() { return micrograph_ctf; }; CTF ReturnMicrographCTFWithOriginalPixelSize(); float ReturnOriginalMicrographPixelSize() { return original_micrograph_pixel_size; }; void SetAllUserParameters( wxString wanted_micrograph_filename, float wanted_original_micrograph_pixel_size, float wanted_acceleration_voltage_in_keV, float wanted_spherical_aberration_in_mm, float wanted_amplitude_contrast, float wanted_additional_phase_shift_in_radians, float wanted_defocus_1_in_angstroms, float wanted_defocus_2_in_angstroms, float wanted_astigmatism_angle_in_degrees, bool wanted_already_have_templates, wxString wanted_templates_filename, bool wanted_average_templates_radially, int wanted_number_of_template_rotations, float wanted_typical_radius_in_angstroms, float wanted_maximum_radius_in_angstroms, float wanted_highest_resolution_to_use, wxString wanted_output_stack_filename, int wanted_output_stack_box_size, int wanted_minimum_distance_from_edges_in_pixels, float wanted_minimum_peak_height_for_candidate_particles, bool wanted_avoid_low_variance_areas, bool wanted_avoid_high_variance_areas, float wanted_low_variance_threshold_in_fwhm, float wanted_high_variance_threshold_in_fwhm, bool wanted_avoid_high_low_mean_areas, int wanted_algorithm_to_find_background, int wanted_number_of_background_boxes, bool wanted_particles_are_white); // Todo: To be made private // Todo: use more appropriate objects to do this. Maybe ParticlePositionAssets, or wxArrays of floats // Use will (mis)use Curve objects to keep track of our results Curve results_x_y; Curve results_height_template; Curve results_rotation; bool write_out_plt; private: // Parameters from the user wxString micrograph_filename; wxString templates_filename; bool already_have_templates; float original_micrograph_pixel_size; float highest_resolution_to_use; float maximum_radius_in_angstroms; float typical_radius_in_angstroms; bool average_templates_radially; int algorithm_to_find_background; int number_of_background_boxes; int number_of_template_rotations; float minimum_peak_height_for_candidate_particles; int output_stack_box_size; bool avoid_low_variance_areas; bool avoid_high_variance_areas; float low_variance_threshold_in_fwhm; float high_variance_threshold_in_fwhm; bool avoid_high_low_mean_areas; int minimum_distance_from_edges_in_pixels; wxString output_stack_filename; bool particles_are_white; // CTF parameters from the user float acceleration_voltage_in_keV; float spherical_aberration_in_mm; float amplitude_contrast; float additional_phase_shift_in_radians; float defocus_1_in_angstroms; float defocus_2_in_angstroms; float astigmatism_angle_in_degrees; // Internal int new_micrograph_dimension_x; int new_micrograph_dimension_y; int new_template_dimension; float pixel_size; float maximum_radius_in_pixels; float typical_radius_in_pixels; int number_of_background_boxes_to_skip; //float minimum_distance_between_picks_in_angstroms; //float minimum_distance_between_picks_in_pixels; int minimum_box_size_for_object_with_psf; int minimum_box_size_for_picking; int number_of_templates; MRCFile micrograph_file; MRCFile template_file; CTF micrograph_ctf; Image *template_image; ProgressBar *my_progress_bar; Curve template_power_spectrum; Curve background_power_spectrum; Curve current_power_spectrum; Curve current_number_of_fourier_elements; Curve temp_curve; Image micrograph; Image micrograph_bp; Image micrograph_whitened; float micrograph_mean; Image local_mean; Image local_sigma; //Image local_sigma_modified; float local_sigma_mode; float local_sigma_fwhm; float local_mean_mode; float local_mean_fwhm; Curve background_whitening_filter; Image maximum_score; Image maximum_score_modified; Image template_rotation_giving_maximum_score; Image template_giving_maximum_score; // Private methods void UpdateMaximumRadiusInPixels(); void UpdateTypicalRadiusInPixels(); void CloseImageFiles(); void FindPeaksAndExtractParticles(); void RemoveHighLowMeanAreasFromTargetFunction(); void RemoveHighLowVarianceAreasFromTargetFunction(); void DoTemplateMatching(); void WhitenMicrographBackground(); void UpdateLocalMeanAndSigma(); void BandPassMicrograph(); void ReadAndResampleMicrograph(); void GenerateATemplate(); void SetupCurveObjects(); void ReadTemplatesFromDisk(); void AllocateTemplateImages(); void DeallocateTemplateImages(); void UpdateMinimumBoxSize(); void OpenMicrographAndUpdateDimensions(); void UpdatePixelSizeFromMicrographDimensions(); void OpenTemplatesAndUpdateDimensions(); void UpdateCTF(); void ComputeLocalMeanAndStandardDeviation(Image *micrograph, Image *mask_image, float mask_radius_in_pixels, long number_of_pixels_within_mask, Image *micrograph_local_mean, Image *micrograph_local_stdev); void SetAreaToIgnore(Image &my_image, int central_pixel_address_x, int central_pixel_address_y, Image *box_image, float wanted_value); void SetCircularAreaToIgnore(Image &my_image, const int central_pixel_address_x, const int central_pixel_address_y, const float wanted_radius, const float wanted_value); void PrepareTemplateForMatching(Image *template_image, Image &prepared_image, float in_plane_rotation, CTF *micrograph_ctf, Curve *whitening_filter); }; ctffind-4.1.14/src/core/progressbar.cpp000066400000000000000000000077361440356052600200140ustar00rootroot00000000000000#include "core_headers.h" ProgressBar::ProgressBar(void) { MyPrintWithDetails("An instance of progress bar has been created with no constructor. This is not allowed.\n"); DEBUG_ABORT; } ProgressBar::~ProgressBar(void) { // How long did the process take? long total_seconds; long total_minutes = 0; long total_hours = 0; total_seconds = last_update_time - start_time; if (total_seconds > 3600) total_hours = total_seconds / 3600; if ((total_seconds - total_hours * 3600) > 60) total_minutes = total_seconds / 60 - total_hours * 60; total_seconds = total_seconds - total_hours * 3600 - total_minutes * 60; if (total_seconds < 0) { total_seconds = 0; } // Set to 100% and end the line.. if (total_number_of_ticks > 1) { wxPrintf(" 100% [=================] done! "); } // Print out how long it took if (total_hours > 999) { wxPrintf("(999h:99m:99s) \n"); } else { wxPrintf("(%lih:",total_hours); // minutes, if less than ten do a preceding 0 wxPrintf("%02lim",total_minutes); // similiar for the seconds wxPrintf("%02lis) \n", total_seconds); fflush(stdout); // we are done so flush and CR! } } ProgressBar::ProgressBar(long wanted_total_number_of_ticks) { total_number_of_ticks = wanted_total_number_of_ticks; // check if there is less than 2 ticks, if so - don't do anything.. if (wanted_total_number_of_ticks > 1) { start_time = time(NULL); last_update_time = start_time; // draw the start state... wxPrintf(" 0% [ ] ???h:??m:??s \r"); fflush(stdout); } } void ProgressBar::Update(long current_tick) { // zero or negative ticks are not allowed, and should indicate an error.. if (current_tick < 1) { MyPrintWithDetails("Called with a tick value less than 1\n"); DEBUG_ABORT; } // if there is less than 2 ticks we don't do anything.. if (total_number_of_ticks > 1) { long seconds_remaining; long minutes_remaining; long hours_remaining; long percent_complete; double current_seconds_per_tick; long remaining_time; long filled_bar_size; long current_time; current_time = time(NULL); // Only proceed if we are less than one second from the previous update time, this // is here to stop incredibly fast processes just spending all their time drawing // the progress bar again and again. // // of course if the process is fast enough it will just spend all it's time getting // the time, then you will have to restrict what ticks you send.. if (current_time - last_update_time>= 1) { last_update_time = current_time; percent_complete = long(myround(100. / double(total_number_of_ticks) * double(current_tick))); current_seconds_per_tick = double(time(NULL) - start_time) / double(current_tick); remaining_time = long(myround((total_number_of_ticks - current_tick) * current_seconds_per_tick)); filled_bar_size = long(myround(double(percent_complete * .3))); if (remaining_time > 3600) hours_remaining = remaining_time / 3600; else hours_remaining = 0; if (remaining_time > 60) minutes_remaining = (remaining_time / 60) - (hours_remaining * 60); else minutes_remaining = 0; seconds_remaining = remaining_time - ((hours_remaining * 60 + minutes_remaining) * 60); // some sanity checking.. if (filled_bar_size > 30) filled_bar_size = 30; // draw out the bar.. starting with percent complete. wxPrintf(" %3li% [",percent_complete); for (long position = 0; position < 30; position++) { if (position < filled_bar_size) wxPrintf("="); else wxPrintf(" "); } wxPrintf("] "); // print out ETA.. if (hours_remaining > 999) { wxPrintf("999h:99m:99s \r"); } else { wxPrintf("%lih:",hours_remaining); // minutes, if less than ten do a preceding 0 wxPrintf("%02lim",minutes_remaining); // similiar for the seconds wxPrintf("%02lis \r", seconds_remaining); fflush(stdout); // we are done so flush and CR! } } } } ctffind-4.1.14/src/core/progressbar.h000066400000000000000000000043231440356052600174460ustar00rootroot00000000000000// // ProgressBar // // Timothy Grant // // 20090109 // // // // A Simple Class to show a basic command line progress bar. It // includes the total percent complete, and also a self estimated // Time Remaining.. // // To use, simply call the constructor with the "number_of_ticks" // required. For example when dealing with images this would // typically be the total number of images - although it can of // course be anything. // // Once the ProgressBar object is constructed it will be printed // to the console in it's initialised form (it is important that // you output no other text during the lifetime of the progress bar // or everything will look a bit weird. In order to update the // progress bar you must call the Update method with the tick // you are currently on (in the above example this would be the // image you are currently working on). // // After finishing you should delete the progress bar, which erases it. // // NOTE : If you call the status bar with one tick it will do nothing. // I implemented this for sanity as it is stupid to have a progress // bar for 1 image or 1 anything really. However rather than write // code in every program that checks how many images there are before // creating a progress bar, I thought it would be easier to just do // the check here. // // A Quick Example, meanfiltering a bunch of images :- // // void main(void) // { // TigrisImage my_image("my_file", 1); // long number_of_images = my_image.number_following + 1; // // ProgressBar *my_progress_bar = new ProgressBar(number_of_images); // // for (long counter = 1; counter <= number_of_images; counter++) // { // input_image.Read(input_filename, counter); // input_image.MeanFilter(filter_size); // input_image.Write(output_filename, counter); // my_progress_bar->Update(counter); // } // // delete my_progress_bar; // } // // class ProgressBar { private: long total_number_of_ticks; long start_time; long last_update_time; public : // Constructors ProgressBar(); ProgressBar(long wanted_total_number_of_ticks); // Destructor ~ProgressBar(); // Methods void Update(long current_tick); }; ctffind-4.1.14/src/core/project.h000066400000000000000000000014711440356052600165640ustar00rootroot00000000000000class Project { public : Database database; bool is_open; wxString project_name; wxFileName project_directory; wxFileName movie_asset_directory; wxFileName image_asset_directory; wxFileName volume_asset_directory; wxFileName ctf_asset_directory; wxFileName particle_position_asset_directory; wxFileName particle_stack_directory; wxFileName class_average_directory; wxFileName parameter_file_directory; wxFileName scratch_directory; double total_cpu_hours; int total_jobs_run; int integer_database_version; Project(); ~Project(); void Close(bool remove_lock = true); bool CreateNewProject(wxFileName database_file, wxString project_directory, wxString project_name); bool OpenProjectFromFile(wxFileName file_to_open); bool ReadMasterSettings(); bool WriteProjectStatisticsToDatabase(); }; ctffind-4.1.14/src/core/randomnumbergenerator.cpp000066400000000000000000000033631440356052600220530ustar00rootroot00000000000000#include "core_headers.h" RandomNumberGenerator::RandomNumberGenerator(bool internal) { use_internal = internal; SetSeed(4711); } RandomNumberGenerator::RandomNumberGenerator(int random_seed, bool internal) { use_internal = internal; SetSeed(random_seed); } // Set seed for random number generator void RandomNumberGenerator::SetSeed(int random_seed) { if (random_seed < 0) { this->random_seed = time(NULL); } else this->random_seed = random_seed; if (use_internal) Internal_srand((unsigned int) this->random_seed); else srand((unsigned int) this->random_seed); } // Return a random number in the interval [-1,1] // from a uniform distribution float RandomNumberGenerator::GetUniformRandom() { float rnd1; float hmax; if (use_internal) { rnd1 = (float)Internal_rand(); hmax = ((float)32767) / 2.0; // wxPrintf("rnd1 = %g\n", rnd1); } else { rnd1 = (float)rand(); hmax = ((float) RAND_MAX) / 2.0; } float rnd2 = (rnd1 - hmax) / hmax; return rnd2; } // Return a random number according to the normal distribution using the // the Box-Muller transformation (polar variant) // standard normal distribution: // p(X) = 1/(2*Pi)^0.5 * exp(-x^2/2) float RandomNumberGenerator::GetNormalRandom() { float x1; float x2; float R; float y1; do { x1 = GetUniformRandom(); x2 = GetUniformRandom(); R = x1 * x1 + x2 * x2; } while (R == 0.0 || R > 1.0); y1 = x1 * sqrtf(-2.0 * log(R) / R); // y2 = x2 * sqrtf(-2.0 * log(R) / R); return y1; } void RandomNumberGenerator::Internal_srand(unsigned int random_seed) { next_seed = random_seed; } int RandomNumberGenerator::Internal_rand() { next_seed = next_seed * 1103515245 + 12345; // wxPrintf("next = %i\n", next_seed); return((unsigned int)(next_seed / 65536) % 32768); } ctffind-4.1.14/src/core/randomnumbergenerator.h000066400000000000000000000014411440356052600215130ustar00rootroot00000000000000/* \brief RandomNumberGenerator class */ class RandomNumberGenerator { public: int random_seed; // Seed for all instances of this class even though it is not declared static! bool use_internal; // Use internal implementation of rand and srand to enable multiple PRNGs within a single program unsigned int next_seed; // State variable for internal PRNG // Constructor RandomNumberGenerator(bool internal = false); RandomNumberGenerator(int random_seed, bool internal = false); // Seed generator void SetSeed(int random_seed); // Generate random numbers from various distributions float GetUniformRandom(); // Uniform random number [-1,1] float GetNormalRandom(); // Normal random number, sigma = 1 void Internal_srand(unsigned int random_seed); int Internal_rand(); }; ctffind-4.1.14/src/core/reconstruct_3d.h000066400000000000000000000066101440356052600200570ustar00rootroot00000000000000/* \brief Reconstruct3D class (derived from Frealign Pinsert) */ class Particle; class Reconstruct3D { public: float pixel_size; float original_pixel_size; float average_occupancy; float average_score; float score_weights_conversion; SymmetryMatrix symmetry_matrices; bool edge_terms_were_added; bool center_mass; int correct_ewald_sphere; Image image_reconstruction; float *ctf_reconstruction; int logical_x_dimension; // !< Logical (X) dimensions of the image., Note that this does not necessarily correspond to memory allocation dimensions (ie physical dimensions). int logical_y_dimension; // !< Logical (Y) dimensions of the image., Note that this does not necessarily correspond to memory allocation dimensions (ie physical dimensions). int logical_z_dimension; // !< Logical (Z) dimensions of the image., Note that this does not necessarily correspond to memory allocation dimensions (ie physical dimensions). int original_x_dimension; int original_y_dimension; int original_z_dimension; int images_processed; Reconstruct3D(float wanted_pixel_size = 0.0, float wanted_average_occupancy = 0.0, float wanted_average_score = 0.0, float wanted_score_weights_conversion = 0.0, int wanted_correct_ewald_sphere = 0); Reconstruct3D(float wanted_pixel_size, float wanted_average_occupancy, float wanted_average_score, float wanted_score_weights_conversion, wxString wanted_symmetry, int wanted_correct_ewald_sphere = 0); Reconstruct3D(int wanted_logical_x_dimension, int wanted_logical_y_dimension, int wanted_logical_z_dimension, float wanted_pixel_size, float wanted_average_occupancy, float wanted_average_score, float wanted_score_weights_conversion, wxString wanted_symmetry, int wanted_correct_ewald_sphere = 0); // constructor with size ~Reconstruct3D(); // destructor void FreeMemory(); void Init(int wanted_logical_x_dimension, int wanted_logical_y_dimension, int wanted_logical_z_dimension, float wanted_pixel_size, float wanted_average_occupancy, float wanted_average_score, float wanted_score_weights_conversion, int wanted_correct_ewald_sphere = 0); void InsertSliceWithCTF(Particle &particle_to_insert, float symmetry_weight = 1.0); void InsertSliceNoCTF(Particle &particle_to_insert, float symmetry_weight = 1.0); void AddByLinearInterpolation(float &wanted_x_coordinate, float &wanted_y_coordinate, float &wanted_z_coordinate, std::complex &wanted_value, std::complex &ctf_value, float wanted_weight, bool complex_ctf = false); void CompleteEdges(); float Correct3DCTF(Image &buffer3d); void DumpArrays(wxString filename, bool insert_even); void ReadArrayHeader(wxString filename, int &logical_x_dimension, int &logical_y_dimension, int &logical_z_dimension, int &original_x_dimension, int &original_y_dimension, int &original_z_dimension, int &images_processed, float &pixel_size, float &original_pixel_size, float &average_occupancy, float &average_score, float &score_weights_conversion, wxString &symmetry_symbol, bool &insert_even, bool ¢er_mass); void ReadArrays(wxString filename); Reconstruct3D operator + (const Reconstruct3D &other); Reconstruct3D &operator = (const Reconstruct3D &other); Reconstruct3D &operator = (const Reconstruct3D *other); Reconstruct3D &operator += (const Reconstruct3D &other); Reconstruct3D &operator += (const Reconstruct3D *other); }; ctffind-4.1.14/src/core/reconstructed_volume.h000066400000000000000000000067251440356052600214000ustar00rootroot00000000000000/* \brief ReconstructedVolume class */ class Reconstruct3D; class NumericTextFile; class ReconstructedVolume { public: float pixel_size; float mask_volume_in_voxels; float molecular_mass_in_kDa; float mask_radius; wxString symmetry_symbol; SymmetryMatrix symmetry_matrices; Image density_map; Image current_projection; // ResolutionStatistics statistics; float current_resolution_limit; float current_ctf; float current_phi; float current_theta; float current_psi; float current_shift_x; float current_shift_y; float current_mask_radius; float current_mask_falloff; bool current_whitening; bool current_swap_quadrants; bool has_been_initialized; bool has_masked_applied; bool was_corrected; // bool has_statistics; bool has_been_filtered; bool whitened_projection; ReconstructedVolume(float wanted_molecular_mass_in_kDa = 0.0); ~ReconstructedVolume(); ReconstructedVolume & operator = (const ReconstructedVolume &t); ReconstructedVolume & operator = (const ReconstructedVolume *t); void Deallocate(); void InitWithReconstruct3D(Reconstruct3D &image_reconstruction, float wanted_pixel_size); void InitWithDimensions(int wanted_logical_x_dimension, int wanted_logical_y_dimension, int wanted_logical_z_dimension, float wanted_pixel_size, wxString = "C1"); void PrepareForProjections(float low_resolution_limit, float high_resolution_limit, bool approximate_binning = false, bool apply_binning = true); // void PrepareForProjections(float resolution_limit, bool approximate_binning = false, bool apply_binning = true); void CalculateProjection(Image &projection, Image &CTF, AnglesAndShifts &angles_and_shifts_of_projection, float mask_radius = 0.0, float mask_falloff = 0.0, float resolution_limit = 1.0, bool swap_quadrants = false, bool apply_shifts = false, bool whiten = false, bool apply_ctf = false, bool abolute_ctf = false); void Calculate3DSimple(Reconstruct3D &reconstruction); void Calculate3DOptimal(Reconstruct3D &reconstruction, ResolutionStatistics &statistics, float weiner_filter_nominater = 1.0f); float Correct3D(float mask_radius = 0.0); void CosineRingMask(float wanted_inner_mask_radius, float wanted_outer_mask_radius, float wanted_mask_edge); void CosineMask(float wanted_mask_radius, float wanted_mask_edge); void OptimalFilter(ResolutionStatistics &statistics); void FinalizeSimple(Reconstruct3D &reconstruction, int &original_box_size, float &original_pixel_size, float &pixel_size, float &inner_mask_radius, float &outer_mask_radius, float &mask_falloff, wxString &output_volume); void FinalizeOptimal(Reconstruct3D &reconstruction, Image &density_map_1, Image &density_map_2, float &original_pixel_size, float &pixel_size, float &inner_mask_radius, float &outer_mask_radius, float &mask_falloff, bool center_mass, wxString &output_volume, NumericTextFile &output_statistics, ResolutionStatistics *copy_of_statistics = NULL, float weiner_filter_nominator = 1.0f); void FinalizeML(Reconstruct3D &reconstruction, Image &density_map_1, Image &density_map_2, float &original_pixel_size, float &pixel_size, float &inner_mask_radius, float &outer_mask_radius, float &mask_falloff, wxString &output_volume, NumericTextFile &output_statistics, ResolutionStatistics *copy_of_statistics = NULL); void Calculate3DML(Reconstruct3D &reconstruction); float ComputeOrientationDistributionEfficiency(Reconstruct3D &reconstruction); }; ctffind-4.1.14/src/core/refinement.h000066400000000000000000000072601440356052600172540ustar00rootroot00000000000000class RefinementResult { public: RefinementResult(); ~RefinementResult(); long position_in_stack; float psi; float theta; float phi; float xshift; float yshift; float defocus1; float defocus2; float defocus_angle; float phase_shift; float occupancy; float logp; float sigma; float score; int image_is_active; }; WX_DECLARE_OBJARRAY(RefinementResult, ArrayofRefinementResults); class ClassRefinementResults { public : ClassRefinementResults(); ~ClassRefinementResults(); ResolutionStatistics class_resolution_statistics; float global_resolution_limit; float high_resolution_limit; float classification_resolution_limit; float low_resolution_limit; float mask_radius; float signed_cc_resolution_limit; float global_mask_radius; int number_results_to_refine; float angular_search_step; float search_range_x; float search_range_y; bool should_focus_classify; float sphere_x_coord; float sphere_y_coord; float sphere_z_coord; float sphere_radius; bool should_refine_ctf; float defocus_search_range; float defocus_search_step; long reconstructed_volume_asset_id; long reconstruction_id; float average_occupancy; float estimated_resolution; bool should_auto_mask; bool should_refine_input_params; bool should_use_supplied_mask; long mask_asset_id; float mask_edge_width; float outside_mask_weight; bool should_low_pass_filter_mask; float filter_resolution; ArrayofRefinementResults particle_refinement_results; }; WX_DECLARE_OBJARRAY(ClassRefinementResults, ArrayofClassRefinementResults); class Refinement { public : Refinement(); ~Refinement(); long refinement_id; long refinement_package_asset_id; wxString name; bool resolution_statistics_are_generated; wxDateTime datetime_of_run; long starting_refinement_id; long number_of_particles; int number_of_classes; float percent_used; int resolution_statistics_box_size; float resolution_statistics_pixel_size; void SizeAndFillWithEmpty(long number_of_particles, int number_of_classes); void UpdateOccupancies(bool use_old_occupancies = true); wxArrayFloat UpdatePSSNR(); wxArrayLong reference_volume_ids; ArrayofClassRefinementResults class_refinement_results; float ReturnChangeInAverageOccupancy(Refinement &other_refinement); RefinementResult ReturnRefinementResultByClassAndPositionInStack(int wanted_class, long wanted_position_in_stack); void WriteSingleClassFrealignParameterFile(wxString filename,int wanted_class, float percent_used_overide = 1.0f, float sigma_override = 0.0f); wxArrayString WriteFrealignParameterFiles(wxString base_filename, float percent_used_overide = 1.0f, float sigma_override = 0.0f); wxArrayString WriteResolutionStatistics(wxString base_filename, float pssnr_division_factor = 1.0f); long ReturnNumberOfActiveParticlesInFirstClass(); int ReturnClassWithHighestOccupanyForGivenParticle(long wanted_particle); ArrayofAngularDistributionHistograms ReturnAngularDistributions(wxString desired_symmetry); void FillAngularDistributionHistogram(wxString wanted_symmetry, int wanted_class, int number_of_theta_bins, int number_of_phi_bins, AngularDistributionHistogram &histogram_to_fill); }; WX_DECLARE_OBJARRAY(Refinement, ArrayofRefinements); class ShortRefinementInfo { public : ShortRefinementInfo(); long refinement_id; long refinement_package_asset_id; wxString name; long number_of_particles; int number_of_classes; wxArrayFloat average_occupancy; wxArrayFloat estimated_resolution; wxArrayLong reconstructed_volume_asset_ids; ShortRefinementInfo & operator = (const Refinement &other_refinement); ShortRefinementInfo & operator = (const Refinement *other_other_refinement); }; WX_DECLARE_OBJARRAY(ShortRefinementInfo, ArrayofShortRefinementInfos); ctffind-4.1.14/src/core/refinement_package.h000066400000000000000000000024731440356052600207300ustar00rootroot00000000000000class RefinementPackageParticleInfo { public : RefinementPackageParticleInfo(); ~RefinementPackageParticleInfo(); long parent_image_id; long position_in_stack; long original_particle_position_asset_id; float x_pos; float y_pos; float pixel_size; float defocus_1; float defocus_2; float defocus_angle; float phase_shift; float spherical_aberration; float amplitude_contrast; float microscope_voltage; }; WX_DECLARE_OBJARRAY(RefinementPackageParticleInfo, ArrayOfRefinmentPackageParticleInfos); class RefinementPackage { public: RefinementPackage(); ~RefinementPackage(); long asset_id; wxString stack_filename; wxString name; int stack_box_size; int number_of_classes; wxString symmetry; double estimated_particle_size_in_angstroms; double estimated_particle_weight_in_kda; double lowest_resolution_of_intial_parameter_generated_3ds; bool stack_has_white_protein; int number_of_run_refinments; long last_refinment_id; wxArrayLong references_for_next_refinement; wxArrayLong refinement_ids; wxArrayLong classification_ids; ArrayOfRefinmentPackageParticleInfos contained_particles; RefinementPackageParticleInfo ReturnParticleInfoByPositionInStack(long wanted_position_in_stack); long ReturnLastRefinementID(); }; WX_DECLARE_OBJARRAY(RefinementPackage, ArrayOfRefinementPackages); ctffind-4.1.14/src/core/resolution_statistics.h000066400000000000000000000046001440356052600215700ustar00rootroot00000000000000/* \brief ResolutionStatistics class */ class NumericTextFile; class ResolutionStatistics { public: Curve FSC; Curve part_FSC; Curve part_SSNR; Curve rec_SSNR; float pixel_size; int number_of_bins; int number_of_bins_extended; // Extend table to include corners in 3D Fourier space ResolutionStatistics(); ResolutionStatistics(float wanted_pixel_size, int box_size = 0); ResolutionStatistics( const ResolutionStatistics &other_statistics); // copy constructor // ~ResolutionStatistics(); ResolutionStatistics & operator = (const ResolutionStatistics &t); ResolutionStatistics & operator = (const ResolutionStatistics *t); void ResampleFrom(ResolutionStatistics &other_statistics, int wanted_number_of_bins = 0); void CopyFrom(ResolutionStatistics &other_statistics, int wanted_number_of_bins = 0); void CopyParticleSSNR(ResolutionStatistics &other_statistics, int wanted_number_of_bins = 0); void ResampleParticleSSNR(ResolutionStatistics &other_statistics, int wanted_number_of_bins = 0); void Init(float wanted_pixel_size, int box_size = 0); void NormalizeVolumeWithParticleSSNR(Image &reconstructed_volume); void CalculateFSC(Image &reconstructed_volume_1, Image &reconstructed_volume_2, bool smooth_curve = false); void CalculateParticleFSCandSSNR(float mask_volume_in_voxels, float molecular_mass_in_kDa); void CalculateParticleSSNR(Image &image_reconstruction, float *ctf_reconstruction, float wanted_mask_volume_fraction = 1.0f); void ZeroToResolution(float resolution_limit); void PrintStatistics(); void WriteStatisticsToFile(NumericTextFile &output_statistics_file, float pssnr_division_factor = 1.0f); void WriteStatisticsToFloatArray(float *float_array, int wanted_class); void ReadStatisticsFromFile(wxString input_file); void GenerateDefaultStatistics(float molecular_mass_in_kDa); int ReturnResolutionShellNumber(float wanted_resolution); float ReturnResolutionNShellsBefore(float wanted_resolution, int number_of_shells); float ReturnResolutionNShellsAfter(float wanted_resolution, int number_of_shells); float ReturnEstimatedResolution(bool use_part_fsc = true); float Return0p8Resolution(bool use_part_fsc = true); float Return0p5Resolution(bool use_part_fsc = true); inline float kDa_to_area_in_pixel(float molecular_mass_in_kDa) { return PI * powf(3.0f * (kDa_to_Angstrom3(molecular_mass_in_kDa) / powf(pixel_size,3)) / 4.0f / PI, 2.0f / 3.0f); }; }; ctffind-4.1.14/src/core/rle3d.h000066400000000000000000000040311440356052600161220ustar00rootroot00000000000000// class for run length incoding - copied and modified from TIGRIS class rle3d_coord { public: int x_pos; int y_pos; int z_pos; long length; int group_number; // this is only used in certain operations, e.g. when working out connected rles. rle3d_coord(); }; class rle3d { private: long allocated_coordinates; long number_of_coordinates; public : long x_size; long y_size; long z_size; long number_of_groups; rle3d_coord *rle_coordinates; rle3d(); ~rle3d(); rle3d(Image &input3d); void AddCoord(long x, long y, long z, long current_length); void EncodeFrom(Image &input3d); //void DecodeTo(Image &output3d); void ConnectedSizeDecodeTo(Image &output3d); void Write(const char *filename); void GroupConnected(); inline void SameGroup(long first, long second) { if (rle_coordinates[first].group_number == 0 && rle_coordinates[second].group_number != 0) { rle_coordinates[first].group_number = rle_coordinates[second].group_number; } else if (rle_coordinates[second].group_number == 0 && rle_coordinates[first].group_number != 0) { rle_coordinates[second].group_number = rle_coordinates[first].group_number; } else if (rle_coordinates[second].group_number == 0 && rle_coordinates[first].group_number == 0) { number_of_groups++; rle_coordinates[first].group_number = number_of_groups; rle_coordinates[second].group_number = number_of_groups; } else { // This is the complicated bit.. if we got here then both are in the same group, but have different // group numbers, so we have to replace all occurences of the first with the last.. long coord_counter; long group_to_replace; long group_to_replace_with; group_to_replace = rle_coordinates[second].group_number; group_to_replace_with = rle_coordinates[first].group_number; for (coord_counter = 0; coord_counter < number_of_coordinates; coord_counter++) { if (rle_coordinates[coord_counter].group_number == group_to_replace) rle_coordinates[coord_counter].group_number = group_to_replace_with; } } } }; ctffind-4.1.14/src/core/run_profiles.cpp000066400000000000000000000230711440356052600201600ustar00rootroot00000000000000#include "core_headers.h" RunCommand::RunCommand() { command_to_run = ""; number_of_copies = 0; delay_time_in_ms = 0; } RunCommand::~RunCommand() { } void RunCommand::SetCommand(wxString wanted_command, int wanted_number_of_copies, int wanted_delay_time_in_ms) { command_to_run = wanted_command; number_of_copies = wanted_number_of_copies; delay_time_in_ms = wanted_delay_time_in_ms; } RunProfile::RunProfile() { id = 1; number_of_run_commands = 0; manager_command = "$command"; run_commands = new RunCommand[5]; number_allocated = 5; executable_name = ""; gui_address = ""; controller_address = ""; } RunProfile::RunProfile( const RunProfile &obj) // copy contructor { id = obj.id; name = obj.name; number_of_run_commands = obj.number_of_run_commands; manager_command = obj.manager_command; number_allocated = obj.number_allocated; executable_name = obj.executable_name; gui_address = obj.gui_address; controller_address = obj.controller_address; run_commands = new RunCommand[number_allocated]; for (long counter = 0; counter < number_of_run_commands; counter++) { run_commands[counter] = obj.run_commands[counter]; } } RunProfile::~RunProfile() { delete [] run_commands; } void RunProfile::AddCommand(RunCommand wanted_command) { // check we have enough memory RunCommand *buffer; if (number_of_run_commands >= number_allocated) { // reallocate.. if (number_allocated < 100) number_allocated *= 2; else number_allocated += 100; buffer = new RunCommand[number_allocated]; for (long counter = 0; counter < number_of_run_commands; counter++) { buffer[counter] = run_commands[counter]; } delete [] run_commands; run_commands = buffer; } // Should be fine for memory, so just add one. run_commands[number_of_run_commands] = wanted_command; number_of_run_commands++; } void RunProfile::AddCommand(wxString wanted_command, int wanted_number_of_copies, int wanted_delay_time_in_ms) { // check we have enough memory RunCommand *buffer; if (number_of_run_commands >= number_allocated) { // reallocate.. if (number_allocated < 100) number_allocated *= 2; else number_allocated += 100; buffer = new RunCommand[number_allocated]; for (long counter = 0; counter < number_of_run_commands; counter++) { buffer[counter] = run_commands[counter]; } delete [] run_commands; run_commands = buffer; } // Should be fine for memory, so just add one. run_commands[number_of_run_commands].command_to_run = wanted_command; run_commands[number_of_run_commands].number_of_copies = wanted_number_of_copies; run_commands[number_of_run_commands].delay_time_in_ms = wanted_delay_time_in_ms; number_of_run_commands++; } void RunProfile::RemoveCommand(int number_to_remove) { MyDebugAssertTrue(number_to_remove >= 0 && number_to_remove < number_of_run_commands, "Error: Trying to remove a command that doesnt't exist"); for (long counter = number_to_remove; counter < number_of_run_commands - 1; counter++) { run_commands[counter] = run_commands[counter + 1]; } number_of_run_commands--; } void RunProfile::RemoveAll() { number_of_run_commands = 0; } long RunProfile::ReturnTotalJobs() { long total_jobs = 0; for (long counter = 0; counter < number_of_run_commands; counter++) { total_jobs += run_commands[counter].number_of_copies; } return total_jobs; } void RunProfile::SubstituteExecutableName(wxString executable_name) { for (long counter = 0; counter < number_of_run_commands; counter++) { run_commands[counter].command_to_run.Replace("$command", executable_name); } } RunProfile & RunProfile::operator = (const RunProfile &t) { // Check for self assignment if(this != &t) { if(this->number_allocated != t.number_allocated) { delete [] this->run_commands; this->run_commands = new RunCommand[t.number_allocated]; this->number_allocated = t.number_allocated; } this->id = t.id; this->name = t.name; this->number_of_run_commands = t.number_of_run_commands; this->manager_command = t.manager_command; this->executable_name = t.executable_name; this->gui_address = t.gui_address; this->controller_address = t.controller_address; for (long counter = 0; counter < t.number_of_run_commands; counter++) { this->run_commands[counter] = t.run_commands[counter]; } } return *this; } RunProfile & RunProfile::operator = (const RunProfile *t) { // Check for self assignment if(this != t) { if(this->number_allocated != t->number_allocated) { delete [] this->run_commands; this->run_commands = new RunCommand[t->number_allocated]; this->number_allocated = t->number_allocated; } this->id = t->id; this->name = t->name; this->number_of_run_commands = t->number_of_run_commands; this->manager_command = t->manager_command; this->executable_name = t->executable_name; this->gui_address = t->gui_address; this->controller_address = t->controller_address; for (long counter = 0; counter < t->number_of_run_commands; counter++) { this->run_commands[counter] = t->run_commands[counter]; } } return *this; } RunProfileManager::RunProfileManager() { current_id_number = 0; number_of_run_profiles = 0; run_profiles = new RunProfile[5]; number_allocated = 5; } RunProfileManager::~RunProfileManager() { delete [] run_profiles; } void RunProfileManager::AddProfile(RunProfile *profile_to_add) { // check we have enough memory RunProfile *buffer; if (number_of_run_profiles >= number_allocated) { // reallocate.. if (number_allocated < 100) number_allocated *= 2; else number_allocated += 100; buffer = new RunProfile[number_allocated]; for (long counter = 0; counter < number_of_run_profiles; counter++) { buffer[counter] = run_profiles[counter]; } delete [] run_profiles; run_profiles = buffer; } // Should be fine for memory, so just add one. run_profiles[number_of_run_profiles] = profile_to_add; number_of_run_profiles++; if (profile_to_add->id > current_id_number) current_id_number = profile_to_add->id; } void RunProfileManager::AddBlankProfile() { // check we have enough memory RunProfile *buffer; if (number_of_run_profiles >= number_allocated) { // reallocate.. if (number_allocated < 100) number_allocated *= 2; else number_allocated += 100; buffer = new RunProfile[number_allocated]; for (long counter = 0; counter < number_of_run_profiles; counter++) { buffer[counter] = run_profiles[counter]; } delete [] run_profiles; run_profiles = buffer; } current_id_number++; run_profiles[number_of_run_profiles].id = current_id_number; run_profiles[number_of_run_profiles].name = "New Profile"; run_profiles[number_of_run_profiles].number_of_run_commands = 0; run_profiles[number_of_run_profiles].manager_command = "$command"; run_profiles[number_of_run_profiles].gui_address = ""; run_profiles[number_of_run_profiles].controller_address = ""; run_profiles[number_of_run_profiles].AddCommand("$command", 2, 10); number_of_run_profiles++; } void RunProfileManager::AddDefaultLocalProfile() { // check we have enough memory RunProfile *buffer; if (number_of_run_profiles >= number_allocated) { // reallocate.. if (number_allocated < 100) number_allocated *= 2; else number_allocated += 100; buffer = new RunProfile[number_allocated]; for (long counter = 0; counter < number_of_run_profiles; counter++) { buffer[counter] = run_profiles[counter]; } delete [] run_profiles; run_profiles = buffer; } wxString execution_command = wxStandardPaths::Get().GetExecutablePath(); execution_command = execution_command.BeforeLast('/'); execution_command += "/$command"; current_id_number++; run_profiles[number_of_run_profiles].id = current_id_number; run_profiles[number_of_run_profiles].name = "Default Local"; run_profiles[number_of_run_profiles].number_of_run_commands = 0; run_profiles[number_of_run_profiles].manager_command = execution_command; run_profiles[number_of_run_profiles].gui_address = ""; run_profiles[number_of_run_profiles].controller_address = ""; int number_of_cores = wxThread::GetCPUCount(); if (number_of_cores == -1) number_of_cores = 1; number_of_cores++; run_profiles[number_of_run_profiles].AddCommand(execution_command, number_of_cores, 10); number_of_run_profiles++; } RunProfile * RunProfileManager::ReturnLastProfilePointer() { return &run_profiles[number_of_run_profiles - 1]; } RunProfile * RunProfileManager::ReturnProfilePointer(int wanted_profile) { return &run_profiles[wanted_profile]; } void RunProfileManager::RemoveProfile(int number_to_remove) { MyDebugAssertTrue(number_to_remove >= 0 && number_to_remove < number_of_run_profiles, "Error: Trying to remove a profile that doesnt't exist"); for (long counter = number_to_remove; counter < number_of_run_profiles - 1; counter++) { run_profiles[counter] = run_profiles[counter + 1]; } number_of_run_profiles--; } void RunProfileManager::RemoveAllProfiles() { number_of_run_profiles = 0; if (number_allocated > 100) { delete [] run_profiles; number_allocated = 100; run_profiles = new RunProfile[number_allocated]; } } wxString RunProfileManager::ReturnProfileName(long wanted_profile) { return run_profiles[wanted_profile].name; } long RunProfileManager::ReturnProfileID(long wanted_profile) { return run_profiles[wanted_profile].id; } long RunProfileManager::ReturnTotalJobs(long wanted_profile) { long total_jobs = 0; for (long counter = 0; counter < run_profiles[wanted_profile].number_of_run_commands; counter++) { total_jobs += run_profiles[wanted_profile].run_commands[counter].number_of_copies; } return total_jobs; } ctffind-4.1.14/src/core/run_profiles.h000066400000000000000000000030571440356052600176270ustar00rootroot00000000000000class RunCommand { public: RunCommand(); ~RunCommand(); wxString command_to_run; int number_of_copies; int delay_time_in_ms; void SetCommand(wxString wanted_command, int wanted_number_of_copies, int wanted_delay_time_in_ms); }; class RunProfile { public: int id; long number_of_run_commands; long number_allocated; public : RunProfile(); RunProfile( const RunProfile &obj); // copy contructor ~RunProfile(); wxString name; wxString manager_command; wxString gui_address; wxString controller_address; RunCommand *run_commands; wxString executable_name; void AddCommand(RunCommand wanted_command); void AddCommand(wxString wanted_command, int wanted_number_of_copies, int wanted_delay_time_in_ms); void RemoveCommand(int number_to_remove); void RemoveAll(); long ReturnTotalJobs(); void SubstituteExecutableName(wxString executable_name); RunProfile & operator = (const RunProfile &t); RunProfile & operator = (const RunProfile *t); }; class RunProfileManager { public: int current_id_number; long number_of_run_profiles; long number_allocated; RunProfile *run_profiles; void AddProfile(RunProfile *profile_to_add); void AddBlankProfile(); void AddDefaultLocalProfile(); void RemoveProfile(int number_to_remove); void RemoveAllProfiles(); RunProfile * ReturnLastProfilePointer(); RunProfile * ReturnProfilePointer(int wanted_profile); wxString ReturnProfileName(long wanted_profile); long ReturnProfileID(long wanted_profile); long ReturnTotalJobs(long wanted_profile); RunProfileManager(); ~RunProfileManager(); }; ctffind-4.1.14/src/core/socket_codes.h000066400000000000000000000031431440356052600175610ustar00rootroot00000000000000#ifndef __SOCKET_CODES_H__ #define __SOCKET_CODES_H__ #define SOCKET_CODE_SIZE 16 #define SETUP_SOCKET_CODES unsigned char socket_input_buffer[SOCKET_CODE_SIZE]; const unsigned char socket_please_identify [] = "JcFG>&P.RuC9,>za"; const unsigned char socket_identification [] = "eTdLfTB2kQs/{7a-"; const unsigned char socket_you_are_connected [] = "J82zjSwYY^-!bF>4"; const unsigned char socket_send_job_details [] = "grThBp6w9fzLg"; const unsigned char socket_ready_to_send_job_package [] = "'8ujA!Lup%PR*!hG"; const unsigned char socket_send_job_package [] = "x3u.8?Kdvx!fPr /* Needed for the definition of va_list */ /* ** Make sure we can call this stuff from C++. */ #ifdef __cplusplus extern "C" { #endif /* ** Provide the ability to override linkage features of the interface. */ #ifndef SQLITE_EXTERN # define SQLITE_EXTERN extern #endif #ifndef SQLITE_API # define SQLITE_API #endif #ifndef SQLITE_CDECL # define SQLITE_CDECL #endif #ifndef SQLITE_APICALL # define SQLITE_APICALL #endif #ifndef SQLITE_STDCALL # define SQLITE_STDCALL SQLITE_APICALL #endif #ifndef SQLITE_CALLBACK # define SQLITE_CALLBACK #endif #ifndef SQLITE_SYSAPI # define SQLITE_SYSAPI #endif /* ** These no-op macros are used in front of interfaces to mark those ** interfaces as either deprecated or experimental. New applications ** should not use deprecated interfaces - they are supported for backwards ** compatibility only. Application writers should be aware that ** experimental interfaces are subject to change in point releases. ** ** These macros used to resolve to various kinds of compiler magic that ** would generate warning messages when they were used. But that ** compiler magic ended up generating such a flurry of bug reports ** that we have taken it all out and gone back to using simple ** noop macros. */ #define SQLITE_DEPRECATED #define SQLITE_EXPERIMENTAL /* ** Ensure these symbols were not defined by some previous header file. */ #ifdef SQLITE_VERSION # undef SQLITE_VERSION #endif #ifdef SQLITE_VERSION_NUMBER # undef SQLITE_VERSION_NUMBER #endif /* ** CAPI3REF: Compile-Time Library Version Numbers ** ** ^(The [SQLITE_VERSION] C preprocessor macro in the sqlite3.h header ** evaluates to a string literal that is the SQLite version in the ** format "X.Y.Z" where X is the major version number (always 3 for ** SQLite3) and Y is the minor version number and Z is the release number.)^ ** ^(The [SQLITE_VERSION_NUMBER] C preprocessor macro resolves to an integer ** with the value (X*1000000 + Y*1000 + Z) where X, Y, and Z are the same ** numbers used in [SQLITE_VERSION].)^ ** The SQLITE_VERSION_NUMBER for any given release of SQLite will also ** be larger than the release from which it is derived. Either Y will ** be held constant and Z will be incremented or else Y will be incremented ** and Z will be reset to zero. ** ** Since [version 3.6.18] ([dateof:3.6.18]), ** SQLite source code has been stored in the ** Fossil configuration management ** system. ^The SQLITE_SOURCE_ID macro evaluates to ** a string which identifies a particular check-in of SQLite ** within its configuration management system. ^The SQLITE_SOURCE_ID ** string contains the date and time of the check-in (UTC) and a SHA1 ** or SHA3-256 hash of the entire source tree. ** ** See also: [sqlite3_libversion()], ** [sqlite3_libversion_number()], [sqlite3_sourceid()], ** [sqlite_version()] and [sqlite_source_id()]. */ #define SQLITE_VERSION "3.20.1" #define SQLITE_VERSION_NUMBER 3020001 #define SQLITE_SOURCE_ID "2017-08-24 16:21:36 8d3a7ea6c5690d6b7c3767558f4f01b511c55463e3f9e64506801fe9b74dce34" /* ** CAPI3REF: Run-Time Library Version Numbers ** KEYWORDS: sqlite3_version sqlite3_sourceid ** ** These interfaces provide the same information as the [SQLITE_VERSION], ** [SQLITE_VERSION_NUMBER], and [SQLITE_SOURCE_ID] C preprocessor macros ** but are associated with the library instead of the header file. ^(Cautious ** programmers might include assert() statements in their application to ** verify that values returned by these interfaces match the macros in ** the header, and thus ensure that the application is ** compiled with matching library and header files. ** ** 
** assert( sqlite3_libversion_number()==SQLITE_VERSION_NUMBER );
** assert( strcmp(sqlite3_sourceid(),SQLITE_SOURCE_ID)==0 );
** assert( strcmp(sqlite3_libversion(),SQLITE_VERSION)==0 );
**
)^ ** ** ^The sqlite3_version[] string constant contains the text of [SQLITE_VERSION] ** macro. ^The sqlite3_libversion() function returns a pointer to the ** to the sqlite3_version[] string constant. The sqlite3_libversion() ** function is provided for use in DLLs since DLL users usually do not have ** direct access to string constants within the DLL. ^The ** sqlite3_libversion_number() function returns an integer equal to ** [SQLITE_VERSION_NUMBER]. ^The sqlite3_sourceid() function returns ** a pointer to a string constant whose value is the same as the ** [SQLITE_SOURCE_ID] C preprocessor macro. ** ** See also: [sqlite_version()] and [sqlite_source_id()]. */ SQLITE_API SQLITE_EXTERN const char sqlite3_version[]; SQLITE_API const char *sqlite3_libversion(void); SQLITE_API const char *sqlite3_sourceid(void); SQLITE_API int sqlite3_libversion_number(void); /* ** CAPI3REF: Run-Time Library Compilation Options Diagnostics ** ** ^The sqlite3_compileoption_used() function returns 0 or 1 ** indicating whether the specified option was defined at ** compile time. ^The SQLITE_ prefix may be omitted from the ** option name passed to sqlite3_compileoption_used(). ** ** ^The sqlite3_compileoption_get() function allows iterating ** over the list of options that were defined at compile time by ** returning the N-th compile time option string. ^If N is out of range, ** sqlite3_compileoption_get() returns a NULL pointer. ^The SQLITE_ ** prefix is omitted from any strings returned by ** sqlite3_compileoption_get(). ** ** ^Support for the diagnostic functions sqlite3_compileoption_used() ** and sqlite3_compileoption_get() may be omitted by specifying the ** [SQLITE_OMIT_COMPILEOPTION_DIAGS] option at compile time. ** ** See also: SQL functions [sqlite_compileoption_used()] and ** [sqlite_compileoption_get()] and the [compile_options pragma]. */ #ifndef SQLITE_OMIT_COMPILEOPTION_DIAGS SQLITE_API int sqlite3_compileoption_used(const char *zOptName); SQLITE_API const char *sqlite3_compileoption_get(int N); #endif /* ** CAPI3REF: Test To See If The Library Is Threadsafe ** ** ^The sqlite3_threadsafe() function returns zero if and only if ** SQLite was compiled with mutexing code omitted due to the ** [SQLITE_THREADSAFE] compile-time option being set to 0. ** ** SQLite can be compiled with or without mutexes. When ** the [SQLITE_THREADSAFE] C preprocessor macro is 1 or 2, mutexes ** are enabled and SQLite is threadsafe. When the ** [SQLITE_THREADSAFE] macro is 0, ** the mutexes are omitted. Without the mutexes, it is not safe ** to use SQLite concurrently from more than one thread. ** ** Enabling mutexes incurs a measurable performance penalty. ** So if speed is of utmost importance, it makes sense to disable ** the mutexes. But for maximum safety, mutexes should be enabled. ** ^The default behavior is for mutexes to be enabled. ** ** This interface can be used by an application to make sure that the ** version of SQLite that it is linking against was compiled with ** the desired setting of the [SQLITE_THREADSAFE] macro. ** ** This interface only reports on the compile-time mutex setting ** of the [SQLITE_THREADSAFE] flag. If SQLite is compiled with ** SQLITE_THREADSAFE=1 or =2 then mutexes are enabled by default but ** can be fully or partially disabled using a call to [sqlite3_config()] ** with the verbs [SQLITE_CONFIG_SINGLETHREAD], [SQLITE_CONFIG_MULTITHREAD], ** or [SQLITE_CONFIG_SERIALIZED]. ^(The return value of the ** sqlite3_threadsafe() function shows only the compile-time setting of ** thread safety, not any run-time changes to that setting made by ** sqlite3_config(). In other words, the return value from sqlite3_threadsafe() ** is unchanged by calls to sqlite3_config().)^ ** ** See the [threading mode] documentation for additional information. */ SQLITE_API int sqlite3_threadsafe(void); /* ** CAPI3REF: Database Connection Handle ** KEYWORDS: {database connection} {database connections} ** ** Each open SQLite database is represented by a pointer to an instance of ** the opaque structure named "sqlite3". It is useful to think of an sqlite3 ** pointer as an object. The [sqlite3_open()], [sqlite3_open16()], and ** [sqlite3_open_v2()] interfaces are its constructors, and [sqlite3_close()] ** and [sqlite3_close_v2()] are its destructors. There are many other ** interfaces (such as ** [sqlite3_prepare_v2()], [sqlite3_create_function()], and ** [sqlite3_busy_timeout()] to name but three) that are methods on an ** sqlite3 object. */ typedef struct sqlite3 sqlite3; /* ** CAPI3REF: 64-Bit Integer Types ** KEYWORDS: sqlite_int64 sqlite_uint64 ** ** Because there is no cross-platform way to specify 64-bit integer types ** SQLite includes typedefs for 64-bit signed and unsigned integers. ** ** The sqlite3_int64 and sqlite3_uint64 are the preferred type definitions. ** The sqlite_int64 and sqlite_uint64 types are supported for backwards ** compatibility only. ** ** ^The sqlite3_int64 and sqlite_int64 types can store integer values ** between -9223372036854775808 and +9223372036854775807 inclusive. ^The ** sqlite3_uint64 and sqlite_uint64 types can store integer values ** between 0 and +18446744073709551615 inclusive. */ #ifdef SQLITE_INT64_TYPE typedef SQLITE_INT64_TYPE sqlite_int64; # ifdef SQLITE_UINT64_TYPE typedef SQLITE_UINT64_TYPE sqlite_uint64; # else typedef unsigned SQLITE_INT64_TYPE sqlite_uint64; # endif #elif defined(_MSC_VER) || defined(__BORLANDC__) typedef __int64 sqlite_int64; typedef unsigned __int64 sqlite_uint64; #else typedef long long int sqlite_int64; typedef unsigned long long int sqlite_uint64; #endif typedef sqlite_int64 sqlite3_int64; typedef sqlite_uint64 sqlite3_uint64; /* ** If compiling for a processor that lacks floating point support, ** substitute integer for floating-point. */ #ifdef SQLITE_OMIT_FLOATING_POINT # define double sqlite3_int64 #endif /* ** CAPI3REF: Closing A Database Connection ** DESTRUCTOR: sqlite3 ** ** ^The sqlite3_close() and sqlite3_close_v2() routines are destructors ** for the [sqlite3] object. ** ^Calls to sqlite3_close() and sqlite3_close_v2() return [SQLITE_OK] if ** the [sqlite3] object is successfully destroyed and all associated ** resources are deallocated. ** ** ^If the database connection is associated with unfinalized prepared ** statements or unfinished sqlite3_backup objects then sqlite3_close() ** will leave the database connection open and return [SQLITE_BUSY]. ** ^If sqlite3_close_v2() is called with unfinalized prepared statements ** and/or unfinished sqlite3_backups, then the database connection becomes ** an unusable "zombie" which will automatically be deallocated when the ** last prepared statement is finalized or the last sqlite3_backup is ** finished. The sqlite3_close_v2() interface is intended for use with ** host languages that are garbage collected, and where the order in which ** destructors are called is arbitrary. ** ** Applications should [sqlite3_finalize | finalize] all [prepared statements], ** [sqlite3_blob_close | close] all [BLOB handles], and ** [sqlite3_backup_finish | finish] all [sqlite3_backup] objects associated ** with the [sqlite3] object prior to attempting to close the object. ^If ** sqlite3_close_v2() is called on a [database connection] that still has ** outstanding [prepared statements], [BLOB handles], and/or ** [sqlite3_backup] objects then it returns [SQLITE_OK] and the deallocation ** of resources is deferred until all [prepared statements], [BLOB handles], ** and [sqlite3_backup] objects are also destroyed. ** ** ^If an [sqlite3] object is destroyed while a transaction is open, ** the transaction is automatically rolled back. ** ** The C parameter to [sqlite3_close(C)] and [sqlite3_close_v2(C)] ** must be either a NULL ** pointer or an [sqlite3] object pointer obtained ** from [sqlite3_open()], [sqlite3_open16()], or ** [sqlite3_open_v2()], and not previously closed. ** ^Calling sqlite3_close() or sqlite3_close_v2() with a NULL pointer ** argument is a harmless no-op. */ SQLITE_API int sqlite3_close(sqlite3*); SQLITE_API int sqlite3_close_v2(sqlite3*); /* ** The type for a callback function. ** This is legacy and deprecated. It is included for historical ** compatibility and is not documented. */ typedef int (*sqlite3_callback)(void*,int,char**, char**); /* ** CAPI3REF: One-Step Query Execution Interface ** METHOD: sqlite3 ** ** The sqlite3_exec() interface is a convenience wrapper around ** [sqlite3_prepare_v2()], [sqlite3_step()], and [sqlite3_finalize()], ** that allows an application to run multiple statements of SQL ** without having to use a lot of C code. ** ** ^The sqlite3_exec() interface runs zero or more UTF-8 encoded, ** semicolon-separate SQL statements passed into its 2nd argument, ** in the context of the [database connection] passed in as its 1st ** argument. ^If the callback function of the 3rd argument to ** sqlite3_exec() is not NULL, then it is invoked for each result row ** coming out of the evaluated SQL statements. ^The 4th argument to ** sqlite3_exec() is relayed through to the 1st argument of each ** callback invocation. ^If the callback pointer to sqlite3_exec() ** is NULL, then no callback is ever invoked and result rows are ** ignored. ** ** ^If an error occurs while evaluating the SQL statements passed into ** sqlite3_exec(), then execution of the current statement stops and ** subsequent statements are skipped. ^If the 5th parameter to sqlite3_exec() ** is not NULL then any error message is written into memory obtained ** from [sqlite3_malloc()] and passed back through the 5th parameter. ** To avoid memory leaks, the application should invoke [sqlite3_free()] ** on error message strings returned through the 5th parameter of ** sqlite3_exec() after the error message string is no longer needed. ** ^If the 5th parameter to sqlite3_exec() is not NULL and no errors ** occur, then sqlite3_exec() sets the pointer in its 5th parameter to ** NULL before returning. ** ** ^If an sqlite3_exec() callback returns non-zero, the sqlite3_exec() ** routine returns SQLITE_ABORT without invoking the callback again and ** without running any subsequent SQL statements. ** ** ^The 2nd argument to the sqlite3_exec() callback function is the ** number of columns in the result. ^The 3rd argument to the sqlite3_exec() ** callback is an array of pointers to strings obtained as if from ** [sqlite3_column_text()], one for each column. ^If an element of a ** result row is NULL then the corresponding string pointer for the ** sqlite3_exec() callback is a NULL pointer. ^The 4th argument to the ** sqlite3_exec() callback is an array of pointers to strings where each ** entry represents the name of corresponding result column as obtained ** from [sqlite3_column_name()]. ** ** ^If the 2nd parameter to sqlite3_exec() is a NULL pointer, a pointer ** to an empty string, or a pointer that contains only whitespace and/or ** SQL comments, then no SQL statements are evaluated and the database ** is not changed. ** ** Restrictions: ** **
    **
  • The application must ensure that the 1st parameter to sqlite3_exec() ** is a valid and open [database connection]. **
  • The application must not close the [database connection] specified by ** the 1st parameter to sqlite3_exec() while sqlite3_exec() is running. **
  • The application must not modify the SQL statement text passed into ** the 2nd parameter of sqlite3_exec() while sqlite3_exec() is running. **
*/ SQLITE_API int sqlite3_exec( sqlite3*, /* An open database */ const char *sql, /* SQL to be evaluated */ int (*callback)(void*,int,char**,char**), /* Callback function */ void *, /* 1st argument to callback */ char **errmsg /* Error msg written here */ ); /* ** CAPI3REF: Result Codes ** KEYWORDS: {result code definitions} ** ** Many SQLite functions return an integer result code from the set shown ** here in order to indicate success or failure. ** ** New error codes may be added in future versions of SQLite. ** ** See also: [extended result code definitions] */ #define SQLITE_OK 0 /* Successful result */ /* beginning-of-error-codes */ #define SQLITE_ERROR 1 /* Generic error */ #define SQLITE_INTERNAL 2 /* Internal logic error in SQLite */ #define SQLITE_PERM 3 /* Access permission denied */ #define SQLITE_ABORT 4 /* Callback routine requested an abort */ #define SQLITE_BUSY 5 /* The database file is locked */ #define SQLITE_LOCKED 6 /* A table in the database is locked */ #define SQLITE_NOMEM 7 /* A malloc() failed */ #define SQLITE_READONLY 8 /* Attempt to write a readonly database */ #define SQLITE_INTERRUPT 9 /* Operation terminated by sqlite3_interrupt()*/ #define SQLITE_IOERR 10 /* Some kind of disk I/O error occurred */ #define SQLITE_CORRUPT 11 /* The database disk image is malformed */ #define SQLITE_NOTFOUND 12 /* Unknown opcode in sqlite3_file_control() */ #define SQLITE_FULL 13 /* Insertion failed because database is full */ #define SQLITE_CANTOPEN 14 /* Unable to open the database file */ #define SQLITE_PROTOCOL 15 /* Database lock protocol error */ #define SQLITE_EMPTY 16 /* Not used */ #define SQLITE_SCHEMA 17 /* The database schema changed */ #define SQLITE_TOOBIG 18 /* String or BLOB exceeds size limit */ #define SQLITE_CONSTRAINT 19 /* Abort due to constraint violation */ #define SQLITE_MISMATCH 20 /* Data type mismatch */ #define SQLITE_MISUSE 21 /* Library used incorrectly */ #define SQLITE_NOLFS 22 /* Uses OS features not supported on host */ #define SQLITE_AUTH 23 /* Authorization denied */ #define SQLITE_FORMAT 24 /* Not used */ #define SQLITE_RANGE 25 /* 2nd parameter to sqlite3_bind out of range */ #define SQLITE_NOTADB 26 /* File opened that is not a database file */ #define SQLITE_NOTICE 27 /* Notifications from sqlite3_log() */ #define SQLITE_WARNING 28 /* Warnings from sqlite3_log() */ #define SQLITE_ROW 100 /* sqlite3_step() has another row ready */ #define SQLITE_DONE 101 /* sqlite3_step() has finished executing */ /* end-of-error-codes */ /* ** CAPI3REF: Extended Result Codes ** KEYWORDS: {extended result code definitions} ** ** In its default configuration, SQLite API routines return one of 30 integer ** [result codes]. However, experience has shown that many of ** these result codes are too coarse-grained. They do not provide as ** much information about problems as programmers might like. In an effort to ** address this, newer versions of SQLite (version 3.3.8 [dateof:3.3.8] ** and later) include ** support for additional result codes that provide more detailed information ** about errors. These [extended result codes] are enabled or disabled ** on a per database connection basis using the ** [sqlite3_extended_result_codes()] API. Or, the extended code for ** the most recent error can be obtained using ** [sqlite3_extended_errcode()]. */ #define SQLITE_IOERR_READ (SQLITE_IOERR | (1<<8)) #define SQLITE_IOERR_SHORT_READ (SQLITE_IOERR | (2<<8)) #define SQLITE_IOERR_WRITE (SQLITE_IOERR | (3<<8)) #define SQLITE_IOERR_FSYNC (SQLITE_IOERR | (4<<8)) #define SQLITE_IOERR_DIR_FSYNC (SQLITE_IOERR | (5<<8)) #define SQLITE_IOERR_TRUNCATE (SQLITE_IOERR | (6<<8)) #define SQLITE_IOERR_FSTAT (SQLITE_IOERR | (7<<8)) #define SQLITE_IOERR_UNLOCK (SQLITE_IOERR | (8<<8)) #define SQLITE_IOERR_RDLOCK (SQLITE_IOERR | (9<<8)) #define SQLITE_IOERR_DELETE (SQLITE_IOERR | (10<<8)) #define SQLITE_IOERR_BLOCKED (SQLITE_IOERR | (11<<8)) #define SQLITE_IOERR_NOMEM (SQLITE_IOERR | (12<<8)) #define SQLITE_IOERR_ACCESS (SQLITE_IOERR | (13<<8)) #define SQLITE_IOERR_CHECKRESERVEDLOCK (SQLITE_IOERR | (14<<8)) #define SQLITE_IOERR_LOCK (SQLITE_IOERR | (15<<8)) #define SQLITE_IOERR_CLOSE (SQLITE_IOERR | (16<<8)) #define SQLITE_IOERR_DIR_CLOSE (SQLITE_IOERR | (17<<8)) #define SQLITE_IOERR_SHMOPEN (SQLITE_IOERR | (18<<8)) #define SQLITE_IOERR_SHMSIZE (SQLITE_IOERR | (19<<8)) #define SQLITE_IOERR_SHMLOCK (SQLITE_IOERR | (20<<8)) #define SQLITE_IOERR_SHMMAP (SQLITE_IOERR | (21<<8)) #define SQLITE_IOERR_SEEK (SQLITE_IOERR | (22<<8)) #define SQLITE_IOERR_DELETE_NOENT (SQLITE_IOERR | (23<<8)) #define SQLITE_IOERR_MMAP (SQLITE_IOERR | (24<<8)) #define SQLITE_IOERR_GETTEMPPATH (SQLITE_IOERR | (25<<8)) #define SQLITE_IOERR_CONVPATH (SQLITE_IOERR | (26<<8)) #define SQLITE_IOERR_VNODE (SQLITE_IOERR | (27<<8)) #define SQLITE_IOERR_AUTH (SQLITE_IOERR | (28<<8)) #define SQLITE_LOCKED_SHAREDCACHE (SQLITE_LOCKED | (1<<8)) #define SQLITE_BUSY_RECOVERY (SQLITE_BUSY | (1<<8)) #define SQLITE_BUSY_SNAPSHOT (SQLITE_BUSY | (2<<8)) #define SQLITE_CANTOPEN_NOTEMPDIR (SQLITE_CANTOPEN | (1<<8)) #define SQLITE_CANTOPEN_ISDIR (SQLITE_CANTOPEN | (2<<8)) #define SQLITE_CANTOPEN_FULLPATH (SQLITE_CANTOPEN | (3<<8)) #define SQLITE_CANTOPEN_CONVPATH (SQLITE_CANTOPEN | (4<<8)) #define SQLITE_CORRUPT_VTAB (SQLITE_CORRUPT | (1<<8)) #define SQLITE_READONLY_RECOVERY (SQLITE_READONLY | (1<<8)) #define SQLITE_READONLY_CANTLOCK (SQLITE_READONLY | (2<<8)) #define SQLITE_READONLY_ROLLBACK (SQLITE_READONLY | (3<<8)) #define SQLITE_READONLY_DBMOVED (SQLITE_READONLY | (4<<8)) #define SQLITE_ABORT_ROLLBACK (SQLITE_ABORT | (2<<8)) #define SQLITE_CONSTRAINT_CHECK (SQLITE_CONSTRAINT | (1<<8)) #define SQLITE_CONSTRAINT_COMMITHOOK (SQLITE_CONSTRAINT | (2<<8)) #define SQLITE_CONSTRAINT_FOREIGNKEY (SQLITE_CONSTRAINT | (3<<8)) #define SQLITE_CONSTRAINT_FUNCTION (SQLITE_CONSTRAINT | (4<<8)) #define SQLITE_CONSTRAINT_NOTNULL (SQLITE_CONSTRAINT | (5<<8)) #define SQLITE_CONSTRAINT_PRIMARYKEY (SQLITE_CONSTRAINT | (6<<8)) #define SQLITE_CONSTRAINT_TRIGGER (SQLITE_CONSTRAINT | (7<<8)) #define SQLITE_CONSTRAINT_UNIQUE (SQLITE_CONSTRAINT | (8<<8)) #define SQLITE_CONSTRAINT_VTAB (SQLITE_CONSTRAINT | (9<<8)) #define SQLITE_CONSTRAINT_ROWID (SQLITE_CONSTRAINT |(10<<8)) #define SQLITE_NOTICE_RECOVER_WAL (SQLITE_NOTICE | (1<<8)) #define SQLITE_NOTICE_RECOVER_ROLLBACK (SQLITE_NOTICE | (2<<8)) #define SQLITE_WARNING_AUTOINDEX (SQLITE_WARNING | (1<<8)) #define SQLITE_AUTH_USER (SQLITE_AUTH | (1<<8)) #define SQLITE_OK_LOAD_PERMANENTLY (SQLITE_OK | (1<<8)) /* ** CAPI3REF: Flags For File Open Operations ** ** These bit values are intended for use in the ** 3rd parameter to the [sqlite3_open_v2()] interface and ** in the 4th parameter to the [sqlite3_vfs.xOpen] method. */ #define SQLITE_OPEN_READONLY 0x00000001 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_READWRITE 0x00000002 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_CREATE 0x00000004 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_DELETEONCLOSE 0x00000008 /* VFS only */ #define SQLITE_OPEN_EXCLUSIVE 0x00000010 /* VFS only */ #define SQLITE_OPEN_AUTOPROXY 0x00000020 /* VFS only */ #define SQLITE_OPEN_URI 0x00000040 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_MEMORY 0x00000080 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_MAIN_DB 0x00000100 /* VFS only */ #define SQLITE_OPEN_TEMP_DB 0x00000200 /* VFS only */ #define SQLITE_OPEN_TRANSIENT_DB 0x00000400 /* VFS only */ #define SQLITE_OPEN_MAIN_JOURNAL 0x00000800 /* VFS only */ #define SQLITE_OPEN_TEMP_JOURNAL 0x00001000 /* VFS only */ #define SQLITE_OPEN_SUBJOURNAL 0x00002000 /* VFS only */ #define SQLITE_OPEN_MASTER_JOURNAL 0x00004000 /* VFS only */ #define SQLITE_OPEN_NOMUTEX 0x00008000 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_FULLMUTEX 0x00010000 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_SHAREDCACHE 0x00020000 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_PRIVATECACHE 0x00040000 /* Ok for sqlite3_open_v2() */ #define SQLITE_OPEN_WAL 0x00080000 /* VFS only */ /* Reserved: 0x00F00000 */ /* ** CAPI3REF: Device Characteristics ** ** The xDeviceCharacteristics method of the [sqlite3_io_methods] ** object returns an integer which is a vector of these ** bit values expressing I/O characteristics of the mass storage ** device that holds the file that the [sqlite3_io_methods] ** refers to. ** ** The SQLITE_IOCAP_ATOMIC property means that all writes of ** any size are atomic. The SQLITE_IOCAP_ATOMICnnn values ** mean that writes of blocks that are nnn bytes in size and ** are aligned to an address which is an integer multiple of ** nnn are atomic. The SQLITE_IOCAP_SAFE_APPEND value means ** that when data is appended to a file, the data is appended ** first then the size of the file is extended, never the other ** way around. The SQLITE_IOCAP_SEQUENTIAL property means that ** information is written to disk in the same order as calls ** to xWrite(). The SQLITE_IOCAP_POWERSAFE_OVERWRITE property means that ** after reboot following a crash or power loss, the only bytes in a ** file that were written at the application level might have changed ** and that adjacent bytes, even bytes within the same sector are ** guaranteed to be unchanged. The SQLITE_IOCAP_UNDELETABLE_WHEN_OPEN ** flag indicates that a file cannot be deleted when open. The ** SQLITE_IOCAP_IMMUTABLE flag indicates that the file is on ** read-only media and cannot be changed even by processes with ** elevated privileges. */ #define SQLITE_IOCAP_ATOMIC 0x00000001 #define SQLITE_IOCAP_ATOMIC512 0x00000002 #define SQLITE_IOCAP_ATOMIC1K 0x00000004 #define SQLITE_IOCAP_ATOMIC2K 0x00000008 #define SQLITE_IOCAP_ATOMIC4K 0x00000010 #define SQLITE_IOCAP_ATOMIC8K 0x00000020 #define SQLITE_IOCAP_ATOMIC16K 0x00000040 #define SQLITE_IOCAP_ATOMIC32K 0x00000080 #define SQLITE_IOCAP_ATOMIC64K 0x00000100 #define SQLITE_IOCAP_SAFE_APPEND 0x00000200 #define SQLITE_IOCAP_SEQUENTIAL 0x00000400 #define SQLITE_IOCAP_UNDELETABLE_WHEN_OPEN 0x00000800 #define SQLITE_IOCAP_POWERSAFE_OVERWRITE 0x00001000 #define SQLITE_IOCAP_IMMUTABLE 0x00002000 /* ** CAPI3REF: File Locking Levels ** ** SQLite uses one of these integer values as the second ** argument to calls it makes to the xLock() and xUnlock() methods ** of an [sqlite3_io_methods] object. */ #define SQLITE_LOCK_NONE 0 #define SQLITE_LOCK_SHARED 1 #define SQLITE_LOCK_RESERVED 2 #define SQLITE_LOCK_PENDING 3 #define SQLITE_LOCK_EXCLUSIVE 4 /* ** CAPI3REF: Synchronization Type Flags ** ** When SQLite invokes the xSync() method of an ** [sqlite3_io_methods] object it uses a combination of ** these integer values as the second argument. ** ** When the SQLITE_SYNC_DATAONLY flag is used, it means that the ** sync operation only needs to flush data to mass storage. Inode ** information need not be flushed. If the lower four bits of the flag ** equal SQLITE_SYNC_NORMAL, that means to use normal fsync() semantics. ** If the lower four bits equal SQLITE_SYNC_FULL, that means ** to use Mac OS X style fullsync instead of fsync(). ** ** Do not confuse the SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL flags ** with the [PRAGMA synchronous]=NORMAL and [PRAGMA synchronous]=FULL ** settings. The [synchronous pragma] determines when calls to the ** xSync VFS method occur and applies uniformly across all platforms. ** The SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL flags determine how ** energetic or rigorous or forceful the sync operations are and ** only make a difference on Mac OSX for the default SQLite code. ** (Third-party VFS implementations might also make the distinction ** between SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL, but among the ** operating systems natively supported by SQLite, only Mac OSX ** cares about the difference.) */ #define SQLITE_SYNC_NORMAL 0x00002 #define SQLITE_SYNC_FULL 0x00003 #define SQLITE_SYNC_DATAONLY 0x00010 /* ** CAPI3REF: OS Interface Open File Handle ** ** An [sqlite3_file] object represents an open file in the ** [sqlite3_vfs | OS interface layer]. Individual OS interface ** implementations will ** want to subclass this object by appending additional fields ** for their own use. The pMethods entry is a pointer to an ** [sqlite3_io_methods] object that defines methods for performing ** I/O operations on the open file. */ typedef struct sqlite3_file sqlite3_file; struct sqlite3_file { const struct sqlite3_io_methods *pMethods; /* Methods for an open file */ }; /* ** CAPI3REF: OS Interface File Virtual Methods Object ** ** Every file opened by the [sqlite3_vfs.xOpen] method populates an ** [sqlite3_file] object (or, more commonly, a subclass of the ** [sqlite3_file] object) with a pointer to an instance of this object. ** This object defines the methods used to perform various operations ** against the open file represented by the [sqlite3_file] object. ** ** If the [sqlite3_vfs.xOpen] method sets the sqlite3_file.pMethods element ** to a non-NULL pointer, then the sqlite3_io_methods.xClose method ** may be invoked even if the [sqlite3_vfs.xOpen] reported that it failed. The ** only way to prevent a call to xClose following a failed [sqlite3_vfs.xOpen] ** is for the [sqlite3_vfs.xOpen] to set the sqlite3_file.pMethods element ** to NULL. ** ** The flags argument to xSync may be one of [SQLITE_SYNC_NORMAL] or ** [SQLITE_SYNC_FULL]. The first choice is the normal fsync(). ** The second choice is a Mac OS X style fullsync. The [SQLITE_SYNC_DATAONLY] ** flag may be ORed in to indicate that only the data of the file ** and not its inode needs to be synced. ** ** The integer values to xLock() and xUnlock() are one of **
    **
  • [SQLITE_LOCK_NONE], **
  • [SQLITE_LOCK_SHARED], **
  • [SQLITE_LOCK_RESERVED], **
  • [SQLITE_LOCK_PENDING], or **
  • [SQLITE_LOCK_EXCLUSIVE]. **
** xLock() increases the lock. xUnlock() decreases the lock. ** The xCheckReservedLock() method checks whether any database connection, ** either in this process or in some other process, is holding a RESERVED, ** PENDING, or EXCLUSIVE lock on the file. It returns true ** if such a lock exists and false otherwise. ** ** The xFileControl() method is a generic interface that allows custom ** VFS implementations to directly control an open file using the ** [sqlite3_file_control()] interface. The second "op" argument is an ** integer opcode. The third argument is a generic pointer intended to ** point to a structure that may contain arguments or space in which to ** write return values. Potential uses for xFileControl() might be ** functions to enable blocking locks with timeouts, to change the ** locking strategy (for example to use dot-file locks), to inquire ** about the status of a lock, or to break stale locks. The SQLite ** core reserves all opcodes less than 100 for its own use. ** A [file control opcodes | list of opcodes] less than 100 is available. ** Applications that define a custom xFileControl method should use opcodes ** greater than 100 to avoid conflicts. VFS implementations should ** return [SQLITE_NOTFOUND] for file control opcodes that they do not ** recognize. ** ** The xSectorSize() method returns the sector size of the ** device that underlies the file. The sector size is the ** minimum write that can be performed without disturbing ** other bytes in the file. The xDeviceCharacteristics() ** method returns a bit vector describing behaviors of the ** underlying device: ** **
    **
  • [SQLITE_IOCAP_ATOMIC] **
  • [SQLITE_IOCAP_ATOMIC512] **
  • [SQLITE_IOCAP_ATOMIC1K] **
  • [SQLITE_IOCAP_ATOMIC2K] **
  • [SQLITE_IOCAP_ATOMIC4K] **
  • [SQLITE_IOCAP_ATOMIC8K] **
  • [SQLITE_IOCAP_ATOMIC16K] **
  • [SQLITE_IOCAP_ATOMIC32K] **
  • [SQLITE_IOCAP_ATOMIC64K] **
  • [SQLITE_IOCAP_SAFE_APPEND] **
  • [SQLITE_IOCAP_SEQUENTIAL] **
  • [SQLITE_IOCAP_UNDELETABLE_WHEN_OPEN] **
  • [SQLITE_IOCAP_POWERSAFE_OVERWRITE] **
  • [SQLITE_IOCAP_IMMUTABLE] **
** ** The SQLITE_IOCAP_ATOMIC property means that all writes of ** any size are atomic. The SQLITE_IOCAP_ATOMICnnn values ** mean that writes of blocks that are nnn bytes in size and ** are aligned to an address which is an integer multiple of ** nnn are atomic. The SQLITE_IOCAP_SAFE_APPEND value means ** that when data is appended to a file, the data is appended ** first then the size of the file is extended, never the other ** way around. The SQLITE_IOCAP_SEQUENTIAL property means that ** information is written to disk in the same order as calls ** to xWrite(). ** ** If xRead() returns SQLITE_IOERR_SHORT_READ it must also fill ** in the unread portions of the buffer with zeros. A VFS that ** fails to zero-fill short reads might seem to work. However, ** failure to zero-fill short reads will eventually lead to ** database corruption. */ typedef struct sqlite3_io_methods sqlite3_io_methods; struct sqlite3_io_methods { int iVersion; int (*xClose)(sqlite3_file*); int (*xRead)(sqlite3_file*, void*, int iAmt, sqlite3_int64 iOfst); int (*xWrite)(sqlite3_file*, const void*, int iAmt, sqlite3_int64 iOfst); int (*xTruncate)(sqlite3_file*, sqlite3_int64 size); int (*xSync)(sqlite3_file*, int flags); int (*xFileSize)(sqlite3_file*, sqlite3_int64 *pSize); int (*xLock)(sqlite3_file*, int); int (*xUnlock)(sqlite3_file*, int); int (*xCheckReservedLock)(sqlite3_file*, int *pResOut); int (*xFileControl)(sqlite3_file*, int op, void *pArg); int (*xSectorSize)(sqlite3_file*); int (*xDeviceCharacteristics)(sqlite3_file*); /* Methods above are valid for version 1 */ int (*xShmMap)(sqlite3_file*, int iPg, int pgsz, int, void volatile**); int (*xShmLock)(sqlite3_file*, int offset, int n, int flags); void (*xShmBarrier)(sqlite3_file*); int (*xShmUnmap)(sqlite3_file*, int deleteFlag); /* Methods above are valid for version 2 */ int (*xFetch)(sqlite3_file*, sqlite3_int64 iOfst, int iAmt, void **pp); int (*xUnfetch)(sqlite3_file*, sqlite3_int64 iOfst, void *p); /* Methods above are valid for version 3 */ /* Additional methods may be added in future releases */ }; /* ** CAPI3REF: Standard File Control Opcodes ** KEYWORDS: {file control opcodes} {file control opcode} ** ** These integer constants are opcodes for the xFileControl method ** of the [sqlite3_io_methods] object and for the [sqlite3_file_control()] ** interface. ** **
    **
  • [[SQLITE_FCNTL_LOCKSTATE]] ** The [SQLITE_FCNTL_LOCKSTATE] opcode is used for debugging. This ** opcode causes the xFileControl method to write the current state of ** the lock (one of [SQLITE_LOCK_NONE], [SQLITE_LOCK_SHARED], ** [SQLITE_LOCK_RESERVED], [SQLITE_LOCK_PENDING], or [SQLITE_LOCK_EXCLUSIVE]) ** into an integer that the pArg argument points to. This capability ** is used during testing and is only available when the SQLITE_TEST ** compile-time option is used. ** **
  • [[SQLITE_FCNTL_SIZE_HINT]] ** The [SQLITE_FCNTL_SIZE_HINT] opcode is used by SQLite to give the VFS ** layer a hint of how large the database file will grow to be during the ** current transaction. This hint is not guaranteed to be accurate but it ** is often close. The underlying VFS might choose to preallocate database ** file space based on this hint in order to help writes to the database ** file run faster. ** **
  • [[SQLITE_FCNTL_CHUNK_SIZE]] ** The [SQLITE_FCNTL_CHUNK_SIZE] opcode is used to request that the VFS ** extends and truncates the database file in chunks of a size specified ** by the user. The fourth argument to [sqlite3_file_control()] should ** point to an integer (type int) containing the new chunk-size to use ** for the nominated database. Allocating database file space in large ** chunks (say 1MB at a time), may reduce file-system fragmentation and ** improve performance on some systems. ** **
  • [[SQLITE_FCNTL_FILE_POINTER]] ** The [SQLITE_FCNTL_FILE_POINTER] opcode is used to obtain a pointer ** to the [sqlite3_file] object associated with a particular database ** connection. See also [SQLITE_FCNTL_JOURNAL_POINTER]. ** **
  • [[SQLITE_FCNTL_JOURNAL_POINTER]] ** The [SQLITE_FCNTL_JOURNAL_POINTER] opcode is used to obtain a pointer ** to the [sqlite3_file] object associated with the journal file (either ** the [rollback journal] or the [write-ahead log]) for a particular database ** connection. See also [SQLITE_FCNTL_FILE_POINTER]. ** **
  • [[SQLITE_FCNTL_SYNC_OMITTED]] ** No longer in use. ** **
  • [[SQLITE_FCNTL_SYNC]] ** The [SQLITE_FCNTL_SYNC] opcode is generated internally by SQLite and ** sent to the VFS immediately before the xSync method is invoked on a ** database file descriptor. Or, if the xSync method is not invoked ** because the user has configured SQLite with ** [PRAGMA synchronous | PRAGMA synchronous=OFF] it is invoked in place ** of the xSync method. In most cases, the pointer argument passed with ** this file-control is NULL. However, if the database file is being synced ** as part of a multi-database commit, the argument points to a nul-terminated ** string containing the transactions master-journal file name. VFSes that ** do not need this signal should silently ignore this opcode. Applications ** should not call [sqlite3_file_control()] with this opcode as doing so may ** disrupt the operation of the specialized VFSes that do require it. ** **
  • [[SQLITE_FCNTL_COMMIT_PHASETWO]] ** The [SQLITE_FCNTL_COMMIT_PHASETWO] opcode is generated internally by SQLite ** and sent to the VFS after a transaction has been committed immediately ** but before the database is unlocked. VFSes that do not need this signal ** should silently ignore this opcode. Applications should not call ** [sqlite3_file_control()] with this opcode as doing so may disrupt the ** operation of the specialized VFSes that do require it. ** **
  • [[SQLITE_FCNTL_WIN32_AV_RETRY]] ** ^The [SQLITE_FCNTL_WIN32_AV_RETRY] opcode is used to configure automatic ** retry counts and intervals for certain disk I/O operations for the ** windows [VFS] in order to provide robustness in the presence of ** anti-virus programs. By default, the windows VFS will retry file read, ** file write, and file delete operations up to 10 times, with a delay ** of 25 milliseconds before the first retry and with the delay increasing ** by an additional 25 milliseconds with each subsequent retry. This ** opcode allows these two values (10 retries and 25 milliseconds of delay) ** to be adjusted. The values are changed for all database connections ** within the same process. The argument is a pointer to an array of two ** integers where the first integer is the new retry count and the second ** integer is the delay. If either integer is negative, then the setting ** is not changed but instead the prior value of that setting is written ** into the array entry, allowing the current retry settings to be ** interrogated. The zDbName parameter is ignored. ** **
  • [[SQLITE_FCNTL_PERSIST_WAL]] ** ^The [SQLITE_FCNTL_PERSIST_WAL] opcode is used to set or query the ** persistent [WAL | Write Ahead Log] setting. By default, the auxiliary ** write ahead log and shared memory files used for transaction control ** are automatically deleted when the latest connection to the database ** closes. Setting persistent WAL mode causes those files to persist after ** close. Persisting the files is useful when other processes that do not ** have write permission on the directory containing the database file want ** to read the database file, as the WAL and shared memory files must exist ** in order for the database to be readable. The fourth parameter to ** [sqlite3_file_control()] for this opcode should be a pointer to an integer. ** That integer is 0 to disable persistent WAL mode or 1 to enable persistent ** WAL mode. If the integer is -1, then it is overwritten with the current ** WAL persistence setting. ** **
  • [[SQLITE_FCNTL_POWERSAFE_OVERWRITE]] ** ^The [SQLITE_FCNTL_POWERSAFE_OVERWRITE] opcode is used to set or query the ** persistent "powersafe-overwrite" or "PSOW" setting. The PSOW setting ** determines the [SQLITE_IOCAP_POWERSAFE_OVERWRITE] bit of the ** xDeviceCharacteristics methods. The fourth parameter to ** [sqlite3_file_control()] for this opcode should be a pointer to an integer. ** That integer is 0 to disable zero-damage mode or 1 to enable zero-damage ** mode. If the integer is -1, then it is overwritten with the current ** zero-damage mode setting. ** **
  • [[SQLITE_FCNTL_OVERWRITE]] ** ^The [SQLITE_FCNTL_OVERWRITE] opcode is invoked by SQLite after opening ** a write transaction to indicate that, unless it is rolled back for some ** reason, the entire database file will be overwritten by the current ** transaction. This is used by VACUUM operations. ** **
  • [[SQLITE_FCNTL_VFSNAME]] ** ^The [SQLITE_FCNTL_VFSNAME] opcode can be used to obtain the names of ** all [VFSes] in the VFS stack. The names are of all VFS shims and the ** final bottom-level VFS are written into memory obtained from ** [sqlite3_malloc()] and the result is stored in the char* variable ** that the fourth parameter of [sqlite3_file_control()] points to. ** The caller is responsible for freeing the memory when done. As with ** all file-control actions, there is no guarantee that this will actually ** do anything. Callers should initialize the char* variable to a NULL ** pointer in case this file-control is not implemented. This file-control ** is intended for diagnostic use only. ** **
  • [[SQLITE_FCNTL_VFS_POINTER]] ** ^The [SQLITE_FCNTL_VFS_POINTER] opcode finds a pointer to the top-level ** [VFSes] currently in use. ^(The argument X in ** sqlite3_file_control(db,SQLITE_FCNTL_VFS_POINTER,X) must be ** of type "[sqlite3_vfs] **". This opcodes will set *X ** to a pointer to the top-level VFS.)^ ** ^When there are multiple VFS shims in the stack, this opcode finds the ** upper-most shim only. ** **
  • [[SQLITE_FCNTL_PRAGMA]] ** ^Whenever a [PRAGMA] statement is parsed, an [SQLITE_FCNTL_PRAGMA] ** file control is sent to the open [sqlite3_file] object corresponding ** to the database file to which the pragma statement refers. ^The argument ** to the [SQLITE_FCNTL_PRAGMA] file control is an array of ** pointers to strings (char**) in which the second element of the array ** is the name of the pragma and the third element is the argument to the ** pragma or NULL if the pragma has no argument. ^The handler for an ** [SQLITE_FCNTL_PRAGMA] file control can optionally make the first element ** of the char** argument point to a string obtained from [sqlite3_mprintf()] ** or the equivalent and that string will become the result of the pragma or ** the error message if the pragma fails. ^If the ** [SQLITE_FCNTL_PRAGMA] file control returns [SQLITE_NOTFOUND], then normal ** [PRAGMA] processing continues. ^If the [SQLITE_FCNTL_PRAGMA] ** file control returns [SQLITE_OK], then the parser assumes that the ** VFS has handled the PRAGMA itself and the parser generates a no-op ** prepared statement if result string is NULL, or that returns a copy ** of the result string if the string is non-NULL. ** ^If the [SQLITE_FCNTL_PRAGMA] file control returns ** any result code other than [SQLITE_OK] or [SQLITE_NOTFOUND], that means ** that the VFS encountered an error while handling the [PRAGMA] and the ** compilation of the PRAGMA fails with an error. ^The [SQLITE_FCNTL_PRAGMA] ** file control occurs at the beginning of pragma statement analysis and so ** it is able to override built-in [PRAGMA] statements. ** **
  • [[SQLITE_FCNTL_BUSYHANDLER]] ** ^The [SQLITE_FCNTL_BUSYHANDLER] ** file-control may be invoked by SQLite on the database file handle ** shortly after it is opened in order to provide a custom VFS with access ** to the connections busy-handler callback. The argument is of type (void **) ** - an array of two (void *) values. The first (void *) actually points ** to a function of type (int (*)(void *)). In order to invoke the connections ** busy-handler, this function should be invoked with the second (void *) in ** the array as the only argument. If it returns non-zero, then the operation ** should be retried. If it returns zero, the custom VFS should abandon the ** current operation. ** **
  • [[SQLITE_FCNTL_TEMPFILENAME]] ** ^Application can invoke the [SQLITE_FCNTL_TEMPFILENAME] file-control ** to have SQLite generate a ** temporary filename using the same algorithm that is followed to generate ** temporary filenames for TEMP tables and other internal uses. The ** argument should be a char** which will be filled with the filename ** written into memory obtained from [sqlite3_malloc()]. The caller should ** invoke [sqlite3_free()] on the result to avoid a memory leak. ** **
  • [[SQLITE_FCNTL_MMAP_SIZE]] ** The [SQLITE_FCNTL_MMAP_SIZE] file control is used to query or set the ** maximum number of bytes that will be used for memory-mapped I/O. ** The argument is a pointer to a value of type sqlite3_int64 that ** is an advisory maximum number of bytes in the file to memory map. The ** pointer is overwritten with the old value. The limit is not changed if ** the value originally pointed to is negative, and so the current limit ** can be queried by passing in a pointer to a negative number. This ** file-control is used internally to implement [PRAGMA mmap_size]. ** **
  • [[SQLITE_FCNTL_TRACE]] ** The [SQLITE_FCNTL_TRACE] file control provides advisory information ** to the VFS about what the higher layers of the SQLite stack are doing. ** This file control is used by some VFS activity tracing [shims]. ** The argument is a zero-terminated string. Higher layers in the ** SQLite stack may generate instances of this file control if ** the [SQLITE_USE_FCNTL_TRACE] compile-time option is enabled. ** **
  • [[SQLITE_FCNTL_HAS_MOVED]] ** The [SQLITE_FCNTL_HAS_MOVED] file control interprets its argument as a ** pointer to an integer and it writes a boolean into that integer depending ** on whether or not the file has been renamed, moved, or deleted since it ** was first opened. ** **
  • [[SQLITE_FCNTL_WIN32_GET_HANDLE]] ** The [SQLITE_FCNTL_WIN32_GET_HANDLE] opcode can be used to obtain the ** underlying native file handle associated with a file handle. This file ** control interprets its argument as a pointer to a native file handle and ** writes the resulting value there. ** **
  • [[SQLITE_FCNTL_WIN32_SET_HANDLE]] ** The [SQLITE_FCNTL_WIN32_SET_HANDLE] opcode is used for debugging. This ** opcode causes the xFileControl method to swap the file handle with the one ** pointed to by the pArg argument. This capability is used during testing ** and only needs to be supported when SQLITE_TEST is defined. ** **
  • [[SQLITE_FCNTL_WAL_BLOCK]] ** The [SQLITE_FCNTL_WAL_BLOCK] is a signal to the VFS layer that it might ** be advantageous to block on the next WAL lock if the lock is not immediately ** available. The WAL subsystem issues this signal during rare ** circumstances in order to fix a problem with priority inversion. ** Applications should not use this file-control. ** **
  • [[SQLITE_FCNTL_ZIPVFS]] ** The [SQLITE_FCNTL_ZIPVFS] opcode is implemented by zipvfs only. All other ** VFS should return SQLITE_NOTFOUND for this opcode. ** **
  • [[SQLITE_FCNTL_RBU]] ** The [SQLITE_FCNTL_RBU] opcode is implemented by the special VFS used by ** the RBU extension only. All other VFS should return SQLITE_NOTFOUND for ** this opcode. **
*/ #define SQLITE_FCNTL_LOCKSTATE 1 #define SQLITE_FCNTL_GET_LOCKPROXYFILE 2 #define SQLITE_FCNTL_SET_LOCKPROXYFILE 3 #define SQLITE_FCNTL_LAST_ERRNO 4 #define SQLITE_FCNTL_SIZE_HINT 5 #define SQLITE_FCNTL_CHUNK_SIZE 6 #define SQLITE_FCNTL_FILE_POINTER 7 #define SQLITE_FCNTL_SYNC_OMITTED 8 #define SQLITE_FCNTL_WIN32_AV_RETRY 9 #define SQLITE_FCNTL_PERSIST_WAL 10 #define SQLITE_FCNTL_OVERWRITE 11 #define SQLITE_FCNTL_VFSNAME 12 #define SQLITE_FCNTL_POWERSAFE_OVERWRITE 13 #define SQLITE_FCNTL_PRAGMA 14 #define SQLITE_FCNTL_BUSYHANDLER 15 #define SQLITE_FCNTL_TEMPFILENAME 16 #define SQLITE_FCNTL_MMAP_SIZE 18 #define SQLITE_FCNTL_TRACE 19 #define SQLITE_FCNTL_HAS_MOVED 20 #define SQLITE_FCNTL_SYNC 21 #define SQLITE_FCNTL_COMMIT_PHASETWO 22 #define SQLITE_FCNTL_WIN32_SET_HANDLE 23 #define SQLITE_FCNTL_WAL_BLOCK 24 #define SQLITE_FCNTL_ZIPVFS 25 #define SQLITE_FCNTL_RBU 26 #define SQLITE_FCNTL_VFS_POINTER 27 #define SQLITE_FCNTL_JOURNAL_POINTER 28 #define SQLITE_FCNTL_WIN32_GET_HANDLE 29 #define SQLITE_FCNTL_PDB 30 /* deprecated names */ #define SQLITE_GET_LOCKPROXYFILE SQLITE_FCNTL_GET_LOCKPROXYFILE #define SQLITE_SET_LOCKPROXYFILE SQLITE_FCNTL_SET_LOCKPROXYFILE #define SQLITE_LAST_ERRNO SQLITE_FCNTL_LAST_ERRNO /* ** CAPI3REF: Mutex Handle ** ** The mutex module within SQLite defines [sqlite3_mutex] to be an ** abstract type for a mutex object. The SQLite core never looks ** at the internal representation of an [sqlite3_mutex]. It only ** deals with pointers to the [sqlite3_mutex] object. ** ** Mutexes are created using [sqlite3_mutex_alloc()]. */ typedef struct sqlite3_mutex sqlite3_mutex; /* ** CAPI3REF: Loadable Extension Thunk ** ** A pointer to the opaque sqlite3_api_routines structure is passed as ** the third parameter to entry points of [loadable extensions]. This ** structure must be typedefed in order to work around compiler warnings ** on some platforms. */ typedef struct sqlite3_api_routines sqlite3_api_routines; /* ** CAPI3REF: OS Interface Object ** ** An instance of the sqlite3_vfs object defines the interface between ** the SQLite core and the underlying operating system. The "vfs" ** in the name of the object stands for "virtual file system". See ** the [VFS | VFS documentation] for further information. ** ** The value of the iVersion field is initially 1 but may be larger in ** future versions of SQLite. Additional fields may be appended to this ** object when the iVersion value is increased. Note that the structure ** of the sqlite3_vfs object changes in the transaction between ** SQLite version 3.5.9 and 3.6.0 and yet the iVersion field was not ** modified. ** ** The szOsFile field is the size of the subclassed [sqlite3_file] ** structure used by this VFS. mxPathname is the maximum length of ** a pathname in this VFS. ** ** Registered sqlite3_vfs objects are kept on a linked list formed by ** the pNext pointer. The [sqlite3_vfs_register()] ** and [sqlite3_vfs_unregister()] interfaces manage this list ** in a thread-safe way. The [sqlite3_vfs_find()] interface ** searches the list. Neither the application code nor the VFS ** implementation should use the pNext pointer. ** ** The pNext field is the only field in the sqlite3_vfs ** structure that SQLite will ever modify. SQLite will only access ** or modify this field while holding a particular static mutex. ** The application should never modify anything within the sqlite3_vfs ** object once the object has been registered. ** ** The zName field holds the name of the VFS module. The name must ** be unique across all VFS modules. ** ** [[sqlite3_vfs.xOpen]] ** ^SQLite guarantees that the zFilename parameter to xOpen ** is either a NULL pointer or string obtained ** from xFullPathname() with an optional suffix added. ** ^If a suffix is added to the zFilename parameter, it will ** consist of a single "-" character followed by no more than ** 11 alphanumeric and/or "-" characters. ** ^SQLite further guarantees that ** the string will be valid and unchanged until xClose() is ** called. Because of the previous sentence, ** the [sqlite3_file] can safely store a pointer to the ** filename if it needs to remember the filename for some reason. ** If the zFilename parameter to xOpen is a NULL pointer then xOpen ** must invent its own temporary name for the file. ^Whenever the ** xFilename parameter is NULL it will also be the case that the ** flags parameter will include [SQLITE_OPEN_DELETEONCLOSE]. ** ** The flags argument to xOpen() includes all bits set in ** the flags argument to [sqlite3_open_v2()]. Or if [sqlite3_open()] ** or [sqlite3_open16()] is used, then flags includes at least ** [SQLITE_OPEN_READWRITE] | [SQLITE_OPEN_CREATE]. ** If xOpen() opens a file read-only then it sets *pOutFlags to ** include [SQLITE_OPEN_READONLY]. Other bits in *pOutFlags may be set. ** ** ^(SQLite will also add one of the following flags to the xOpen() ** call, depending on the object being opened: ** **
    **
  • [SQLITE_OPEN_MAIN_DB] **
  • [SQLITE_OPEN_MAIN_JOURNAL] **
  • [SQLITE_OPEN_TEMP_DB] **
  • [SQLITE_OPEN_TEMP_JOURNAL] **
  • [SQLITE_OPEN_TRANSIENT_DB] **
  • [SQLITE_OPEN_SUBJOURNAL] **
  • [SQLITE_OPEN_MASTER_JOURNAL] **
  • [SQLITE_OPEN_WAL] **
)^ ** ** The file I/O implementation can use the object type flags to ** change the way it deals with files. For example, an application ** that does not care about crash recovery or rollback might make ** the open of a journal file a no-op. Writes to this journal would ** also be no-ops, and any attempt to read the journal would return ** SQLITE_IOERR. Or the implementation might recognize that a database ** file will be doing page-aligned sector reads and writes in a random ** order and set up its I/O subsystem accordingly. ** ** SQLite might also add one of the following flags to the xOpen method: ** **
    **
  • [SQLITE_OPEN_DELETEONCLOSE] **
  • [SQLITE_OPEN_EXCLUSIVE] **
** ** The [SQLITE_OPEN_DELETEONCLOSE] flag means the file should be ** deleted when it is closed. ^The [SQLITE_OPEN_DELETEONCLOSE] ** will be set for TEMP databases and their journals, transient ** databases, and subjournals. ** ** ^The [SQLITE_OPEN_EXCLUSIVE] flag is always used in conjunction ** with the [SQLITE_OPEN_CREATE] flag, which are both directly ** analogous to the O_EXCL and O_CREAT flags of the POSIX open() ** API. The SQLITE_OPEN_EXCLUSIVE flag, when paired with the ** SQLITE_OPEN_CREATE, is used to indicate that file should always ** be created, and that it is an error if it already exists. ** It is not used to indicate the file should be opened ** for exclusive access. ** ** ^At least szOsFile bytes of memory are allocated by SQLite ** to hold the [sqlite3_file] structure passed as the third ** argument to xOpen. The xOpen method does not have to ** allocate the structure; it should just fill it in. Note that ** the xOpen method must set the sqlite3_file.pMethods to either ** a valid [sqlite3_io_methods] object or to NULL. xOpen must do ** this even if the open fails. SQLite expects that the sqlite3_file.pMethods ** element will be valid after xOpen returns regardless of the success ** or failure of the xOpen call. ** ** [[sqlite3_vfs.xAccess]] ** ^The flags argument to xAccess() may be [SQLITE_ACCESS_EXISTS] ** to test for the existence of a file, or [SQLITE_ACCESS_READWRITE] to ** test whether a file is readable and writable, or [SQLITE_ACCESS_READ] ** to test whether a file is at least readable. The file can be a ** directory. ** ** ^SQLite will always allocate at least mxPathname+1 bytes for the ** output buffer xFullPathname. The exact size of the output buffer ** is also passed as a parameter to both methods. If the output buffer ** is not large enough, [SQLITE_CANTOPEN] should be returned. Since this is ** handled as a fatal error by SQLite, vfs implementations should endeavor ** to prevent this by setting mxPathname to a sufficiently large value. ** ** The xRandomness(), xSleep(), xCurrentTime(), and xCurrentTimeInt64() ** interfaces are not strictly a part of the filesystem, but they are ** included in the VFS structure for completeness. ** The xRandomness() function attempts to return nBytes bytes ** of good-quality randomness into zOut. The return value is ** the actual number of bytes of randomness obtained. ** The xSleep() method causes the calling thread to sleep for at ** least the number of microseconds given. ^The xCurrentTime() ** method returns a Julian Day Number for the current date and time as ** a floating point value. ** ^The xCurrentTimeInt64() method returns, as an integer, the Julian ** Day Number multiplied by 86400000 (the number of milliseconds in ** a 24-hour day). ** ^SQLite will use the xCurrentTimeInt64() method to get the current ** date and time if that method is available (if iVersion is 2 or ** greater and the function pointer is not NULL) and will fall back ** to xCurrentTime() if xCurrentTimeInt64() is unavailable. ** ** ^The xSetSystemCall(), xGetSystemCall(), and xNestSystemCall() interfaces ** are not used by the SQLite core. These optional interfaces are provided ** by some VFSes to facilitate testing of the VFS code. By overriding ** system calls with functions under its control, a test program can ** simulate faults and error conditions that would otherwise be difficult ** or impossible to induce. The set of system calls that can be overridden ** varies from one VFS to another, and from one version of the same VFS to the ** next. Applications that use these interfaces must be prepared for any ** or all of these interfaces to be NULL or for their behavior to change ** from one release to the next. Applications must not attempt to access ** any of these methods if the iVersion of the VFS is less than 3. */ typedef struct sqlite3_vfs sqlite3_vfs; typedef void (*sqlite3_syscall_ptr)(void); struct sqlite3_vfs { int iVersion; /* Structure version number (currently 3) */ int szOsFile; /* Size of subclassed sqlite3_file */ int mxPathname; /* Maximum file pathname length */ sqlite3_vfs *pNext; /* Next registered VFS */ const char *zName; /* Name of this virtual file system */ void *pAppData; /* Pointer to application-specific data */ int (*xOpen)(sqlite3_vfs*, const char *zName, sqlite3_file*, int flags, int *pOutFlags); int (*xDelete)(sqlite3_vfs*, const char *zName, int syncDir); int (*xAccess)(sqlite3_vfs*, const char *zName, int flags, int *pResOut); int (*xFullPathname)(sqlite3_vfs*, const char *zName, int nOut, char *zOut); void *(*xDlOpen)(sqlite3_vfs*, const char *zFilename); void (*xDlError)(sqlite3_vfs*, int nByte, char *zErrMsg); void (*(*xDlSym)(sqlite3_vfs*,void*, const char *zSymbol))(void); void (*xDlClose)(sqlite3_vfs*, void*); int (*xRandomness)(sqlite3_vfs*, int nByte, char *zOut); int (*xSleep)(sqlite3_vfs*, int microseconds); int (*xCurrentTime)(sqlite3_vfs*, double*); int (*xGetLastError)(sqlite3_vfs*, int, char *); /* ** The methods above are in version 1 of the sqlite_vfs object ** definition. Those that follow are added in version 2 or later */ int (*xCurrentTimeInt64)(sqlite3_vfs*, sqlite3_int64*); /* ** The methods above are in versions 1 and 2 of the sqlite_vfs object. ** Those below are for version 3 and greater. */ int (*xSetSystemCall)(sqlite3_vfs*, const char *zName, sqlite3_syscall_ptr); sqlite3_syscall_ptr (*xGetSystemCall)(sqlite3_vfs*, const char *zName); const char *(*xNextSystemCall)(sqlite3_vfs*, const char *zName); /* ** The methods above are in versions 1 through 3 of the sqlite_vfs object. ** New fields may be appended in future versions. The iVersion ** value will increment whenever this happens. */ }; /* ** CAPI3REF: Flags for the xAccess VFS method ** ** These integer constants can be used as the third parameter to ** the xAccess method of an [sqlite3_vfs] object. They determine ** what kind of permissions the xAccess method is looking for. ** With SQLITE_ACCESS_EXISTS, the xAccess method ** simply checks whether the file exists. ** With SQLITE_ACCESS_READWRITE, the xAccess method ** checks whether the named directory is both readable and writable ** (in other words, if files can be added, removed, and renamed within ** the directory). ** The SQLITE_ACCESS_READWRITE constant is currently used only by the ** [temp_store_directory pragma], though this could change in a future ** release of SQLite. ** With SQLITE_ACCESS_READ, the xAccess method ** checks whether the file is readable. The SQLITE_ACCESS_READ constant is ** currently unused, though it might be used in a future release of ** SQLite. */ #define SQLITE_ACCESS_EXISTS 0 #define SQLITE_ACCESS_READWRITE 1 /* Used by PRAGMA temp_store_directory */ #define SQLITE_ACCESS_READ 2 /* Unused */ /* ** CAPI3REF: Flags for the xShmLock VFS method ** ** These integer constants define the various locking operations ** allowed by the xShmLock method of [sqlite3_io_methods]. The ** following are the only legal combinations of flags to the ** xShmLock method: ** **
    **
  • SQLITE_SHM_LOCK | SQLITE_SHM_SHARED **
  • SQLITE_SHM_LOCK | SQLITE_SHM_EXCLUSIVE **
  • SQLITE_SHM_UNLOCK | SQLITE_SHM_SHARED **
  • SQLITE_SHM_UNLOCK | SQLITE_SHM_EXCLUSIVE **
** ** When unlocking, the same SHARED or EXCLUSIVE flag must be supplied as ** was given on the corresponding lock. ** ** The xShmLock method can transition between unlocked and SHARED or ** between unlocked and EXCLUSIVE. It cannot transition between SHARED ** and EXCLUSIVE. */ #define SQLITE_SHM_UNLOCK 1 #define SQLITE_SHM_LOCK 2 #define SQLITE_SHM_SHARED 4 #define SQLITE_SHM_EXCLUSIVE 8 /* ** CAPI3REF: Maximum xShmLock index ** ** The xShmLock method on [sqlite3_io_methods] may use values ** between 0 and this upper bound as its "offset" argument. ** The SQLite core will never attempt to acquire or release a ** lock outside of this range */ #define SQLITE_SHM_NLOCK 8 /* ** CAPI3REF: Initialize The SQLite Library ** ** ^The sqlite3_initialize() routine initializes the ** SQLite library. ^The sqlite3_shutdown() routine ** deallocates any resources that were allocated by sqlite3_initialize(). ** These routines are designed to aid in process initialization and ** shutdown on embedded systems. Workstation applications using ** SQLite normally do not need to invoke either of these routines. ** ** A call to sqlite3_initialize() is an "effective" call if it is ** the first time sqlite3_initialize() is invoked during the lifetime of ** the process, or if it is the first time sqlite3_initialize() is invoked ** following a call to sqlite3_shutdown(). ^(Only an effective call ** of sqlite3_initialize() does any initialization. All other calls ** are harmless no-ops.)^ ** ** A call to sqlite3_shutdown() is an "effective" call if it is the first ** call to sqlite3_shutdown() since the last sqlite3_initialize(). ^(Only ** an effective call to sqlite3_shutdown() does any deinitialization. ** All other valid calls to sqlite3_shutdown() are harmless no-ops.)^ ** ** The sqlite3_initialize() interface is threadsafe, but sqlite3_shutdown() ** is not. The sqlite3_shutdown() interface must only be called from a ** single thread. All open [database connections] must be closed and all ** other SQLite resources must be deallocated prior to invoking ** sqlite3_shutdown(). ** ** Among other things, ^sqlite3_initialize() will invoke ** sqlite3_os_init(). Similarly, ^sqlite3_shutdown() ** will invoke sqlite3_os_end(). ** ** ^The sqlite3_initialize() routine returns [SQLITE_OK] on success. ** ^If for some reason, sqlite3_initialize() is unable to initialize ** the library (perhaps it is unable to allocate a needed resource such ** as a mutex) it returns an [error code] other than [SQLITE_OK]. ** ** ^The sqlite3_initialize() routine is called internally by many other ** SQLite interfaces so that an application usually does not need to ** invoke sqlite3_initialize() directly. For example, [sqlite3_open()] ** calls sqlite3_initialize() so the SQLite library will be automatically ** initialized when [sqlite3_open()] is called if it has not be initialized ** already. ^However, if SQLite is compiled with the [SQLITE_OMIT_AUTOINIT] ** compile-time option, then the automatic calls to sqlite3_initialize() ** are omitted and the application must call sqlite3_initialize() directly ** prior to using any other SQLite interface. For maximum portability, ** it is recommended that applications always invoke sqlite3_initialize() ** directly prior to using any other SQLite interface. Future releases ** of SQLite may require this. In other words, the behavior exhibited ** when SQLite is compiled with [SQLITE_OMIT_AUTOINIT] might become the ** default behavior in some future release of SQLite. ** ** The sqlite3_os_init() routine does operating-system specific ** initialization of the SQLite library. The sqlite3_os_end() ** routine undoes the effect of sqlite3_os_init(). Typical tasks ** performed by these routines include allocation or deallocation ** of static resources, initialization of global variables, ** setting up a default [sqlite3_vfs] module, or setting up ** a default configuration using [sqlite3_config()]. ** ** The application should never invoke either sqlite3_os_init() ** or sqlite3_os_end() directly. The application should only invoke ** sqlite3_initialize() and sqlite3_shutdown(). The sqlite3_os_init() ** interface is called automatically by sqlite3_initialize() and ** sqlite3_os_end() is called by sqlite3_shutdown(). Appropriate ** implementations for sqlite3_os_init() and sqlite3_os_end() ** are built into SQLite when it is compiled for Unix, Windows, or OS/2. ** When [custom builds | built for other platforms] ** (using the [SQLITE_OS_OTHER=1] compile-time ** option) the application must supply a suitable implementation for ** sqlite3_os_init() and sqlite3_os_end(). An application-supplied ** implementation of sqlite3_os_init() or sqlite3_os_end() ** must return [SQLITE_OK] on success and some other [error code] upon ** failure. */ SQLITE_API int sqlite3_initialize(void); SQLITE_API int sqlite3_shutdown(void); SQLITE_API int sqlite3_os_init(void); SQLITE_API int sqlite3_os_end(void); /* ** CAPI3REF: Configuring The SQLite Library ** ** The sqlite3_config() interface is used to make global configuration ** changes to SQLite in order to tune SQLite to the specific needs of ** the application. The default configuration is recommended for most ** applications and so this routine is usually not necessary. It is ** provided to support rare applications with unusual needs. ** ** The sqlite3_config() interface is not threadsafe. The application ** must ensure that no other SQLite interfaces are invoked by other ** threads while sqlite3_config() is running. ** ** The sqlite3_config() interface ** may only be invoked prior to library initialization using ** [sqlite3_initialize()] or after shutdown by [sqlite3_shutdown()]. ** ^If sqlite3_config() is called after [sqlite3_initialize()] and before ** [sqlite3_shutdown()] then it will return SQLITE_MISUSE. ** Note, however, that ^sqlite3_config() can be called as part of the ** implementation of an application-defined [sqlite3_os_init()]. ** ** The first argument to sqlite3_config() is an integer ** [configuration option] that determines ** what property of SQLite is to be configured. Subsequent arguments ** vary depending on the [configuration option] ** in the first argument. ** ** ^When a configuration option is set, sqlite3_config() returns [SQLITE_OK]. ** ^If the option is unknown or SQLite is unable to set the option ** then this routine returns a non-zero [error code]. */ SQLITE_API int sqlite3_config(int, ...); /* ** CAPI3REF: Configure database connections ** METHOD: sqlite3 ** ** The sqlite3_db_config() interface is used to make configuration ** changes to a [database connection]. The interface is similar to ** [sqlite3_config()] except that the changes apply to a single ** [database connection] (specified in the first argument). ** ** The second argument to sqlite3_db_config(D,V,...) is the ** [SQLITE_DBCONFIG_LOOKASIDE | configuration verb] - an integer code ** that indicates what aspect of the [database connection] is being configured. ** Subsequent arguments vary depending on the configuration verb. ** ** ^Calls to sqlite3_db_config() return SQLITE_OK if and only if ** the call is considered successful. */ SQLITE_API int sqlite3_db_config(sqlite3*, int op, ...); /* ** CAPI3REF: Memory Allocation Routines ** ** An instance of this object defines the interface between SQLite ** and low-level memory allocation routines. ** ** This object is used in only one place in the SQLite interface. ** A pointer to an instance of this object is the argument to ** [sqlite3_config()] when the configuration option is ** [SQLITE_CONFIG_MALLOC] or [SQLITE_CONFIG_GETMALLOC]. ** By creating an instance of this object ** and passing it to [sqlite3_config]([SQLITE_CONFIG_MALLOC]) ** during configuration, an application can specify an alternative ** memory allocation subsystem for SQLite to use for all of its ** dynamic memory needs. ** ** Note that SQLite comes with several [built-in memory allocators] ** that are perfectly adequate for the overwhelming majority of applications ** and that this object is only useful to a tiny minority of applications ** with specialized memory allocation requirements. This object is ** also used during testing of SQLite in order to specify an alternative ** memory allocator that simulates memory out-of-memory conditions in ** order to verify that SQLite recovers gracefully from such ** conditions. ** ** The xMalloc, xRealloc, and xFree methods must work like the ** malloc(), realloc() and free() functions from the standard C library. ** ^SQLite guarantees that the second argument to ** xRealloc is always a value returned by a prior call to xRoundup. ** ** xSize should return the allocated size of a memory allocation ** previously obtained from xMalloc or xRealloc. The allocated size ** is always at least as big as the requested size but may be larger. ** ** The xRoundup method returns what would be the allocated size of ** a memory allocation given a particular requested size. Most memory ** allocators round up memory allocations at least to the next multiple ** of 8. Some allocators round up to a larger multiple or to a power of 2. ** Every memory allocation request coming in through [sqlite3_malloc()] ** or [sqlite3_realloc()] first calls xRoundup. If xRoundup returns 0, ** that causes the corresponding memory allocation to fail. ** ** The xInit method initializes the memory allocator. For example, ** it might allocate any require mutexes or initialize internal data ** structures. The xShutdown method is invoked (indirectly) by ** [sqlite3_shutdown()] and should deallocate any resources acquired ** by xInit. The pAppData pointer is used as the only parameter to ** xInit and xShutdown. ** ** SQLite holds the [SQLITE_MUTEX_STATIC_MASTER] mutex when it invokes ** the xInit method, so the xInit method need not be threadsafe. The ** xShutdown method is only called from [sqlite3_shutdown()] so it does ** not need to be threadsafe either. For all other methods, SQLite ** holds the [SQLITE_MUTEX_STATIC_MEM] mutex as long as the ** [SQLITE_CONFIG_MEMSTATUS] configuration option is turned on (which ** it is by default) and so the methods are automatically serialized. ** However, if [SQLITE_CONFIG_MEMSTATUS] is disabled, then the other ** methods must be threadsafe or else make their own arrangements for ** serialization. ** ** SQLite will never invoke xInit() more than once without an intervening ** call to xShutdown(). */ typedef struct sqlite3_mem_methods sqlite3_mem_methods; struct sqlite3_mem_methods { void *(*xMalloc)(int); /* Memory allocation function */ void (*xFree)(void*); /* Free a prior allocation */ void *(*xRealloc)(void*,int); /* Resize an allocation */ int (*xSize)(void*); /* Return the size of an allocation */ int (*xRoundup)(int); /* Round up request size to allocation size */ int (*xInit)(void*); /* Initialize the memory allocator */ void (*xShutdown)(void*); /* Deinitialize the memory allocator */ void *pAppData; /* Argument to xInit() and xShutdown() */ }; /* ** CAPI3REF: Configuration Options ** KEYWORDS: {configuration option} ** ** These constants are the available integer configuration options that ** can be passed as the first argument to the [sqlite3_config()] interface. ** ** New configuration options may be added in future releases of SQLite. ** Existing configuration options might be discontinued. Applications ** should check the return code from [sqlite3_config()] to make sure that ** the call worked. The [sqlite3_config()] interface will return a ** non-zero [error code] if a discontinued or unsupported configuration option ** is invoked. ** **
** [[SQLITE_CONFIG_SINGLETHREAD]]
SQLITE_CONFIG_SINGLETHREAD
**
There are no arguments to this option. ^This option sets the ** [threading mode] to Single-thread. In other words, it disables ** all mutexing and puts SQLite into a mode where it can only be used ** by a single thread. ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** it is not possible to change the [threading mode] from its default ** value of Single-thread and so [sqlite3_config()] will return ** [SQLITE_ERROR] if called with the SQLITE_CONFIG_SINGLETHREAD ** configuration option.
** ** [[SQLITE_CONFIG_MULTITHREAD]]
SQLITE_CONFIG_MULTITHREAD
**
There are no arguments to this option. ^This option sets the ** [threading mode] to Multi-thread. In other words, it disables ** mutexing on [database connection] and [prepared statement] objects. ** The application is responsible for serializing access to ** [database connections] and [prepared statements]. But other mutexes ** are enabled so that SQLite will be safe to use in a multi-threaded ** environment as long as no two threads attempt to use the same ** [database connection] at the same time. ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** it is not possible to set the Multi-thread [threading mode] and ** [sqlite3_config()] will return [SQLITE_ERROR] if called with the ** SQLITE_CONFIG_MULTITHREAD configuration option.
** ** [[SQLITE_CONFIG_SERIALIZED]]
SQLITE_CONFIG_SERIALIZED
**
There are no arguments to this option. ^This option sets the ** [threading mode] to Serialized. In other words, this option enables ** all mutexes including the recursive ** mutexes on [database connection] and [prepared statement] objects. ** In this mode (which is the default when SQLite is compiled with ** [SQLITE_THREADSAFE=1]) the SQLite library will itself serialize access ** to [database connections] and [prepared statements] so that the ** application is free to use the same [database connection] or the ** same [prepared statement] in different threads at the same time. ** ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** it is not possible to set the Serialized [threading mode] and ** [sqlite3_config()] will return [SQLITE_ERROR] if called with the ** SQLITE_CONFIG_SERIALIZED configuration option.
** ** [[SQLITE_CONFIG_MALLOC]]
SQLITE_CONFIG_MALLOC
**
^(The SQLITE_CONFIG_MALLOC option takes a single argument which is ** a pointer to an instance of the [sqlite3_mem_methods] structure. ** The argument specifies ** alternative low-level memory allocation routines to be used in place of ** the memory allocation routines built into SQLite.)^ ^SQLite makes ** its own private copy of the content of the [sqlite3_mem_methods] structure ** before the [sqlite3_config()] call returns.
** ** [[SQLITE_CONFIG_GETMALLOC]]
SQLITE_CONFIG_GETMALLOC
**
^(The SQLITE_CONFIG_GETMALLOC option takes a single argument which ** is a pointer to an instance of the [sqlite3_mem_methods] structure. ** The [sqlite3_mem_methods] ** structure is filled with the currently defined memory allocation routines.)^ ** This option can be used to overload the default memory allocation ** routines with a wrapper that simulations memory allocation failure or ** tracks memory usage, for example.
** ** [[SQLITE_CONFIG_MEMSTATUS]]
SQLITE_CONFIG_MEMSTATUS
**
^The SQLITE_CONFIG_MEMSTATUS option takes single argument of type int, ** interpreted as a boolean, which enables or disables the collection of ** memory allocation statistics. ^(When memory allocation statistics are ** disabled, the following SQLite interfaces become non-operational: **
    **
  • [sqlite3_memory_used()] **
  • [sqlite3_memory_highwater()] **
  • [sqlite3_soft_heap_limit64()] **
  • [sqlite3_status64()] **
)^ ** ^Memory allocation statistics are enabled by default unless SQLite is ** compiled with [SQLITE_DEFAULT_MEMSTATUS]=0 in which case memory ** allocation statistics are disabled by default. **
** ** [[SQLITE_CONFIG_SCRATCH]]
SQLITE_CONFIG_SCRATCH
**
^The SQLITE_CONFIG_SCRATCH option specifies a static memory buffer ** that SQLite can use for scratch memory. ^(There are three arguments ** to SQLITE_CONFIG_SCRATCH: A pointer an 8-byte ** aligned memory buffer from which the scratch allocations will be ** drawn, the size of each scratch allocation (sz), ** and the maximum number of scratch allocations (N).)^ ** The first argument must be a pointer to an 8-byte aligned buffer ** of at least sz*N bytes of memory. ** ^SQLite will not use more than one scratch buffers per thread. ** ^SQLite will never request a scratch buffer that is more than 6 ** times the database page size. ** ^If SQLite needs needs additional ** scratch memory beyond what is provided by this configuration option, then ** [sqlite3_malloc()] will be used to obtain the memory needed.

** ^When the application provides any amount of scratch memory using ** SQLITE_CONFIG_SCRATCH, SQLite avoids unnecessary large ** [sqlite3_malloc|heap allocations]. ** This can help [Robson proof|prevent memory allocation failures] due to heap ** fragmentation in low-memory embedded systems. **

** ** [[SQLITE_CONFIG_PAGECACHE]]
SQLITE_CONFIG_PAGECACHE
**
^The SQLITE_CONFIG_PAGECACHE option specifies a memory pool ** that SQLite can use for the database page cache with the default page ** cache implementation. ** This configuration option is a no-op if an application-define page ** cache implementation is loaded using the [SQLITE_CONFIG_PCACHE2]. ** ^There are three arguments to SQLITE_CONFIG_PAGECACHE: A pointer to ** 8-byte aligned memory (pMem), the size of each page cache line (sz), ** and the number of cache lines (N). ** The sz argument should be the size of the largest database page ** (a power of two between 512 and 65536) plus some extra bytes for each ** page header. ^The number of extra bytes needed by the page header ** can be determined using [SQLITE_CONFIG_PCACHE_HDRSZ]. ** ^It is harmless, apart from the wasted memory, ** for the sz parameter to be larger than necessary. The pMem ** argument must be either a NULL pointer or a pointer to an 8-byte ** aligned block of memory of at least sz*N bytes, otherwise ** subsequent behavior is undefined. ** ^When pMem is not NULL, SQLite will strive to use the memory provided ** to satisfy page cache needs, falling back to [sqlite3_malloc()] if ** a page cache line is larger than sz bytes or if all of the pMem buffer ** is exhausted. ** ^If pMem is NULL and N is non-zero, then each database connection ** does an initial bulk allocation for page cache memory ** from [sqlite3_malloc()] sufficient for N cache lines if N is positive or ** of -1024*N bytes if N is negative, . ^If additional ** page cache memory is needed beyond what is provided by the initial ** allocation, then SQLite goes to [sqlite3_malloc()] separately for each ** additional cache line.
** ** [[SQLITE_CONFIG_HEAP]]
SQLITE_CONFIG_HEAP
**
^The SQLITE_CONFIG_HEAP option specifies a static memory buffer ** that SQLite will use for all of its dynamic memory allocation needs ** beyond those provided for by [SQLITE_CONFIG_SCRATCH] and ** [SQLITE_CONFIG_PAGECACHE]. ** ^The SQLITE_CONFIG_HEAP option is only available if SQLite is compiled ** with either [SQLITE_ENABLE_MEMSYS3] or [SQLITE_ENABLE_MEMSYS5] and returns ** [SQLITE_ERROR] if invoked otherwise. ** ^There are three arguments to SQLITE_CONFIG_HEAP: ** An 8-byte aligned pointer to the memory, ** the number of bytes in the memory buffer, and the minimum allocation size. ** ^If the first pointer (the memory pointer) is NULL, then SQLite reverts ** to using its default memory allocator (the system malloc() implementation), ** undoing any prior invocation of [SQLITE_CONFIG_MALLOC]. ^If the ** memory pointer is not NULL then the alternative memory ** allocator is engaged to handle all of SQLites memory allocation needs. ** The first pointer (the memory pointer) must be aligned to an 8-byte ** boundary or subsequent behavior of SQLite will be undefined. ** The minimum allocation size is capped at 2**12. Reasonable values ** for the minimum allocation size are 2**5 through 2**8.
** ** [[SQLITE_CONFIG_MUTEX]]
SQLITE_CONFIG_MUTEX
**
^(The SQLITE_CONFIG_MUTEX option takes a single argument which is a ** pointer to an instance of the [sqlite3_mutex_methods] structure. ** The argument specifies alternative low-level mutex routines to be used ** in place the mutex routines built into SQLite.)^ ^SQLite makes a copy of ** the content of the [sqlite3_mutex_methods] structure before the call to ** [sqlite3_config()] returns. ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** the entire mutexing subsystem is omitted from the build and hence calls to ** [sqlite3_config()] with the SQLITE_CONFIG_MUTEX configuration option will ** return [SQLITE_ERROR].
** ** [[SQLITE_CONFIG_GETMUTEX]]
SQLITE_CONFIG_GETMUTEX
**
^(The SQLITE_CONFIG_GETMUTEX option takes a single argument which ** is a pointer to an instance of the [sqlite3_mutex_methods] structure. The ** [sqlite3_mutex_methods] ** structure is filled with the currently defined mutex routines.)^ ** This option can be used to overload the default mutex allocation ** routines with a wrapper used to track mutex usage for performance ** profiling or testing, for example. ^If SQLite is compiled with ** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then ** the entire mutexing subsystem is omitted from the build and hence calls to ** [sqlite3_config()] with the SQLITE_CONFIG_GETMUTEX configuration option will ** return [SQLITE_ERROR].
** ** [[SQLITE_CONFIG_LOOKASIDE]]
SQLITE_CONFIG_LOOKASIDE
**
^(The SQLITE_CONFIG_LOOKASIDE option takes two arguments that determine ** the default size of lookaside memory on each [database connection]. ** The first argument is the ** size of each lookaside buffer slot and the second is the number of ** slots allocated to each database connection.)^ ^(SQLITE_CONFIG_LOOKASIDE ** sets the default lookaside size. The [SQLITE_DBCONFIG_LOOKASIDE] ** option to [sqlite3_db_config()] can be used to change the lookaside ** configuration on individual connections.)^
** ** [[SQLITE_CONFIG_PCACHE2]]
SQLITE_CONFIG_PCACHE2
**
^(The SQLITE_CONFIG_PCACHE2 option takes a single argument which is ** a pointer to an [sqlite3_pcache_methods2] object. This object specifies ** the interface to a custom page cache implementation.)^ ** ^SQLite makes a copy of the [sqlite3_pcache_methods2] object.
** ** [[SQLITE_CONFIG_GETPCACHE2]]
SQLITE_CONFIG_GETPCACHE2
**
^(The SQLITE_CONFIG_GETPCACHE2 option takes a single argument which ** is a pointer to an [sqlite3_pcache_methods2] object. SQLite copies of ** the current page cache implementation into that object.)^
** ** [[SQLITE_CONFIG_LOG]]
SQLITE_CONFIG_LOG
**
The SQLITE_CONFIG_LOG option is used to configure the SQLite ** global [error log]. ** (^The SQLITE_CONFIG_LOG option takes two arguments: a pointer to a ** function with a call signature of void(*)(void*,int,const char*), ** and a pointer to void. ^If the function pointer is not NULL, it is ** invoked by [sqlite3_log()] to process each logging event. ^If the ** function pointer is NULL, the [sqlite3_log()] interface becomes a no-op. ** ^The void pointer that is the second argument to SQLITE_CONFIG_LOG is ** passed through as the first parameter to the application-defined logger ** function whenever that function is invoked. ^The second parameter to ** the logger function is a copy of the first parameter to the corresponding ** [sqlite3_log()] call and is intended to be a [result code] or an ** [extended result code]. ^The third parameter passed to the logger is ** log message after formatting via [sqlite3_snprintf()]. ** The SQLite logging interface is not reentrant; the logger function ** supplied by the application must not invoke any SQLite interface. ** In a multi-threaded application, the application-defined logger ** function must be threadsafe.
** ** [[SQLITE_CONFIG_URI]]
SQLITE_CONFIG_URI **
^(The SQLITE_CONFIG_URI option takes a single argument of type int. ** If non-zero, then URI handling is globally enabled. If the parameter is zero, ** then URI handling is globally disabled.)^ ^If URI handling is globally ** enabled, all filenames passed to [sqlite3_open()], [sqlite3_open_v2()], ** [sqlite3_open16()] or ** specified as part of [ATTACH] commands are interpreted as URIs, regardless ** of whether or not the [SQLITE_OPEN_URI] flag is set when the database ** connection is opened. ^If it is globally disabled, filenames are ** only interpreted as URIs if the SQLITE_OPEN_URI flag is set when the ** database connection is opened. ^(By default, URI handling is globally ** disabled. The default value may be changed by compiling with the ** [SQLITE_USE_URI] symbol defined.)^ ** ** [[SQLITE_CONFIG_COVERING_INDEX_SCAN]]
SQLITE_CONFIG_COVERING_INDEX_SCAN **
^The SQLITE_CONFIG_COVERING_INDEX_SCAN option takes a single integer ** argument which is interpreted as a boolean in order to enable or disable ** the use of covering indices for full table scans in the query optimizer. ** ^The default setting is determined ** by the [SQLITE_ALLOW_COVERING_INDEX_SCAN] compile-time option, or is "on" ** if that compile-time option is omitted. ** The ability to disable the use of covering indices for full table scans ** is because some incorrectly coded legacy applications might malfunction ** when the optimization is enabled. Providing the ability to ** disable the optimization allows the older, buggy application code to work ** without change even with newer versions of SQLite. ** ** [[SQLITE_CONFIG_PCACHE]] [[SQLITE_CONFIG_GETPCACHE]] **
SQLITE_CONFIG_PCACHE and SQLITE_CONFIG_GETPCACHE **
These options are obsolete and should not be used by new code. ** They are retained for backwards compatibility but are now no-ops. **
** ** [[SQLITE_CONFIG_SQLLOG]] **
SQLITE_CONFIG_SQLLOG **
This option is only available if sqlite is compiled with the ** [SQLITE_ENABLE_SQLLOG] pre-processor macro defined. The first argument should ** be a pointer to a function of type void(*)(void*,sqlite3*,const char*, int). ** The second should be of type (void*). The callback is invoked by the library ** in three separate circumstances, identified by the value passed as the ** fourth parameter. If the fourth parameter is 0, then the database connection ** passed as the second argument has just been opened. The third argument ** points to a buffer containing the name of the main database file. If the ** fourth parameter is 1, then the SQL statement that the third parameter ** points to has just been executed. Or, if the fourth parameter is 2, then ** the connection being passed as the second parameter is being closed. The ** third parameter is passed NULL In this case. An example of using this ** configuration option can be seen in the "test_sqllog.c" source file in ** the canonical SQLite source tree.
** ** [[SQLITE_CONFIG_MMAP_SIZE]] **
SQLITE_CONFIG_MMAP_SIZE **
^SQLITE_CONFIG_MMAP_SIZE takes two 64-bit integer (sqlite3_int64) values ** that are the default mmap size limit (the default setting for ** [PRAGMA mmap_size]) and the maximum allowed mmap size limit. ** ^The default setting can be overridden by each database connection using ** either the [PRAGMA mmap_size] command, or by using the ** [SQLITE_FCNTL_MMAP_SIZE] file control. ^(The maximum allowed mmap size ** will be silently truncated if necessary so that it does not exceed the ** compile-time maximum mmap size set by the ** [SQLITE_MAX_MMAP_SIZE] compile-time option.)^ ** ^If either argument to this option is negative, then that argument is ** changed to its compile-time default. ** ** [[SQLITE_CONFIG_WIN32_HEAPSIZE]] **
SQLITE_CONFIG_WIN32_HEAPSIZE **
^The SQLITE_CONFIG_WIN32_HEAPSIZE option is only available if SQLite is ** compiled for Windows with the [SQLITE_WIN32_MALLOC] pre-processor macro ** defined. ^SQLITE_CONFIG_WIN32_HEAPSIZE takes a 32-bit unsigned integer value ** that specifies the maximum size of the created heap. ** ** [[SQLITE_CONFIG_PCACHE_HDRSZ]] **
SQLITE_CONFIG_PCACHE_HDRSZ **
^The SQLITE_CONFIG_PCACHE_HDRSZ option takes a single parameter which ** is a pointer to an integer and writes into that integer the number of extra ** bytes per page required for each page in [SQLITE_CONFIG_PAGECACHE]. ** The amount of extra space required can change depending on the compiler, ** target platform, and SQLite version. ** ** [[SQLITE_CONFIG_PMASZ]] **
SQLITE_CONFIG_PMASZ **
^The SQLITE_CONFIG_PMASZ option takes a single parameter which ** is an unsigned integer and sets the "Minimum PMA Size" for the multithreaded ** sorter to that integer. The default minimum PMA Size is set by the ** [SQLITE_SORTER_PMASZ] compile-time option. New threads are launched ** to help with sort operations when multithreaded sorting ** is enabled (using the [PRAGMA threads] command) and the amount of content ** to be sorted exceeds the page size times the minimum of the ** [PRAGMA cache_size] setting and this value. ** ** [[SQLITE_CONFIG_STMTJRNL_SPILL]] **
SQLITE_CONFIG_STMTJRNL_SPILL **
^The SQLITE_CONFIG_STMTJRNL_SPILL option takes a single parameter which ** becomes the [statement journal] spill-to-disk threshold. ** [Statement journals] are held in memory until their size (in bytes) ** exceeds this threshold, at which point they are written to disk. ** Or if the threshold is -1, statement journals are always held ** exclusively in memory. ** Since many statement journals never become large, setting the spill ** threshold to a value such as 64KiB can greatly reduce the amount of ** I/O required to support statement rollback. ** The default value for this setting is controlled by the ** [SQLITE_STMTJRNL_SPILL] compile-time option. **
*/ #define SQLITE_CONFIG_SINGLETHREAD 1 /* nil */ #define SQLITE_CONFIG_MULTITHREAD 2 /* nil */ #define SQLITE_CONFIG_SERIALIZED 3 /* nil */ #define SQLITE_CONFIG_MALLOC 4 /* sqlite3_mem_methods* */ #define SQLITE_CONFIG_GETMALLOC 5 /* sqlite3_mem_methods* */ #define SQLITE_CONFIG_SCRATCH 6 /* void*, int sz, int N */ #define SQLITE_CONFIG_PAGECACHE 7 /* void*, int sz, int N */ #define SQLITE_CONFIG_HEAP 8 /* void*, int nByte, int min */ #define SQLITE_CONFIG_MEMSTATUS 9 /* boolean */ #define SQLITE_CONFIG_MUTEX 10 /* sqlite3_mutex_methods* */ #define SQLITE_CONFIG_GETMUTEX 11 /* sqlite3_mutex_methods* */ /* previously SQLITE_CONFIG_CHUNKALLOC 12 which is now unused. */ #define SQLITE_CONFIG_LOOKASIDE 13 /* int int */ #define SQLITE_CONFIG_PCACHE 14 /* no-op */ #define SQLITE_CONFIG_GETPCACHE 15 /* no-op */ #define SQLITE_CONFIG_LOG 16 /* xFunc, void* */ #define SQLITE_CONFIG_URI 17 /* int */ #define SQLITE_CONFIG_PCACHE2 18 /* sqlite3_pcache_methods2* */ #define SQLITE_CONFIG_GETPCACHE2 19 /* sqlite3_pcache_methods2* */ #define SQLITE_CONFIG_COVERING_INDEX_SCAN 20 /* int */ #define SQLITE_CONFIG_SQLLOG 21 /* xSqllog, void* */ #define SQLITE_CONFIG_MMAP_SIZE 22 /* sqlite3_int64, sqlite3_int64 */ #define SQLITE_CONFIG_WIN32_HEAPSIZE 23 /* int nByte */ #define SQLITE_CONFIG_PCACHE_HDRSZ 24 /* int *psz */ #define SQLITE_CONFIG_PMASZ 25 /* unsigned int szPma */ #define SQLITE_CONFIG_STMTJRNL_SPILL 26 /* int nByte */ /* ** CAPI3REF: Database Connection Configuration Options ** ** These constants are the available integer configuration options that ** can be passed as the second argument to the [sqlite3_db_config()] interface. ** ** New configuration options may be added in future releases of SQLite. ** Existing configuration options might be discontinued. Applications ** should check the return code from [sqlite3_db_config()] to make sure that ** the call worked. ^The [sqlite3_db_config()] interface will return a ** non-zero [error code] if a discontinued or unsupported configuration option ** is invoked. ** **
**
SQLITE_DBCONFIG_LOOKASIDE
**
^This option takes three additional arguments that determine the ** [lookaside memory allocator] configuration for the [database connection]. ** ^The first argument (the third parameter to [sqlite3_db_config()] is a ** pointer to a memory buffer to use for lookaside memory. ** ^The first argument after the SQLITE_DBCONFIG_LOOKASIDE verb ** may be NULL in which case SQLite will allocate the ** lookaside buffer itself using [sqlite3_malloc()]. ^The second argument is the ** size of each lookaside buffer slot. ^The third argument is the number of ** slots. The size of the buffer in the first argument must be greater than ** or equal to the product of the second and third arguments. The buffer ** must be aligned to an 8-byte boundary. ^If the second argument to ** SQLITE_DBCONFIG_LOOKASIDE is not a multiple of 8, it is internally ** rounded down to the next smaller multiple of 8. ^(The lookaside memory ** configuration for a database connection can only be changed when that ** connection is not currently using lookaside memory, or in other words ** when the "current value" returned by ** [sqlite3_db_status](D,[SQLITE_CONFIG_LOOKASIDE],...) is zero. ** Any attempt to change the lookaside memory configuration when lookaside ** memory is in use leaves the configuration unchanged and returns ** [SQLITE_BUSY].)^
** **
SQLITE_DBCONFIG_ENABLE_FKEY
**
^This option is used to enable or disable the enforcement of ** [foreign key constraints]. There should be two additional arguments. ** The first argument is an integer which is 0 to disable FK enforcement, ** positive to enable FK enforcement or negative to leave FK enforcement ** unchanged. The second parameter is a pointer to an integer into which ** is written 0 or 1 to indicate whether FK enforcement is off or on ** following this call. The second parameter may be a NULL pointer, in ** which case the FK enforcement setting is not reported back.
** **
SQLITE_DBCONFIG_ENABLE_TRIGGER
**
^This option is used to enable or disable [CREATE TRIGGER | triggers]. ** There should be two additional arguments. ** The first argument is an integer which is 0 to disable triggers, ** positive to enable triggers or negative to leave the setting unchanged. ** The second parameter is a pointer to an integer into which ** is written 0 or 1 to indicate whether triggers are disabled or enabled ** following this call. The second parameter may be a NULL pointer, in ** which case the trigger setting is not reported back.
** **
SQLITE_DBCONFIG_ENABLE_FTS3_TOKENIZER
**
^This option is used to enable or disable the two-argument ** version of the [fts3_tokenizer()] function which is part of the ** [FTS3] full-text search engine extension. ** There should be two additional arguments. ** The first argument is an integer which is 0 to disable fts3_tokenizer() or ** positive to enable fts3_tokenizer() or negative to leave the setting ** unchanged. ** The second parameter is a pointer to an integer into which ** is written 0 or 1 to indicate whether fts3_tokenizer is disabled or enabled ** following this call. The second parameter may be a NULL pointer, in ** which case the new setting is not reported back.
** **
SQLITE_DBCONFIG_ENABLE_LOAD_EXTENSION
**
^This option is used to enable or disable the [sqlite3_load_extension()] ** interface independently of the [load_extension()] SQL function. ** The [sqlite3_enable_load_extension()] API enables or disables both the ** C-API [sqlite3_load_extension()] and the SQL function [load_extension()]. ** There should be two additional arguments. ** When the first argument to this interface is 1, then only the C-API is ** enabled and the SQL function remains disabled. If the first argument to ** this interface is 0, then both the C-API and the SQL function are disabled. ** If the first argument is -1, then no changes are made to state of either the ** C-API or the SQL function. ** The second parameter is a pointer to an integer into which ** is written 0 or 1 to indicate whether [sqlite3_load_extension()] interface ** is disabled or enabled following this call. The second parameter may ** be a NULL pointer, in which case the new setting is not reported back. **
** **
SQLITE_DBCONFIG_MAINDBNAME
**
^This option is used to change the name of the "main" database ** schema. ^The sole argument is a pointer to a constant UTF8 string ** which will become the new schema name in place of "main". ^SQLite ** does not make a copy of the new main schema name string, so the application ** must ensure that the argument passed into this DBCONFIG option is unchanged ** until after the database connection closes. **
** **
SQLITE_DBCONFIG_NO_CKPT_ON_CLOSE
**
Usually, when a database in wal mode is closed or detached from a ** database handle, SQLite checks if this will mean that there are now no ** connections at all to the database. If so, it performs a checkpoint ** operation before closing the connection. This option may be used to ** override this behaviour. The first parameter passed to this operation ** is an integer - non-zero to disable checkpoints-on-close, or zero (the ** default) to enable them. The second parameter is a pointer to an integer ** into which is written 0 or 1 to indicate whether checkpoints-on-close ** have been disabled - 0 if they are not disabled, 1 if they are. **
** **
SQLITE_DBCONFIG_ENABLE_QPSG
**
^(The SQLITE_DBCONFIG_ENABLE_QPSG option activates or deactivates ** the [query planner stability guarantee] (QPSG). When the QPSG is active, ** a single SQL query statement will always use the same algorithm regardless ** of values of [bound parameters].)^ The QPSG disables some query optimizations ** that look at the values of bound parameters, which can make some queries ** slower. But the QPSG has the advantage of more predictable behavior. With ** the QPSG active, SQLite will always use the same query plan in the field as ** was used during testing in the lab. **
** **
*/ #define SQLITE_DBCONFIG_MAINDBNAME 1000 /* const char* */ #define SQLITE_DBCONFIG_LOOKASIDE 1001 /* void* int int */ #define SQLITE_DBCONFIG_ENABLE_FKEY 1002 /* int int* */ #define SQLITE_DBCONFIG_ENABLE_TRIGGER 1003 /* int int* */ #define SQLITE_DBCONFIG_ENABLE_FTS3_TOKENIZER 1004 /* int int* */ #define SQLITE_DBCONFIG_ENABLE_LOAD_EXTENSION 1005 /* int int* */ #define SQLITE_DBCONFIG_NO_CKPT_ON_CLOSE 1006 /* int int* */ #define SQLITE_DBCONFIG_ENABLE_QPSG 1007 /* int int* */ /* ** CAPI3REF: Enable Or Disable Extended Result Codes ** METHOD: sqlite3 ** ** ^The sqlite3_extended_result_codes() routine enables or disables the ** [extended result codes] feature of SQLite. ^The extended result ** codes are disabled by default for historical compatibility. */ SQLITE_API int sqlite3_extended_result_codes(sqlite3*, int onoff); /* ** CAPI3REF: Last Insert Rowid ** METHOD: sqlite3 ** ** ^Each entry in most SQLite tables (except for [WITHOUT ROWID] tables) ** has a unique 64-bit signed ** integer key called the [ROWID | "rowid"]. ^The rowid is always available ** as an undeclared column named ROWID, OID, or _ROWID_ as long as those ** names are not also used by explicitly declared columns. ^If ** the table has a column of type [INTEGER PRIMARY KEY] then that column ** is another alias for the rowid. ** ** ^The sqlite3_last_insert_rowid(D) interface usually returns the [rowid] of ** the most recent successful [INSERT] into a rowid table or [virtual table] ** on database connection D. ^Inserts into [WITHOUT ROWID] tables are not ** recorded. ^If no successful [INSERT]s into rowid tables have ever occurred ** on the database connection D, then sqlite3_last_insert_rowid(D) returns ** zero. ** ** As well as being set automatically as rows are inserted into database ** tables, the value returned by this function may be set explicitly by ** [sqlite3_set_last_insert_rowid()] ** ** Some virtual table implementations may INSERT rows into rowid tables as ** part of committing a transaction (e.g. to flush data accumulated in memory ** to disk). In this case subsequent calls to this function return the rowid ** associated with these internal INSERT operations, which leads to ** unintuitive results. Virtual table implementations that do write to rowid ** tables in this way can avoid this problem by restoring the original ** rowid value using [sqlite3_set_last_insert_rowid()] before returning ** control to the user. ** ** ^(If an [INSERT] occurs within a trigger then this routine will ** return the [rowid] of the inserted row as long as the trigger is ** running. Once the trigger program ends, the value returned ** by this routine reverts to what it was before the trigger was fired.)^ ** ** ^An [INSERT] that fails due to a constraint violation is not a ** successful [INSERT] and does not change the value returned by this ** routine. ^Thus INSERT OR FAIL, INSERT OR IGNORE, INSERT OR ROLLBACK, ** and INSERT OR ABORT make no changes to the return value of this ** routine when their insertion fails. ^(When INSERT OR REPLACE ** encounters a constraint violation, it does not fail. The ** INSERT continues to completion after deleting rows that caused ** the constraint problem so INSERT OR REPLACE will always change ** the return value of this interface.)^ ** ** ^For the purposes of this routine, an [INSERT] is considered to ** be successful even if it is subsequently rolled back. ** ** This function is accessible to SQL statements via the ** [last_insert_rowid() SQL function]. ** ** If a separate thread performs a new [INSERT] on the same ** database connection while the [sqlite3_last_insert_rowid()] ** function is running and thus changes the last insert [rowid], ** then the value returned by [sqlite3_last_insert_rowid()] is ** unpredictable and might not equal either the old or the new ** last insert [rowid]. */ SQLITE_API sqlite3_int64 sqlite3_last_insert_rowid(sqlite3*); /* ** CAPI3REF: Set the Last Insert Rowid value. ** METHOD: sqlite3 ** ** The sqlite3_set_last_insert_rowid(D, R) method allows the application to ** set the value returned by calling sqlite3_last_insert_rowid(D) to R ** without inserting a row into the database. */ SQLITE_API void sqlite3_set_last_insert_rowid(sqlite3*,sqlite3_int64); /* ** CAPI3REF: Count The Number Of Rows Modified ** METHOD: sqlite3 ** ** ^This function returns the number of rows modified, inserted or ** deleted by the most recently completed INSERT, UPDATE or DELETE ** statement on the database connection specified by the only parameter. ** ^Executing any other type of SQL statement does not modify the value ** returned by this function. ** ** ^Only changes made directly by the INSERT, UPDATE or DELETE statement are ** considered - auxiliary changes caused by [CREATE TRIGGER | triggers], ** [foreign key actions] or [REPLACE] constraint resolution are not counted. ** ** Changes to a view that are intercepted by ** [INSTEAD OF trigger | INSTEAD OF triggers] are not counted. ^The value ** returned by sqlite3_changes() immediately after an INSERT, UPDATE or ** DELETE statement run on a view is always zero. Only changes made to real ** tables are counted. ** ** Things are more complicated if the sqlite3_changes() function is ** executed while a trigger program is running. This may happen if the ** program uses the [changes() SQL function], or if some other callback ** function invokes sqlite3_changes() directly. Essentially: ** **
    **
  • ^(Before entering a trigger program the value returned by ** sqlite3_changes() function is saved. After the trigger program ** has finished, the original value is restored.)^ ** **
  • ^(Within a trigger program each INSERT, UPDATE and DELETE ** statement sets the value returned by sqlite3_changes() ** upon completion as normal. Of course, this value will not include ** any changes performed by sub-triggers, as the sqlite3_changes() ** value will be saved and restored after each sub-trigger has run.)^ **
** ** ^This means that if the changes() SQL function (or similar) is used ** by the first INSERT, UPDATE or DELETE statement within a trigger, it ** returns the value as set when the calling statement began executing. ** ^If it is used by the second or subsequent such statement within a trigger ** program, the value returned reflects the number of rows modified by the ** previous INSERT, UPDATE or DELETE statement within the same trigger. ** ** See also the [sqlite3_total_changes()] interface, the ** [count_changes pragma], and the [changes() SQL function]. ** ** If a separate thread makes changes on the same database connection ** while [sqlite3_changes()] is running then the value returned ** is unpredictable and not meaningful. */ SQLITE_API int sqlite3_changes(sqlite3*); /* ** CAPI3REF: Total Number Of Rows Modified ** METHOD: sqlite3 ** ** ^This function returns the total number of rows inserted, modified or ** deleted by all [INSERT], [UPDATE] or [DELETE] statements completed ** since the database connection was opened, including those executed as ** part of trigger programs. ^Executing any other type of SQL statement ** does not affect the value returned by sqlite3_total_changes(). ** ** ^Changes made as part of [foreign key actions] are included in the ** count, but those made as part of REPLACE constraint resolution are ** not. ^Changes to a view that are intercepted by INSTEAD OF triggers ** are not counted. ** ** See also the [sqlite3_changes()] interface, the ** [count_changes pragma], and the [total_changes() SQL function]. ** ** If a separate thread makes changes on the same database connection ** while [sqlite3_total_changes()] is running then the value ** returned is unpredictable and not meaningful. */ SQLITE_API int sqlite3_total_changes(sqlite3*); /* ** CAPI3REF: Interrupt A Long-Running Query ** METHOD: sqlite3 ** ** ^This function causes any pending database operation to abort and ** return at its earliest opportunity. This routine is typically ** called in response to a user action such as pressing "Cancel" ** or Ctrl-C where the user wants a long query operation to halt ** immediately. ** ** ^It is safe to call this routine from a thread different from the ** thread that is currently running the database operation. But it ** is not safe to call this routine with a [database connection] that ** is closed or might close before sqlite3_interrupt() returns. ** ** ^If an SQL operation is very nearly finished at the time when ** sqlite3_interrupt() is called, then it might not have an opportunity ** to be interrupted and might continue to completion. ** ** ^An SQL operation that is interrupted will return [SQLITE_INTERRUPT]. ** ^If the interrupted SQL operation is an INSERT, UPDATE, or DELETE ** that is inside an explicit transaction, then the entire transaction ** will be rolled back automatically. ** ** ^The sqlite3_interrupt(D) call is in effect until all currently running ** SQL statements on [database connection] D complete. ^Any new SQL statements ** that are started after the sqlite3_interrupt() call and before the ** running statements reaches zero are interrupted as if they had been ** running prior to the sqlite3_interrupt() call. ^New SQL statements ** that are started after the running statement count reaches zero are ** not effected by the sqlite3_interrupt(). ** ^A call to sqlite3_interrupt(D) that occurs when there are no running ** SQL statements is a no-op and has no effect on SQL statements ** that are started after the sqlite3_interrupt() call returns. */ SQLITE_API void sqlite3_interrupt(sqlite3*); /* ** CAPI3REF: Determine If An SQL Statement Is Complete ** ** These routines are useful during command-line input to determine if the ** currently entered text seems to form a complete SQL statement or ** if additional input is needed before sending the text into ** SQLite for parsing. ^These routines return 1 if the input string ** appears to be a complete SQL statement. ^A statement is judged to be ** complete if it ends with a semicolon token and is not a prefix of a ** well-formed CREATE TRIGGER statement. ^Semicolons that are embedded within ** string literals or quoted identifier names or comments are not ** independent tokens (they are part of the token in which they are ** embedded) and thus do not count as a statement terminator. ^Whitespace ** and comments that follow the final semicolon are ignored. ** ** ^These routines return 0 if the statement is incomplete. ^If a ** memory allocation fails, then SQLITE_NOMEM is returned. ** ** ^These routines do not parse the SQL statements thus ** will not detect syntactically incorrect SQL. ** ** ^(If SQLite has not been initialized using [sqlite3_initialize()] prior ** to invoking sqlite3_complete16() then sqlite3_initialize() is invoked ** automatically by sqlite3_complete16(). If that initialization fails, ** then the return value from sqlite3_complete16() will be non-zero ** regardless of whether or not the input SQL is complete.)^ ** ** The input to [sqlite3_complete()] must be a zero-terminated ** UTF-8 string. ** ** The input to [sqlite3_complete16()] must be a zero-terminated ** UTF-16 string in native byte order. */ SQLITE_API int sqlite3_complete(const char *sql); SQLITE_API int sqlite3_complete16(const void *sql); /* ** CAPI3REF: Register A Callback To Handle SQLITE_BUSY Errors ** KEYWORDS: {busy-handler callback} {busy handler} ** METHOD: sqlite3 ** ** ^The sqlite3_busy_handler(D,X,P) routine sets a callback function X ** that might be invoked with argument P whenever ** an attempt is made to access a database table associated with ** [database connection] D when another thread ** or process has the table locked. ** The sqlite3_busy_handler() interface is used to implement ** [sqlite3_busy_timeout()] and [PRAGMA busy_timeout]. ** ** ^If the busy callback is NULL, then [SQLITE_BUSY] ** is returned immediately upon encountering the lock. ^If the busy callback ** is not NULL, then the callback might be invoked with two arguments. ** ** ^The first argument to the busy handler is a copy of the void* pointer which ** is the third argument to sqlite3_busy_handler(). ^The second argument to ** the busy handler callback is the number of times that the busy handler has ** been invoked previously for the same locking event. ^If the ** busy callback returns 0, then no additional attempts are made to ** access the database and [SQLITE_BUSY] is returned ** to the application. ** ^If the callback returns non-zero, then another attempt ** is made to access the database and the cycle repeats. ** ** The presence of a busy handler does not guarantee that it will be invoked ** when there is lock contention. ^If SQLite determines that invoking the busy ** handler could result in a deadlock, it will go ahead and return [SQLITE_BUSY] ** to the application instead of invoking the ** busy handler. ** Consider a scenario where one process is holding a read lock that ** it is trying to promote to a reserved lock and ** a second process is holding a reserved lock that it is trying ** to promote to an exclusive lock. The first process cannot proceed ** because it is blocked by the second and the second process cannot ** proceed because it is blocked by the first. If both processes ** invoke the busy handlers, neither will make any progress. Therefore, ** SQLite returns [SQLITE_BUSY] for the first process, hoping that this ** will induce the first process to release its read lock and allow ** the second process to proceed. ** ** ^The default busy callback is NULL. ** ** ^(There can only be a single busy handler defined for each ** [database connection]. Setting a new busy handler clears any ** previously set handler.)^ ^Note that calling [sqlite3_busy_timeout()] ** or evaluating [PRAGMA busy_timeout=N] will change the ** busy handler and thus clear any previously set busy handler. ** ** The busy callback should not take any actions which modify the ** database connection that invoked the busy handler. In other words, ** the busy handler is not reentrant. Any such actions ** result in undefined behavior. ** ** A busy handler must not close the database connection ** or [prepared statement] that invoked the busy handler. */ SQLITE_API int sqlite3_busy_handler(sqlite3*,int(*)(void*,int),void*); /* ** CAPI3REF: Set A Busy Timeout ** METHOD: sqlite3 ** ** ^This routine sets a [sqlite3_busy_handler | busy handler] that sleeps ** for a specified amount of time when a table is locked. ^The handler ** will sleep multiple times until at least "ms" milliseconds of sleeping ** have accumulated. ^After at least "ms" milliseconds of sleeping, ** the handler returns 0 which causes [sqlite3_step()] to return ** [SQLITE_BUSY]. ** ** ^Calling this routine with an argument less than or equal to zero ** turns off all busy handlers. ** ** ^(There can only be a single busy handler for a particular ** [database connection] at any given moment. If another busy handler ** was defined (using [sqlite3_busy_handler()]) prior to calling ** this routine, that other busy handler is cleared.)^ ** ** See also: [PRAGMA busy_timeout] */ SQLITE_API int sqlite3_busy_timeout(sqlite3*, int ms); /* ** CAPI3REF: Convenience Routines For Running Queries ** METHOD: sqlite3 ** ** This is a legacy interface that is preserved for backwards compatibility. ** Use of this interface is not recommended. ** ** Definition: A result table is memory data structure created by the ** [sqlite3_get_table()] interface. A result table records the ** complete query results from one or more queries. ** ** The table conceptually has a number of rows and columns. But ** these numbers are not part of the result table itself. These ** numbers are obtained separately. Let N be the number of rows ** and M be the number of columns. ** ** A result table is an array of pointers to zero-terminated UTF-8 strings. ** There are (N+1)*M elements in the array. The first M pointers point ** to zero-terminated strings that contain the names of the columns. ** The remaining entries all point to query results. NULL values result ** in NULL pointers. All other values are in their UTF-8 zero-terminated ** string representation as returned by [sqlite3_column_text()]. ** ** A result table might consist of one or more memory allocations. ** It is not safe to pass a result table directly to [sqlite3_free()]. ** A result table should be deallocated using [sqlite3_free_table()]. ** ** ^(As an example of the result table format, suppose a query result ** is as follows: ** ** 
**        Name        | Age
**        -----------------------
**        Alice       | 43
**        Bob         | 28
**        Cindy       | 21
**
** ** There are two column (M==2) and three rows (N==3). Thus the ** result table has 8 entries. Suppose the result table is stored ** in an array names azResult. Then azResult holds this content: ** ** 
**        azResult[0] = "Name";
**        azResult[1] = "Age";
**        azResult[2] = "Alice";
**        azResult[3] = "43";
**        azResult[4] = "Bob";
**        azResult[5] = "28";
**        azResult[6] = "Cindy";
**        azResult[7] = "21";
**
)^ ** ** ^The sqlite3_get_table() function evaluates one or more ** semicolon-separated SQL statements in the zero-terminated UTF-8 ** string of its 2nd parameter and returns a result table to the ** pointer given in its 3rd parameter. ** ** After the application has finished with the result from sqlite3_get_table(), ** it must pass the result table pointer to sqlite3_free_table() in order to ** release the memory that was malloced. Because of the way the ** [sqlite3_malloc()] happens within sqlite3_get_table(), the calling ** function must not try to call [sqlite3_free()] directly. Only ** [sqlite3_free_table()] is able to release the memory properly and safely. ** ** The sqlite3_get_table() interface is implemented as a wrapper around ** [sqlite3_exec()]. The sqlite3_get_table() routine does not have access ** to any internal data structures of SQLite. It uses only the public ** interface defined here. As a consequence, errors that occur in the ** wrapper layer outside of the internal [sqlite3_exec()] call are not ** reflected in subsequent calls to [sqlite3_errcode()] or ** [sqlite3_errmsg()]. */ SQLITE_API int sqlite3_get_table( sqlite3 *db, /* An open database */ const char *zSql, /* SQL to be evaluated */ char ***pazResult, /* Results of the query */ int *pnRow, /* Number of result rows written here */ int *pnColumn, /* Number of result columns written here */ char **pzErrmsg /* Error msg written here */ ); SQLITE_API void sqlite3_free_table(char **result); /* ** CAPI3REF: Formatted String Printing Functions ** ** These routines are work-alikes of the "printf()" family of functions ** from the standard C library. ** These routines understand most of the common K&R formatting options, ** plus some additional non-standard formats, detailed below. ** Note that some of the more obscure formatting options from recent ** C-library standards are omitted from this implementation. ** ** ^The sqlite3_mprintf() and sqlite3_vmprintf() routines write their ** results into memory obtained from [sqlite3_malloc()]. ** The strings returned by these two routines should be ** released by [sqlite3_free()]. ^Both routines return a ** NULL pointer if [sqlite3_malloc()] is unable to allocate enough ** memory to hold the resulting string. ** ** ^(The sqlite3_snprintf() routine is similar to "snprintf()" from ** the standard C library. The result is written into the ** buffer supplied as the second parameter whose size is given by ** the first parameter. Note that the order of the ** first two parameters is reversed from snprintf().)^ This is an ** historical accident that cannot be fixed without breaking ** backwards compatibility. ^(Note also that sqlite3_snprintf() ** returns a pointer to its buffer instead of the number of ** characters actually written into the buffer.)^ We admit that ** the number of characters written would be a more useful return ** value but we cannot change the implementation of sqlite3_snprintf() ** now without breaking compatibility. ** ** ^As long as the buffer size is greater than zero, sqlite3_snprintf() ** guarantees that the buffer is always zero-terminated. ^The first ** parameter "n" is the total size of the buffer, including space for ** the zero terminator. So the longest string that can be completely ** written will be n-1 characters. ** ** ^The sqlite3_vsnprintf() routine is a varargs version of sqlite3_snprintf(). ** ** These routines all implement some additional formatting ** options that are useful for constructing SQL statements. ** All of the usual printf() formatting options apply. In addition, there ** is are "%q", "%Q", "%w" and "%z" options. ** ** ^(The %q option works like %s in that it substitutes a nul-terminated ** string from the argument list. But %q also doubles every '\'' character. ** %q is designed for use inside a string literal.)^ By doubling each '\'' ** character it escapes that character and allows it to be inserted into ** the string. ** ** For example, assume the string variable zText contains text as follows: ** ** 
**  char *zText = "It's a happy day!";
**
** ** One can use this text in an SQL statement as follows: ** ** 
**  char *zSQL = sqlite3_mprintf("INSERT INTO table VALUES('%q')", zText);
**  sqlite3_exec(db, zSQL, 0, 0, 0);
**  sqlite3_free(zSQL);
**
** ** Because the %q format string is used, the '\'' character in zText ** is escaped and the SQL generated is as follows: ** ** 
**  INSERT INTO table1 VALUES('It''s a happy day!')
**
** ** This is correct. Had we used %s instead of %q, the generated SQL ** would have looked like this: ** ** 
**  INSERT INTO table1 VALUES('It's a happy day!');
**
** ** This second example is an SQL syntax error. As a general rule you should ** always use %q instead of %s when inserting text into a string literal. ** ** ^(The %Q option works like %q except it also adds single quotes around ** the outside of the total string. Additionally, if the parameter in the ** argument list is a NULL pointer, %Q substitutes the text "NULL" (without ** single quotes).)^ So, for example, one could say: ** ** 
**  char *zSQL = sqlite3_mprintf("INSERT INTO table VALUES(%Q)", zText);
**  sqlite3_exec(db, zSQL, 0, 0, 0);
**  sqlite3_free(zSQL);
**
** ** The code above will render a correct SQL statement in the zSQL ** variable even if the zText variable is a NULL pointer. ** ** ^(The "%w" formatting option is like "%q" except that it expects to ** be contained within double-quotes instead of single quotes, and it ** escapes the double-quote character instead of the single-quote ** character.)^ The "%w" formatting option is intended for safely inserting ** table and column names into a constructed SQL statement. ** ** ^(The "%z" formatting option works like "%s" but with the ** addition that after the string has been read and copied into ** the result, [sqlite3_free()] is called on the input string.)^ */ SQLITE_API char *sqlite3_mprintf(const char*,...); SQLITE_API char *sqlite3_vmprintf(const char*, va_list); SQLITE_API char *sqlite3_snprintf(int,char*,const char*, ...); SQLITE_API char *sqlite3_vsnprintf(int,char*,const char*, va_list); /* ** CAPI3REF: Memory Allocation Subsystem ** ** The SQLite core uses these three routines for all of its own ** internal memory allocation needs. "Core" in the previous sentence ** does not include operating-system specific VFS implementation. The ** Windows VFS uses native malloc() and free() for some operations. ** ** ^The sqlite3_malloc() routine returns a pointer to a block ** of memory at least N bytes in length, where N is the parameter. ** ^If sqlite3_malloc() is unable to obtain sufficient free ** memory, it returns a NULL pointer. ^If the parameter N to ** sqlite3_malloc() is zero or negative then sqlite3_malloc() returns ** a NULL pointer. ** ** ^The sqlite3_malloc64(N) routine works just like ** sqlite3_malloc(N) except that N is an unsigned 64-bit integer instead ** of a signed 32-bit integer. ** ** ^Calling sqlite3_free() with a pointer previously returned ** by sqlite3_malloc() or sqlite3_realloc() releases that memory so ** that it might be reused. ^The sqlite3_free() routine is ** a no-op if is called with a NULL pointer. Passing a NULL pointer ** to sqlite3_free() is harmless. After being freed, memory ** should neither be read nor written. Even reading previously freed ** memory might result in a segmentation fault or other severe error. ** Memory corruption, a segmentation fault, or other severe error ** might result if sqlite3_free() is called with a non-NULL pointer that ** was not obtained from sqlite3_malloc() or sqlite3_realloc(). ** ** ^The sqlite3_realloc(X,N) interface attempts to resize a ** prior memory allocation X to be at least N bytes. ** ^If the X parameter to sqlite3_realloc(X,N) ** is a NULL pointer then its behavior is identical to calling ** sqlite3_malloc(N). ** ^If the N parameter to sqlite3_realloc(X,N) is zero or ** negative then the behavior is exactly the same as calling ** sqlite3_free(X). ** ^sqlite3_realloc(X,N) returns a pointer to a memory allocation ** of at least N bytes in size or NULL if insufficient memory is available. ** ^If M is the size of the prior allocation, then min(N,M) bytes ** of the prior allocation are copied into the beginning of buffer returned ** by sqlite3_realloc(X,N) and the prior allocation is freed. ** ^If sqlite3_realloc(X,N) returns NULL and N is positive, then the ** prior allocation is not freed. ** ** ^The sqlite3_realloc64(X,N) interfaces works the same as ** sqlite3_realloc(X,N) except that N is a 64-bit unsigned integer instead ** of a 32-bit signed integer. ** ** ^If X is a memory allocation previously obtained from sqlite3_malloc(), ** sqlite3_malloc64(), sqlite3_realloc(), or sqlite3_realloc64(), then ** sqlite3_msize(X) returns the size of that memory allocation in bytes. ** ^The value returned by sqlite3_msize(X) might be larger than the number ** of bytes requested when X was allocated. ^If X is a NULL pointer then ** sqlite3_msize(X) returns zero. If X points to something that is not ** the beginning of memory allocation, or if it points to a formerly ** valid memory allocation that has now been freed, then the behavior ** of sqlite3_msize(X) is undefined and possibly harmful. ** ** ^The memory returned by sqlite3_malloc(), sqlite3_realloc(), ** sqlite3_malloc64(), and sqlite3_realloc64() ** is always aligned to at least an 8 byte boundary, or to a ** 4 byte boundary if the [SQLITE_4_BYTE_ALIGNED_MALLOC] compile-time ** option is used. ** ** In SQLite version 3.5.0 and 3.5.1, it was possible to define ** the SQLITE_OMIT_MEMORY_ALLOCATION which would cause the built-in ** implementation of these routines to be omitted. That capability ** is no longer provided. Only built-in memory allocators can be used. ** ** Prior to SQLite version 3.7.10, the Windows OS interface layer called ** the system malloc() and free() directly when converting ** filenames between the UTF-8 encoding used by SQLite ** and whatever filename encoding is used by the particular Windows ** installation. Memory allocation errors were detected, but ** they were reported back as [SQLITE_CANTOPEN] or ** [SQLITE_IOERR] rather than [SQLITE_NOMEM]. ** ** The pointer arguments to [sqlite3_free()] and [sqlite3_realloc()] ** must be either NULL or else pointers obtained from a prior ** invocation of [sqlite3_malloc()] or [sqlite3_realloc()] that have ** not yet been released. ** ** The application must not read or write any part of ** a block of memory after it has been released using ** [sqlite3_free()] or [sqlite3_realloc()]. */ SQLITE_API void *sqlite3_malloc(int); SQLITE_API void *sqlite3_malloc64(sqlite3_uint64); SQLITE_API void *sqlite3_realloc(void*, int); SQLITE_API void *sqlite3_realloc64(void*, sqlite3_uint64); SQLITE_API void sqlite3_free(void*); SQLITE_API sqlite3_uint64 sqlite3_msize(void*); /* ** CAPI3REF: Memory Allocator Statistics ** ** SQLite provides these two interfaces for reporting on the status ** of the [sqlite3_malloc()], [sqlite3_free()], and [sqlite3_realloc()] ** routines, which form the built-in memory allocation subsystem. ** ** ^The [sqlite3_memory_used()] routine returns the number of bytes ** of memory currently outstanding (malloced but not freed). ** ^The [sqlite3_memory_highwater()] routine returns the maximum ** value of [sqlite3_memory_used()] since the high-water mark ** was last reset. ^The values returned by [sqlite3_memory_used()] and ** [sqlite3_memory_highwater()] include any overhead ** added by SQLite in its implementation of [sqlite3_malloc()], ** but not overhead added by the any underlying system library ** routines that [sqlite3_malloc()] may call. ** ** ^The memory high-water mark is reset to the current value of ** [sqlite3_memory_used()] if and only if the parameter to ** [sqlite3_memory_highwater()] is true. ^The value returned ** by [sqlite3_memory_highwater(1)] is the high-water mark ** prior to the reset. */ SQLITE_API sqlite3_int64 sqlite3_memory_used(void); SQLITE_API sqlite3_int64 sqlite3_memory_highwater(int resetFlag); /* ** CAPI3REF: Pseudo-Random Number Generator ** ** SQLite contains a high-quality pseudo-random number generator (PRNG) used to ** select random [ROWID | ROWIDs] when inserting new records into a table that ** already uses the largest possible [ROWID]. The PRNG is also used for ** the build-in random() and randomblob() SQL functions. This interface allows ** applications to access the same PRNG for other purposes. ** ** ^A call to this routine stores N bytes of randomness into buffer P. ** ^The P parameter can be a NULL pointer. ** ** ^If this routine has not been previously called or if the previous ** call had N less than one or a NULL pointer for P, then the PRNG is ** seeded using randomness obtained from the xRandomness method of ** the default [sqlite3_vfs] object. ** ^If the previous call to this routine had an N of 1 or more and a ** non-NULL P then the pseudo-randomness is generated ** internally and without recourse to the [sqlite3_vfs] xRandomness ** method. */ SQLITE_API void sqlite3_randomness(int N, void *P); /* ** CAPI3REF: Compile-Time Authorization Callbacks ** METHOD: sqlite3 ** KEYWORDS: {authorizer callback} ** ** ^This routine registers an authorizer callback with a particular ** [database connection], supplied in the first argument. ** ^The authorizer callback is invoked as SQL statements are being compiled ** by [sqlite3_prepare()] or its variants [sqlite3_prepare_v2()], ** [sqlite3_prepare_v3()], [sqlite3_prepare16()], [sqlite3_prepare16_v2()], ** and [sqlite3_prepare16_v3()]. ^At various ** points during the compilation process, as logic is being created ** to perform various actions, the authorizer callback is invoked to ** see if those actions are allowed. ^The authorizer callback should ** return [SQLITE_OK] to allow the action, [SQLITE_IGNORE] to disallow the ** specific action but allow the SQL statement to continue to be ** compiled, or [SQLITE_DENY] to cause the entire SQL statement to be ** rejected with an error. ^If the authorizer callback returns ** any value other than [SQLITE_IGNORE], [SQLITE_OK], or [SQLITE_DENY] ** then the [sqlite3_prepare_v2()] or equivalent call that triggered ** the authorizer will fail with an error message. ** ** When the callback returns [SQLITE_OK], that means the operation ** requested is ok. ^When the callback returns [SQLITE_DENY], the ** [sqlite3_prepare_v2()] or equivalent call that triggered the ** authorizer will fail with an error message explaining that ** access is denied. ** ** ^The first parameter to the authorizer callback is a copy of the third ** parameter to the sqlite3_set_authorizer() interface. ^The second parameter ** to the callback is an integer [SQLITE_COPY | action code] that specifies ** the particular action to be authorized. ^The third through sixth parameters ** to the callback are either NULL pointers or zero-terminated strings ** that contain additional details about the action to be authorized. ** Applications must always be prepared to encounter a NULL pointer in any ** of the third through the sixth parameters of the authorization callback. ** ** ^If the action code is [SQLITE_READ] ** and the callback returns [SQLITE_IGNORE] then the ** [prepared statement] statement is constructed to substitute ** a NULL value in place of the table column that would have ** been read if [SQLITE_OK] had been returned. The [SQLITE_IGNORE] ** return can be used to deny an untrusted user access to individual ** columns of a table. ** ^When a table is referenced by a [SELECT] but no column values are ** extracted from that table (for example in a query like ** "SELECT count(*) FROM tab") then the [SQLITE_READ] authorizer callback ** is invoked once for that table with a column name that is an empty string. ** ^If the action code is [SQLITE_DELETE] and the callback returns ** [SQLITE_IGNORE] then the [DELETE] operation proceeds but the ** [truncate optimization] is disabled and all rows are deleted individually. ** ** An authorizer is used when [sqlite3_prepare | preparing] ** SQL statements from an untrusted source, to ensure that the SQL statements ** do not try to access data they are not allowed to see, or that they do not ** try to execute malicious statements that damage the database. For ** example, an application may allow a user to enter arbitrary ** SQL queries for evaluation by a database. But the application does ** not want the user to be able to make arbitrary changes to the ** database. An authorizer could then be put in place while the ** user-entered SQL is being [sqlite3_prepare | prepared] that ** disallows everything except [SELECT] statements. ** ** Applications that need to process SQL from untrusted sources ** might also consider lowering resource limits using [sqlite3_limit()] ** and limiting database size using the [max_page_count] [PRAGMA] ** in addition to using an authorizer. ** ** ^(Only a single authorizer can be in place on a database connection ** at a time. Each call to sqlite3_set_authorizer overrides the ** previous call.)^ ^Disable the authorizer by installing a NULL callback. ** The authorizer is disabled by default. ** ** The authorizer callback must not do anything that will modify ** the database connection that invoked the authorizer callback. ** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their ** database connections for the meaning of "modify" in this paragraph. ** ** ^When [sqlite3_prepare_v2()] is used to prepare a statement, the ** statement might be re-prepared during [sqlite3_step()] due to a ** schema change. Hence, the application should ensure that the ** correct authorizer callback remains in place during the [sqlite3_step()]. ** ** ^Note that the authorizer callback is invoked only during ** [sqlite3_prepare()] or its variants. Authorization is not ** performed during statement evaluation in [sqlite3_step()], unless ** as stated in the previous paragraph, sqlite3_step() invokes ** sqlite3_prepare_v2() to reprepare a statement after a schema change. */ SQLITE_API int sqlite3_set_authorizer( sqlite3*, int (*xAuth)(void*,int,const char*,const char*,const char*,const char*), void *pUserData ); /* ** CAPI3REF: Authorizer Return Codes ** ** The [sqlite3_set_authorizer | authorizer callback function] must ** return either [SQLITE_OK] or one of these two constants in order ** to signal SQLite whether or not the action is permitted. See the ** [sqlite3_set_authorizer | authorizer documentation] for additional ** information. ** ** Note that SQLITE_IGNORE is also used as a [conflict resolution mode] ** returned from the [sqlite3_vtab_on_conflict()] interface. */ #define SQLITE_DENY 1 /* Abort the SQL statement with an error */ #define SQLITE_IGNORE 2 /* Don't allow access, but don't generate an error */ /* ** CAPI3REF: Authorizer Action Codes ** ** The [sqlite3_set_authorizer()] interface registers a callback function ** that is invoked to authorize certain SQL statement actions. The ** second parameter to the callback is an integer code that specifies ** what action is being authorized. These are the integer action codes that ** the authorizer callback may be passed. ** ** These action code values signify what kind of operation is to be ** authorized. The 3rd and 4th parameters to the authorization ** callback function will be parameters or NULL depending on which of these ** codes is used as the second parameter. ^(The 5th parameter to the ** authorizer callback is the name of the database ("main", "temp", ** etc.) if applicable.)^ ^The 6th parameter to the authorizer callback ** is the name of the inner-most trigger or view that is responsible for ** the access attempt or NULL if this access attempt is directly from ** top-level SQL code. */ /******************************************* 3rd ************ 4th ***********/ #define SQLITE_CREATE_INDEX 1 /* Index Name Table Name */ #define SQLITE_CREATE_TABLE 2 /* Table Name NULL */ #define SQLITE_CREATE_TEMP_INDEX 3 /* Index Name Table Name */ #define SQLITE_CREATE_TEMP_TABLE 4 /* Table Name NULL */ #define SQLITE_CREATE_TEMP_TRIGGER 5 /* Trigger Name Table Name */ #define SQLITE_CREATE_TEMP_VIEW 6 /* View Name NULL */ #define SQLITE_CREATE_TRIGGER 7 /* Trigger Name Table Name */ #define SQLITE_CREATE_VIEW 8 /* View Name NULL */ #define SQLITE_DELETE 9 /* Table Name NULL */ #define SQLITE_DROP_INDEX 10 /* Index Name Table Name */ #define SQLITE_DROP_TABLE 11 /* Table Name NULL */ #define SQLITE_DROP_TEMP_INDEX 12 /* Index Name Table Name */ #define SQLITE_DROP_TEMP_TABLE 13 /* Table Name NULL */ #define SQLITE_DROP_TEMP_TRIGGER 14 /* Trigger Name Table Name */ #define SQLITE_DROP_TEMP_VIEW 15 /* View Name NULL */ #define SQLITE_DROP_TRIGGER 16 /* Trigger Name Table Name */ #define SQLITE_DROP_VIEW 17 /* View Name NULL */ #define SQLITE_INSERT 18 /* Table Name NULL */ #define SQLITE_PRAGMA 19 /* Pragma Name 1st arg or NULL */ #define SQLITE_READ 20 /* Table Name Column Name */ #define SQLITE_SELECT 21 /* NULL NULL */ #define SQLITE_TRANSACTION 22 /* Operation NULL */ #define SQLITE_UPDATE 23 /* Table Name Column Name */ #define SQLITE_ATTACH 24 /* Filename NULL */ #define SQLITE_DETACH 25 /* Database Name NULL */ #define SQLITE_ALTER_TABLE 26 /* Database Name Table Name */ #define SQLITE_REINDEX 27 /* Index Name NULL */ #define SQLITE_ANALYZE 28 /* Table Name NULL */ #define SQLITE_CREATE_VTABLE 29 /* Table Name Module Name */ #define SQLITE_DROP_VTABLE 30 /* Table Name Module Name */ #define SQLITE_FUNCTION 31 /* NULL Function Name */ #define SQLITE_SAVEPOINT 32 /* Operation Savepoint Name */ #define SQLITE_COPY 0 /* No longer used */ #define SQLITE_RECURSIVE 33 /* NULL NULL */ /* ** CAPI3REF: Tracing And Profiling Functions ** METHOD: sqlite3 ** ** These routines are deprecated. Use the [sqlite3_trace_v2()] interface ** instead of the routines described here. ** ** These routines register callback functions that can be used for ** tracing and profiling the execution of SQL statements. ** ** ^The callback function registered by sqlite3_trace() is invoked at ** various times when an SQL statement is being run by [sqlite3_step()]. ** ^The sqlite3_trace() callback is invoked with a UTF-8 rendering of the ** SQL statement text as the statement first begins executing. ** ^(Additional sqlite3_trace() callbacks might occur ** as each triggered subprogram is entered. The callbacks for triggers ** contain a UTF-8 SQL comment that identifies the trigger.)^ ** ** The [SQLITE_TRACE_SIZE_LIMIT] compile-time option can be used to limit ** the length of [bound parameter] expansion in the output of sqlite3_trace(). ** ** ^The callback function registered by sqlite3_profile() is invoked ** as each SQL statement finishes. ^The profile callback contains ** the original statement text and an estimate of wall-clock time ** of how long that statement took to run. ^The profile callback ** time is in units of nanoseconds, however the current implementation ** is only capable of millisecond resolution so the six least significant ** digits in the time are meaningless. Future versions of SQLite ** might provide greater resolution on the profiler callback. The ** sqlite3_profile() function is considered experimental and is ** subject to change in future versions of SQLite. */ SQLITE_API SQLITE_DEPRECATED void *sqlite3_trace(sqlite3*, void(*xTrace)(void*,const char*), void*); SQLITE_API SQLITE_DEPRECATED void *sqlite3_profile(sqlite3*, void(*xProfile)(void*,const char*,sqlite3_uint64), void*); /* ** CAPI3REF: SQL Trace Event Codes ** KEYWORDS: SQLITE_TRACE ** ** These constants identify classes of events that can be monitored ** using the [sqlite3_trace_v2()] tracing logic. The third argument ** to [sqlite3_trace_v2()] is an OR-ed combination of one or more of ** the following constants. ^The first argument to the trace callback ** is one of the following constants. ** ** New tracing constants may be added in future releases. ** ** ^A trace callback has four arguments: xCallback(T,C,P,X). ** ^The T argument is one of the integer type codes above. ** ^The C argument is a copy of the context pointer passed in as the ** fourth argument to [sqlite3_trace_v2()]. ** The P and X arguments are pointers whose meanings depend on T. ** **
** [[SQLITE_TRACE_STMT]]
SQLITE_TRACE_STMT
**
^An SQLITE_TRACE_STMT callback is invoked when a prepared statement ** first begins running and possibly at other times during the ** execution of the prepared statement, such as at the start of each ** trigger subprogram. ^The P argument is a pointer to the ** [prepared statement]. ^The X argument is a pointer to a string which ** is the unexpanded SQL text of the prepared statement or an SQL comment ** that indicates the invocation of a trigger. ^The callback can compute ** the same text that would have been returned by the legacy [sqlite3_trace()] ** interface by using the X argument when X begins with "--" and invoking ** [sqlite3_expanded_sql(P)] otherwise. ** ** [[SQLITE_TRACE_PROFILE]]
SQLITE_TRACE_PROFILE
**
^An SQLITE_TRACE_PROFILE callback provides approximately the same ** information as is provided by the [sqlite3_profile()] callback. ** ^The P argument is a pointer to the [prepared statement] and the ** X argument points to a 64-bit integer which is the estimated of ** the number of nanosecond that the prepared statement took to run. ** ^The SQLITE_TRACE_PROFILE callback is invoked when the statement finishes. ** ** [[SQLITE_TRACE_ROW]]
SQLITE_TRACE_ROW
**
^An SQLITE_TRACE_ROW callback is invoked whenever a prepared ** statement generates a single row of result. ** ^The P argument is a pointer to the [prepared statement] and the ** X argument is unused. ** ** [[SQLITE_TRACE_CLOSE]]
SQLITE_TRACE_CLOSE
**
^An SQLITE_TRACE_CLOSE callback is invoked when a database ** connection closes. ** ^The P argument is a pointer to the [database connection] object ** and the X argument is unused. **
*/ #define SQLITE_TRACE_STMT 0x01 #define SQLITE_TRACE_PROFILE 0x02 #define SQLITE_TRACE_ROW 0x04 #define SQLITE_TRACE_CLOSE 0x08 /* ** CAPI3REF: SQL Trace Hook ** METHOD: sqlite3 ** ** ^The sqlite3_trace_v2(D,M,X,P) interface registers a trace callback ** function X against [database connection] D, using property mask M ** and context pointer P. ^If the X callback is ** NULL or if the M mask is zero, then tracing is disabled. The ** M argument should be the bitwise OR-ed combination of ** zero or more [SQLITE_TRACE] constants. ** ** ^Each call to either sqlite3_trace() or sqlite3_trace_v2() overrides ** (cancels) any prior calls to sqlite3_trace() or sqlite3_trace_v2(). ** ** ^The X callback is invoked whenever any of the events identified by ** mask M occur. ^The integer return value from the callback is currently ** ignored, though this may change in future releases. Callback ** implementations should return zero to ensure future compatibility. ** ** ^A trace callback is invoked with four arguments: callback(T,C,P,X). ** ^The T argument is one of the [SQLITE_TRACE] ** constants to indicate why the callback was invoked. ** ^The C argument is a copy of the context pointer. ** The P and X arguments are pointers whose meanings depend on T. ** ** The sqlite3_trace_v2() interface is intended to replace the legacy ** interfaces [sqlite3_trace()] and [sqlite3_profile()], both of which ** are deprecated. */ SQLITE_API int sqlite3_trace_v2( sqlite3*, unsigned uMask, int(*xCallback)(unsigned,void*,void*,void*), void *pCtx ); /* ** CAPI3REF: Query Progress Callbacks ** METHOD: sqlite3 ** ** ^The sqlite3_progress_handler(D,N,X,P) interface causes the callback ** function X to be invoked periodically during long running calls to ** [sqlite3_exec()], [sqlite3_step()] and [sqlite3_get_table()] for ** database connection D. An example use for this ** interface is to keep a GUI updated during a large query. ** ** ^The parameter P is passed through as the only parameter to the ** callback function X. ^The parameter N is the approximate number of ** [virtual machine instructions] that are evaluated between successive ** invocations of the callback X. ^If N is less than one then the progress ** handler is disabled. ** ** ^Only a single progress handler may be defined at one time per ** [database connection]; setting a new progress handler cancels the ** old one. ^Setting parameter X to NULL disables the progress handler. ** ^The progress handler is also disabled by setting N to a value less ** than 1. ** ** ^If the progress callback returns non-zero, the operation is ** interrupted. This feature can be used to implement a ** "Cancel" button on a GUI progress dialog box. ** ** The progress handler callback must not do anything that will modify ** the database connection that invoked the progress handler. ** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their ** database connections for the meaning of "modify" in this paragraph. ** */ SQLITE_API void sqlite3_progress_handler(sqlite3*, int, int(*)(void*), void*); /* ** CAPI3REF: Opening A New Database Connection ** CONSTRUCTOR: sqlite3 ** ** ^These routines open an SQLite database file as specified by the ** filename argument. ^The filename argument is interpreted as UTF-8 for ** sqlite3_open() and sqlite3_open_v2() and as UTF-16 in the native byte ** order for sqlite3_open16(). ^(A [database connection] handle is usually ** returned in *ppDb, even if an error occurs. The only exception is that ** if SQLite is unable to allocate memory to hold the [sqlite3] object, ** a NULL will be written into *ppDb instead of a pointer to the [sqlite3] ** object.)^ ^(If the database is opened (and/or created) successfully, then ** [SQLITE_OK] is returned. Otherwise an [error code] is returned.)^ ^The ** [sqlite3_errmsg()] or [sqlite3_errmsg16()] routines can be used to obtain ** an English language description of the error following a failure of any ** of the sqlite3_open() routines. ** ** ^The default encoding will be UTF-8 for databases created using ** sqlite3_open() or sqlite3_open_v2(). ^The default encoding for databases ** created using sqlite3_open16() will be UTF-16 in the native byte order. ** ** Whether or not an error occurs when it is opened, resources ** associated with the [database connection] handle should be released by ** passing it to [sqlite3_close()] when it is no longer required. ** ** The sqlite3_open_v2() interface works like sqlite3_open() ** except that it accepts two additional parameters for additional control ** over the new database connection. ^(The flags parameter to ** sqlite3_open_v2() can take one of ** the following three values, optionally combined with the ** [SQLITE_OPEN_NOMUTEX], [SQLITE_OPEN_FULLMUTEX], [SQLITE_OPEN_SHAREDCACHE], ** [SQLITE_OPEN_PRIVATECACHE], and/or [SQLITE_OPEN_URI] flags:)^ ** **
** ^(
[SQLITE_OPEN_READONLY]
**
The database is opened in read-only mode. If the database does not ** already exist, an error is returned.
)^ ** ** ^(
[SQLITE_OPEN_READWRITE]
**
The database is opened for reading and writing if possible, or reading ** only if the file is write protected by the operating system. In either ** case the database must already exist, otherwise an error is returned.
)^ ** ** ^(
[SQLITE_OPEN_READWRITE] | [SQLITE_OPEN_CREATE]
**
The database is opened for reading and writing, and is created if ** it does not already exist. This is the behavior that is always used for ** sqlite3_open() and sqlite3_open16().
)^ **
** ** If the 3rd parameter to sqlite3_open_v2() is not one of the ** combinations shown above optionally combined with other ** [SQLITE_OPEN_READONLY | SQLITE_OPEN_* bits] ** then the behavior is undefined. ** ** ^If the [SQLITE_OPEN_NOMUTEX] flag is set, then the database connection ** opens in the multi-thread [threading mode] as long as the single-thread ** mode has not been set at compile-time or start-time. ^If the ** [SQLITE_OPEN_FULLMUTEX] flag is set then the database connection opens ** in the serialized [threading mode] unless single-thread was ** previously selected at compile-time or start-time. ** ^The [SQLITE_OPEN_SHAREDCACHE] flag causes the database connection to be ** eligible to use [shared cache mode], regardless of whether or not shared ** cache is enabled using [sqlite3_enable_shared_cache()]. ^The ** [SQLITE_OPEN_PRIVATECACHE] flag causes the database connection to not ** participate in [shared cache mode] even if it is enabled. ** ** ^The fourth parameter to sqlite3_open_v2() is the name of the ** [sqlite3_vfs] object that defines the operating system interface that ** the new database connection should use. ^If the fourth parameter is ** a NULL pointer then the default [sqlite3_vfs] object is used. ** ** ^If the filename is ":memory:", then a private, temporary in-memory database ** is created for the connection. ^This in-memory database will vanish when ** the database connection is closed. Future versions of SQLite might ** make use of additional special filenames that begin with the ":" character. ** It is recommended that when a database filename actually does begin with ** a ":" character you should prefix the filename with a pathname such as ** "./" to avoid ambiguity. ** ** ^If the filename is an empty string, then a private, temporary ** on-disk database will be created. ^This private database will be ** automatically deleted as soon as the database connection is closed. ** ** [[URI filenames in sqlite3_open()]]

URI Filenames

** ** ^If [URI filename] interpretation is enabled, and the filename argument ** begins with "file:", then the filename is interpreted as a URI. ^URI ** filename interpretation is enabled if the [SQLITE_OPEN_URI] flag is ** set in the fourth argument to sqlite3_open_v2(), or if it has ** been enabled globally using the [SQLITE_CONFIG_URI] option with the ** [sqlite3_config()] method or by the [SQLITE_USE_URI] compile-time option. ** As of SQLite version 3.7.7, URI filename interpretation is turned off ** by default, but future releases of SQLite might enable URI filename ** interpretation by default. See "[URI filenames]" for additional ** information. ** ** URI filenames are parsed according to RFC 3986. ^If the URI contains an ** authority, then it must be either an empty string or the string ** "localhost". ^If the authority is not an empty string or "localhost", an ** error is returned to the caller. ^The fragment component of a URI, if ** present, is ignored. ** ** ^SQLite uses the path component of the URI as the name of the disk file ** which contains the database. ^If the path begins with a '/' character, ** then it is interpreted as an absolute path. ^If the path does not begin ** with a '/' (meaning that the authority section is omitted from the URI) ** then the path is interpreted as a relative path. ** ^(On windows, the first component of an absolute path ** is a drive specification (e.g. "C:").)^ ** ** [[core URI query parameters]] ** The query component of a URI may contain parameters that are interpreted ** either by SQLite itself, or by a [VFS | custom VFS implementation]. ** SQLite and its built-in [VFSes] interpret the ** following query parameters: ** **
    **
  • vfs: ^The "vfs" parameter may be used to specify the name of ** a VFS object that provides the operating system interface that should ** be used to access the database file on disk. ^If this option is set to ** an empty string the default VFS object is used. ^Specifying an unknown ** VFS is an error. ^If sqlite3_open_v2() is used and the vfs option is ** present, then the VFS specified by the option takes precedence over ** the value passed as the fourth parameter to sqlite3_open_v2(). ** **
  • mode: ^(The mode parameter may be set to either "ro", "rw", ** "rwc", or "memory". Attempting to set it to any other value is ** an error)^. ** ^If "ro" is specified, then the database is opened for read-only ** access, just as if the [SQLITE_OPEN_READONLY] flag had been set in the ** third argument to sqlite3_open_v2(). ^If the mode option is set to ** "rw", then the database is opened for read-write (but not create) ** access, as if SQLITE_OPEN_READWRITE (but not SQLITE_OPEN_CREATE) had ** been set. ^Value "rwc" is equivalent to setting both ** SQLITE_OPEN_READWRITE and SQLITE_OPEN_CREATE. ^If the mode option is ** set to "memory" then a pure [in-memory database] that never reads ** or writes from disk is used. ^It is an error to specify a value for ** the mode parameter that is less restrictive than that specified by ** the flags passed in the third parameter to sqlite3_open_v2(). ** **
  • cache: ^The cache parameter may be set to either "shared" or ** "private". ^Setting it to "shared" is equivalent to setting the ** SQLITE_OPEN_SHAREDCACHE bit in the flags argument passed to ** sqlite3_open_v2(). ^Setting the cache parameter to "private" is ** equivalent to setting the SQLITE_OPEN_PRIVATECACHE bit. ** ^If sqlite3_open_v2() is used and the "cache" parameter is present in ** a URI filename, its value overrides any behavior requested by setting ** SQLITE_OPEN_PRIVATECACHE or SQLITE_OPEN_SHAREDCACHE flag. ** **
  • psow: ^The psow parameter indicates whether or not the ** [powersafe overwrite] property does or does not apply to the ** storage media on which the database file resides. ** **
  • nolock: ^The nolock parameter is a boolean query parameter ** which if set disables file locking in rollback journal modes. This ** is useful for accessing a database on a filesystem that does not ** support locking. Caution: Database corruption might result if two ** or more processes write to the same database and any one of those ** processes uses nolock=1. ** **
  • immutable: ^The immutable parameter is a boolean query ** parameter that indicates that the database file is stored on ** read-only media. ^When immutable is set, SQLite assumes that the ** database file cannot be changed, even by a process with higher ** privilege, and so the database is opened read-only and all locking ** and change detection is disabled. Caution: Setting the immutable ** property on a database file that does in fact change can result ** in incorrect query results and/or [SQLITE_CORRUPT] errors. ** See also: [SQLITE_IOCAP_IMMUTABLE]. ** **
** ** ^Specifying an unknown parameter in the query component of a URI is not an ** error. Future versions of SQLite might understand additional query ** parameters. See "[query parameters with special meaning to SQLite]" for ** additional information. ** ** [[URI filename examples]]

URI filename examples

** ** **
URI filenames Results **
file:data.db ** Open the file "data.db" in the current directory. **
file:/home/fred/data.db
** file:///home/fred/data.db
** file://localhost/home/fred/data.db
** Open the database file "/home/fred/data.db". **
file://darkstar/home/fred/data.db ** An error. "darkstar" is not a recognized authority. **
** file:///C:/Documents%20and%20Settings/fred/Desktop/data.db ** Windows only: Open the file "data.db" on fred's desktop on drive ** C:. Note that the %20 escaping in this example is not strictly ** necessary - space characters can be used literally ** in URI filenames. **
file:data.db?mode=ro&cache=private ** Open file "data.db" in the current directory for read-only access. ** Regardless of whether or not shared-cache mode is enabled by ** default, use a private cache. **
file:/home/fred/data.db?vfs=unix-dotfile ** Open file "/home/fred/data.db". Use the special VFS "unix-dotfile" ** that uses dot-files in place of posix advisory locking. **
file:data.db?mode=readonly ** An error. "readonly" is not a valid option for the "mode" parameter. **
** ** ^URI hexadecimal escape sequences (%HH) are supported within the path and ** query components of a URI. A hexadecimal escape sequence consists of a ** percent sign - "%" - followed by exactly two hexadecimal digits ** specifying an octet value. ^Before the path or query components of a ** URI filename are interpreted, they are encoded using UTF-8 and all ** hexadecimal escape sequences replaced by a single byte containing the ** corresponding octet. If this process generates an invalid UTF-8 encoding, ** the results are undefined. ** ** Note to Windows users: The encoding used for the filename argument ** of sqlite3_open() and sqlite3_open_v2() must be UTF-8, not whatever ** codepage is currently defined. Filenames containing international ** characters must be converted to UTF-8 prior to passing them into ** sqlite3_open() or sqlite3_open_v2(). ** ** Note to Windows Runtime users: The temporary directory must be set ** prior to calling sqlite3_open() or sqlite3_open_v2(). Otherwise, various ** features that require the use of temporary files may fail. ** ** See also: [sqlite3_temp_directory] */ SQLITE_API int sqlite3_open( const char *filename, /* Database filename (UTF-8) */ sqlite3 **ppDb /* OUT: SQLite db handle */ ); SQLITE_API int sqlite3_open16( const void *filename, /* Database filename (UTF-16) */ sqlite3 **ppDb /* OUT: SQLite db handle */ ); SQLITE_API int sqlite3_open_v2( const char *filename, /* Database filename (UTF-8) */ sqlite3 **ppDb, /* OUT: SQLite db handle */ int flags, /* Flags */ const char *zVfs /* Name of VFS module to use */ ); /* ** CAPI3REF: Obtain Values For URI Parameters ** ** These are utility routines, useful to VFS implementations, that check ** to see if a database file was a URI that contained a specific query ** parameter, and if so obtains the value of that query parameter. ** ** If F is the database filename pointer passed into the xOpen() method of ** a VFS implementation when the flags parameter to xOpen() has one or ** more of the [SQLITE_OPEN_URI] or [SQLITE_OPEN_MAIN_DB] bits set and ** P is the name of the query parameter, then ** sqlite3_uri_parameter(F,P) returns the value of the P ** parameter if it exists or a NULL pointer if P does not appear as a ** query parameter on F. If P is a query parameter of F ** has no explicit value, then sqlite3_uri_parameter(F,P) returns ** a pointer to an empty string. ** ** The sqlite3_uri_boolean(F,P,B) routine assumes that P is a boolean ** parameter and returns true (1) or false (0) according to the value ** of P. The sqlite3_uri_boolean(F,P,B) routine returns true (1) if the ** value of query parameter P is one of "yes", "true", or "on" in any ** case or if the value begins with a non-zero number. The ** sqlite3_uri_boolean(F,P,B) routines returns false (0) if the value of ** query parameter P is one of "no", "false", or "off" in any case or ** if the value begins with a numeric zero. If P is not a query ** parameter on F or if the value of P is does not match any of the ** above, then sqlite3_uri_boolean(F,P,B) returns (B!=0). ** ** The sqlite3_uri_int64(F,P,D) routine converts the value of P into a ** 64-bit signed integer and returns that integer, or D if P does not ** exist. If the value of P is something other than an integer, then ** zero is returned. ** ** If F is a NULL pointer, then sqlite3_uri_parameter(F,P) returns NULL and ** sqlite3_uri_boolean(F,P,B) returns B. If F is not a NULL pointer and ** is not a database file pathname pointer that SQLite passed into the xOpen ** VFS method, then the behavior of this routine is undefined and probably ** undesirable. */ SQLITE_API const char *sqlite3_uri_parameter(const char *zFilename, const char *zParam); SQLITE_API int sqlite3_uri_boolean(const char *zFile, const char *zParam, int bDefault); SQLITE_API sqlite3_int64 sqlite3_uri_int64(const char*, const char*, sqlite3_int64); /* ** CAPI3REF: Error Codes And Messages ** METHOD: sqlite3 ** ** ^If the most recent sqlite3_* API call associated with ** [database connection] D failed, then the sqlite3_errcode(D) interface ** returns the numeric [result code] or [extended result code] for that ** API call. ** If the most recent API call was successful, ** then the return value from sqlite3_errcode() is undefined. ** ^The sqlite3_extended_errcode() ** interface is the same except that it always returns the ** [extended result code] even when extended result codes are ** disabled. ** ** ^The sqlite3_errmsg() and sqlite3_errmsg16() return English-language ** text that describes the error, as either UTF-8 or UTF-16 respectively. ** ^(Memory to hold the error message string is managed internally. ** The application does not need to worry about freeing the result. ** However, the error string might be overwritten or deallocated by ** subsequent calls to other SQLite interface functions.)^ ** ** ^The sqlite3_errstr() interface returns the English-language text ** that describes the [result code], as UTF-8. ** ^(Memory to hold the error message string is managed internally ** and must not be freed by the application)^. ** ** When the serialized [threading mode] is in use, it might be the ** case that a second error occurs on a separate thread in between ** the time of the first error and the call to these interfaces. ** When that happens, the second error will be reported since these ** interfaces always report the most recent result. To avoid ** this, each thread can obtain exclusive use of the [database connection] D ** by invoking [sqlite3_mutex_enter]([sqlite3_db_mutex](D)) before beginning ** to use D and invoking [sqlite3_mutex_leave]([sqlite3_db_mutex](D)) after ** all calls to the interfaces listed here are completed. ** ** If an interface fails with SQLITE_MISUSE, that means the interface ** was invoked incorrectly by the application. In that case, the ** error code and message may or may not be set. */ SQLITE_API int sqlite3_errcode(sqlite3 *db); SQLITE_API int sqlite3_extended_errcode(sqlite3 *db); SQLITE_API const char *sqlite3_errmsg(sqlite3*); SQLITE_API const void *sqlite3_errmsg16(sqlite3*); SQLITE_API const char *sqlite3_errstr(int); /* ** CAPI3REF: Prepared Statement Object ** KEYWORDS: {prepared statement} {prepared statements} ** ** An instance of this object represents a single SQL statement that ** has been compiled into binary form and is ready to be evaluated. ** ** Think of each SQL statement as a separate computer program. The ** original SQL text is source code. A prepared statement object ** is the compiled object code. All SQL must be converted into a ** prepared statement before it can be run. ** ** The life-cycle of a prepared statement object usually goes like this: ** **
    **
  1. Create the prepared statement object using [sqlite3_prepare_v2()]. **
  2. Bind values to [parameters] using the sqlite3_bind_*() ** interfaces. **
  3. Run the SQL by calling [sqlite3_step()] one or more times. **
  4. Reset the prepared statement using [sqlite3_reset()] then go back ** to step 2. Do this zero or more times. **
  5. Destroy the object using [sqlite3_finalize()]. **
*/ typedef struct sqlite3_stmt sqlite3_stmt; /* ** CAPI3REF: Run-time Limits ** METHOD: sqlite3 ** ** ^(This interface allows the size of various constructs to be limited ** on a connection by connection basis. The first parameter is the ** [database connection] whose limit is to be set or queried. The ** second parameter is one of the [limit categories] that define a ** class of constructs to be size limited. The third parameter is the ** new limit for that construct.)^ ** ** ^If the new limit is a negative number, the limit is unchanged. ** ^(For each limit category SQLITE_LIMIT_NAME there is a ** [limits | hard upper bound] ** set at compile-time by a C preprocessor macro called ** [limits | SQLITE_MAX_NAME]. ** (The "_LIMIT_" in the name is changed to "_MAX_".))^ ** ^Attempts to increase a limit above its hard upper bound are ** silently truncated to the hard upper bound. ** ** ^Regardless of whether or not the limit was changed, the ** [sqlite3_limit()] interface returns the prior value of the limit. ** ^Hence, to find the current value of a limit without changing it, ** simply invoke this interface with the third parameter set to -1. ** ** Run-time limits are intended for use in applications that manage ** both their own internal database and also databases that are controlled ** by untrusted external sources. An example application might be a ** web browser that has its own databases for storing history and ** separate databases controlled by JavaScript applications downloaded ** off the Internet. The internal databases can be given the ** large, default limits. Databases managed by external sources can ** be given much smaller limits designed to prevent a denial of service ** attack. Developers might also want to use the [sqlite3_set_authorizer()] ** interface to further control untrusted SQL. The size of the database ** created by an untrusted script can be contained using the ** [max_page_count] [PRAGMA]. ** ** New run-time limit categories may be added in future releases. */ SQLITE_API int sqlite3_limit(sqlite3*, int id, int newVal); /* ** CAPI3REF: Run-Time Limit Categories ** KEYWORDS: {limit category} {*limit categories} ** ** These constants define various performance limits ** that can be lowered at run-time using [sqlite3_limit()]. ** The synopsis of the meanings of the various limits is shown below. ** Additional information is available at [limits | Limits in SQLite]. ** **
** [[SQLITE_LIMIT_LENGTH]] ^(
SQLITE_LIMIT_LENGTH
**
The maximum size of any string or BLOB or table row, in bytes.
)^ ** ** [[SQLITE_LIMIT_SQL_LENGTH]] ^(
SQLITE_LIMIT_SQL_LENGTH
**
The maximum length of an SQL statement, in bytes.
)^ ** ** [[SQLITE_LIMIT_COLUMN]] ^(
SQLITE_LIMIT_COLUMN
**
The maximum number of columns in a table definition or in the ** result set of a [SELECT] or the maximum number of columns in an index ** or in an ORDER BY or GROUP BY clause.
)^ ** ** [[SQLITE_LIMIT_EXPR_DEPTH]] ^(
SQLITE_LIMIT_EXPR_DEPTH
**
The maximum depth of the parse tree on any expression.
)^ ** ** [[SQLITE_LIMIT_COMPOUND_SELECT]] ^(
SQLITE_LIMIT_COMPOUND_SELECT
**
The maximum number of terms in a compound SELECT statement.
)^ ** ** [[SQLITE_LIMIT_VDBE_OP]] ^(
SQLITE_LIMIT_VDBE_OP
**
The maximum number of instructions in a virtual machine program ** used to implement an SQL statement. If [sqlite3_prepare_v2()] or ** the equivalent tries to allocate space for more than this many opcodes ** in a single prepared statement, an SQLITE_NOMEM error is returned.
)^ ** ** [[SQLITE_LIMIT_FUNCTION_ARG]] ^(
SQLITE_LIMIT_FUNCTION_ARG
**
The maximum number of arguments on a function.
)^ ** ** [[SQLITE_LIMIT_ATTACHED]] ^(
SQLITE_LIMIT_ATTACHED
**
The maximum number of [ATTACH | attached databases].)^
** ** [[SQLITE_LIMIT_LIKE_PATTERN_LENGTH]] ** ^(
SQLITE_LIMIT_LIKE_PATTERN_LENGTH
**
The maximum length of the pattern argument to the [LIKE] or ** [GLOB] operators.
)^ ** ** [[SQLITE_LIMIT_VARIABLE_NUMBER]] ** ^(
SQLITE_LIMIT_VARIABLE_NUMBER
**
The maximum index number of any [parameter] in an SQL statement.)^ ** ** [[SQLITE_LIMIT_TRIGGER_DEPTH]] ^(
SQLITE_LIMIT_TRIGGER_DEPTH
**
The maximum depth of recursion for triggers.
)^ ** ** [[SQLITE_LIMIT_WORKER_THREADS]] ^(
SQLITE_LIMIT_WORKER_THREADS
**
The maximum number of auxiliary worker threads that a single ** [prepared statement] may start.
)^ **
*/ #define SQLITE_LIMIT_LENGTH 0 #define SQLITE_LIMIT_SQL_LENGTH 1 #define SQLITE_LIMIT_COLUMN 2 #define SQLITE_LIMIT_EXPR_DEPTH 3 #define SQLITE_LIMIT_COMPOUND_SELECT 4 #define SQLITE_LIMIT_VDBE_OP 5 #define SQLITE_LIMIT_FUNCTION_ARG 6 #define SQLITE_LIMIT_ATTACHED 7 #define SQLITE_LIMIT_LIKE_PATTERN_LENGTH 8 #define SQLITE_LIMIT_VARIABLE_NUMBER 9 #define SQLITE_LIMIT_TRIGGER_DEPTH 10 #define SQLITE_LIMIT_WORKER_THREADS 11 /* ** CAPI3REF: Prepare Flags ** ** These constants define various flags that can be passed into ** "prepFlags" parameter of the [sqlite3_prepare_v3()] and ** [sqlite3_prepare16_v3()] interfaces. ** ** New flags may be added in future releases of SQLite. ** **
** [[SQLITE_PREPARE_PERSISTENT]] ^(
SQLITE_PREPARE_PERSISTENT
**
The SQLITE_PREPARE_PERSISTENT flag is a hint to the query planner ** that the prepared statement will be retained for a long time and ** probably reused many times.)^ ^Without this flag, [sqlite3_prepare_v3()] ** and [sqlite3_prepare16_v3()] assume that the prepared statement will ** be used just once or at most a few times and then destroyed using ** [sqlite3_finalize()] relatively soon. The current implementation acts ** on this hint by avoiding the use of [lookaside memory] so as not to ** deplete the limited store of lookaside memory. Future versions of ** SQLite may act on this hint differently. **
*/ #define SQLITE_PREPARE_PERSISTENT 0x01 /* ** CAPI3REF: Compiling An SQL Statement ** KEYWORDS: {SQL statement compiler} ** METHOD: sqlite3 ** CONSTRUCTOR: sqlite3_stmt ** ** To execute an SQL statement, it must first be compiled into a byte-code ** program using one of these routines. Or, in other words, these routines ** are constructors for the [prepared statement] object. ** ** The preferred routine to use is [sqlite3_prepare_v2()]. The ** [sqlite3_prepare()] interface is legacy and should be avoided. ** [sqlite3_prepare_v3()] has an extra "prepFlags" option that is used ** for special purposes. ** ** The use of the UTF-8 interfaces is preferred, as SQLite currently ** does all parsing using UTF-8. The UTF-16 interfaces are provided ** as a convenience. The UTF-16 interfaces work by converting the ** input text into UTF-8, then invoking the corresponding UTF-8 interface. ** ** The first argument, "db", is a [database connection] obtained from a ** prior successful call to [sqlite3_open()], [sqlite3_open_v2()] or ** [sqlite3_open16()]. The database connection must not have been closed. ** ** The second argument, "zSql", is the statement to be compiled, encoded ** as either UTF-8 or UTF-16. The sqlite3_prepare(), sqlite3_prepare_v2(), ** and sqlite3_prepare_v3() ** interfaces use UTF-8, and sqlite3_prepare16(), sqlite3_prepare16_v2(), ** and sqlite3_prepare16_v3() use UTF-16. ** ** ^If the nByte argument is negative, then zSql is read up to the ** first zero terminator. ^If nByte is positive, then it is the ** number of bytes read from zSql. ^If nByte is zero, then no prepared ** statement is generated. ** If the caller knows that the supplied string is nul-terminated, then ** there is a small performance advantage to passing an nByte parameter that ** is the number of bytes in the input string including ** the nul-terminator. ** ** ^If pzTail is not NULL then *pzTail is made to point to the first byte ** past the end of the first SQL statement in zSql. These routines only ** compile the first statement in zSql, so *pzTail is left pointing to ** what remains uncompiled. ** ** ^*ppStmt is left pointing to a compiled [prepared statement] that can be ** executed using [sqlite3_step()]. ^If there is an error, *ppStmt is set ** to NULL. ^If the input text contains no SQL (if the input is an empty ** string or a comment) then *ppStmt is set to NULL. ** The calling procedure is responsible for deleting the compiled ** SQL statement using [sqlite3_finalize()] after it has finished with it. ** ppStmt may not be NULL. ** ** ^On success, the sqlite3_prepare() family of routines return [SQLITE_OK]; ** otherwise an [error code] is returned. ** ** The sqlite3_prepare_v2(), sqlite3_prepare_v3(), sqlite3_prepare16_v2(), ** and sqlite3_prepare16_v3() interfaces are recommended for all new programs. ** The older interfaces (sqlite3_prepare() and sqlite3_prepare16()) ** are retained for backwards compatibility, but their use is discouraged. ** ^In the "vX" interfaces, the prepared statement ** that is returned (the [sqlite3_stmt] object) contains a copy of the ** original SQL text. This causes the [sqlite3_step()] interface to ** behave differently in three ways: ** **
    **
  1. ** ^If the database schema changes, instead of returning [SQLITE_SCHEMA] as it ** always used to do, [sqlite3_step()] will automatically recompile the SQL ** statement and try to run it again. As many as [SQLITE_MAX_SCHEMA_RETRY] ** retries will occur before sqlite3_step() gives up and returns an error. **
    2. ** **
  2. ** ^When an error occurs, [sqlite3_step()] will return one of the detailed ** [error codes] or [extended error codes]. ^The legacy behavior was that ** [sqlite3_step()] would only return a generic [SQLITE_ERROR] result code ** and the application would have to make a second call to [sqlite3_reset()] ** in order to find the underlying cause of the problem. With the "v2" prepare ** interfaces, the underlying reason for the error is returned immediately. **
    3. ** **
  3. ** ^If the specific value bound to [parameter | host parameter] in the ** WHERE clause might influence the choice of query plan for a statement, ** then the statement will be automatically recompiled, as if there had been ** a schema change, on the first [sqlite3_step()] call following any change ** to the [sqlite3_bind_text | bindings] of that [parameter]. ** ^The specific value of WHERE-clause [parameter] might influence the ** choice of query plan if the parameter is the left-hand side of a [LIKE] ** or [GLOB] operator or if the parameter is compared to an indexed column ** and the [SQLITE_ENABLE_STAT3] compile-time option is enabled. **
    4. ** **

    ^sqlite3_prepare_v3() differs from sqlite3_prepare_v2() only in having ** the extra prepFlags parameter, which is a bit array consisting of zero or ** more of the [SQLITE_PREPARE_PERSISTENT|SQLITE_PREPARE_*] flags. ^The ** sqlite3_prepare_v2() interface works exactly the same as ** sqlite3_prepare_v3() with a zero prepFlags parameter. **

*/ SQLITE_API int sqlite3_prepare( sqlite3 *db, /* Database handle */ const char *zSql, /* SQL statement, UTF-8 encoded */ int nByte, /* Maximum length of zSql in bytes. */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const char **pzTail /* OUT: Pointer to unused portion of zSql */ ); SQLITE_API int sqlite3_prepare_v2( sqlite3 *db, /* Database handle */ const char *zSql, /* SQL statement, UTF-8 encoded */ int nByte, /* Maximum length of zSql in bytes. */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const char **pzTail /* OUT: Pointer to unused portion of zSql */ ); SQLITE_API int sqlite3_prepare_v3( sqlite3 *db, /* Database handle */ const char *zSql, /* SQL statement, UTF-8 encoded */ int nByte, /* Maximum length of zSql in bytes. */ unsigned int prepFlags, /* Zero or more SQLITE_PREPARE_ flags */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const char **pzTail /* OUT: Pointer to unused portion of zSql */ ); SQLITE_API int sqlite3_prepare16( sqlite3 *db, /* Database handle */ const void *zSql, /* SQL statement, UTF-16 encoded */ int nByte, /* Maximum length of zSql in bytes. */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const void **pzTail /* OUT: Pointer to unused portion of zSql */ ); SQLITE_API int sqlite3_prepare16_v2( sqlite3 *db, /* Database handle */ const void *zSql, /* SQL statement, UTF-16 encoded */ int nByte, /* Maximum length of zSql in bytes. */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const void **pzTail /* OUT: Pointer to unused portion of zSql */ ); SQLITE_API int sqlite3_prepare16_v3( sqlite3 *db, /* Database handle */ const void *zSql, /* SQL statement, UTF-16 encoded */ int nByte, /* Maximum length of zSql in bytes. */ unsigned int prepFlags, /* Zero or more SQLITE_PREPARE_ flags */ sqlite3_stmt **ppStmt, /* OUT: Statement handle */ const void **pzTail /* OUT: Pointer to unused portion of zSql */ ); /* ** CAPI3REF: Retrieving Statement SQL ** METHOD: sqlite3_stmt ** ** ^The sqlite3_sql(P) interface returns a pointer to a copy of the UTF-8 ** SQL text used to create [prepared statement] P if P was ** created by [sqlite3_prepare_v2()], [sqlite3_prepare_v3()], ** [sqlite3_prepare16_v2()], or [sqlite3_prepare16_v3()]. ** ^The sqlite3_expanded_sql(P) interface returns a pointer to a UTF-8 ** string containing the SQL text of prepared statement P with ** [bound parameters] expanded. ** ** ^(For example, if a prepared statement is created using the SQL ** text "SELECT $abc,:xyz" and if parameter $abc is bound to integer 2345 ** and parameter :xyz is unbound, then sqlite3_sql() will return ** the original string, "SELECT $abc,:xyz" but sqlite3_expanded_sql() ** will return "SELECT 2345,NULL".)^ ** ** ^The sqlite3_expanded_sql() interface returns NULL if insufficient memory ** is available to hold the result, or if the result would exceed the ** the maximum string length determined by the [SQLITE_LIMIT_LENGTH]. ** ** ^The [SQLITE_TRACE_SIZE_LIMIT] compile-time option limits the size of ** bound parameter expansions. ^The [SQLITE_OMIT_TRACE] compile-time ** option causes sqlite3_expanded_sql() to always return NULL. ** ** ^The string returned by sqlite3_sql(P) is managed by SQLite and is ** automatically freed when the prepared statement is finalized. ** ^The string returned by sqlite3_expanded_sql(P), on the other hand, ** is obtained from [sqlite3_malloc()] and must be free by the application ** by passing it to [sqlite3_free()]. */ SQLITE_API const char *sqlite3_sql(sqlite3_stmt *pStmt); SQLITE_API char *sqlite3_expanded_sql(sqlite3_stmt *pStmt); /* ** CAPI3REF: Determine If An SQL Statement Writes The Database ** METHOD: sqlite3_stmt ** ** ^The sqlite3_stmt_readonly(X) interface returns true (non-zero) if ** and only if the [prepared statement] X makes no direct changes to ** the content of the database file. ** ** Note that [application-defined SQL functions] or ** [virtual tables] might change the database indirectly as a side effect. ** ^(For example, if an application defines a function "eval()" that ** calls [sqlite3_exec()], then the following SQL statement would ** change the database file through side-effects: ** ** 
**    SELECT eval('DELETE FROM t1') FROM t2;
**
** ** But because the [SELECT] statement does not change the database file ** directly, sqlite3_stmt_readonly() would still return true.)^ ** ** ^Transaction control statements such as [BEGIN], [COMMIT], [ROLLBACK], ** [SAVEPOINT], and [RELEASE] cause sqlite3_stmt_readonly() to return true, ** since the statements themselves do not actually modify the database but ** rather they control the timing of when other statements modify the ** database. ^The [ATTACH] and [DETACH] statements also cause ** sqlite3_stmt_readonly() to return true since, while those statements ** change the configuration of a database connection, they do not make ** changes to the content of the database files on disk. ** ^The sqlite3_stmt_readonly() interface returns true for [BEGIN] since ** [BEGIN] merely sets internal flags, but the [BEGIN|BEGIN IMMEDIATE] and ** [BEGIN|BEGIN EXCLUSIVE] commands do touch the database and so ** sqlite3_stmt_readonly() returns false for those commands. */ SQLITE_API int sqlite3_stmt_readonly(sqlite3_stmt *pStmt); /* ** CAPI3REF: Determine If A Prepared Statement Has Been Reset ** METHOD: sqlite3_stmt ** ** ^The sqlite3_stmt_busy(S) interface returns true (non-zero) if the ** [prepared statement] S has been stepped at least once using ** [sqlite3_step(S)] but has neither run to completion (returned ** [SQLITE_DONE] from [sqlite3_step(S)]) nor ** been reset using [sqlite3_reset(S)]. ^The sqlite3_stmt_busy(S) ** interface returns false if S is a NULL pointer. If S is not a ** NULL pointer and is not a pointer to a valid [prepared statement] ** object, then the behavior is undefined and probably undesirable. ** ** This interface can be used in combination [sqlite3_next_stmt()] ** to locate all prepared statements associated with a database ** connection that are in need of being reset. This can be used, ** for example, in diagnostic routines to search for prepared ** statements that are holding a transaction open. */ SQLITE_API int sqlite3_stmt_busy(sqlite3_stmt*); /* ** CAPI3REF: Dynamically Typed Value Object ** KEYWORDS: {protected sqlite3_value} {unprotected sqlite3_value} ** ** SQLite uses the sqlite3_value object to represent all values ** that can be stored in a database table. SQLite uses dynamic typing ** for the values it stores. ^Values stored in sqlite3_value objects ** can be integers, floating point values, strings, BLOBs, or NULL. ** ** An sqlite3_value object may be either "protected" or "unprotected". ** Some interfaces require a protected sqlite3_value. Other interfaces ** will accept either a protected or an unprotected sqlite3_value. ** Every interface that accepts sqlite3_value arguments specifies ** whether or not it requires a protected sqlite3_value. The ** [sqlite3_value_dup()] interface can be used to construct a new ** protected sqlite3_value from an unprotected sqlite3_value. ** ** The terms "protected" and "unprotected" refer to whether or not ** a mutex is held. An internal mutex is held for a protected ** sqlite3_value object but no mutex is held for an unprotected ** sqlite3_value object. If SQLite is compiled to be single-threaded ** (with [SQLITE_THREADSAFE=0] and with [sqlite3_threadsafe()] returning 0) ** or if SQLite is run in one of reduced mutex modes ** [SQLITE_CONFIG_SINGLETHREAD] or [SQLITE_CONFIG_MULTITHREAD] ** then there is no distinction between protected and unprotected ** sqlite3_value objects and they can be used interchangeably. However, ** for maximum code portability it is recommended that applications ** still make the distinction between protected and unprotected ** sqlite3_value objects even when not strictly required. ** ** ^The sqlite3_value objects that are passed as parameters into the ** implementation of [application-defined SQL functions] are protected. ** ^The sqlite3_value object returned by ** [sqlite3_column_value()] is unprotected. ** Unprotected sqlite3_value objects may only be used with ** [sqlite3_result_value()] and [sqlite3_bind_value()]. ** The [sqlite3_value_blob | sqlite3_value_type()] family of ** interfaces require protected sqlite3_value objects. */ typedef struct sqlite3_value sqlite3_value; /* ** CAPI3REF: SQL Function Context Object ** ** The context in which an SQL function executes is stored in an ** sqlite3_context object. ^A pointer to an sqlite3_context object ** is always first parameter to [application-defined SQL functions]. ** The application-defined SQL function implementation will pass this ** pointer through into calls to [sqlite3_result_int | sqlite3_result()], ** [sqlite3_aggregate_context()], [sqlite3_user_data()], ** [sqlite3_context_db_handle()], [sqlite3_get_auxdata()], ** and/or [sqlite3_set_auxdata()]. */ typedef struct sqlite3_context sqlite3_context; /* ** CAPI3REF: Binding Values To Prepared Statements ** KEYWORDS: {host parameter} {host parameters} {host parameter name} ** KEYWORDS: {SQL parameter} {SQL parameters} {parameter binding} ** METHOD: sqlite3_stmt ** ** ^(In the SQL statement text input to [sqlite3_prepare_v2()] and its variants, ** literals may be replaced by a [parameter] that matches one of following ** templates: ** **
    **
  • ? **
  • ?NNN **
  • :VVV **
  • @VVV **
  • $VVV **
** ** In the templates above, NNN represents an integer literal, ** and VVV represents an alphanumeric identifier.)^ ^The values of these ** parameters (also called "host parameter names" or "SQL parameters") ** can be set using the sqlite3_bind_*() routines defined here. ** ** ^The first argument to the sqlite3_bind_*() routines is always ** a pointer to the [sqlite3_stmt] object returned from ** [sqlite3_prepare_v2()] or its variants. ** ** ^The second argument is the index of the SQL parameter to be set. ** ^The leftmost SQL parameter has an index of 1. ^When the same named ** SQL parameter is used more than once, second and subsequent ** occurrences have the same index as the first occurrence. ** ^The index for named parameters can be looked up using the ** [sqlite3_bind_parameter_index()] API if desired. ^The index ** for "?NNN" parameters is the value of NNN. ** ^The NNN value must be between 1 and the [sqlite3_limit()] ** parameter [SQLITE_LIMIT_VARIABLE_NUMBER] (default value: 999). ** ** ^The third argument is the value to bind to the parameter. ** ^If the third parameter to sqlite3_bind_text() or sqlite3_bind_text16() ** or sqlite3_bind_blob() is a NULL pointer then the fourth parameter ** is ignored and the end result is the same as sqlite3_bind_null(). ** ** ^(In those routines that have a fourth argument, its value is the ** number of bytes in the parameter. To be clear: the value is the ** number of bytes in the value, not the number of characters.)^ ** ^If the fourth parameter to sqlite3_bind_text() or sqlite3_bind_text16() ** is negative, then the length of the string is ** the number of bytes up to the first zero terminator. ** If the fourth parameter to sqlite3_bind_blob() is negative, then ** the behavior is undefined. ** If a non-negative fourth parameter is provided to sqlite3_bind_text() ** or sqlite3_bind_text16() or sqlite3_bind_text64() then ** that parameter must be the byte offset ** where the NUL terminator would occur assuming the string were NUL ** terminated. If any NUL characters occur at byte offsets less than ** the value of the fourth parameter then the resulting string value will ** contain embedded NULs. The result of expressions involving strings ** with embedded NULs is undefined. ** ** ^The fifth argument to the BLOB and string binding interfaces ** is a destructor used to dispose of the BLOB or ** string after SQLite has finished with it. ^The destructor is called ** to dispose of the BLOB or string even if the call to bind API fails. ** ^If the fifth argument is ** the special value [SQLITE_STATIC], then SQLite assumes that the ** information is in static, unmanaged space and does not need to be freed. ** ^If the fifth argument has the value [SQLITE_TRANSIENT], then ** SQLite makes its own private copy of the data immediately, before ** the sqlite3_bind_*() routine returns. ** ** ^The sixth argument to sqlite3_bind_text64() must be one of ** [SQLITE_UTF8], [SQLITE_UTF16], [SQLITE_UTF16BE], or [SQLITE_UTF16LE] ** to specify the encoding of the text in the third parameter. If ** the sixth argument to sqlite3_bind_text64() is not one of the ** allowed values shown above, or if the text encoding is different ** from the encoding specified by the sixth parameter, then the behavior ** is undefined. ** ** ^The sqlite3_bind_zeroblob() routine binds a BLOB of length N that ** is filled with zeroes. ^A zeroblob uses a fixed amount of memory ** (just an integer to hold its size) while it is being processed. ** Zeroblobs are intended to serve as placeholders for BLOBs whose ** content is later written using ** [sqlite3_blob_open | incremental BLOB I/O] routines. ** ^A negative value for the zeroblob results in a zero-length BLOB. ** ** ^The sqlite3_bind_pointer(S,I,P,T,D) routine causes the I-th parameter in ** [prepared statement] S to have an SQL value of NULL, but to also be ** associated with the pointer P of type T. ^D is either a NULL pointer or ** a pointer to a destructor function for P. ^SQLite will invoke the ** destructor D with a single argument of P when it is finished using ** P. The T parameter should be a static string, preferably a string ** literal. The sqlite3_bind_pointer() routine is part of the ** [pointer passing interface] added for SQLite 3.20.0. ** ** ^If any of the sqlite3_bind_*() routines are called with a NULL pointer ** for the [prepared statement] or with a prepared statement for which ** [sqlite3_step()] has been called more recently than [sqlite3_reset()], ** then the call will return [SQLITE_MISUSE]. If any sqlite3_bind_() ** routine is passed a [prepared statement] that has been finalized, the ** result is undefined and probably harmful. ** ** ^Bindings are not cleared by the [sqlite3_reset()] routine. ** ^Unbound parameters are interpreted as NULL. ** ** ^The sqlite3_bind_* routines return [SQLITE_OK] on success or an ** [error code] if anything goes wrong. ** ^[SQLITE_TOOBIG] might be returned if the size of a string or BLOB ** exceeds limits imposed by [sqlite3_limit]([SQLITE_LIMIT_LENGTH]) or ** [SQLITE_MAX_LENGTH]. ** ^[SQLITE_RANGE] is returned if the parameter ** index is out of range. ^[SQLITE_NOMEM] is returned if malloc() fails. ** ** See also: [sqlite3_bind_parameter_count()], ** [sqlite3_bind_parameter_name()], and [sqlite3_bind_parameter_index()]. */ SQLITE_API int sqlite3_bind_blob(sqlite3_stmt*, int, const void*, int n, void(*)(void*)); SQLITE_API int sqlite3_bind_blob64(sqlite3_stmt*, int, const void*, sqlite3_uint64, void(*)(void*)); SQLITE_API int sqlite3_bind_double(sqlite3_stmt*, int, double); SQLITE_API int sqlite3_bind_int(sqlite3_stmt*, int, int); SQLITE_API int sqlite3_bind_int64(sqlite3_stmt*, int, sqlite3_int64); SQLITE_API int sqlite3_bind_null(sqlite3_stmt*, int); SQLITE_API int sqlite3_bind_text(sqlite3_stmt*,int,const char*,int,void(*)(void*)); SQLITE_API int sqlite3_bind_text16(sqlite3_stmt*, int, const void*, int, void(*)(void*)); SQLITE_API int sqlite3_bind_text64(sqlite3_stmt*, int, const char*, sqlite3_uint64, void(*)(void*), unsigned char encoding); SQLITE_API int sqlite3_bind_value(sqlite3_stmt*, int, const sqlite3_value*); SQLITE_API int sqlite3_bind_pointer(sqlite3_stmt*, int, void*, const char*,void(*)(void*)); SQLITE_API int sqlite3_bind_zeroblob(sqlite3_stmt*, int, int n); SQLITE_API int sqlite3_bind_zeroblob64(sqlite3_stmt*, int, sqlite3_uint64); /* ** CAPI3REF: Number Of SQL Parameters ** METHOD: sqlite3_stmt ** ** ^This routine can be used to find the number of [SQL parameters] ** in a [prepared statement]. SQL parameters are tokens of the ** form "?", "?NNN", ":AAA", "$AAA", or "@AAA" that serve as ** placeholders for values that are [sqlite3_bind_blob | bound] ** to the parameters at a later time. ** ** ^(This routine actually returns the index of the largest (rightmost) ** parameter. For all forms except ?NNN, this will correspond to the ** number of unique parameters. If parameters of the ?NNN form are used, ** there may be gaps in the list.)^ ** ** See also: [sqlite3_bind_blob|sqlite3_bind()], ** [sqlite3_bind_parameter_name()], and ** [sqlite3_bind_parameter_index()]. */ SQLITE_API int sqlite3_bind_parameter_count(sqlite3_stmt*); /* ** CAPI3REF: Name Of A Host Parameter ** METHOD: sqlite3_stmt ** ** ^The sqlite3_bind_parameter_name(P,N) interface returns ** the name of the N-th [SQL parameter] in the [prepared statement] P. ** ^(SQL parameters of the form "?NNN" or ":AAA" or "@AAA" or "$AAA" ** have a name which is the string "?NNN" or ":AAA" or "@AAA" or "$AAA" ** respectively. ** In other words, the initial ":" or "$" or "@" or "?" ** is included as part of the name.)^ ** ^Parameters of the form "?" without a following integer have no name ** and are referred to as "nameless" or "anonymous parameters". ** ** ^The first host parameter has an index of 1, not 0. ** ** ^If the value N is out of range or if the N-th parameter is ** nameless, then NULL is returned. ^The returned string is ** always in UTF-8 encoding even if the named parameter was ** originally specified as UTF-16 in [sqlite3_prepare16()], ** [sqlite3_prepare16_v2()], or [sqlite3_prepare16_v3()]. ** ** See also: [sqlite3_bind_blob|sqlite3_bind()], ** [sqlite3_bind_parameter_count()], and ** [sqlite3_bind_parameter_index()]. */ SQLITE_API const char *sqlite3_bind_parameter_name(sqlite3_stmt*, int); /* ** CAPI3REF: Index Of A Parameter With A Given Name ** METHOD: sqlite3_stmt ** ** ^Return the index of an SQL parameter given its name. ^The ** index value returned is suitable for use as the second ** parameter to [sqlite3_bind_blob|sqlite3_bind()]. ^A zero ** is returned if no matching parameter is found. ^The parameter ** name must be given in UTF-8 even if the original statement ** was prepared from UTF-16 text using [sqlite3_prepare16_v2()] or ** [sqlite3_prepare16_v3()]. ** ** See also: [sqlite3_bind_blob|sqlite3_bind()], ** [sqlite3_bind_parameter_count()], and ** [sqlite3_bind_parameter_name()]. */ SQLITE_API int sqlite3_bind_parameter_index(sqlite3_stmt*, const char *zName); /* ** CAPI3REF: Reset All Bindings On A Prepared Statement ** METHOD: sqlite3_stmt ** ** ^Contrary to the intuition of many, [sqlite3_reset()] does not reset ** the [sqlite3_bind_blob | bindings] on a [prepared statement]. ** ^Use this routine to reset all host parameters to NULL. */ SQLITE_API int sqlite3_clear_bindings(sqlite3_stmt*); /* ** CAPI3REF: Number Of Columns In A Result Set ** METHOD: sqlite3_stmt ** ** ^Return the number of columns in the result set returned by the ** [prepared statement]. ^If this routine returns 0, that means the ** [prepared statement] returns no data (for example an [UPDATE]). ** ^However, just because this routine returns a positive number does not ** mean that one or more rows of data will be returned. ^A SELECT statement ** will always have a positive sqlite3_column_count() but depending on the ** WHERE clause constraints and the table content, it might return no rows. ** ** See also: [sqlite3_data_count()] */ SQLITE_API int sqlite3_column_count(sqlite3_stmt *pStmt); /* ** CAPI3REF: Column Names In A Result Set ** METHOD: sqlite3_stmt ** ** ^These routines return the name assigned to a particular column ** in the result set of a [SELECT] statement. ^The sqlite3_column_name() ** interface returns a pointer to a zero-terminated UTF-8 string ** and sqlite3_column_name16() returns a pointer to a zero-terminated ** UTF-16 string. ^The first parameter is the [prepared statement] ** that implements the [SELECT] statement. ^The second parameter is the ** column number. ^The leftmost column is number 0. ** ** ^The returned string pointer is valid until either the [prepared statement] ** is destroyed by [sqlite3_finalize()] or until the statement is automatically ** reprepared by the first call to [sqlite3_step()] for a particular run ** or until the next call to ** sqlite3_column_name() or sqlite3_column_name16() on the same column. ** ** ^If sqlite3_malloc() fails during the processing of either routine ** (for example during a conversion from UTF-8 to UTF-16) then a ** NULL pointer is returned. ** ** ^The name of a result column is the value of the "AS" clause for ** that column, if there is an AS clause. If there is no AS clause ** then the name of the column is unspecified and may change from ** one release of SQLite to the next. */ SQLITE_API const char *sqlite3_column_name(sqlite3_stmt*, int N); SQLITE_API const void *sqlite3_column_name16(sqlite3_stmt*, int N); /* ** CAPI3REF: Source Of Data In A Query Result ** METHOD: sqlite3_stmt ** ** ^These routines provide a means to determine the database, table, and ** table column that is the origin of a particular result column in ** [SELECT] statement. ** ^The name of the database or table or column can be returned as ** either a UTF-8 or UTF-16 string. ^The _database_ routines return ** the database name, the _table_ routines return the table name, and ** the origin_ routines return the column name. ** ^The returned string is valid until the [prepared statement] is destroyed ** using [sqlite3_finalize()] or until the statement is automatically ** reprepared by the first call to [sqlite3_step()] for a particular run ** or until the same information is requested ** again in a different encoding. ** ** ^The names returned are the original un-aliased names of the ** database, table, and column. ** ** ^The first argument to these interfaces is a [prepared statement]. ** ^These functions return information about the Nth result column returned by ** the statement, where N is the second function argument. ** ^The left-most column is column 0 for these routines. ** ** ^If the Nth column returned by the statement is an expression or ** subquery and is not a column value, then all of these functions return ** NULL. ^These routine might also return NULL if a memory allocation error ** occurs. ^Otherwise, they return the name of the attached database, table, ** or column that query result column was extracted from. ** ** ^As with all other SQLite APIs, those whose names end with "16" return ** UTF-16 encoded strings and the other functions return UTF-8. ** ** ^These APIs are only available if the library was compiled with the ** [SQLITE_ENABLE_COLUMN_METADATA] C-preprocessor symbol. ** ** If two or more threads call one or more of these routines against the same ** prepared statement and column at the same time then the results are ** undefined. ** ** If two or more threads call one or more ** [sqlite3_column_database_name | column metadata interfaces] ** for the same [prepared statement] and result column ** at the same time then the results are undefined. */ SQLITE_API const char *sqlite3_column_database_name(sqlite3_stmt*,int); SQLITE_API const void *sqlite3_column_database_name16(sqlite3_stmt*,int); SQLITE_API const char *sqlite3_column_table_name(sqlite3_stmt*,int); SQLITE_API const void *sqlite3_column_table_name16(sqlite3_stmt*,int); SQLITE_API const char *sqlite3_column_origin_name(sqlite3_stmt*,int); SQLITE_API const void *sqlite3_column_origin_name16(sqlite3_stmt*,int); /* ** CAPI3REF: Declared Datatype Of A Query Result ** METHOD: sqlite3_stmt ** ** ^(The first parameter is a [prepared statement]. ** If this statement is a [SELECT] statement and the Nth column of the ** returned result set of that [SELECT] is a table column (not an ** expression or subquery) then the declared type of the table ** column is returned.)^ ^If the Nth column of the result set is an ** expression or subquery, then a NULL pointer is returned. ** ^The returned string is always UTF-8 encoded. ** ** ^(For example, given the database schema: ** ** CREATE TABLE t1(c1 VARIANT); ** ** and the following statement to be compiled: ** ** SELECT c1 + 1, c1 FROM t1; ** ** this routine would return the string "VARIANT" for the second result ** column (i==1), and a NULL pointer for the first result column (i==0).)^ ** ** ^SQLite uses dynamic run-time typing. ^So just because a column ** is declared to contain a particular type does not mean that the ** data stored in that column is of the declared type. SQLite is ** strongly typed, but the typing is dynamic not static. ^Type ** is associated with individual values, not with the containers ** used to hold those values. */ SQLITE_API const char *sqlite3_column_decltype(sqlite3_stmt*,int); SQLITE_API const void *sqlite3_column_decltype16(sqlite3_stmt*,int); /* ** CAPI3REF: Evaluate An SQL Statement ** METHOD: sqlite3_stmt ** ** After a [prepared statement] has been prepared using any of ** [sqlite3_prepare_v2()], [sqlite3_prepare_v3()], [sqlite3_prepare16_v2()], ** or [sqlite3_prepare16_v3()] or one of the legacy ** interfaces [sqlite3_prepare()] or [sqlite3_prepare16()], this function ** must be called one or more times to evaluate the statement. ** ** The details of the behavior of the sqlite3_step() interface depend ** on whether the statement was prepared using the newer "vX" interfaces ** [sqlite3_prepare_v3()], [sqlite3_prepare_v2()], [sqlite3_prepare16_v3()], ** [sqlite3_prepare16_v2()] or the older legacy ** interfaces [sqlite3_prepare()] and [sqlite3_prepare16()]. The use of the ** new "vX" interface is recommended for new applications but the legacy ** interface will continue to be supported. ** ** ^In the legacy interface, the return value will be either [SQLITE_BUSY], ** [SQLITE_DONE], [SQLITE_ROW], [SQLITE_ERROR], or [SQLITE_MISUSE]. ** ^With the "v2" interface, any of the other [result codes] or ** [extended result codes] might be returned as well. ** ** ^[SQLITE_BUSY] means that the database engine was unable to acquire the ** database locks it needs to do its job. ^If the statement is a [COMMIT] ** or occurs outside of an explicit transaction, then you can retry the ** statement. If the statement is not a [COMMIT] and occurs within an ** explicit transaction then you should rollback the transaction before ** continuing. ** ** ^[SQLITE_DONE] means that the statement has finished executing ** successfully. sqlite3_step() should not be called again on this virtual ** machine without first calling [sqlite3_reset()] to reset the virtual ** machine back to its initial state. ** ** ^If the SQL statement being executed returns any data, then [SQLITE_ROW] ** is returned each time a new row of data is ready for processing by the ** caller. The values may be accessed using the [column access functions]. ** sqlite3_step() is called again to retrieve the next row of data. ** ** ^[SQLITE_ERROR] means that a run-time error (such as a constraint ** violation) has occurred. sqlite3_step() should not be called again on ** the VM. More information may be found by calling [sqlite3_errmsg()]. ** ^With the legacy interface, a more specific error code (for example, ** [SQLITE_INTERRUPT], [SQLITE_SCHEMA], [SQLITE_CORRUPT], and so forth) ** can be obtained by calling [sqlite3_reset()] on the ** [prepared statement]. ^In the "v2" interface, ** the more specific error code is returned directly by sqlite3_step(). ** ** [SQLITE_MISUSE] means that the this routine was called inappropriately. ** Perhaps it was called on a [prepared statement] that has ** already been [sqlite3_finalize | finalized] or on one that had ** previously returned [SQLITE_ERROR] or [SQLITE_DONE]. Or it could ** be the case that the same database connection is being used by two or ** more threads at the same moment in time. ** ** For all versions of SQLite up to and including 3.6.23.1, a call to ** [sqlite3_reset()] was required after sqlite3_step() returned anything ** other than [SQLITE_ROW] before any subsequent invocation of ** sqlite3_step(). Failure to reset the prepared statement using ** [sqlite3_reset()] would result in an [SQLITE_MISUSE] return from ** sqlite3_step(). But after [version 3.6.23.1] ([dateof:3.6.23.1]), ** sqlite3_step() began ** calling [sqlite3_reset()] automatically in this circumstance rather ** than returning [SQLITE_MISUSE]. This is not considered a compatibility ** break because any application that ever receives an SQLITE_MISUSE error ** is broken by definition. The [SQLITE_OMIT_AUTORESET] compile-time option ** can be used to restore the legacy behavior. ** ** Goofy Interface Alert: In the legacy interface, the sqlite3_step() ** API always returns a generic error code, [SQLITE_ERROR], following any ** error other than [SQLITE_BUSY] and [SQLITE_MISUSE]. You must call ** [sqlite3_reset()] or [sqlite3_finalize()] in order to find one of the ** specific [error codes] that better describes the error. ** We admit that this is a goofy design. The problem has been fixed ** with the "v2" interface. If you prepare all of your SQL statements ** using [sqlite3_prepare_v3()] or [sqlite3_prepare_v2()] ** or [sqlite3_prepare16_v2()] or [sqlite3_prepare16_v3()] instead ** of the legacy [sqlite3_prepare()] and [sqlite3_prepare16()] interfaces, ** then the more specific [error codes] are returned directly ** by sqlite3_step(). The use of the "vX" interfaces is recommended. */ SQLITE_API int sqlite3_step(sqlite3_stmt*); /* ** CAPI3REF: Number of columns in a result set ** METHOD: sqlite3_stmt ** ** ^The sqlite3_data_count(P) interface returns the number of columns in the ** current row of the result set of [prepared statement] P. ** ^If prepared statement P does not have results ready to return ** (via calls to the [sqlite3_column_int | sqlite3_column_*()] of ** interfaces) then sqlite3_data_count(P) returns 0. ** ^The sqlite3_data_count(P) routine also returns 0 if P is a NULL pointer. ** ^The sqlite3_data_count(P) routine returns 0 if the previous call to ** [sqlite3_step](P) returned [SQLITE_DONE]. ^The sqlite3_data_count(P) ** will return non-zero if previous call to [sqlite3_step](P) returned ** [SQLITE_ROW], except in the case of the [PRAGMA incremental_vacuum] ** where it always returns zero since each step of that multi-step ** pragma returns 0 columns of data. ** ** See also: [sqlite3_column_count()] */ SQLITE_API int sqlite3_data_count(sqlite3_stmt *pStmt); /* ** CAPI3REF: Fundamental Datatypes ** KEYWORDS: SQLITE_TEXT ** ** ^(Every value in SQLite has one of five fundamental datatypes: ** **
    **
  • 64-bit signed integer **
  • 64-bit IEEE floating point number **
  • string **
  • BLOB **
  • NULL **
)^ ** ** These constants are codes for each of those types. ** ** Note that the SQLITE_TEXT constant was also used in SQLite version 2 ** for a completely different meaning. Software that links against both ** SQLite version 2 and SQLite version 3 should use SQLITE3_TEXT, not ** SQLITE_TEXT. */ #define SQLITE_INTEGER 1 #define SQLITE_FLOAT 2 #define SQLITE_BLOB 4 #define SQLITE_NULL 5 #ifdef SQLITE_TEXT # undef SQLITE_TEXT #else # define SQLITE_TEXT 3 #endif #define SQLITE3_TEXT 3 /* ** CAPI3REF: Result Values From A Query ** KEYWORDS: {column access functions} ** METHOD: sqlite3_stmt ** ** Summary: **
**
sqlite3_column_blob→BLOB result **
sqlite3_column_double→REAL result **
sqlite3_column_int→32-bit INTEGER result **
sqlite3_column_int64→64-bit INTEGER result **
sqlite3_column_text→UTF-8 TEXT result **
sqlite3_column_text16→UTF-16 TEXT result **
sqlite3_column_value→The result as an ** [sqlite3_value|unprotected sqlite3_value] object. **
    **
sqlite3_column_bytes→Size of a BLOB ** or a UTF-8 TEXT result in bytes **
sqlite3_column_bytes16   ** →  Size of UTF-16 ** TEXT in bytes **
sqlite3_column_type→Default ** datatype of the result **
** ** Details: ** ** ^These routines return information about a single column of the current ** result row of a query. ^In every case the first argument is a pointer ** to the [prepared statement] that is being evaluated (the [sqlite3_stmt*] ** that was returned from [sqlite3_prepare_v2()] or one of its variants) ** and the second argument is the index of the column for which information ** should be returned. ^The leftmost column of the result set has the index 0. ** ^The number of columns in the result can be determined using ** [sqlite3_column_count()]. ** ** If the SQL statement does not currently point to a valid row, or if the ** column index is out of range, the result is undefined. ** These routines may only be called when the most recent call to ** [sqlite3_step()] has returned [SQLITE_ROW] and neither ** [sqlite3_reset()] nor [sqlite3_finalize()] have been called subsequently. ** If any of these routines are called after [sqlite3_reset()] or ** [sqlite3_finalize()] or after [sqlite3_step()] has returned ** something other than [SQLITE_ROW], the results are undefined. ** If [sqlite3_step()] or [sqlite3_reset()] or [sqlite3_finalize()] ** are called from a different thread while any of these routines ** are pending, then the results are undefined. ** ** The first six interfaces (_blob, _double, _int, _int64, _text, and _text16) ** each return the value of a result column in a specific data format. If ** the result column is not initially in the requested format (for example, ** if the query returns an integer but the sqlite3_column_text() interface ** is used to extract the value) then an automatic type conversion is performed. ** ** ^The sqlite3_column_type() routine returns the ** [SQLITE_INTEGER | datatype code] for the initial data type ** of the result column. ^The returned value is one of [SQLITE_INTEGER], ** [SQLITE_FLOAT], [SQLITE_TEXT], [SQLITE_BLOB], or [SQLITE_NULL]. ** The return value of sqlite3_column_type() can be used to decide which ** of the first six interface should be used to extract the column value. ** The value returned by sqlite3_column_type() is only meaningful if no ** automatic type conversions have occurred for the value in question. ** After a type conversion, the result of calling sqlite3_column_type() ** is undefined, though harmless. Future ** versions of SQLite may change the behavior of sqlite3_column_type() ** following a type conversion. ** ** If the result is a BLOB or a TEXT string, then the sqlite3_column_bytes() ** or sqlite3_column_bytes16() interfaces can be used to determine the size ** of that BLOB or string. ** ** ^If the result is a BLOB or UTF-8 string then the sqlite3_column_bytes() ** routine returns the number of bytes in that BLOB or string. ** ^If the result is a UTF-16 string, then sqlite3_column_bytes() converts ** the string to UTF-8 and then returns the number of bytes. ** ^If the result is a numeric value then sqlite3_column_bytes() uses ** [sqlite3_snprintf()] to convert that value to a UTF-8 string and returns ** the number of bytes in that string. ** ^If the result is NULL, then sqlite3_column_bytes() returns zero. ** ** ^If the result is a BLOB or UTF-16 string then the sqlite3_column_bytes16() ** routine returns the number of bytes in that BLOB or string. ** ^If the result is a UTF-8 string, then sqlite3_column_bytes16() converts ** the string to UTF-16 and then returns the number of bytes. ** ^If the result is a numeric value then sqlite3_column_bytes16() uses ** [sqlite3_snprintf()] to convert that value to a UTF-16 string and returns ** the number of bytes in that string. ** ^If the result is NULL, then sqlite3_column_bytes16() returns zero. ** ** ^The values returned by [sqlite3_column_bytes()] and ** [sqlite3_column_bytes16()] do not include the zero terminators at the end ** of the string. ^For clarity: the values returned by ** [sqlite3_column_bytes()] and [sqlite3_column_bytes16()] are the number of ** bytes in the string, not the number of characters. ** ** ^Strings returned by sqlite3_column_text() and sqlite3_column_text16(), ** even empty strings, are always zero-terminated. ^The return ** value from sqlite3_column_blob() for a zero-length BLOB is a NULL pointer. ** ** Warning: ^The object returned by [sqlite3_column_value()] is an ** [unprotected sqlite3_value] object. In a multithreaded environment, ** an unprotected sqlite3_value object may only be used safely with ** [sqlite3_bind_value()] and [sqlite3_result_value()]. ** If the [unprotected sqlite3_value] object returned by ** [sqlite3_column_value()] is used in any other way, including calls ** to routines like [sqlite3_value_int()], [sqlite3_value_text()], ** or [sqlite3_value_bytes()], the behavior is not threadsafe. ** Hence, the sqlite3_column_value() interface ** is normally only useful within the implementation of ** [application-defined SQL functions] or [virtual tables], not within ** top-level application code. ** ** The these routines may attempt to convert the datatype of the result. ** ^For example, if the internal representation is FLOAT and a text result ** is requested, [sqlite3_snprintf()] is used internally to perform the ** conversion automatically. ^(The following table details the conversions ** that are applied: ** **
** **
Internal
Type 		Requested
Type 		Conversion ** **
NULL INTEGER Result is 0 **
NULL FLOAT Result is 0.0 **
NULL TEXT Result is a NULL pointer **
NULL BLOB Result is a NULL pointer **
INTEGER FLOAT Convert from integer to float **
INTEGER TEXT ASCII rendering of the integer **
INTEGER BLOB Same as INTEGER->TEXT **
FLOAT INTEGER [CAST] to INTEGER **
FLOAT TEXT ASCII rendering of the float **
FLOAT BLOB [CAST] to BLOB **
TEXT INTEGER [CAST] to INTEGER **
TEXT FLOAT [CAST] to REAL **
TEXT BLOB No change **
BLOB INTEGER [CAST] to INTEGER **
BLOB FLOAT [CAST] to REAL **
BLOB TEXT Add a zero terminator if needed **
**
)^ ** ** Note that when type conversions occur, pointers returned by prior ** calls to sqlite3_column_blob(), sqlite3_column_text(), and/or ** sqlite3_column_text16() may be invalidated. ** Type conversions and pointer invalidations might occur ** in the following cases: ** **
    **
  • The initial content is a BLOB and sqlite3_column_text() or ** sqlite3_column_text16() is called. A zero-terminator might ** need to be added to the string.
    • **
  • The initial content is UTF-8 text and sqlite3_column_bytes16() or ** sqlite3_column_text16() is called. The content must be converted ** to UTF-16.
    • **
  • The initial content is UTF-16 text and sqlite3_column_bytes() or ** sqlite3_column_text() is called. The content must be converted ** to UTF-8.
    • **
** ** ^Conversions between UTF-16be and UTF-16le are always done in place and do ** not invalidate a prior pointer, though of course the content of the buffer ** that the prior pointer references will have been modified. Other kinds ** of conversion are done in place when it is possible, but sometimes they ** are not possible and in those cases prior pointers are invalidated. ** ** The safest policy is to invoke these routines ** in one of the following ways: ** **
    **
  • sqlite3_column_text() followed by sqlite3_column_bytes()
    • **
  • sqlite3_column_blob() followed by sqlite3_column_bytes()
    • **
  • sqlite3_column_text16() followed by sqlite3_column_bytes16()
    • **
** ** In other words, you should call sqlite3_column_text(), ** sqlite3_column_blob(), or sqlite3_column_text16() first to force the result ** into the desired format, then invoke sqlite3_column_bytes() or ** sqlite3_column_bytes16() to find the size of the result. Do not mix calls ** to sqlite3_column_text() or sqlite3_column_blob() with calls to ** sqlite3_column_bytes16(), and do not mix calls to sqlite3_column_text16() ** with calls to sqlite3_column_bytes(). ** ** ^The pointers returned are valid until a type conversion occurs as ** described above, or until [sqlite3_step()] or [sqlite3_reset()] or ** [sqlite3_finalize()] is called. ^The memory space used to hold strings ** and BLOBs is freed automatically. Do not pass the pointers returned ** from [sqlite3_column_blob()], [sqlite3_column_text()], etc. into ** [sqlite3_free()]. ** ** ^(If a memory allocation error occurs during the evaluation of any ** of these routines, a default value is returned. The default value ** is either the integer 0, the floating point number 0.0, or a NULL ** pointer. Subsequent calls to [sqlite3_errcode()] will return ** [SQLITE_NOMEM].)^ */ SQLITE_API const void *sqlite3_column_blob(sqlite3_stmt*, int iCol); SQLITE_API double sqlite3_column_double(sqlite3_stmt*, int iCol); SQLITE_API int sqlite3_column_int(sqlite3_stmt*, int iCol); SQLITE_API sqlite3_int64 sqlite3_column_int64(sqlite3_stmt*, int iCol); SQLITE_API const unsigned char *sqlite3_column_text(sqlite3_stmt*, int iCol); SQLITE_API const void *sqlite3_column_text16(sqlite3_stmt*, int iCol); SQLITE_API sqlite3_value *sqlite3_column_value(sqlite3_stmt*, int iCol); SQLITE_API int sqlite3_column_bytes(sqlite3_stmt*, int iCol); SQLITE_API int sqlite3_column_bytes16(sqlite3_stmt*, int iCol); SQLITE_API int sqlite3_column_type(sqlite3_stmt*, int iCol); /* ** CAPI3REF: Destroy A Prepared Statement Object ** DESTRUCTOR: sqlite3_stmt ** ** ^The sqlite3_finalize() function is called to delete a [prepared statement]. ** ^If the most recent evaluation of the statement encountered no errors ** or if the statement is never been evaluated, then sqlite3_finalize() returns ** SQLITE_OK. ^If the most recent evaluation of statement S failed, then ** sqlite3_finalize(S) returns the appropriate [error code] or ** [extended error code]. ** ** ^The sqlite3_finalize(S) routine can be called at any point during ** the life cycle of [prepared statement] S: ** before statement S is ever evaluated, after ** one or more calls to [sqlite3_reset()], or after any call ** to [sqlite3_step()] regardless of whether or not the statement has ** completed execution. ** ** ^Invoking sqlite3_finalize() on a NULL pointer is a harmless no-op. ** ** The application must finalize every [prepared statement] in order to avoid ** resource leaks. It is a grievous error for the application to try to use ** a prepared statement after it has been finalized. Any use of a prepared ** statement after it has been finalized can result in undefined and ** undesirable behavior such as segfaults and heap corruption. */ SQLITE_API int sqlite3_finalize(sqlite3_stmt *pStmt); /* ** CAPI3REF: Reset A Prepared Statement Object ** METHOD: sqlite3_stmt ** ** The sqlite3_reset() function is called to reset a [prepared statement] ** object back to its initial state, ready to be re-executed. ** ^Any SQL statement variables that had values bound to them using ** the [sqlite3_bind_blob | sqlite3_bind_*() API] retain their values. ** Use [sqlite3_clear_bindings()] to reset the bindings. ** ** ^The [sqlite3_reset(S)] interface resets the [prepared statement] S ** back to the beginning of its program. ** ** ^If the most recent call to [sqlite3_step(S)] for the ** [prepared statement] S returned [SQLITE_ROW] or [SQLITE_DONE], ** or if [sqlite3_step(S)] has never before been called on S, ** then [sqlite3_reset(S)] returns [SQLITE_OK]. ** ** ^If the most recent call to [sqlite3_step(S)] for the ** [prepared statement] S indicated an error, then ** [sqlite3_reset(S)] returns an appropriate [error code]. ** ** ^The [sqlite3_reset(S)] interface does not change the values ** of any [sqlite3_bind_blob|bindings] on the [prepared statement] S. */ SQLITE_API int sqlite3_reset(sqlite3_stmt *pStmt); /* ** CAPI3REF: Create Or Redefine SQL Functions ** KEYWORDS: {function creation routines} ** KEYWORDS: {application-defined SQL function} ** KEYWORDS: {application-defined SQL functions} ** METHOD: sqlite3 ** ** ^These functions (collectively known as "function creation routines") ** are used to add SQL functions or aggregates or to redefine the behavior ** of existing SQL functions or aggregates. The only differences between ** these routines are the text encoding expected for ** the second parameter (the name of the function being created) ** and the presence or absence of a destructor callback for ** the application data pointer. ** ** ^The first parameter is the [database connection] to which the SQL ** function is to be added. ^If an application uses more than one database ** connection then application-defined SQL functions must be added ** to each database connection separately. ** ** ^The second parameter is the name of the SQL function to be created or ** redefined. ^The length of the name is limited to 255 bytes in a UTF-8 ** representation, exclusive of the zero-terminator. ^Note that the name ** length limit is in UTF-8 bytes, not characters nor UTF-16 bytes. ** ^Any attempt to create a function with a longer name ** will result in [SQLITE_MISUSE] being returned. ** ** ^The third parameter (nArg) ** is the number of arguments that the SQL function or ** aggregate takes. ^If this parameter is -1, then the SQL function or ** aggregate may take any number of arguments between 0 and the limit ** set by [sqlite3_limit]([SQLITE_LIMIT_FUNCTION_ARG]). If the third ** parameter is less than -1 or greater than 127 then the behavior is ** undefined. ** ** ^The fourth parameter, eTextRep, specifies what ** [SQLITE_UTF8 | text encoding] this SQL function prefers for ** its parameters. The application should set this parameter to ** [SQLITE_UTF16LE] if the function implementation invokes ** [sqlite3_value_text16le()] on an input, or [SQLITE_UTF16BE] if the ** implementation invokes [sqlite3_value_text16be()] on an input, or ** [SQLITE_UTF16] if [sqlite3_value_text16()] is used, or [SQLITE_UTF8] ** otherwise. ^The same SQL function may be registered multiple times using ** different preferred text encodings, with different implementations for ** each encoding. ** ^When multiple implementations of the same function are available, SQLite ** will pick the one that involves the least amount of data conversion. ** ** ^The fourth parameter may optionally be ORed with [SQLITE_DETERMINISTIC] ** to signal that the function will always return the same result given ** the same inputs within a single SQL statement. Most SQL functions are ** deterministic. The built-in [random()] SQL function is an example of a ** function that is not deterministic. The SQLite query planner is able to ** perform additional optimizations on deterministic functions, so use ** of the [SQLITE_DETERMINISTIC] flag is recommended where possible. ** ** ^(The fifth parameter is an arbitrary pointer. The implementation of the ** function can gain access to this pointer using [sqlite3_user_data()].)^ ** ** ^The sixth, seventh and eighth parameters, xFunc, xStep and xFinal, are ** pointers to C-language functions that implement the SQL function or ** aggregate. ^A scalar SQL function requires an implementation of the xFunc ** callback only; NULL pointers must be passed as the xStep and xFinal ** parameters. ^An aggregate SQL function requires an implementation of xStep ** and xFinal and NULL pointer must be passed for xFunc. ^To delete an existing ** SQL function or aggregate, pass NULL pointers for all three function ** callbacks. ** ** ^(If the ninth parameter to sqlite3_create_function_v2() is not NULL, ** then it is destructor for the application data pointer. ** The destructor is invoked when the function is deleted, either by being ** overloaded or when the database connection closes.)^ ** ^The destructor is also invoked if the call to ** sqlite3_create_function_v2() fails. ** ^When the destructor callback of the tenth parameter is invoked, it ** is passed a single argument which is a copy of the application data ** pointer which was the fifth parameter to sqlite3_create_function_v2(). ** ** ^It is permitted to register multiple implementations of the same ** functions with the same name but with either differing numbers of ** arguments or differing preferred text encodings. ^SQLite will use ** the implementation that most closely matches the way in which the ** SQL function is used. ^A function implementation with a non-negative ** nArg parameter is a better match than a function implementation with ** a negative nArg. ^A function where the preferred text encoding ** matches the database encoding is a better ** match than a function where the encoding is different. ** ^A function where the encoding difference is between UTF16le and UTF16be ** is a closer match than a function where the encoding difference is ** between UTF8 and UTF16. ** ** ^Built-in functions may be overloaded by new application-defined functions. ** ** ^An application-defined function is permitted to call other ** SQLite interfaces. However, such calls must not ** close the database connection nor finalize or reset the prepared ** statement in which the function is running. */ SQLITE_API int sqlite3_create_function( sqlite3 *db, const char *zFunctionName, int nArg, int eTextRep, void *pApp, void (*xFunc)(sqlite3_context*,int,sqlite3_value**), void (*xStep)(sqlite3_context*,int,sqlite3_value**), void (*xFinal)(sqlite3_context*) ); SQLITE_API int sqlite3_create_function16( sqlite3 *db, const void *zFunctionName, int nArg, int eTextRep, void *pApp, void (*xFunc)(sqlite3_context*,int,sqlite3_value**), void (*xStep)(sqlite3_context*,int,sqlite3_value**), void (*xFinal)(sqlite3_context*) ); SQLITE_API int sqlite3_create_function_v2( sqlite3 *db, const char *zFunctionName, int nArg, int eTextRep, void *pApp, void (*xFunc)(sqlite3_context*,int,sqlite3_value**), void (*xStep)(sqlite3_context*,int,sqlite3_value**), void (*xFinal)(sqlite3_context*), void(*xDestroy)(void*) ); /* ** CAPI3REF: Text Encodings ** ** These constant define integer codes that represent the various ** text encodings supported by SQLite. */ #define SQLITE_UTF8 1 /* IMP: R-37514-35566 */ #define SQLITE_UTF16LE 2 /* IMP: R-03371-37637 */ #define SQLITE_UTF16BE 3 /* IMP: R-51971-34154 */ #define SQLITE_UTF16 4 /* Use native byte order */ #define SQLITE_ANY 5 /* Deprecated */ #define SQLITE_UTF16_ALIGNED 8 /* sqlite3_create_collation only */ /* ** CAPI3REF: Function Flags ** ** These constants may be ORed together with the ** [SQLITE_UTF8 | preferred text encoding] as the fourth argument ** to [sqlite3_create_function()], [sqlite3_create_function16()], or ** [sqlite3_create_function_v2()]. */ #define SQLITE_DETERMINISTIC 0x800 /* ** CAPI3REF: Deprecated Functions ** DEPRECATED ** ** These functions are [deprecated]. In order to maintain ** backwards compatibility with older code, these functions continue ** to be supported. However, new applications should avoid ** the use of these functions. To encourage programmers to avoid ** these functions, we will not explain what they do. */ #ifndef SQLITE_OMIT_DEPRECATED SQLITE_API SQLITE_DEPRECATED int sqlite3_aggregate_count(sqlite3_context*); SQLITE_API SQLITE_DEPRECATED int sqlite3_expired(sqlite3_stmt*); SQLITE_API SQLITE_DEPRECATED int sqlite3_transfer_bindings(sqlite3_stmt*, sqlite3_stmt*); SQLITE_API SQLITE_DEPRECATED int sqlite3_global_recover(void); SQLITE_API SQLITE_DEPRECATED void sqlite3_thread_cleanup(void); SQLITE_API SQLITE_DEPRECATED int sqlite3_memory_alarm(void(*)(void*,sqlite3_int64,int), void*,sqlite3_int64); #endif /* ** CAPI3REF: Obtaining SQL Values ** METHOD: sqlite3_value ** ** Summary: **
**
sqlite3_value_blob→BLOB value **
sqlite3_value_double→REAL value **
sqlite3_value_int→32-bit INTEGER value **
sqlite3_value_int64→64-bit INTEGER value **
sqlite3_value_pointer→Pointer value **
sqlite3_value_text→UTF-8 TEXT value **
sqlite3_value_text16→UTF-16 TEXT value in ** the native byteorder **
sqlite3_value_text16be→UTF-16be TEXT value **
sqlite3_value_text16le→UTF-16le TEXT value **
    **
sqlite3_value_bytes→Size of a BLOB ** or a UTF-8 TEXT in bytes **
sqlite3_value_bytes16   ** →  Size of UTF-16 ** TEXT in bytes **
sqlite3_value_type→Default ** datatype of the value **
sqlite3_value_numeric_type   ** →  Best numeric datatype of the value **
** ** Details: ** ** These routines extract type, size, and content information from ** [protected sqlite3_value] objects. Protected sqlite3_value objects ** are used to pass parameter information into implementation of ** [application-defined SQL functions] and [virtual tables]. ** ** These routines work only with [protected sqlite3_value] objects. ** Any attempt to use these routines on an [unprotected sqlite3_value] ** is not threadsafe. ** ** ^These routines work just like the corresponding [column access functions] ** except that these routines take a single [protected sqlite3_value] object ** pointer instead of a [sqlite3_stmt*] pointer and an integer column number. ** ** ^The sqlite3_value_text16() interface extracts a UTF-16 string ** in the native byte-order of the host machine. ^The ** sqlite3_value_text16be() and sqlite3_value_text16le() interfaces ** extract UTF-16 strings as big-endian and little-endian respectively. ** ** ^If [sqlite3_value] object V was initialized ** using [sqlite3_bind_pointer(S,I,P,X,D)] or [sqlite3_result_pointer(C,P,X,D)] ** and if X and Y are strings that compare equal according to strcmp(X,Y), ** then sqlite3_value_pointer(V,Y) will return the pointer P. ^Otherwise, ** sqlite3_value_pointer(V,Y) returns a NULL. The sqlite3_bind_pointer() ** routine is part of the [pointer passing interface] added for SQLite 3.20.0. ** ** ^(The sqlite3_value_type(V) interface returns the ** [SQLITE_INTEGER | datatype code] for the initial datatype of the ** [sqlite3_value] object V. The returned value is one of [SQLITE_INTEGER], ** [SQLITE_FLOAT], [SQLITE_TEXT], [SQLITE_BLOB], or [SQLITE_NULL].)^ ** Other interfaces might change the datatype for an sqlite3_value object. ** For example, if the datatype is initially SQLITE_INTEGER and ** sqlite3_value_text(V) is called to extract a text value for that ** integer, then subsequent calls to sqlite3_value_type(V) might return ** SQLITE_TEXT. Whether or not a persistent internal datatype conversion ** occurs is undefined and may change from one release of SQLite to the next. ** ** ^(The sqlite3_value_numeric_type() interface attempts to apply ** numeric affinity to the value. This means that an attempt is ** made to convert the value to an integer or floating point. If ** such a conversion is possible without loss of information (in other ** words, if the value is a string that looks like a number) ** then the conversion is performed. Otherwise no conversion occurs. ** The [SQLITE_INTEGER | datatype] after conversion is returned.)^ ** ** Please pay particular attention to the fact that the pointer returned ** from [sqlite3_value_blob()], [sqlite3_value_text()], or ** [sqlite3_value_text16()] can be invalidated by a subsequent call to ** [sqlite3_value_bytes()], [sqlite3_value_bytes16()], [sqlite3_value_text()], ** or [sqlite3_value_text16()]. ** ** These routines must be called from the same thread as ** the SQL function that supplied the [sqlite3_value*] parameters. */ SQLITE_API const void *sqlite3_value_blob(sqlite3_value*); SQLITE_API double sqlite3_value_double(sqlite3_value*); SQLITE_API int sqlite3_value_int(sqlite3_value*); SQLITE_API sqlite3_int64 sqlite3_value_int64(sqlite3_value*); SQLITE_API void *sqlite3_value_pointer(sqlite3_value*, const char*); SQLITE_API const unsigned char *sqlite3_value_text(sqlite3_value*); SQLITE_API const void *sqlite3_value_text16(sqlite3_value*); SQLITE_API const void *sqlite3_value_text16le(sqlite3_value*); SQLITE_API const void *sqlite3_value_text16be(sqlite3_value*); SQLITE_API int sqlite3_value_bytes(sqlite3_value*); SQLITE_API int sqlite3_value_bytes16(sqlite3_value*); SQLITE_API int sqlite3_value_type(sqlite3_value*); SQLITE_API int sqlite3_value_numeric_type(sqlite3_value*); /* ** CAPI3REF: Finding The Subtype Of SQL Values ** METHOD: sqlite3_value ** ** The sqlite3_value_subtype(V) function returns the subtype for ** an [application-defined SQL function] argument V. The subtype ** information can be used to pass a limited amount of context from ** one SQL function to another. Use the [sqlite3_result_subtype()] ** routine to set the subtype for the return value of an SQL function. */ SQLITE_API unsigned int sqlite3_value_subtype(sqlite3_value*); /* ** CAPI3REF: Copy And Free SQL Values ** METHOD: sqlite3_value ** ** ^The sqlite3_value_dup(V) interface makes a copy of the [sqlite3_value] ** object D and returns a pointer to that copy. ^The [sqlite3_value] returned ** is a [protected sqlite3_value] object even if the input is not. ** ^The sqlite3_value_dup(V) interface returns NULL if V is NULL or if a ** memory allocation fails. ** ** ^The sqlite3_value_free(V) interface frees an [sqlite3_value] object ** previously obtained from [sqlite3_value_dup()]. ^If V is a NULL pointer ** then sqlite3_value_free(V) is a harmless no-op. */ SQLITE_API sqlite3_value *sqlite3_value_dup(const sqlite3_value*); SQLITE_API void sqlite3_value_free(sqlite3_value*); /* ** CAPI3REF: Obtain Aggregate Function Context ** METHOD: sqlite3_context ** ** Implementations of aggregate SQL functions use this ** routine to allocate memory for storing their state. ** ** ^The first time the sqlite3_aggregate_context(C,N) routine is called ** for a particular aggregate function, SQLite ** allocates N of memory, zeroes out that memory, and returns a pointer ** to the new memory. ^On second and subsequent calls to ** sqlite3_aggregate_context() for the same aggregate function instance, ** the same buffer is returned. Sqlite3_aggregate_context() is normally ** called once for each invocation of the xStep callback and then one ** last time when the xFinal callback is invoked. ^(When no rows match ** an aggregate query, the xStep() callback of the aggregate function ** implementation is never called and xFinal() is called exactly once. ** In those cases, sqlite3_aggregate_context() might be called for the ** first time from within xFinal().)^ ** ** ^The sqlite3_aggregate_context(C,N) routine returns a NULL pointer ** when first called if N is less than or equal to zero or if a memory ** allocate error occurs. ** ** ^(The amount of space allocated by sqlite3_aggregate_context(C,N) is ** determined by the N parameter on first successful call. Changing the ** value of N in subsequent call to sqlite3_aggregate_context() within ** the same aggregate function instance will not resize the memory ** allocation.)^ Within the xFinal callback, it is customary to set ** N=0 in calls to sqlite3_aggregate_context(C,N) so that no ** pointless memory allocations occur. ** ** ^SQLite automatically frees the memory allocated by ** sqlite3_aggregate_context() when the aggregate query concludes. ** ** The first parameter must be a copy of the ** [sqlite3_context | SQL function context] that is the first parameter ** to the xStep or xFinal callback routine that implements the aggregate ** function. ** ** This routine must be called from the same thread in which ** the aggregate SQL function is running. */ SQLITE_API void *sqlite3_aggregate_context(sqlite3_context*, int nBytes); /* ** CAPI3REF: User Data For Functions ** METHOD: sqlite3_context ** ** ^The sqlite3_user_data() interface returns a copy of ** the pointer that was the pUserData parameter (the 5th parameter) ** of the [sqlite3_create_function()] ** and [sqlite3_create_function16()] routines that originally ** registered the application defined function. ** ** This routine must be called from the same thread in which ** the application-defined function is running. */ SQLITE_API void *sqlite3_user_data(sqlite3_context*); /* ** CAPI3REF: Database Connection For Functions ** METHOD: sqlite3_context ** ** ^The sqlite3_context_db_handle() interface returns a copy of ** the pointer to the [database connection] (the 1st parameter) ** of the [sqlite3_create_function()] ** and [sqlite3_create_function16()] routines that originally ** registered the application defined function. */ SQLITE_API sqlite3 *sqlite3_context_db_handle(sqlite3_context*); /* ** CAPI3REF: Function Auxiliary Data ** METHOD: sqlite3_context ** ** These functions may be used by (non-aggregate) SQL functions to ** associate metadata with argument values. If the same value is passed to ** multiple invocations of the same SQL function during query execution, under ** some circumstances the associated metadata may be preserved. An example ** of where this might be useful is in a regular-expression matching ** function. The compiled version of the regular expression can be stored as ** metadata associated with the pattern string. ** Then as long as the pattern string remains the same, ** the compiled regular expression can be reused on multiple ** invocations of the same function. ** ** ^The sqlite3_get_auxdata(C,N) interface returns a pointer to the metadata ** associated by the sqlite3_set_auxdata(C,N,P,X) function with the Nth argument ** value to the application-defined function. ^N is zero for the left-most ** function argument. ^If there is no metadata ** associated with the function argument, the sqlite3_get_auxdata(C,N) interface ** returns a NULL pointer. ** ** ^The sqlite3_set_auxdata(C,N,P,X) interface saves P as metadata for the N-th ** argument of the application-defined function. ^Subsequent ** calls to sqlite3_get_auxdata(C,N) return P from the most recent ** sqlite3_set_auxdata(C,N,P,X) call if the metadata is still valid or ** NULL if the metadata has been discarded. ** ^After each call to sqlite3_set_auxdata(C,N,P,X) where X is not NULL, ** SQLite will invoke the destructor function X with parameter P exactly ** once, when the metadata is discarded. ** SQLite is free to discard the metadata at any time, including:
    **
  • ^(when the corresponding function parameter changes)^, or **
  • ^(when [sqlite3_reset()] or [sqlite3_finalize()] is called for the ** SQL statement)^, or **
  • ^(when sqlite3_set_auxdata() is invoked again on the same ** parameter)^, or **
  • ^(during the original sqlite3_set_auxdata() call when a memory ** allocation error occurs.)^
** ** Note the last bullet in particular. The destructor X in ** sqlite3_set_auxdata(C,N,P,X) might be called immediately, before the ** sqlite3_set_auxdata() interface even returns. Hence sqlite3_set_auxdata() ** should be called near the end of the function implementation and the ** function implementation should not make any use of P after ** sqlite3_set_auxdata() has been called. ** ** ^(In practice, metadata is preserved between function calls for ** function parameters that are compile-time constants, including literal ** values and [parameters] and expressions composed from the same.)^ ** ** The value of the N parameter to these interfaces should be non-negative. ** Future enhancements may make use of negative N values to define new ** kinds of function caching behavior. ** ** These routines must be called from the same thread in which ** the SQL function is running. */ SQLITE_API void *sqlite3_get_auxdata(sqlite3_context*, int N); SQLITE_API void sqlite3_set_auxdata(sqlite3_context*, int N, void*, void (*)(void*)); /* ** CAPI3REF: Constants Defining Special Destructor Behavior ** ** These are special values for the destructor that is passed in as the ** final argument to routines like [sqlite3_result_blob()]. ^If the destructor ** argument is SQLITE_STATIC, it means that the content pointer is constant ** and will never change. It does not need to be destroyed. ^The ** SQLITE_TRANSIENT value means that the content will likely change in ** the near future and that SQLite should make its own private copy of ** the content before returning. ** ** The typedef is necessary to work around problems in certain ** C++ compilers. */ typedef void (*sqlite3_destructor_type)(void*); #define SQLITE_STATIC ((sqlite3_destructor_type)0) #define SQLITE_TRANSIENT ((sqlite3_destructor_type)-1) /* ** CAPI3REF: Setting The Result Of An SQL Function ** METHOD: sqlite3_context ** ** These routines are used by the xFunc or xFinal callbacks that ** implement SQL functions and aggregates. See ** [sqlite3_create_function()] and [sqlite3_create_function16()] ** for additional information. ** ** These functions work very much like the [parameter binding] family of ** functions used to bind values to host parameters in prepared statements. ** Refer to the [SQL parameter] documentation for additional information. ** ** ^The sqlite3_result_blob() interface sets the result from ** an application-defined function to be the BLOB whose content is pointed ** to by the second parameter and which is N bytes long where N is the ** third parameter. ** ** ^The sqlite3_result_zeroblob(C,N) and sqlite3_result_zeroblob64(C,N) ** interfaces set the result of the application-defined function to be ** a BLOB containing all zero bytes and N bytes in size. ** ** ^The sqlite3_result_double() interface sets the result from ** an application-defined function to be a floating point value specified ** by its 2nd argument. ** ** ^The sqlite3_result_error() and sqlite3_result_error16() functions ** cause the implemented SQL function to throw an exception. ** ^SQLite uses the string pointed to by the ** 2nd parameter of sqlite3_result_error() or sqlite3_result_error16() ** as the text of an error message. ^SQLite interprets the error ** message string from sqlite3_result_error() as UTF-8. ^SQLite ** interprets the string from sqlite3_result_error16() as UTF-16 in native ** byte order. ^If the third parameter to sqlite3_result_error() ** or sqlite3_result_error16() is negative then SQLite takes as the error ** message all text up through the first zero character. ** ^If the third parameter to sqlite3_result_error() or ** sqlite3_result_error16() is non-negative then SQLite takes that many ** bytes (not characters) from the 2nd parameter as the error message. ** ^The sqlite3_result_error() and sqlite3_result_error16() ** routines make a private copy of the error message text before ** they return. Hence, the calling function can deallocate or ** modify the text after they return without harm. ** ^The sqlite3_result_error_code() function changes the error code ** returned by SQLite as a result of an error in a function. ^By default, ** the error code is SQLITE_ERROR. ^A subsequent call to sqlite3_result_error() ** or sqlite3_result_error16() resets the error code to SQLITE_ERROR. ** ** ^The sqlite3_result_error_toobig() interface causes SQLite to throw an ** error indicating that a string or BLOB is too long to represent. ** ** ^The sqlite3_result_error_nomem() interface causes SQLite to throw an ** error indicating that a memory allocation failed. ** ** ^The sqlite3_result_int() interface sets the return value ** of the application-defined function to be the 32-bit signed integer ** value given in the 2nd argument. ** ^The sqlite3_result_int64() interface sets the return value ** of the application-defined function to be the 64-bit signed integer ** value given in the 2nd argument. ** ** ^The sqlite3_result_null() interface sets the return value ** of the application-defined function to be NULL. ** ** ^The sqlite3_result_text(), sqlite3_result_text16(), ** sqlite3_result_text16le(), and sqlite3_result_text16be() interfaces ** set the return value of the application-defined function to be ** a text string which is represented as UTF-8, UTF-16 native byte order, ** UTF-16 little endian, or UTF-16 big endian, respectively. ** ^The sqlite3_result_text64() interface sets the return value of an ** application-defined function to be a text string in an encoding ** specified by the fifth (and last) parameter, which must be one ** of [SQLITE_UTF8], [SQLITE_UTF16], [SQLITE_UTF16BE], or [SQLITE_UTF16LE]. ** ^SQLite takes the text result from the application from ** the 2nd parameter of the sqlite3_result_text* interfaces. ** ^If the 3rd parameter to the sqlite3_result_text* interfaces ** is negative, then SQLite takes result text from the 2nd parameter ** through the first zero character. ** ^If the 3rd parameter to the sqlite3_result_text* interfaces ** is non-negative, then as many bytes (not characters) of the text ** pointed to by the 2nd parameter are taken as the application-defined ** function result. If the 3rd parameter is non-negative, then it ** must be the byte offset into the string where the NUL terminator would ** appear if the string where NUL terminated. If any NUL characters occur ** in the string at a byte offset that is less than the value of the 3rd ** parameter, then the resulting string will contain embedded NULs and the ** result of expressions operating on strings with embedded NULs is undefined. ** ^If the 4th parameter to the sqlite3_result_text* interfaces ** or sqlite3_result_blob is a non-NULL pointer, then SQLite calls that ** function as the destructor on the text or BLOB result when it has ** finished using that result. ** ^If the 4th parameter to the sqlite3_result_text* interfaces or to ** sqlite3_result_blob is the special constant SQLITE_STATIC, then SQLite ** assumes that the text or BLOB result is in constant space and does not ** copy the content of the parameter nor call a destructor on the content ** when it has finished using that result. ** ^If the 4th parameter to the sqlite3_result_text* interfaces ** or sqlite3_result_blob is the special constant SQLITE_TRANSIENT ** then SQLite makes a copy of the result into space obtained ** from [sqlite3_malloc()] before it returns. ** ** ^The sqlite3_result_value() interface sets the result of ** the application-defined function to be a copy of the ** [unprotected sqlite3_value] object specified by the 2nd parameter. ^The ** sqlite3_result_value() interface makes a copy of the [sqlite3_value] ** so that the [sqlite3_value] specified in the parameter may change or ** be deallocated after sqlite3_result_value() returns without harm. ** ^A [protected sqlite3_value] object may always be used where an ** [unprotected sqlite3_value] object is required, so either ** kind of [sqlite3_value] object can be used with this interface. ** ** ^The sqlite3_result_pointer(C,P,T,D) interface sets the result to an ** SQL NULL value, just like [sqlite3_result_null(C)], except that it ** also associates the host-language pointer P or type T with that ** NULL value such that the pointer can be retrieved within an ** [application-defined SQL function] using [sqlite3_value_pointer()]. ** ^If the D parameter is not NULL, then it is a pointer to a destructor ** for the P parameter. ^SQLite invokes D with P as its only argument ** when SQLite is finished with P. The T parameter should be a static ** string and preferably a string literal. The sqlite3_result_pointer() ** routine is part of the [pointer passing interface] added for SQLite 3.20.0. ** ** If these routines are called from within the different thread ** than the one containing the application-defined function that received ** the [sqlite3_context] pointer, the results are undefined. */ SQLITE_API void sqlite3_result_blob(sqlite3_context*, const void*, int, void(*)(void*)); SQLITE_API void sqlite3_result_blob64(sqlite3_context*,const void*, sqlite3_uint64,void(*)(void*)); SQLITE_API void sqlite3_result_double(sqlite3_context*, double); SQLITE_API void sqlite3_result_error(sqlite3_context*, const char*, int); SQLITE_API void sqlite3_result_error16(sqlite3_context*, const void*, int); SQLITE_API void sqlite3_result_error_toobig(sqlite3_context*); SQLITE_API void sqlite3_result_error_nomem(sqlite3_context*); SQLITE_API void sqlite3_result_error_code(sqlite3_context*, int); SQLITE_API void sqlite3_result_int(sqlite3_context*, int); SQLITE_API void sqlite3_result_int64(sqlite3_context*, sqlite3_int64); SQLITE_API void sqlite3_result_null(sqlite3_context*); SQLITE_API void sqlite3_result_text(sqlite3_context*, const char*, int, void(*)(void*)); SQLITE_API void sqlite3_result_text64(sqlite3_context*, const char*,sqlite3_uint64, void(*)(void*), unsigned char encoding); SQLITE_API void sqlite3_result_text16(sqlite3_context*, const void*, int, void(*)(void*)); SQLITE_API void sqlite3_result_text16le(sqlite3_context*, const void*, int,void(*)(void*)); SQLITE_API void sqlite3_result_text16be(sqlite3_context*, const void*, int,void(*)(void*)); SQLITE_API void sqlite3_result_value(sqlite3_context*, sqlite3_value*); SQLITE_API void sqlite3_result_pointer(sqlite3_context*, void*,const char*,void(*)(void*)); SQLITE_API void sqlite3_result_zeroblob(sqlite3_context*, int n); SQLITE_API int sqlite3_result_zeroblob64(sqlite3_context*, sqlite3_uint64 n); /* ** CAPI3REF: Setting The Subtype Of An SQL Function ** METHOD: sqlite3_context ** ** The sqlite3_result_subtype(C,T) function causes the subtype of ** the result from the [application-defined SQL function] with ** [sqlite3_context] C to be the value T. Only the lower 8 bits ** of the subtype T are preserved in current versions of SQLite; ** higher order bits are discarded. ** The number of subtype bytes preserved by SQLite might increase ** in future releases of SQLite. */ SQLITE_API void sqlite3_result_subtype(sqlite3_context*,unsigned int); /* ** CAPI3REF: Define New Collating Sequences ** METHOD: sqlite3 ** ** ^These functions add, remove, or modify a [collation] associated ** with the [database connection] specified as the first argument. ** ** ^The name of the collation is a UTF-8 string ** for sqlite3_create_collation() and sqlite3_create_collation_v2() ** and a UTF-16 string in native byte order for sqlite3_create_collation16(). ** ^Collation names that compare equal according to [sqlite3_strnicmp()] are ** considered to be the same name. ** ** ^(The third argument (eTextRep) must be one of the constants: **
    **
  • [SQLITE_UTF8], **
  • [SQLITE_UTF16LE], **
  • [SQLITE_UTF16BE], **
  • [SQLITE_UTF16], or **
  • [SQLITE_UTF16_ALIGNED]. **
)^ ** ^The eTextRep argument determines the encoding of strings passed ** to the collating function callback, xCallback. ** ^The [SQLITE_UTF16] and [SQLITE_UTF16_ALIGNED] values for eTextRep ** force strings to be UTF16 with native byte order. ** ^The [SQLITE_UTF16_ALIGNED] value for eTextRep forces strings to begin ** on an even byte address. ** ** ^The fourth argument, pArg, is an application data pointer that is passed ** through as the first argument to the collating function callback. ** ** ^The fifth argument, xCallback, is a pointer to the collating function. ** ^Multiple collating functions can be registered using the same name but ** with different eTextRep parameters and SQLite will use whichever ** function requires the least amount of data transformation. ** ^If the xCallback argument is NULL then the collating function is ** deleted. ^When all collating functions having the same name are deleted, ** that collation is no longer usable. ** ** ^The collating function callback is invoked with a copy of the pArg ** application data pointer and with two strings in the encoding specified ** by the eTextRep argument. The collating function must return an ** integer that is negative, zero, or positive ** if the first string is less than, equal to, or greater than the second, ** respectively. A collating function must always return the same answer ** given the same inputs. If two or more collating functions are registered ** to the same collation name (using different eTextRep values) then all ** must give an equivalent answer when invoked with equivalent strings. ** The collating function must obey the following properties for all ** strings A, B, and C: ** **
    **
  1. If A==B then B==A. **
  2. If A==B and B==C then A==C. **
  3. If A<B THEN B>A. **
  4. If A<B and B<C then A<C. **
** ** If a collating function fails any of the above constraints and that ** collating function is registered and used, then the behavior of SQLite ** is undefined. ** ** ^The sqlite3_create_collation_v2() works like sqlite3_create_collation() ** with the addition that the xDestroy callback is invoked on pArg when ** the collating function is deleted. ** ^Collating functions are deleted when they are overridden by later ** calls to the collation creation functions or when the ** [database connection] is closed using [sqlite3_close()]. ** ** ^The xDestroy callback is not called if the ** sqlite3_create_collation_v2() function fails. Applications that invoke ** sqlite3_create_collation_v2() with a non-NULL xDestroy argument should ** check the return code and dispose of the application data pointer ** themselves rather than expecting SQLite to deal with it for them. ** This is different from every other SQLite interface. The inconsistency ** is unfortunate but cannot be changed without breaking backwards ** compatibility. ** ** See also: [sqlite3_collation_needed()] and [sqlite3_collation_needed16()]. */ SQLITE_API int sqlite3_create_collation( sqlite3*, const char *zName, int eTextRep, void *pArg, int(*xCompare)(void*,int,const void*,int,const void*) ); SQLITE_API int sqlite3_create_collation_v2( sqlite3*, const char *zName, int eTextRep, void *pArg, int(*xCompare)(void*,int,const void*,int,const void*), void(*xDestroy)(void*) ); SQLITE_API int sqlite3_create_collation16( sqlite3*, const void *zName, int eTextRep, void *pArg, int(*xCompare)(void*,int,const void*,int,const void*) ); /* ** CAPI3REF: Collation Needed Callbacks ** METHOD: sqlite3 ** ** ^To avoid having to register all collation sequences before a database ** can be used, a single callback function may be registered with the ** [database connection] to be invoked whenever an undefined collation ** sequence is required. ** ** ^If the function is registered using the sqlite3_collation_needed() API, ** then it is passed the names of undefined collation sequences as strings ** encoded in UTF-8. ^If sqlite3_collation_needed16() is used, ** the names are passed as UTF-16 in machine native byte order. ** ^A call to either function replaces the existing collation-needed callback. ** ** ^(When the callback is invoked, the first argument passed is a copy ** of the second argument to sqlite3_collation_needed() or ** sqlite3_collation_needed16(). The second argument is the database ** connection. The third argument is one of [SQLITE_UTF8], [SQLITE_UTF16BE], ** or [SQLITE_UTF16LE], indicating the most desirable form of the collation ** sequence function required. The fourth parameter is the name of the ** required collation sequence.)^ ** ** The callback function should register the desired collation using ** [sqlite3_create_collation()], [sqlite3_create_collation16()], or ** [sqlite3_create_collation_v2()]. */ SQLITE_API int sqlite3_collation_needed( sqlite3*, void*, void(*)(void*,sqlite3*,int eTextRep,const char*) ); SQLITE_API int sqlite3_collation_needed16( sqlite3*, void*, void(*)(void*,sqlite3*,int eTextRep,const void*) ); #ifdef SQLITE_HAS_CODEC /* ** Specify the key for an encrypted database. This routine should be ** called right after sqlite3_open(). ** ** The code to implement this API is not available in the public release ** of SQLite. */ SQLITE_API int sqlite3_key( sqlite3 *db, /* Database to be rekeyed */ const void *pKey, int nKey /* The key */ ); SQLITE_API int sqlite3_key_v2( sqlite3 *db, /* Database to be rekeyed */ const char *zDbName, /* Name of the database */ const void *pKey, int nKey /* The key */ ); /* ** Change the key on an open database. If the current database is not ** encrypted, this routine will encrypt it. If pNew==0 or nNew==0, the ** database is decrypted. ** ** The code to implement this API is not available in the public release ** of SQLite. */ SQLITE_API int sqlite3_rekey( sqlite3 *db, /* Database to be rekeyed */ const void *pKey, int nKey /* The new key */ ); SQLITE_API int sqlite3_rekey_v2( sqlite3 *db, /* Database to be rekeyed */ const char *zDbName, /* Name of the database */ const void *pKey, int nKey /* The new key */ ); /* ** Specify the activation key for a SEE database. Unless ** activated, none of the SEE routines will work. */ SQLITE_API void sqlite3_activate_see( const char *zPassPhrase /* Activation phrase */ ); #endif #ifdef SQLITE_ENABLE_CEROD /* ** Specify the activation key for a CEROD database. Unless ** activated, none of the CEROD routines will work. */ SQLITE_API void sqlite3_activate_cerod( const char *zPassPhrase /* Activation phrase */ ); #endif /* ** CAPI3REF: Suspend Execution For A Short Time ** ** The sqlite3_sleep() function causes the current thread to suspend execution ** for at least a number of milliseconds specified in its parameter. ** ** If the operating system does not support sleep requests with ** millisecond time resolution, then the time will be rounded up to ** the nearest second. The number of milliseconds of sleep actually ** requested from the operating system is returned. ** ** ^SQLite implements this interface by calling the xSleep() ** method of the default [sqlite3_vfs] object. If the xSleep() method ** of the default VFS is not implemented correctly, or not implemented at ** all, then the behavior of sqlite3_sleep() may deviate from the description ** in the previous paragraphs. */ SQLITE_API int sqlite3_sleep(int); /* ** CAPI3REF: Name Of The Folder Holding Temporary Files ** ** ^(If this global variable is made to point to a string which is ** the name of a folder (a.k.a. directory), then all temporary files ** created by SQLite when using a built-in [sqlite3_vfs | VFS] ** will be placed in that directory.)^ ^If this variable ** is a NULL pointer, then SQLite performs a search for an appropriate ** temporary file directory. ** ** Applications are strongly discouraged from using this global variable. ** It is required to set a temporary folder on Windows Runtime (WinRT). ** But for all other platforms, it is highly recommended that applications ** neither read nor write this variable. This global variable is a relic ** that exists for backwards compatibility of legacy applications and should ** be avoided in new projects. ** ** It is not safe to read or modify this variable in more than one ** thread at a time. It is not safe to read or modify this variable ** if a [database connection] is being used at the same time in a separate ** thread. ** It is intended that this variable be set once ** as part of process initialization and before any SQLite interface ** routines have been called and that this variable remain unchanged ** thereafter. ** ** ^The [temp_store_directory pragma] may modify this variable and cause ** it to point to memory obtained from [sqlite3_malloc]. ^Furthermore, ** the [temp_store_directory pragma] always assumes that any string ** that this variable points to is held in memory obtained from ** [sqlite3_malloc] and the pragma may attempt to free that memory ** using [sqlite3_free]. ** Hence, if this variable is modified directly, either it should be ** made NULL or made to point to memory obtained from [sqlite3_malloc] ** or else the use of the [temp_store_directory pragma] should be avoided. ** Except when requested by the [temp_store_directory pragma], SQLite ** does not free the memory that sqlite3_temp_directory points to. If ** the application wants that memory to be freed, it must do ** so itself, taking care to only do so after all [database connection] ** objects have been destroyed. ** ** Note to Windows Runtime users: The temporary directory must be set ** prior to calling [sqlite3_open] or [sqlite3_open_v2]. Otherwise, various ** features that require the use of temporary files may fail. Here is an ** example of how to do this using C++ with the Windows Runtime: ** ** 
** LPCWSTR zPath = Windows::Storage::ApplicationData::Current->
**       TemporaryFolder->Path->Data();
** char zPathBuf[MAX_PATH + 1];
** memset(zPathBuf, 0, sizeof(zPathBuf));
** WideCharToMultiByte(CP_UTF8, 0, zPath, -1, zPathBuf, sizeof(zPathBuf),
**       NULL, NULL);
** sqlite3_temp_directory = sqlite3_mprintf("%s", zPathBuf);
**
*/ SQLITE_API SQLITE_EXTERN char *sqlite3_temp_directory; /* ** CAPI3REF: Name Of The Folder Holding Database Files ** ** ^(If this global variable is made to point to a string which is ** the name of a folder (a.k.a. directory), then all database files ** specified with a relative pathname and created or accessed by ** SQLite when using a built-in windows [sqlite3_vfs | VFS] will be assumed ** to be relative to that directory.)^ ^If this variable is a NULL ** pointer, then SQLite assumes that all database files specified ** with a relative pathname are relative to the current directory ** for the process. Only the windows VFS makes use of this global ** variable; it is ignored by the unix VFS. ** ** Changing the value of this variable while a database connection is ** open can result in a corrupt database. ** ** It is not safe to read or modify this variable in more than one ** thread at a time. It is not safe to read or modify this variable ** if a [database connection] is being used at the same time in a separate ** thread. ** It is intended that this variable be set once ** as part of process initialization and before any SQLite interface ** routines have been called and that this variable remain unchanged ** thereafter. ** ** ^The [data_store_directory pragma] may modify this variable and cause ** it to point to memory obtained from [sqlite3_malloc]. ^Furthermore, ** the [data_store_directory pragma] always assumes that any string ** that this variable points to is held in memory obtained from ** [sqlite3_malloc] and the pragma may attempt to free that memory ** using [sqlite3_free]. ** Hence, if this variable is modified directly, either it should be ** made NULL or made to point to memory obtained from [sqlite3_malloc] ** or else the use of the [data_store_directory pragma] should be avoided. */ SQLITE_API SQLITE_EXTERN char *sqlite3_data_directory; /* ** CAPI3REF: Test For Auto-Commit Mode ** KEYWORDS: {autocommit mode} ** METHOD: sqlite3 ** ** ^The sqlite3_get_autocommit() interface returns non-zero or ** zero if the given database connection is or is not in autocommit mode, ** respectively. ^Autocommit mode is on by default. ** ^Autocommit mode is disabled by a [BEGIN] statement. ** ^Autocommit mode is re-enabled by a [COMMIT] or [ROLLBACK]. ** ** If certain kinds of errors occur on a statement within a multi-statement ** transaction (errors including [SQLITE_FULL], [SQLITE_IOERR], ** [SQLITE_NOMEM], [SQLITE_BUSY], and [SQLITE_INTERRUPT]) then the ** transaction might be rolled back automatically. The only way to ** find out whether SQLite automatically rolled back the transaction after ** an error is to use this function. ** ** If another thread changes the autocommit status of the database ** connection while this routine is running, then the return value ** is undefined. */ SQLITE_API int sqlite3_get_autocommit(sqlite3*); /* ** CAPI3REF: Find The Database Handle Of A Prepared Statement ** METHOD: sqlite3_stmt ** ** ^The sqlite3_db_handle interface returns the [database connection] handle ** to which a [prepared statement] belongs. ^The [database connection] ** returned by sqlite3_db_handle is the same [database connection] ** that was the first argument ** to the [sqlite3_prepare_v2()] call (or its variants) that was used to ** create the statement in the first place. */ SQLITE_API sqlite3 *sqlite3_db_handle(sqlite3_stmt*); /* ** CAPI3REF: Return The Filename For A Database Connection ** METHOD: sqlite3 ** ** ^The sqlite3_db_filename(D,N) interface returns a pointer to a filename ** associated with database N of connection D. ^The main database file ** has the name "main". If there is no attached database N on the database ** connection D, or if database N is a temporary or in-memory database, then ** a NULL pointer is returned. ** ** ^The filename returned by this function is the output of the ** xFullPathname method of the [VFS]. ^In other words, the filename ** will be an absolute pathname, even if the filename used ** to open the database originally was a URI or relative pathname. */ SQLITE_API const char *sqlite3_db_filename(sqlite3 *db, const char *zDbName); /* ** CAPI3REF: Determine if a database is read-only ** METHOD: sqlite3 ** ** ^The sqlite3_db_readonly(D,N) interface returns 1 if the database N ** of connection D is read-only, 0 if it is read/write, or -1 if N is not ** the name of a database on connection D. */ SQLITE_API int sqlite3_db_readonly(sqlite3 *db, const char *zDbName); /* ** CAPI3REF: Find the next prepared statement ** METHOD: sqlite3 ** ** ^This interface returns a pointer to the next [prepared statement] after ** pStmt associated with the [database connection] pDb. ^If pStmt is NULL ** then this interface returns a pointer to the first prepared statement ** associated with the database connection pDb. ^If no prepared statement ** satisfies the conditions of this routine, it returns NULL. ** ** The [database connection] pointer D in a call to ** [sqlite3_next_stmt(D,S)] must refer to an open database ** connection and in particular must not be a NULL pointer. */ SQLITE_API sqlite3_stmt *sqlite3_next_stmt(sqlite3 *pDb, sqlite3_stmt *pStmt); /* ** CAPI3REF: Commit And Rollback Notification Callbacks ** METHOD: sqlite3 ** ** ^The sqlite3_commit_hook() interface registers a callback ** function to be invoked whenever a transaction is [COMMIT | committed]. ** ^Any callback set by a previous call to sqlite3_commit_hook() ** for the same database connection is overridden. ** ^The sqlite3_rollback_hook() interface registers a callback ** function to be invoked whenever a transaction is [ROLLBACK | rolled back]. ** ^Any callback set by a previous call to sqlite3_rollback_hook() ** for the same database connection is overridden. ** ^The pArg argument is passed through to the callback. ** ^If the callback on a commit hook function returns non-zero, ** then the commit is converted into a rollback. ** ** ^The sqlite3_commit_hook(D,C,P) and sqlite3_rollback_hook(D,C,P) functions ** return the P argument from the previous call of the same function ** on the same [database connection] D, or NULL for ** the first call for each function on D. ** ** The commit and rollback hook callbacks are not reentrant. ** The callback implementation must not do anything that will modify ** the database connection that invoked the callback. Any actions ** to modify the database connection must be deferred until after the ** completion of the [sqlite3_step()] call that triggered the commit ** or rollback hook in the first place. ** Note that running any other SQL statements, including SELECT statements, ** or merely calling [sqlite3_prepare_v2()] and [sqlite3_step()] will modify ** the database connections for the meaning of "modify" in this paragraph. ** ** ^Registering a NULL function disables the callback. ** ** ^When the commit hook callback routine returns zero, the [COMMIT] ** operation is allowed to continue normally. ^If the commit hook ** returns non-zero, then the [COMMIT] is converted into a [ROLLBACK]. ** ^The rollback hook is invoked on a rollback that results from a commit ** hook returning non-zero, just as it would be with any other rollback. ** ** ^For the purposes of this API, a transaction is said to have been ** rolled back if an explicit "ROLLBACK" statement is executed, or ** an error or constraint causes an implicit rollback to occur. ** ^The rollback callback is not invoked if a transaction is ** automatically rolled back because the database connection is closed. ** ** See also the [sqlite3_update_hook()] interface. */ SQLITE_API void *sqlite3_commit_hook(sqlite3*, int(*)(void*), void*); SQLITE_API void *sqlite3_rollback_hook(sqlite3*, void(*)(void *), void*); /* ** CAPI3REF: Data Change Notification Callbacks ** METHOD: sqlite3 ** ** ^The sqlite3_update_hook() interface registers a callback function ** with the [database connection] identified by the first argument ** to be invoked whenever a row is updated, inserted or deleted in ** a [rowid table]. ** ^Any callback set by a previous call to this function ** for the same database connection is overridden. ** ** ^The second argument is a pointer to the function to invoke when a ** row is updated, inserted or deleted in a rowid table. ** ^The first argument to the callback is a copy of the third argument ** to sqlite3_update_hook(). ** ^The second callback argument is one of [SQLITE_INSERT], [SQLITE_DELETE], ** or [SQLITE_UPDATE], depending on the operation that caused the callback ** to be invoked. ** ^The third and fourth arguments to the callback contain pointers to the ** database and table name containing the affected row. ** ^The final callback parameter is the [rowid] of the row. ** ^In the case of an update, this is the [rowid] after the update takes place. ** ** ^(The update hook is not invoked when internal system tables are ** modified (i.e. sqlite_master and sqlite_sequence).)^ ** ^The update hook is not invoked when [WITHOUT ROWID] tables are modified. ** ** ^In the current implementation, the update hook ** is not invoked when conflicting rows are deleted because of an ** [ON CONFLICT | ON CONFLICT REPLACE] clause. ^Nor is the update hook ** invoked when rows are deleted using the [truncate optimization]. ** The exceptions defined in this paragraph might change in a future ** release of SQLite. ** ** The update hook implementation must not do anything that will modify ** the database connection that invoked the update hook. Any actions ** to modify the database connection must be deferred until after the ** completion of the [sqlite3_step()] call that triggered the update hook. ** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their ** database connections for the meaning of "modify" in this paragraph. ** ** ^The sqlite3_update_hook(D,C,P) function ** returns the P argument from the previous call ** on the same [database connection] D, or NULL for ** the first call on D. ** ** See also the [sqlite3_commit_hook()], [sqlite3_rollback_hook()], ** and [sqlite3_preupdate_hook()] interfaces. */ SQLITE_API void *sqlite3_update_hook( sqlite3*, void(*)(void *,int ,char const *,char const *,sqlite3_int64), void* ); /* ** CAPI3REF: Enable Or Disable Shared Pager Cache ** ** ^(This routine enables or disables the sharing of the database cache ** and schema data structures between [database connection | connections] ** to the same database. Sharing is enabled if the argument is true ** and disabled if the argument is false.)^ ** ** ^Cache sharing is enabled and disabled for an entire process. ** This is a change as of SQLite [version 3.5.0] ([dateof:3.5.0]). ** In prior versions of SQLite, ** sharing was enabled or disabled for each thread separately. ** ** ^(The cache sharing mode set by this interface effects all subsequent ** calls to [sqlite3_open()], [sqlite3_open_v2()], and [sqlite3_open16()]. ** Existing database connections continue use the sharing mode ** that was in effect at the time they were opened.)^ ** ** ^(This routine returns [SQLITE_OK] if shared cache was enabled or disabled ** successfully. An [error code] is returned otherwise.)^ ** ** ^Shared cache is disabled by default. But this might change in ** future releases of SQLite. Applications that care about shared ** cache setting should set it explicitly. ** ** Note: This method is disabled on MacOS X 10.7 and iOS version 5.0 ** and will always return SQLITE_MISUSE. On those systems, ** shared cache mode should be enabled per-database connection via ** [sqlite3_open_v2()] with [SQLITE_OPEN_SHAREDCACHE]. ** ** This interface is threadsafe on processors where writing a ** 32-bit integer is atomic. ** ** See Also: [SQLite Shared-Cache Mode] */ SQLITE_API int sqlite3_enable_shared_cache(int); /* ** CAPI3REF: Attempt To Free Heap Memory ** ** ^The sqlite3_release_memory() interface attempts to free N bytes ** of heap memory by deallocating non-essential memory allocations ** held by the database library. Memory used to cache database ** pages to improve performance is an example of non-essential memory. ** ^sqlite3_release_memory() returns the number of bytes actually freed, ** which might be more or less than the amount requested. ** ^The sqlite3_release_memory() routine is a no-op returning zero ** if SQLite is not compiled with [SQLITE_ENABLE_MEMORY_MANAGEMENT]. ** ** See also: [sqlite3_db_release_memory()] */ SQLITE_API int sqlite3_release_memory(int); /* ** CAPI3REF: Free Memory Used By A Database Connection ** METHOD: sqlite3 ** ** ^The sqlite3_db_release_memory(D) interface attempts to free as much heap ** memory as possible from database connection D. Unlike the ** [sqlite3_release_memory()] interface, this interface is in effect even ** when the [SQLITE_ENABLE_MEMORY_MANAGEMENT] compile-time option is ** omitted. ** ** See also: [sqlite3_release_memory()] */ SQLITE_API int sqlite3_db_release_memory(sqlite3*); /* ** CAPI3REF: Impose A Limit On Heap Size ** ** ^The sqlite3_soft_heap_limit64() interface sets and/or queries the ** soft limit on the amount of heap memory that may be allocated by SQLite. ** ^SQLite strives to keep heap memory utilization below the soft heap ** limit by reducing the number of pages held in the page cache ** as heap memory usages approaches the limit. ** ^The soft heap limit is "soft" because even though SQLite strives to stay ** below the limit, it will exceed the limit rather than generate ** an [SQLITE_NOMEM] error. In other words, the soft heap limit ** is advisory only. ** ** ^The return value from sqlite3_soft_heap_limit64() is the size of ** the soft heap limit prior to the call, or negative in the case of an ** error. ^If the argument N is negative ** then no change is made to the soft heap limit. Hence, the current ** size of the soft heap limit can be determined by invoking ** sqlite3_soft_heap_limit64() with a negative argument. ** ** ^If the argument N is zero then the soft heap limit is disabled. ** ** ^(The soft heap limit is not enforced in the current implementation ** if one or more of following conditions are true: ** **
    **
  • The soft heap limit is set to zero. **
  • Memory accounting is disabled using a combination of the ** [sqlite3_config]([SQLITE_CONFIG_MEMSTATUS],...) start-time option and ** the [SQLITE_DEFAULT_MEMSTATUS] compile-time option. **
  • An alternative page cache implementation is specified using ** [sqlite3_config]([SQLITE_CONFIG_PCACHE2],...). **
  • The page cache allocates from its own memory pool supplied ** by [sqlite3_config]([SQLITE_CONFIG_PAGECACHE],...) rather than ** from the heap. **
)^ ** ** Beginning with SQLite [version 3.7.3] ([dateof:3.7.3]), ** the soft heap limit is enforced ** regardless of whether or not the [SQLITE_ENABLE_MEMORY_MANAGEMENT] ** compile-time option is invoked. With [SQLITE_ENABLE_MEMORY_MANAGEMENT], ** the soft heap limit is enforced on every memory allocation. Without ** [SQLITE_ENABLE_MEMORY_MANAGEMENT], the soft heap limit is only enforced ** when memory is allocated by the page cache. Testing suggests that because ** the page cache is the predominate memory user in SQLite, most ** applications will achieve adequate soft heap limit enforcement without ** the use of [SQLITE_ENABLE_MEMORY_MANAGEMENT]. ** ** The circumstances under which SQLite will enforce the soft heap limit may ** changes in future releases of SQLite. */ SQLITE_API sqlite3_int64 sqlite3_soft_heap_limit64(sqlite3_int64 N); /* ** CAPI3REF: Deprecated Soft Heap Limit Interface ** DEPRECATED ** ** This is a deprecated version of the [sqlite3_soft_heap_limit64()] ** interface. This routine is provided for historical compatibility ** only. All new applications should use the ** [sqlite3_soft_heap_limit64()] interface rather than this one. */ SQLITE_API SQLITE_DEPRECATED void sqlite3_soft_heap_limit(int N); /* ** CAPI3REF: Extract Metadata About A Column Of A Table ** METHOD: sqlite3 ** ** ^(The sqlite3_table_column_metadata(X,D,T,C,....) routine returns ** information about column C of table T in database D ** on [database connection] X.)^ ^The sqlite3_table_column_metadata() ** interface returns SQLITE_OK and fills in the non-NULL pointers in ** the final five arguments with appropriate values if the specified ** column exists. ^The sqlite3_table_column_metadata() interface returns ** SQLITE_ERROR and if the specified column does not exist. ** ^If the column-name parameter to sqlite3_table_column_metadata() is a ** NULL pointer, then this routine simply checks for the existence of the ** table and returns SQLITE_OK if the table exists and SQLITE_ERROR if it ** does not. If the table name parameter T in a call to ** sqlite3_table_column_metadata(X,D,T,C,...) is NULL then the result is ** undefined behavior. ** ** ^The column is identified by the second, third and fourth parameters to ** this function. ^(The second parameter is either the name of the database ** (i.e. "main", "temp", or an attached database) containing the specified ** table or NULL.)^ ^If it is NULL, then all attached databases are searched ** for the table using the same algorithm used by the database engine to ** resolve unqualified table references. ** ** ^The third and fourth parameters to this function are the table and column ** name of the desired column, respectively. ** ** ^Metadata is returned by writing to the memory locations passed as the 5th ** and subsequent parameters to this function. ^Any of these arguments may be ** NULL, in which case the corresponding element of metadata is omitted. ** ** ^(
** **
Parameter Output
Type 		Description ** **
5th const char* Data type **
6th const char* Name of default collation sequence **
7th int True if column has a NOT NULL constraint **
8th int True if column is part of the PRIMARY KEY **
9th int True if column is [AUTOINCREMENT] **
**
)^ ** ** ^The memory pointed to by the character pointers returned for the ** declaration type and collation sequence is valid until the next ** call to any SQLite API function. ** ** ^If the specified table is actually a view, an [error code] is returned. ** ** ^If the specified column is "rowid", "oid" or "_rowid_" and the table ** is not a [WITHOUT ROWID] table and an ** [INTEGER PRIMARY KEY] column has been explicitly declared, then the output ** parameters are set for the explicitly declared column. ^(If there is no ** [INTEGER PRIMARY KEY] column, then the outputs ** for the [rowid] are set as follows: ** ** 
**     data type: "INTEGER"
**     collation sequence: "BINARY"
**     not null: 0
**     primary key: 1
**     auto increment: 0
**
)^ ** ** ^This function causes all database schemas to be read from disk and ** parsed, if that has not already been done, and returns an error if ** any errors are encountered while loading the schema. */ SQLITE_API int sqlite3_table_column_metadata( sqlite3 *db, /* Connection handle */ const char *zDbName, /* Database name or NULL */ const char *zTableName, /* Table name */ const char *zColumnName, /* Column name */ char const **pzDataType, /* OUTPUT: Declared data type */ char const **pzCollSeq, /* OUTPUT: Collation sequence name */ int *pNotNull, /* OUTPUT: True if NOT NULL constraint exists */ int *pPrimaryKey, /* OUTPUT: True if column part of PK */ int *pAutoinc /* OUTPUT: True if column is auto-increment */ ); /* ** CAPI3REF: Load An Extension ** METHOD: sqlite3 ** ** ^This interface loads an SQLite extension library from the named file. ** ** ^The sqlite3_load_extension() interface attempts to load an ** [SQLite extension] library contained in the file zFile. If ** the file cannot be loaded directly, attempts are made to load ** with various operating-system specific extensions added. ** So for example, if "samplelib" cannot be loaded, then names like ** "samplelib.so" or "samplelib.dylib" or "samplelib.dll" might ** be tried also. ** ** ^The entry point is zProc. ** ^(zProc may be 0, in which case SQLite will try to come up with an ** entry point name on its own. It first tries "sqlite3_extension_init". ** If that does not work, it constructs a name "sqlite3_X_init" where the ** X is consists of the lower-case equivalent of all ASCII alphabetic ** characters in the filename from the last "/" to the first following ** "." and omitting any initial "lib".)^ ** ^The sqlite3_load_extension() interface returns ** [SQLITE_OK] on success and [SQLITE_ERROR] if something goes wrong. ** ^If an error occurs and pzErrMsg is not 0, then the ** [sqlite3_load_extension()] interface shall attempt to ** fill *pzErrMsg with error message text stored in memory ** obtained from [sqlite3_malloc()]. The calling function ** should free this memory by calling [sqlite3_free()]. ** ** ^Extension loading must be enabled using ** [sqlite3_enable_load_extension()] or ** [sqlite3_db_config](db,[SQLITE_DBCONFIG_ENABLE_LOAD_EXTENSION],1,NULL) ** prior to calling this API, ** otherwise an error will be returned. ** ** Security warning: It is recommended that the ** [SQLITE_DBCONFIG_ENABLE_LOAD_EXTENSION] method be used to enable only this ** interface. The use of the [sqlite3_enable_load_extension()] interface ** should be avoided. This will keep the SQL function [load_extension()] ** disabled and prevent SQL injections from giving attackers ** access to extension loading capabilities. ** ** See also the [load_extension() SQL function]. */ SQLITE_API int sqlite3_load_extension( sqlite3 *db, /* Load the extension into this database connection */ const char *zFile, /* Name of the shared library containing extension */ const char *zProc, /* Entry point. Derived from zFile if 0 */ char **pzErrMsg /* Put error message here if not 0 */ ); /* ** CAPI3REF: Enable Or Disable Extension Loading ** METHOD: sqlite3 ** ** ^So as not to open security holes in older applications that are ** unprepared to deal with [extension loading], and as a means of disabling ** [extension loading] while evaluating user-entered SQL, the following API ** is provided to turn the [sqlite3_load_extension()] mechanism on and off. ** ** ^Extension loading is off by default. ** ^Call the sqlite3_enable_load_extension() routine with onoff==1 ** to turn extension loading on and call it with onoff==0 to turn ** it back off again. ** ** ^This interface enables or disables both the C-API ** [sqlite3_load_extension()] and the SQL function [load_extension()]. ** ^(Use [sqlite3_db_config](db,[SQLITE_DBCONFIG_ENABLE_LOAD_EXTENSION],..) ** to enable or disable only the C-API.)^ ** ** Security warning: It is recommended that extension loading ** be disabled using the [SQLITE_DBCONFIG_ENABLE_LOAD_EXTENSION] method ** rather than this interface, so the [load_extension()] SQL function ** remains disabled. This will prevent SQL injections from giving attackers ** access to extension loading capabilities. */ SQLITE_API int sqlite3_enable_load_extension(sqlite3 *db, int onoff); /* ** CAPI3REF: Automatically Load Statically Linked Extensions ** ** ^This interface causes the xEntryPoint() function to be invoked for ** each new [database connection] that is created. The idea here is that ** xEntryPoint() is the entry point for a statically linked [SQLite extension] ** that is to be automatically loaded into all new database connections. ** ** ^(Even though the function prototype shows that xEntryPoint() takes ** no arguments and returns void, SQLite invokes xEntryPoint() with three ** arguments and expects an integer result as if the signature of the ** entry point where as follows: ** ** 
**    int xEntryPoint(
**      sqlite3 *db,
**      const char **pzErrMsg,
**      const struct sqlite3_api_routines *pThunk
**    );
**
)^ ** ** If the xEntryPoint routine encounters an error, it should make *pzErrMsg ** point to an appropriate error message (obtained from [sqlite3_mprintf()]) ** and return an appropriate [error code]. ^SQLite ensures that *pzErrMsg ** is NULL before calling the xEntryPoint(). ^SQLite will invoke ** [sqlite3_free()] on *pzErrMsg after xEntryPoint() returns. ^If any ** xEntryPoint() returns an error, the [sqlite3_open()], [sqlite3_open16()], ** or [sqlite3_open_v2()] call that provoked the xEntryPoint() will fail. ** ** ^Calling sqlite3_auto_extension(X) with an entry point X that is already ** on the list of automatic extensions is a harmless no-op. ^No entry point ** will be called more than once for each database connection that is opened. ** ** See also: [sqlite3_reset_auto_extension()] ** and [sqlite3_cancel_auto_extension()] */ SQLITE_API int sqlite3_auto_extension(void(*xEntryPoint)(void)); /* ** CAPI3REF: Cancel Automatic Extension Loading ** ** ^The [sqlite3_cancel_auto_extension(X)] interface unregisters the ** initialization routine X that was registered using a prior call to ** [sqlite3_auto_extension(X)]. ^The [sqlite3_cancel_auto_extension(X)] ** routine returns 1 if initialization routine X was successfully ** unregistered and it returns 0 if X was not on the list of initialization ** routines. */ SQLITE_API int sqlite3_cancel_auto_extension(void(*xEntryPoint)(void)); /* ** CAPI3REF: Reset Automatic Extension Loading ** ** ^This interface disables all automatic extensions previously ** registered using [sqlite3_auto_extension()]. */ SQLITE_API void sqlite3_reset_auto_extension(void); /* ** The interface to the virtual-table mechanism is currently considered ** to be experimental. The interface might change in incompatible ways. ** If this is a problem for you, do not use the interface at this time. ** ** When the virtual-table mechanism stabilizes, we will declare the ** interface fixed, support it indefinitely, and remove this comment. */ /* ** Structures used by the virtual table interface */ typedef struct sqlite3_vtab sqlite3_vtab; typedef struct sqlite3_index_info sqlite3_index_info; typedef struct sqlite3_vtab_cursor sqlite3_vtab_cursor; typedef struct sqlite3_module sqlite3_module; /* ** CAPI3REF: Virtual Table Object ** KEYWORDS: sqlite3_module {virtual table module} ** ** This structure, sometimes called a "virtual table module", ** defines the implementation of a [virtual tables]. ** This structure consists mostly of methods for the module. ** ** ^A virtual table module is created by filling in a persistent ** instance of this structure and passing a pointer to that instance ** to [sqlite3_create_module()] or [sqlite3_create_module_v2()]. ** ^The registration remains valid until it is replaced by a different ** module or until the [database connection] closes. The content ** of this structure must not change while it is registered with ** any database connection. */ struct sqlite3_module { int iVersion; int (*xCreate)(sqlite3*, void *pAux, int argc, const char *const*argv, sqlite3_vtab **ppVTab, char**); int (*xConnect)(sqlite3*, void *pAux, int argc, const char *const*argv, sqlite3_vtab **ppVTab, char**); int (*xBestIndex)(sqlite3_vtab *pVTab, sqlite3_index_info*); int (*xDisconnect)(sqlite3_vtab *pVTab); int (*xDestroy)(sqlite3_vtab *pVTab); int (*xOpen)(sqlite3_vtab *pVTab, sqlite3_vtab_cursor **ppCursor); int (*xClose)(sqlite3_vtab_cursor*); int (*xFilter)(sqlite3_vtab_cursor*, int idxNum, const char *idxStr, int argc, sqlite3_value **argv); int (*xNext)(sqlite3_vtab_cursor*); int (*xEof)(sqlite3_vtab_cursor*); int (*xColumn)(sqlite3_vtab_cursor*, sqlite3_context*, int); int (*xRowid)(sqlite3_vtab_cursor*, sqlite3_int64 *pRowid); int (*xUpdate)(sqlite3_vtab *, int, sqlite3_value **, sqlite3_int64 *); int (*xBegin)(sqlite3_vtab *pVTab); int (*xSync)(sqlite3_vtab *pVTab); int (*xCommit)(sqlite3_vtab *pVTab); int (*xRollback)(sqlite3_vtab *pVTab); int (*xFindFunction)(sqlite3_vtab *pVtab, int nArg, const char *zName, void (**pxFunc)(sqlite3_context*,int,sqlite3_value**), void **ppArg); int (*xRename)(sqlite3_vtab *pVtab, const char *zNew); /* The methods above are in version 1 of the sqlite_module object. Those ** below are for version 2 and greater. */ int (*xSavepoint)(sqlite3_vtab *pVTab, int); int (*xRelease)(sqlite3_vtab *pVTab, int); int (*xRollbackTo)(sqlite3_vtab *pVTab, int); }; /* ** CAPI3REF: Virtual Table Indexing Information ** KEYWORDS: sqlite3_index_info ** ** The sqlite3_index_info structure and its substructures is used as part ** of the [virtual table] interface to ** pass information into and receive the reply from the [xBestIndex] ** method of a [virtual table module]. The fields under **Inputs** are the ** inputs to xBestIndex and are read-only. xBestIndex inserts its ** results into the **Outputs** fields. ** ** ^(The aConstraint[] array records WHERE clause constraints of the form: ** **
column OP expr
** ** where OP is =, <, <=, >, or >=.)^ ^(The particular operator is ** stored in aConstraint[].op using one of the ** [SQLITE_INDEX_CONSTRAINT_EQ | SQLITE_INDEX_CONSTRAINT_ values].)^ ** ^(The index of the column is stored in ** aConstraint[].iColumn.)^ ^(aConstraint[].usable is TRUE if the ** expr on the right-hand side can be evaluated (and thus the constraint ** is usable) and false if it cannot.)^ ** ** ^The optimizer automatically inverts terms of the form "expr OP column" ** and makes other simplifications to the WHERE clause in an attempt to ** get as many WHERE clause terms into the form shown above as possible. ** ^The aConstraint[] array only reports WHERE clause terms that are ** relevant to the particular virtual table being queried. ** ** ^Information about the ORDER BY clause is stored in aOrderBy[]. ** ^Each term of aOrderBy records a column of the ORDER BY clause. ** ** The colUsed field indicates which columns of the virtual table may be ** required by the current scan. Virtual table columns are numbered from ** zero in the order in which they appear within the CREATE TABLE statement ** passed to sqlite3_declare_vtab(). For the first 63 columns (columns 0-62), ** the corresponding bit is set within the colUsed mask if the column may be ** required by SQLite. If the table has at least 64 columns and any column ** to the right of the first 63 is required, then bit 63 of colUsed is also ** set. In other words, column iCol may be required if the expression ** (colUsed & ((sqlite3_uint64)1 << (iCol>=63 ? 63 : iCol))) evaluates to ** non-zero. ** ** The [xBestIndex] method must fill aConstraintUsage[] with information ** about what parameters to pass to xFilter. ^If argvIndex>0 then ** the right-hand side of the corresponding aConstraint[] is evaluated ** and becomes the argvIndex-th entry in argv. ^(If aConstraintUsage[].omit ** is true, then the constraint is assumed to be fully handled by the ** virtual table and is not checked again by SQLite.)^ ** ** ^The idxNum and idxPtr values are recorded and passed into the ** [xFilter] method. ** ^[sqlite3_free()] is used to free idxPtr if and only if ** needToFreeIdxPtr is true. ** ** ^The orderByConsumed means that output from [xFilter]/[xNext] will occur in ** the correct order to satisfy the ORDER BY clause so that no separate ** sorting step is required. ** ** ^The estimatedCost value is an estimate of the cost of a particular ** strategy. A cost of N indicates that the cost of the strategy is similar ** to a linear scan of an SQLite table with N rows. A cost of log(N) ** indicates that the expense of the operation is similar to that of a ** binary search on a unique indexed field of an SQLite table with N rows. ** ** ^The estimatedRows value is an estimate of the number of rows that ** will be returned by the strategy. ** ** The xBestIndex method may optionally populate the idxFlags field with a ** mask of SQLITE_INDEX_SCAN_* flags. Currently there is only one such flag - ** SQLITE_INDEX_SCAN_UNIQUE. If the xBestIndex method sets this flag, SQLite ** assumes that the strategy may visit at most one row. ** ** Additionally, if xBestIndex sets the SQLITE_INDEX_SCAN_UNIQUE flag, then ** SQLite also assumes that if a call to the xUpdate() method is made as ** part of the same statement to delete or update a virtual table row and the ** implementation returns SQLITE_CONSTRAINT, then there is no need to rollback ** any database changes. In other words, if the xUpdate() returns ** SQLITE_CONSTRAINT, the database contents must be exactly as they were ** before xUpdate was called. By contrast, if SQLITE_INDEX_SCAN_UNIQUE is not ** set and xUpdate returns SQLITE_CONSTRAINT, any database changes made by ** the xUpdate method are automatically rolled back by SQLite. ** ** IMPORTANT: The estimatedRows field was added to the sqlite3_index_info ** structure for SQLite [version 3.8.2] ([dateof:3.8.2]). ** If a virtual table extension is ** used with an SQLite version earlier than 3.8.2, the results of attempting ** to read or write the estimatedRows field are undefined (but are likely ** to included crashing the application). The estimatedRows field should ** therefore only be used if [sqlite3_libversion_number()] returns a ** value greater than or equal to 3008002. Similarly, the idxFlags field ** was added for [version 3.9.0] ([dateof:3.9.0]). ** It may therefore only be used if ** sqlite3_libversion_number() returns a value greater than or equal to ** 3009000. */ struct sqlite3_index_info { /* Inputs */ int nConstraint; /* Number of entries in aConstraint */ struct sqlite3_index_constraint { int iColumn; /* Column constrained. -1 for ROWID */ unsigned char op; /* Constraint operator */ unsigned char usable; /* True if this constraint is usable */ int iTermOffset; /* Used internally - xBestIndex should ignore */ } *aConstraint; /* Table of WHERE clause constraints */ int nOrderBy; /* Number of terms in the ORDER BY clause */ struct sqlite3_index_orderby { int iColumn; /* Column number */ unsigned char desc; /* True for DESC. False for ASC. */ } *aOrderBy; /* The ORDER BY clause */ /* Outputs */ struct sqlite3_index_constraint_usage { int argvIndex; /* if >0, constraint is part of argv to xFilter */ unsigned char omit; /* Do not code a test for this constraint */ } *aConstraintUsage; int idxNum; /* Number used to identify the index */ char *idxStr; /* String, possibly obtained from sqlite3_malloc */ int needToFreeIdxStr; /* Free idxStr using sqlite3_free() if true */ int orderByConsumed; /* True if output is already ordered */ double estimatedCost; /* Estimated cost of using this index */ /* Fields below are only available in SQLite 3.8.2 and later */ sqlite3_int64 estimatedRows; /* Estimated number of rows returned */ /* Fields below are only available in SQLite 3.9.0 and later */ int idxFlags; /* Mask of SQLITE_INDEX_SCAN_* flags */ /* Fields below are only available in SQLite 3.10.0 and later */ sqlite3_uint64 colUsed; /* Input: Mask of columns used by statement */ }; /* ** CAPI3REF: Virtual Table Scan Flags */ #define SQLITE_INDEX_SCAN_UNIQUE 1 /* Scan visits at most 1 row */ /* ** CAPI3REF: Virtual Table Constraint Operator Codes ** ** These macros defined the allowed values for the ** [sqlite3_index_info].aConstraint[].op field. Each value represents ** an operator that is part of a constraint term in the wHERE clause of ** a query that uses a [virtual table]. */ #define SQLITE_INDEX_CONSTRAINT_EQ 2 #define SQLITE_INDEX_CONSTRAINT_GT 4 #define SQLITE_INDEX_CONSTRAINT_LE 8 #define SQLITE_INDEX_CONSTRAINT_LT 16 #define SQLITE_INDEX_CONSTRAINT_GE 32 #define SQLITE_INDEX_CONSTRAINT_MATCH 64 #define SQLITE_INDEX_CONSTRAINT_LIKE 65 #define SQLITE_INDEX_CONSTRAINT_GLOB 66 #define SQLITE_INDEX_CONSTRAINT_REGEXP 67 /* ** CAPI3REF: Register A Virtual Table Implementation ** METHOD: sqlite3 ** ** ^These routines are used to register a new [virtual table module] name. ** ^Module names must be registered before ** creating a new [virtual table] using the module and before using a ** preexisting [virtual table] for the module. ** ** ^The module name is registered on the [database connection] specified ** by the first parameter. ^The name of the module is given by the ** second parameter. ^The third parameter is a pointer to ** the implementation of the [virtual table module]. ^The fourth ** parameter is an arbitrary client data pointer that is passed through ** into the [xCreate] and [xConnect] methods of the virtual table module ** when a new virtual table is be being created or reinitialized. ** ** ^The sqlite3_create_module_v2() interface has a fifth parameter which ** is a pointer to a destructor for the pClientData. ^SQLite will ** invoke the destructor function (if it is not NULL) when SQLite ** no longer needs the pClientData pointer. ^The destructor will also ** be invoked if the call to sqlite3_create_module_v2() fails. ** ^The sqlite3_create_module() ** interface is equivalent to sqlite3_create_module_v2() with a NULL ** destructor. */ SQLITE_API int sqlite3_create_module( sqlite3 *db, /* SQLite connection to register module with */ const char *zName, /* Name of the module */ const sqlite3_module *p, /* Methods for the module */ void *pClientData /* Client data for xCreate/xConnect */ ); SQLITE_API int sqlite3_create_module_v2( sqlite3 *db, /* SQLite connection to register module with */ const char *zName, /* Name of the module */ const sqlite3_module *p, /* Methods for the module */ void *pClientData, /* Client data for xCreate/xConnect */ void(*xDestroy)(void*) /* Module destructor function */ ); /* ** CAPI3REF: Virtual Table Instance Object ** KEYWORDS: sqlite3_vtab ** ** Every [virtual table module] implementation uses a subclass ** of this object to describe a particular instance ** of the [virtual table]. Each subclass will ** be tailored to the specific needs of the module implementation. ** The purpose of this superclass is to define certain fields that are ** common to all module implementations. ** ** ^Virtual tables methods can set an error message by assigning a ** string obtained from [sqlite3_mprintf()] to zErrMsg. The method should ** take care that any prior string is freed by a call to [sqlite3_free()] ** prior to assigning a new string to zErrMsg. ^After the error message ** is delivered up to the client application, the string will be automatically ** freed by sqlite3_free() and the zErrMsg field will be zeroed. */ struct sqlite3_vtab { const sqlite3_module *pModule; /* The module for this virtual table */ int nRef; /* Number of open cursors */ char *zErrMsg; /* Error message from sqlite3_mprintf() */ /* Virtual table implementations will typically add additional fields */ }; /* ** CAPI3REF: Virtual Table Cursor Object ** KEYWORDS: sqlite3_vtab_cursor {virtual table cursor} ** ** Every [virtual table module] implementation uses a subclass of the ** following structure to describe cursors that point into the ** [virtual table] and are used ** to loop through the virtual table. Cursors are created using the ** [sqlite3_module.xOpen | xOpen] method of the module and are destroyed ** by the [sqlite3_module.xClose | xClose] method. Cursors are used ** by the [xFilter], [xNext], [xEof], [xColumn], and [xRowid] methods ** of the module. Each module implementation will define ** the content of a cursor structure to suit its own needs. ** ** This superclass exists in order to define fields of the cursor that ** are common to all implementations. */ struct sqlite3_vtab_cursor { sqlite3_vtab *pVtab; /* Virtual table of this cursor */ /* Virtual table implementations will typically add additional fields */ }; /* ** CAPI3REF: Declare The Schema Of A Virtual Table ** ** ^The [xCreate] and [xConnect] methods of a ** [virtual table module] call this interface ** to declare the format (the names and datatypes of the columns) of ** the virtual tables they implement. */ SQLITE_API int sqlite3_declare_vtab(sqlite3*, const char *zSQL); /* ** CAPI3REF: Overload A Function For A Virtual Table ** METHOD: sqlite3 ** ** ^(Virtual tables can provide alternative implementations of functions ** using the [xFindFunction] method of the [virtual table module]. ** But global versions of those functions ** must exist in order to be overloaded.)^ ** ** ^(This API makes sure a global version of a function with a particular ** name and number of parameters exists. If no such function exists ** before this API is called, a new function is created.)^ ^The implementation ** of the new function always causes an exception to be thrown. So ** the new function is not good for anything by itself. Its only ** purpose is to be a placeholder function that can be overloaded ** by a [virtual table]. */ SQLITE_API int sqlite3_overload_function(sqlite3*, const char *zFuncName, int nArg); /* ** The interface to the virtual-table mechanism defined above (back up ** to a comment remarkably similar to this one) is currently considered ** to be experimental. The interface might change in incompatible ways. ** If this is a problem for you, do not use the interface at this time. ** ** When the virtual-table mechanism stabilizes, we will declare the ** interface fixed, support it indefinitely, and remove this comment. */ /* ** CAPI3REF: A Handle To An Open BLOB ** KEYWORDS: {BLOB handle} {BLOB handles} ** ** An instance of this object represents an open BLOB on which ** [sqlite3_blob_open | incremental BLOB I/O] can be performed. ** ^Objects of this type are created by [sqlite3_blob_open()] ** and destroyed by [sqlite3_blob_close()]. ** ^The [sqlite3_blob_read()] and [sqlite3_blob_write()] interfaces ** can be used to read or write small subsections of the BLOB. ** ^The [sqlite3_blob_bytes()] interface returns the size of the BLOB in bytes. */ typedef struct sqlite3_blob sqlite3_blob; /* ** CAPI3REF: Open A BLOB For Incremental I/O ** METHOD: sqlite3 ** CONSTRUCTOR: sqlite3_blob ** ** ^(This interfaces opens a [BLOB handle | handle] to the BLOB located ** in row iRow, column zColumn, table zTable in database zDb; ** in other words, the same BLOB that would be selected by: ** ** 
**     SELECT zColumn FROM zDb.zTable WHERE [rowid] = iRow;
**
)^ ** ** ^(Parameter zDb is not the filename that contains the database, but ** rather the symbolic name of the database. For attached databases, this is ** the name that appears after the AS keyword in the [ATTACH] statement. ** For the main database file, the database name is "main". For TEMP ** tables, the database name is "temp".)^ ** ** ^If the flags parameter is non-zero, then the BLOB is opened for read ** and write access. ^If the flags parameter is zero, the BLOB is opened for ** read-only access. ** ** ^(On success, [SQLITE_OK] is returned and the new [BLOB handle] is stored ** in *ppBlob. Otherwise an [error code] is returned and, unless the error ** code is SQLITE_MISUSE, *ppBlob is set to NULL.)^ ^This means that, provided ** the API is not misused, it is always safe to call [sqlite3_blob_close()] ** on *ppBlob after this function it returns. ** ** This function fails with SQLITE_ERROR if any of the following are true: **
    **
  • ^(Database zDb does not exist)^, **
  • ^(Table zTable does not exist within database zDb)^, **
  • ^(Table zTable is a WITHOUT ROWID table)^, **
  • ^(Column zColumn does not exist)^, **
  • ^(Row iRow is not present in the table)^, **
  • ^(The specified column of row iRow contains a value that is not ** a TEXT or BLOB value)^, **
  • ^(Column zColumn is part of an index, PRIMARY KEY or UNIQUE ** constraint and the blob is being opened for read/write access)^, **
  • ^([foreign key constraints | Foreign key constraints] are enabled, ** column zColumn is part of a [child key] definition and the blob is ** being opened for read/write access)^. **
** ** ^Unless it returns SQLITE_MISUSE, this function sets the ** [database connection] error code and message accessible via ** [sqlite3_errcode()] and [sqlite3_errmsg()] and related functions. ** ** A BLOB referenced by sqlite3_blob_open() may be read using the ** [sqlite3_blob_read()] interface and modified by using ** [sqlite3_blob_write()]. The [BLOB handle] can be moved to a ** different row of the same table using the [sqlite3_blob_reopen()] ** interface. However, the column, table, or database of a [BLOB handle] ** cannot be changed after the [BLOB handle] is opened. ** ** ^(If the row that a BLOB handle points to is modified by an ** [UPDATE], [DELETE], or by [ON CONFLICT] side-effects ** then the BLOB handle is marked as "expired". ** This is true if any column of the row is changed, even a column ** other than the one the BLOB handle is open on.)^ ** ^Calls to [sqlite3_blob_read()] and [sqlite3_blob_write()] for ** an expired BLOB handle fail with a return code of [SQLITE_ABORT]. ** ^(Changes written into a BLOB prior to the BLOB expiring are not ** rolled back by the expiration of the BLOB. Such changes will eventually ** commit if the transaction continues to completion.)^ ** ** ^Use the [sqlite3_blob_bytes()] interface to determine the size of ** the opened blob. ^The size of a blob may not be changed by this ** interface. Use the [UPDATE] SQL command to change the size of a ** blob. ** ** ^The [sqlite3_bind_zeroblob()] and [sqlite3_result_zeroblob()] interfaces ** and the built-in [zeroblob] SQL function may be used to create a ** zero-filled blob to read or write using the incremental-blob interface. ** ** To avoid a resource leak, every open [BLOB handle] should eventually ** be released by a call to [sqlite3_blob_close()]. ** ** See also: [sqlite3_blob_close()], ** [sqlite3_blob_reopen()], [sqlite3_blob_read()], ** [sqlite3_blob_bytes()], [sqlite3_blob_write()]. */ SQLITE_API int sqlite3_blob_open( sqlite3*, const char *zDb, const char *zTable, const char *zColumn, sqlite3_int64 iRow, int flags, sqlite3_blob **ppBlob ); /* ** CAPI3REF: Move a BLOB Handle to a New Row ** METHOD: sqlite3_blob ** ** ^This function is used to move an existing [BLOB handle] so that it points ** to a different row of the same database table. ^The new row is identified ** by the rowid value passed as the second argument. Only the row can be ** changed. ^The database, table and column on which the blob handle is open ** remain the same. Moving an existing [BLOB handle] to a new row is ** faster than closing the existing handle and opening a new one. ** ** ^(The new row must meet the same criteria as for [sqlite3_blob_open()] - ** it must exist and there must be either a blob or text value stored in ** the nominated column.)^ ^If the new row is not present in the table, or if ** it does not contain a blob or text value, or if another error occurs, an ** SQLite error code is returned and the blob handle is considered aborted. ** ^All subsequent calls to [sqlite3_blob_read()], [sqlite3_blob_write()] or ** [sqlite3_blob_reopen()] on an aborted blob handle immediately return ** SQLITE_ABORT. ^Calling [sqlite3_blob_bytes()] on an aborted blob handle ** always returns zero. ** ** ^This function sets the database handle error code and message. */ SQLITE_API int sqlite3_blob_reopen(sqlite3_blob *, sqlite3_int64); /* ** CAPI3REF: Close A BLOB Handle ** DESTRUCTOR: sqlite3_blob ** ** ^This function closes an open [BLOB handle]. ^(The BLOB handle is closed ** unconditionally. Even if this routine returns an error code, the ** handle is still closed.)^ ** ** ^If the blob handle being closed was opened for read-write access, and if ** the database is in auto-commit mode and there are no other open read-write ** blob handles or active write statements, the current transaction is ** committed. ^If an error occurs while committing the transaction, an error ** code is returned and the transaction rolled back. ** ** Calling this function with an argument that is not a NULL pointer or an ** open blob handle results in undefined behaviour. ^Calling this routine ** with a null pointer (such as would be returned by a failed call to ** [sqlite3_blob_open()]) is a harmless no-op. ^Otherwise, if this function ** is passed a valid open blob handle, the values returned by the ** sqlite3_errcode() and sqlite3_errmsg() functions are set before returning. */ SQLITE_API int sqlite3_blob_close(sqlite3_blob *); /* ** CAPI3REF: Return The Size Of An Open BLOB ** METHOD: sqlite3_blob ** ** ^Returns the size in bytes of the BLOB accessible via the ** successfully opened [BLOB handle] in its only argument. ^The ** incremental blob I/O routines can only read or overwriting existing ** blob content; they cannot change the size of a blob. ** ** This routine only works on a [BLOB handle] which has been created ** by a prior successful call to [sqlite3_blob_open()] and which has not ** been closed by [sqlite3_blob_close()]. Passing any other pointer in ** to this routine results in undefined and probably undesirable behavior. */ SQLITE_API int sqlite3_blob_bytes(sqlite3_blob *); /* ** CAPI3REF: Read Data From A BLOB Incrementally ** METHOD: sqlite3_blob ** ** ^(This function is used to read data from an open [BLOB handle] into a ** caller-supplied buffer. N bytes of data are copied into buffer Z ** from the open BLOB, starting at offset iOffset.)^ ** ** ^If offset iOffset is less than N bytes from the end of the BLOB, ** [SQLITE_ERROR] is returned and no data is read. ^If N or iOffset is ** less than zero, [SQLITE_ERROR] is returned and no data is read. ** ^The size of the blob (and hence the maximum value of N+iOffset) ** can be determined using the [sqlite3_blob_bytes()] interface. ** ** ^An attempt to read from an expired [BLOB handle] fails with an ** error code of [SQLITE_ABORT]. ** ** ^(On success, sqlite3_blob_read() returns SQLITE_OK. ** Otherwise, an [error code] or an [extended error code] is returned.)^ ** ** This routine only works on a [BLOB handle] which has been created ** by a prior successful call to [sqlite3_blob_open()] and which has not ** been closed by [sqlite3_blob_close()]. Passing any other pointer in ** to this routine results in undefined and probably undesirable behavior. ** ** See also: [sqlite3_blob_write()]. */ SQLITE_API int sqlite3_blob_read(sqlite3_blob *, void *Z, int N, int iOffset); /* ** CAPI3REF: Write Data Into A BLOB Incrementally ** METHOD: sqlite3_blob ** ** ^(This function is used to write data into an open [BLOB handle] from a ** caller-supplied buffer. N bytes of data are copied from the buffer Z ** into the open BLOB, starting at offset iOffset.)^ ** ** ^(On success, sqlite3_blob_write() returns SQLITE_OK. ** Otherwise, an [error code] or an [extended error code] is returned.)^ ** ^Unless SQLITE_MISUSE is returned, this function sets the ** [database connection] error code and message accessible via ** [sqlite3_errcode()] and [sqlite3_errmsg()] and related functions. ** ** ^If the [BLOB handle] passed as the first argument was not opened for ** writing (the flags parameter to [sqlite3_blob_open()] was zero), ** this function returns [SQLITE_READONLY]. ** ** This function may only modify the contents of the BLOB; it is ** not possible to increase the size of a BLOB using this API. ** ^If offset iOffset is less than N bytes from the end of the BLOB, ** [SQLITE_ERROR] is returned and no data is written. The size of the ** BLOB (and hence the maximum value of N+iOffset) can be determined ** using the [sqlite3_blob_bytes()] interface. ^If N or iOffset are less ** than zero [SQLITE_ERROR] is returned and no data is written. ** ** ^An attempt to write to an expired [BLOB handle] fails with an ** error code of [SQLITE_ABORT]. ^Writes to the BLOB that occurred ** before the [BLOB handle] expired are not rolled back by the ** expiration of the handle, though of course those changes might ** have been overwritten by the statement that expired the BLOB handle ** or by other independent statements. ** ** This routine only works on a [BLOB handle] which has been created ** by a prior successful call to [sqlite3_blob_open()] and which has not ** been closed by [sqlite3_blob_close()]. Passing any other pointer in ** to this routine results in undefined and probably undesirable behavior. ** ** See also: [sqlite3_blob_read()]. */ SQLITE_API int sqlite3_blob_write(sqlite3_blob *, const void *z, int n, int iOffset); /* ** CAPI3REF: Virtual File System Objects ** ** A virtual filesystem (VFS) is an [sqlite3_vfs] object ** that SQLite uses to interact ** with the underlying operating system. Most SQLite builds come with a ** single default VFS that is appropriate for the host computer. ** New VFSes can be registered and existing VFSes can be unregistered. ** The following interfaces are provided. ** ** ^The sqlite3_vfs_find() interface returns a pointer to a VFS given its name. ** ^Names are case sensitive. ** ^Names are zero-terminated UTF-8 strings. ** ^If there is no match, a NULL pointer is returned. ** ^If zVfsName is NULL then the default VFS is returned. ** ** ^New VFSes are registered with sqlite3_vfs_register(). ** ^Each new VFS becomes the default VFS if the makeDflt flag is set. ** ^The same VFS can be registered multiple times without injury. ** ^To make an existing VFS into the default VFS, register it again ** with the makeDflt flag set. If two different VFSes with the ** same name are registered, the behavior is undefined. If a ** VFS is registered with a name that is NULL or an empty string, ** then the behavior is undefined. ** ** ^Unregister a VFS with the sqlite3_vfs_unregister() interface. ** ^(If the default VFS is unregistered, another VFS is chosen as ** the default. The choice for the new VFS is arbitrary.)^ */ SQLITE_API sqlite3_vfs *sqlite3_vfs_find(const char *zVfsName); SQLITE_API int sqlite3_vfs_register(sqlite3_vfs*, int makeDflt); SQLITE_API int sqlite3_vfs_unregister(sqlite3_vfs*); /* ** CAPI3REF: Mutexes ** ** The SQLite core uses these routines for thread ** synchronization. Though they are intended for internal ** use by SQLite, code that links against SQLite is ** permitted to use any of these routines. ** ** The SQLite source code contains multiple implementations ** of these mutex routines. An appropriate implementation ** is selected automatically at compile-time. The following ** implementations are available in the SQLite core: ** **
    **
  • SQLITE_MUTEX_PTHREADS **
  • SQLITE_MUTEX_W32 **
  • SQLITE_MUTEX_NOOP **
** ** The SQLITE_MUTEX_NOOP implementation is a set of routines ** that does no real locking and is appropriate for use in ** a single-threaded application. The SQLITE_MUTEX_PTHREADS and ** SQLITE_MUTEX_W32 implementations are appropriate for use on Unix ** and Windows. ** ** If SQLite is compiled with the SQLITE_MUTEX_APPDEF preprocessor ** macro defined (with "-DSQLITE_MUTEX_APPDEF=1"), then no mutex ** implementation is included with the library. In this case the ** application must supply a custom mutex implementation using the ** [SQLITE_CONFIG_MUTEX] option of the sqlite3_config() function ** before calling sqlite3_initialize() or any other public sqlite3_ ** function that calls sqlite3_initialize(). ** ** ^The sqlite3_mutex_alloc() routine allocates a new ** mutex and returns a pointer to it. ^The sqlite3_mutex_alloc() ** routine returns NULL if it is unable to allocate the requested ** mutex. The argument to sqlite3_mutex_alloc() must one of these ** integer constants: ** **
    **
  • SQLITE_MUTEX_FAST **
  • SQLITE_MUTEX_RECURSIVE **
  • SQLITE_MUTEX_STATIC_MASTER **
  • SQLITE_MUTEX_STATIC_MEM **
  • SQLITE_MUTEX_STATIC_OPEN **
  • SQLITE_MUTEX_STATIC_PRNG **
  • SQLITE_MUTEX_STATIC_LRU **
  • SQLITE_MUTEX_STATIC_PMEM **
  • SQLITE_MUTEX_STATIC_APP1 **
  • SQLITE_MUTEX_STATIC_APP2 **
  • SQLITE_MUTEX_STATIC_APP3 **
  • SQLITE_MUTEX_STATIC_VFS1 **
  • SQLITE_MUTEX_STATIC_VFS2 **
  • SQLITE_MUTEX_STATIC_VFS3 **
** ** ^The first two constants (SQLITE_MUTEX_FAST and SQLITE_MUTEX_RECURSIVE) ** cause sqlite3_mutex_alloc() to create ** a new mutex. ^The new mutex is recursive when SQLITE_MUTEX_RECURSIVE ** is used but not necessarily so when SQLITE_MUTEX_FAST is used. ** The mutex implementation does not need to make a distinction ** between SQLITE_MUTEX_RECURSIVE and SQLITE_MUTEX_FAST if it does ** not want to. SQLite will only request a recursive mutex in ** cases where it really needs one. If a faster non-recursive mutex ** implementation is available on the host platform, the mutex subsystem ** might return such a mutex in response to SQLITE_MUTEX_FAST. ** ** ^The other allowed parameters to sqlite3_mutex_alloc() (anything other ** than SQLITE_MUTEX_FAST and SQLITE_MUTEX_RECURSIVE) each return ** a pointer to a static preexisting mutex. ^Nine static mutexes are ** used by the current version of SQLite. Future versions of SQLite ** may add additional static mutexes. Static mutexes are for internal ** use by SQLite only. Applications that use SQLite mutexes should ** use only the dynamic mutexes returned by SQLITE_MUTEX_FAST or ** SQLITE_MUTEX_RECURSIVE. ** ** ^Note that if one of the dynamic mutex parameters (SQLITE_MUTEX_FAST ** or SQLITE_MUTEX_RECURSIVE) is used then sqlite3_mutex_alloc() ** returns a different mutex on every call. ^For the static ** mutex types, the same mutex is returned on every call that has ** the same type number. ** ** ^The sqlite3_mutex_free() routine deallocates a previously ** allocated dynamic mutex. Attempting to deallocate a static ** mutex results in undefined behavior. ** ** ^The sqlite3_mutex_enter() and sqlite3_mutex_try() routines attempt ** to enter a mutex. ^If another thread is already within the mutex, ** sqlite3_mutex_enter() will block and sqlite3_mutex_try() will return ** SQLITE_BUSY. ^The sqlite3_mutex_try() interface returns [SQLITE_OK] ** upon successful entry. ^(Mutexes created using ** SQLITE_MUTEX_RECURSIVE can be entered multiple times by the same thread. ** In such cases, the ** mutex must be exited an equal number of times before another thread ** can enter.)^ If the same thread tries to enter any mutex other ** than an SQLITE_MUTEX_RECURSIVE more than once, the behavior is undefined. ** ** ^(Some systems (for example, Windows 95) do not support the operation ** implemented by sqlite3_mutex_try(). On those systems, sqlite3_mutex_try() ** will always return SQLITE_BUSY. The SQLite core only ever uses ** sqlite3_mutex_try() as an optimization so this is acceptable ** behavior.)^ ** ** ^The sqlite3_mutex_leave() routine exits a mutex that was ** previously entered by the same thread. The behavior ** is undefined if the mutex is not currently entered by the ** calling thread or is not currently allocated. ** ** ^If the argument to sqlite3_mutex_enter(), sqlite3_mutex_try(), or ** sqlite3_mutex_leave() is a NULL pointer, then all three routines ** behave as no-ops. ** ** See also: [sqlite3_mutex_held()] and [sqlite3_mutex_notheld()]. */ SQLITE_API sqlite3_mutex *sqlite3_mutex_alloc(int); SQLITE_API void sqlite3_mutex_free(sqlite3_mutex*); SQLITE_API void sqlite3_mutex_enter(sqlite3_mutex*); SQLITE_API int sqlite3_mutex_try(sqlite3_mutex*); SQLITE_API void sqlite3_mutex_leave(sqlite3_mutex*); /* ** CAPI3REF: Mutex Methods Object ** ** An instance of this structure defines the low-level routines ** used to allocate and use mutexes. ** ** Usually, the default mutex implementations provided by SQLite are ** sufficient, however the application has the option of substituting a custom ** implementation for specialized deployments or systems for which SQLite ** does not provide a suitable implementation. In this case, the application ** creates and populates an instance of this structure to pass ** to sqlite3_config() along with the [SQLITE_CONFIG_MUTEX] option. ** Additionally, an instance of this structure can be used as an ** output variable when querying the system for the current mutex ** implementation, using the [SQLITE_CONFIG_GETMUTEX] option. ** ** ^The xMutexInit method defined by this structure is invoked as ** part of system initialization by the sqlite3_initialize() function. ** ^The xMutexInit routine is called by SQLite exactly once for each ** effective call to [sqlite3_initialize()]. ** ** ^The xMutexEnd method defined by this structure is invoked as ** part of system shutdown by the sqlite3_shutdown() function. The ** implementation of this method is expected to release all outstanding ** resources obtained by the mutex methods implementation, especially ** those obtained by the xMutexInit method. ^The xMutexEnd() ** interface is invoked exactly once for each call to [sqlite3_shutdown()]. ** ** ^(The remaining seven methods defined by this structure (xMutexAlloc, ** xMutexFree, xMutexEnter, xMutexTry, xMutexLeave, xMutexHeld and ** xMutexNotheld) implement the following interfaces (respectively): ** **
    **
  • [sqlite3_mutex_alloc()]
    • **
  • [sqlite3_mutex_free()]
    • **
  • [sqlite3_mutex_enter()]
    • **
  • [sqlite3_mutex_try()]
    • **
  • [sqlite3_mutex_leave()]
    • **
  • [sqlite3_mutex_held()]
    • **
  • [sqlite3_mutex_notheld()]
    • **
)^ ** ** The only difference is that the public sqlite3_XXX functions enumerated ** above silently ignore any invocations that pass a NULL pointer instead ** of a valid mutex handle. The implementations of the methods defined ** by this structure are not required to handle this case, the results ** of passing a NULL pointer instead of a valid mutex handle are undefined ** (i.e. it is acceptable to provide an implementation that segfaults if ** it is passed a NULL pointer). ** ** The xMutexInit() method must be threadsafe. It must be harmless to ** invoke xMutexInit() multiple times within the same process and without ** intervening calls to xMutexEnd(). Second and subsequent calls to ** xMutexInit() must be no-ops. ** ** xMutexInit() must not use SQLite memory allocation ([sqlite3_malloc()] ** and its associates). Similarly, xMutexAlloc() must not use SQLite memory ** allocation for a static mutex. ^However xMutexAlloc() may use SQLite ** memory allocation for a fast or recursive mutex. ** ** ^SQLite will invoke the xMutexEnd() method when [sqlite3_shutdown()] is ** called, but only if the prior call to xMutexInit returned SQLITE_OK. ** If xMutexInit fails in any way, it is expected to clean up after itself ** prior to returning. */ typedef struct sqlite3_mutex_methods sqlite3_mutex_methods; struct sqlite3_mutex_methods { int (*xMutexInit)(void); int (*xMutexEnd)(void); sqlite3_mutex *(*xMutexAlloc)(int); void (*xMutexFree)(sqlite3_mutex *); void (*xMutexEnter)(sqlite3_mutex *); int (*xMutexTry)(sqlite3_mutex *); void (*xMutexLeave)(sqlite3_mutex *); int (*xMutexHeld)(sqlite3_mutex *); int (*xMutexNotheld)(sqlite3_mutex *); }; /* ** CAPI3REF: Mutex Verification Routines ** ** The sqlite3_mutex_held() and sqlite3_mutex_notheld() routines ** are intended for use inside assert() statements. The SQLite core ** never uses these routines except inside an assert() and applications ** are advised to follow the lead of the core. The SQLite core only ** provides implementations for these routines when it is compiled ** with the SQLITE_DEBUG flag. External mutex implementations ** are only required to provide these routines if SQLITE_DEBUG is ** defined and if NDEBUG is not defined. ** ** These routines should return true if the mutex in their argument ** is held or not held, respectively, by the calling thread. ** ** The implementation is not required to provide versions of these ** routines that actually work. If the implementation does not provide working ** versions of these routines, it should at least provide stubs that always ** return true so that one does not get spurious assertion failures. ** ** If the argument to sqlite3_mutex_held() is a NULL pointer then ** the routine should return 1. This seems counter-intuitive since ** clearly the mutex cannot be held if it does not exist. But ** the reason the mutex does not exist is because the build is not ** using mutexes. And we do not want the assert() containing the ** call to sqlite3_mutex_held() to fail, so a non-zero return is ** the appropriate thing to do. The sqlite3_mutex_notheld() ** interface should also return 1 when given a NULL pointer. */ #ifndef NDEBUG SQLITE_API int sqlite3_mutex_held(sqlite3_mutex*); SQLITE_API int sqlite3_mutex_notheld(sqlite3_mutex*); #endif /* ** CAPI3REF: Mutex Types ** ** The [sqlite3_mutex_alloc()] interface takes a single argument ** which is one of these integer constants. ** ** The set of static mutexes may change from one SQLite release to the ** next. Applications that override the built-in mutex logic must be ** prepared to accommodate additional static mutexes. */ #define SQLITE_MUTEX_FAST 0 #define SQLITE_MUTEX_RECURSIVE 1 #define SQLITE_MUTEX_STATIC_MASTER 2 #define SQLITE_MUTEX_STATIC_MEM 3 /* sqlite3_malloc() */ #define SQLITE_MUTEX_STATIC_MEM2 4 /* NOT USED */ #define SQLITE_MUTEX_STATIC_OPEN 4 /* sqlite3BtreeOpen() */ #define SQLITE_MUTEX_STATIC_PRNG 5 /* sqlite3_randomness() */ #define SQLITE_MUTEX_STATIC_LRU 6 /* lru page list */ #define SQLITE_MUTEX_STATIC_LRU2 7 /* NOT USED */ #define SQLITE_MUTEX_STATIC_PMEM 7 /* sqlite3PageMalloc() */ #define SQLITE_MUTEX_STATIC_APP1 8 /* For use by application */ #define SQLITE_MUTEX_STATIC_APP2 9 /* For use by application */ #define SQLITE_MUTEX_STATIC_APP3 10 /* For use by application */ #define SQLITE_MUTEX_STATIC_VFS1 11 /* For use by built-in VFS */ #define SQLITE_MUTEX_STATIC_VFS2 12 /* For use by extension VFS */ #define SQLITE_MUTEX_STATIC_VFS3 13 /* For use by application VFS */ /* ** CAPI3REF: Retrieve the mutex for a database connection ** METHOD: sqlite3 ** ** ^This interface returns a pointer the [sqlite3_mutex] object that ** serializes access to the [database connection] given in the argument ** when the [threading mode] is Serialized. ** ^If the [threading mode] is Single-thread or Multi-thread then this ** routine returns a NULL pointer. */ SQLITE_API sqlite3_mutex *sqlite3_db_mutex(sqlite3*); /* ** CAPI3REF: Low-Level Control Of Database Files ** METHOD: sqlite3 ** ** ^The [sqlite3_file_control()] interface makes a direct call to the ** xFileControl method for the [sqlite3_io_methods] object associated ** with a particular database identified by the second argument. ^The ** name of the database is "main" for the main database or "temp" for the ** TEMP database, or the name that appears after the AS keyword for ** databases that are added using the [ATTACH] SQL command. ** ^A NULL pointer can be used in place of "main" to refer to the ** main database file. ** ^The third and fourth parameters to this routine ** are passed directly through to the second and third parameters of ** the xFileControl method. ^The return value of the xFileControl ** method becomes the return value of this routine. ** ** ^The SQLITE_FCNTL_FILE_POINTER value for the op parameter causes ** a pointer to the underlying [sqlite3_file] object to be written into ** the space pointed to by the 4th parameter. ^The SQLITE_FCNTL_FILE_POINTER ** case is a short-circuit path which does not actually invoke the ** underlying sqlite3_io_methods.xFileControl method. ** ** ^If the second parameter (zDbName) does not match the name of any ** open database file, then SQLITE_ERROR is returned. ^This error ** code is not remembered and will not be recalled by [sqlite3_errcode()] ** or [sqlite3_errmsg()]. The underlying xFileControl method might ** also return SQLITE_ERROR. There is no way to distinguish between ** an incorrect zDbName and an SQLITE_ERROR return from the underlying ** xFileControl method. ** ** See also: [SQLITE_FCNTL_LOCKSTATE] */ SQLITE_API int sqlite3_file_control(sqlite3*, const char *zDbName, int op, void*); /* ** CAPI3REF: Testing Interface ** ** ^The sqlite3_test_control() interface is used to read out internal ** state of SQLite and to inject faults into SQLite for testing ** purposes. ^The first parameter is an operation code that determines ** the number, meaning, and operation of all subsequent parameters. ** ** This interface is not for use by applications. It exists solely ** for verifying the correct operation of the SQLite library. Depending ** on how the SQLite library is compiled, this interface might not exist. ** ** The details of the operation codes, their meanings, the parameters ** they take, and what they do are all subject to change without notice. ** Unlike most of the SQLite API, this function is not guaranteed to ** operate consistently from one release to the next. */ SQLITE_API int sqlite3_test_control(int op, ...); /* ** CAPI3REF: Testing Interface Operation Codes ** ** These constants are the valid operation code parameters used ** as the first argument to [sqlite3_test_control()]. ** ** These parameters and their meanings are subject to change ** without notice. These values are for testing purposes only. ** Applications should not use any of these parameters or the ** [sqlite3_test_control()] interface. */ #define SQLITE_TESTCTRL_FIRST 5 #define SQLITE_TESTCTRL_PRNG_SAVE 5 #define SQLITE_TESTCTRL_PRNG_RESTORE 6 #define SQLITE_TESTCTRL_PRNG_RESET 7 #define SQLITE_TESTCTRL_BITVEC_TEST 8 #define SQLITE_TESTCTRL_FAULT_INSTALL 9 #define SQLITE_TESTCTRL_BENIGN_MALLOC_HOOKS 10 #define SQLITE_TESTCTRL_PENDING_BYTE 11 #define SQLITE_TESTCTRL_ASSERT 12 #define SQLITE_TESTCTRL_ALWAYS 13 #define SQLITE_TESTCTRL_RESERVE 14 #define SQLITE_TESTCTRL_OPTIMIZATIONS 15 #define SQLITE_TESTCTRL_ISKEYWORD 16 #define SQLITE_TESTCTRL_SCRATCHMALLOC 17 #define SQLITE_TESTCTRL_LOCALTIME_FAULT 18 #define SQLITE_TESTCTRL_EXPLAIN_STMT 19 /* NOT USED */ #define SQLITE_TESTCTRL_ONCE_RESET_THRESHOLD 19 #define SQLITE_TESTCTRL_NEVER_CORRUPT 20 #define SQLITE_TESTCTRL_VDBE_COVERAGE 21 #define SQLITE_TESTCTRL_BYTEORDER 22 #define SQLITE_TESTCTRL_ISINIT 23 #define SQLITE_TESTCTRL_SORTER_MMAP 24 #define SQLITE_TESTCTRL_IMPOSTER 25 #define SQLITE_TESTCTRL_LAST 25 /* ** CAPI3REF: SQLite Runtime Status ** ** ^These interfaces are used to retrieve runtime status information ** about the performance of SQLite, and optionally to reset various ** highwater marks. ^The first argument is an integer code for ** the specific parameter to measure. ^(Recognized integer codes ** are of the form [status parameters | SQLITE_STATUS_...].)^ ** ^The current value of the parameter is returned into *pCurrent. ** ^The highest recorded value is returned in *pHighwater. ^If the ** resetFlag is true, then the highest record value is reset after ** *pHighwater is written. ^(Some parameters do not record the highest ** value. For those parameters ** nothing is written into *pHighwater and the resetFlag is ignored.)^ ** ^(Other parameters record only the highwater mark and not the current ** value. For these latter parameters nothing is written into *pCurrent.)^ ** ** ^The sqlite3_status() and sqlite3_status64() routines return ** SQLITE_OK on success and a non-zero [error code] on failure. ** ** If either the current value or the highwater mark is too large to ** be represented by a 32-bit integer, then the values returned by ** sqlite3_status() are undefined. ** ** See also: [sqlite3_db_status()] */ SQLITE_API int sqlite3_status(int op, int *pCurrent, int *pHighwater, int resetFlag); SQLITE_API int sqlite3_status64( int op, sqlite3_int64 *pCurrent, sqlite3_int64 *pHighwater, int resetFlag ); /* ** CAPI3REF: Status Parameters ** KEYWORDS: {status parameters} ** ** These integer constants designate various run-time status parameters ** that can be returned by [sqlite3_status()]. ** **
** [[SQLITE_STATUS_MEMORY_USED]] ^(
SQLITE_STATUS_MEMORY_USED
**
This parameter is the current amount of memory checked out ** using [sqlite3_malloc()], either directly or indirectly. The ** figure includes calls made to [sqlite3_malloc()] by the application ** and internal memory usage by the SQLite library. Scratch memory ** controlled by [SQLITE_CONFIG_SCRATCH] and auxiliary page-cache ** memory controlled by [SQLITE_CONFIG_PAGECACHE] is not included in ** this parameter. The amount returned is the sum of the allocation ** sizes as reported by the xSize method in [sqlite3_mem_methods].
)^ ** ** [[SQLITE_STATUS_MALLOC_SIZE]] ^(
SQLITE_STATUS_MALLOC_SIZE
**
This parameter records the largest memory allocation request ** handed to [sqlite3_malloc()] or [sqlite3_realloc()] (or their ** internal equivalents). Only the value returned in the ** *pHighwater parameter to [sqlite3_status()] is of interest. ** The value written into the *pCurrent parameter is undefined.
)^ ** ** [[SQLITE_STATUS_MALLOC_COUNT]] ^(
SQLITE_STATUS_MALLOC_COUNT
**
This parameter records the number of separate memory allocations ** currently checked out.
)^ ** ** [[SQLITE_STATUS_PAGECACHE_USED]] ^(
SQLITE_STATUS_PAGECACHE_USED
**
This parameter returns the number of pages used out of the ** [pagecache memory allocator] that was configured using ** [SQLITE_CONFIG_PAGECACHE]. The ** value returned is in pages, not in bytes.
)^ ** ** [[SQLITE_STATUS_PAGECACHE_OVERFLOW]] ** ^(
SQLITE_STATUS_PAGECACHE_OVERFLOW
**
This parameter returns the number of bytes of page cache ** allocation which could not be satisfied by the [SQLITE_CONFIG_PAGECACHE] ** buffer and where forced to overflow to [sqlite3_malloc()]. The ** returned value includes allocations that overflowed because they ** where too large (they were larger than the "sz" parameter to ** [SQLITE_CONFIG_PAGECACHE]) and allocations that overflowed because ** no space was left in the page cache.
)^ ** ** [[SQLITE_STATUS_PAGECACHE_SIZE]] ^(
SQLITE_STATUS_PAGECACHE_SIZE
**
This parameter records the largest memory allocation request ** handed to [pagecache memory allocator]. Only the value returned in the ** *pHighwater parameter to [sqlite3_status()] is of interest. ** The value written into the *pCurrent parameter is undefined.
)^ ** ** [[SQLITE_STATUS_SCRATCH_USED]] ^(
SQLITE_STATUS_SCRATCH_USED
**
This parameter returns the number of allocations used out of the ** [scratch memory allocator] configured using ** [SQLITE_CONFIG_SCRATCH]. The value returned is in allocations, not ** in bytes. Since a single thread may only have one scratch allocation ** outstanding at time, this parameter also reports the number of threads ** using scratch memory at the same time.
)^ ** ** [[SQLITE_STATUS_SCRATCH_OVERFLOW]] ^(
SQLITE_STATUS_SCRATCH_OVERFLOW
**
This parameter returns the number of bytes of scratch memory ** allocation which could not be satisfied by the [SQLITE_CONFIG_SCRATCH] ** buffer and where forced to overflow to [sqlite3_malloc()]. The values ** returned include overflows because the requested allocation was too ** larger (that is, because the requested allocation was larger than the ** "sz" parameter to [SQLITE_CONFIG_SCRATCH]) and because no scratch buffer ** slots were available. **
)^ ** ** [[SQLITE_STATUS_SCRATCH_SIZE]] ^(
SQLITE_STATUS_SCRATCH_SIZE
**
This parameter records the largest memory allocation request ** handed to [scratch memory allocator]. Only the value returned in the ** *pHighwater parameter to [sqlite3_status()] is of interest. ** The value written into the *pCurrent parameter is undefined.
)^ ** ** [[SQLITE_STATUS_PARSER_STACK]] ^(
SQLITE_STATUS_PARSER_STACK
**
The *pHighwater parameter records the deepest parser stack. ** The *pCurrent value is undefined. The *pHighwater value is only ** meaningful if SQLite is compiled with [YYTRACKMAXSTACKDEPTH].
)^ **
** ** New status parameters may be added from time to time. */ #define SQLITE_STATUS_MEMORY_USED 0 #define SQLITE_STATUS_PAGECACHE_USED 1 #define SQLITE_STATUS_PAGECACHE_OVERFLOW 2 #define SQLITE_STATUS_SCRATCH_USED 3 #define SQLITE_STATUS_SCRATCH_OVERFLOW 4 #define SQLITE_STATUS_MALLOC_SIZE 5 #define SQLITE_STATUS_PARSER_STACK 6 #define SQLITE_STATUS_PAGECACHE_SIZE 7 #define SQLITE_STATUS_SCRATCH_SIZE 8 #define SQLITE_STATUS_MALLOC_COUNT 9 /* ** CAPI3REF: Database Connection Status ** METHOD: sqlite3 ** ** ^This interface is used to retrieve runtime status information ** about a single [database connection]. ^The first argument is the ** database connection object to be interrogated. ^The second argument ** is an integer constant, taken from the set of ** [SQLITE_DBSTATUS options], that ** determines the parameter to interrogate. The set of ** [SQLITE_DBSTATUS options] is likely ** to grow in future releases of SQLite. ** ** ^The current value of the requested parameter is written into *pCur ** and the highest instantaneous value is written into *pHiwtr. ^If ** the resetFlg is true, then the highest instantaneous value is ** reset back down to the current value. ** ** ^The sqlite3_db_status() routine returns SQLITE_OK on success and a ** non-zero [error code] on failure. ** ** See also: [sqlite3_status()] and [sqlite3_stmt_status()]. */ SQLITE_API int sqlite3_db_status(sqlite3*, int op, int *pCur, int *pHiwtr, int resetFlg); /* ** CAPI3REF: Status Parameters for database connections ** KEYWORDS: {SQLITE_DBSTATUS options} ** ** These constants are the available integer "verbs" that can be passed as ** the second argument to the [sqlite3_db_status()] interface. ** ** New verbs may be added in future releases of SQLite. Existing verbs ** might be discontinued. Applications should check the return code from ** [sqlite3_db_status()] to make sure that the call worked. ** The [sqlite3_db_status()] interface will return a non-zero error code ** if a discontinued or unsupported verb is invoked. ** **
** [[SQLITE_DBSTATUS_LOOKASIDE_USED]] ^(
SQLITE_DBSTATUS_LOOKASIDE_USED
**
This parameter returns the number of lookaside memory slots currently ** checked out.
)^ ** ** [[SQLITE_DBSTATUS_LOOKASIDE_HIT]] ^(
SQLITE_DBSTATUS_LOOKASIDE_HIT
**
This parameter returns the number malloc attempts that were ** satisfied using lookaside memory. Only the high-water value is meaningful; ** the current value is always zero.)^ ** ** [[SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE]] ** ^(
SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE
**
This parameter returns the number malloc attempts that might have ** been satisfied using lookaside memory but failed due to the amount of ** memory requested being larger than the lookaside slot size. ** Only the high-water value is meaningful; ** the current value is always zero.)^ ** ** [[SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL]] ** ^(
SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL
**
This parameter returns the number malloc attempts that might have ** been satisfied using lookaside memory but failed due to all lookaside ** memory already being in use. ** Only the high-water value is meaningful; ** the current value is always zero.)^ ** ** [[SQLITE_DBSTATUS_CACHE_USED]] ^(
SQLITE_DBSTATUS_CACHE_USED
**
This parameter returns the approximate number of bytes of heap ** memory used by all pager caches associated with the database connection.)^ ** ^The highwater mark associated with SQLITE_DBSTATUS_CACHE_USED is always 0. ** ** [[SQLITE_DBSTATUS_CACHE_USED_SHARED]] ** ^(
SQLITE_DBSTATUS_CACHE_USED_SHARED
**
This parameter is similar to DBSTATUS_CACHE_USED, except that if a ** pager cache is shared between two or more connections the bytes of heap ** memory used by that pager cache is divided evenly between the attached ** connections.)^ In other words, if none of the pager caches associated ** with the database connection are shared, this request returns the same ** value as DBSTATUS_CACHE_USED. Or, if one or more or the pager caches are ** shared, the value returned by this call will be smaller than that returned ** by DBSTATUS_CACHE_USED. ^The highwater mark associated with ** SQLITE_DBSTATUS_CACHE_USED_SHARED is always 0. ** ** [[SQLITE_DBSTATUS_SCHEMA_USED]] ^(
SQLITE_DBSTATUS_SCHEMA_USED
**
This parameter returns the approximate number of bytes of heap ** memory used to store the schema for all databases associated ** with the connection - main, temp, and any [ATTACH]-ed databases.)^ ** ^The full amount of memory used by the schemas is reported, even if the ** schema memory is shared with other database connections due to ** [shared cache mode] being enabled. ** ^The highwater mark associated with SQLITE_DBSTATUS_SCHEMA_USED is always 0. ** ** [[SQLITE_DBSTATUS_STMT_USED]] ^(
SQLITE_DBSTATUS_STMT_USED
**
This parameter returns the approximate number of bytes of heap ** and lookaside memory used by all prepared statements associated with ** the database connection.)^ ** ^The highwater mark associated with SQLITE_DBSTATUS_STMT_USED is always 0. **
** ** [[SQLITE_DBSTATUS_CACHE_HIT]] ^(
SQLITE_DBSTATUS_CACHE_HIT
**
This parameter returns the number of pager cache hits that have ** occurred.)^ ^The highwater mark associated with SQLITE_DBSTATUS_CACHE_HIT ** is always 0. **
** ** [[SQLITE_DBSTATUS_CACHE_MISS]] ^(
SQLITE_DBSTATUS_CACHE_MISS
**
This parameter returns the number of pager cache misses that have ** occurred.)^ ^The highwater mark associated with SQLITE_DBSTATUS_CACHE_MISS ** is always 0. **
** ** [[SQLITE_DBSTATUS_CACHE_WRITE]] ^(
SQLITE_DBSTATUS_CACHE_WRITE
**
This parameter returns the number of dirty cache entries that have ** been written to disk. Specifically, the number of pages written to the ** wal file in wal mode databases, or the number of pages written to the ** database file in rollback mode databases. Any pages written as part of ** transaction rollback or database recovery operations are not included. ** If an IO or other error occurs while writing a page to disk, the effect ** on subsequent SQLITE_DBSTATUS_CACHE_WRITE requests is undefined.)^ ^The ** highwater mark associated with SQLITE_DBSTATUS_CACHE_WRITE is always 0. **
** ** [[SQLITE_DBSTATUS_DEFERRED_FKS]] ^(
SQLITE_DBSTATUS_DEFERRED_FKS
**
This parameter returns zero for the current value if and only if ** all foreign key constraints (deferred or immediate) have been ** resolved.)^ ^The highwater mark is always 0. **
**
*/ #define SQLITE_DBSTATUS_LOOKASIDE_USED 0 #define SQLITE_DBSTATUS_CACHE_USED 1 #define SQLITE_DBSTATUS_SCHEMA_USED 2 #define SQLITE_DBSTATUS_STMT_USED 3 #define SQLITE_DBSTATUS_LOOKASIDE_HIT 4 #define SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE 5 #define SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL 6 #define SQLITE_DBSTATUS_CACHE_HIT 7 #define SQLITE_DBSTATUS_CACHE_MISS 8 #define SQLITE_DBSTATUS_CACHE_WRITE 9 #define SQLITE_DBSTATUS_DEFERRED_FKS 10 #define SQLITE_DBSTATUS_CACHE_USED_SHARED 11 #define SQLITE_DBSTATUS_MAX 11 /* Largest defined DBSTATUS */ /* ** CAPI3REF: Prepared Statement Status ** METHOD: sqlite3_stmt ** ** ^(Each prepared statement maintains various ** [SQLITE_STMTSTATUS counters] that measure the number ** of times it has performed specific operations.)^ These counters can ** be used to monitor the performance characteristics of the prepared ** statements. For example, if the number of table steps greatly exceeds ** the number of table searches or result rows, that would tend to indicate ** that the prepared statement is using a full table scan rather than ** an index. ** ** ^(This interface is used to retrieve and reset counter values from ** a [prepared statement]. The first argument is the prepared statement ** object to be interrogated. The second argument ** is an integer code for a specific [SQLITE_STMTSTATUS counter] ** to be interrogated.)^ ** ^The current value of the requested counter is returned. ** ^If the resetFlg is true, then the counter is reset to zero after this ** interface call returns. ** ** See also: [sqlite3_status()] and [sqlite3_db_status()]. */ SQLITE_API int sqlite3_stmt_status(sqlite3_stmt*, int op,int resetFlg); /* ** CAPI3REF: Status Parameters for prepared statements ** KEYWORDS: {SQLITE_STMTSTATUS counter} {SQLITE_STMTSTATUS counters} ** ** These preprocessor macros define integer codes that name counter ** values associated with the [sqlite3_stmt_status()] interface. ** The meanings of the various counters are as follows: ** **
** [[SQLITE_STMTSTATUS_FULLSCAN_STEP]]
SQLITE_STMTSTATUS_FULLSCAN_STEP
**
^This is the number of times that SQLite has stepped forward in ** a table as part of a full table scan. Large numbers for this counter ** may indicate opportunities for performance improvement through ** careful use of indices.
** ** [[SQLITE_STMTSTATUS_SORT]]
SQLITE_STMTSTATUS_SORT
**
^This is the number of sort operations that have occurred. ** A non-zero value in this counter may indicate an opportunity to ** improvement performance through careful use of indices.
** ** [[SQLITE_STMTSTATUS_AUTOINDEX]]
SQLITE_STMTSTATUS_AUTOINDEX
**
^This is the number of rows inserted into transient indices that ** were created automatically in order to help joins run faster. ** A non-zero value in this counter may indicate an opportunity to ** improvement performance by adding permanent indices that do not ** need to be reinitialized each time the statement is run.
** ** [[SQLITE_STMTSTATUS_VM_STEP]]
SQLITE_STMTSTATUS_VM_STEP
**
^This is the number of virtual machine operations executed ** by the prepared statement if that number is less than or equal ** to 2147483647. The number of virtual machine operations can be ** used as a proxy for the total work done by the prepared statement. ** If the number of virtual machine operations exceeds 2147483647 ** then the value returned by this statement status code is undefined. ** ** [[SQLITE_STMTSTATUS_REPREPARE]]
SQLITE_STMTSTATUS_REPREPARE
**
^This is the number of times that the prepare statement has been ** automatically regenerated due to schema changes or change to ** [bound parameters] that might affect the query plan. ** ** [[SQLITE_STMTSTATUS_RUN]]
SQLITE_STMTSTATUS_RUN
**
^This is the number of times that the prepared statement has ** been run. A single "run" for the purposes of this counter is one ** or more calls to [sqlite3_step()] followed by a call to [sqlite3_reset()]. ** The counter is incremented on the first [sqlite3_step()] call of each ** cycle. ** ** [[SQLITE_STMTSTATUS_MEMUSED]]
SQLITE_STMTSTATUS_MEMUSED
**
^This is the approximate number of bytes of heap memory ** used to store the prepared statement. ^This value is not actually ** a counter, and so the resetFlg parameter to sqlite3_stmt_status() ** is ignored when the opcode is SQLITE_STMTSTATUS_MEMUSED. **
**
*/ #define SQLITE_STMTSTATUS_FULLSCAN_STEP 1 #define SQLITE_STMTSTATUS_SORT 2 #define SQLITE_STMTSTATUS_AUTOINDEX 3 #define SQLITE_STMTSTATUS_VM_STEP 4 #define SQLITE_STMTSTATUS_REPREPARE 5 #define SQLITE_STMTSTATUS_RUN 6 #define SQLITE_STMTSTATUS_MEMUSED 99 /* ** CAPI3REF: Custom Page Cache Object ** ** The sqlite3_pcache type is opaque. It is implemented by ** the pluggable module. The SQLite core has no knowledge of ** its size or internal structure and never deals with the ** sqlite3_pcache object except by holding and passing pointers ** to the object. ** ** See [sqlite3_pcache_methods2] for additional information. */ typedef struct sqlite3_pcache sqlite3_pcache; /* ** CAPI3REF: Custom Page Cache Object ** ** The sqlite3_pcache_page object represents a single page in the ** page cache. The page cache will allocate instances of this ** object. Various methods of the page cache use pointers to instances ** of this object as parameters or as their return value. ** ** See [sqlite3_pcache_methods2] for additional information. */ typedef struct sqlite3_pcache_page sqlite3_pcache_page; struct sqlite3_pcache_page { void *pBuf; /* The content of the page */ void *pExtra; /* Extra information associated with the page */ }; /* ** CAPI3REF: Application Defined Page Cache. ** KEYWORDS: {page cache} ** ** ^(The [sqlite3_config]([SQLITE_CONFIG_PCACHE2], ...) interface can ** register an alternative page cache implementation by passing in an ** instance of the sqlite3_pcache_methods2 structure.)^ ** In many applications, most of the heap memory allocated by ** SQLite is used for the page cache. ** By implementing a ** custom page cache using this API, an application can better control ** the amount of memory consumed by SQLite, the way in which ** that memory is allocated and released, and the policies used to ** determine exactly which parts of a database file are cached and for ** how long. ** ** The alternative page cache mechanism is an ** extreme measure that is only needed by the most demanding applications. ** The built-in page cache is recommended for most uses. ** ** ^(The contents of the sqlite3_pcache_methods2 structure are copied to an ** internal buffer by SQLite within the call to [sqlite3_config]. Hence ** the application may discard the parameter after the call to ** [sqlite3_config()] returns.)^ ** ** [[the xInit() page cache method]] ** ^(The xInit() method is called once for each effective ** call to [sqlite3_initialize()])^ ** (usually only once during the lifetime of the process). ^(The xInit() ** method is passed a copy of the sqlite3_pcache_methods2.pArg value.)^ ** The intent of the xInit() method is to set up global data structures ** required by the custom page cache implementation. ** ^(If the xInit() method is NULL, then the ** built-in default page cache is used instead of the application defined ** page cache.)^ ** ** [[the xShutdown() page cache method]] ** ^The xShutdown() method is called by [sqlite3_shutdown()]. ** It can be used to clean up ** any outstanding resources before process shutdown, if required. ** ^The xShutdown() method may be NULL. ** ** ^SQLite automatically serializes calls to the xInit method, ** so the xInit method need not be threadsafe. ^The ** xShutdown method is only called from [sqlite3_shutdown()] so it does ** not need to be threadsafe either. All other methods must be threadsafe ** in multithreaded applications. ** ** ^SQLite will never invoke xInit() more than once without an intervening ** call to xShutdown(). ** ** [[the xCreate() page cache methods]] ** ^SQLite invokes the xCreate() method to construct a new cache instance. ** SQLite will typically create one cache instance for each open database file, ** though this is not guaranteed. ^The ** first parameter, szPage, is the size in bytes of the pages that must ** be allocated by the cache. ^szPage will always a power of two. ^The ** second parameter szExtra is a number of bytes of extra storage ** associated with each page cache entry. ^The szExtra parameter will ** a number less than 250. SQLite will use the ** extra szExtra bytes on each page to store metadata about the underlying ** database page on disk. The value passed into szExtra depends ** on the SQLite version, the target platform, and how SQLite was compiled. ** ^The third argument to xCreate(), bPurgeable, is true if the cache being ** created will be used to cache database pages of a file stored on disk, or ** false if it is used for an in-memory database. The cache implementation ** does not have to do anything special based with the value of bPurgeable; ** it is purely advisory. ^On a cache where bPurgeable is false, SQLite will ** never invoke xUnpin() except to deliberately delete a page. ** ^In other words, calls to xUnpin() on a cache with bPurgeable set to ** false will always have the "discard" flag set to true. ** ^Hence, a cache created with bPurgeable false will ** never contain any unpinned pages. ** ** [[the xCachesize() page cache method]] ** ^(The xCachesize() method may be called at any time by SQLite to set the ** suggested maximum cache-size (number of pages stored by) the cache ** instance passed as the first argument. This is the value configured using ** the SQLite "[PRAGMA cache_size]" command.)^ As with the bPurgeable ** parameter, the implementation is not required to do anything with this ** value; it is advisory only. ** ** [[the xPagecount() page cache methods]] ** The xPagecount() method must return the number of pages currently ** stored in the cache, both pinned and unpinned. ** ** [[the xFetch() page cache methods]] ** The xFetch() method locates a page in the cache and returns a pointer to ** an sqlite3_pcache_page object associated with that page, or a NULL pointer. ** The pBuf element of the returned sqlite3_pcache_page object will be a ** pointer to a buffer of szPage bytes used to store the content of a ** single database page. The pExtra element of sqlite3_pcache_page will be ** a pointer to the szExtra bytes of extra storage that SQLite has requested ** for each entry in the page cache. ** ** The page to be fetched is determined by the key. ^The minimum key value ** is 1. After it has been retrieved using xFetch, the page is considered ** to be "pinned". ** ** If the requested page is already in the page cache, then the page cache ** implementation must return a pointer to the page buffer with its content ** intact. If the requested page is not already in the cache, then the ** cache implementation should use the value of the createFlag ** parameter to help it determined what action to take: ** ** **
createFlag Behavior when page is not already in cache **
0 Do not allocate a new page. Return NULL. **
1 Allocate a new page if it easy and convenient to do so. ** Otherwise return NULL. **
2 Make every effort to allocate a new page. Only return ** NULL if allocating a new page is effectively impossible. **
** ** ^(SQLite will normally invoke xFetch() with a createFlag of 0 or 1. SQLite ** will only use a createFlag of 2 after a prior call with a createFlag of 1 ** failed.)^ In between the to xFetch() calls, SQLite may ** attempt to unpin one or more cache pages by spilling the content of ** pinned pages to disk and synching the operating system disk cache. ** ** [[the xUnpin() page cache method]] ** ^xUnpin() is called by SQLite with a pointer to a currently pinned page ** as its second argument. If the third parameter, discard, is non-zero, ** then the page must be evicted from the cache. ** ^If the discard parameter is ** zero, then the page may be discarded or retained at the discretion of ** page cache implementation. ^The page cache implementation ** may choose to evict unpinned pages at any time. ** ** The cache must not perform any reference counting. A single ** call to xUnpin() unpins the page regardless of the number of prior calls ** to xFetch(). ** ** [[the xRekey() page cache methods]] ** The xRekey() method is used to change the key value associated with the ** page passed as the second argument. If the cache ** previously contains an entry associated with newKey, it must be ** discarded. ^Any prior cache entry associated with newKey is guaranteed not ** to be pinned. ** ** When SQLite calls the xTruncate() method, the cache must discard all ** existing cache entries with page numbers (keys) greater than or equal ** to the value of the iLimit parameter passed to xTruncate(). If any ** of these pages are pinned, they are implicitly unpinned, meaning that ** they can be safely discarded. ** ** [[the xDestroy() page cache method]] ** ^The xDestroy() method is used to delete a cache allocated by xCreate(). ** All resources associated with the specified cache should be freed. ^After ** calling the xDestroy() method, SQLite considers the [sqlite3_pcache*] ** handle invalid, and will not use it with any other sqlite3_pcache_methods2 ** functions. ** ** [[the xShrink() page cache method]] ** ^SQLite invokes the xShrink() method when it wants the page cache to ** free up as much of heap memory as possible. The page cache implementation ** is not obligated to free any memory, but well-behaved implementations should ** do their best. */ typedef struct sqlite3_pcache_methods2 sqlite3_pcache_methods2; struct sqlite3_pcache_methods2 { int iVersion; void *pArg; int (*xInit)(void*); void (*xShutdown)(void*); sqlite3_pcache *(*xCreate)(int szPage, int szExtra, int bPurgeable); void (*xCachesize)(sqlite3_pcache*, int nCachesize); int (*xPagecount)(sqlite3_pcache*); sqlite3_pcache_page *(*xFetch)(sqlite3_pcache*, unsigned key, int createFlag); void (*xUnpin)(sqlite3_pcache*, sqlite3_pcache_page*, int discard); void (*xRekey)(sqlite3_pcache*, sqlite3_pcache_page*, unsigned oldKey, unsigned newKey); void (*xTruncate)(sqlite3_pcache*, unsigned iLimit); void (*xDestroy)(sqlite3_pcache*); void (*xShrink)(sqlite3_pcache*); }; /* ** This is the obsolete pcache_methods object that has now been replaced ** by sqlite3_pcache_methods2. This object is not used by SQLite. It is ** retained in the header file for backwards compatibility only. */ typedef struct sqlite3_pcache_methods sqlite3_pcache_methods; struct sqlite3_pcache_methods { void *pArg; int (*xInit)(void*); void (*xShutdown)(void*); sqlite3_pcache *(*xCreate)(int szPage, int bPurgeable); void (*xCachesize)(sqlite3_pcache*, int nCachesize); int (*xPagecount)(sqlite3_pcache*); void *(*xFetch)(sqlite3_pcache*, unsigned key, int createFlag); void (*xUnpin)(sqlite3_pcache*, void*, int discard); void (*xRekey)(sqlite3_pcache*, void*, unsigned oldKey, unsigned newKey); void (*xTruncate)(sqlite3_pcache*, unsigned iLimit); void (*xDestroy)(sqlite3_pcache*); }; /* ** CAPI3REF: Online Backup Object ** ** The sqlite3_backup object records state information about an ongoing ** online backup operation. ^The sqlite3_backup object is created by ** a call to [sqlite3_backup_init()] and is destroyed by a call to ** [sqlite3_backup_finish()]. ** ** See Also: [Using the SQLite Online Backup API] */ typedef struct sqlite3_backup sqlite3_backup; /* ** CAPI3REF: Online Backup API. ** ** The backup API copies the content of one database into another. ** It is useful either for creating backups of databases or ** for copying in-memory databases to or from persistent files. ** ** See Also: [Using the SQLite Online Backup API] ** ** ^SQLite holds a write transaction open on the destination database file ** for the duration of the backup operation. ** ^The source database is read-locked only while it is being read; ** it is not locked continuously for the entire backup operation. ** ^Thus, the backup may be performed on a live source database without ** preventing other database connections from ** reading or writing to the source database while the backup is underway. ** ** ^(To perform a backup operation: **
    **
  1. sqlite3_backup_init() is called once to initialize the ** backup, **
  2. sqlite3_backup_step() is called one or more times to transfer ** the data between the two databases, and finally **
  3. sqlite3_backup_finish() is called to release all resources ** associated with the backup operation. **
)^ ** There should be exactly one call to sqlite3_backup_finish() for each ** successful call to sqlite3_backup_init(). ** ** [[sqlite3_backup_init()]] sqlite3_backup_init() ** ** ^The D and N arguments to sqlite3_backup_init(D,N,S,M) are the ** [database connection] associated with the destination database ** and the database name, respectively. ** ^The database name is "main" for the main database, "temp" for the ** temporary database, or the name specified after the AS keyword in ** an [ATTACH] statement for an attached database. ** ^The S and M arguments passed to ** sqlite3_backup_init(D,N,S,M) identify the [database connection] ** and database name of the source database, respectively. ** ^The source and destination [database connections] (parameters S and D) ** must be different or else sqlite3_backup_init(D,N,S,M) will fail with ** an error. ** ** ^A call to sqlite3_backup_init() will fail, returning NULL, if ** there is already a read or read-write transaction open on the ** destination database. ** ** ^If an error occurs within sqlite3_backup_init(D,N,S,M), then NULL is ** returned and an error code and error message are stored in the ** destination [database connection] D. ** ^The error code and message for the failed call to sqlite3_backup_init() ** can be retrieved using the [sqlite3_errcode()], [sqlite3_errmsg()], and/or ** [sqlite3_errmsg16()] functions. ** ^A successful call to sqlite3_backup_init() returns a pointer to an ** [sqlite3_backup] object. ** ^The [sqlite3_backup] object may be used with the sqlite3_backup_step() and ** sqlite3_backup_finish() functions to perform the specified backup ** operation. ** ** [[sqlite3_backup_step()]] sqlite3_backup_step() ** ** ^Function sqlite3_backup_step(B,N) will copy up to N pages between ** the source and destination databases specified by [sqlite3_backup] object B. ** ^If N is negative, all remaining source pages are copied. ** ^If sqlite3_backup_step(B,N) successfully copies N pages and there ** are still more pages to be copied, then the function returns [SQLITE_OK]. ** ^If sqlite3_backup_step(B,N) successfully finishes copying all pages ** from source to destination, then it returns [SQLITE_DONE]. ** ^If an error occurs while running sqlite3_backup_step(B,N), ** then an [error code] is returned. ^As well as [SQLITE_OK] and ** [SQLITE_DONE], a call to sqlite3_backup_step() may return [SQLITE_READONLY], ** [SQLITE_NOMEM], [SQLITE_BUSY], [SQLITE_LOCKED], or an ** [SQLITE_IOERR_ACCESS | SQLITE_IOERR_XXX] extended error code. ** ** ^(The sqlite3_backup_step() might return [SQLITE_READONLY] if **
    **
  1. the destination database was opened read-only, or **
  2. the destination database is using write-ahead-log journaling ** and the destination and source page sizes differ, or **
  3. the destination database is an in-memory database and the ** destination and source page sizes differ. **
)^ ** ** ^If sqlite3_backup_step() cannot obtain a required file-system lock, then ** the [sqlite3_busy_handler | busy-handler function] ** is invoked (if one is specified). ^If the ** busy-handler returns non-zero before the lock is available, then ** [SQLITE_BUSY] is returned to the caller. ^In this case the call to ** sqlite3_backup_step() can be retried later. ^If the source ** [database connection] ** is being used to write to the source database when sqlite3_backup_step() ** is called, then [SQLITE_LOCKED] is returned immediately. ^Again, in this ** case the call to sqlite3_backup_step() can be retried later on. ^(If ** [SQLITE_IOERR_ACCESS | SQLITE_IOERR_XXX], [SQLITE_NOMEM], or ** [SQLITE_READONLY] is returned, then ** there is no point in retrying the call to sqlite3_backup_step(). These ** errors are considered fatal.)^ The application must accept ** that the backup operation has failed and pass the backup operation handle ** to the sqlite3_backup_finish() to release associated resources. ** ** ^The first call to sqlite3_backup_step() obtains an exclusive lock ** on the destination file. ^The exclusive lock is not released until either ** sqlite3_backup_finish() is called or the backup operation is complete ** and sqlite3_backup_step() returns [SQLITE_DONE]. ^Every call to ** sqlite3_backup_step() obtains a [shared lock] on the source database that ** lasts for the duration of the sqlite3_backup_step() call. ** ^Because the source database is not locked between calls to ** sqlite3_backup_step(), the source database may be modified mid-way ** through the backup process. ^If the source database is modified by an ** external process or via a database connection other than the one being ** used by the backup operation, then the backup will be automatically ** restarted by the next call to sqlite3_backup_step(). ^If the source ** database is modified by the using the same database connection as is used ** by the backup operation, then the backup database is automatically ** updated at the same time. ** ** [[sqlite3_backup_finish()]] sqlite3_backup_finish() ** ** When sqlite3_backup_step() has returned [SQLITE_DONE], or when the ** application wishes to abandon the backup operation, the application ** should destroy the [sqlite3_backup] by passing it to sqlite3_backup_finish(). ** ^The sqlite3_backup_finish() interfaces releases all ** resources associated with the [sqlite3_backup] object. ** ^If sqlite3_backup_step() has not yet returned [SQLITE_DONE], then any ** active write-transaction on the destination database is rolled back. ** The [sqlite3_backup] object is invalid ** and may not be used following a call to sqlite3_backup_finish(). ** ** ^The value returned by sqlite3_backup_finish is [SQLITE_OK] if no ** sqlite3_backup_step() errors occurred, regardless or whether or not ** sqlite3_backup_step() completed. ** ^If an out-of-memory condition or IO error occurred during any prior ** sqlite3_backup_step() call on the same [sqlite3_backup] object, then ** sqlite3_backup_finish() returns the corresponding [error code]. ** ** ^A return of [SQLITE_BUSY] or [SQLITE_LOCKED] from sqlite3_backup_step() ** is not a permanent error and does not affect the return value of ** sqlite3_backup_finish(). ** ** [[sqlite3_backup_remaining()]] [[sqlite3_backup_pagecount()]] ** sqlite3_backup_remaining() and sqlite3_backup_pagecount() ** ** ^The sqlite3_backup_remaining() routine returns the number of pages still ** to be backed up at the conclusion of the most recent sqlite3_backup_step(). ** ^The sqlite3_backup_pagecount() routine returns the total number of pages ** in the source database at the conclusion of the most recent ** sqlite3_backup_step(). ** ^(The values returned by these functions are only updated by ** sqlite3_backup_step(). If the source database is modified in a way that ** changes the size of the source database or the number of pages remaining, ** those changes are not reflected in the output of sqlite3_backup_pagecount() ** and sqlite3_backup_remaining() until after the next ** sqlite3_backup_step().)^ ** ** Concurrent Usage of Database Handles ** ** ^The source [database connection] may be used by the application for other ** purposes while a backup operation is underway or being initialized. ** ^If SQLite is compiled and configured to support threadsafe database ** connections, then the source database connection may be used concurrently ** from within other threads. ** ** However, the application must guarantee that the destination ** [database connection] is not passed to any other API (by any thread) after ** sqlite3_backup_init() is called and before the corresponding call to ** sqlite3_backup_finish(). SQLite does not currently check to see ** if the application incorrectly accesses the destination [database connection] ** and so no error code is reported, but the operations may malfunction ** nevertheless. Use of the destination database connection while a ** backup is in progress might also also cause a mutex deadlock. ** ** If running in [shared cache mode], the application must ** guarantee that the shared cache used by the destination database ** is not accessed while the backup is running. In practice this means ** that the application must guarantee that the disk file being ** backed up to is not accessed by any connection within the process, ** not just the specific connection that was passed to sqlite3_backup_init(). ** ** The [sqlite3_backup] object itself is partially threadsafe. Multiple ** threads may safely make multiple concurrent calls to sqlite3_backup_step(). ** However, the sqlite3_backup_remaining() and sqlite3_backup_pagecount() ** APIs are not strictly speaking threadsafe. If they are invoked at the ** same time as another thread is invoking sqlite3_backup_step() it is ** possible that they return invalid values. */ SQLITE_API sqlite3_backup *sqlite3_backup_init( sqlite3 *pDest, /* Destination database handle */ const char *zDestName, /* Destination database name */ sqlite3 *pSource, /* Source database handle */ const char *zSourceName /* Source database name */ ); SQLITE_API int sqlite3_backup_step(sqlite3_backup *p, int nPage); SQLITE_API int sqlite3_backup_finish(sqlite3_backup *p); SQLITE_API int sqlite3_backup_remaining(sqlite3_backup *p); SQLITE_API int sqlite3_backup_pagecount(sqlite3_backup *p); /* ** CAPI3REF: Unlock Notification ** METHOD: sqlite3 ** ** ^When running in shared-cache mode, a database operation may fail with ** an [SQLITE_LOCKED] error if the required locks on the shared-cache or ** individual tables within the shared-cache cannot be obtained. See ** [SQLite Shared-Cache Mode] for a description of shared-cache locking. ** ^This API may be used to register a callback that SQLite will invoke ** when the connection currently holding the required lock relinquishes it. ** ^This API is only available if the library was compiled with the ** [SQLITE_ENABLE_UNLOCK_NOTIFY] C-preprocessor symbol defined. ** ** See Also: [Using the SQLite Unlock Notification Feature]. ** ** ^Shared-cache locks are released when a database connection concludes ** its current transaction, either by committing it or rolling it back. ** ** ^When a connection (known as the blocked connection) fails to obtain a ** shared-cache lock and SQLITE_LOCKED is returned to the caller, the ** identity of the database connection (the blocking connection) that ** has locked the required resource is stored internally. ^After an ** application receives an SQLITE_LOCKED error, it may call the ** sqlite3_unlock_notify() method with the blocked connection handle as ** the first argument to register for a callback that will be invoked ** when the blocking connections current transaction is concluded. ^The ** callback is invoked from within the [sqlite3_step] or [sqlite3_close] ** call that concludes the blocking connections transaction. ** ** ^(If sqlite3_unlock_notify() is called in a multi-threaded application, ** there is a chance that the blocking connection will have already ** concluded its transaction by the time sqlite3_unlock_notify() is invoked. ** If this happens, then the specified callback is invoked immediately, ** from within the call to sqlite3_unlock_notify().)^ ** ** ^If the blocked connection is attempting to obtain a write-lock on a ** shared-cache table, and more than one other connection currently holds ** a read-lock on the same table, then SQLite arbitrarily selects one of ** the other connections to use as the blocking connection. ** ** ^(There may be at most one unlock-notify callback registered by a ** blocked connection. If sqlite3_unlock_notify() is called when the ** blocked connection already has a registered unlock-notify callback, ** then the new callback replaces the old.)^ ^If sqlite3_unlock_notify() is ** called with a NULL pointer as its second argument, then any existing ** unlock-notify callback is canceled. ^The blocked connections ** unlock-notify callback may also be canceled by closing the blocked ** connection using [sqlite3_close()]. ** ** The unlock-notify callback is not reentrant. If an application invokes ** any sqlite3_xxx API functions from within an unlock-notify callback, a ** crash or deadlock may be the result. ** ** ^Unless deadlock is detected (see below), sqlite3_unlock_notify() always ** returns SQLITE_OK. ** ** Callback Invocation Details ** ** When an unlock-notify callback is registered, the application provides a ** single void* pointer that is passed to the callback when it is invoked. ** However, the signature of the callback function allows SQLite to pass ** it an array of void* context pointers. The first argument passed to ** an unlock-notify callback is a pointer to an array of void* pointers, ** and the second is the number of entries in the array. ** ** When a blocking connections transaction is concluded, there may be ** more than one blocked connection that has registered for an unlock-notify ** callback. ^If two or more such blocked connections have specified the ** same callback function, then instead of invoking the callback function ** multiple times, it is invoked once with the set of void* context pointers ** specified by the blocked connections bundled together into an array. ** This gives the application an opportunity to prioritize any actions ** related to the set of unblocked database connections. ** ** Deadlock Detection ** ** Assuming that after registering for an unlock-notify callback a ** database waits for the callback to be issued before taking any further ** action (a reasonable assumption), then using this API may cause the ** application to deadlock. For example, if connection X is waiting for ** connection Y's transaction to be concluded, and similarly connection ** Y is waiting on connection X's transaction, then neither connection ** will proceed and the system may remain deadlocked indefinitely. ** ** To avoid this scenario, the sqlite3_unlock_notify() performs deadlock ** detection. ^If a given call to sqlite3_unlock_notify() would put the ** system in a deadlocked state, then SQLITE_LOCKED is returned and no ** unlock-notify callback is registered. The system is said to be in ** a deadlocked state if connection A has registered for an unlock-notify ** callback on the conclusion of connection B's transaction, and connection ** B has itself registered for an unlock-notify callback when connection ** A's transaction is concluded. ^Indirect deadlock is also detected, so ** the system is also considered to be deadlocked if connection B has ** registered for an unlock-notify callback on the conclusion of connection ** C's transaction, where connection C is waiting on connection A. ^Any ** number of levels of indirection are allowed. ** ** The "DROP TABLE" Exception ** ** When a call to [sqlite3_step()] returns SQLITE_LOCKED, it is almost ** always appropriate to call sqlite3_unlock_notify(). There is however, ** one exception. When executing a "DROP TABLE" or "DROP INDEX" statement, ** SQLite checks if there are any currently executing SELECT statements ** that belong to the same connection. If there are, SQLITE_LOCKED is ** returned. In this case there is no "blocking connection", so invoking ** sqlite3_unlock_notify() results in the unlock-notify callback being ** invoked immediately. If the application then re-attempts the "DROP TABLE" ** or "DROP INDEX" query, an infinite loop might be the result. ** ** One way around this problem is to check the extended error code returned ** by an sqlite3_step() call. ^(If there is a blocking connection, then the ** extended error code is set to SQLITE_LOCKED_SHAREDCACHE. Otherwise, in ** the special "DROP TABLE/INDEX" case, the extended error code is just ** SQLITE_LOCKED.)^ */ SQLITE_API int sqlite3_unlock_notify( sqlite3 *pBlocked, /* Waiting connection */ void (*xNotify)(void **apArg, int nArg), /* Callback function to invoke */ void *pNotifyArg /* Argument to pass to xNotify */ ); /* ** CAPI3REF: String Comparison ** ** ^The [sqlite3_stricmp()] and [sqlite3_strnicmp()] APIs allow applications ** and extensions to compare the contents of two buffers containing UTF-8 ** strings in a case-independent fashion, using the same definition of "case ** independence" that SQLite uses internally when comparing identifiers. */ SQLITE_API int sqlite3_stricmp(const char *, const char *); SQLITE_API int sqlite3_strnicmp(const char *, const char *, int); /* ** CAPI3REF: String Globbing * ** ^The [sqlite3_strglob(P,X)] interface returns zero if and only if ** string X matches the [GLOB] pattern P. ** ^The definition of [GLOB] pattern matching used in ** [sqlite3_strglob(P,X)] is the same as for the "X GLOB P" operator in the ** SQL dialect understood by SQLite. ^The [sqlite3_strglob(P,X)] function ** is case sensitive. ** ** Note that this routine returns zero on a match and non-zero if the strings ** do not match, the same as [sqlite3_stricmp()] and [sqlite3_strnicmp()]. ** ** See also: [sqlite3_strlike()]. */ SQLITE_API int sqlite3_strglob(const char *zGlob, const char *zStr); /* ** CAPI3REF: String LIKE Matching * ** ^The [sqlite3_strlike(P,X,E)] interface returns zero if and only if ** string X matches the [LIKE] pattern P with escape character E. ** ^The definition of [LIKE] pattern matching used in ** [sqlite3_strlike(P,X,E)] is the same as for the "X LIKE P ESCAPE E" ** operator in the SQL dialect understood by SQLite. ^For "X LIKE P" without ** the ESCAPE clause, set the E parameter of [sqlite3_strlike(P,X,E)] to 0. ** ^As with the LIKE operator, the [sqlite3_strlike(P,X,E)] function is case ** insensitive - equivalent upper and lower case ASCII characters match ** one another. ** ** ^The [sqlite3_strlike(P,X,E)] function matches Unicode characters, though ** only ASCII characters are case folded. ** ** Note that this routine returns zero on a match and non-zero if the strings ** do not match, the same as [sqlite3_stricmp()] and [sqlite3_strnicmp()]. ** ** See also: [sqlite3_strglob()]. */ SQLITE_API int sqlite3_strlike(const char *zGlob, const char *zStr, unsigned int cEsc); /* ** CAPI3REF: Error Logging Interface ** ** ^The [sqlite3_log()] interface writes a message into the [error log] ** established by the [SQLITE_CONFIG_LOG] option to [sqlite3_config()]. ** ^If logging is enabled, the zFormat string and subsequent arguments are ** used with [sqlite3_snprintf()] to generate the final output string. ** ** The sqlite3_log() interface is intended for use by extensions such as ** virtual tables, collating functions, and SQL functions. While there is ** nothing to prevent an application from calling sqlite3_log(), doing so ** is considered bad form. ** ** The zFormat string must not be NULL. ** ** To avoid deadlocks and other threading problems, the sqlite3_log() routine ** will not use dynamically allocated memory. The log message is stored in ** a fixed-length buffer on the stack. If the log message is longer than ** a few hundred characters, it will be truncated to the length of the ** buffer. */ SQLITE_API void sqlite3_log(int iErrCode, const char *zFormat, ...); /* ** CAPI3REF: Write-Ahead Log Commit Hook ** METHOD: sqlite3 ** ** ^The [sqlite3_wal_hook()] function is used to register a callback that ** is invoked each time data is committed to a database in wal mode. ** ** ^(The callback is invoked by SQLite after the commit has taken place and ** the associated write-lock on the database released)^, so the implementation ** may read, write or [checkpoint] the database as required. ** ** ^The first parameter passed to the callback function when it is invoked ** is a copy of the third parameter passed to sqlite3_wal_hook() when ** registering the callback. ^The second is a copy of the database handle. ** ^The third parameter is the name of the database that was written to - ** either "main" or the name of an [ATTACH]-ed database. ^The fourth parameter ** is the number of pages currently in the write-ahead log file, ** including those that were just committed. ** ** The callback function should normally return [SQLITE_OK]. ^If an error ** code is returned, that error will propagate back up through the ** SQLite code base to cause the statement that provoked the callback ** to report an error, though the commit will have still occurred. If the ** callback returns [SQLITE_ROW] or [SQLITE_DONE], or if it returns a value ** that does not correspond to any valid SQLite error code, the results ** are undefined. ** ** A single database handle may have at most a single write-ahead log callback ** registered at one time. ^Calling [sqlite3_wal_hook()] replaces any ** previously registered write-ahead log callback. ^Note that the ** [sqlite3_wal_autocheckpoint()] interface and the ** [wal_autocheckpoint pragma] both invoke [sqlite3_wal_hook()] and will ** overwrite any prior [sqlite3_wal_hook()] settings. */ SQLITE_API void *sqlite3_wal_hook( sqlite3*, int(*)(void *,sqlite3*,const char*,int), void* ); /* ** CAPI3REF: Configure an auto-checkpoint ** METHOD: sqlite3 ** ** ^The [sqlite3_wal_autocheckpoint(D,N)] is a wrapper around ** [sqlite3_wal_hook()] that causes any database on [database connection] D ** to automatically [checkpoint] ** after committing a transaction if there are N or ** more frames in the [write-ahead log] file. ^Passing zero or ** a negative value as the nFrame parameter disables automatic ** checkpoints entirely. ** ** ^The callback registered by this function replaces any existing callback ** registered using [sqlite3_wal_hook()]. ^Likewise, registering a callback ** using [sqlite3_wal_hook()] disables the automatic checkpoint mechanism ** configured by this function. ** ** ^The [wal_autocheckpoint pragma] can be used to invoke this interface ** from SQL. ** ** ^Checkpoints initiated by this mechanism are ** [sqlite3_wal_checkpoint_v2|PASSIVE]. ** ** ^Every new [database connection] defaults to having the auto-checkpoint ** enabled with a threshold of 1000 or [SQLITE_DEFAULT_WAL_AUTOCHECKPOINT] ** pages. The use of this interface ** is only necessary if the default setting is found to be suboptimal ** for a particular application. */ SQLITE_API int sqlite3_wal_autocheckpoint(sqlite3 *db, int N); /* ** CAPI3REF: Checkpoint a database ** METHOD: sqlite3 ** ** ^(The sqlite3_wal_checkpoint(D,X) is equivalent to ** [sqlite3_wal_checkpoint_v2](D,X,[SQLITE_CHECKPOINT_PASSIVE],0,0).)^ ** ** In brief, sqlite3_wal_checkpoint(D,X) causes the content in the ** [write-ahead log] for database X on [database connection] D to be ** transferred into the database file and for the write-ahead log to ** be reset. See the [checkpointing] documentation for addition ** information. ** ** This interface used to be the only way to cause a checkpoint to ** occur. But then the newer and more powerful [sqlite3_wal_checkpoint_v2()] ** interface was added. This interface is retained for backwards ** compatibility and as a convenience for applications that need to manually ** start a callback but which do not need the full power (and corresponding ** complication) of [sqlite3_wal_checkpoint_v2()]. */ SQLITE_API int sqlite3_wal_checkpoint(sqlite3 *db, const char *zDb); /* ** CAPI3REF: Checkpoint a database ** METHOD: sqlite3 ** ** ^(The sqlite3_wal_checkpoint_v2(D,X,M,L,C) interface runs a checkpoint ** operation on database X of [database connection] D in mode M. Status ** information is written back into integers pointed to by L and C.)^ ** ^(The M parameter must be a valid [checkpoint mode]:)^ ** **
**
SQLITE_CHECKPOINT_PASSIVE
** ^Checkpoint as many frames as possible without waiting for any database ** readers or writers to finish, then sync the database file if all frames ** in the log were checkpointed. ^The [busy-handler callback] ** is never invoked in the SQLITE_CHECKPOINT_PASSIVE mode. ** ^On the other hand, passive mode might leave the checkpoint unfinished ** if there are concurrent readers or writers. ** **
SQLITE_CHECKPOINT_FULL
** ^This mode blocks (it invokes the ** [sqlite3_busy_handler|busy-handler callback]) until there is no ** database writer and all readers are reading from the most recent database ** snapshot. ^It then checkpoints all frames in the log file and syncs the ** database file. ^This mode blocks new database writers while it is pending, ** but new database readers are allowed to continue unimpeded. ** **
SQLITE_CHECKPOINT_RESTART
** ^This mode works the same way as SQLITE_CHECKPOINT_FULL with the addition ** that after checkpointing the log file it blocks (calls the ** [busy-handler callback]) ** until all readers are reading from the database file only. ^This ensures ** that the next writer will restart the log file from the beginning. ** ^Like SQLITE_CHECKPOINT_FULL, this mode blocks new ** database writer attempts while it is pending, but does not impede readers. ** **
SQLITE_CHECKPOINT_TRUNCATE
** ^This mode works the same way as SQLITE_CHECKPOINT_RESTART with the ** addition that it also truncates the log file to zero bytes just prior ** to a successful return. **
** ** ^If pnLog is not NULL, then *pnLog is set to the total number of frames in ** the log file or to -1 if the checkpoint could not run because ** of an error or because the database is not in [WAL mode]. ^If pnCkpt is not ** NULL,then *pnCkpt is set to the total number of checkpointed frames in the ** log file (including any that were already checkpointed before the function ** was called) or to -1 if the checkpoint could not run due to an error or ** because the database is not in WAL mode. ^Note that upon successful ** completion of an SQLITE_CHECKPOINT_TRUNCATE, the log file will have been ** truncated to zero bytes and so both *pnLog and *pnCkpt will be set to zero. ** ** ^All calls obtain an exclusive "checkpoint" lock on the database file. ^If ** any other process is running a checkpoint operation at the same time, the ** lock cannot be obtained and SQLITE_BUSY is returned. ^Even if there is a ** busy-handler configured, it will not be invoked in this case. ** ** ^The SQLITE_CHECKPOINT_FULL, RESTART and TRUNCATE modes also obtain the ** exclusive "writer" lock on the database file. ^If the writer lock cannot be ** obtained immediately, and a busy-handler is configured, it is invoked and ** the writer lock retried until either the busy-handler returns 0 or the lock ** is successfully obtained. ^The busy-handler is also invoked while waiting for ** database readers as described above. ^If the busy-handler returns 0 before ** the writer lock is obtained or while waiting for database readers, the ** checkpoint operation proceeds from that point in the same way as ** SQLITE_CHECKPOINT_PASSIVE - checkpointing as many frames as possible ** without blocking any further. ^SQLITE_BUSY is returned in this case. ** ** ^If parameter zDb is NULL or points to a zero length string, then the ** specified operation is attempted on all WAL databases [attached] to ** [database connection] db. In this case the ** values written to output parameters *pnLog and *pnCkpt are undefined. ^If ** an SQLITE_BUSY error is encountered when processing one or more of the ** attached WAL databases, the operation is still attempted on any remaining ** attached databases and SQLITE_BUSY is returned at the end. ^If any other ** error occurs while processing an attached database, processing is abandoned ** and the error code is returned to the caller immediately. ^If no error ** (SQLITE_BUSY or otherwise) is encountered while processing the attached ** databases, SQLITE_OK is returned. ** ** ^If database zDb is the name of an attached database that is not in WAL ** mode, SQLITE_OK is returned and both *pnLog and *pnCkpt set to -1. ^If ** zDb is not NULL (or a zero length string) and is not the name of any ** attached database, SQLITE_ERROR is returned to the caller. ** ** ^Unless it returns SQLITE_MISUSE, ** the sqlite3_wal_checkpoint_v2() interface ** sets the error information that is queried by ** [sqlite3_errcode()] and [sqlite3_errmsg()]. ** ** ^The [PRAGMA wal_checkpoint] command can be used to invoke this interface ** from SQL. */ SQLITE_API int sqlite3_wal_checkpoint_v2( sqlite3 *db, /* Database handle */ const char *zDb, /* Name of attached database (or NULL) */ int eMode, /* SQLITE_CHECKPOINT_* value */ int *pnLog, /* OUT: Size of WAL log in frames */ int *pnCkpt /* OUT: Total number of frames checkpointed */ ); /* ** CAPI3REF: Checkpoint Mode Values ** KEYWORDS: {checkpoint mode} ** ** These constants define all valid values for the "checkpoint mode" passed ** as the third parameter to the [sqlite3_wal_checkpoint_v2()] interface. ** See the [sqlite3_wal_checkpoint_v2()] documentation for details on the ** meaning of each of these checkpoint modes. */ #define SQLITE_CHECKPOINT_PASSIVE 0 /* Do as much as possible w/o blocking */ #define SQLITE_CHECKPOINT_FULL 1 /* Wait for writers, then checkpoint */ #define SQLITE_CHECKPOINT_RESTART 2 /* Like FULL but wait for for readers */ #define SQLITE_CHECKPOINT_TRUNCATE 3 /* Like RESTART but also truncate WAL */ /* ** CAPI3REF: Virtual Table Interface Configuration ** ** This function may be called by either the [xConnect] or [xCreate] method ** of a [virtual table] implementation to configure ** various facets of the virtual table interface. ** ** If this interface is invoked outside the context of an xConnect or ** xCreate virtual table method then the behavior is undefined. ** ** At present, there is only one option that may be configured using ** this function. (See [SQLITE_VTAB_CONSTRAINT_SUPPORT].) Further options ** may be added in the future. */ SQLITE_API int sqlite3_vtab_config(sqlite3*, int op, ...); /* ** CAPI3REF: Virtual Table Configuration Options ** ** These macros define the various options to the ** [sqlite3_vtab_config()] interface that [virtual table] implementations ** can use to customize and optimize their behavior. ** **
**
SQLITE_VTAB_CONSTRAINT_SUPPORT **
Calls of the form ** [sqlite3_vtab_config](db,SQLITE_VTAB_CONSTRAINT_SUPPORT,X) are supported, ** where X is an integer. If X is zero, then the [virtual table] whose ** [xCreate] or [xConnect] method invoked [sqlite3_vtab_config()] does not ** support constraints. In this configuration (which is the default) if ** a call to the [xUpdate] method returns [SQLITE_CONSTRAINT], then the entire ** statement is rolled back as if [ON CONFLICT | OR ABORT] had been ** specified as part of the users SQL statement, regardless of the actual ** ON CONFLICT mode specified. ** ** If X is non-zero, then the virtual table implementation guarantees ** that if [xUpdate] returns [SQLITE_CONSTRAINT], it will do so before ** any modifications to internal or persistent data structures have been made. ** If the [ON CONFLICT] mode is ABORT, FAIL, IGNORE or ROLLBACK, SQLite ** is able to roll back a statement or database transaction, and abandon ** or continue processing the current SQL statement as appropriate. ** If the ON CONFLICT mode is REPLACE and the [xUpdate] method returns ** [SQLITE_CONSTRAINT], SQLite handles this as if the ON CONFLICT mode ** had been ABORT. ** ** Virtual table implementations that are required to handle OR REPLACE ** must do so within the [xUpdate] method. If a call to the ** [sqlite3_vtab_on_conflict()] function indicates that the current ON ** CONFLICT policy is REPLACE, the virtual table implementation should ** silently replace the appropriate rows within the xUpdate callback and ** return SQLITE_OK. Or, if this is not possible, it may return ** SQLITE_CONSTRAINT, in which case SQLite falls back to OR ABORT ** constraint handling. **
*/ #define SQLITE_VTAB_CONSTRAINT_SUPPORT 1 /* ** CAPI3REF: Determine The Virtual Table Conflict Policy ** ** This function may only be called from within a call to the [xUpdate] method ** of a [virtual table] implementation for an INSERT or UPDATE operation. ^The ** value returned is one of [SQLITE_ROLLBACK], [SQLITE_IGNORE], [SQLITE_FAIL], ** [SQLITE_ABORT], or [SQLITE_REPLACE], according to the [ON CONFLICT] mode ** of the SQL statement that triggered the call to the [xUpdate] method of the ** [virtual table]. */ SQLITE_API int sqlite3_vtab_on_conflict(sqlite3 *); /* ** CAPI3REF: Conflict resolution modes ** KEYWORDS: {conflict resolution mode} ** ** These constants are returned by [sqlite3_vtab_on_conflict()] to ** inform a [virtual table] implementation what the [ON CONFLICT] mode ** is for the SQL statement being evaluated. ** ** Note that the [SQLITE_IGNORE] constant is also used as a potential ** return value from the [sqlite3_set_authorizer()] callback and that ** [SQLITE_ABORT] is also a [result code]. */ #define SQLITE_ROLLBACK 1 /* #define SQLITE_IGNORE 2 // Also used by sqlite3_authorizer() callback */ #define SQLITE_FAIL 3 /* #define SQLITE_ABORT 4 // Also an error code */ #define SQLITE_REPLACE 5 /* ** CAPI3REF: Prepared Statement Scan Status Opcodes ** KEYWORDS: {scanstatus options} ** ** The following constants can be used for the T parameter to the ** [sqlite3_stmt_scanstatus(S,X,T,V)] interface. Each constant designates a ** different metric for sqlite3_stmt_scanstatus() to return. ** ** When the value returned to V is a string, space to hold that string is ** managed by the prepared statement S and will be automatically freed when ** S is finalized. ** **
** [[SQLITE_SCANSTAT_NLOOP]]
SQLITE_SCANSTAT_NLOOP
**
^The [sqlite3_int64] variable pointed to by the T parameter will be ** set to the total number of times that the X-th loop has run.
** ** [[SQLITE_SCANSTAT_NVISIT]]
SQLITE_SCANSTAT_NVISIT
**
^The [sqlite3_int64] variable pointed to by the T parameter will be set ** to the total number of rows examined by all iterations of the X-th loop.
** ** [[SQLITE_SCANSTAT_EST]]
SQLITE_SCANSTAT_EST
**
^The "double" variable pointed to by the T parameter will be set to the ** query planner's estimate for the average number of rows output from each ** iteration of the X-th loop. If the query planner's estimates was accurate, ** then this value will approximate the quotient NVISIT/NLOOP and the ** product of this value for all prior loops with the same SELECTID will ** be the NLOOP value for the current loop. ** ** [[SQLITE_SCANSTAT_NAME]]
SQLITE_SCANSTAT_NAME
**
^The "const char *" variable pointed to by the T parameter will be set ** to a zero-terminated UTF-8 string containing the name of the index or table ** used for the X-th loop. ** ** [[SQLITE_SCANSTAT_EXPLAIN]]
SQLITE_SCANSTAT_EXPLAIN
**
^The "const char *" variable pointed to by the T parameter will be set ** to a zero-terminated UTF-8 string containing the [EXPLAIN QUERY PLAN] ** description for the X-th loop. ** ** [[SQLITE_SCANSTAT_SELECTID]]
SQLITE_SCANSTAT_SELECT
**
^The "int" variable pointed to by the T parameter will be set to the ** "select-id" for the X-th loop. The select-id identifies which query or ** subquery the loop is part of. The main query has a select-id of zero. ** The select-id is the same value as is output in the first column ** of an [EXPLAIN QUERY PLAN] query. **
*/ #define SQLITE_SCANSTAT_NLOOP 0 #define SQLITE_SCANSTAT_NVISIT 1 #define SQLITE_SCANSTAT_EST 2 #define SQLITE_SCANSTAT_NAME 3 #define SQLITE_SCANSTAT_EXPLAIN 4 #define SQLITE_SCANSTAT_SELECTID 5 /* ** CAPI3REF: Prepared Statement Scan Status ** METHOD: sqlite3_stmt ** ** This interface returns information about the predicted and measured ** performance for pStmt. Advanced applications can use this ** interface to compare the predicted and the measured performance and ** issue warnings and/or rerun [ANALYZE] if discrepancies are found. ** ** Since this interface is expected to be rarely used, it is only ** available if SQLite is compiled using the [SQLITE_ENABLE_STMT_SCANSTATUS] ** compile-time option. ** ** The "iScanStatusOp" parameter determines which status information to return. ** The "iScanStatusOp" must be one of the [scanstatus options] or the behavior ** of this interface is undefined. ** ^The requested measurement is written into a variable pointed to by ** the "pOut" parameter. ** Parameter "idx" identifies the specific loop to retrieve statistics for. ** Loops are numbered starting from zero. ^If idx is out of range - less than ** zero or greater than or equal to the total number of loops used to implement ** the statement - a non-zero value is returned and the variable that pOut ** points to is unchanged. ** ** ^Statistics might not be available for all loops in all statements. ^In cases ** where there exist loops with no available statistics, this function behaves ** as if the loop did not exist - it returns non-zero and leave the variable ** that pOut points to unchanged. ** ** See also: [sqlite3_stmt_scanstatus_reset()] */ SQLITE_API int sqlite3_stmt_scanstatus( sqlite3_stmt *pStmt, /* Prepared statement for which info desired */ int idx, /* Index of loop to report on */ int iScanStatusOp, /* Information desired. SQLITE_SCANSTAT_* */ void *pOut /* Result written here */ ); /* ** CAPI3REF: Zero Scan-Status Counters ** METHOD: sqlite3_stmt ** ** ^Zero all [sqlite3_stmt_scanstatus()] related event counters. ** ** This API is only available if the library is built with pre-processor ** symbol [SQLITE_ENABLE_STMT_SCANSTATUS] defined. */ SQLITE_API void sqlite3_stmt_scanstatus_reset(sqlite3_stmt*); /* ** CAPI3REF: Flush caches to disk mid-transaction ** ** ^If a write-transaction is open on [database connection] D when the ** [sqlite3_db_cacheflush(D)] interface invoked, any dirty ** pages in the pager-cache that are not currently in use are written out ** to disk. A dirty page may be in use if a database cursor created by an ** active SQL statement is reading from it, or if it is page 1 of a database ** file (page 1 is always "in use"). ^The [sqlite3_db_cacheflush(D)] ** interface flushes caches for all schemas - "main", "temp", and ** any [attached] databases. ** ** ^If this function needs to obtain extra database locks before dirty pages ** can be flushed to disk, it does so. ^If those locks cannot be obtained ** immediately and there is a busy-handler callback configured, it is invoked ** in the usual manner. ^If the required lock still cannot be obtained, then ** the database is skipped and an attempt made to flush any dirty pages ** belonging to the next (if any) database. ^If any databases are skipped ** because locks cannot be obtained, but no other error occurs, this ** function returns SQLITE_BUSY. ** ** ^If any other error occurs while flushing dirty pages to disk (for ** example an IO error or out-of-memory condition), then processing is ** abandoned and an SQLite [error code] is returned to the caller immediately. ** ** ^Otherwise, if no error occurs, [sqlite3_db_cacheflush()] returns SQLITE_OK. ** ** ^This function does not set the database handle error code or message ** returned by the [sqlite3_errcode()] and [sqlite3_errmsg()] functions. */ SQLITE_API int sqlite3_db_cacheflush(sqlite3*); /* ** CAPI3REF: The pre-update hook. ** ** ^These interfaces are only available if SQLite is compiled using the ** [SQLITE_ENABLE_PREUPDATE_HOOK] compile-time option. ** ** ^The [sqlite3_preupdate_hook()] interface registers a callback function ** that is invoked prior to each [INSERT], [UPDATE], and [DELETE] operation ** on a database table. ** ^At most one preupdate hook may be registered at a time on a single ** [database connection]; each call to [sqlite3_preupdate_hook()] overrides ** the previous setting. ** ^The preupdate hook is disabled by invoking [sqlite3_preupdate_hook()] ** with a NULL pointer as the second parameter. ** ^The third parameter to [sqlite3_preupdate_hook()] is passed through as ** the first parameter to callbacks. ** ** ^The preupdate hook only fires for changes to real database tables; the ** preupdate hook is not invoked for changes to [virtual tables] or to ** system tables like sqlite_master or sqlite_stat1. ** ** ^The second parameter to the preupdate callback is a pointer to ** the [database connection] that registered the preupdate hook. ** ^The third parameter to the preupdate callback is one of the constants ** [SQLITE_INSERT], [SQLITE_DELETE], or [SQLITE_UPDATE] to identify the ** kind of update operation that is about to occur. ** ^(The fourth parameter to the preupdate callback is the name of the ** database within the database connection that is being modified. This ** will be "main" for the main database or "temp" for TEMP tables or ** the name given after the AS keyword in the [ATTACH] statement for attached ** databases.)^ ** ^The fifth parameter to the preupdate callback is the name of the ** table that is being modified. ** ** For an UPDATE or DELETE operation on a [rowid table], the sixth ** parameter passed to the preupdate callback is the initial [rowid] of the ** row being modified or deleted. For an INSERT operation on a rowid table, ** or any operation on a WITHOUT ROWID table, the value of the sixth ** parameter is undefined. For an INSERT or UPDATE on a rowid table the ** seventh parameter is the final rowid value of the row being inserted ** or updated. The value of the seventh parameter passed to the callback ** function is not defined for operations on WITHOUT ROWID tables, or for ** INSERT operations on rowid tables. ** ** The [sqlite3_preupdate_old()], [sqlite3_preupdate_new()], ** [sqlite3_preupdate_count()], and [sqlite3_preupdate_depth()] interfaces ** provide additional information about a preupdate event. These routines ** may only be called from within a preupdate callback. Invoking any of ** these routines from outside of a preupdate callback or with a ** [database connection] pointer that is different from the one supplied ** to the preupdate callback results in undefined and probably undesirable ** behavior. ** ** ^The [sqlite3_preupdate_count(D)] interface returns the number of columns ** in the row that is being inserted, updated, or deleted. ** ** ^The [sqlite3_preupdate_old(D,N,P)] interface writes into P a pointer to ** a [protected sqlite3_value] that contains the value of the Nth column of ** the table row before it is updated. The N parameter must be between 0 ** and one less than the number of columns or the behavior will be ** undefined. This must only be used within SQLITE_UPDATE and SQLITE_DELETE ** preupdate callbacks; if it is used by an SQLITE_INSERT callback then the ** behavior is undefined. The [sqlite3_value] that P points to ** will be destroyed when the preupdate callback returns. ** ** ^The [sqlite3_preupdate_new(D,N,P)] interface writes into P a pointer to ** a [protected sqlite3_value] that contains the value of the Nth column of ** the table row after it is updated. The N parameter must be between 0 ** and one less than the number of columns or the behavior will be ** undefined. This must only be used within SQLITE_INSERT and SQLITE_UPDATE ** preupdate callbacks; if it is used by an SQLITE_DELETE callback then the ** behavior is undefined. The [sqlite3_value] that P points to ** will be destroyed when the preupdate callback returns. ** ** ^The [sqlite3_preupdate_depth(D)] interface returns 0 if the preupdate ** callback was invoked as a result of a direct insert, update, or delete ** operation; or 1 for inserts, updates, or deletes invoked by top-level ** triggers; or 2 for changes resulting from triggers called by top-level ** triggers; and so forth. ** ** See also: [sqlite3_update_hook()] */ #if defined(SQLITE_ENABLE_PREUPDATE_HOOK) SQLITE_API void *sqlite3_preupdate_hook( sqlite3 *db, void(*xPreUpdate)( void *pCtx, /* Copy of third arg to preupdate_hook() */ sqlite3 *db, /* Database handle */ int op, /* SQLITE_UPDATE, DELETE or INSERT */ char const *zDb, /* Database name */ char const *zName, /* Table name */ sqlite3_int64 iKey1, /* Rowid of row about to be deleted/updated */ sqlite3_int64 iKey2 /* New rowid value (for a rowid UPDATE) */ ), void* ); SQLITE_API int sqlite3_preupdate_old(sqlite3 *, int, sqlite3_value **); SQLITE_API int sqlite3_preupdate_count(sqlite3 *); SQLITE_API int sqlite3_preupdate_depth(sqlite3 *); SQLITE_API int sqlite3_preupdate_new(sqlite3 *, int, sqlite3_value **); #endif /* ** CAPI3REF: Low-level system error code ** ** ^Attempt to return the underlying operating system error code or error ** number that caused the most recent I/O error or failure to open a file. ** The return value is OS-dependent. For example, on unix systems, after ** [sqlite3_open_v2()] returns [SQLITE_CANTOPEN], this interface could be ** called to get back the underlying "errno" that caused the problem, such ** as ENOSPC, EAUTH, EISDIR, and so forth. */ SQLITE_API int sqlite3_system_errno(sqlite3*); /* ** CAPI3REF: Database Snapshot ** KEYWORDS: {snapshot} {sqlite3_snapshot} ** EXPERIMENTAL ** ** An instance of the snapshot object records the state of a [WAL mode] ** database for some specific point in history. ** ** In [WAL mode], multiple [database connections] that are open on the ** same database file can each be reading a different historical version ** of the database file. When a [database connection] begins a read ** transaction, that connection sees an unchanging copy of the database ** as it existed for the point in time when the transaction first started. ** Subsequent changes to the database from other connections are not seen ** by the reader until a new read transaction is started. ** ** The sqlite3_snapshot object records state information about an historical ** version of the database file so that it is possible to later open a new read ** transaction that sees that historical version of the database rather than ** the most recent version. ** ** The constructor for this object is [sqlite3_snapshot_get()]. The ** [sqlite3_snapshot_open()] method causes a fresh read transaction to refer ** to an historical snapshot (if possible). The destructor for ** sqlite3_snapshot objects is [sqlite3_snapshot_free()]. */ typedef struct sqlite3_snapshot { unsigned char hidden[48]; } sqlite3_snapshot; /* ** CAPI3REF: Record A Database Snapshot ** EXPERIMENTAL ** ** ^The [sqlite3_snapshot_get(D,S,P)] interface attempts to make a ** new [sqlite3_snapshot] object that records the current state of ** schema S in database connection D. ^On success, the ** [sqlite3_snapshot_get(D,S,P)] interface writes a pointer to the newly ** created [sqlite3_snapshot] object into *P and returns SQLITE_OK. ** If there is not already a read-transaction open on schema S when ** this function is called, one is opened automatically. ** ** The following must be true for this function to succeed. If any of ** the following statements are false when sqlite3_snapshot_get() is ** called, SQLITE_ERROR is returned. The final value of *P is undefined ** in this case. ** **
    **
  • The database handle must be in [autocommit mode]. ** **
  • Schema S of [database connection] D must be a [WAL mode] database. ** **
  • There must not be a write transaction open on schema S of database ** connection D. ** **
  • One or more transactions must have been written to the current wal ** file since it was created on disk (by any connection). This means ** that a snapshot cannot be taken on a wal mode database with no wal ** file immediately after it is first opened. At least one transaction ** must be written to it first. **
** ** This function may also return SQLITE_NOMEM. If it is called with the ** database handle in autocommit mode but fails for some other reason, ** whether or not a read transaction is opened on schema S is undefined. ** ** The [sqlite3_snapshot] object returned from a successful call to ** [sqlite3_snapshot_get()] must be freed using [sqlite3_snapshot_free()] ** to avoid a memory leak. ** ** The [sqlite3_snapshot_get()] interface is only available when the ** SQLITE_ENABLE_SNAPSHOT compile-time option is used. */ SQLITE_API SQLITE_EXPERIMENTAL int sqlite3_snapshot_get( sqlite3 *db, const char *zSchema, sqlite3_snapshot **ppSnapshot ); /* ** CAPI3REF: Start a read transaction on an historical snapshot ** EXPERIMENTAL ** ** ^The [sqlite3_snapshot_open(D,S,P)] interface starts a ** read transaction for schema S of ** [database connection] D such that the read transaction ** refers to historical [snapshot] P, rather than the most ** recent change to the database. ** ^The [sqlite3_snapshot_open()] interface returns SQLITE_OK on success ** or an appropriate [error code] if it fails. ** ** ^In order to succeed, a call to [sqlite3_snapshot_open(D,S,P)] must be ** the first operation following the [BEGIN] that takes the schema S ** out of [autocommit mode]. ** ^In other words, schema S must not currently be in ** a transaction for [sqlite3_snapshot_open(D,S,P)] to work, but the ** database connection D must be out of [autocommit mode]. ** ^A [snapshot] will fail to open if it has been overwritten by a ** [checkpoint]. ** ^(A call to [sqlite3_snapshot_open(D,S,P)] will fail if the ** database connection D does not know that the database file for ** schema S is in [WAL mode]. A database connection might not know ** that the database file is in [WAL mode] if there has been no prior ** I/O on that database connection, or if the database entered [WAL mode] ** after the most recent I/O on the database connection.)^ ** (Hint: Run "[PRAGMA application_id]" against a newly opened ** database connection in order to make it ready to use snapshots.) ** ** The [sqlite3_snapshot_open()] interface is only available when the ** SQLITE_ENABLE_SNAPSHOT compile-time option is used. */ SQLITE_API SQLITE_EXPERIMENTAL int sqlite3_snapshot_open( sqlite3 *db, const char *zSchema, sqlite3_snapshot *pSnapshot ); /* ** CAPI3REF: Destroy a snapshot ** EXPERIMENTAL ** ** ^The [sqlite3_snapshot_free(P)] interface destroys [sqlite3_snapshot] P. ** The application must eventually free every [sqlite3_snapshot] object ** using this routine to avoid a memory leak. ** ** The [sqlite3_snapshot_free()] interface is only available when the ** SQLITE_ENABLE_SNAPSHOT compile-time option is used. */ SQLITE_API SQLITE_EXPERIMENTAL void sqlite3_snapshot_free(sqlite3_snapshot*); /* ** CAPI3REF: Compare the ages of two snapshot handles. ** EXPERIMENTAL ** ** The sqlite3_snapshot_cmp(P1, P2) interface is used to compare the ages ** of two valid snapshot handles. ** ** If the two snapshot handles are not associated with the same database ** file, the result of the comparison is undefined. ** ** Additionally, the result of the comparison is only valid if both of the ** snapshot handles were obtained by calling sqlite3_snapshot_get() since the ** last time the wal file was deleted. The wal file is deleted when the ** database is changed back to rollback mode or when the number of database ** clients drops to zero. If either snapshot handle was obtained before the ** wal file was last deleted, the value returned by this function ** is undefined. ** ** Otherwise, this API returns a negative value if P1 refers to an older ** snapshot than P2, zero if the two handles refer to the same database ** snapshot, and a positive value if P1 is a newer snapshot than P2. */ SQLITE_API SQLITE_EXPERIMENTAL int sqlite3_snapshot_cmp( sqlite3_snapshot *p1, sqlite3_snapshot *p2 ); /* ** CAPI3REF: Recover snapshots from a wal file ** EXPERIMENTAL ** ** If all connections disconnect from a database file but do not perform ** a checkpoint, the existing wal file is opened along with the database ** file the next time the database is opened. At this point it is only ** possible to successfully call sqlite3_snapshot_open() to open the most ** recent snapshot of the database (the one at the head of the wal file), ** even though the wal file may contain other valid snapshots for which ** clients have sqlite3_snapshot handles. ** ** This function attempts to scan the wal file associated with database zDb ** of database handle db and make all valid snapshots available to ** sqlite3_snapshot_open(). It is an error if there is already a read ** transaction open on the database, or if the database is not a wal mode ** database. ** ** SQLITE_OK is returned if successful, or an SQLite error code otherwise. */ SQLITE_API SQLITE_EXPERIMENTAL int sqlite3_snapshot_recover(sqlite3 *db, const char *zDb); /* ** Undo the hack that converts floating point types to integer for ** builds on processors without floating point support. */ #ifdef SQLITE_OMIT_FLOATING_POINT # undef double #endif #ifdef __cplusplus } /* End of the 'extern "C"' block */ #endif #endif /* SQLITE3_H */ /******** Begin file sqlite3rtree.h *********/ /* ** 2010 August 30 ** ** The author disclaims copyright to this source code. In place of ** a legal notice, here is a blessing: ** ** May you do good and not evil. ** May you find forgiveness for yourself and forgive others. ** May you share freely, never taking more than you give. ** ************************************************************************* */ #ifndef _SQLITE3RTREE_H_ #define _SQLITE3RTREE_H_ #ifdef __cplusplus extern "C" { #endif typedef struct sqlite3_rtree_geometry sqlite3_rtree_geometry; typedef struct sqlite3_rtree_query_info sqlite3_rtree_query_info; /* The double-precision datatype used by RTree depends on the ** SQLITE_RTREE_INT_ONLY compile-time option. */ #ifdef SQLITE_RTREE_INT_ONLY typedef sqlite3_int64 sqlite3_rtree_dbl; #else typedef double sqlite3_rtree_dbl; #endif /* ** Register a geometry callback named zGeom that can be used as part of an ** R-Tree geometry query as follows: ** ** SELECT ... FROM WHERE MATCH $zGeom(... params ...) */ SQLITE_API int sqlite3_rtree_geometry_callback( sqlite3 *db, const char *zGeom, int (*xGeom)(sqlite3_rtree_geometry*, int, sqlite3_rtree_dbl*,int*), void *pContext ); /* ** A pointer to a structure of the following type is passed as the first ** argument to callbacks registered using rtree_geometry_callback(). */ struct sqlite3_rtree_geometry { void *pContext; /* Copy of pContext passed to s_r_g_c() */ int nParam; /* Size of array aParam[] */ sqlite3_rtree_dbl *aParam; /* Parameters passed to SQL geom function */ void *pUser; /* Callback implementation user data */ void (*xDelUser)(void *); /* Called by SQLite to clean up pUser */ }; /* ** Register a 2nd-generation geometry callback named zScore that can be ** used as part of an R-Tree geometry query as follows: ** ** SELECT ... FROM WHERE MATCH $zQueryFunc(... params ...) */ SQLITE_API int sqlite3_rtree_query_callback( sqlite3 *db, const char *zQueryFunc, int (*xQueryFunc)(sqlite3_rtree_query_info*), void *pContext, void (*xDestructor)(void*) ); /* ** A pointer to a structure of the following type is passed as the ** argument to scored geometry callback registered using ** sqlite3_rtree_query_callback(). ** ** Note that the first 5 fields of this structure are identical to ** sqlite3_rtree_geometry. This structure is a subclass of ** sqlite3_rtree_geometry. */ struct sqlite3_rtree_query_info { void *pContext; /* pContext from when function registered */ int nParam; /* Number of function parameters */ sqlite3_rtree_dbl *aParam; /* value of function parameters */ void *pUser; /* callback can use this, if desired */ void (*xDelUser)(void*); /* function to free pUser */ sqlite3_rtree_dbl *aCoord; /* Coordinates of node or entry to check */ unsigned int *anQueue; /* Number of pending entries in the queue */ int nCoord; /* Number of coordinates */ int iLevel; /* Level of current node or entry */ int mxLevel; /* The largest iLevel value in the tree */ sqlite3_int64 iRowid; /* Rowid for current entry */ sqlite3_rtree_dbl rParentScore; /* Score of parent node */ int eParentWithin; /* Visibility of parent node */ int eWithin; /* OUT: Visiblity */ sqlite3_rtree_dbl rScore; /* OUT: Write the score here */ /* The following fields are only available in 3.8.11 and later */ sqlite3_value **apSqlParam; /* Original SQL values of parameters */ }; /* ** Allowed values for sqlite3_rtree_query.eWithin and .eParentWithin. */ #define NOT_WITHIN 0 /* Object completely outside of query region */ #define PARTLY_WITHIN 1 /* Object partially overlaps query region */ #define FULLY_WITHIN 2 /* Object fully contained within query region */ #ifdef __cplusplus } /* end of the 'extern "C"' block */ #endif #endif /* ifndef _SQLITE3RTREE_H_ */ /******** End of sqlite3rtree.h *********/ /******** Begin file sqlite3session.h *********/ #if !defined(__SQLITESESSION_H_) && defined(SQLITE_ENABLE_SESSION) #define __SQLITESESSION_H_ 1 /* ** Make sure we can call this stuff from C++. */ #ifdef __cplusplus extern "C" { #endif /* ** CAPI3REF: Session Object Handle */ typedef struct sqlite3_session sqlite3_session; /* ** CAPI3REF: Changeset Iterator Handle */ typedef struct sqlite3_changeset_iter sqlite3_changeset_iter; /* ** CAPI3REF: Create A New Session Object ** ** Create a new session object attached to database handle db. If successful, ** a pointer to the new object is written to *ppSession and SQLITE_OK is ** returned. If an error occurs, *ppSession is set to NULL and an SQLite ** error code (e.g. SQLITE_NOMEM) is returned. ** ** It is possible to create multiple session objects attached to a single ** database handle. ** ** Session objects created using this function should be deleted using the ** [sqlite3session_delete()] function before the database handle that they ** are attached to is itself closed. If the database handle is closed before ** the session object is deleted, then the results of calling any session ** module function, including [sqlite3session_delete()] on the session object ** are undefined. ** ** Because the session module uses the [sqlite3_preupdate_hook()] API, it ** is not possible for an application to register a pre-update hook on a ** database handle that has one or more session objects attached. Nor is ** it possible to create a session object attached to a database handle for ** which a pre-update hook is already defined. The results of attempting ** either of these things are undefined. ** ** The session object will be used to create changesets for tables in ** database zDb, where zDb is either "main", or "temp", or the name of an ** attached database. It is not an error if database zDb is not attached ** to the database when the session object is created. */ SQLITE_API int sqlite3session_create( sqlite3 *db, /* Database handle */ const char *zDb, /* Name of db (e.g. "main") */ sqlite3_session **ppSession /* OUT: New session object */ ); /* ** CAPI3REF: Delete A Session Object ** ** Delete a session object previously allocated using ** [sqlite3session_create()]. Once a session object has been deleted, the ** results of attempting to use pSession with any other session module ** function are undefined. ** ** Session objects must be deleted before the database handle to which they ** are attached is closed. Refer to the documentation for ** [sqlite3session_create()] for details. */ SQLITE_API void sqlite3session_delete(sqlite3_session *pSession); /* ** CAPI3REF: Enable Or Disable A Session Object ** ** Enable or disable the recording of changes by a session object. When ** enabled, a session object records changes made to the database. When ** disabled - it does not. A newly created session object is enabled. ** Refer to the documentation for [sqlite3session_changeset()] for further ** details regarding how enabling and disabling a session object affects ** the eventual changesets. ** ** Passing zero to this function disables the session. Passing a value ** greater than zero enables it. Passing a value less than zero is a ** no-op, and may be used to query the current state of the session. ** ** The return value indicates the final state of the session object: 0 if ** the session is disabled, or 1 if it is enabled. */ SQLITE_API int sqlite3session_enable(sqlite3_session *pSession, int bEnable); /* ** CAPI3REF: Set Or Clear the Indirect Change Flag ** ** Each change recorded by a session object is marked as either direct or ** indirect. A change is marked as indirect if either: ** **
    **
  • The session object "indirect" flag is set when the change is ** made, or **
  • The change is made by an SQL trigger or foreign key action ** instead of directly as a result of a users SQL statement. **
** ** If a single row is affected by more than one operation within a session, ** then the change is considered indirect if all operations meet the criteria ** for an indirect change above, or direct otherwise. ** ** This function is used to set, clear or query the session object indirect ** flag. If the second argument passed to this function is zero, then the ** indirect flag is cleared. If it is greater than zero, the indirect flag ** is set. Passing a value less than zero does not modify the current value ** of the indirect flag, and may be used to query the current state of the ** indirect flag for the specified session object. ** ** The return value indicates the final state of the indirect flag: 0 if ** it is clear, or 1 if it is set. */ SQLITE_API int sqlite3session_indirect(sqlite3_session *pSession, int bIndirect); /* ** CAPI3REF: Attach A Table To A Session Object ** ** If argument zTab is not NULL, then it is the name of a table to attach ** to the session object passed as the first argument. All subsequent changes ** made to the table while the session object is enabled will be recorded. See ** documentation for [sqlite3session_changeset()] for further details. ** ** Or, if argument zTab is NULL, then changes are recorded for all tables ** in the database. If additional tables are added to the database (by ** executing "CREATE TABLE" statements) after this call is made, changes for ** the new tables are also recorded. ** ** Changes can only be recorded for tables that have a PRIMARY KEY explicitly ** defined as part of their CREATE TABLE statement. It does not matter if the ** PRIMARY KEY is an "INTEGER PRIMARY KEY" (rowid alias) or not. The PRIMARY ** KEY may consist of a single column, or may be a composite key. ** ** It is not an error if the named table does not exist in the database. Nor ** is it an error if the named table does not have a PRIMARY KEY. However, ** no changes will be recorded in either of these scenarios. ** ** Changes are not recorded for individual rows that have NULL values stored ** in one or more of their PRIMARY KEY columns. ** ** SQLITE_OK is returned if the call completes without error. Or, if an error ** occurs, an SQLite error code (e.g. SQLITE_NOMEM) is returned. */ SQLITE_API int sqlite3session_attach( sqlite3_session *pSession, /* Session object */ const char *zTab /* Table name */ ); /* ** CAPI3REF: Set a table filter on a Session Object. ** ** The second argument (xFilter) is the "filter callback". For changes to rows ** in tables that are not attached to the Session object, the filter is called ** to determine whether changes to the table's rows should be tracked or not. ** If xFilter returns 0, changes is not tracked. Note that once a table is ** attached, xFilter will not be called again. */ SQLITE_API void sqlite3session_table_filter( sqlite3_session *pSession, /* Session object */ int(*xFilter)( void *pCtx, /* Copy of third arg to _filter_table() */ const char *zTab /* Table name */ ), void *pCtx /* First argument passed to xFilter */ ); /* ** CAPI3REF: Generate A Changeset From A Session Object ** ** Obtain a changeset containing changes to the tables attached to the ** session object passed as the first argument. If successful, ** set *ppChangeset to point to a buffer containing the changeset ** and *pnChangeset to the size of the changeset in bytes before returning ** SQLITE_OK. If an error occurs, set both *ppChangeset and *pnChangeset to ** zero and return an SQLite error code. ** ** A changeset consists of zero or more INSERT, UPDATE and/or DELETE changes, ** each representing a change to a single row of an attached table. An INSERT ** change contains the values of each field of a new database row. A DELETE ** contains the original values of each field of a deleted database row. An ** UPDATE change contains the original values of each field of an updated ** database row along with the updated values for each updated non-primary-key ** column. It is not possible for an UPDATE change to represent a change that ** modifies the values of primary key columns. If such a change is made, it ** is represented in a changeset as a DELETE followed by an INSERT. ** ** Changes are not recorded for rows that have NULL values stored in one or ** more of their PRIMARY KEY columns. If such a row is inserted or deleted, ** no corresponding change is present in the changesets returned by this ** function. If an existing row with one or more NULL values stored in ** PRIMARY KEY columns is updated so that all PRIMARY KEY columns are non-NULL, ** only an INSERT is appears in the changeset. Similarly, if an existing row ** with non-NULL PRIMARY KEY values is updated so that one or more of its ** PRIMARY KEY columns are set to NULL, the resulting changeset contains a ** DELETE change only. ** ** The contents of a changeset may be traversed using an iterator created ** using the [sqlite3changeset_start()] API. A changeset may be applied to ** a database with a compatible schema using the [sqlite3changeset_apply()] ** API. ** ** Within a changeset generated by this function, all changes related to a ** single table are grouped together. In other words, when iterating through ** a changeset or when applying a changeset to a database, all changes related ** to a single table are processed before moving on to the next table. Tables ** are sorted in the same order in which they were attached (or auto-attached) ** to the sqlite3_session object. The order in which the changes related to ** a single table are stored is undefined. ** ** Following a successful call to this function, it is the responsibility of ** the caller to eventually free the buffer that *ppChangeset points to using ** [sqlite3_free()]. ** **

Changeset Generation

** ** Once a table has been attached to a session object, the session object ** records the primary key values of all new rows inserted into the table. ** It also records the original primary key and other column values of any ** deleted or updated rows. For each unique primary key value, data is only ** recorded once - the first time a row with said primary key is inserted, ** updated or deleted in the lifetime of the session. ** ** There is one exception to the previous paragraph: when a row is inserted, ** updated or deleted, if one or more of its primary key columns contain a ** NULL value, no record of the change is made. ** ** The session object therefore accumulates two types of records - those ** that consist of primary key values only (created when the user inserts ** a new record) and those that consist of the primary key values and the ** original values of other table columns (created when the users deletes ** or updates a record). ** ** When this function is called, the requested changeset is created using ** both the accumulated records and the current contents of the database ** file. Specifically: ** **
    **
  • For each record generated by an insert, the database is queried ** for a row with a matching primary key. If one is found, an INSERT ** change is added to the changeset. If no such row is found, no change ** is added to the changeset. ** **
  • For each record generated by an update or delete, the database is ** queried for a row with a matching primary key. If such a row is ** found and one or more of the non-primary key fields have been ** modified from their original values, an UPDATE change is added to ** the changeset. Or, if no such row is found in the table, a DELETE ** change is added to the changeset. If there is a row with a matching ** primary key in the database, but all fields contain their original ** values, no change is added to the changeset. **
** ** This means, amongst other things, that if a row is inserted and then later ** deleted while a session object is active, neither the insert nor the delete ** will be present in the changeset. Or if a row is deleted and then later a ** row with the same primary key values inserted while a session object is ** active, the resulting changeset will contain an UPDATE change instead of ** a DELETE and an INSERT. ** ** When a session object is disabled (see the [sqlite3session_enable()] API), ** it does not accumulate records when rows are inserted, updated or deleted. ** This may appear to have some counter-intuitive effects if a single row ** is written to more than once during a session. For example, if a row ** is inserted while a session object is enabled, then later deleted while ** the same session object is disabled, no INSERT record will appear in the ** changeset, even though the delete took place while the session was disabled. ** Or, if one field of a row is updated while a session is disabled, and ** another field of the same row is updated while the session is enabled, the ** resulting changeset will contain an UPDATE change that updates both fields. */ SQLITE_API int sqlite3session_changeset( sqlite3_session *pSession, /* Session object */ int *pnChangeset, /* OUT: Size of buffer at *ppChangeset */ void **ppChangeset /* OUT: Buffer containing changeset */ ); /* ** CAPI3REF: Load The Difference Between Tables Into A Session ** ** If it is not already attached to the session object passed as the first ** argument, this function attaches table zTbl in the same manner as the ** [sqlite3session_attach()] function. If zTbl does not exist, or if it ** does not have a primary key, this function is a no-op (but does not return ** an error). ** ** Argument zFromDb must be the name of a database ("main", "temp" etc.) ** attached to the same database handle as the session object that contains ** a table compatible with the table attached to the session by this function. ** A table is considered compatible if it: ** **
    **
  • Has the same name, **
  • Has the same set of columns declared in the same order, and **
  • Has the same PRIMARY KEY definition. **
** ** If the tables are not compatible, SQLITE_SCHEMA is returned. If the tables ** are compatible but do not have any PRIMARY KEY columns, it is not an error ** but no changes are added to the session object. As with other session ** APIs, tables without PRIMARY KEYs are simply ignored. ** ** This function adds a set of changes to the session object that could be ** used to update the table in database zFrom (call this the "from-table") ** so that its content is the same as the table attached to the session ** object (call this the "to-table"). Specifically: ** **
    **
  • For each row (primary key) that exists in the to-table but not in ** the from-table, an INSERT record is added to the session object. ** **
  • For each row (primary key) that exists in the to-table but not in ** the from-table, a DELETE record is added to the session object. ** **
  • For each row (primary key) that exists in both tables, but features ** different non-PK values in each, an UPDATE record is added to the ** session. **
** ** To clarify, if this function is called and then a changeset constructed ** using [sqlite3session_changeset()], then after applying that changeset to ** database zFrom the contents of the two compatible tables would be ** identical. ** ** It an error if database zFrom does not exist or does not contain the ** required compatible table. ** ** If the operation successful, SQLITE_OK is returned. Otherwise, an SQLite ** error code. In this case, if argument pzErrMsg is not NULL, *pzErrMsg ** may be set to point to a buffer containing an English language error ** message. It is the responsibility of the caller to free this buffer using ** sqlite3_free(). */ SQLITE_API int sqlite3session_diff( sqlite3_session *pSession, const char *zFromDb, const char *zTbl, char **pzErrMsg ); /* ** CAPI3REF: Generate A Patchset From A Session Object ** ** The differences between a patchset and a changeset are that: ** **
    **
  • DELETE records consist of the primary key fields only. The ** original values of other fields are omitted. **
  • The original values of any modified fields are omitted from ** UPDATE records. **
** ** A patchset blob may be used with up to date versions of all ** sqlite3changeset_xxx API functions except for sqlite3changeset_invert(), ** which returns SQLITE_CORRUPT if it is passed a patchset. Similarly, ** attempting to use a patchset blob with old versions of the ** sqlite3changeset_xxx APIs also provokes an SQLITE_CORRUPT error. ** ** Because the non-primary key "old.*" fields are omitted, no ** SQLITE_CHANGESET_DATA conflicts can be detected or reported if a patchset ** is passed to the sqlite3changeset_apply() API. Other conflict types work ** in the same way as for changesets. ** ** Changes within a patchset are ordered in the same way as for changesets ** generated by the sqlite3session_changeset() function (i.e. all changes for ** a single table are grouped together, tables appear in the order in which ** they were attached to the session object). */ SQLITE_API int sqlite3session_patchset( sqlite3_session *pSession, /* Session object */ int *pnPatchset, /* OUT: Size of buffer at *ppChangeset */ void **ppPatchset /* OUT: Buffer containing changeset */ ); /* ** CAPI3REF: Test if a changeset has recorded any changes. ** ** Return non-zero if no changes to attached tables have been recorded by ** the session object passed as the first argument. Otherwise, if one or ** more changes have been recorded, return zero. ** ** Even if this function returns zero, it is possible that calling ** [sqlite3session_changeset()] on the session handle may still return a ** changeset that contains no changes. This can happen when a row in ** an attached table is modified and then later on the original values ** are restored. However, if this function returns non-zero, then it is ** guaranteed that a call to sqlite3session_changeset() will return a ** changeset containing zero changes. */ SQLITE_API int sqlite3session_isempty(sqlite3_session *pSession); /* ** CAPI3REF: Create An Iterator To Traverse A Changeset ** ** Create an iterator used to iterate through the contents of a changeset. ** If successful, *pp is set to point to the iterator handle and SQLITE_OK ** is returned. Otherwise, if an error occurs, *pp is set to zero and an ** SQLite error code is returned. ** ** The following functions can be used to advance and query a changeset ** iterator created by this function: ** **
    **
  • [sqlite3changeset_next()] **
  • [sqlite3changeset_op()] **
  • [sqlite3changeset_new()] **
  • [sqlite3changeset_old()] **
** ** It is the responsibility of the caller to eventually destroy the iterator ** by passing it to [sqlite3changeset_finalize()]. The buffer containing the ** changeset (pChangeset) must remain valid until after the iterator is ** destroyed. ** ** Assuming the changeset blob was created by one of the ** [sqlite3session_changeset()], [sqlite3changeset_concat()] or ** [sqlite3changeset_invert()] functions, all changes within the changeset ** that apply to a single table are grouped together. This means that when ** an application iterates through a changeset using an iterator created by ** this function, all changes that relate to a single table are visited ** consecutively. There is no chance that the iterator will visit a change ** the applies to table X, then one for table Y, and then later on visit ** another change for table X. */ SQLITE_API int sqlite3changeset_start( sqlite3_changeset_iter **pp, /* OUT: New changeset iterator handle */ int nChangeset, /* Size of changeset blob in bytes */ void *pChangeset /* Pointer to blob containing changeset */ ); /* ** CAPI3REF: Advance A Changeset Iterator ** ** This function may only be used with iterators created by function ** [sqlite3changeset_start()]. If it is called on an iterator passed to ** a conflict-handler callback by [sqlite3changeset_apply()], SQLITE_MISUSE ** is returned and the call has no effect. ** ** Immediately after an iterator is created by sqlite3changeset_start(), it ** does not point to any change in the changeset. Assuming the changeset ** is not empty, the first call to this function advances the iterator to ** point to the first change in the changeset. Each subsequent call advances ** the iterator to point to the next change in the changeset (if any). If ** no error occurs and the iterator points to a valid change after a call ** to sqlite3changeset_next() has advanced it, SQLITE_ROW is returned. ** Otherwise, if all changes in the changeset have already been visited, ** SQLITE_DONE is returned. ** ** If an error occurs, an SQLite error code is returned. Possible error ** codes include SQLITE_CORRUPT (if the changeset buffer is corrupt) or ** SQLITE_NOMEM. */ SQLITE_API int sqlite3changeset_next(sqlite3_changeset_iter *pIter); /* ** CAPI3REF: Obtain The Current Operation From A Changeset Iterator ** ** The pIter argument passed to this function may either be an iterator ** passed to a conflict-handler by [sqlite3changeset_apply()], or an iterator ** created by [sqlite3changeset_start()]. In the latter case, the most recent ** call to [sqlite3changeset_next()] must have returned [SQLITE_ROW]. If this ** is not the case, this function returns [SQLITE_MISUSE]. ** ** If argument pzTab is not NULL, then *pzTab is set to point to a ** nul-terminated utf-8 encoded string containing the name of the table ** affected by the current change. The buffer remains valid until either ** sqlite3changeset_next() is called on the iterator or until the ** conflict-handler function returns. If pnCol is not NULL, then *pnCol is ** set to the number of columns in the table affected by the change. If ** pbIncorrect is not NULL, then *pbIndirect is set to true (1) if the change ** is an indirect change, or false (0) otherwise. See the documentation for ** [sqlite3session_indirect()] for a description of direct and indirect ** changes. Finally, if pOp is not NULL, then *pOp is set to one of ** [SQLITE_INSERT], [SQLITE_DELETE] or [SQLITE_UPDATE], depending on the ** type of change that the iterator currently points to. ** ** If no error occurs, SQLITE_OK is returned. If an error does occur, an ** SQLite error code is returned. The values of the output variables may not ** be trusted in this case. */ SQLITE_API int sqlite3changeset_op( sqlite3_changeset_iter *pIter, /* Iterator object */ const char **pzTab, /* OUT: Pointer to table name */ int *pnCol, /* OUT: Number of columns in table */ int *pOp, /* OUT: SQLITE_INSERT, DELETE or UPDATE */ int *pbIndirect /* OUT: True for an 'indirect' change */ ); /* ** CAPI3REF: Obtain The Primary Key Definition Of A Table ** ** For each modified table, a changeset includes the following: ** **
    **
  • The number of columns in the table, and **
  • Which of those columns make up the tables PRIMARY KEY. **
** ** This function is used to find which columns comprise the PRIMARY KEY of ** the table modified by the change that iterator pIter currently points to. ** If successful, *pabPK is set to point to an array of nCol entries, where ** nCol is the number of columns in the table. Elements of *pabPK are set to ** 0x01 if the corresponding column is part of the tables primary key, or ** 0x00 if it is not. ** ** If argument pnCol is not NULL, then *pnCol is set to the number of columns ** in the table. ** ** If this function is called when the iterator does not point to a valid ** entry, SQLITE_MISUSE is returned and the output variables zeroed. Otherwise, ** SQLITE_OK is returned and the output variables populated as described ** above. */ SQLITE_API int sqlite3changeset_pk( sqlite3_changeset_iter *pIter, /* Iterator object */ unsigned char **pabPK, /* OUT: Array of boolean - true for PK cols */ int *pnCol /* OUT: Number of entries in output array */ ); /* ** CAPI3REF: Obtain old.* Values From A Changeset Iterator ** ** The pIter argument passed to this function may either be an iterator ** passed to a conflict-handler by [sqlite3changeset_apply()], or an iterator ** created by [sqlite3changeset_start()]. In the latter case, the most recent ** call to [sqlite3changeset_next()] must have returned SQLITE_ROW. ** Furthermore, it may only be called if the type of change that the iterator ** currently points to is either [SQLITE_DELETE] or [SQLITE_UPDATE]. Otherwise, ** this function returns [SQLITE_MISUSE] and sets *ppValue to NULL. ** ** Argument iVal must be greater than or equal to 0, and less than the number ** of columns in the table affected by the current change. Otherwise, ** [SQLITE_RANGE] is returned and *ppValue is set to NULL. ** ** If successful, this function sets *ppValue to point to a protected ** sqlite3_value object containing the iVal'th value from the vector of ** original row values stored as part of the UPDATE or DELETE change and ** returns SQLITE_OK. The name of the function comes from the fact that this ** is similar to the "old.*" columns available to update or delete triggers. ** ** If some other error occurs (e.g. an OOM condition), an SQLite error code ** is returned and *ppValue is set to NULL. */ SQLITE_API int sqlite3changeset_old( sqlite3_changeset_iter *pIter, /* Changeset iterator */ int iVal, /* Column number */ sqlite3_value **ppValue /* OUT: Old value (or NULL pointer) */ ); /* ** CAPI3REF: Obtain new.* Values From A Changeset Iterator ** ** The pIter argument passed to this function may either be an iterator ** passed to a conflict-handler by [sqlite3changeset_apply()], or an iterator ** created by [sqlite3changeset_start()]. In the latter case, the most recent ** call to [sqlite3changeset_next()] must have returned SQLITE_ROW. ** Furthermore, it may only be called if the type of change that the iterator ** currently points to is either [SQLITE_UPDATE] or [SQLITE_INSERT]. Otherwise, ** this function returns [SQLITE_MISUSE] and sets *ppValue to NULL. ** ** Argument iVal must be greater than or equal to 0, and less than the number ** of columns in the table affected by the current change. Otherwise, ** [SQLITE_RANGE] is returned and *ppValue is set to NULL. ** ** If successful, this function sets *ppValue to point to a protected ** sqlite3_value object containing the iVal'th value from the vector of ** new row values stored as part of the UPDATE or INSERT change and ** returns SQLITE_OK. If the change is an UPDATE and does not include ** a new value for the requested column, *ppValue is set to NULL and ** SQLITE_OK returned. The name of the function comes from the fact that ** this is similar to the "new.*" columns available to update or delete ** triggers. ** ** If some other error occurs (e.g. an OOM condition), an SQLite error code ** is returned and *ppValue is set to NULL. */ SQLITE_API int sqlite3changeset_new( sqlite3_changeset_iter *pIter, /* Changeset iterator */ int iVal, /* Column number */ sqlite3_value **ppValue /* OUT: New value (or NULL pointer) */ ); /* ** CAPI3REF: Obtain Conflicting Row Values From A Changeset Iterator ** ** This function should only be used with iterator objects passed to a ** conflict-handler callback by [sqlite3changeset_apply()] with either ** [SQLITE_CHANGESET_DATA] or [SQLITE_CHANGESET_CONFLICT]. If this function ** is called on any other iterator, [SQLITE_MISUSE] is returned and *ppValue ** is set to NULL. ** ** Argument iVal must be greater than or equal to 0, and less than the number ** of columns in the table affected by the current change. Otherwise, ** [SQLITE_RANGE] is returned and *ppValue is set to NULL. ** ** If successful, this function sets *ppValue to point to a protected ** sqlite3_value object containing the iVal'th value from the ** "conflicting row" associated with the current conflict-handler callback ** and returns SQLITE_OK. ** ** If some other error occurs (e.g. an OOM condition), an SQLite error code ** is returned and *ppValue is set to NULL. */ SQLITE_API int sqlite3changeset_conflict( sqlite3_changeset_iter *pIter, /* Changeset iterator */ int iVal, /* Column number */ sqlite3_value **ppValue /* OUT: Value from conflicting row */ ); /* ** CAPI3REF: Determine The Number Of Foreign Key Constraint Violations ** ** This function may only be called with an iterator passed to an ** SQLITE_CHANGESET_FOREIGN_KEY conflict handler callback. In this case ** it sets the output variable to the total number of known foreign key ** violations in the destination database and returns SQLITE_OK. ** ** In all other cases this function returns SQLITE_MISUSE. */ SQLITE_API int sqlite3changeset_fk_conflicts( sqlite3_changeset_iter *pIter, /* Changeset iterator */ int *pnOut /* OUT: Number of FK violations */ ); /* ** CAPI3REF: Finalize A Changeset Iterator ** ** This function is used to finalize an iterator allocated with ** [sqlite3changeset_start()]. ** ** This function should only be called on iterators created using the ** [sqlite3changeset_start()] function. If an application calls this ** function with an iterator passed to a conflict-handler by ** [sqlite3changeset_apply()], [SQLITE_MISUSE] is immediately returned and the ** call has no effect. ** ** If an error was encountered within a call to an sqlite3changeset_xxx() ** function (for example an [SQLITE_CORRUPT] in [sqlite3changeset_next()] or an ** [SQLITE_NOMEM] in [sqlite3changeset_new()]) then an error code corresponding ** to that error is returned by this function. Otherwise, SQLITE_OK is ** returned. This is to allow the following pattern (pseudo-code): ** ** sqlite3changeset_start(); ** while( SQLITE_ROW==sqlite3changeset_next() ){ ** // Do something with change. ** } ** rc = sqlite3changeset_finalize(); ** if( rc!=SQLITE_OK ){ ** // An error has occurred ** } */ SQLITE_API int sqlite3changeset_finalize(sqlite3_changeset_iter *pIter); /* ** CAPI3REF: Invert A Changeset ** ** This function is used to "invert" a changeset object. Applying an inverted ** changeset to a database reverses the effects of applying the uninverted ** changeset. Specifically: ** **
    **
  • Each DELETE change is changed to an INSERT, and **
  • Each INSERT change is changed to a DELETE, and **
  • For each UPDATE change, the old.* and new.* values are exchanged. **
** ** This function does not change the order in which changes appear within ** the changeset. It merely reverses the sense of each individual change. ** ** If successful, a pointer to a buffer containing the inverted changeset ** is stored in *ppOut, the size of the same buffer is stored in *pnOut, and ** SQLITE_OK is returned. If an error occurs, both *pnOut and *ppOut are ** zeroed and an SQLite error code returned. ** ** It is the responsibility of the caller to eventually call sqlite3_free() ** on the *ppOut pointer to free the buffer allocation following a successful ** call to this function. ** ** WARNING/TODO: This function currently assumes that the input is a valid ** changeset. If it is not, the results are undefined. */ SQLITE_API int sqlite3changeset_invert( int nIn, const void *pIn, /* Input changeset */ int *pnOut, void **ppOut /* OUT: Inverse of input */ ); /* ** CAPI3REF: Concatenate Two Changeset Objects ** ** This function is used to concatenate two changesets, A and B, into a ** single changeset. The result is a changeset equivalent to applying ** changeset A followed by changeset B. ** ** This function combines the two input changesets using an ** sqlite3_changegroup object. Calling it produces similar results as the ** following code fragment: ** ** sqlite3_changegroup *pGrp; ** rc = sqlite3_changegroup_new(&pGrp); ** if( rc==SQLITE_OK ) rc = sqlite3changegroup_add(pGrp, nA, pA); ** if( rc==SQLITE_OK ) rc = sqlite3changegroup_add(pGrp, nB, pB); ** if( rc==SQLITE_OK ){ ** rc = sqlite3changegroup_output(pGrp, pnOut, ppOut); ** }else{ ** *ppOut = 0; ** *pnOut = 0; ** } ** ** Refer to the sqlite3_changegroup documentation below for details. */ SQLITE_API int sqlite3changeset_concat( int nA, /* Number of bytes in buffer pA */ void *pA, /* Pointer to buffer containing changeset A */ int nB, /* Number of bytes in buffer pB */ void *pB, /* Pointer to buffer containing changeset B */ int *pnOut, /* OUT: Number of bytes in output changeset */ void **ppOut /* OUT: Buffer containing output changeset */ ); /* ** CAPI3REF: Changegroup Handle */ typedef struct sqlite3_changegroup sqlite3_changegroup; /* ** CAPI3REF: Create A New Changegroup Object ** ** An sqlite3_changegroup object is used to combine two or more changesets ** (or patchsets) into a single changeset (or patchset). A single changegroup ** object may combine changesets or patchsets, but not both. The output is ** always in the same format as the input. ** ** If successful, this function returns SQLITE_OK and populates (*pp) with ** a pointer to a new sqlite3_changegroup object before returning. The caller ** should eventually free the returned object using a call to ** sqlite3changegroup_delete(). If an error occurs, an SQLite error code ** (i.e. SQLITE_NOMEM) is returned and *pp is set to NULL. ** ** The usual usage pattern for an sqlite3_changegroup object is as follows: ** **
    **
  • It is created using a call to sqlite3changegroup_new(). ** **
  • Zero or more changesets (or patchsets) are added to the object ** by calling sqlite3changegroup_add(). ** **
  • The result of combining all input changesets together is obtained ** by the application via a call to sqlite3changegroup_output(). ** **
  • The object is deleted using a call to sqlite3changegroup_delete(). **
** ** Any number of calls to add() and output() may be made between the calls to ** new() and delete(), and in any order. ** ** As well as the regular sqlite3changegroup_add() and ** sqlite3changegroup_output() functions, also available are the streaming ** versions sqlite3changegroup_add_strm() and sqlite3changegroup_output_strm(). */ SQLITE_API int sqlite3changegroup_new(sqlite3_changegroup **pp); /* ** CAPI3REF: Add A Changeset To A Changegroup ** ** Add all changes within the changeset (or patchset) in buffer pData (size ** nData bytes) to the changegroup. ** ** If the buffer contains a patchset, then all prior calls to this function ** on the same changegroup object must also have specified patchsets. Or, if ** the buffer contains a changeset, so must have the earlier calls to this ** function. Otherwise, SQLITE_ERROR is returned and no changes are added ** to the changegroup. ** ** Rows within the changeset and changegroup are identified by the values in ** their PRIMARY KEY columns. A change in the changeset is considered to ** apply to the same row as a change already present in the changegroup if ** the two rows have the same primary key. ** ** Changes to rows that do not already appear in the changegroup are ** simply copied into it. Or, if both the new changeset and the changegroup ** contain changes that apply to a single row, the final contents of the ** changegroup depends on the type of each change, as follows: ** ** ** ** **
Existing Change New Change Output Change **
INSERT INSERT ** The new change is ignored. This case does not occur if the new ** changeset was recorded immediately after the changesets already ** added to the changegroup. **
INSERT UPDATE ** The INSERT change remains in the changegroup. The values in the ** INSERT change are modified as if the row was inserted by the ** existing change and then updated according to the new change. **
INSERT DELETE ** The existing INSERT is removed from the changegroup. The DELETE is ** not added. **
UPDATE INSERT ** The new change is ignored. This case does not occur if the new ** changeset was recorded immediately after the changesets already ** added to the changegroup. **
UPDATE UPDATE ** The existing UPDATE remains within the changegroup. It is amended ** so that the accompanying values are as if the row was updated once ** by the existing change and then again by the new change. **
UPDATE DELETE ** The existing UPDATE is replaced by the new DELETE within the ** changegroup. **
DELETE INSERT ** If one or more of the column values in the row inserted by the ** new change differ from those in the row deleted by the existing ** change, the existing DELETE is replaced by an UPDATE within the ** changegroup. Otherwise, if the inserted row is exactly the same ** as the deleted row, the existing DELETE is simply discarded. **
DELETE UPDATE ** The new change is ignored. This case does not occur if the new ** changeset was recorded immediately after the changesets already ** added to the changegroup. **
DELETE DELETE ** The new change is ignored. This case does not occur if the new ** changeset was recorded immediately after the changesets already ** added to the changegroup. **
** ** If the new changeset contains changes to a table that is already present ** in the changegroup, then the number of columns and the position of the ** primary key columns for the table must be consistent. If this is not the ** case, this function fails with SQLITE_SCHEMA. If the input changeset ** appears to be corrupt and the corruption is detected, SQLITE_CORRUPT is ** returned. Or, if an out-of-memory condition occurs during processing, this ** function returns SQLITE_NOMEM. In all cases, if an error occurs the ** final contents of the changegroup is undefined. ** ** If no error occurs, SQLITE_OK is returned. */ SQLITE_API int sqlite3changegroup_add(sqlite3_changegroup*, int nData, void *pData); /* ** CAPI3REF: Obtain A Composite Changeset From A Changegroup ** ** Obtain a buffer containing a changeset (or patchset) representing the ** current contents of the changegroup. If the inputs to the changegroup ** were themselves changesets, the output is a changeset. Or, if the ** inputs were patchsets, the output is also a patchset. ** ** As with the output of the sqlite3session_changeset() and ** sqlite3session_patchset() functions, all changes related to a single ** table are grouped together in the output of this function. Tables appear ** in the same order as for the very first changeset added to the changegroup. ** If the second or subsequent changesets added to the changegroup contain ** changes for tables that do not appear in the first changeset, they are ** appended onto the end of the output changeset, again in the order in ** which they are first encountered. ** ** If an error occurs, an SQLite error code is returned and the output ** variables (*pnData) and (*ppData) are set to 0. Otherwise, SQLITE_OK ** is returned and the output variables are set to the size of and a ** pointer to the output buffer, respectively. In this case it is the ** responsibility of the caller to eventually free the buffer using a ** call to sqlite3_free(). */ SQLITE_API int sqlite3changegroup_output( sqlite3_changegroup*, int *pnData, /* OUT: Size of output buffer in bytes */ void **ppData /* OUT: Pointer to output buffer */ ); /* ** CAPI3REF: Delete A Changegroup Object */ SQLITE_API void sqlite3changegroup_delete(sqlite3_changegroup*); /* ** CAPI3REF: Apply A Changeset To A Database ** ** Apply a changeset to a database. This function attempts to update the ** "main" database attached to handle db with the changes found in the ** changeset passed via the second and third arguments. ** ** The fourth argument (xFilter) passed to this function is the "filter ** callback". If it is not NULL, then for each table affected by at least one ** change in the changeset, the filter callback is invoked with ** the table name as the second argument, and a copy of the context pointer ** passed as the sixth argument to this function as the first. If the "filter ** callback" returns zero, then no attempt is made to apply any changes to ** the table. Otherwise, if the return value is non-zero or the xFilter ** argument to this function is NULL, all changes related to the table are ** attempted. ** ** For each table that is not excluded by the filter callback, this function ** tests that the target database contains a compatible table. A table is ** considered compatible if all of the following are true: ** **
    **
  • The table has the same name as the name recorded in the ** changeset, and **
  • The table has at least as many columns as recorded in the ** changeset, and **
  • The table has primary key columns in the same position as ** recorded in the changeset. **
** ** If there is no compatible table, it is not an error, but none of the ** changes associated with the table are applied. A warning message is issued ** via the sqlite3_log() mechanism with the error code SQLITE_SCHEMA. At most ** one such warning is issued for each table in the changeset. ** ** For each change for which there is a compatible table, an attempt is made ** to modify the table contents according to the UPDATE, INSERT or DELETE ** change. If a change cannot be applied cleanly, the conflict handler ** function passed as the fifth argument to sqlite3changeset_apply() may be ** invoked. A description of exactly when the conflict handler is invoked for ** each type of change is below. ** ** Unlike the xFilter argument, xConflict may not be passed NULL. The results ** of passing anything other than a valid function pointer as the xConflict ** argument are undefined. ** ** Each time the conflict handler function is invoked, it must return one ** of [SQLITE_CHANGESET_OMIT], [SQLITE_CHANGESET_ABORT] or ** [SQLITE_CHANGESET_REPLACE]. SQLITE_CHANGESET_REPLACE may only be returned ** if the second argument passed to the conflict handler is either ** SQLITE_CHANGESET_DATA or SQLITE_CHANGESET_CONFLICT. If the conflict-handler ** returns an illegal value, any changes already made are rolled back and ** the call to sqlite3changeset_apply() returns SQLITE_MISUSE. Different ** actions are taken by sqlite3changeset_apply() depending on the value ** returned by each invocation of the conflict-handler function. Refer to ** the documentation for the three ** [SQLITE_CHANGESET_OMIT|available return values] for details. ** **
**
DELETE Changes
** For each DELETE change, this function checks if the target database ** contains a row with the same primary key value (or values) as the ** original row values stored in the changeset. If it does, and the values ** stored in all non-primary key columns also match the values stored in ** the changeset the row is deleted from the target database. ** ** If a row with matching primary key values is found, but one or more of ** the non-primary key fields contains a value different from the original ** row value stored in the changeset, the conflict-handler function is ** invoked with [SQLITE_CHANGESET_DATA] as the second argument. If the ** database table has more columns than are recorded in the changeset, ** only the values of those non-primary key fields are compared against ** the current database contents - any trailing database table columns ** are ignored. ** ** If no row with matching primary key values is found in the database, ** the conflict-handler function is invoked with [SQLITE_CHANGESET_NOTFOUND] ** passed as the second argument. ** ** If the DELETE operation is attempted, but SQLite returns SQLITE_CONSTRAINT ** (which can only happen if a foreign key constraint is violated), the ** conflict-handler function is invoked with [SQLITE_CHANGESET_CONSTRAINT] ** passed as the second argument. This includes the case where the DELETE ** operation is attempted because an earlier call to the conflict handler ** function returned [SQLITE_CHANGESET_REPLACE]. ** **
INSERT Changes
** For each INSERT change, an attempt is made to insert the new row into ** the database. If the changeset row contains fewer fields than the ** database table, the trailing fields are populated with their default ** values. ** ** If the attempt to insert the row fails because the database already ** contains a row with the same primary key values, the conflict handler ** function is invoked with the second argument set to ** [SQLITE_CHANGESET_CONFLICT]. ** ** If the attempt to insert the row fails because of some other constraint ** violation (e.g. NOT NULL or UNIQUE), the conflict handler function is ** invoked with the second argument set to [SQLITE_CHANGESET_CONSTRAINT]. ** This includes the case where the INSERT operation is re-attempted because ** an earlier call to the conflict handler function returned ** [SQLITE_CHANGESET_REPLACE]. ** **
UPDATE Changes
** For each UPDATE change, this function checks if the target database ** contains a row with the same primary key value (or values) as the ** original row values stored in the changeset. If it does, and the values ** stored in all modified non-primary key columns also match the values ** stored in the changeset the row is updated within the target database. ** ** If a row with matching primary key values is found, but one or more of ** the modified non-primary key fields contains a value different from an ** original row value stored in the changeset, the conflict-handler function ** is invoked with [SQLITE_CHANGESET_DATA] as the second argument. Since ** UPDATE changes only contain values for non-primary key fields that are ** to be modified, only those fields need to match the original values to ** avoid the SQLITE_CHANGESET_DATA conflict-handler callback. ** ** If no row with matching primary key values is found in the database, ** the conflict-handler function is invoked with [SQLITE_CHANGESET_NOTFOUND] ** passed as the second argument. ** ** If the UPDATE operation is attempted, but SQLite returns ** SQLITE_CONSTRAINT, the conflict-handler function is invoked with ** [SQLITE_CHANGESET_CONSTRAINT] passed as the second argument. ** This includes the case where the UPDATE operation is attempted after ** an earlier call to the conflict handler function returned ** [SQLITE_CHANGESET_REPLACE]. **
** ** It is safe to execute SQL statements, including those that write to the ** table that the callback related to, from within the xConflict callback. ** This can be used to further customize the applications conflict ** resolution strategy. ** ** All changes made by this function are enclosed in a savepoint transaction. ** If any other error (aside from a constraint failure when attempting to ** write to the target database) occurs, then the savepoint transaction is ** rolled back, restoring the target database to its original state, and an ** SQLite error code returned. */ SQLITE_API int sqlite3changeset_apply( sqlite3 *db, /* Apply change to "main" db of this handle */ int nChangeset, /* Size of changeset in bytes */ void *pChangeset, /* Changeset blob */ int(*xFilter)( void *pCtx, /* Copy of sixth arg to _apply() */ const char *zTab /* Table name */ ), int(*xConflict)( void *pCtx, /* Copy of sixth arg to _apply() */ int eConflict, /* DATA, MISSING, CONFLICT, CONSTRAINT */ sqlite3_changeset_iter *p /* Handle describing change and conflict */ ), void *pCtx /* First argument passed to xConflict */ ); /* ** CAPI3REF: Constants Passed To The Conflict Handler ** ** Values that may be passed as the second argument to a conflict-handler. ** **
**
SQLITE_CHANGESET_DATA
** The conflict handler is invoked with CHANGESET_DATA as the second argument ** when processing a DELETE or UPDATE change if a row with the required ** PRIMARY KEY fields is present in the database, but one or more other ** (non primary-key) fields modified by the update do not contain the ** expected "before" values. ** ** The conflicting row, in this case, is the database row with the matching ** primary key. ** **
SQLITE_CHANGESET_NOTFOUND
** The conflict handler is invoked with CHANGESET_NOTFOUND as the second ** argument when processing a DELETE or UPDATE change if a row with the ** required PRIMARY KEY fields is not present in the database. ** ** There is no conflicting row in this case. The results of invoking the ** sqlite3changeset_conflict() API are undefined. ** **
SQLITE_CHANGESET_CONFLICT
** CHANGESET_CONFLICT is passed as the second argument to the conflict ** handler while processing an INSERT change if the operation would result ** in duplicate primary key values. ** ** The conflicting row in this case is the database row with the matching ** primary key. ** **
SQLITE_CHANGESET_FOREIGN_KEY
** If foreign key handling is enabled, and applying a changeset leaves the ** database in a state containing foreign key violations, the conflict ** handler is invoked with CHANGESET_FOREIGN_KEY as the second argument ** exactly once before the changeset is committed. If the conflict handler ** returns CHANGESET_OMIT, the changes, including those that caused the ** foreign key constraint violation, are committed. Or, if it returns ** CHANGESET_ABORT, the changeset is rolled back. ** ** No current or conflicting row information is provided. The only function ** it is possible to call on the supplied sqlite3_changeset_iter handle ** is sqlite3changeset_fk_conflicts(). ** **
SQLITE_CHANGESET_CONSTRAINT
** If any other constraint violation occurs while applying a change (i.e. ** a UNIQUE, CHECK or NOT NULL constraint), the conflict handler is ** invoked with CHANGESET_CONSTRAINT as the second argument. ** ** There is no conflicting row in this case. The results of invoking the ** sqlite3changeset_conflict() API are undefined. ** **
*/ #define SQLITE_CHANGESET_DATA 1 #define SQLITE_CHANGESET_NOTFOUND 2 #define SQLITE_CHANGESET_CONFLICT 3 #define SQLITE_CHANGESET_CONSTRAINT 4 #define SQLITE_CHANGESET_FOREIGN_KEY 5 /* ** CAPI3REF: Constants Returned By The Conflict Handler ** ** A conflict handler callback must return one of the following three values. ** **
**
SQLITE_CHANGESET_OMIT
** If a conflict handler returns this value no special action is taken. The ** change that caused the conflict is not applied. The session module ** continues to the next change in the changeset. ** **
SQLITE_CHANGESET_REPLACE
** This value may only be returned if the second argument to the conflict ** handler was SQLITE_CHANGESET_DATA or SQLITE_CHANGESET_CONFLICT. If this ** is not the case, any changes applied so far are rolled back and the ** call to sqlite3changeset_apply() returns SQLITE_MISUSE. ** ** If CHANGESET_REPLACE is returned by an SQLITE_CHANGESET_DATA conflict ** handler, then the conflicting row is either updated or deleted, depending ** on the type of change. ** ** If CHANGESET_REPLACE is returned by an SQLITE_CHANGESET_CONFLICT conflict ** handler, then the conflicting row is removed from the database and a ** second attempt to apply the change is made. If this second attempt fails, ** the original row is restored to the database before continuing. ** **
SQLITE_CHANGESET_ABORT
** If this value is returned, any changes applied so far are rolled back ** and the call to sqlite3changeset_apply() returns SQLITE_ABORT. **
*/ #define SQLITE_CHANGESET_OMIT 0 #define SQLITE_CHANGESET_REPLACE 1 #define SQLITE_CHANGESET_ABORT 2 /* ** CAPI3REF: Streaming Versions of API functions. ** ** The six streaming API xxx_strm() functions serve similar purposes to the ** corresponding non-streaming API functions: ** ** ** **
Streaming functionNon-streaming equivalent
sqlite3changeset_apply_str[sqlite3changeset_apply] **
sqlite3changeset_concat_str[sqlite3changeset_concat] **
sqlite3changeset_invert_str[sqlite3changeset_invert] **
sqlite3changeset_start_str[sqlite3changeset_start] **
sqlite3session_changeset_str[sqlite3session_changeset] **
sqlite3session_patchset_str[sqlite3session_patchset] **
** ** Non-streaming functions that accept changesets (or patchsets) as input ** require that the entire changeset be stored in a single buffer in memory. ** Similarly, those that return a changeset or patchset do so by returning ** a pointer to a single large buffer allocated using sqlite3_malloc(). ** Normally this is convenient. However, if an application running in a ** low-memory environment is required to handle very large changesets, the ** large contiguous memory allocations required can become onerous. ** ** In order to avoid this problem, instead of a single large buffer, input ** is passed to a streaming API functions by way of a callback function that ** the sessions module invokes to incrementally request input data as it is ** required. In all cases, a pair of API function parameters such as ** ** 
**        int nChangeset,
**        void *pChangeset,
**
** ** Is replaced by: ** ** 
**        int (*xInput)(void *pIn, void *pData, int *pnData),
**        void *pIn,
**
** ** Each time the xInput callback is invoked by the sessions module, the first ** argument passed is a copy of the supplied pIn context pointer. The second ** argument, pData, points to a buffer (*pnData) bytes in size. Assuming no ** error occurs the xInput method should copy up to (*pnData) bytes of data ** into the buffer and set (*pnData) to the actual number of bytes copied ** before returning SQLITE_OK. If the input is completely exhausted, (*pnData) ** should be set to zero to indicate this. Or, if an error occurs, an SQLite ** error code should be returned. In all cases, if an xInput callback returns ** an error, all processing is abandoned and the streaming API function ** returns a copy of the error code to the caller. ** ** In the case of sqlite3changeset_start_strm(), the xInput callback may be ** invoked by the sessions module at any point during the lifetime of the ** iterator. If such an xInput callback returns an error, the iterator enters ** an error state, whereby all subsequent calls to iterator functions ** immediately fail with the same error code as returned by xInput. ** ** Similarly, streaming API functions that return changesets (or patchsets) ** return them in chunks by way of a callback function instead of via a ** pointer to a single large buffer. In this case, a pair of parameters such ** as: ** ** 
**        int *pnChangeset,
**        void **ppChangeset,
**
** ** Is replaced by: ** ** 
**        int (*xOutput)(void *pOut, const void *pData, int nData),
**        void *pOut
**
** ** The xOutput callback is invoked zero or more times to return data to ** the application. The first parameter passed to each call is a copy of the ** pOut pointer supplied by the application. The second parameter, pData, ** points to a buffer nData bytes in size containing the chunk of output ** data being returned. If the xOutput callback successfully processes the ** supplied data, it should return SQLITE_OK to indicate success. Otherwise, ** it should return some other SQLite error code. In this case processing ** is immediately abandoned and the streaming API function returns a copy ** of the xOutput error code to the application. ** ** The sessions module never invokes an xOutput callback with the third ** parameter set to a value less than or equal to zero. Other than this, ** no guarantees are made as to the size of the chunks of data returned. */ SQLITE_API int sqlite3changeset_apply_strm( sqlite3 *db, /* Apply change to "main" db of this handle */ int (*xInput)(void *pIn, void *pData, int *pnData), /* Input function */ void *pIn, /* First arg for xInput */ int(*xFilter)( void *pCtx, /* Copy of sixth arg to _apply() */ const char *zTab /* Table name */ ), int(*xConflict)( void *pCtx, /* Copy of sixth arg to _apply() */ int eConflict, /* DATA, MISSING, CONFLICT, CONSTRAINT */ sqlite3_changeset_iter *p /* Handle describing change and conflict */ ), void *pCtx /* First argument passed to xConflict */ ); SQLITE_API int sqlite3changeset_concat_strm( int (*xInputA)(void *pIn, void *pData, int *pnData), void *pInA, int (*xInputB)(void *pIn, void *pData, int *pnData), void *pInB, int (*xOutput)(void *pOut, const void *pData, int nData), void *pOut ); SQLITE_API int sqlite3changeset_invert_strm( int (*xInput)(void *pIn, void *pData, int *pnData), void *pIn, int (*xOutput)(void *pOut, const void *pData, int nData), void *pOut ); SQLITE_API int sqlite3changeset_start_strm( sqlite3_changeset_iter **pp, int (*xInput)(void *pIn, void *pData, int *pnData), void *pIn ); SQLITE_API int sqlite3session_changeset_strm( sqlite3_session *pSession, int (*xOutput)(void *pOut, const void *pData, int nData), void *pOut ); SQLITE_API int sqlite3session_patchset_strm( sqlite3_session *pSession, int (*xOutput)(void *pOut, const void *pData, int nData), void *pOut ); SQLITE_API int sqlite3changegroup_add_strm(sqlite3_changegroup*, int (*xInput)(void *pIn, void *pData, int *pnData), void *pIn ); SQLITE_API int sqlite3changegroup_output_strm(sqlite3_changegroup*, int (*xOutput)(void *pOut, const void *pData, int nData), void *pOut ); /* ** Make sure we can call this stuff from C++. */ #ifdef __cplusplus } #endif #endif /* !defined(__SQLITESESSION_H_) && defined(SQLITE_ENABLE_SESSION) */ /******** End of sqlite3session.h *********/ /******** Begin file fts5.h *********/ /* ** 2014 May 31 ** ** The author disclaims copyright to this source code. In place of ** a legal notice, here is a blessing: ** ** May you do good and not evil. ** May you find forgiveness for yourself and forgive others. ** May you share freely, never taking more than you give. ** ****************************************************************************** ** ** Interfaces to extend FTS5. Using the interfaces defined in this file, ** FTS5 may be extended with: ** ** * custom tokenizers, and ** * custom auxiliary functions. */ #ifndef _FTS5_H #define _FTS5_H #ifdef __cplusplus extern "C" { #endif /************************************************************************* ** CUSTOM AUXILIARY FUNCTIONS ** ** Virtual table implementations may overload SQL functions by implementing ** the sqlite3_module.xFindFunction() method. */ typedef struct Fts5ExtensionApi Fts5ExtensionApi; typedef struct Fts5Context Fts5Context; typedef struct Fts5PhraseIter Fts5PhraseIter; typedef void (*fts5_extension_function)( const Fts5ExtensionApi *pApi, /* API offered by current FTS version */ Fts5Context *pFts, /* First arg to pass to pApi functions */ sqlite3_context *pCtx, /* Context for returning result/error */ int nVal, /* Number of values in apVal[] array */ sqlite3_value **apVal /* Array of trailing arguments */ ); struct Fts5PhraseIter { const unsigned char *a; const unsigned char *b; }; /* ** EXTENSION API FUNCTIONS ** ** xUserData(pFts): ** Return a copy of the context pointer the extension function was ** registered with. ** ** xColumnTotalSize(pFts, iCol, pnToken): ** If parameter iCol is less than zero, set output variable *pnToken ** to the total number of tokens in the FTS5 table. Or, if iCol is ** non-negative but less than the number of columns in the table, return ** the total number of tokens in column iCol, considering all rows in ** the FTS5 table. ** ** If parameter iCol is greater than or equal to the number of columns ** in the table, SQLITE_RANGE is returned. Or, if an error occurs (e.g. ** an OOM condition or IO error), an appropriate SQLite error code is ** returned. ** ** xColumnCount(pFts): ** Return the number of columns in the table. ** ** xColumnSize(pFts, iCol, pnToken): ** If parameter iCol is less than zero, set output variable *pnToken ** to the total number of tokens in the current row. Or, if iCol is ** non-negative but less than the number of columns in the table, set ** *pnToken to the number of tokens in column iCol of the current row. ** ** If parameter iCol is greater than or equal to the number of columns ** in the table, SQLITE_RANGE is returned. Or, if an error occurs (e.g. ** an OOM condition or IO error), an appropriate SQLite error code is ** returned. ** ** This function may be quite inefficient if used with an FTS5 table ** created with the "columnsize=0" option. ** ** xColumnText: ** This function attempts to retrieve the text of column iCol of the ** current document. If successful, (*pz) is set to point to a buffer ** containing the text in utf-8 encoding, (*pn) is set to the size in bytes ** (not characters) of the buffer and SQLITE_OK is returned. Otherwise, ** if an error occurs, an SQLite error code is returned and the final values ** of (*pz) and (*pn) are undefined. ** ** xPhraseCount: ** Returns the number of phrases in the current query expression. ** ** xPhraseSize: ** Returns the number of tokens in phrase iPhrase of the query. Phrases ** are numbered starting from zero. ** ** xInstCount: ** Set *pnInst to the total number of occurrences of all phrases within ** the query within the current row. Return SQLITE_OK if successful, or ** an error code (i.e. SQLITE_NOMEM) if an error occurs. ** ** This API can be quite slow if used with an FTS5 table created with the ** "detail=none" or "detail=column" option. If the FTS5 table is created ** with either "detail=none" or "detail=column" and "content=" option ** (i.e. if it is a contentless table), then this API always returns 0. ** ** xInst: ** Query for the details of phrase match iIdx within the current row. ** Phrase matches are numbered starting from zero, so the iIdx argument ** should be greater than or equal to zero and smaller than the value ** output by xInstCount(). ** ** Usually, output parameter *piPhrase is set to the phrase number, *piCol ** to the column in which it occurs and *piOff the token offset of the ** first token of the phrase. The exception is if the table was created ** with the offsets=0 option specified. In this case *piOff is always ** set to -1. ** ** Returns SQLITE_OK if successful, or an error code (i.e. SQLITE_NOMEM) ** if an error occurs. ** ** This API can be quite slow if used with an FTS5 table created with the ** "detail=none" or "detail=column" option. ** ** xRowid: ** Returns the rowid of the current row. ** ** xTokenize: ** Tokenize text using the tokenizer belonging to the FTS5 table. ** ** xQueryPhrase(pFts5, iPhrase, pUserData, xCallback): ** This API function is used to query the FTS table for phrase iPhrase ** of the current query. Specifically, a query equivalent to: ** ** ... FROM ftstable WHERE ftstable MATCH $p ORDER BY rowid ** ** with $p set to a phrase equivalent to the phrase iPhrase of the ** current query is executed. Any column filter that applies to ** phrase iPhrase of the current query is included in $p. For each ** row visited, the callback function passed as the fourth argument ** is invoked. The context and API objects passed to the callback ** function may be used to access the properties of each matched row. ** Invoking Api.xUserData() returns a copy of the pointer passed as ** the third argument to pUserData. ** ** If the callback function returns any value other than SQLITE_OK, the ** query is abandoned and the xQueryPhrase function returns immediately. ** If the returned value is SQLITE_DONE, xQueryPhrase returns SQLITE_OK. ** Otherwise, the error code is propagated upwards. ** ** If the query runs to completion without incident, SQLITE_OK is returned. ** Or, if some error occurs before the query completes or is aborted by ** the callback, an SQLite error code is returned. ** ** ** xSetAuxdata(pFts5, pAux, xDelete) ** ** Save the pointer passed as the second argument as the extension functions ** "auxiliary data". The pointer may then be retrieved by the current or any ** future invocation of the same fts5 extension function made as part of ** of the same MATCH query using the xGetAuxdata() API. ** ** Each extension function is allocated a single auxiliary data slot for ** each FTS query (MATCH expression). If the extension function is invoked ** more than once for a single FTS query, then all invocations share a ** single auxiliary data context. ** ** If there is already an auxiliary data pointer when this function is ** invoked, then it is replaced by the new pointer. If an xDelete callback ** was specified along with the original pointer, it is invoked at this ** point. ** ** The xDelete callback, if one is specified, is also invoked on the ** auxiliary data pointer after the FTS5 query has finished. ** ** If an error (e.g. an OOM condition) occurs within this function, an ** the auxiliary data is set to NULL and an error code returned. If the ** xDelete parameter was not NULL, it is invoked on the auxiliary data ** pointer before returning. ** ** ** xGetAuxdata(pFts5, bClear) ** ** Returns the current auxiliary data pointer for the fts5 extension ** function. See the xSetAuxdata() method for details. ** ** If the bClear argument is non-zero, then the auxiliary data is cleared ** (set to NULL) before this function returns. In this case the xDelete, ** if any, is not invoked. ** ** ** xRowCount(pFts5, pnRow) ** ** This function is used to retrieve the total number of rows in the table. ** In other words, the same value that would be returned by: ** ** SELECT count(*) FROM ftstable; ** ** xPhraseFirst() ** This function is used, along with type Fts5PhraseIter and the xPhraseNext ** method, to iterate through all instances of a single query phrase within ** the current row. This is the same information as is accessible via the ** xInstCount/xInst APIs. While the xInstCount/xInst APIs are more convenient ** to use, this API may be faster under some circumstances. To iterate ** through instances of phrase iPhrase, use the following code: ** ** Fts5PhraseIter iter; ** int iCol, iOff; ** for(pApi->xPhraseFirst(pFts, iPhrase, &iter, &iCol, &iOff); ** iCol>=0; ** pApi->xPhraseNext(pFts, &iter, &iCol, &iOff) ** ){ ** // An instance of phrase iPhrase at offset iOff of column iCol ** } ** ** The Fts5PhraseIter structure is defined above. Applications should not ** modify this structure directly - it should only be used as shown above ** with the xPhraseFirst() and xPhraseNext() API methods (and by ** xPhraseFirstColumn() and xPhraseNextColumn() as illustrated below). ** ** This API can be quite slow if used with an FTS5 table created with the ** "detail=none" or "detail=column" option. If the FTS5 table is created ** with either "detail=none" or "detail=column" and "content=" option ** (i.e. if it is a contentless table), then this API always iterates ** through an empty set (all calls to xPhraseFirst() set iCol to -1). ** ** xPhraseNext() ** See xPhraseFirst above. ** ** xPhraseFirstColumn() ** This function and xPhraseNextColumn() are similar to the xPhraseFirst() ** and xPhraseNext() APIs described above. The difference is that instead ** of iterating through all instances of a phrase in the current row, these ** APIs are used to iterate through the set of columns in the current row ** that contain one or more instances of a specified phrase. For example: ** ** Fts5PhraseIter iter; ** int iCol; ** for(pApi->xPhraseFirstColumn(pFts, iPhrase, &iter, &iCol); ** iCol>=0; ** pApi->xPhraseNextColumn(pFts, &iter, &iCol) ** ){ ** // Column iCol contains at least one instance of phrase iPhrase ** } ** ** This API can be quite slow if used with an FTS5 table created with the ** "detail=none" option. If the FTS5 table is created with either ** "detail=none" "content=" option (i.e. if it is a contentless table), ** then this API always iterates through an empty set (all calls to ** xPhraseFirstColumn() set iCol to -1). ** ** The information accessed using this API and its companion ** xPhraseFirstColumn() may also be obtained using xPhraseFirst/xPhraseNext ** (or xInst/xInstCount). The chief advantage of this API is that it is ** significantly more efficient than those alternatives when used with ** "detail=column" tables. ** ** xPhraseNextColumn() ** See xPhraseFirstColumn above. */ struct Fts5ExtensionApi { int iVersion; /* Currently always set to 3 */ void *(*xUserData)(Fts5Context*); int (*xColumnCount)(Fts5Context*); int (*xRowCount)(Fts5Context*, sqlite3_int64 *pnRow); int (*xColumnTotalSize)(Fts5Context*, int iCol, sqlite3_int64 *pnToken); int (*xTokenize)(Fts5Context*, const char *pText, int nText, /* Text to tokenize */ void *pCtx, /* Context passed to xToken() */ int (*xToken)(void*, int, const char*, int, int, int) /* Callback */ ); int (*xPhraseCount)(Fts5Context*); int (*xPhraseSize)(Fts5Context*, int iPhrase); int (*xInstCount)(Fts5Context*, int *pnInst); int (*xInst)(Fts5Context*, int iIdx, int *piPhrase, int *piCol, int *piOff); sqlite3_int64 (*xRowid)(Fts5Context*); int (*xColumnText)(Fts5Context*, int iCol, const char **pz, int *pn); int (*xColumnSize)(Fts5Context*, int iCol, int *pnToken); int (*xQueryPhrase)(Fts5Context*, int iPhrase, void *pUserData, int(*)(const Fts5ExtensionApi*,Fts5Context*,void*) ); int (*xSetAuxdata)(Fts5Context*, void *pAux, void(*xDelete)(void*)); void *(*xGetAuxdata)(Fts5Context*, int bClear); int (*xPhraseFirst)(Fts5Context*, int iPhrase, Fts5PhraseIter*, int*, int*); void (*xPhraseNext)(Fts5Context*, Fts5PhraseIter*, int *piCol, int *piOff); int (*xPhraseFirstColumn)(Fts5Context*, int iPhrase, Fts5PhraseIter*, int*); void (*xPhraseNextColumn)(Fts5Context*, Fts5PhraseIter*, int *piCol); }; /* ** CUSTOM AUXILIARY FUNCTIONS *************************************************************************/ /************************************************************************* ** CUSTOM TOKENIZERS ** ** Applications may also register custom tokenizer types. A tokenizer ** is registered by providing fts5 with a populated instance of the ** following structure. All structure methods must be defined, setting ** any member of the fts5_tokenizer struct to NULL leads to undefined ** behaviour. The structure methods are expected to function as follows: ** ** xCreate: ** This function is used to allocate and initialize a tokenizer instance. ** A tokenizer instance is required to actually tokenize text. ** ** The first argument passed to this function is a copy of the (void*) ** pointer provided by the application when the fts5_tokenizer object ** was registered with FTS5 (the third argument to xCreateTokenizer()). ** The second and third arguments are an array of nul-terminated strings ** containing the tokenizer arguments, if any, specified following the ** tokenizer name as part of the CREATE VIRTUAL TABLE statement used ** to create the FTS5 table. ** ** The final argument is an output variable. If successful, (*ppOut) ** should be set to point to the new tokenizer handle and SQLITE_OK ** returned. If an error occurs, some value other than SQLITE_OK should ** be returned. In this case, fts5 assumes that the final value of *ppOut ** is undefined. ** ** xDelete: ** This function is invoked to delete a tokenizer handle previously ** allocated using xCreate(). Fts5 guarantees that this function will ** be invoked exactly once for each successful call to xCreate(). ** ** xTokenize: ** This function is expected to tokenize the nText byte string indicated ** by argument pText. pText may or may not be nul-terminated. The first ** argument passed to this function is a pointer to an Fts5Tokenizer object ** returned by an earlier call to xCreate(). ** ** The second argument indicates the reason that FTS5 is requesting ** tokenization of the supplied text. This is always one of the following ** four values: ** **
  • FTS5_TOKENIZE_DOCUMENT - A document is being inserted into ** or removed from the FTS table. The tokenizer is being invoked to ** determine the set of tokens to add to (or delete from) the ** FTS index. ** **
  • FTS5_TOKENIZE_QUERY - A MATCH query is being executed ** against the FTS index. The tokenizer is being called to tokenize ** a bareword or quoted string specified as part of the query. ** **
  • (FTS5_TOKENIZE_QUERY | FTS5_TOKENIZE_PREFIX) - Same as ** FTS5_TOKENIZE_QUERY, except that the bareword or quoted string is ** followed by a "*" character, indicating that the last token ** returned by the tokenizer will be treated as a token prefix. ** **
  • FTS5_TOKENIZE_AUX - The tokenizer is being invoked to ** satisfy an fts5_api.xTokenize() request made by an auxiliary ** function. Or an fts5_api.xColumnSize() request made by the same ** on a columnsize=0 database. **
** ** For each token in the input string, the supplied callback xToken() must ** be invoked. The first argument to it should be a copy of the pointer ** passed as the second argument to xTokenize(). The third and fourth ** arguments are a pointer to a buffer containing the token text, and the ** size of the token in bytes. The 4th and 5th arguments are the byte offsets ** of the first byte of and first byte immediately following the text from ** which the token is derived within the input. ** ** The second argument passed to the xToken() callback ("tflags") should ** normally be set to 0. The exception is if the tokenizer supports ** synonyms. In this case see the discussion below for details. ** ** FTS5 assumes the xToken() callback is invoked for each token in the ** order that they occur within the input text. ** ** If an xToken() callback returns any value other than SQLITE_OK, then ** the tokenization should be abandoned and the xTokenize() method should ** immediately return a copy of the xToken() return value. Or, if the ** input buffer is exhausted, xTokenize() should return SQLITE_OK. Finally, ** if an error occurs with the xTokenize() implementation itself, it ** may abandon the tokenization and return any error code other than ** SQLITE_OK or SQLITE_DONE. ** ** SYNONYM SUPPORT ** ** Custom tokenizers may also support synonyms. Consider a case in which a ** user wishes to query for a phrase such as "first place". Using the ** built-in tokenizers, the FTS5 query 'first + place' will match instances ** of "first place" within the document set, but not alternative forms ** such as "1st place". In some applications, it would be better to match ** all instances of "first place" or "1st place" regardless of which form ** the user specified in the MATCH query text. ** ** There are several ways to approach this in FTS5: ** **
  1. By mapping all synonyms to a single token. In this case, the ** In the above example, this means that the tokenizer returns the ** same token for inputs "first" and "1st". Say that token is in ** fact "first", so that when the user inserts the document "I won ** 1st place" entries are added to the index for tokens "i", "won", ** "first" and "place". If the user then queries for '1st + place', ** the tokenizer substitutes "first" for "1st" and the query works ** as expected. ** **
  2. By adding multiple synonyms for a single term to the FTS index. ** In this case, when tokenizing query text, the tokenizer may ** provide multiple synonyms for a single term within the document. ** FTS5 then queries the index for each synonym individually. For ** example, faced with the query: ** ** ** ... MATCH 'first place' ** ** the tokenizer offers both "1st" and "first" as synonyms for the ** first token in the MATCH query and FTS5 effectively runs a query ** similar to: ** ** ** ... MATCH '(first OR 1st) place' ** ** except that, for the purposes of auxiliary functions, the query ** still appears to contain just two phrases - "(first OR 1st)" ** being treated as a single phrase. ** **
  3. By adding multiple synonyms for a single term to the FTS index. ** Using this method, when tokenizing document text, the tokenizer ** provides multiple synonyms for each token. So that when a ** document such as "I won first place" is tokenized, entries are ** added to the FTS index for "i", "won", "first", "1st" and ** "place". ** ** This way, even if the tokenizer does not provide synonyms ** when tokenizing query text (it should not - to do would be ** inefficient), it doesn't matter if the user queries for ** 'first + place' or '1st + place', as there are entires in the ** FTS index corresponding to both forms of the first token. **
** ** Whether it is parsing document or query text, any call to xToken that ** specifies a tflags argument with the FTS5_TOKEN_COLOCATED bit ** is considered to supply a synonym for the previous token. For example, ** when parsing the document "I won first place", a tokenizer that supports ** synonyms would call xToken() 5 times, as follows: ** ** ** xToken(pCtx, 0, "i", 1, 0, 1); ** xToken(pCtx, 0, "won", 3, 2, 5); ** xToken(pCtx, 0, "first", 5, 6, 11); ** xToken(pCtx, FTS5_TOKEN_COLOCATED, "1st", 3, 6, 11); ** xToken(pCtx, 0, "place", 5, 12, 17); ** ** ** It is an error to specify the FTS5_TOKEN_COLOCATED flag the first time ** xToken() is called. Multiple synonyms may be specified for a single token ** by making multiple calls to xToken(FTS5_TOKEN_COLOCATED) in sequence. ** There is no limit to the number of synonyms that may be provided for a ** single token. ** ** In many cases, method (1) above is the best approach. It does not add ** extra data to the FTS index or require FTS5 to query for multiple terms, ** so it is efficient in terms of disk space and query speed. However, it ** does not support prefix queries very well. If, as suggested above, the ** token "first" is subsituted for "1st" by the tokenizer, then the query: ** ** ** ... MATCH '1s*' ** ** will not match documents that contain the token "1st" (as the tokenizer ** will probably not map "1s" to any prefix of "first"). ** ** For full prefix support, method (3) may be preferred. In this case, ** because the index contains entries for both "first" and "1st", prefix ** queries such as 'fi*' or '1s*' will match correctly. However, because ** extra entries are added to the FTS index, this method uses more space ** within the database. ** ** Method (2) offers a midpoint between (1) and (3). Using this method, ** a query such as '1s*' will match documents that contain the literal ** token "1st", but not "first" (assuming the tokenizer is not able to ** provide synonyms for prefixes). However, a non-prefix query like '1st' ** will match against "1st" and "first". This method does not require ** extra disk space, as no extra entries are added to the FTS index. ** On the other hand, it may require more CPU cycles to run MATCH queries, ** as separate queries of the FTS index are required for each synonym. ** ** When using methods (2) or (3), it is important that the tokenizer only ** provide synonyms when tokenizing document text (method (2)) or query ** text (method (3)), not both. Doing so will not cause any errors, but is ** inefficient. */ typedef struct Fts5Tokenizer Fts5Tokenizer; typedef struct fts5_tokenizer fts5_tokenizer; struct fts5_tokenizer { int (*xCreate)(void*, const char **azArg, int nArg, Fts5Tokenizer **ppOut); void (*xDelete)(Fts5Tokenizer*); int (*xTokenize)(Fts5Tokenizer*, void *pCtx, int flags, /* Mask of FTS5_TOKENIZE_* flags */ const char *pText, int nText, int (*xToken)( void *pCtx, /* Copy of 2nd argument to xTokenize() */ int tflags, /* Mask of FTS5_TOKEN_* flags */ const char *pToken, /* Pointer to buffer containing token */ int nToken, /* Size of token in bytes */ int iStart, /* Byte offset of token within input text */ int iEnd /* Byte offset of end of token within input text */ ) ); }; /* Flags that may be passed as the third argument to xTokenize() */ #define FTS5_TOKENIZE_QUERY 0x0001 #define FTS5_TOKENIZE_PREFIX 0x0002 #define FTS5_TOKENIZE_DOCUMENT 0x0004 #define FTS5_TOKENIZE_AUX 0x0008 /* Flags that may be passed by the tokenizer implementation back to FTS5 ** as the third argument to the supplied xToken callback. */ #define FTS5_TOKEN_COLOCATED 0x0001 /* Same position as prev. token */ /* ** END OF CUSTOM TOKENIZERS *************************************************************************/ /************************************************************************* ** FTS5 EXTENSION REGISTRATION API */ typedef struct fts5_api fts5_api; struct fts5_api { int iVersion; /* Currently always set to 2 */ /* Create a new tokenizer */ int (*xCreateTokenizer)( fts5_api *pApi, const char *zName, void *pContext, fts5_tokenizer *pTokenizer, void (*xDestroy)(void*) ); /* Find an existing tokenizer */ int (*xFindTokenizer)( fts5_api *pApi, const char *zName, void **ppContext, fts5_tokenizer *pTokenizer ); /* Create a new auxiliary function */ int (*xCreateFunction)( fts5_api *pApi, const char *zName, void *pContext, fts5_extension_function xFunction, void (*xDestroy)(void*) ); }; /* ** END OF REGISTRATION API *************************************************************************/ #ifdef __cplusplus } /* end of the 'extern "C"' block */ #endif #endif /* _FTS5_H */ /******** End of fts5.h *********/ ctffind-4.1.14/src/core/symmetry_matrix.cpp000066400000000000000000001233671440356052600207370ustar00rootroot00000000000000#include "core_headers.h" SymmetryMatrix::SymmetryMatrix() { rot_mat = NULL; number_of_matrices = 0; // MyPrintWithDetails("Error: Constructor must be called with symmetry symbol\n"); // DEBUG_ABORT; } SymmetryMatrix::SymmetryMatrix(wxString wanted_symmetry_symbol) { Init(wanted_symmetry_symbol); } void SymmetryMatrix::Init(wxString wanted_symmetry_symbol) { wxChar symmetry_type; long symmetry_number; wanted_symmetry_symbol = wanted_symmetry_symbol.Trim(); wanted_symmetry_symbol = wanted_symmetry_symbol.Trim(false); if (wanted_symmetry_symbol.Length() < 1) { MyPrintWithDetails("Error: Must specify symmetry symbol\n"); DEBUG_ABORT; } symmetry_type = wanted_symmetry_symbol.Capitalize()[0]; if (wanted_symmetry_symbol.Length() == 1) { symmetry_number = 0; } else { if (! wanted_symmetry_symbol.Mid(1).ToLong(&symmetry_number)) { MyPrintWithDetails("Error: Invalid n after symmetry symbol: %s\n", wanted_symmetry_symbol.Mid(1)); DEBUG_ABORT; } } symmetry_symbol = wanted_symmetry_symbol; if (symmetry_type == 'C') { int i; float angle; float delta_angle; if (symmetry_number == 0) { MyPrintWithDetails("Error: Invalid n after symmetry symbol\n"); DEBUG_ABORT; } number_of_matrices = symmetry_number; if (rot_mat != NULL) { delete [] rot_mat; } rot_mat = new RotationMatrix[number_of_matrices]; // wxPrintf("Initializing Cn symmetry matrices with n = %i\n",number_of_matrices); delta_angle = 2.0 * PI / number_of_matrices; for (i = 0; i < number_of_matrices; i++) { angle = i * delta_angle; rot_mat[i].SetToValues(cosf(angle), sinf(angle), 0.000000,-sinf(angle), cosf(angle), 0.000000, 0.000000, 0.000000, 1.000000); } return; } if (symmetry_type == 'D') { int i; float angle; float delta_angle; if (symmetry_number == 0) { MyPrintWithDetails("Error: Invalid n after symmetry symbol\n"); DEBUG_ABORT; } number_of_matrices = symmetry_number; if (rot_mat != NULL) { delete [] rot_mat; } rot_mat = new RotationMatrix[2 * number_of_matrices]; // wxPrintf("Initializing Dn symmetry matrices with n = %i\n",number_of_matrices); delta_angle = 2.0 * PI / number_of_matrices; for (i = 0; i < number_of_matrices; i++) { angle = i * delta_angle; rot_mat[i].SetToValues(cosf(angle), sinf(angle), 0.000000,-sinf(angle), cosf(angle), 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[i + number_of_matrices].SetToValues(cosf(angle),-sinf(angle), 0.000000,-sinf(angle),-cosf(angle), 0.000000, 0.000000, 0.000000,-1.000000); } number_of_matrices = 2 * number_of_matrices; return; } if (symmetry_type == 'T') { // wxPrintf("Initializing T symmetry matrices...\n"); number_of_matrices = 12; if (rot_mat != NULL) { delete [] rot_mat; } rot_mat = new RotationMatrix[number_of_matrices]; if (symmetry_number < 2) { rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues( 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[ 2].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000); rot_mat[ 3].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 4].SetToValues( 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[ 5].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 6].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[ 7].SetToValues( 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[ 8].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 9].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[10].SetToValues( 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[11].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000); /* rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 2].SetToValues( 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[ 3].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 4].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 5].SetToValues( 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[ 6].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[ 7].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000); rot_mat[ 8].SetToValues( 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[ 9].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[10].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000); rot_mat[11].SetToValues( 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); */ return; } // Use octahedral conventions according to Relion. if (symmetry_number == 2) { rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues(-0.500005,-0.288678,-0.816495, 0.288671, 0.833331,-0.471411, 0.816493,-0.471410,-0.333332); rot_mat[ 2].SetToValues( 0.500005,-0.288678,-0.816495,-0.866021,-0.166669,-0.471411, 0.000007, 0.942809,-0.333332); rot_mat[ 3].SetToValues( 0.000000, 0.577356,-0.816495, 0.577350,-0.666662,-0.471411,-0.816500,-0.471399,-0.333332); rot_mat[ 4].SetToValues( 0.500000, 0.288675, 0.816500, 0.866028,-0.166665,-0.471400,-0.000006, 0.942810,-0.333330); rot_mat[ 5].SetToValues(-0.500000, 0.288675, 0.816500,-0.288678, 0.833335,-0.471400,-0.816494,-0.471410,-0.333330); rot_mat[ 6].SetToValues( 0.000000,-0.577350, 0.816500,-0.577350,-0.666670,-0.471400, 0.816500,-0.471400,-0.333330); rot_mat[ 7].SetToValues( 0.500000,-0.866025, 0.000000,-0.288672,-0.166665, 0.942810,-0.816497,-0.471405,-0.333330); rot_mat[ 8].SetToValues( 0.500000, 0.866025, 0.000000, 0.288672,-0.166665, 0.942810, 0.816497,-0.471405,-0.333330); rot_mat[ 9].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 0.333330, 0.942810, 0.000000, 0.942810,-0.333330); rot_mat[10].SetToValues(-0.500000, 0.866025, 0.000000,-0.866025,-0.500000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[11].SetToValues(-0.500000,-0.866025, 0.000000, 0.866025,-0.500000, 0.000000, 0.000000, 0.000000, 1.000000); return; } } if (symmetry_type == 'O') { // wxPrintf("Initializing O symmetry matrices...\n"); number_of_matrices = 24; if (rot_mat != NULL) { delete [] rot_mat; } rot_mat = new RotationMatrix[number_of_matrices]; rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues( 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[ 2].SetToValues( 0.000000, 0.000000,-1.000000, 0.000000,-1.000000, 0.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 3].SetToValues( 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[ 4].SetToValues( 0.000000, 0.000000,-1.000000, 0.000000, 1.000000, 0.000000, 1.000000, 0.000000, 0.000000); rot_mat[ 5].SetToValues( 0.000000, 0.000000, 1.000000, 0.000000, 1.000000, 0.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 6].SetToValues( 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[ 7].SetToValues( 0.000000, 0.000000, 1.000000, 0.000000,-1.000000, 0.000000, 1.000000, 0.000000, 0.000000); rot_mat[ 8].SetToValues( 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[ 9].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000); rot_mat[10].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000,-1.000000, 0.000000); rot_mat[11].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000); rot_mat[12].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 1.000000, 0.000000); rot_mat[13].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 1.000000, 0.000000); rot_mat[14].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000); rot_mat[15].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000,-1.000000, 0.000000); rot_mat[16].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000); rot_mat[17].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[18].SetToValues( 0.000000,-1.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[19].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[20].SetToValues( 0.000000, 1.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[21].SetToValues( 0.000000, 1.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[22].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[23].SetToValues( 0.000000,-1.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000); /* rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 2].SetToValues( 0.000000, 0.000000,-1.000000, 0.000000,-1.000000, 0.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 3].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 4].SetToValues( 0.000000, 0.000000, 1.000000, 0.000000, 1.000000, 0.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 5].SetToValues( 0.000000, 0.000000,-1.000000, 0.000000, 1.000000, 0.000000, 1.000000, 0.000000, 0.000000); rot_mat[ 6].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000); rot_mat[ 7].SetToValues( 0.000000, 0.000000, 1.000000, 0.000000,-1.000000, 0.000000, 1.000000, 0.000000, 0.000000); rot_mat[ 8].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000); rot_mat[ 9].SetToValues( 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[10].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000,-1.000000, 0.000000); rot_mat[11].SetToValues( 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[12].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000,-1.000000, 0.000000); rot_mat[13].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 1.000000, 0.000000); rot_mat[14].SetToValues( 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[15].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 1.000000, 0.000000); rot_mat[16].SetToValues( 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[17].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[18].SetToValues( 0.000000,-1.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[19].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[20].SetToValues( 0.000000, 1.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[21].SetToValues( 0.000000,-1.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[22].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[23].SetToValues( 0.000000, 1.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000); */ return; } if (symmetry_type == 'I') { // wxPrintf("Initializing I symmetry matrices...\n"); number_of_matrices = 60; if (rot_mat != NULL) { delete [] rot_mat; } rot_mat = new RotationMatrix[number_of_matrices]; if (symmetry_number < 2) { rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues(-0.500000,-0.309017,-0.809017,-0.309017,-0.809017, 0.500000,-0.809017, 0.500000, 0.309017); rot_mat[ 2].SetToValues(-0.309017,-0.809017,-0.500000, 0.809017,-0.500000, 0.309017,-0.500000,-0.309017, 0.809017); rot_mat[ 3].SetToValues( 0.309017,-0.809017,-0.500000, 0.809017, 0.500000,-0.309017, 0.500000,-0.309017, 0.809017); rot_mat[ 4].SetToValues( 0.500000,-0.309017,-0.809017,-0.309017, 0.809017,-0.500000, 0.809017, 0.500000, 0.309017); rot_mat[ 5].SetToValues( 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[ 6].SetToValues( 0.809017,-0.500000,-0.309017,-0.500000,-0.309017,-0.809017, 0.309017, 0.809017,-0.500000); rot_mat[ 7].SetToValues( 0.500000, 0.309017,-0.809017,-0.309017,-0.809017,-0.500000,-0.809017, 0.500000,-0.309017); rot_mat[ 8].SetToValues(-0.500000, 0.309017,-0.809017, 0.309017,-0.809017,-0.500000,-0.809017,-0.500000, 0.309017); rot_mat[ 9].SetToValues(-0.809017,-0.500000,-0.309017, 0.500000,-0.309017,-0.809017, 0.309017,-0.809017, 0.500000); rot_mat[10].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000); rot_mat[11].SetToValues(-0.309017,-0.809017, 0.500000, 0.809017,-0.500000,-0.309017, 0.500000, 0.309017, 0.809017); rot_mat[12].SetToValues( 0.809017,-0.500000, 0.309017, 0.500000, 0.309017,-0.809017, 0.309017, 0.809017, 0.500000); rot_mat[13].SetToValues( 0.809017, 0.500000,-0.309017,-0.500000, 0.309017,-0.809017,-0.309017, 0.809017, 0.500000); rot_mat[14].SetToValues(-0.309017, 0.809017,-0.500000,-0.809017,-0.500000,-0.309017,-0.500000, 0.309017, 0.809017); rot_mat[15].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[16].SetToValues(-0.500000,-0.309017,-0.809017, 0.309017, 0.809017,-0.500000, 0.809017,-0.500000,-0.309017); rot_mat[17].SetToValues(-0.309017,-0.809017,-0.500000,-0.809017, 0.500000,-0.309017, 0.500000, 0.309017,-0.809017); rot_mat[18].SetToValues( 0.309017,-0.809017,-0.500000,-0.809017,-0.500000, 0.309017,-0.500000, 0.309017,-0.809017); rot_mat[19].SetToValues( 0.500000,-0.309017,-0.809017, 0.309017,-0.809017, 0.500000,-0.809017,-0.500000,-0.309017); rot_mat[20].SetToValues( 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[21].SetToValues( 0.809017,-0.500000,-0.309017, 0.500000, 0.309017, 0.809017,-0.309017,-0.809017, 0.500000); rot_mat[22].SetToValues( 0.500000, 0.309017,-0.809017, 0.309017, 0.809017, 0.500000, 0.809017,-0.500000, 0.309017); rot_mat[23].SetToValues(-0.500000, 0.309017,-0.809017,-0.309017, 0.809017, 0.500000, 0.809017, 0.500000,-0.309017); rot_mat[24].SetToValues(-0.809017,-0.500000,-0.309017,-0.500000, 0.309017, 0.809017,-0.309017, 0.809017,-0.500000); rot_mat[25].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000); rot_mat[26].SetToValues(-0.309017,-0.809017, 0.500000,-0.809017, 0.500000, 0.309017,-0.500000,-0.309017,-0.809017); rot_mat[27].SetToValues( 0.809017,-0.500000, 0.309017,-0.500000,-0.309017, 0.809017,-0.309017,-0.809017,-0.500000); rot_mat[28].SetToValues( 0.809017, 0.500000,-0.309017, 0.500000,-0.309017, 0.809017, 0.309017,-0.809017,-0.500000); rot_mat[29].SetToValues(-0.309017, 0.809017,-0.500000, 0.809017, 0.500000, 0.309017, 0.500000,-0.309017,-0.809017); rot_mat[30].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[31].SetToValues( 0.500000, 0.309017, 0.809017,-0.309017,-0.809017, 0.500000, 0.809017,-0.500000,-0.309017); rot_mat[32].SetToValues( 0.309017, 0.809017, 0.500000, 0.809017,-0.500000, 0.309017, 0.500000, 0.309017,-0.809017); rot_mat[33].SetToValues(-0.309017, 0.809017, 0.500000, 0.809017, 0.500000,-0.309017,-0.500000, 0.309017,-0.809017); rot_mat[34].SetToValues(-0.500000, 0.309017, 0.809017,-0.309017, 0.809017,-0.500000,-0.809017,-0.500000,-0.309017); rot_mat[35].SetToValues( 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[36].SetToValues(-0.809017, 0.500000, 0.309017,-0.500000,-0.309017,-0.809017,-0.309017,-0.809017, 0.500000); rot_mat[37].SetToValues(-0.500000,-0.309017, 0.809017,-0.309017,-0.809017,-0.500000, 0.809017,-0.500000, 0.309017); rot_mat[38].SetToValues( 0.500000,-0.309017, 0.809017, 0.309017,-0.809017,-0.500000, 0.809017, 0.500000,-0.309017); rot_mat[39].SetToValues( 0.809017, 0.500000, 0.309017, 0.500000,-0.309017,-0.809017,-0.309017, 0.809017,-0.500000); rot_mat[40].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000); rot_mat[41].SetToValues( 0.309017, 0.809017,-0.500000, 0.809017,-0.500000,-0.309017,-0.500000,-0.309017,-0.809017); rot_mat[42].SetToValues(-0.809017, 0.500000,-0.309017, 0.500000, 0.309017,-0.809017,-0.309017,-0.809017,-0.500000); rot_mat[43].SetToValues(-0.809017,-0.500000, 0.309017,-0.500000, 0.309017,-0.809017, 0.309017,-0.809017,-0.500000); rot_mat[44].SetToValues( 0.309017,-0.809017, 0.500000,-0.809017,-0.500000,-0.309017, 0.500000,-0.309017,-0.809017); rot_mat[45].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[46].SetToValues( 0.500000, 0.309017, 0.809017, 0.309017, 0.809017,-0.500000,-0.809017, 0.500000, 0.309017); rot_mat[47].SetToValues( 0.309017, 0.809017, 0.500000,-0.809017, 0.500000,-0.309017,-0.500000,-0.309017, 0.809017); rot_mat[48].SetToValues(-0.309017, 0.809017, 0.500000,-0.809017,-0.500000, 0.309017, 0.500000,-0.309017, 0.809017); rot_mat[49].SetToValues(-0.500000, 0.309017, 0.809017, 0.309017,-0.809017, 0.500000, 0.809017, 0.500000, 0.309017); rot_mat[50].SetToValues( 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[51].SetToValues(-0.809017, 0.500000, 0.309017, 0.500000, 0.309017, 0.809017, 0.309017, 0.809017,-0.500000); rot_mat[52].SetToValues(-0.500000,-0.309017, 0.809017, 0.309017, 0.809017, 0.500000,-0.809017, 0.500000,-0.309017); rot_mat[53].SetToValues( 0.500000,-0.309017, 0.809017,-0.309017, 0.809017, 0.500000,-0.809017,-0.500000, 0.309017); rot_mat[54].SetToValues( 0.809017, 0.500000, 0.309017,-0.500000, 0.309017, 0.809017, 0.309017,-0.809017, 0.500000); rot_mat[55].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000); rot_mat[56].SetToValues( 0.309017, 0.809017,-0.500000,-0.809017, 0.500000, 0.309017, 0.500000, 0.309017, 0.809017); rot_mat[57].SetToValues(-0.809017, 0.500000,-0.309017,-0.500000,-0.309017, 0.809017, 0.309017, 0.809017, 0.500000); rot_mat[58].SetToValues(-0.809017,-0.500000, 0.309017, 0.500000,-0.309017, 0.809017,-0.309017, 0.809017, 0.500000); rot_mat[59].SetToValues( 0.309017,-0.809017, 0.500000, 0.809017, 0.500000, 0.309017,-0.500000, 0.309017, 0.809017); /* rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues(-0.500000,-0.309017,-0.809017,-0.309017,-0.809017, 0.500000,-0.809017, 0.500000, 0.309017); rot_mat[ 2].SetToValues(-0.309017, 0.809017,-0.500000,-0.809017,-0.500000,-0.309017,-0.500000, 0.309017, 0.809017); rot_mat[ 3].SetToValues( 0.309017, 0.809017, 0.500000,-0.809017, 0.500000,-0.309017,-0.500000,-0.309017, 0.809017); rot_mat[ 4].SetToValues( 0.500000,-0.309017, 0.809017,-0.309017, 0.809017, 0.500000,-0.809017,-0.500000, 0.309017); rot_mat[ 5].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 6].SetToValues( 0.809017,-0.500000, 0.309017,-0.500000,-0.309017, 0.809017,-0.309017,-0.809017,-0.500000); rot_mat[ 7].SetToValues( 0.500000,-0.309017,-0.809017, 0.309017,-0.809017, 0.500000,-0.809017,-0.500000,-0.309017); rot_mat[ 8].SetToValues(-0.500000, 0.309017,-0.809017, 0.309017,-0.809017,-0.500000,-0.809017,-0.500000, 0.309017); rot_mat[ 9].SetToValues(-0.809017, 0.500000, 0.309017,-0.500000,-0.309017,-0.809017,-0.309017,-0.809017, 0.500000); rot_mat[10].SetToValues( 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[11].SetToValues(-0.309017, 0.809017, 0.500000,-0.809017,-0.500000, 0.309017, 0.500000,-0.309017, 0.809017); rot_mat[12].SetToValues( 0.809017, 0.500000, 0.309017,-0.500000, 0.309017, 0.809017, 0.309017,-0.809017, 0.500000); rot_mat[13].SetToValues( 0.809017,-0.500000,-0.309017, 0.500000, 0.309017, 0.809017,-0.309017,-0.809017, 0.500000); rot_mat[14].SetToValues(-0.309017,-0.809017,-0.500000, 0.809017,-0.500000, 0.309017,-0.500000,-0.309017, 0.809017); rot_mat[15].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[16].SetToValues(-0.500000, 0.309017, 0.809017,-0.309017, 0.809017,-0.500000,-0.809017,-0.500000,-0.309017); rot_mat[17].SetToValues(-0.309017,-0.809017, 0.500000,-0.809017, 0.500000, 0.309017,-0.500000,-0.309017,-0.809017); rot_mat[18].SetToValues( 0.309017,-0.809017,-0.500000,-0.809017,-0.500000, 0.309017,-0.500000, 0.309017,-0.809017); rot_mat[19].SetToValues( 0.500000, 0.309017,-0.809017,-0.309017,-0.809017,-0.500000,-0.809017, 0.500000,-0.309017); rot_mat[20].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000); rot_mat[21].SetToValues( 0.809017, 0.500000,-0.309017,-0.500000, 0.309017,-0.809017,-0.309017, 0.809017, 0.500000); rot_mat[22].SetToValues( 0.500000, 0.309017, 0.809017, 0.309017, 0.809017,-0.500000,-0.809017, 0.500000, 0.309017); rot_mat[23].SetToValues(-0.500000,-0.309017, 0.809017, 0.309017, 0.809017, 0.500000,-0.809017, 0.500000,-0.309017); rot_mat[24].SetToValues(-0.809017,-0.500000,-0.309017,-0.500000, 0.309017, 0.809017,-0.309017, 0.809017,-0.500000); rot_mat[25].SetToValues( 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[26].SetToValues(-0.309017,-0.809017,-0.500000,-0.809017, 0.500000,-0.309017, 0.500000, 0.309017,-0.809017); rot_mat[27].SetToValues( 0.809017,-0.500000,-0.309017,-0.500000,-0.309017,-0.809017, 0.309017, 0.809017,-0.500000); rot_mat[28].SetToValues( 0.809017, 0.500000, 0.309017, 0.500000,-0.309017,-0.809017,-0.309017, 0.809017,-0.500000); rot_mat[29].SetToValues(-0.309017, 0.809017, 0.500000, 0.809017, 0.500000,-0.309017,-0.500000, 0.309017,-0.809017); rot_mat[30].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[31].SetToValues( 0.500000,-0.309017, 0.809017, 0.309017,-0.809017,-0.500000, 0.809017, 0.500000,-0.309017); rot_mat[32].SetToValues( 0.309017, 0.809017, 0.500000, 0.809017,-0.500000, 0.309017, 0.500000, 0.309017,-0.809017); rot_mat[33].SetToValues(-0.309017, 0.809017,-0.500000, 0.809017, 0.500000, 0.309017, 0.500000,-0.309017,-0.809017); rot_mat[34].SetToValues(-0.500000,-0.309017,-0.809017, 0.309017, 0.809017,-0.500000, 0.809017,-0.500000,-0.309017); rot_mat[35].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000); rot_mat[36].SetToValues(-0.809017,-0.500000,-0.309017, 0.500000,-0.309017,-0.809017, 0.309017,-0.809017, 0.500000); rot_mat[37].SetToValues(-0.500000,-0.309017, 0.809017,-0.309017,-0.809017,-0.500000, 0.809017,-0.500000, 0.309017); rot_mat[38].SetToValues( 0.500000, 0.309017, 0.809017,-0.309017,-0.809017, 0.500000, 0.809017,-0.500000,-0.309017); rot_mat[39].SetToValues( 0.809017, 0.500000,-0.309017, 0.500000,-0.309017, 0.809017, 0.309017,-0.809017,-0.500000); rot_mat[40].SetToValues( 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[41].SetToValues( 0.309017, 0.809017,-0.500000, 0.809017,-0.500000,-0.309017,-0.500000,-0.309017,-0.809017); rot_mat[42].SetToValues(-0.809017, 0.500000,-0.309017, 0.500000, 0.309017,-0.809017,-0.309017,-0.809017,-0.500000); rot_mat[43].SetToValues(-0.809017,-0.500000, 0.309017,-0.500000, 0.309017,-0.809017, 0.309017,-0.809017,-0.500000); rot_mat[44].SetToValues( 0.309017,-0.809017, 0.500000,-0.809017,-0.500000,-0.309017, 0.500000,-0.309017,-0.809017); rot_mat[45].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[46].SetToValues( 0.500000, 0.309017,-0.809017, 0.309017, 0.809017, 0.500000, 0.809017,-0.500000, 0.309017); rot_mat[47].SetToValues( 0.309017,-0.809017,-0.500000, 0.809017, 0.500000,-0.309017, 0.500000,-0.309017, 0.809017); rot_mat[48].SetToValues(-0.309017,-0.809017, 0.500000, 0.809017,-0.500000,-0.309017, 0.500000, 0.309017, 0.809017); rot_mat[49].SetToValues(-0.500000, 0.309017, 0.809017, 0.309017,-0.809017, 0.500000, 0.809017, 0.500000, 0.309017); rot_mat[50].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000); rot_mat[51].SetToValues(-0.809017, 0.500000, 0.309017, 0.500000, 0.309017, 0.809017, 0.309017, 0.809017,-0.500000); rot_mat[52].SetToValues(-0.500000, 0.309017,-0.809017,-0.309017, 0.809017, 0.500000, 0.809017, 0.500000,-0.309017); rot_mat[53].SetToValues( 0.500000,-0.309017,-0.809017,-0.309017, 0.809017,-0.500000, 0.809017, 0.500000, 0.309017); rot_mat[54].SetToValues( 0.809017,-0.500000, 0.309017, 0.500000, 0.309017,-0.809017, 0.309017, 0.809017, 0.500000); rot_mat[55].SetToValues( 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[56].SetToValues( 0.309017,-0.809017, 0.500000, 0.809017, 0.500000, 0.309017,-0.500000, 0.309017, 0.809017); rot_mat[57].SetToValues(-0.809017,-0.500000, 0.309017, 0.500000,-0.309017, 0.809017,-0.309017, 0.809017, 0.500000); rot_mat[58].SetToValues(-0.809017, 0.500000,-0.309017,-0.500000,-0.309017, 0.809017, 0.309017, 0.809017, 0.500000); rot_mat[59].SetToValues( 0.309017, 0.809017,-0.500000,-0.809017, 0.500000, 0.309017, 0.500000, 0.309017, 0.809017); */ return; } // Use icosahedral conventions according to Crowther et al. if (symmetry_number == 2) { rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues( 0.500000,-0.809017,-0.309017,-0.809017,-0.309017,-0.500000, 0.309017, 0.500000,-0.809017); rot_mat[ 2].SetToValues( 0.309017,-0.500000, 0.809017,-0.500000,-0.809017,-0.309017, 0.809017,-0.309017,-0.500000); rot_mat[ 3].SetToValues(-0.309017, 0.500000, 0.809017,-0.500000,-0.809017, 0.309017, 0.809017,-0.309017, 0.500000); rot_mat[ 4].SetToValues(-0.500000, 0.809017,-0.309017,-0.809017,-0.309017, 0.500000, 0.309017, 0.500000, 0.809017); rot_mat[ 5].SetToValues( 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[ 6].SetToValues(-0.309017,-0.500000, 0.809017, 0.500000,-0.809017,-0.309017, 0.809017, 0.309017, 0.500000); rot_mat[ 7].SetToValues(-0.809017, 0.309017, 0.500000, 0.309017,-0.500000, 0.809017, 0.500000, 0.809017, 0.309017); rot_mat[ 8].SetToValues(-0.809017, 0.309017,-0.500000,-0.309017, 0.500000, 0.809017, 0.500000, 0.809017,-0.309017); rot_mat[ 9].SetToValues(-0.309017,-0.500000,-0.809017,-0.500000, 0.809017,-0.309017, 0.809017, 0.309017,-0.500000); rot_mat[10].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000); rot_mat[11].SetToValues(-0.809017,-0.309017,-0.500000,-0.309017,-0.500000, 0.809017,-0.500000, 0.809017, 0.309017); rot_mat[12].SetToValues(-0.500000,-0.809017,-0.309017,-0.809017, 0.309017, 0.500000,-0.309017, 0.500000,-0.809017); rot_mat[13].SetToValues(-0.500000,-0.809017, 0.309017,-0.809017, 0.309017,-0.500000, 0.309017,-0.500000,-0.809017); rot_mat[14].SetToValues(-0.809017,-0.309017, 0.500000,-0.309017,-0.500000,-0.809017, 0.500000,-0.809017, 0.309017); rot_mat[15].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[16].SetToValues( 0.500000,-0.809017,-0.309017, 0.809017, 0.309017, 0.500000,-0.309017,-0.500000, 0.809017); rot_mat[17].SetToValues( 0.309017,-0.500000, 0.809017, 0.500000, 0.809017, 0.309017,-0.809017, 0.309017, 0.500000); rot_mat[18].SetToValues(-0.309017, 0.500000, 0.809017, 0.500000, 0.809017,-0.309017,-0.809017, 0.309017,-0.500000); rot_mat[19].SetToValues(-0.500000, 0.809017,-0.309017, 0.809017, 0.309017,-0.500000,-0.309017,-0.500000,-0.809017); rot_mat[20].SetToValues( 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[21].SetToValues(-0.309017,-0.500000, 0.809017,-0.500000, 0.809017, 0.309017,-0.809017,-0.309017,-0.500000); rot_mat[22].SetToValues(-0.809017, 0.309017, 0.500000,-0.309017, 0.500000,-0.809017,-0.500000,-0.809017,-0.309017); rot_mat[23].SetToValues(-0.809017, 0.309017,-0.500000, 0.309017,-0.500000,-0.809017,-0.500000,-0.809017, 0.309017); rot_mat[24].SetToValues(-0.309017,-0.500000,-0.809017, 0.500000,-0.809017, 0.309017,-0.809017,-0.309017, 0.500000); rot_mat[25].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000); rot_mat[26].SetToValues(-0.809017,-0.309017,-0.500000, 0.309017, 0.500000,-0.809017, 0.500000,-0.809017,-0.309017); rot_mat[27].SetToValues(-0.500000,-0.809017,-0.309017, 0.809017,-0.309017,-0.500000, 0.309017,-0.500000, 0.809017); rot_mat[28].SetToValues(-0.500000,-0.809017, 0.309017, 0.809017,-0.309017, 0.500000,-0.309017, 0.500000, 0.809017); rot_mat[29].SetToValues(-0.809017,-0.309017, 0.500000, 0.309017, 0.500000, 0.809017,-0.500000, 0.809017,-0.309017); rot_mat[30].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[31].SetToValues(-0.500000, 0.809017, 0.309017,-0.809017,-0.309017,-0.500000,-0.309017,-0.500000, 0.809017); rot_mat[32].SetToValues(-0.309017, 0.500000,-0.809017,-0.500000,-0.809017,-0.309017,-0.809017, 0.309017, 0.500000); rot_mat[33].SetToValues( 0.309017,-0.500000,-0.809017,-0.500000,-0.809017, 0.309017,-0.809017, 0.309017,-0.500000); rot_mat[34].SetToValues( 0.500000,-0.809017, 0.309017,-0.809017,-0.309017, 0.500000,-0.309017,-0.500000,-0.809017); rot_mat[35].SetToValues( 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[36].SetToValues( 0.309017, 0.500000,-0.809017, 0.500000,-0.809017,-0.309017,-0.809017,-0.309017,-0.500000); rot_mat[37].SetToValues( 0.809017,-0.309017,-0.500000, 0.309017,-0.500000, 0.809017,-0.500000,-0.809017,-0.309017); rot_mat[38].SetToValues( 0.809017,-0.309017, 0.500000,-0.309017, 0.500000, 0.809017,-0.500000,-0.809017, 0.309017); rot_mat[39].SetToValues( 0.309017, 0.500000, 0.809017,-0.500000, 0.809017,-0.309017,-0.809017,-0.309017, 0.500000); rot_mat[40].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000); rot_mat[41].SetToValues( 0.809017, 0.309017, 0.500000,-0.309017,-0.500000, 0.809017, 0.500000,-0.809017,-0.309017); rot_mat[42].SetToValues( 0.500000, 0.809017, 0.309017,-0.809017, 0.309017, 0.500000, 0.309017,-0.500000, 0.809017); rot_mat[43].SetToValues( 0.500000, 0.809017,-0.309017,-0.809017, 0.309017,-0.500000,-0.309017, 0.500000, 0.809017); rot_mat[44].SetToValues( 0.809017, 0.309017,-0.500000,-0.309017,-0.500000,-0.809017,-0.500000, 0.809017,-0.309017); rot_mat[45].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[46].SetToValues(-0.500000, 0.809017, 0.309017, 0.809017, 0.309017, 0.500000, 0.309017, 0.500000,-0.809017); rot_mat[47].SetToValues(-0.309017, 0.500000,-0.809017, 0.500000, 0.809017, 0.309017, 0.809017,-0.309017,-0.500000); rot_mat[48].SetToValues( 0.309017,-0.500000,-0.809017, 0.500000, 0.809017,-0.309017, 0.809017,-0.309017, 0.500000); rot_mat[49].SetToValues( 0.500000,-0.809017, 0.309017, 0.809017, 0.309017,-0.500000, 0.309017, 0.500000, 0.809017); rot_mat[50].SetToValues( 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[51].SetToValues( 0.309017, 0.500000,-0.809017,-0.500000, 0.809017, 0.309017, 0.809017, 0.309017, 0.500000); rot_mat[52].SetToValues( 0.809017,-0.309017,-0.500000,-0.309017, 0.500000,-0.809017, 0.500000, 0.809017, 0.309017); rot_mat[53].SetToValues( 0.809017,-0.309017, 0.500000, 0.309017,-0.500000,-0.809017, 0.500000, 0.809017,-0.309017); rot_mat[54].SetToValues( 0.309017, 0.500000, 0.809017, 0.500000,-0.809017, 0.309017, 0.809017, 0.309017,-0.500000); rot_mat[55].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000); rot_mat[56].SetToValues( 0.809017, 0.309017, 0.500000, 0.309017, 0.500000,-0.809017,-0.500000, 0.809017, 0.309017); rot_mat[57].SetToValues( 0.500000, 0.809017, 0.309017, 0.809017,-0.309017,-0.500000,-0.309017, 0.500000,-0.809017); rot_mat[58].SetToValues( 0.500000, 0.809017,-0.309017, 0.809017,-0.309017, 0.500000, 0.309017,-0.500000,-0.809017); rot_mat[59].SetToValues( 0.809017, 0.309017,-0.500000, 0.309017, 0.500000, 0.809017, 0.500000,-0.809017, 0.309017); /* rot_mat[ 0].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[ 1].SetToValues( 0.500000,-0.809017, 0.309017,-0.809017,-0.309017, 0.500000,-0.309017,-0.500000,-0.809017); rot_mat[ 2].SetToValues( 0.309017,-0.500000, 0.809017,-0.500000,-0.809017,-0.309017, 0.809017,-0.309017,-0.500000); rot_mat[ 3].SetToValues(-0.309017,-0.500000, 0.809017, 0.500000,-0.809017,-0.309017, 0.809017, 0.309017, 0.500000); rot_mat[ 4].SetToValues(-0.500000,-0.809017, 0.309017, 0.809017,-0.309017, 0.500000,-0.309017, 0.500000, 0.809017); rot_mat[ 5].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000); rot_mat[ 6].SetToValues(-0.309017, 0.500000, 0.809017,-0.500000,-0.809017, 0.309017, 0.809017,-0.309017, 0.500000); rot_mat[ 7].SetToValues(-0.809017, 0.309017, 0.500000, 0.309017,-0.500000, 0.809017, 0.500000, 0.809017, 0.309017); rot_mat[ 8].SetToValues(-0.809017,-0.309017, 0.500000, 0.309017, 0.500000, 0.809017,-0.500000, 0.809017,-0.309017); rot_mat[ 9].SetToValues(-0.309017,-0.500000, 0.809017,-0.500000, 0.809017, 0.309017,-0.809017,-0.309017,-0.500000); rot_mat[10].SetToValues( 0.000000, 0.000000, 1.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[11].SetToValues(-0.809017,-0.309017,-0.500000,-0.309017,-0.500000, 0.809017,-0.500000, 0.809017, 0.309017); rot_mat[12].SetToValues(-0.500000,-0.809017,-0.309017,-0.809017, 0.309017, 0.500000,-0.309017, 0.500000,-0.809017); rot_mat[13].SetToValues(-0.500000,-0.809017, 0.309017,-0.809017, 0.309017,-0.500000, 0.309017,-0.500000,-0.809017); rot_mat[14].SetToValues(-0.809017,-0.309017, 0.500000,-0.309017,-0.500000,-0.809017, 0.500000,-0.809017, 0.309017); rot_mat[15].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000); rot_mat[16].SetToValues( 0.500000, 0.809017,-0.309017,-0.809017, 0.309017,-0.500000,-0.309017, 0.500000, 0.809017); rot_mat[17].SetToValues( 0.309017, 0.500000,-0.809017,-0.500000, 0.809017, 0.309017, 0.809017, 0.309017, 0.500000); rot_mat[18].SetToValues(-0.309017, 0.500000,-0.809017, 0.500000, 0.809017, 0.309017, 0.809017,-0.309017,-0.500000); rot_mat[19].SetToValues(-0.500000, 0.809017,-0.309017, 0.809017, 0.309017,-0.500000,-0.309017,-0.500000,-0.809017); rot_mat[20].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000); rot_mat[21].SetToValues(-0.309017,-0.500000,-0.809017,-0.500000, 0.809017,-0.309017, 0.809017, 0.309017,-0.500000); rot_mat[22].SetToValues(-0.809017,-0.309017,-0.500000, 0.309017, 0.500000,-0.809017, 0.500000,-0.809017,-0.309017); rot_mat[23].SetToValues(-0.809017, 0.309017,-0.500000, 0.309017,-0.500000,-0.809017,-0.500000,-0.809017, 0.309017); rot_mat[24].SetToValues(-0.309017, 0.500000,-0.809017,-0.500000,-0.809017,-0.309017,-0.809017, 0.309017, 0.500000); rot_mat[25].SetToValues( 0.000000, 0.000000,-1.000000,-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[26].SetToValues(-0.809017, 0.309017, 0.500000,-0.309017, 0.500000,-0.809017,-0.500000,-0.809017,-0.309017); rot_mat[27].SetToValues(-0.500000, 0.809017, 0.309017,-0.809017,-0.309017,-0.500000,-0.309017,-0.500000, 0.809017); rot_mat[28].SetToValues(-0.500000, 0.809017,-0.309017,-0.809017,-0.309017, 0.500000, 0.309017, 0.500000, 0.809017); rot_mat[29].SetToValues(-0.809017, 0.309017,-0.500000,-0.309017, 0.500000, 0.809017, 0.500000, 0.809017,-0.309017); rot_mat[30].SetToValues(-1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[31].SetToValues(-0.500000,-0.809017,-0.309017, 0.809017,-0.309017,-0.500000, 0.309017,-0.500000, 0.809017); rot_mat[32].SetToValues(-0.309017,-0.500000,-0.809017, 0.500000,-0.809017, 0.309017,-0.809017,-0.309017, 0.500000); rot_mat[33].SetToValues( 0.309017,-0.500000,-0.809017,-0.500000,-0.809017, 0.309017,-0.809017, 0.309017,-0.500000); rot_mat[34].SetToValues( 0.500000,-0.809017,-0.309017,-0.809017,-0.309017,-0.500000, 0.309017, 0.500000,-0.809017); rot_mat[35].SetToValues( 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000); rot_mat[36].SetToValues( 0.309017, 0.500000,-0.809017, 0.500000,-0.809017,-0.309017,-0.809017,-0.309017,-0.500000); rot_mat[37].SetToValues( 0.809017, 0.309017,-0.500000,-0.309017,-0.500000,-0.809017,-0.500000, 0.809017,-0.309017); rot_mat[38].SetToValues( 0.809017,-0.309017,-0.500000,-0.309017, 0.500000,-0.809017, 0.500000, 0.809017, 0.309017); rot_mat[39].SetToValues( 0.309017,-0.500000,-0.809017, 0.500000, 0.809017,-0.309017, 0.809017,-0.309017, 0.500000); rot_mat[40].SetToValues( 0.000000, 0.000000,-1.000000, 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000); rot_mat[41].SetToValues( 0.809017,-0.309017, 0.500000, 0.309017,-0.500000,-0.809017, 0.500000, 0.809017,-0.309017); rot_mat[42].SetToValues( 0.500000,-0.809017, 0.309017, 0.809017, 0.309017,-0.500000, 0.309017, 0.500000, 0.809017); rot_mat[43].SetToValues( 0.500000,-0.809017,-0.309017, 0.809017, 0.309017, 0.500000,-0.309017,-0.500000, 0.809017); rot_mat[44].SetToValues( 0.809017,-0.309017,-0.500000, 0.309017,-0.500000, 0.809017,-0.500000,-0.809017,-0.309017); rot_mat[45].SetToValues( 1.000000, 0.000000, 0.000000, 0.000000,-1.000000, 0.000000, 0.000000, 0.000000,-1.000000); rot_mat[46].SetToValues(-0.500000, 0.809017, 0.309017, 0.809017, 0.309017, 0.500000, 0.309017, 0.500000,-0.809017); rot_mat[47].SetToValues(-0.309017, 0.500000, 0.809017, 0.500000, 0.809017,-0.309017,-0.809017, 0.309017,-0.500000); rot_mat[48].SetToValues( 0.309017, 0.500000, 0.809017,-0.500000, 0.809017,-0.309017,-0.809017,-0.309017, 0.500000); rot_mat[49].SetToValues( 0.500000, 0.809017, 0.309017,-0.809017, 0.309017, 0.500000, 0.309017,-0.500000, 0.809017); rot_mat[50].SetToValues( 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000); rot_mat[51].SetToValues( 0.309017,-0.500000, 0.809017, 0.500000, 0.809017, 0.309017,-0.809017, 0.309017, 0.500000); rot_mat[52].SetToValues( 0.809017,-0.309017, 0.500000,-0.309017, 0.500000, 0.809017,-0.500000,-0.809017, 0.309017); rot_mat[53].SetToValues( 0.809017, 0.309017, 0.500000,-0.309017,-0.500000, 0.809017, 0.500000,-0.809017,-0.309017); rot_mat[54].SetToValues( 0.309017, 0.500000, 0.809017, 0.500000,-0.809017, 0.309017, 0.809017, 0.309017,-0.500000); rot_mat[55].SetToValues( 0.000000, 0.000000, 1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000); rot_mat[56].SetToValues( 0.809017, 0.309017,-0.500000, 0.309017, 0.500000, 0.809017, 0.500000,-0.809017, 0.309017); rot_mat[57].SetToValues( 0.500000, 0.809017,-0.309017, 0.809017,-0.309017, 0.500000, 0.309017,-0.500000,-0.809017); rot_mat[58].SetToValues( 0.500000, 0.809017, 0.309017, 0.809017,-0.309017,-0.500000,-0.309017, 0.500000,-0.809017); rot_mat[59].SetToValues( 0.809017, 0.309017, 0.500000, 0.309017, 0.500000,-0.809017,-0.500000, 0.809017, 0.309017); */ return; } } MyPrintWithDetails("Error: Invalid symmetry symbol\n"); DEBUG_ABORT; } SymmetryMatrix::~SymmetryMatrix() { if (rot_mat != NULL) { delete [] rot_mat; } } void SymmetryMatrix::PrintMatrices() { MyDebugAssertTrue(rot_mat != NULL, "Symmetry matrices have not been calculated"); for (int i = 0; i < number_of_matrices; i++) { wxPrintf("\n%9.6f,%9.6f,%9.6f\n%9.6f,%9.6f,%9.6f\n%9.6f,%9.6f,%9.6f\n",rot_mat[i].m[0][0],rot_mat[i].m[1][0],rot_mat[i].m[2][0], rot_mat[i].m[0][1],rot_mat[i].m[1][1],rot_mat[i].m[2][1],rot_mat[i].m[0][2],rot_mat[i].m[1][2],rot_mat[i].m[2][2]); } } ctffind-4.1.14/src/core/symmetry_matrix.h000066400000000000000000000007121440356052600203700ustar00rootroot00000000000000/* \brief SymmetryMatrix class */ // Matrices generated using Frealign code, implemented in tool generate_symmetry_matrices.exe class SymmetryMatrix { public: wxString symmetry_symbol; int number_of_matrices; RotationMatrix *rot_mat; /* 3D rotation matrix array*/ SymmetryMatrix(); SymmetryMatrix(wxString wanted_symmetry_symbol); ~SymmetryMatrix(); void Init(wxString wanted_symmetry_symbol); void PrintMatrices(); }; ctffind-4.1.14/src/core/tiff/000077500000000000000000000000001440356052600156725ustar00rootroot00000000000000ctffind-4.1.14/src/core/tiff/tiff.h000066400000000000000000001062231440356052600167770ustar00rootroot00000000000000/* $Id: tiff.h,v 1.69 2014-04-02 17:23:06 fwarmerdam Exp $ */ /* * Copyright (c) 1988-1997 Sam Leffler * Copyright (c) 1991-1997 Silicon Graphics, Inc. * * Permission to use, copy, modify, distribute, and sell this software and * its documentation for any purpose is hereby granted without fee, provided * that (i) the above copyright notices and this permission notice appear in * all copies of the software and related documentation, and (ii) the names of * Sam Leffler and Silicon Graphics may not be used in any advertising or * publicity relating to the software without the specific, prior written * permission of Sam Leffler and Silicon Graphics. * * THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, * EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY * WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. * * IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR * ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, * OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, * WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF * LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE * OF THIS SOFTWARE. */ #ifndef _TIFF_ #define _TIFF_ #include "tiffconf.h" /* * Tag Image File Format (TIFF) * * Based on Rev 6.0 from: * Developer's Desk * Aldus Corporation * 411 First Ave. South * Suite 200 * Seattle, WA 98104 * 206-622-5500 * * (http://partners.adobe.com/asn/developer/PDFS/TN/TIFF6.pdf) * * For BigTIFF design notes see the following links * http://www.remotesensing.org/libtiff/bigtiffdesign.html * http://www.awaresystems.be/imaging/tiff/bigtiff.html */ #define TIFF_VERSION_CLASSIC 42 #define TIFF_VERSION_BIG 43 #define TIFF_BIGENDIAN 0x4d4d #define TIFF_LITTLEENDIAN 0x4949 #define MDI_LITTLEENDIAN 0x5045 #define MDI_BIGENDIAN 0x4550 /* * Intrinsic data types required by the file format: * * 8-bit quantities int8/uint8 * 16-bit quantities int16/uint16 * 32-bit quantities int32/uint32 * 64-bit quantities int64/uint64 * strings unsigned char* */ typedef TIFF_INT8_T int8; typedef TIFF_UINT8_T uint8; typedef TIFF_INT16_T int16; typedef TIFF_UINT16_T uint16; typedef TIFF_INT32_T int32; typedef TIFF_UINT32_T uint32; typedef TIFF_INT64_T int64; typedef TIFF_UINT64_T uint64; /* * Some types as promoted in a variable argument list * We use uint16_vap rather then directly using int, because this way * we document the type we actually want to pass through, conceptually, * rather then confusing the issue by merely stating the type it gets * promoted to */ typedef int uint16_vap; /* * TIFF header. */ typedef struct { uint16 tiff_magic; /* magic number (defines byte order) */ uint16 tiff_version; /* TIFF version number */ } TIFFHeaderCommon; typedef struct { uint16 tiff_magic; /* magic number (defines byte order) */ uint16 tiff_version; /* TIFF version number */ uint32 tiff_diroff; /* byte offset to first directory */ } TIFFHeaderClassic; typedef struct { uint16 tiff_magic; /* magic number (defines byte order) */ uint16 tiff_version; /* TIFF version number */ uint16 tiff_offsetsize; /* size of offsets, should be 8 */ uint16 tiff_unused; /* unused word, should be 0 */ uint64 tiff_diroff; /* byte offset to first directory */ } TIFFHeaderBig; /* * NB: In the comments below, * - items marked with a + are obsoleted by revision 5.0, * - items marked with a ! are introduced in revision 6.0. * - items marked with a % are introduced post revision 6.0. * - items marked with a $ are obsoleted by revision 6.0. * - items marked with a & are introduced by Adobe DNG specification. */ /* * Tag data type information. * * Note: RATIONALs are the ratio of two 32-bit integer values. */ typedef enum { TIFF_NOTYPE = 0, /* placeholder */ TIFF_BYTE = 1, /* 8-bit unsigned integer */ TIFF_ASCII = 2, /* 8-bit bytes w/ last byte null */ TIFF_SHORT = 3, /* 16-bit unsigned integer */ TIFF_LONG = 4, /* 32-bit unsigned integer */ TIFF_RATIONAL = 5, /* 64-bit unsigned fraction */ TIFF_SBYTE = 6, /* !8-bit signed integer */ TIFF_UNDEFINED = 7, /* !8-bit untyped data */ TIFF_SSHORT = 8, /* !16-bit signed integer */ TIFF_SLONG = 9, /* !32-bit signed integer */ TIFF_SRATIONAL = 10, /* !64-bit signed fraction */ TIFF_FLOAT = 11, /* !32-bit IEEE floating point */ TIFF_DOUBLE = 12, /* !64-bit IEEE floating point */ TIFF_IFD = 13, /* %32-bit unsigned integer (offset) */ TIFF_LONG8 = 16, /* BigTIFF 64-bit unsigned integer */ TIFF_SLONG8 = 17, /* BigTIFF 64-bit signed integer */ TIFF_IFD8 = 18 /* BigTIFF 64-bit unsigned integer (offset) */ } TIFFDataType; /* * TIFF Tag Definitions. */ #define TIFFTAG_SUBFILETYPE 254 /* subfile data descriptor */ #define FILETYPE_REDUCEDIMAGE 0x1 /* reduced resolution version */ #define FILETYPE_PAGE 0x2 /* one page of many */ #define FILETYPE_MASK 0x4 /* transparency mask */ #define TIFFTAG_OSUBFILETYPE 255 /* +kind of data in subfile */ #define OFILETYPE_IMAGE 1 /* full resolution image data */ #define OFILETYPE_REDUCEDIMAGE 2 /* reduced size image data */ #define OFILETYPE_PAGE 3 /* one page of many */ #define TIFFTAG_IMAGEWIDTH 256 /* image width in pixels */ #define TIFFTAG_IMAGELENGTH 257 /* image height in pixels */ #define TIFFTAG_BITSPERSAMPLE 258 /* bits per channel (sample) */ #define TIFFTAG_COMPRESSION 259 /* data compression technique */ #define COMPRESSION_NONE 1 /* dump mode */ #define COMPRESSION_CCITTRLE 2 /* CCITT modified Huffman RLE */ #define COMPRESSION_CCITTFAX3 3 /* CCITT Group 3 fax encoding */ #define COMPRESSION_CCITT_T4 3 /* CCITT T.4 (TIFF 6 name) */ #define COMPRESSION_CCITTFAX4 4 /* CCITT Group 4 fax encoding */ #define COMPRESSION_CCITT_T6 4 /* CCITT T.6 (TIFF 6 name) */ #define COMPRESSION_LZW 5 /* Lempel-Ziv & Welch */ #define COMPRESSION_OJPEG 6 /* !6.0 JPEG */ #define COMPRESSION_JPEG 7 /* %JPEG DCT compression */ #define COMPRESSION_T85 9 /* !TIFF/FX T.85 JBIG compression */ #define COMPRESSION_T43 10 /* !TIFF/FX T.43 colour by layered JBIG compression */ #define COMPRESSION_NEXT 32766 /* NeXT 2-bit RLE */ #define COMPRESSION_CCITTRLEW 32771 /* #1 w/ word alignment */ #define COMPRESSION_PACKBITS 32773 /* Macintosh RLE */ #define COMPRESSION_THUNDERSCAN 32809 /* ThunderScan RLE */ /* codes 32895-32898 are reserved for ANSI IT8 TIFF/IT */ #define COMPRESSION_DCS 32947 /* Kodak DCS encoding */ #define COMPRESSION_JBIG 34661 /* ISO JBIG */ #define COMPRESSION_SGILOG 34676 /* SGI Log Luminance RLE */ #define COMPRESSION_SGILOG24 34677 /* SGI Log 24-bit packed */ #define COMPRESSION_JP2000 34712 /* Leadtools JPEG2000 */ #define COMPRESSION_LZMA 34925 /* LZMA2 */ #define TIFFTAG_PHOTOMETRIC 262 /* photometric interpretation */ #define PHOTOMETRIC_MINISWHITE 0 /* min value is white */ #define PHOTOMETRIC_MINISBLACK 1 /* min value is black */ #define PHOTOMETRIC_RGB 2 /* RGB color model */ #define PHOTOMETRIC_PALETTE 3 /* color map indexed */ #define PHOTOMETRIC_MASK 4 /* $holdout mask */ #define PHOTOMETRIC_SEPARATED 5 /* !color separations */ #define PHOTOMETRIC_YCBCR 6 /* !CCIR 601 */ #define PHOTOMETRIC_CIELAB 8 /* !1976 CIE L*a*b* */ #define PHOTOMETRIC_ICCLAB 9 /* ICC L*a*b* [Adobe TIFF Technote 4] */ #define PHOTOMETRIC_ITULAB 10 /* ITU L*a*b* */ #define PHOTOMETRIC_CFA 32803 /* color filter array */ #define PHOTOMETRIC_LOGL 32844 /* CIE Log2(L) */ #define PHOTOMETRIC_LOGLUV 32845 /* CIE Log2(L) (u',v') */ #define TIFFTAG_THRESHHOLDING 263 /* +thresholding used on data */ #define THRESHHOLD_BILEVEL 1 /* b&w art scan */ #define THRESHHOLD_HALFTONE 2 /* or dithered scan */ #define THRESHHOLD_ERRORDIFFUSE 3 /* usually floyd-steinberg */ #define TIFFTAG_CELLWIDTH 264 /* +dithering matrix width */ #define TIFFTAG_CELLLENGTH 265 /* +dithering matrix height */ #define TIFFTAG_FILLORDER 266 /* data order within a byte */ #define FILLORDER_MSB2LSB 1 /* most significant -> least */ #define FILLORDER_LSB2MSB 2 /* least significant -> most */ #define TIFFTAG_DOCUMENTNAME 269 /* name of doc. image is from */ #define TIFFTAG_IMAGEDESCRIPTION 270 /* info about image */ #define TIFFTAG_MAKE 271 /* scanner manufacturer name */ #define TIFFTAG_MODEL 272 /* scanner model name/number */ #define TIFFTAG_STRIPOFFSETS 273 /* offsets to data strips */ #define TIFFTAG_ORIENTATION 274 /* +image orientation */ #define ORIENTATION_TOPLEFT 1 /* row 0 top, col 0 lhs */ #define ORIENTATION_TOPRIGHT 2 /* row 0 top, col 0 rhs */ #define ORIENTATION_BOTRIGHT 3 /* row 0 bottom, col 0 rhs */ #define ORIENTATION_BOTLEFT 4 /* row 0 bottom, col 0 lhs */ #define ORIENTATION_LEFTTOP 5 /* row 0 lhs, col 0 top */ #define ORIENTATION_RIGHTTOP 6 /* row 0 rhs, col 0 top */ #define ORIENTATION_RIGHTBOT 7 /* row 0 rhs, col 0 bottom */ #define ORIENTATION_LEFTBOT 8 /* row 0 lhs, col 0 bottom */ #define TIFFTAG_SAMPLESPERPIXEL 277 /* samples per pixel */ #define TIFFTAG_ROWSPERSTRIP 278 /* rows per strip of data */ #define TIFFTAG_STRIPBYTECOUNTS 279 /* bytes counts for strips */ #define TIFFTAG_MINSAMPLEVALUE 280 /* +minimum sample value */ #define TIFFTAG_MAXSAMPLEVALUE 281 /* +maximum sample value */ #define TIFFTAG_XRESOLUTION 282 /* pixels/resolution in x */ #define TIFFTAG_YRESOLUTION 283 /* pixels/resolution in y */ #define TIFFTAG_PLANARCONFIG 284 /* storage organization */ #define PLANARCONFIG_CONTIG 1 /* single image plane */ #define PLANARCONFIG_SEPARATE 2 /* separate planes of data */ #define TIFFTAG_PAGENAME 285 /* page name image is from */ #define TIFFTAG_XPOSITION 286 /* x page offset of image lhs */ #define TIFFTAG_YPOSITION 287 /* y page offset of image lhs */ #define TIFFTAG_FREEOFFSETS 288 /* +byte offset to free block */ #define TIFFTAG_FREEBYTECOUNTS 289 /* +sizes of free blocks */ #define TIFFTAG_GRAYRESPONSEUNIT 290 /* $gray scale curve accuracy */ #define GRAYRESPONSEUNIT_10S 1 /* tenths of a unit */ #define GRAYRESPONSEUNIT_100S 2 /* hundredths of a unit */ #define GRAYRESPONSEUNIT_1000S 3 /* thousandths of a unit */ #define GRAYRESPONSEUNIT_10000S 4 /* ten-thousandths of a unit */ #define GRAYRESPONSEUNIT_100000S 5 /* hundred-thousandths */ #define TIFFTAG_GRAYRESPONSECURVE 291 /* $gray scale response curve */ #define TIFFTAG_GROUP3OPTIONS 292 /* 32 flag bits */ #define TIFFTAG_T4OPTIONS 292 /* TIFF 6.0 proper name alias */ #define GROUP3OPT_2DENCODING 0x1 /* 2-dimensional coding */ #define GROUP3OPT_UNCOMPRESSED 0x2 /* data not compressed */ #define GROUP3OPT_FILLBITS 0x4 /* fill to byte boundary */ #define TIFFTAG_GROUP4OPTIONS 293 /* 32 flag bits */ #define TIFFTAG_T6OPTIONS 293 /* TIFF 6.0 proper name */ #define GROUP4OPT_UNCOMPRESSED 0x2 /* data not compressed */ #define TIFFTAG_RESOLUTIONUNIT 296 /* units of resolutions */ #define RESUNIT_NONE 1 /* no meaningful units */ #define RESUNIT_INCH 2 /* english */ #define RESUNIT_CENTIMETER 3 /* metric */ #define TIFFTAG_PAGENUMBER 297 /* page numbers of multi-page */ #define TIFFTAG_COLORRESPONSEUNIT 300 /* $color curve accuracy */ #define COLORRESPONSEUNIT_10S 1 /* tenths of a unit */ #define COLORRESPONSEUNIT_100S 2 /* hundredths of a unit */ #define COLORRESPONSEUNIT_1000S 3 /* thousandths of a unit */ #define COLORRESPONSEUNIT_10000S 4 /* ten-thousandths of a unit */ #define COLORRESPONSEUNIT_100000S 5 /* hundred-thousandths */ #define TIFFTAG_TRANSFERFUNCTION 301 /* !colorimetry info */ #define TIFFTAG_SOFTWARE 305 /* name & release */ #define TIFFTAG_DATETIME 306 /* creation date and time */ #define TIFFTAG_ARTIST 315 /* creator of image */ #define TIFFTAG_HOSTCOMPUTER 316 /* machine where created */ #define TIFFTAG_PREDICTOR 317 /* prediction scheme w/ LZW */ #define PREDICTOR_NONE 1 /* no prediction scheme used */ #define PREDICTOR_HORIZONTAL 2 /* horizontal differencing */ #define PREDICTOR_FLOATINGPOINT 3 /* floating point predictor */ #define TIFFTAG_WHITEPOINT 318 /* image white point */ #define TIFFTAG_PRIMARYCHROMATICITIES 319 /* !primary chromaticities */ #define TIFFTAG_COLORMAP 320 /* RGB map for pallette image */ #define TIFFTAG_HALFTONEHINTS 321 /* !highlight+shadow info */ #define TIFFTAG_TILEWIDTH 322 /* !tile width in pixels */ #define TIFFTAG_TILELENGTH 323 /* !tile height in pixels */ #define TIFFTAG_TILEOFFSETS 324 /* !offsets to data tiles */ #define TIFFTAG_TILEBYTECOUNTS 325 /* !byte counts for tiles */ #define TIFFTAG_BADFAXLINES 326 /* lines w/ wrong pixel count */ #define TIFFTAG_CLEANFAXDATA 327 /* regenerated line info */ #define CLEANFAXDATA_CLEAN 0 /* no errors detected */ #define CLEANFAXDATA_REGENERATED 1 /* receiver regenerated lines */ #define CLEANFAXDATA_UNCLEAN 2 /* uncorrected errors exist */ #define TIFFTAG_CONSECUTIVEBADFAXLINES 328 /* max consecutive bad lines */ #define TIFFTAG_SUBIFD 330 /* subimage descriptors */ #define TIFFTAG_INKSET 332 /* !inks in separated image */ #define INKSET_CMYK 1 /* !cyan-magenta-yellow-black color */ #define INKSET_MULTIINK 2 /* !multi-ink or hi-fi color */ #define TIFFTAG_INKNAMES 333 /* !ascii names of inks */ #define TIFFTAG_NUMBEROFINKS 334 /* !number of inks */ #define TIFFTAG_DOTRANGE 336 /* !0% and 100% dot codes */ #define TIFFTAG_TARGETPRINTER 337 /* !separation target */ #define TIFFTAG_EXTRASAMPLES 338 /* !info about extra samples */ #define EXTRASAMPLE_UNSPECIFIED 0 /* !unspecified data */ #define EXTRASAMPLE_ASSOCALPHA 1 /* !associated alpha data */ #define EXTRASAMPLE_UNASSALPHA 2 /* !unassociated alpha data */ #define TIFFTAG_SAMPLEFORMAT 339 /* !data sample format */ #define SAMPLEFORMAT_UINT 1 /* !unsigned integer data */ #define SAMPLEFORMAT_INT 2 /* !signed integer data */ #define SAMPLEFORMAT_IEEEFP 3 /* !IEEE floating point data */ #define SAMPLEFORMAT_VOID 4 /* !untyped data */ #define SAMPLEFORMAT_COMPLEXINT 5 /* !complex signed int */ #define SAMPLEFORMAT_COMPLEXIEEEFP 6 /* !complex ieee floating */ #define TIFFTAG_SMINSAMPLEVALUE 340 /* !variable MinSampleValue */ #define TIFFTAG_SMAXSAMPLEVALUE 341 /* !variable MaxSampleValue */ #define TIFFTAG_CLIPPATH 343 /* %ClipPath [Adobe TIFF technote 2] */ #define TIFFTAG_XCLIPPATHUNITS 344 /* %XClipPathUnits [Adobe TIFF technote 2] */ #define TIFFTAG_YCLIPPATHUNITS 345 /* %YClipPathUnits [Adobe TIFF technote 2] */ #define TIFFTAG_INDEXED 346 /* %Indexed [Adobe TIFF Technote 3] */ #define TIFFTAG_JPEGTABLES 347 /* %JPEG table stream */ #define TIFFTAG_OPIPROXY 351 /* %OPI Proxy [Adobe TIFF technote] */ /* Tags 400-435 are from the TIFF/FX spec */ #define TIFFTAG_GLOBALPARAMETERSIFD 400 /* ! */ #define TIFFTAG_PROFILETYPE 401 /* ! */ #define PROFILETYPE_UNSPECIFIED 0 /* ! */ #define PROFILETYPE_G3_FAX 1 /* ! */ #define TIFFTAG_FAXPROFILE 402 /* ! */ #define FAXPROFILE_S 1 /* !TIFF/FX FAX profile S */ #define FAXPROFILE_F 2 /* !TIFF/FX FAX profile F */ #define FAXPROFILE_J 3 /* !TIFF/FX FAX profile J */ #define FAXPROFILE_C 4 /* !TIFF/FX FAX profile C */ #define FAXPROFILE_L 5 /* !TIFF/FX FAX profile L */ #define FAXPROFILE_M 6 /* !TIFF/FX FAX profile LM */ #define TIFFTAG_CODINGMETHODS 403 /* !TIFF/FX coding methods */ #define CODINGMETHODS_T4_1D (1 << 1) /* !T.4 1D */ #define CODINGMETHODS_T4_2D (1 << 2) /* !T.4 2D */ #define CODINGMETHODS_T6 (1 << 3) /* !T.6 */ #define CODINGMETHODS_T85 (1 << 4) /* !T.85 JBIG */ #define CODINGMETHODS_T42 (1 << 5) /* !T.42 JPEG */ #define CODINGMETHODS_T43 (1 << 6) /* !T.43 colour by layered JBIG */ #define TIFFTAG_VERSIONYEAR 404 /* !TIFF/FX version year */ #define TIFFTAG_MODENUMBER 405 /* !TIFF/FX mode number */ #define TIFFTAG_DECODE 433 /* !TIFF/FX decode */ #define TIFFTAG_IMAGEBASECOLOR 434 /* !TIFF/FX image base colour */ #define TIFFTAG_T82OPTIONS 435 /* !TIFF/FX T.82 options */ /* * Tags 512-521 are obsoleted by Technical Note #2 which specifies a * revised JPEG-in-TIFF scheme. */ #define TIFFTAG_JPEGPROC 512 /* !JPEG processing algorithm */ #define JPEGPROC_BASELINE 1 /* !baseline sequential */ #define JPEGPROC_LOSSLESS 14 /* !Huffman coded lossless */ #define TIFFTAG_JPEGIFOFFSET 513 /* !pointer to SOI marker */ #define TIFFTAG_JPEGIFBYTECOUNT 514 /* !JFIF stream length */ #define TIFFTAG_JPEGRESTARTINTERVAL 515 /* !restart interval length */ #define TIFFTAG_JPEGLOSSLESSPREDICTORS 517 /* !lossless proc predictor */ #define TIFFTAG_JPEGPOINTTRANSFORM 518 /* !lossless point transform */ #define TIFFTAG_JPEGQTABLES 519 /* !Q matrice offsets */ #define TIFFTAG_JPEGDCTABLES 520 /* !DCT table offsets */ #define TIFFTAG_JPEGACTABLES 521 /* !AC coefficient offsets */ #define TIFFTAG_YCBCRCOEFFICIENTS 529 /* !RGB -> YCbCr transform */ #define TIFFTAG_YCBCRSUBSAMPLING 530 /* !YCbCr subsampling factors */ #define TIFFTAG_YCBCRPOSITIONING 531 /* !subsample positioning */ #define YCBCRPOSITION_CENTERED 1 /* !as in PostScript Level 2 */ #define YCBCRPOSITION_COSITED 2 /* !as in CCIR 601-1 */ #define TIFFTAG_REFERENCEBLACKWHITE 532 /* !colorimetry info */ #define TIFFTAG_STRIPROWCOUNTS 559 /* !TIFF/FX strip row counts */ #define TIFFTAG_XMLPACKET 700 /* %XML packet [Adobe XMP Specification, January 2004 */ #define TIFFTAG_OPIIMAGEID 32781 /* %OPI ImageID [Adobe TIFF technote] */ /* tags 32952-32956 are private tags registered to Island Graphics */ #define TIFFTAG_REFPTS 32953 /* image reference points */ #define TIFFTAG_REGIONTACKPOINT 32954 /* region-xform tack point */ #define TIFFTAG_REGIONWARPCORNERS 32955 /* warp quadrilateral */ #define TIFFTAG_REGIONAFFINE 32956 /* affine transformation mat */ /* tags 32995-32999 are private tags registered to SGI */ #define TIFFTAG_MATTEING 32995 /* $use ExtraSamples */ #define TIFFTAG_DATATYPE 32996 /* $use SampleFormat */ #define TIFFTAG_IMAGEDEPTH 32997 /* z depth of image */ #define TIFFTAG_TILEDEPTH 32998 /* z depth/data tile */ /* tags 33300-33309 are private tags registered to Pixar */ /* * TIFFTAG_PIXAR_IMAGEFULLWIDTH and TIFFTAG_PIXAR_IMAGEFULLLENGTH * are set when an image has been cropped out of a larger image. * They reflect the size of the original uncropped image. * The TIFFTAG_XPOSITION and TIFFTAG_YPOSITION can be used * to determine the position of the smaller image in the larger one. */ #define TIFFTAG_PIXAR_IMAGEFULLWIDTH 33300 /* full image size in x */ #define TIFFTAG_PIXAR_IMAGEFULLLENGTH 33301 /* full image size in y */ /* Tags 33302-33306 are used to identify special image modes and data * used by Pixar's texture formats. */ #define TIFFTAG_PIXAR_TEXTUREFORMAT 33302 /* texture map format */ #define TIFFTAG_PIXAR_WRAPMODES 33303 /* s & t wrap modes */ #define TIFFTAG_PIXAR_FOVCOT 33304 /* cotan(fov) for env. maps */ #define TIFFTAG_PIXAR_MATRIX_WORLDTOSCREEN 33305 #define TIFFTAG_PIXAR_MATRIX_WORLDTOCAMERA 33306 /* tag 33405 is a private tag registered to Eastman Kodak */ #define TIFFTAG_WRITERSERIALNUMBER 33405 /* device serial number */ #define TIFFTAG_CFAREPEATPATTERNDIM 33421 /* dimensions of CFA pattern */ #define TIFFTAG_CFAPATTERN 33422 /* color filter array pattern */ /* tag 33432 is listed in the 6.0 spec w/ unknown ownership */ #define TIFFTAG_COPYRIGHT 33432 /* copyright string */ /* IPTC TAG from RichTIFF specifications */ #define TIFFTAG_RICHTIFFIPTC 33723 /* 34016-34029 are reserved for ANSI IT8 TIFF/IT */ #define TIFFTAG_STONITS 37439 /* Sample value to Nits */ /* tag 34929 is a private tag registered to FedEx */ #define TIFFTAG_FEDEX_EDR 34929 /* unknown use */ #define TIFFTAG_INTEROPERABILITYIFD 40965 /* Pointer to Interoperability private directory */ /* Adobe Digital Negative (DNG) format tags */ #define TIFFTAG_DNGVERSION 50706 /* &DNG version number */ #define TIFFTAG_DNGBACKWARDVERSION 50707 /* &DNG compatibility version */ #define TIFFTAG_UNIQUECAMERAMODEL 50708 /* &name for the camera model */ #define TIFFTAG_LOCALIZEDCAMERAMODEL 50709 /* &localized camera model name */ #define TIFFTAG_CFAPLANECOLOR 50710 /* &CFAPattern->LinearRaw space mapping */ #define TIFFTAG_CFALAYOUT 50711 /* &spatial layout of the CFA */ #define TIFFTAG_LINEARIZATIONTABLE 50712 /* &lookup table description */ #define TIFFTAG_BLACKLEVELREPEATDIM 50713 /* &repeat pattern size for the BlackLevel tag */ #define TIFFTAG_BLACKLEVEL 50714 /* &zero light encoding level */ #define TIFFTAG_BLACKLEVELDELTAH 50715 /* &zero light encoding level differences (columns) */ #define TIFFTAG_BLACKLEVELDELTAV 50716 /* &zero light encoding level differences (rows) */ #define TIFFTAG_WHITELEVEL 50717 /* &fully saturated encoding level */ #define TIFFTAG_DEFAULTSCALE 50718 /* &default scale factors */ #define TIFFTAG_DEFAULTCROPORIGIN 50719 /* &origin of the final image area */ #define TIFFTAG_DEFAULTCROPSIZE 50720 /* &size of the final image area */ #define TIFFTAG_COLORMATRIX1 50721 /* &XYZ->reference color space transformation matrix 1 */ #define TIFFTAG_COLORMATRIX2 50722 /* &XYZ->reference color space transformation matrix 2 */ #define TIFFTAG_CAMERACALIBRATION1 50723 /* &calibration matrix 1 */ #define TIFFTAG_CAMERACALIBRATION2 50724 /* &calibration matrix 2 */ #define TIFFTAG_REDUCTIONMATRIX1 50725 /* &dimensionality reduction matrix 1 */ #define TIFFTAG_REDUCTIONMATRIX2 50726 /* &dimensionality reduction matrix 2 */ #define TIFFTAG_ANALOGBALANCE 50727 /* &gain applied the stored raw values*/ #define TIFFTAG_ASSHOTNEUTRAL 50728 /* &selected white balance in linear reference space */ #define TIFFTAG_ASSHOTWHITEXY 50729 /* &selected white balance in x-y chromaticity coordinates */ #define TIFFTAG_BASELINEEXPOSURE 50730 /* &how much to move the zero point */ #define TIFFTAG_BASELINENOISE 50731 /* &relative noise level */ #define TIFFTAG_BASELINESHARPNESS 50732 /* &relative amount of sharpening */ #define TIFFTAG_BAYERGREENSPLIT 50733 /* &how closely the values of the green pixels in the blue/green rows track the values of the green pixels in the red/green rows */ #define TIFFTAG_LINEARRESPONSELIMIT 50734 /* &non-linear encoding range */ #define TIFFTAG_CAMERASERIALNUMBER 50735 /* &camera's serial number */ #define TIFFTAG_LENSINFO 50736 /* info about the lens */ #define TIFFTAG_CHROMABLURRADIUS 50737 /* &chroma blur radius */ #define TIFFTAG_ANTIALIASSTRENGTH 50738 /* &relative strength of the camera's anti-alias filter */ #define TIFFTAG_SHADOWSCALE 50739 /* &used by Adobe Camera Raw */ #define TIFFTAG_DNGPRIVATEDATA 50740 /* &manufacturer's private data */ #define TIFFTAG_MAKERNOTESAFETY 50741 /* &whether the EXIF MakerNote tag is safe to preserve along with the rest of the EXIF data */ #define TIFFTAG_CALIBRATIONILLUMINANT1 50778 /* &illuminant 1 */ #define TIFFTAG_CALIBRATIONILLUMINANT2 50779 /* &illuminant 2 */ #define TIFFTAG_BESTQUALITYSCALE 50780 /* &best quality multiplier */ #define TIFFTAG_RAWDATAUNIQUEID 50781 /* &unique identifier for the raw image data */ #define TIFFTAG_ORIGINALRAWFILENAME 50827 /* &file name of the original raw file */ #define TIFFTAG_ORIGINALRAWFILEDATA 50828 /* &contents of the original raw file */ #define TIFFTAG_ACTIVEAREA 50829 /* &active (non-masked) pixels of the sensor */ #define TIFFTAG_MASKEDAREAS 50830 /* &list of coordinates of fully masked pixels */ #define TIFFTAG_ASSHOTICCPROFILE 50831 /* &these two tags used to */ #define TIFFTAG_ASSHOTPREPROFILEMATRIX 50832 /* map cameras's color space into ICC profile space */ #define TIFFTAG_CURRENTICCPROFILE 50833 /* & */ #define TIFFTAG_CURRENTPREPROFILEMATRIX 50834 /* & */ /* tag 65535 is an undefined tag used by Eastman Kodak */ #define TIFFTAG_DCSHUESHIFTVALUES 65535 /* hue shift correction data */ /* * The following are ``pseudo tags'' that can be used to control * codec-specific functionality. These tags are not written to file. * Note that these values start at 0xffff+1 so that they'll never * collide with Aldus-assigned tags. * * If you want your private pseudo tags ``registered'' (i.e. added to * this file), please post a bug report via the tracking system at * http://www.remotesensing.org/libtiff/bugs.html with the appropriate * C definitions to add. */ #define TIFFTAG_FAXMODE 65536 /* Group 3/4 format control */ #define FAXMODE_CLASSIC 0x0000 /* default, include RTC */ #define FAXMODE_NORTC 0x0001 /* no RTC at end of data */ #define FAXMODE_NOEOL 0x0002 /* no EOL code at end of row */ #define FAXMODE_BYTEALIGN 0x0004 /* byte align row */ #define FAXMODE_WORDALIGN 0x0008 /* word align row */ #define FAXMODE_CLASSF FAXMODE_NORTC /* TIFF Class F */ #define TIFFTAG_JPEGQUALITY 65537 /* Compression quality level */ /* Note: quality level is on the IJG 0-100 scale. Default value is 75 */ #define TIFFTAG_JPEGCOLORMODE 65538 /* Auto RGB<=>YCbCr convert? */ #define JPEGCOLORMODE_RAW 0x0000 /* no conversion (default) */ #define JPEGCOLORMODE_RGB 0x0001 /* do auto conversion */ #define TIFFTAG_JPEGTABLESMODE 65539 /* What to put in JPEGTables */ #define JPEGTABLESMODE_QUANT 0x0001 /* include quantization tbls */ #define JPEGTABLESMODE_HUFF 0x0002 /* include Huffman tbls */ /* Note: default is JPEGTABLESMODE_QUANT | JPEGTABLESMODE_HUFF */ #define TIFFTAG_FAXFILLFUNC 65540 /* G3/G4 fill function */ #define TIFFTAG_PIXARLOGDATAFMT 65549 /* PixarLogCodec I/O data sz */ #define PIXARLOGDATAFMT_8BIT 0 /* regular u_char samples */ #define PIXARLOGDATAFMT_8BITABGR 1 /* ABGR-order u_chars */ #define PIXARLOGDATAFMT_11BITLOG 2 /* 11-bit log-encoded (raw) */ #define PIXARLOGDATAFMT_12BITPICIO 3 /* as per PICIO (1.0==2048) */ #define PIXARLOGDATAFMT_16BIT 4 /* signed short samples */ #define PIXARLOGDATAFMT_FLOAT 5 /* IEEE float samples */ /* 65550-65556 are allocated to Oceana Matrix */ #define TIFFTAG_DCSIMAGERTYPE 65550 /* imager model & filter */ #define DCSIMAGERMODEL_M3 0 /* M3 chip (1280 x 1024) */ #define DCSIMAGERMODEL_M5 1 /* M5 chip (1536 x 1024) */ #define DCSIMAGERMODEL_M6 2 /* M6 chip (3072 x 2048) */ #define DCSIMAGERFILTER_IR 0 /* infrared filter */ #define DCSIMAGERFILTER_MONO 1 /* monochrome filter */ #define DCSIMAGERFILTER_CFA 2 /* color filter array */ #define DCSIMAGERFILTER_OTHER 3 /* other filter */ #define TIFFTAG_DCSINTERPMODE 65551 /* interpolation mode */ #define DCSINTERPMODE_NORMAL 0x0 /* whole image, default */ #define DCSINTERPMODE_PREVIEW 0x1 /* preview of image (384x256) */ #define TIFFTAG_DCSBALANCEARRAY 65552 /* color balance values */ #define TIFFTAG_DCSCORRECTMATRIX 65553 /* color correction values */ #define TIFFTAG_DCSGAMMA 65554 /* gamma value */ #define TIFFTAG_DCSTOESHOULDERPTS 65555 /* toe & shoulder points */ #define TIFFTAG_DCSCALIBRATIONFD 65556 /* calibration file desc */ /* Note: quality level is on the ZLIB 1-9 scale. Default value is -1 */ #define TIFFTAG_ZIPQUALITY 65557 /* compression quality level */ #define TIFFTAG_PIXARLOGQUALITY 65558 /* PixarLog uses same scale */ /* 65559 is allocated to Oceana Matrix */ #define TIFFTAG_DCSCLIPRECTANGLE 65559 /* area of image to acquire */ #define TIFFTAG_SGILOGDATAFMT 65560 /* SGILog user data format */ #define SGILOGDATAFMT_FLOAT 0 /* IEEE float samples */ #define SGILOGDATAFMT_16BIT 1 /* 16-bit samples */ #define SGILOGDATAFMT_RAW 2 /* uninterpreted data */ #define SGILOGDATAFMT_8BIT 3 /* 8-bit RGB monitor values */ #define TIFFTAG_SGILOGENCODE 65561 /* SGILog data encoding control*/ #define SGILOGENCODE_NODITHER 0 /* do not dither encoded values*/ #define SGILOGENCODE_RANDITHER 1 /* randomly dither encd values */ #define TIFFTAG_LZMAPRESET 65562 /* LZMA2 preset (compression level) */ #define TIFFTAG_PERSAMPLE 65563 /* interface for per sample tags */ #define PERSAMPLE_MERGED 0 /* present as a single value */ #define PERSAMPLE_MULTI 1 /* present as multiple values */ /* * EXIF tags */ #define EXIFTAG_EXPOSURETIME 33434 /* Exposure time */ #define EXIFTAG_FNUMBER 33437 /* F number */ #define EXIFTAG_EXPOSUREPROGRAM 34850 /* Exposure program */ #define EXIFTAG_SPECTRALSENSITIVITY 34852 /* Spectral sensitivity */ #define EXIFTAG_ISOSPEEDRATINGS 34855 /* ISO speed rating */ #define EXIFTAG_OECF 34856 /* Optoelectric conversion factor */ #define EXIFTAG_EXIFVERSION 36864 /* Exif version */ #define EXIFTAG_DATETIMEORIGINAL 36867 /* Date and time of original data generation */ #define EXIFTAG_DATETIMEDIGITIZED 36868 /* Date and time of digital data generation */ #define EXIFTAG_COMPONENTSCONFIGURATION 37121 /* Meaning of each component */ #define EXIFTAG_COMPRESSEDBITSPERPIXEL 37122 /* Image compression mode */ #define EXIFTAG_SHUTTERSPEEDVALUE 37377 /* Shutter speed */ #define EXIFTAG_APERTUREVALUE 37378 /* Aperture */ #define EXIFTAG_BRIGHTNESSVALUE 37379 /* Brightness */ #define EXIFTAG_EXPOSUREBIASVALUE 37380 /* Exposure bias */ #define EXIFTAG_MAXAPERTUREVALUE 37381 /* Maximum lens aperture */ #define EXIFTAG_SUBJECTDISTANCE 37382 /* Subject distance */ #define EXIFTAG_METERINGMODE 37383 /* Metering mode */ #define EXIFTAG_LIGHTSOURCE 37384 /* Light source */ #define EXIFTAG_FLASH 37385 /* Flash */ #define EXIFTAG_FOCALLENGTH 37386 /* Lens focal length */ #define EXIFTAG_SUBJECTAREA 37396 /* Subject area */ #define EXIFTAG_MAKERNOTE 37500 /* Manufacturer notes */ #define EXIFTAG_USERCOMMENT 37510 /* User comments */ #define EXIFTAG_SUBSECTIME 37520 /* DateTime subseconds */ #define EXIFTAG_SUBSECTIMEORIGINAL 37521 /* DateTimeOriginal subseconds */ #define EXIFTAG_SUBSECTIMEDIGITIZED 37522 /* DateTimeDigitized subseconds */ #define EXIFTAG_FLASHPIXVERSION 40960 /* Supported Flashpix version */ #define EXIFTAG_COLORSPACE 40961 /* Color space information */ #define EXIFTAG_PIXELXDIMENSION 40962 /* Valid image width */ #define EXIFTAG_PIXELYDIMENSION 40963 /* Valid image height */ #define EXIFTAG_RELATEDSOUNDFILE 40964 /* Related audio file */ #define EXIFTAG_FLASHENERGY 41483 /* Flash energy */ #define EXIFTAG_SPATIALFREQUENCYRESPONSE 41484 /* Spatial frequency response */ #define EXIFTAG_FOCALPLANEXRESOLUTION 41486 /* Focal plane X resolution */ #define EXIFTAG_FOCALPLANEYRESOLUTION 41487 /* Focal plane Y resolution */ #define EXIFTAG_FOCALPLANERESOLUTIONUNIT 41488 /* Focal plane resolution unit */ #define EXIFTAG_SUBJECTLOCATION 41492 /* Subject location */ #define EXIFTAG_EXPOSUREINDEX 41493 /* Exposure index */ #define EXIFTAG_SENSINGMETHOD 41495 /* Sensing method */ #define EXIFTAG_FILESOURCE 41728 /* File source */ #define EXIFTAG_SCENETYPE 41729 /* Scene type */ #define EXIFTAG_CFAPATTERN 41730 /* CFA pattern */ #define EXIFTAG_CUSTOMRENDERED 41985 /* Custom image processing */ #define EXIFTAG_EXPOSUREMODE 41986 /* Exposure mode */ #define EXIFTAG_WHITEBALANCE 41987 /* White balance */ #define EXIFTAG_DIGITALZOOMRATIO 41988 /* Digital zoom ratio */ #define EXIFTAG_FOCALLENGTHIN35MMFILM 41989 /* Focal length in 35 mm film */ #define EXIFTAG_SCENECAPTURETYPE 41990 /* Scene capture type */ #define EXIFTAG_GAINCONTROL 41991 /* Gain control */ #define EXIFTAG_CONTRAST 41992 /* Contrast */ #define EXIFTAG_SATURATION 41993 /* Saturation */ #define EXIFTAG_SHARPNESS 41994 /* Sharpness */ #define EXIFTAG_DEVICESETTINGDESCRIPTION 41995 /* Device settings description */ #define EXIFTAG_SUBJECTDISTANCERANGE 41996 /* Subject distance range */ #define EXIFTAG_GAINCONTROL 41991 /* Gain control */ #define EXIFTAG_GAINCONTROL 41991 /* Gain control */ #define EXIFTAG_IMAGEUNIQUEID 42016 /* Unique image ID */ #endif /* _TIFF_ */ /* vim: set ts=8 sts=8 sw=8 noet: */ /* * Local Variables: * mode: c * c-basic-offset: 8 * fill-column: 78 * End: */ ctffind-4.1.14/src/core/tiff/tiffconf.h000066400000000000000000000065451440356052600176530ustar00rootroot00000000000000/* libtiff/tiffconf.h. Generated from tiffconf.h.in by configure. */ /* Configuration defines for installed libtiff. This file maintained for backward compatibility. Do not use definitions from this file in your programs. */ #ifndef _TIFFCONF_ #define _TIFFCONF_ /* Signed 16-bit type */ #define TIFF_INT16_T signed short /* Signed 32-bit type */ #define TIFF_INT32_T signed int /* Signed 64-bit type */ #define TIFF_INT64_T signed long /* Signed 8-bit type */ #define TIFF_INT8_T signed char /* Unsigned 16-bit type */ #define TIFF_UINT16_T unsigned short /* Unsigned 32-bit type */ #define TIFF_UINT32_T unsigned int /* Unsigned 64-bit type */ #define TIFF_UINT64_T unsigned long /* Unsigned 8-bit type */ #define TIFF_UINT8_T unsigned char /* Signed size type */ #define TIFF_SSIZE_T signed long /* Pointer difference type */ #define TIFF_PTRDIFF_T ptrdiff_t /* Define to 1 if the system has the type `int16'. */ /* #undef HAVE_INT16 */ /* Define to 1 if the system has the type `int32'. */ /* #undef HAVE_INT32 */ /* Define to 1 if the system has the type `int8'. */ /* #undef HAVE_INT8 */ /* Compatibility stuff. */ /* Define as 0 or 1 according to the floating point format suported by the machine */ #define HAVE_IEEEFP 1 /* Set the native cpu bit order (FILLORDER_LSB2MSB or FILLORDER_MSB2LSB) */ #define HOST_FILLORDER FILLORDER_LSB2MSB /* Native cpu byte order: 1 if big-endian (Motorola) or 0 if little-endian (Intel) */ #define HOST_BIGENDIAN 0 /* Support CCITT Group 3 & 4 algorithms */ #define CCITT_SUPPORT 1 /* Support JPEG compression (requires IJG JPEG library) */ #define JPEG_SUPPORT 1 /* Support JBIG compression (requires JBIG-KIT library) */ #define JBIG_SUPPORT 1 /* Support LogLuv high dynamic range encoding */ #define LOGLUV_SUPPORT 1 /* Support LZW algorithm */ #define LZW_SUPPORT 1 /* Support NeXT 2-bit RLE algorithm */ #define NEXT_SUPPORT 1 /* Support Old JPEG compresson (read contrib/ojpeg/README first! Compilation fails with unpatched IJG JPEG library) */ #define OJPEG_SUPPORT 1 /* Support Macintosh PackBits algorithm */ #define PACKBITS_SUPPORT 1 /* Support Pixar log-format algorithm (requires Zlib) */ #define PIXARLOG_SUPPORT 1 /* Support ThunderScan 4-bit RLE algorithm */ #define THUNDER_SUPPORT 1 /* Support Deflate compression */ #define ZIP_SUPPORT 1 /* Support strip chopping (whether or not to convert single-strip uncompressed images to mutiple strips of ~8Kb to reduce memory usage) */ #define STRIPCHOP_DEFAULT TIFF_STRIPCHOP /* Enable SubIFD tag (330) support */ #define SUBIFD_SUPPORT 1 /* Treat extra sample as alpha (default enabled). The RGBA interface will treat a fourth sample with no EXTRASAMPLE_ value as being ASSOCALPHA. Many packages produce RGBA files but don't mark the alpha properly. */ #define DEFAULT_EXTRASAMPLE_AS_ALPHA 1 /* Pick up YCbCr subsampling info from the JPEG data stream to support files lacking the tag (default enabled). */ #define CHECK_JPEG_YCBCR_SUBSAMPLING 1 /* Support MS MDI magic number files as TIFF */ #define MDI_SUPPORT 1 /* * Feature support definitions. * XXX: These macros are obsoleted. Don't use them in your apps! * Macros stays here for backward compatibility and should be always defined. */ #define COLORIMETRY_SUPPORT #define YCBCR_SUPPORT #define CMYK_SUPPORT #define ICC_SUPPORT #define PHOTOSHOP_SUPPORT #define IPTC_SUPPORT #endif /* _TIFFCONF_ */ ctffind-4.1.14/src/core/tiff/tiffio.h000066400000000000000000000547331440356052600173370ustar00rootroot00000000000000/* $Id: tiffio.h,v 1.91 2012-07-29 15:45:29 tgl Exp $ */ /* * Copyright (c) 1988-1997 Sam Leffler * Copyright (c) 1991-1997 Silicon Graphics, Inc. * * Permission to use, copy, modify, distribute, and sell this software and * its documentation for any purpose is hereby granted without fee, provided * that (i) the above copyright notices and this permission notice appear in * all copies of the software and related documentation, and (ii) the names of * Sam Leffler and Silicon Graphics may not be used in any advertising or * publicity relating to the software without the specific, prior written * permission of Sam Leffler and Silicon Graphics. * * THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, * EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY * WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. * * IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR * ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, * OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, * WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF * LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE * OF THIS SOFTWARE. */ #ifndef _TIFFIO_ #define _TIFFIO_ /* * TIFF I/O Library Definitions. */ #include "tiff.h" #include "tiffvers.h" /* * TIFF is defined as an incomplete type to hide the * library's internal data structures from clients. */ typedef struct tiff TIFF; /* * The following typedefs define the intrinsic size of * data types used in the *exported* interfaces. These * definitions depend on the proper definition of types * in tiff.h. Note also that the varargs interface used * to pass tag types and values uses the types defined in * tiff.h directly. * * NB: ttag_t is unsigned int and not unsigned short because * ANSI C requires that the type before the ellipsis be a * promoted type (i.e. one of int, unsigned int, pointer, * or double) and because we defined pseudo-tags that are * outside the range of legal Aldus-assigned tags. * NB: tsize_t is int32 and not uint32 because some functions * return -1. * NB: toff_t is not off_t for many reasons; TIFFs max out at * 32-bit file offsets, and BigTIFF maxes out at 64-bit * offsets being the most important, and to ensure use of * a consistently unsigned type across architectures. * Prior to libtiff 4.0, this was an unsigned 32 bit type. */ /* * this is the machine addressing size type, only it's signed, so make it * int32 on 32bit machines, int64 on 64bit machines */ typedef TIFF_SSIZE_T tmsize_t; typedef uint64 toff_t; /* file offset */ /* the following are deprecated and should be replaced by their defining counterparts */ typedef uint32 ttag_t; /* directory tag */ typedef uint16 tdir_t; /* directory index */ typedef uint16 tsample_t; /* sample number */ typedef uint32 tstrile_t; /* strip or tile number */ typedef tstrile_t tstrip_t; /* strip number */ typedef tstrile_t ttile_t; /* tile number */ typedef tmsize_t tsize_t; /* i/o size in bytes */ typedef void* tdata_t; /* image data ref */ #if !defined(__WIN32__) && (defined(_WIN32) || defined(WIN32)) #define __WIN32__ #endif /* * On windows you should define USE_WIN32_FILEIO if you are using tif_win32.c * or AVOID_WIN32_FILEIO if you are using something else (like tif_unix.c). * * By default tif_unix.c is assumed. */ #if defined(_WINDOWS) || defined(__WIN32__) || defined(_Windows) # if !defined(__CYGWIN) && !defined(AVOID_WIN32_FILEIO) && !defined(USE_WIN32_FILEIO) # define AVOID_WIN32_FILEIO # endif #endif #if defined(USE_WIN32_FILEIO) # define VC_EXTRALEAN # include # ifdef __WIN32__ DECLARE_HANDLE(thandle_t); /* Win32 file handle */ # else typedef HFILE thandle_t; /* client data handle */ # endif /* __WIN32__ */ #else typedef void* thandle_t; /* client data handle */ #endif /* USE_WIN32_FILEIO */ /* * Flags to pass to TIFFPrintDirectory to control * printing of data structures that are potentially * very large. Bit-or these flags to enable printing * multiple items. */ #define TIFFPRINT_NONE 0x0 /* no extra info */ #define TIFFPRINT_STRIPS 0x1 /* strips/tiles info */ #define TIFFPRINT_CURVES 0x2 /* color/gray response curves */ #define TIFFPRINT_COLORMAP 0x4 /* colormap */ #define TIFFPRINT_JPEGQTABLES 0x100 /* JPEG Q matrices */ #define TIFFPRINT_JPEGACTABLES 0x200 /* JPEG AC tables */ #define TIFFPRINT_JPEGDCTABLES 0x200 /* JPEG DC tables */ /* * Colour conversion stuff */ /* reference white */ #define D65_X0 (95.0470F) #define D65_Y0 (100.0F) #define D65_Z0 (108.8827F) #define D50_X0 (96.4250F) #define D50_Y0 (100.0F) #define D50_Z0 (82.4680F) /* Structure for holding information about a display device. */ typedef unsigned char TIFFRGBValue; /* 8-bit samples */ typedef struct { float d_mat[3][3]; /* XYZ -> luminance matrix */ float d_YCR; /* Light o/p for reference white */ float d_YCG; float d_YCB; uint32 d_Vrwr; /* Pixel values for ref. white */ uint32 d_Vrwg; uint32 d_Vrwb; float d_Y0R; /* Residual light for black pixel */ float d_Y0G; float d_Y0B; float d_gammaR; /* Gamma values for the three guns */ float d_gammaG; float d_gammaB; } TIFFDisplay; typedef struct { /* YCbCr->RGB support */ TIFFRGBValue* clamptab; /* range clamping table */ int* Cr_r_tab; int* Cb_b_tab; int32* Cr_g_tab; int32* Cb_g_tab; int32* Y_tab; } TIFFYCbCrToRGB; typedef struct { /* CIE Lab 1976->RGB support */ int range; /* Size of conversion table */ #define CIELABTORGB_TABLE_RANGE 1500 float rstep, gstep, bstep; float X0, Y0, Z0; /* Reference white point */ TIFFDisplay display; float Yr2r[CIELABTORGB_TABLE_RANGE + 1]; /* Conversion of Yr to r */ float Yg2g[CIELABTORGB_TABLE_RANGE + 1]; /* Conversion of Yg to g */ float Yb2b[CIELABTORGB_TABLE_RANGE + 1]; /* Conversion of Yb to b */ } TIFFCIELabToRGB; /* * RGBA-style image support. */ typedef struct _TIFFRGBAImage TIFFRGBAImage; /* * The image reading and conversion routines invoke * ``put routines'' to copy/image/whatever tiles of * raw image data. A default set of routines are * provided to convert/copy raw image data to 8-bit * packed ABGR format rasters. Applications can supply * alternate routines that unpack the data into a * different format or, for example, unpack the data * and draw the unpacked raster on the display. */ typedef void (*tileContigRoutine) (TIFFRGBAImage*, uint32*, uint32, uint32, uint32, uint32, int32, int32, unsigned char*); typedef void (*tileSeparateRoutine) (TIFFRGBAImage*, uint32*, uint32, uint32, uint32, uint32, int32, int32, unsigned char*, unsigned char*, unsigned char*, unsigned char*); /* * RGBA-reader state. */ struct _TIFFRGBAImage { TIFF* tif; /* image handle */ int stoponerr; /* stop on read error */ int isContig; /* data is packed/separate */ int alpha; /* type of alpha data present */ uint32 width; /* image width */ uint32 height; /* image height */ uint16 bitspersample; /* image bits/sample */ uint16 samplesperpixel; /* image samples/pixel */ uint16 orientation; /* image orientation */ uint16 req_orientation; /* requested orientation */ uint16 photometric; /* image photometric interp */ uint16* redcmap; /* colormap pallete */ uint16* greencmap; uint16* bluecmap; /* get image data routine */ int (*get)(TIFFRGBAImage*, uint32*, uint32, uint32); /* put decoded strip/tile */ union { void (*any)(TIFFRGBAImage*); tileContigRoutine contig; tileSeparateRoutine separate; } put; TIFFRGBValue* Map; /* sample mapping array */ uint32** BWmap; /* black&white map */ uint32** PALmap; /* palette image map */ TIFFYCbCrToRGB* ycbcr; /* YCbCr conversion state */ TIFFCIELabToRGB* cielab; /* CIE L*a*b conversion state */ uint8* UaToAa; /* Unassociated alpha to associated alpha convertion LUT */ uint8* Bitdepth16To8; /* LUT for conversion from 16bit to 8bit values */ int row_offset; int col_offset; }; /* * Macros for extracting components from the * packed ABGR form returned by TIFFReadRGBAImage. */ #define TIFFGetR(abgr) ((abgr) & 0xff) #define TIFFGetG(abgr) (((abgr) >> 8) & 0xff) #define TIFFGetB(abgr) (((abgr) >> 16) & 0xff) #define TIFFGetA(abgr) (((abgr) >> 24) & 0xff) /* * A CODEC is a software package that implements decoding, * encoding, or decoding+encoding of a compression algorithm. * The library provides a collection of builtin codecs. * More codecs may be registered through calls to the library * and/or the builtin implementations may be overridden. */ typedef int (*TIFFInitMethod)(TIFF*, int); typedef struct { char* name; uint16 scheme; TIFFInitMethod init; } TIFFCodec; #include #include /* share internal LogLuv conversion routines? */ #ifndef LOGLUV_PUBLIC #define LOGLUV_PUBLIC 1 #endif #if !defined(__GNUC__) && !defined(__attribute__) # define __attribute__(x) /*nothing*/ #endif #if defined(c_plusplus) || defined(__cplusplus) extern "C" { #endif typedef void (*TIFFErrorHandler)(const char*, const char*, va_list); typedef void (*TIFFErrorHandlerExt)(thandle_t, const char*, const char*, va_list); typedef tmsize_t (*TIFFReadWriteProc)(thandle_t, void*, tmsize_t); typedef toff_t (*TIFFSeekProc)(thandle_t, toff_t, int); typedef int (*TIFFCloseProc)(thandle_t); typedef toff_t (*TIFFSizeProc)(thandle_t); typedef int (*TIFFMapFileProc)(thandle_t, void** base, toff_t* size); typedef void (*TIFFUnmapFileProc)(thandle_t, void* base, toff_t size); typedef void (*TIFFExtendProc)(TIFF*); extern const char* TIFFGetVersion(void); extern const TIFFCodec* TIFFFindCODEC(uint16); extern TIFFCodec* TIFFRegisterCODEC(uint16, const char*, TIFFInitMethod); extern void TIFFUnRegisterCODEC(TIFFCodec*); extern int TIFFIsCODECConfigured(uint16); extern TIFFCodec* TIFFGetConfiguredCODECs(void); /* * Auxiliary functions. */ extern void* _TIFFmalloc(tmsize_t s); extern void* _TIFFrealloc(void* p, tmsize_t s); extern void _TIFFmemset(void* p, int v, tmsize_t c); extern void _TIFFmemcpy(void* d, const void* s, tmsize_t c); extern int _TIFFmemcmp(const void* p1, const void* p2, tmsize_t c); extern void _TIFFfree(void* p); /* ** Stuff, related to tag handling and creating custom tags. */ extern int TIFFGetTagListCount( TIFF * ); extern uint32 TIFFGetTagListEntry( TIFF *, int tag_index ); #define TIFF_ANY TIFF_NOTYPE /* for field descriptor searching */ #define TIFF_VARIABLE -1 /* marker for variable length tags */ #define TIFF_SPP -2 /* marker for SamplesPerPixel tags */ #define TIFF_VARIABLE2 -3 /* marker for uint32 var-length tags */ #define FIELD_CUSTOM 65 typedef struct _TIFFField TIFFField; typedef struct _TIFFFieldArray TIFFFieldArray; extern const TIFFField* TIFFFindField(TIFF *, uint32, TIFFDataType); extern const TIFFField* TIFFFieldWithTag(TIFF*, uint32); extern const TIFFField* TIFFFieldWithName(TIFF*, const char *); extern uint32 TIFFFieldTag(const TIFFField*); extern const char* TIFFFieldName(const TIFFField*); extern TIFFDataType TIFFFieldDataType(const TIFFField*); extern int TIFFFieldPassCount(const TIFFField*); extern int TIFFFieldReadCount(const TIFFField*); extern int TIFFFieldWriteCount(const TIFFField*); typedef int (*TIFFVSetMethod)(TIFF*, uint32, va_list); typedef int (*TIFFVGetMethod)(TIFF*, uint32, va_list); typedef void (*TIFFPrintMethod)(TIFF*, FILE*, long); typedef struct { TIFFVSetMethod vsetfield; /* tag set routine */ TIFFVGetMethod vgetfield; /* tag get routine */ TIFFPrintMethod printdir; /* directory print routine */ } TIFFTagMethods; extern TIFFTagMethods *TIFFAccessTagMethods(TIFF *); extern void *TIFFGetClientInfo(TIFF *, const char *); extern void TIFFSetClientInfo(TIFF *, void *, const char *); extern void TIFFCleanup(TIFF* tif); extern void TIFFClose(TIFF* tif); extern int TIFFFlush(TIFF* tif); extern int TIFFFlushData(TIFF* tif); extern int TIFFGetField(TIFF* tif, uint32 tag, ...); extern int TIFFVGetField(TIFF* tif, uint32 tag, va_list ap); extern int TIFFGetFieldDefaulted(TIFF* tif, uint32 tag, ...); extern int TIFFVGetFieldDefaulted(TIFF* tif, uint32 tag, va_list ap); extern int TIFFReadDirectory(TIFF* tif); extern int TIFFReadCustomDirectory(TIFF* tif, toff_t diroff, const TIFFFieldArray* infoarray); extern int TIFFReadEXIFDirectory(TIFF* tif, toff_t diroff); extern uint64 TIFFScanlineSize64(TIFF* tif); extern tmsize_t TIFFScanlineSize(TIFF* tif); extern uint64 TIFFRasterScanlineSize64(TIFF* tif); extern tmsize_t TIFFRasterScanlineSize(TIFF* tif); extern uint64 TIFFStripSize64(TIFF* tif); extern tmsize_t TIFFStripSize(TIFF* tif); extern uint64 TIFFRawStripSize64(TIFF* tif, uint32 strip); extern tmsize_t TIFFRawStripSize(TIFF* tif, uint32 strip); extern uint64 TIFFVStripSize64(TIFF* tif, uint32 nrows); extern tmsize_t TIFFVStripSize(TIFF* tif, uint32 nrows); extern uint64 TIFFTileRowSize64(TIFF* tif); extern tmsize_t TIFFTileRowSize(TIFF* tif); extern uint64 TIFFTileSize64(TIFF* tif); extern tmsize_t TIFFTileSize(TIFF* tif); extern uint64 TIFFVTileSize64(TIFF* tif, uint32 nrows); extern tmsize_t TIFFVTileSize(TIFF* tif, uint32 nrows); extern uint32 TIFFDefaultStripSize(TIFF* tif, uint32 request); extern void TIFFDefaultTileSize(TIFF*, uint32*, uint32*); extern int TIFFFileno(TIFF*); extern int TIFFSetFileno(TIFF*, int); extern thandle_t TIFFClientdata(TIFF*); extern thandle_t TIFFSetClientdata(TIFF*, thandle_t); extern int TIFFGetMode(TIFF*); extern int TIFFSetMode(TIFF*, int); extern int TIFFIsTiled(TIFF*); extern int TIFFIsByteSwapped(TIFF*); extern int TIFFIsUpSampled(TIFF*); extern int TIFFIsMSB2LSB(TIFF*); extern int TIFFIsBigEndian(TIFF*); extern TIFFReadWriteProc TIFFGetReadProc(TIFF*); extern TIFFReadWriteProc TIFFGetWriteProc(TIFF*); extern TIFFSeekProc TIFFGetSeekProc(TIFF*); extern TIFFCloseProc TIFFGetCloseProc(TIFF*); extern TIFFSizeProc TIFFGetSizeProc(TIFF*); extern TIFFMapFileProc TIFFGetMapFileProc(TIFF*); extern TIFFUnmapFileProc TIFFGetUnmapFileProc(TIFF*); extern uint32 TIFFCurrentRow(TIFF*); extern uint16 TIFFCurrentDirectory(TIFF*); extern uint16 TIFFNumberOfDirectories(TIFF*); extern uint64 TIFFCurrentDirOffset(TIFF*); extern uint32 TIFFCurrentStrip(TIFF*); extern uint32 TIFFCurrentTile(TIFF* tif); extern int TIFFReadBufferSetup(TIFF* tif, void* bp, tmsize_t size); extern int TIFFWriteBufferSetup(TIFF* tif, void* bp, tmsize_t size); extern int TIFFSetupStrips(TIFF *); extern int TIFFWriteCheck(TIFF*, int, const char *); extern void TIFFFreeDirectory(TIFF*); extern int TIFFCreateDirectory(TIFF*); extern int TIFFCreateCustomDirectory(TIFF*,const TIFFFieldArray*); extern int TIFFCreateEXIFDirectory(TIFF*); extern int TIFFLastDirectory(TIFF*); extern int TIFFSetDirectory(TIFF*, uint16); extern int TIFFSetSubDirectory(TIFF*, uint64); extern int TIFFUnlinkDirectory(TIFF*, uint16); extern int TIFFSetField(TIFF*, uint32, ...); extern int TIFFVSetField(TIFF*, uint32, va_list); extern int TIFFUnsetField(TIFF*, uint32); extern int TIFFWriteDirectory(TIFF *); extern int TIFFWriteCustomDirectory(TIFF *, uint64 *); extern int TIFFCheckpointDirectory(TIFF *); extern int TIFFRewriteDirectory(TIFF *); #if defined(c_plusplus) || defined(__cplusplus) extern void TIFFPrintDirectory(TIFF*, FILE*, long = 0); extern int TIFFReadScanline(TIFF* tif, void* buf, uint32 row, uint16 sample = 0); extern int TIFFWriteScanline(TIFF* tif, void* buf, uint32 row, uint16 sample = 0); extern int TIFFReadRGBAImage(TIFF*, uint32, uint32, uint32*, int = 0); extern int TIFFReadRGBAImageOriented(TIFF*, uint32, uint32, uint32*, int = ORIENTATION_BOTLEFT, int = 0); #else extern void TIFFPrintDirectory(TIFF*, FILE*, long); extern int TIFFReadScanline(TIFF* tif, void* buf, uint32 row, uint16 sample); extern int TIFFWriteScanline(TIFF* tif, void* buf, uint32 row, uint16 sample); extern int TIFFReadRGBAImage(TIFF*, uint32, uint32, uint32*, int); extern int TIFFReadRGBAImageOriented(TIFF*, uint32, uint32, uint32*, int, int); #endif extern int TIFFReadRGBAStrip(TIFF*, uint32, uint32 * ); extern int TIFFReadRGBATile(TIFF*, uint32, uint32, uint32 * ); extern int TIFFRGBAImageOK(TIFF*, char [1024]); extern int TIFFRGBAImageBegin(TIFFRGBAImage*, TIFF*, int, char [1024]); extern int TIFFRGBAImageGet(TIFFRGBAImage*, uint32*, uint32, uint32); extern void TIFFRGBAImageEnd(TIFFRGBAImage*); extern TIFF* TIFFOpen(const char*, const char*); # ifdef __WIN32__ extern TIFF* TIFFOpenW(const wchar_t*, const char*); # endif /* __WIN32__ */ extern TIFF* TIFFFdOpen(int, const char*, const char*); extern TIFF* TIFFClientOpen(const char*, const char*, thandle_t, TIFFReadWriteProc, TIFFReadWriteProc, TIFFSeekProc, TIFFCloseProc, TIFFSizeProc, TIFFMapFileProc, TIFFUnmapFileProc); extern const char* TIFFFileName(TIFF*); extern const char* TIFFSetFileName(TIFF*, const char *); extern void TIFFError(const char*, const char*, ...) __attribute__((__format__ (__printf__,2,3))); extern void TIFFErrorExt(thandle_t, const char*, const char*, ...) __attribute__((__format__ (__printf__,3,4))); extern void TIFFWarning(const char*, const char*, ...) __attribute__((__format__ (__printf__,2,3))); extern void TIFFWarningExt(thandle_t, const char*, const char*, ...) __attribute__((__format__ (__printf__,3,4))); extern TIFFErrorHandler TIFFSetErrorHandler(TIFFErrorHandler); extern TIFFErrorHandlerExt TIFFSetErrorHandlerExt(TIFFErrorHandlerExt); extern TIFFErrorHandler TIFFSetWarningHandler(TIFFErrorHandler); extern TIFFErrorHandlerExt TIFFSetWarningHandlerExt(TIFFErrorHandlerExt); extern TIFFExtendProc TIFFSetTagExtender(TIFFExtendProc); extern uint32 TIFFComputeTile(TIFF* tif, uint32 x, uint32 y, uint32 z, uint16 s); extern int TIFFCheckTile(TIFF* tif, uint32 x, uint32 y, uint32 z, uint16 s); extern uint32 TIFFNumberOfTiles(TIFF*); extern tmsize_t TIFFReadTile(TIFF* tif, void* buf, uint32 x, uint32 y, uint32 z, uint16 s); extern tmsize_t TIFFWriteTile(TIFF* tif, void* buf, uint32 x, uint32 y, uint32 z, uint16 s); extern uint32 TIFFComputeStrip(TIFF*, uint32, uint16); extern uint32 TIFFNumberOfStrips(TIFF*); extern tmsize_t TIFFReadEncodedStrip(TIFF* tif, uint32 strip, void* buf, tmsize_t size); extern tmsize_t TIFFReadRawStrip(TIFF* tif, uint32 strip, void* buf, tmsize_t size); extern tmsize_t TIFFReadEncodedTile(TIFF* tif, uint32 tile, void* buf, tmsize_t size); extern tmsize_t TIFFReadRawTile(TIFF* tif, uint32 tile, void* buf, tmsize_t size); extern tmsize_t TIFFWriteEncodedStrip(TIFF* tif, uint32 strip, void* data, tmsize_t cc); extern tmsize_t TIFFWriteRawStrip(TIFF* tif, uint32 strip, void* data, tmsize_t cc); extern tmsize_t TIFFWriteEncodedTile(TIFF* tif, uint32 tile, void* data, tmsize_t cc); extern tmsize_t TIFFWriteRawTile(TIFF* tif, uint32 tile, void* data, tmsize_t cc); extern int TIFFDataWidth(TIFFDataType); /* table of tag datatype widths */ extern void TIFFSetWriteOffset(TIFF* tif, toff_t off); extern void TIFFSwabShort(uint16*); extern void TIFFSwabLong(uint32*); extern void TIFFSwabLong8(uint64*); extern void TIFFSwabFloat(float*); extern void TIFFSwabDouble(double*); extern void TIFFSwabArrayOfShort(uint16* wp, tmsize_t n); extern void TIFFSwabArrayOfTriples(uint8* tp, tmsize_t n); extern void TIFFSwabArrayOfLong(uint32* lp, tmsize_t n); extern void TIFFSwabArrayOfLong8(uint64* lp, tmsize_t n); extern void TIFFSwabArrayOfFloat(float* fp, tmsize_t n); extern void TIFFSwabArrayOfDouble(double* dp, tmsize_t n); extern void TIFFReverseBits(uint8* cp, tmsize_t n); extern const unsigned char* TIFFGetBitRevTable(int); #ifdef LOGLUV_PUBLIC #define U_NEU 0.210526316 #define V_NEU 0.473684211 #define UVSCALE 410. extern double LogL16toY(int); extern double LogL10toY(int); extern void XYZtoRGB24(float*, uint8*); extern int uv_decode(double*, double*, int); extern void LogLuv24toXYZ(uint32, float*); extern void LogLuv32toXYZ(uint32, float*); #if defined(c_plusplus) || defined(__cplusplus) extern int LogL16fromY(double, int = SGILOGENCODE_NODITHER); extern int LogL10fromY(double, int = SGILOGENCODE_NODITHER); extern int uv_encode(double, double, int = SGILOGENCODE_NODITHER); extern uint32 LogLuv24fromXYZ(float*, int = SGILOGENCODE_NODITHER); extern uint32 LogLuv32fromXYZ(float*, int = SGILOGENCODE_NODITHER); #else extern int LogL16fromY(double, int); extern int LogL10fromY(double, int); extern int uv_encode(double, double, int); extern uint32 LogLuv24fromXYZ(float*, int); extern uint32 LogLuv32fromXYZ(float*, int); #endif #endif /* LOGLUV_PUBLIC */ extern int TIFFCIELabToRGBInit(TIFFCIELabToRGB*, const TIFFDisplay *, float*); extern void TIFFCIELabToXYZ(TIFFCIELabToRGB *, uint32, int32, int32, float *, float *, float *); extern void TIFFXYZToRGB(TIFFCIELabToRGB *, float, float, float, uint32 *, uint32 *, uint32 *); extern int TIFFYCbCrToRGBInit(TIFFYCbCrToRGB*, float*, float*); extern void TIFFYCbCrtoRGB(TIFFYCbCrToRGB *, uint32, int32, int32, uint32 *, uint32 *, uint32 *); /**************************************************************************** * O B S O L E T E D I N T E R F A C E S * * Don't use this stuff in your applications, it may be removed in the future * libtiff versions. ****************************************************************************/ typedef struct { ttag_t field_tag; /* field's tag */ short field_readcount; /* read count/TIFF_VARIABLE/TIFF_SPP */ short field_writecount; /* write count/TIFF_VARIABLE */ TIFFDataType field_type; /* type of associated data */ unsigned short field_bit; /* bit in fieldsset bit vector */ unsigned char field_oktochange; /* if true, can change while writing */ unsigned char field_passcount; /* if true, pass dir count on set */ char *field_name; /* ASCII name */ } TIFFFieldInfo; extern int TIFFMergeFieldInfo(TIFF*, const TIFFFieldInfo[], uint32); #if defined(c_plusplus) || defined(__cplusplus) } #endif #endif /* _TIFFIO_ */ /* vim: set ts=8 sts=8 sw=8 noet: */ /* * Local Variables: * mode: c * c-basic-offset: 8 * fill-column: 78 * End: */ ctffind-4.1.14/src/core/tiff/tiffvers.h000066400000000000000000000006321440356052600176740ustar00rootroot00000000000000#define TIFFLIB_VERSION_STR "LIBTIFF, Version 4.0.6\nCopyright (c) 1988-1996 Sam Leffler\nCopyright (c) 1991-1996 Silicon Graphics, Inc." /* * This define can be used in code that requires * compilation-related definitions specific to a * version or versions of the library. Runtime * version checking should be done based on the * string returned by TIFFGetVersion. */ #define TIFFLIB_VERSION 20150912 ctffind-4.1.14/src/core/tiff_file.cpp000066400000000000000000000304761440356052600174070ustar00rootroot00000000000000#include "core_headers.h" TiffFile::TiffFile() { tif = NULL; logical_dimension_x = 0; logical_dimension_y = 0; number_of_images = 0; this_is_in_mastronarde_4bit_hack_format = false; } TiffFile::TiffFile(std::string wanted_filename, bool overwrite) { OpenFile(wanted_filename, overwrite); } TiffFile::~TiffFile() { CloseFile(); } bool TiffFile::OpenFile(std::string wanted_filename, bool overwrite, bool wait_for_file_to_exist) { MyDebugAssertFalse(tif != NULL,"File already open: %s",wanted_filename); MyDebugAssertFalse(wait_for_file_to_exist,"Waiting for file to exist not implemented for tif files"); bool file_already_exists = DoesFileExist(wanted_filename); bool return_value = true; // if overwrite is specified, then we delete the file nomatter what.. if (overwrite) file_already_exists = false; if (file_already_exists) { // We open to read/write tif = TIFFOpen(wanted_filename.c_str(),"rc"); return_value = ReadLogicalDimensionsFromDisk(); } else { // We just open to write tif = TIFFOpen(wanted_filename.c_str(),"w"); } filename = wanted_filename; pixel_size = 1.0; //TODO: work out out to grab the pixel size from SerialEM/IMOD-style TIFF files return return_value; } void TiffFile::CloseFile() { if (tif != NULL) TIFFClose(tif); tif = NULL; } void TiffFile::PrintInfo() { wxPrintf("Filename : %s\n",filename.GetFullName()); wxPrintf("Dimensions: %i %i %i\n",ReturnXSize(),ReturnYSize(),ReturnZSize()); } bool TiffFile::ReadLogicalDimensionsFromDisk() { MyDebugAssertTrue(tif != NULL,"File must be open"); // Loop through all the TIFF directories and check they all have the same x,y dimensions int set_dir_ret = TIFFSetDirectory(tif,0); bool return_value = (set_dir_ret == 1); int dircount = 1; uint32 original_x = 0; uint32 current_x = 0; uint32 current_y = 0; TIFFGetField(tif,TIFFTAG_IMAGEWIDTH,¤t_x); TIFFGetField(tif,TIFFTAG_IMAGELENGTH,¤t_y); // Serial EM has the option to write out 4-bit compressed tif. They way that this is done is to do it as an 8-bit with // half the x dimension. If the file has specific dimensions, it is assumed to be 4-bit. I've copied the check directly // from David Mastronarde. - see function comments for sizeCanBe4BitK2SuperRes if (sizeCanBe4BitK2SuperRes(current_x, current_y) == 1) { logical_dimension_x = current_x * 2; logical_dimension_y = current_y; this_is_in_mastronarde_4bit_hack_format = true; } else { logical_dimension_x = current_x; logical_dimension_y = current_y; this_is_in_mastronarde_4bit_hack_format = false; } original_x = current_x; const bool check_dimensions_of_every_image = true; if (check_dimensions_of_every_image) { // This takes ages when importing TIFFs // TODO: check e.g. IMOD to see if there's a quicker way to check a TIFF is valid while (TIFFReadDirectory(tif)) { dircount++; TIFFGetField(tif,TIFFTAG_IMAGEWIDTH,¤t_x); TIFFGetField(tif,TIFFTAG_IMAGELENGTH,¤t_y); if (current_x != original_x || logical_dimension_y != current_y) { MyPrintfRed("Oops. Image %i of file %s has dimensions %i,%i, whereas previous images had dimensions %i,%i\n",dircount,current_x,current_y,original_x,logical_dimension_y); return_value = false; } } number_of_images = dircount; } else { // This doesnt' seem to be significantly faster than the other way to do it. number_of_images = TIFFNumberOfDirectories(tif); } return return_value; } void TiffFile::ReadSliceFromDisk(int slice_number, float * output_array) { ReadSlicesFromDisk(slice_number, slice_number, output_array); } void TiffFile::ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array) { MyDebugAssertTrue(tif != NULL,"File must be open"); MyDebugAssertTrue(start_slice > 0 && end_slice >= start_slice && end_slice <= number_of_images,"Bad start or end slice number"); unsigned int bits_per_sample = 0; unsigned int samples_per_pixel = 0; unsigned int sample_format = 0; unsigned int rows_per_strip = 0; long output_counter; tstrip_t strip_counter; tmsize_t number_of_bytes_placed_in_buffer; for (unsigned int directory_counter = start_slice-1; directory_counter < end_slice; directory_counter ++ ) { TIFFSetDirectory(tif,directory_counter); // We don't support tiles, only strips if (TIFFIsTiled(tif)) { MyPrintfRed("Error. Cannot read tiled TIF files. Filename = %s, Directory # %i. Number of tiles per image = %i\n",filename.GetFullPath(),directory_counter,TIFFNumberOfTiles(tif)); } // Get bit depth etc TIFFGetField(tif, TIFFTAG_BITSPERSAMPLE, &bits_per_sample); TIFFGetField(tif, TIFFTAG_SAMPLESPERPIXEL, &samples_per_pixel); if (samples_per_pixel != 1) { MyPrintfRed("Error. Unsupported number of samples per pixel: %i. Filename = %s, Directory # %i\n",samples_per_pixel,filename.GetFullPath(),directory_counter); } TIFFGetField(tif, TIFFTAG_SAMPLEFORMAT, &sample_format); // How many rows per strip? TIFFGetField(tif, TIFFTAG_ROWSPERSTRIP, &rows_per_strip); // Copy & cast data from these rows into the output array switch (sample_format) { case SAMPLEFORMAT_UINT: switch (bits_per_sample) { case 8: { uint8 * buf = new uint8[TIFFStripSize(tif)]; // Serial EM has the option to write out 4-bit compressed tif. They way that this is done is to do it as an 8-bit with // half the x dimension. If the file has specific dimensions, it is assumed to be 4-bit. I've copied the check directly // from David Mastronarde. - see function comments for sizeCanBe4BitK2SuperRes if (this_is_in_mastronarde_4bit_hack_format == true) // this is 4-bit { uint8 hi_4bits; uint8 low_4bits; number_of_bytes_placed_in_buffer = TIFFReadEncodedStrip(tif, strip_counter, (char *) buf, (tsize_t) -1); //wxPrintf("%i %i %i\n",int(number_of_bytes_placed_in_buffer),int(rows_per_strip), int(rows_per_strip * ReturnXSize())); if (strip_counter < TIFFNumberOfStrips(tif) - 1) MyDebugAssertTrue(number_of_bytes_placed_in_buffer == rows_per_strip * ReturnXSize(),"Unexpected number of bytes in uint8 buffer"); for (strip_counter = 0; strip_counter < TIFFNumberOfStrips(tif); strip_counter++) { number_of_bytes_placed_in_buffer = TIFFReadEncodedStrip(tif, strip_counter, (char *) buf, (tsize_t) -1); if (strip_counter < TIFFNumberOfStrips(tif) - 1) MyDebugAssertTrue(number_of_bytes_placed_in_buffer == rows_per_strip * ReturnXSize() / 2,"Unexpected number of bytes in uint8 buffer"); output_counter = strip_counter * rows_per_strip * ReturnXSize() + ((directory_counter - start_slice + 1) * ReturnXSize() * ReturnYSize()); for (long counter = 0; counter < number_of_bytes_placed_in_buffer; counter ++) { low_4bits = buf[counter] & 0x0F; hi_4bits = (buf[counter]>>4) & 0x0F; output_array[output_counter] = float(low_4bits); output_counter ++; output_array[output_counter] = float(hi_4bits); output_counter ++; } } } else // not 4-bit { for (strip_counter = 0; strip_counter < TIFFNumberOfStrips(tif); strip_counter++) { number_of_bytes_placed_in_buffer = TIFFReadEncodedStrip(tif, strip_counter, (char *) buf, (tsize_t) -1); if (strip_counter < TIFFNumberOfStrips(tif) - 1) MyDebugAssertTrue(number_of_bytes_placed_in_buffer == rows_per_strip * ReturnXSize(),"Unexpected number of bytes in uint8 buffer"); output_counter = strip_counter * rows_per_strip * ReturnXSize() + ((directory_counter - start_slice + 1) * ReturnXSize() * ReturnYSize()); for (long counter = 0; counter < number_of_bytes_placed_in_buffer; counter ++) { output_array[output_counter] = buf[counter]; output_counter ++; } } } delete [] buf; } break; case 16: { uint16 * buf = new uint16[TIFFStripSize(tif)/2]; for (strip_counter = 0; strip_counter < TIFFNumberOfStrips(tif); strip_counter++) { number_of_bytes_placed_in_buffer = TIFFReadEncodedStrip(tif, strip_counter, (char *) buf, (tsize_t) -1); MyDebugAssertTrue(number_of_bytes_placed_in_buffer == rows_per_strip * ReturnXSize() * 2,"Unexpected number of bytes in uint16 buffer"); output_counter = strip_counter * rows_per_strip * ReturnXSize() + ((directory_counter - start_slice + 1) * ReturnXSize() * ReturnYSize()); for (long counter = 0; counter < number_of_bytes_placed_in_buffer/2; counter ++) { output_array[output_counter] = buf[counter]; output_counter++; } } delete [] buf; } break; default: MyPrintfRed("Error. Unsupported uint bit depth: %i. Filename = %s, Directory # %i\n",bits_per_sample,filename.GetFullPath(),directory_counter); break; } break; case SAMPLEFORMAT_INT: switch (bits_per_sample) { case 16: { int16 * buf = new int16[TIFFStripSize(tif)/2]; for (strip_counter = 0; strip_counter < TIFFNumberOfStrips(tif); strip_counter++) { number_of_bytes_placed_in_buffer = TIFFReadEncodedStrip(tif, strip_counter, (char *) buf, (tsize_t) -1); MyDebugAssertTrue(number_of_bytes_placed_in_buffer == rows_per_strip * ReturnXSize() * 2,"Unexpected number of bytes in uint16 buffer"); output_counter = strip_counter * rows_per_strip * ReturnXSize() + ((directory_counter - start_slice + 1) * ReturnXSize() * ReturnYSize()); for (long counter = 0; counter < number_of_bytes_placed_in_buffer/2; counter ++) { output_array[output_counter] = buf[counter]; output_counter++; } } delete [] buf; } break; default: MyPrintfRed("Error. Unsupported int bit depth: %i. Filename = %s, Directory # %i\n",bits_per_sample,filename.GetFullPath(),directory_counter); break; } break; case SAMPLEFORMAT_IEEEFP: { switch (bits_per_sample) { case 32: { float * buf = new float[TIFFStripSize(tif)/4]; for (strip_counter = 0; strip_counter < TIFFNumberOfStrips(tif); strip_counter++) { number_of_bytes_placed_in_buffer = TIFFReadEncodedStrip(tif, strip_counter, (char *) buf, (tsize_t) -1); MyDebugAssertTrue(number_of_bytes_placed_in_buffer == rows_per_strip * ReturnXSize() * 4,"Unexpected number of bytes in float buffer"); output_counter = strip_counter * rows_per_strip * ReturnXSize() + ((directory_counter - start_slice + 1) * ReturnXSize() * ReturnYSize()); for (long counter = 0; counter < number_of_bytes_placed_in_buffer/4; counter ++) { output_array[output_counter] = buf[counter]; output_counter ++; } } delete [] buf; } break; default: MyPrintfRed("Error. Unsupported float bit depth: %i. Filename = %s, Directory # %i\n",bits_per_sample,filename.GetFullPath(),directory_counter); break; } break; } break; default: MyPrintfRed("Error. Unsupported sample format: %i. Filename = %s, Directory # %i\n",sample_format,filename.GetFullPath(),directory_counter); break; } // Annoyingly, we need to swap the order of the lines to be "compatible" with MRC files etc { float * temp_line = new float[ReturnXSize()]; long address_of_start_of_slice = (directory_counter - start_slice + 1) * ReturnXSize() * ReturnYSize(); long address_of_start_of_line = address_of_start_of_slice; long address_of_start_of_other_line = address_of_start_of_slice + (ReturnYSize()-1)*ReturnXSize(); long counter; for (long line_counter = 0; line_counter < ReturnYSize()/2; line_counter++) { // Copy current line to a buffer for (counter = 0; counter < ReturnXSize(); counter ++ ) { temp_line[counter] = output_array[counter+address_of_start_of_line]; } // Copy other line to current line for (counter = 0; counter < ReturnXSize(); counter ++ ) { output_array[counter+address_of_start_of_line] = output_array[counter+address_of_start_of_other_line]; } // Copy line from buffer to other line for (counter = 0; counter < ReturnXSize(); counter ++ ) { output_array[counter+address_of_start_of_other_line] = temp_line[counter]; } // Get ready for next iteration address_of_start_of_line += ReturnXSize(); address_of_start_of_other_line -= ReturnXSize(); } delete [] temp_line; } } // end of loop over slices } void TiffFile::WriteSliceToDisk(int slice_number, float * input_array) { WriteSlicesToDisk(slice_number, slice_number, input_array); } void TiffFile::WriteSlicesToDisk(int start_slice, int end_slice, float * input_array) { MyDebugAssertTrue(false,"Not implemented yet"); } ctffind-4.1.14/src/core/tiff_file.h000066400000000000000000000021561440356052600170460ustar00rootroot00000000000000class TiffFile : public AbstractImageFile { private: TIFF * tif; int logical_dimension_x; int logical_dimension_y; int number_of_images; bool this_is_in_mastronarde_4bit_hack_format; float pixel_size; bool ReadLogicalDimensionsFromDisk(); public: TiffFile(); TiffFile(std::string wanted_filename, bool overwrite = false); ~TiffFile(); inline int ReturnXSize() {return logical_dimension_x;}; inline int ReturnYSize() {return logical_dimension_y;}; inline int ReturnZSize() {return number_of_images;}; inline int ReturnNumberOfSlices() {return number_of_images;}; inline float ReturnPixelSize() {return pixel_size;}; inline bool IsOpen() {if (tif) {return true;} else { return false;}}; bool OpenFile(std::string filename, bool overwrite = false, bool wait_for_file_to_exist = false); void CloseFile(); void ReadSliceFromDisk(int slice_number, float *output_array); void ReadSlicesFromDisk(int start_slice, int end_slice, float *output_array); void WriteSliceToDisk(int slice_number, float *input_array); void WriteSlicesToDisk(int start_slice, int end_slice, float *input_array); void PrintInfo(); }; ctffind-4.1.14/src/core/userinput.cpp000066400000000000000000000764611440356052600175220ustar00rootroot00000000000000#include "core_headers.h" UserInput::UserInput() { std::cout << "Warning, UserInput Class declared with no program name!" << std::endl << std::endl; Init("default", "0.0"); } UserInput::UserInput(const char *program_name, float program_version) { Init(program_name, wxString::Format("%0.2f",program_version)); } UserInput::UserInput(const char *program_name, wxString program_version) { Init(program_name, program_version); } UserInput::~UserInput() { if (input_is_a_tty == true) { // we need to carry over any unused defaults! if (defaults_file != 0 && new_defaults_file != 0) CarryOverDefaults(); if (defaults_file != 0) fclose(defaults_file); if (new_defaults_file != 0) { fclose(new_defaults_file); remove(defaults_filename); rename(new_defaults_filename, defaults_filename); remove(new_defaults_filename); } } } void UserInput::AskQuestion(const char *question_text, const char *help_text, const char *default_value, char *received_input) { int current_length; char temp_string[1000]; for (int i=0; i<1000;i++) { temp_string[i] = 0; } strcpy (temp_string, question_text); if (input_is_a_tty == true && default_value[0] != 0) { strcat (temp_string, " ["); strcat (temp_string, default_value); strcat (temp_string, "]"); current_length = 50 - strlen(temp_string); if (current_length >= 0) { wxPrintf("%s ", question_text); MyPrintfCyan("[%s]", default_value); } else { wxPrintf("%s\n", question_text); MyPrintfCyan("[%s]", default_value); current_length = 48 - strlen(default_value); } } else { current_length = 50 - strlen(temp_string); wxPrintf("%s", question_text); } for (long temp_counter = 0; temp_counter < current_length; temp_counter++) { wxPrintf(" "); } wxPrintf(" : "); // get some input.. std::cin.getline(received_input, 1000); if (received_input[0] == '*') exit(0); // user request exit else if (received_input[0] == 0) { if (input_is_a_tty == false) { wxPrintf("\n Error: Blank answer in scripted mode, exiting...\n\n"); exit(-1); } else strcpy(received_input, default_value); } else if (received_input[0] == '?') { wxPrintf("\n%s\n\n", help_text); } } void UserInput::Init(const char *program_name, wxString program_version) { int counter; defaults_file = NULL; new_defaults_file = NULL; for (counter = 0; counter < 1000; counter++) { defaults_filename[counter] = 0; new_defaults_filename[counter] = 0; } for (counter = 0; counter < 10000; counter++) { memory_string[counter] = 0; } input_is_a_tty = InputIsATerminal(); output_is_a_tty = OutputIsAtTerminal(); if (input_is_a_tty) { for (counter = 0; counter < 1000; counter++) { defaults_filename[counter] = 0; new_defaults_filename[counter] = 0; } defaults_filename[0] = '.'; strcat(defaults_filename, program_name); strcat(defaults_filename, ".dff"); new_defaults_filename[0] = '.'; strcat(new_defaults_filename, "current"); strcat(new_defaults_filename, program_name); strcat(new_defaults_filename, ".dff"); defaults_file = fopen(defaults_filename, "r"); new_defaults_file = fopen(new_defaults_filename, "w+"); if (new_defaults_file == 0) wxPrintf("\n\nError Can't open defaults file! for writing\n\n"); } wxPrintf("\n\n ** Welcome to %s **\n\n", program_name); for (counter = 0; counter < strlen(program_name) / 2; counter++) wxPrintf(" "); wxPrintf(" Version : %s\n", program_version); for (counter = 0; counter < strlen(program_name) / 2; counter++) wxPrintf(" "); wxPrintf(" Compiled : %s\n", __DATE__); for (counter = 0; counter < strlen(program_name) / 2; counter++) wxPrintf(" "); wxPrintf(" Mode : "); if (input_is_a_tty == true) wxPrintf("Interactive\n\n"); else wxPrintf("Scripted\n\n"); } bool UserInput::GetYesNoFromUser(const char * my_text, const char * help_text, const char * wanted_default_value) { char input[1000]; char default_value[1000]; for (int i=0; i<1000;i++) { input[i] = 0; default_value[i] = 0; } // Sort out the defaults.. GetDefault(my_text, wanted_default_value, default_value); while (1==1) { AskQuestion(my_text, help_text, default_value, input); if (input[0] == 'y' || input[0] == 'Y') { DoGotValidAnswer(my_text, input); return true; } else if (input[0] == 'n' || input[0] == 'N') { DoGotValidAnswer(my_text, input); return false; } DoGotInvalidAnswer(); } } float UserInput::GetFloatFromUser(const char * my_text, const char * help_text, const char * wanted_default_value, float min_value, float max_value) { float my_float; char default_value[1000]; char input[1000]; for (int i=0; i<1000;i++) { default_value[i] = 0; input[i] = 0; } // Sort out the defaults.. GetDefault(my_text, wanted_default_value, default_value); while (1==1) { AskQuestion(my_text, help_text, default_value, input); if (input[0] == 45 || input[0] == 46) { if (input[1] >= 48 && input[1] <= 57) { my_float=atof(input); if (my_float >= min_value && my_float <= max_value) { DoGotValidAnswer(my_text, input); return my_float; } else { if (output_is_a_tty == true) { MyPrintfRed("\nError: Number outside of acceptable range!\n\n"); } else { wxPrintf("\nError: Number outside of acceptable range!\n\n"); } } } } else if (input[0] >= 48 && input[0] <= 57) { my_float=atof(input); if (my_float >= min_value && my_float <= max_value) { DoGotValidAnswer(my_text, input); return my_float; } else { if (output_is_a_tty == true) { MyPrintfRed("\nError: Number outside of acceptable range!\n\n"); } else { wxPrintf("\nError: Number outside of acceptable range!\n\n"); } } } DoGotInvalidAnswer(); } } int UserInput::GetIntFromUser(const char * my_text, const char * help_text, const char * wanted_default_value, int min_value, int max_value) { int my_int; char input[1000]; char default_value[1000]; for (int i=0; i<1000;i++) { input[i] = 0; default_value[i] = 0; } GetDefault(my_text, wanted_default_value, default_value); while (1==1) { AskQuestion(my_text, help_text, default_value, input); if (input[0] == 45) { if (input[1] >= 48 && input[1] <= 57) { my_int=atoi(input); if (my_int >= min_value && my_int <= max_value) { DoGotValidAnswer(my_text, input); return my_int; } else { if (output_is_a_tty == true) { MyPrintfRed("\nError: Number outside of acceptable range!\n\n"); } else { wxPrintf("\nError: Number outside of acceptable range!\n\n"); } } } } else if (input[0] >= 48 && input[0] <= 57) { my_int=atoi(input); if (my_int >= min_value && my_int <= max_value) { DoGotValidAnswer(my_text, input); return my_int; } else { if (output_is_a_tty == true) { MyPrintfRed("\nError: Number outside of acceptable range!\n\n"); } else { wxPrintf("\nError: Number outside of acceptable range!\n\n"); } } } DoGotInvalidAnswer(); } } std::string UserInput::GetStringFromUser(const char * my_text, const char * help_text, const char * wanted_default_value) { char input[1000]; char default_value[1000]; for (int i=0; i<1000;i++) { input[i] = 0; default_value[i] = 0; } GetDefault(my_text, wanted_default_value, default_value); while (1==1) { AskQuestion(my_text, help_text, default_value, input); if (input[0] != 0 && input[0] != '?') { DoGotValidAnswer(my_text, input); std::string my_string(input); return my_string; } DoGotInvalidAnswer(); } } std::string UserInput::GetSymmetryFromUser(const char * my_text, const char * help_text, const char * wanted_default_value) { char input[1000]; char default_value[1000]; for (int i=0; i<1000;i++) { input[i] = 0; default_value[i] = 0; } GetDefault(my_text, wanted_default_value, default_value); while (1==1) { AskQuestion(my_text, help_text, default_value, input); if (input[0] != 0 && input[0] != '?') { wxString supplied_input = input; wxChar symmetry_type; long symmetry_number; if (supplied_input.Length() < 1) { if (output_is_a_tty == true) { MyPrintfRed("\nError: Must specify symmetry symbol!\n\n"); } else { wxPrintf("\nError: Must specify symmetry symbol!\n\n"); } } else { symmetry_type = supplied_input.Capitalize()[0]; if (supplied_input.Length() == 1) { symmetry_number = 0; } else { if (! supplied_input.Mid(1).ToLong(&symmetry_number)) { symmetry_number = -1; if (output_is_a_tty == true) { MyPrintfRed("\nError: Unrecognized symmetry number!\n\n"); } else { wxPrintf("\nError: Unrecognized symmetry number!\n\n"); } } } if (symmetry_number >= 0) { if ((symmetry_type == 'C' || symmetry_type == 'D') && symmetry_number > 0) { DoGotValidAnswer(my_text, input); std::string my_string(input); return my_string; } if (symmetry_type == 'T' && (symmetry_number < 3)) { DoGotValidAnswer(my_text, input); std::string my_string(input); return my_string; } if (symmetry_type == 'O' && (symmetry_number == 0)) { DoGotValidAnswer(my_text, input); std::string my_string(input); return my_string; } if (symmetry_type == 'I' && (symmetry_number < 3)) { DoGotValidAnswer(my_text, input); std::string my_string(input); return my_string; } if (output_is_a_tty == true) { MyPrintfRed("\nError: Unrecognized symmetry!\n\n"); } else { wxPrintf("\nError: Unrecognized symmetry!\n\n"); } } } } } DoGotInvalidAnswer(); } std::string UserInput::GetFilenameFromUser(const char * my_text, const char * help_text, const char * wanted_default_value, bool must_exist) { char input[1000]; char default_value[1000]; for (int i=0; i<1000;i++) { input[i] = 0; default_value[i] = 0; } GetDefault(my_text, wanted_default_value, default_value); while (1==1) { AskQuestion(my_text, help_text, default_value, input); if (input[0] != 0 && input[0] != '?') { if (must_exist == false) { DoGotValidAnswer(my_text, input); std::string my_string(input); return my_string; } else { // check the file exits.. if (wxFileName::FileExists(input) == true) { DoGotValidAnswer(my_text, input); std::string my_string(input); return my_string; } else { if (output_is_a_tty == true) { MyPrintfRed("\nError: File does not exist, please provide an existing file!\n\n"); } else { wxPrintf("\nError: File does not exist, please provide an existing file!\n\n"); } } } } DoGotInvalidAnswer(); } } void UserInput::GetDefault(const char *my_text, const char *default_default_value, char *default_value) { default_value[0] = 0; if (defaults_file != 0 && input_is_a_tty == true) { int file_check = 1; char label_temp[1000]; char current_label[1000]; default_value[0] = 0; for ( int i=0; i<1000;i++) { current_label[i] = 0; label_temp[i] = 0; } rewind(defaults_file); while(file_check != EOF) { while(file_check != EOF) { file_check = fscanf(defaults_file, "%s", label_temp); strcat(current_label, label_temp); if (current_label[int(strlen(current_label)) - 1] == ':' && current_label[int(strlen(current_label)) - 2] == ':') { current_label[int(strlen(current_label)) - 2] = 0; break; } else strcat(current_label, " "); } file_check = fscanf(defaults_file, "%s", default_value); if (strcmp (current_label, my_text) == 0) { // we have found a matching default so finish! break; } else { default_value[0] = 0; current_label[0] = 0; } } } if (default_default_value[0] != 0 && default_value[0] == 0 && input_is_a_tty == true) strcpy(default_value, default_default_value); } void UserInput::DoGotValidAnswer(const char *question_text, const char *new_default) { if (new_defaults_file != 0 && input_is_a_tty == true) fprintf (new_defaults_file, "%s:: %s\n", question_text, new_default); if (input_is_a_tty == false) wxPrintf("%s\n", new_default); } void UserInput::DoGotInvalidAnswer() { // if we got here and we are in scripted mode, something went wrong. if (input_is_a_tty == false) { wxPrintf("\n Error: Running as script, and answer is not recognized...\n\n"); exit(-1); } } void UserInput::CarryOverDefaults() { if (input_is_a_tty == true) { int file_check = 1; int file_check_newfile = 1; char current_label[1000]; char current_label_newfile[1000]; char current_default[1000]; char current_default_newfile[1000]; char label_temp[1000]; char label_temp_newfile[1000]; bool is_present; long file_pos; for (int i=0; i<1000;i++) { current_label[i] = 0; current_label_newfile[i] = 0; current_default[i] = 0; current_default_newfile[i] = 0; label_temp[i] = 0; label_temp_newfile[i] = 0; } rewind(defaults_file); file_pos = ftell ( new_defaults_file ); current_label_newfile[0] = 0; while(file_check != EOF) { current_label[0] = 0; while(file_check != EOF) { file_check = fscanf(defaults_file, "%s", label_temp); strcat(current_label, label_temp); if (current_label[int(strlen(current_label)) - 1] == ':' && current_label[int(strlen(current_label)) - 2] == ':') { current_label[int(strlen(current_label)) - 2] = 0; file_check = fscanf(defaults_file, "%s", current_default); break; } else strcat(current_label, " "); } if (file_check == EOF) break; // search for that in the defaults file we are writing... rewind (new_defaults_file); file_check_newfile = 1; is_present = false; while(file_check_newfile != EOF) { file_check_newfile = fscanf(new_defaults_file, "%s", label_temp_newfile); strcat(current_label_newfile, label_temp_newfile); if (current_label_newfile[int(strlen(current_label_newfile)) - 1] == ':' && current_label_newfile[int(strlen(current_label_newfile)) - 2] == ':') { current_label_newfile[int(strlen(current_label_newfile)) - 2] = 0; file_check_newfile = fscanf(new_defaults_file, "%s", current_default_newfile); if (strcmp (current_label, current_label_newfile) == 0) { is_present = true; break; } else current_label_newfile[0] = 0; } else strcat(current_label_newfile, " "); } if (is_present == false) { // it doesn't exist so write it at the end fseek(new_defaults_file, file_pos, SEEK_SET); fprintf(new_defaults_file, "%s:: %s\n", current_label, current_default); file_pos = ftell ( new_defaults_file ); } } } } /* void UserInput::GetTextFromUser(char *text_buffer, const char * my_text, const char * help_text, const char * wanted_default_value = 0) { while(1==1) { std::cout << my_text << " : "; std::cin.getline(text_buffer, 100); if (text_buffer[0] == '?') std::cout << std::endl << help_text << std::endl << std::endl; else if (text_buffer[0] != 0) break; } } */ /* void UserInput::GetPLTFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * wanted_default_value) { // status of 0 means i don't care // status of 1 means must exist // status of 2 means wipe it, error if can't FILE *input; char PLTFilename[1010]; char default_value[1000]; long current_length = 0; default_value[0] = 0; // Sort out the defaults.. if (defaults_file != 0) { // look for a default matching the input text.. GetDefault(my_text, default_value); } if (wanted_default_value != 0 && default_value[0] == 0) strcpy(default_value, wanted_default_value); while (1==1) { char temp_string[1000]; strcpy (temp_string, my_text); if (default_value[0] != 0) { strcat (temp_string, " ["); strcat (temp_string, default_value); strcat (temp_string, "]"); } current_length = 50 - strlen(temp_string); std::cout << temp_string; for (long temp_counter = 0; temp_counter < current_length; temp_counter++) { std::cout << " "; } std::cout << " : "; std::cin.getline(Filename, 500); if (Filename[0] == '*') exit(0); if (Filename[0] == 0) strcpy(Filename, default_value); strcpy(PLTFilename, Filename); strcat(PLTFilename, ".plt"); if (Filename[0] == '?') std::cout << std::endl << help_text << std::endl << std::endl; else if (Filename[0] != 0) { if (status == 0) {fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break;} else if (status == 1) { input = fopen(PLTFilename, "rb"); if (input==NULL) { perror ("This error has occurred (ReadPLT) : "); } else { fclose(input); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } else if (status == 2) { input = fopen(PLTFilename, "r+b"); if (input == 0) { input = fopen(PLTFilename, "w+b"); } if (input == NULL) { std::cout << "\n\nI can't open the output file for some reason.. quitting...\n\n"; exit(-1); } else { fclose(input); remove(PLTFilename); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } } } } void UserInput::GetTXTFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * wanted_default_value) { // status of 0 means i don't care // status of 1 means must exist // status of 2 means wipe it, error if can't FILE *input; char TXTFilename[1010]; char default_value[1000]; long current_length = 0; default_value[0] = 0; // Sort out the defaults.. if (defaults_file != 0) { // look for a default matching the input text.. GetDefault(my_text, default_value); } if (wanted_default_value != 0 && default_value[0] == 0) strcpy(default_value, wanted_default_value); while (1==1) { char temp_string[1000]; strcpy (temp_string, my_text); if (default_value[0] != 0) { strcat (temp_string, " ["); strcat (temp_string, default_value); strcat (temp_string, "]"); } current_length = 50 - strlen(temp_string); std::cout << temp_string; for (long temp_counter = 0; temp_counter < current_length; temp_counter++) { std::cout << " "; } std::cout << " : "; std::cin.getline(Filename, 500); if (Filename[0] == '*') exit(0); if (Filename[0] == 0) strcpy(Filename, default_value); strcpy(TXTFilename, Filename); strcat(TXTFilename, ".txt"); if (Filename[0] == '?') std::cout << std::endl << help_text << std::endl << std::endl; else if (Filename[0] != 0) { if (status == 0) {fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break;} else if (status == 1) { input = fopen(TXTFilename, "rb"); if (input==NULL) { perror ("This error has occurred (ReadTXT) : "); } else { fclose(input); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } else if (status == 2) { input = fopen(TXTFilename, "r+b"); if (input == 0) { input = fopen(TXTFilename, "w+b"); } if (input == NULL) { std::cout << "\n\nI can't open the output file for some reason.. quitting...\n\n"; exit(-1); } else { fclose(input); remove(TXTFilename); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } } } } void UserInput::GetGeneralFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char *extension, const char * wanted_default_value) { // status of 0 means i don't care // status of 1 means must exist // status of 2 means wipe it, error if can't FILE *input; char GeneralFilename[1010]; char default_value[1000]; long current_length = 0; default_value[0] = 0; // Sort out the defaults.. if (defaults_file != 0) { // look for a default matching the input text.. GetDefault(my_text, default_value); } if (wanted_default_value != 0 && default_value[0] == 0) strcpy(default_value, wanted_default_value); while (1==1) { char temp_string[1000]; strcpy (temp_string, my_text); if (default_value[0] != 0) { strcat (temp_string, " ["); strcat (temp_string, default_value); strcat (temp_string, "]"); } current_length = 50 - strlen(temp_string); std::cout << temp_string; for (long temp_counter = 0; temp_counter < current_length; temp_counter++) { std::cout << " "; } std::cout << " : "; std::cin.getline(Filename, 500); if (Filename[0] == '*') exit(0); if (Filename[0] == 0) strcpy(Filename, default_value); strcpy(GeneralFilename, Filename); strcat(GeneralFilename, "."); strcat(GeneralFilename, extension); if (Filename[0] == '?') std::cout << std::endl << help_text << std::endl << std::endl; else if (Filename[0] != 0) { if (status == 0) {fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break;} else if (status == 1) { input = fopen(GeneralFilename, "rb"); if (input==NULL) { perror ("This error has occurred (ReadGeneral) : "); } else { fclose(input); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } else if (status == 2) { input = fopen(GeneralFilename, "r+b"); if (input == 0) { input = fopen(GeneralFilename, "w+b"); } if (input == NULL) { std::cout << "\n\nI can't open the output file for some reason.. quitting...\n\n"; exit(-1); } else { fclose(input); remove(GeneralFilename); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } } } } void UserInput::GetPlainFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * wanted_default_value) { // status of 0 means i don't care // status of 1 means must exist // status of 2 means wipe it, error if can't FILE *input; char GeneralFilename[1010]; char default_value[1000]; long current_length = 0; default_value[0] = 0; // Sort out the defaults.. if (defaults_file != 0) { // look for a default matching the input text.. GetDefault(my_text, default_value); } if (wanted_default_value != 0 && default_value[0] == 0) strcpy(default_value, wanted_default_value); while (1==1) { char temp_string[1000]; strcpy (temp_string, my_text); if (default_value[0] != 0) { strcat (temp_string, " ["); strcat (temp_string, default_value); strcat (temp_string, "]"); } current_length = 50 - strlen(temp_string); std::cout << temp_string; for (long temp_counter = 0; temp_counter < current_length; temp_counter++) { std::cout << " "; } std::cout << " : "; std::cin.getline(Filename, 500); if (Filename[0] == '*') exit(0); if (Filename[0] == 0) strcpy(Filename, default_value); if (Filename[0] == '?') std::cout << std::endl << help_text << std::endl << std::endl; else if (Filename[0] != 0) { if (status == 0) {fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break;} else if (status == 1) { input = fopen(Filename, "rb"); if (input==NULL) { perror ("This error has occurred (ReadGeneral) : "); } else { fclose(input); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } else if (status == 2) { input = fopen(Filename, "r+b"); if (input == 0) { input = fopen(Filename, "w+b"); } if (input == NULL) { std::cout << "\n\nI can't open the output file for some reason.. quitting...\n\n"; exit(-1); } else { fclose(input); // remove(GeneralFilename); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } } } } void UserInput::GetCLSFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * wanted_default_value) { // status of 0 means i don't care // status of 1 means must exist // status of 2 means wipe it, error if can't FILE *input; char CLSFilename[1010]; char default_value[1000]; long current_length = 0; default_value[0] = 0; // Sort out the defaults.. if (defaults_file != 0) { // look for a default matching the input text.. GetDefault(my_text, default_value); } if (wanted_default_value != 0 && default_value[0] == 0) strcpy(default_value, wanted_default_value); while (1==1) { char temp_string[1000]; strcpy (temp_string, my_text); if (default_value[0] != 0) { strcat (temp_string, " ["); strcat (temp_string, default_value); strcat (temp_string, "]"); } current_length = 50 - strlen(temp_string); std::cout << temp_string; for (long temp_counter = 0; temp_counter < current_length; temp_counter++) { std::cout << " "; } std::cout << " : "; std::cin.getline(Filename, 500); if (Filename[0] == '*') exit(0); if (Filename[0] == 0) strcpy(Filename, default_value); strcpy(CLSFilename, Filename); strcat(CLSFilename, ".cls"); if (Filename[0] == '?') std::cout << std::endl << help_text << std::endl << std::endl; else if (Filename[0] != 0) { if (status == 0) {fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break;} else if (status == 1) { input = fopen(CLSFilename, "rb"); if (input==NULL) { perror ("This error has occurred (ReadCLS) : "); } else { fclose(input); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } else if (status == 2) { input = fopen(CLSFilename, "r+b"); if (input == 0) { input = fopen(CLSFilename, "w+b"); } if (input == NULL) { std::cout << "\n\nI can't open the output file for some reason.. quitting...\n\n"; exit(-1); } else { fclose(input); remove(CLSFilename); fprintf (new_defaults_file, "%s:: %s\n", my_text, Filename); break; } } } } } void UserInput::GetSymmetryFromUser(char *symmetry_type, long *symmetry_number, const char * my_text, const char * help_text, const char * wanted_default_value) { long current_length = 0; char default_value[1000]; default_value[0] = 0; char Option[1000]; // Sort out the defaults.. if (defaults_file != 0) { // look for a default matching the input text.. GetDefault(my_text, default_value); } if (wanted_default_value != 0 && default_value[0] == 0) strcpy(default_value, wanted_default_value); while (1==1) { char temp_string[1000]; strcpy (temp_string, my_text); if (default_value[0] != 0) { strcat (temp_string, " ["); strcat (temp_string, default_value); strcat (temp_string, "]"); } current_length = 50 - strlen(temp_string); std::cout << temp_string; for (long temp_counter = 0; temp_counter < current_length; temp_counter++) { std::cout << " "; } std::cout << " : "; std::cin.getline(Option, 500); if (Option[0] == '*') exit(0); if (Option[0] == '?') std::cout << std::endl << help_text << std::endl << std::endl; if (Option[0] == 0) strcpy(Option, default_value); if (Option[0] == 'C' || Option[0] == 'c') { symmetry_type[0] = 'C'; Option[0] = '0'; symmetry_number[0] = long(atoi(Option)); if (symmetry_number[0] != 0) { Option[0] = 'C'; fprintf (new_defaults_file, "%s:: %s\n", my_text, Option); break; } } else if (Option[0] == 'D' || Option[0] == 'd') { symmetry_type[0] = 'D'; Option[0] = '0'; symmetry_number[0] = long(atoi(Option)); if (symmetry_number[0] != 0) { Option[0] = 'D'; fprintf (new_defaults_file, "%s:: %s\n", my_text, Option); break; } } else if (Option[0] == 'I' || Option[0] == 'i') { symmetry_type[0] = 'I'; symmetry_number[0] = 1; if (symmetry_number[0] != 0) { Option[0] = 'I'; fprintf (new_defaults_file, "%s:: %s\n", my_text, Option); break; } } else if (Option[0] == 'O' || Option[0] == 'o') { symmetry_type[0] = 'O'; symmetry_number[0] = 1; if (symmetry_number[0] != 0) { Option[0] = 'O'; fprintf (new_defaults_file, "%s:: %s\n", my_text, Option); break; } } else if (Option[0] == 'T' || Option[0] == 't') { symmetry_type[0] = 'T'; symmetry_number[0] = 1; if (symmetry_number[0] != 0) { Option[0] = 'T'; fprintf (new_defaults_file, "%s:: %s\n", my_text, Option); break; } } } } long UserInput::GetOptionFromUser(char *option_list, long number_of_options, const char * my_text, const char * help_text, const char * wanted_default_value) { long current_length = 0; char default_value[1000]; default_value[0] = 0; char Option[1000]; long counter; // Sort out the defaults.. if (defaults_file != 0) { // look for a default matching the input text.. GetDefault(my_text, default_value); } if (wanted_default_value != 0 && default_value[0] == 0) strcpy(default_value, wanted_default_value); while (1==1) { char temp_string[1000]; strcpy (temp_string, my_text); if (default_value[0] != 0) { strcat (temp_string, " ["); strcat (temp_string, default_value); strcat (temp_string, "]"); } current_length = 50 - strlen(temp_string); std::cout << temp_string; for (long temp_counter = 0; temp_counter < current_length; temp_counter++) { std::cout << " "; } std::cout << " : "; std::cin.getline(Option, 500); if (Option[0] == '*') exit(0); if (Option[0] == 0) strcpy(Option, default_value); for (counter = 0; counter < number_of_options; counter++) { if (Option[0] == option_list[counter]) { fprintf (new_defaults_file, "%s:: %s\n", my_text, Option); return counter; } } } }*/ ctffind-4.1.14/src/core/userinput.h000066400000000000000000000064211440356052600171540ustar00rootroot00000000000000// User Input Class :- class UserInput { private: void Init(const char *program_name, wxString program_version); FILE *defaults_file; FILE *new_defaults_file; char defaults_filename[1000]; char new_defaults_filename[1000]; char memory_string[10000]; void GetDefault(const char *my_text, const char *default_default_value, char *default_value); void CarryOverDefaults(); void DoGotValidAnswer(const char *question_text, const char *new_default); void DoGotInvalidAnswer(); bool output_is_a_tty; bool input_is_a_tty; public: // Constructors UserInput(); UserInput(const char *program_name, float program_version); UserInput(const char *program_name, wxString program_version); ~UserInput(); // Methods void AskQuestion(const char *question_text, const char *help_text, const char *default_value, char *received_input); float GetFloatFromUser(const char * my_text, const char * help_text, const char * wanted_default_value = 0, float min_value = -FLT_MAX, float max_value = FLT_MAX); int GetIntFromUser(const char * my_text, const char * help_text, const char * wanted_default_value = 0, int min_value = INT_MIN, int max_value = INT_MAX); std::string GetFilenameFromUser(const char * my_question_text, const char * help_text, const char * wanted_default_value = 0, bool must_exist = false); std::string GetStringFromUser(const char * my_question_text, const char * help_text, const char * wanted_default_value = 0); std::string GetSymmetryFromUser(const char * my_question_text, const char * help_text, const char * wanted_default_value = 0); bool GetYesNoFromUser(const char * my_test, const char * help_text, const char * wanted_default_value = 0); //void GetTextFromUser(char *text_buffer, const char * my_text, const char * help_text, const char * wanted_default_value = 0); //void GetTXTFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * wanted_default_value = 0); //void GetPLTFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * wanted_default_value = 0); // void GetCLSFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * wanted_default_value = 0); //void GetPlainFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * wanted_default_value); //void GetGeneralFilenameFromUser(char *Filename, const char * my_text, const char * help_text, long status, const char * extension, const char * wanted_default_value); //void GetSymmetryFromUser(char *symmetry_type, long *symmetry_number, const char * my_text, const char * help_text, const char * wanted_default_value = 0); //long GetOptionFromUser(char *option_list, long number_of_options, const char * my_text, const char * help_text, const char * wanted_default_value = 0); }; ctffind-4.1.14/src/core/va04.cpp000066400000000000000000000332421440356052600162240ustar00rootroot00000000000000/* va04_ctffind.f -- translated by f2c (version 20100827). You must link the resulting object file with libf2c: on Microsoft Windows system, link with libf2c.lib; on Linux or Unix systems, link with .../path/to/libf2c.a -lm or, if you install libf2c.a in a standard place, with -lf2c -lm -- in that order, at the end of the command line, as in cc *.o -lf2c -lm Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., http://www.netlib.org/f2c/libf2c.zip */ #include #ifdef __cplusplus extern "C" { #endif #include "f2c.h" /* Table of constant values */ static int c__1 = 1; /* ****************************************************************************** */ /* Subroutine */ int calcfx_(int *nx, float *xpar, float *rf, float *ain, float *cs, float *wl, float *wgh1, float *wgh2, float *thetatr, float * rmin2, float *rmax2, int *nxyz, float *hw, float *dast) { /* CALCULATES NEW VALUE FOR F TO INPUT TO SUBROUTINE VA04A */ /* ****************************************************************************** */ /* RF=-EVALCTF(CS,WL,WGH1,WGH2,XPAR(1),XPAR(2),XPAR(3), */ /* + THETATR,HW,AIN,NXYZ,RMIN2,RMAX2,DAST) */ /* Parameter adjustments */ --nxyz; --ain; --xpar; /* Function Body */ *rf = (float)-1.; return 0; } /* calcfx_ */ /* ************************************************************************** */ ///* Subroutine */ int va04a_(real *x, real *e, integer *n, real *f, real * // escale, integer *iprint, integer *icon, integer *maxit, real *ain, // real *cs, real *wl, real *wgh1, real *wgh2, real *thetatr, real * // rmin2, real *rmax2, integer *nxyz, real *hw, real *dast) //{ //int va04a_(integer *n, real *e, real *escale, int *num_function_calls, float (*target_function) (void* parameters, float[]), void *parameters, real *f, // integer *iprint, integer *icon, integer *maxit, real *x) int va04a_(int *n, float *e, float *escale, int *num_function_calls, float (*target_function) (void* parameters, float[]), void *parameters, float *f, int *iprint, int *icon, int *maxit, float *x) { /* Format strings */ static char fmt_19[] = "(5x,\002VA04A MAXIMUM CHANGE DOES NOT ALTER FUNCTION\002)"; static char fmt_52[] = "(/1x,\002ITERATION\002,i5,i15,\002 FUNCTION VALUES\002,10x,\002F =\002,e21.14/(5e24.14))"; static char fmt_80[] = "(5x,\002VA04A ACCURACY LIMITED BY ERRORS IN F\002)"; /* System generated locals */ int i__1, i__2, maxx = 100 * *maxit; double r__1, r__2; /* Builtin functions */ int s_wsfe(cilist *), e_wsfe(); // double r_sign(real *, real *), sqrt(doublereal); int do_fio(int *, char *, ftnlen); /* Local variables */ int icnt = 0; static double a, b, d__, xs[11]; static int i__, j, k; // work array w must have at least dimension n * (n + 3) static double w[154], da, db, fa, dd, fb, fc, dc, di, fi, dl; static int jj; static double fp; static int is; static double aaa; static int ind, jjj, jil, inn, ixp; static double tmp, sum, dacc, dmag; static int nfcc; static double dmax__, scer, ddmag, fkeep, fhold, ddmax; static int iline, idirn, iterc, itone; static double fprev; extern /* Subroutine */ int calcfx_(int *, float *, float *, float *, float *, float *, float *, float *, float *, float *, float *, int *, float *, float *); static int isgrad; /* Fortran I/O blocks */ static cilist io___32 = { 0, 6, 0, fmt_19, 0 }; static cilist io___42 = { 0, 6, 0, fmt_52, 0 }; static cilist io___45 = { 0, 6, 0, fmt_80, 0 }; /* ************************************************************************** */ /* STANDARD FORTRAN 66 (A VERIFIED PFORT SUBROUTINE) */ /* W[N*(N+3)] */ /* Parameter adjustments */ //--nxyz; //--ain; --e; --x; /* Function Body */ ddmag = *escale * (float).1; scer = (float).05 / *escale; jj = *n * *n + *n; jjj = jj + *n; k = *n + 1; nfcc = 1; ind = 1; inn = 1; i__1 = *n; for (i__ = 1; i__ <= i__1; i__++) {xs[i__] = x[i__];}; for (i__ = 1; i__ <= i__1; ++i__) { i__2 = *n; for (j = 1; j <= i__2; ++j) { w[k - 1] = (float)0.; if (i__ - j != 0) { goto L4; } else { goto L3; } L3: w[k - 1] = (r__1 = e[i__], dabs(r__1)); w[i__ - 1] = *escale; L4: ++k; /* L2: */ } /* L1: */ } iterc = 1; isgrad = 2; //calcfx_(n, &x[1], f, &ain[1], cs, wl, wgh1, wgh2, thetatr, rmin2, rmax2, & // nxyz[1], hw, dast); icnt++; if (icnt > maxx) goto L999; *f = target_function(parameters, x + 1); fkeep = dabs(*f) + dabs(*f); L5: itone = 1; fp = *f; sum = (float)0.; ixp = jj; i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { ++ixp; w[ixp - 1] = x[i__]; /* L6: */ } idirn = *n + 1; iline = 1; L7: dmax__ = w[iline - 1]; dacc = dmax__ * scer; /* Computing MIN */ r__1 = ddmag, r__2 = dmax__ * (float).1; dmag = dmin(r__1,r__2); /* Computing MAX */ r__1 = dmag, r__2 = dacc * (float)20.; dmag = dmax(r__1,r__2); ddmax = dmag * (float)10.; switch (itone) { case 1: goto L70; case 2: goto L70; case 3: goto L71; } L70: dl = (float)0.; d__ = dmag; fprev = *f; is = 5; fa = *f; da = dl; L8: dd = d__ - dl; dl = d__; L58: k = idirn; i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { x[i__] += dd * w[k - 1]; ++k; /* L9: */ } //calcfx_(n, &x[1], f, &ain[1], cs, wl, wgh1, wgh2, thetatr, rmin2, rmax2, & // nxyz[1], hw, dast); icnt++; if (icnt > maxx) goto L999; *f = target_function(parameters, x + 1); ++nfcc; switch (is) { case 1: goto L10; case 2: goto L11; case 3: goto L12; case 4: goto L13; case 5: goto L14; case 6: goto L96; } L14: if ((r__1 = *f - fa) < (float)0.) { goto L15; } else if (r__1 == 0) { goto L16; } else { goto L24; } L16: if (dabs(d__) - dmax__ <= (float)0.) { goto L17; } else { goto L18; } L17: d__ += d__; goto L8; L18: //s_wsfe(&io___32); //e_wsfe(); // Removed this statement since it does not seem to be very informative // wxPrintf("Warning(VA04): maximum change does not alter target function\n"); goto L20; L15: fb = *f; db = d__; goto L21; L24: fb = fa; db = da; fa = *f; da = d__; L21: switch (isgrad) { case 1: goto L83; case 2: goto L23; } L23: d__ = db + db - da; is = 1; goto L8; L83: d__ = (da + db - (fa - fb) / (da - db)) * (float).5; is = 4; if ((da - d__) * (d__ - db) >= (float)0.) { goto L8; } else { goto L25; } L25: is = 1; if ((r__1 = d__ - db, dabs(r__1)) - ddmax <= (float)0.) { goto L8; } else { goto L26; } L26: r__1 = db - da; d__ = db + copysign(ddmax, r__1); //d__ = db + r_sign(&ddmax, &r__1); is = 1; ddmax += ddmax; ddmag += ddmag; if (ddmax - dmax__ <= (float)0.) { goto L8; } else { goto L27; } L27: ddmax = dmax__; goto L8; L13: if (*f - fa >= (float)0.) { goto L23; } else { goto L28; } L28: fc = fb; dc = db; L29: fb = *f; db = d__; goto L30; L12: if (*f - fb <= (float)0.) { goto L28; } else { goto L31; } L31: fa = *f; da = d__; goto L30; L11: if (*f - fb >= (float)0.) { goto L10; } else { goto L32; } L32: fa = fb; da = db; goto L29; L71: dl = (float)1.; ddmax = (float)5.; fa = fp; da = (float)-1.; fb = fhold; db = (float)0.; d__ = (float)1.; L10: fc = *f; dc = d__; L30: a = (db - dc) * (fa - fc); b = (dc - da) * (fb - fc); if ((a + b) * (da - dc) <= (float)0.) { goto L33; } else { goto L34; } L33: fa = fb; da = db; fb = fc; db = dc; goto L26; L34: d__ = (a * (db + dc) + b * (da + dc)) * (float).5 / (a + b); di = db; fi = fb; if (fb - fc <= (float)0.) { goto L44; } else { goto L43; } L43: di = dc; fi = fc; L44: switch (itone) { case 1: goto L86; case 2: goto L86; case 3: goto L85; } L85: itone = 2; goto L45; L86: if ((r__1 = d__ - di, dabs(r__1)) - dacc <= (float)0.) { goto L41; } else { goto L93; } L93: if ((r__1 = d__ - di, dabs(r__1)) - dabs(d__) * (float).03 <= (float)0.) { goto L41; } else { goto L45; } L45: if ((da - dc) * (dc - d__) >= (float)0.) { goto L46; } else { goto L47; } L46: fa = fb; da = db; fb = fc; db = dc; goto L25; L47: is = 2; if ((db - d__) * (d__ - dc) >= (float)0.) { goto L8; } else { goto L48; } L48: is = 3; goto L8; L41: *f = fi; d__ = di - dl; dd = sqrt((dc - db) * (dc - da) * (da - db) / (a + b)); i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { x[i__] += d__ * w[idirn - 1]; w[idirn - 1] = dd * w[idirn - 1]; ++idirn; /* L49: */ } if (dd == (float)0.) { dd = (float)1e-10; } w[iline - 1] /= dd; ++iline; if (*iprint - 1 != 0) { goto L51; } else { goto L50; } L50: switch (*iprint) { case 1: goto L51; case 2: goto L53; } L51: switch (itone) { case 1: goto L55; case 2: goto L38; } L55: if (fprev - *f - sum >= (float)0.) { goto L95; } else { goto L94; } L95: sum = fprev - *f; jil = iline; L94: if (idirn - jj <= 0) { goto L7; } else { goto L84; } L84: switch (ind) { case 1: goto L92; case 2: goto L72; } L92: fhold = *f; is = 6; ixp = jj; i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { ++ixp; w[ixp - 1] = x[i__] - w[ixp - 1]; /* L59: */ } dd = (float)1.; goto L58; L96: switch (ind) { case 1: goto L112; case 2: goto L87; } L112: if (fp - *f <= (float)0.) { goto L37; } else { goto L91; } L91: /* Computing 2nd power */ r__1 = fp - *f; d__ = (fp + *f - fhold * (float)2.) * (float)2. / (r__1 * r__1); /* Computing 2nd power */ r__1 = fp - fhold - sum; if (d__ * (r__1 * r__1) - sum >= (float)0.) { goto L37; } else { goto L87; } L87: j = jil * *n + 1; if (j - jj <= 0) { goto L60; } else { goto L61; } L60: i__1 = jj; for (i__ = j; i__ <= i__1; ++i__) { k = i__ - *n; w[k - 1] = w[i__ - 1]; /* L62: */ } i__1 = *n; for (i__ = jil; i__ <= i__1; ++i__) { w[i__ - 2] = w[i__ - 1]; /* L97: */ } L61: idirn -= *n; itone = 3; k = idirn; ixp = jj; aaa = (float)0.; i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { ++ixp; w[k - 1] = w[ixp - 1]; if (aaa - (r__1 = w[k - 1] / e[i__], dabs(r__1)) >= (float)0.) { goto L67; } else { goto L66; } L66: aaa = (r__1 = w[k - 1] / e[i__], dabs(r__1)); L67: ++k; /* L65: */ } ddmag = (float)1.; if (aaa == (float)0.) { aaa = (float)1e-10; } w[*n - 1] = *escale / aaa; iline = *n; goto L7; L37: ixp = jj; aaa = (float)0.; *f = fhold; i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { ++ixp; x[i__] -= w[ixp - 1]; if (aaa * (r__1 = e[i__], dabs(r__1)) - (r__2 = w[ixp - 1], dabs(r__2) ) >= (float)0.) { goto L99; } else { goto L98; } L98: aaa = (r__1 = w[ixp - 1] / e[i__], dabs(r__1)); L99: ; } goto L72; L38: aaa *= di + (float)1.; switch (ind) { case 1: goto L72; case 2: goto L106; } L72: if (*iprint - 2 >= 0) { goto L50; } else { goto L53; } L53: switch (ind) { case 1: goto L109; case 2: goto L88; } L109: if (aaa - (float).1 <= (float)0.) { goto L89; } else { goto L76; } L89: switch (*icon) { case 1: goto L20; case 2: goto L116; } L116: ind = 2; switch (inn) { case 1: goto L100; case 2: goto L101; } L100: inn = 2; k = jjj; i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { ++k; w[k - 1] = x[i__]; x[i__] += e[i__] * (float)10.; /* L102: */ } fkeep = *f; //calcfx_(n, &x[1], f, &ain[1], cs, wl, wgh1, wgh2, thetatr, rmin2, rmax2, & // nxyz[1], hw, dast); icnt++; if (icnt > maxx) goto L999; *f = target_function(parameters, x + 1); ++nfcc; ddmag = (float)0.; goto L108; L76: if (*f - fp >= (float)0.) { goto L78; } else { goto L35; } L78: //s_wsfe(&io___45); //e_wsfe(); // Removed this statement since it does not seem to be very informative // wxPrintf("Warning(VA04): accuracy limited by errors in target function\n"); goto L20; L88: ind = 1; L35: tmp = fp - *f; if (tmp > (float)0.) { ddmag = sqrt(tmp) * (float).4; } else { ddmag = (float)0.; } isgrad = 1; L108: ++iterc; if (iterc - *maxit <= 0) { goto L5; } else { goto L81; } L81: /* 81 WRITE(6,82) MAXIT */ /* L82: */ if (*f - fkeep <= (float)0.) { goto L20; } else { goto L110; } L110: *f = fkeep; i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { ++jjj; x[i__] = w[jjj - 1]; /* L111: */ } goto L20; L101: jil = 1; fp = fkeep; if ((r__1 = *f - fkeep) < (float)0.) { goto L105; } else if (r__1 == 0) { goto L78; } else { goto L104; } L104: jil = 2; fp = *f; *f = fkeep; L105: ixp = jj; i__1 = *n; for (i__ = 1; i__ <= i__1; ++i__) { ++ixp; k = ixp + *n; switch (jil) { case 1: goto L114; case 2: goto L115; } L114: w[ixp - 1] = w[k - 1]; goto L113; L115: w[ixp - 1] = x[i__]; x[i__] = w[k - 1]; L113: ; } jil = 2; goto L92; L106: if (aaa - (float).1 <= (float)0.) { goto L20; } else { goto L107; } L20: return 0; L107: inn = 1; goto L35; L999: for (i__ = 1; i__ <= i__1; i__++) {x[i__] = xs[i__];}; *f = target_function(parameters, x + 1); // Removed this statement since it does not seem to be very informative // wxPrintf("Warning(VA04): Endless loop safety catch, icnt = %i\n", icnt); return 0; } /* va04a_ */ #ifdef __cplusplus } #endif ctffind-4.1.14/src/programs/000077500000000000000000000000001440356052600156445ustar00rootroot00000000000000ctffind-4.1.14/src/programs/ctffind/000077500000000000000000000000001440356052600172615ustar00rootroot00000000000000ctffind-4.1.14/src/programs/ctffind/ctffind.cpp000066400000000000000000004174531440356052600214200ustar00rootroot00000000000000#include "../../core/core_headers.h" //#define threshold_spectrum #define use_epa_rather_than_zero_counting const std::string ctffind_version = "4.1.14"; /* * Changelog * - 4.1.14 * -- bug fixes (memory, equiphase averaging) * -- bug fixes from David Mastronarde (fixed/known phase shift) * - 4.1.13 * -- EPA bug fixed (affected 4.1.12 only) * - 4.1.12 * -- diagnostic image includes radial "equi-phase" average of experimental spectrum in bottom right quadrant * -- new "equi-phase averaging" code will probably replace zero-counting eventually * -- bug fix (affected diagnostics for all 4.x): at very high resolution, Cs dominates and the phase aberration decreases * -- bug fix (affected 4.1.11): fitting was only done up to 5Å * -- slow, exhaustive search is no longer the default (since astigmatism-related bugs appear fixed) * -- Number of OpenMP threads defaults to 1 and can be set by: * --- using interactive user input (under expert options) * --- using the -j command-line option (overrides interactive user input) * -- printout timing information * - 4.1.11 * -- speed-ups from David Mastronarde, including OpenMP threading of the exhaustive search * -- score is now a normalized cross-correlation coefficient (David Mastronarde) * - 4.1.10 * -- astimatism-related bug fixes from David Mastronarde * - 4.1.9 * -- FRC is between a re-normalized version of the amplitude spectrum, to emphasize phase of the Thon rings over their relative amplitudes * -- tweaked criteria for "fit resolution" * -- tweaked FRC computation * -- astigmatism restraint is off by default * -- fixed bug affecting astigmatism * -- tweaked background subtraction (thanks Niko!) - helps with noisy VPP spectra */ class CtffindApp : public MyApp { public: bool DoCalculation(); void DoInteractiveUserInput(); void AddCommandLineOptions(); private: }; class ImageCTFComparison { public: ImageCTFComparison(int wanted_number_of_images, CTF wanted_ctf, float wanted_pixel_size, bool should_find_phase_shift, bool wanted_astigmatism_is_known, float wanted_known_astigmatism, float wanted_known_astigmatism_angle, bool should_fit_defocus_sweep); ~ImageCTFComparison(); void SetImage(int wanted_image_number, Image *new_image); void SetCTF(CTF new_ctf); CTF ReturnCTF(); bool AstigmatismIsKnown(); float ReturnKnownAstigmatism(); float ReturnKnownAstigmatismAngle(); bool FindPhaseShift(); void SetupQuickCorrelation(); int number_of_images; Image *img; // Usually an amplitude spectrum, or an array of amplitude spectra int number_to_correlate; double norm_image; double image_mean; float *azimuths; float *spatial_frequency_squared; int *addresses; private: CTF ctf; float pixel_size; bool find_phase_shift; bool astigmatism_is_known; float known_astigmatism; float known_astigmatism_angle; bool fit_defocus_sweep; }; class CurveCTFComparison { public: float *curve; // Usually the 1D rotational average of the amplitude spectrum of an image int number_of_bins; float reciprocal_pixel_size; // In reciprocal pixels CTF ctf; bool find_phase_shift; }; ImageCTFComparison::ImageCTFComparison(int wanted_number_of_images, CTF wanted_ctf, float wanted_pixel_size, bool should_find_phase_shift, bool wanted_astigmatism_is_known, float wanted_known_astigmatism, float wanted_known_astigmatism_angle, bool should_fit_defocus_sweep) { MyDebugAssertTrue(wanted_number_of_images > 0, "Bad wanted number of images: %i\n",wanted_number_of_images); number_of_images = wanted_number_of_images; img = new Image [wanted_number_of_images]; ctf = wanted_ctf; pixel_size = wanted_pixel_size; find_phase_shift = should_find_phase_shift; astigmatism_is_known = wanted_astigmatism_is_known; known_astigmatism = wanted_known_astigmatism; known_astigmatism_angle = wanted_known_astigmatism_angle; fit_defocus_sweep = should_fit_defocus_sweep; azimuths = NULL; spatial_frequency_squared = NULL; addresses = NULL; number_to_correlate = 0; image_mean = 0.0; norm_image = 0.0; } ImageCTFComparison::~ImageCTFComparison() { for (int image_counter = 0; image_counter < number_of_images; image_counter++) { img[image_counter].Deallocate(); } delete [] img; delete [] azimuths; delete [] spatial_frequency_squared; delete [] addresses; number_to_correlate = 0; } void ImageCTFComparison::SetImage(int wanted_image_number, Image *new_image) { MyDebugAssertTrue(wanted_image_number >= 0 && wanted_image_number < number_of_images, "Wanted image number (%i) is out of bounds", wanted_image_number); img[wanted_image_number].CopyFrom(new_image); } void ImageCTFComparison::SetCTF(CTF new_ctf) { ctf = new_ctf; } void ImageCTFComparison::SetupQuickCorrelation() { img[0].SetupQuickCorrelationWithCTF(ctf, number_to_correlate, norm_image, image_mean, NULL, NULL, NULL); azimuths = new float[number_to_correlate]; spatial_frequency_squared = new float[number_to_correlate]; addresses = new int[number_to_correlate]; img[0].SetupQuickCorrelationWithCTF(ctf, number_to_correlate, norm_image, image_mean, addresses, spatial_frequency_squared, azimuths); } CTF ImageCTFComparison::ReturnCTF() { return ctf; } bool ImageCTFComparison::AstigmatismIsKnown() { return astigmatism_is_known; } float ImageCTFComparison::ReturnKnownAstigmatism() { return known_astigmatism; } float ImageCTFComparison::ReturnKnownAstigmatismAngle() { return known_astigmatism_angle; } bool ImageCTFComparison::FindPhaseShift() { return find_phase_shift; } // This is the function which will be minimised float CtffindObjectiveFunction(void *scoring_parameters, float array_of_values[] ) { ImageCTFComparison *comparison_object = reinterpret_cast < ImageCTFComparison *> (scoring_parameters); MyDebugAssertFalse(std::isnan(array_of_values[0]),"DF1 is NaN!"); MyDebugAssertFalse(std::isnan(array_of_values[1]),"DF2 is NaN!"); CTF my_ctf = comparison_object->ReturnCTF(); if (comparison_object->AstigmatismIsKnown()) { MyDebugAssertTrue(comparison_object->ReturnKnownAstigmatism() >= 0.0,"Known asitgmatism must be >= 0.0"); my_ctf.SetDefocus(array_of_values[0],array_of_values[0] - comparison_object->ReturnKnownAstigmatism(), comparison_object->ReturnKnownAstigmatismAngle()); } else { my_ctf.SetDefocus(array_of_values[0],array_of_values[1],array_of_values[2]); } if (comparison_object->FindPhaseShift()) { if (comparison_object->AstigmatismIsKnown()) { my_ctf.SetAdditionalPhaseShift(array_of_values[1]); } else { my_ctf.SetAdditionalPhaseShift(array_of_values[3]); } } // Evaluate the function float score; if (my_ctf.GetDefocus1() == 0.0f && my_ctf.GetDefocus2() == 0.0f && my_ctf.GetSphericalAberration() == 0.0f) { // When defocus = 0.0 and cs = 0.0, CTF is constant and the scoring function breaks down score = 0.0; } else { if (comparison_object->number_to_correlate) { score = - comparison_object->img[0].QuickCorrelationWithCTF(my_ctf, comparison_object->number_to_correlate, comparison_object->norm_image, comparison_object->image_mean, comparison_object->addresses, comparison_object->spatial_frequency_squared, comparison_object->azimuths); } else { score = - comparison_object->img[0].GetCorrelationWithCTF(my_ctf); } } //MyDebugPrint("(CtffindObjectiveFunction) D1 = %6.2f pxl D2 = %6.2f pxl, PhaseShift = %6.3f rad, Ast = %5.2f rad, Low freq = %f 1/pxl, High freq = %f 1/pxl, Score = %g\n",my_ctf.GetDefocus1(),my_ctf.GetDefocus2(),my_ctf.GetAdditionalPhaseShift(), my_ctf.GetAstigmatismAzimuth(),my_ctf.GetLowestFrequencyForFitting(),my_ctf.GetHighestFrequencyForFitting(),score); MyDebugAssertFalse(std::isnan(score),"Score is NaN!"); return score; } //#pragma GCC push_options //#pragma GCC optimize ("O0") // This is the function which will be minimised when dealing with 1D fitting float CtffindCurveObjectiveFunction(void *scoring_parameters, float array_of_values[] ) { CurveCTFComparison *comparison_object = reinterpret_cast < CurveCTFComparison *> (scoring_parameters); CTF my_ctf = comparison_object->ctf; my_ctf.SetDefocus(array_of_values[0],array_of_values[0],0.0); if (comparison_object->find_phase_shift) { my_ctf.SetAdditionalPhaseShift(array_of_values[1]); } // Compute the cross-correlation double cross_product = 0.0; double norm_curve = 0.0; double norm_ctf = 0.0; int number_of_values = 0; int bin_counter; float current_spatial_frequency_squared; const float lowest_freq = pow(my_ctf.GetLowestFrequencyForFitting(),2); const float highest_freq = pow(my_ctf.GetHighestFrequencyForFitting(),2); float current_ctf_value; for ( bin_counter = 0 ; bin_counter < comparison_object->number_of_bins; bin_counter ++ ) { current_spatial_frequency_squared = pow(float(bin_counter)*comparison_object->reciprocal_pixel_size,2); if (current_spatial_frequency_squared > lowest_freq && current_spatial_frequency_squared < highest_freq) { current_ctf_value = fabsf(my_ctf.Evaluate(current_spatial_frequency_squared,0.0)); MyDebugAssertTrue(current_ctf_value >= -1.0 && current_ctf_value <= 1.0,"Bad ctf value: %f",current_ctf_value); number_of_values++; cross_product += comparison_object->curve[bin_counter] * current_ctf_value; norm_curve += pow(comparison_object->curve[bin_counter],2); norm_ctf += pow(current_ctf_value,2); } } MyDebugAssertTrue(norm_ctf > 0.0,"Bad norm_ctf: %f\n", norm_ctf); MyDebugAssertTrue(norm_curve > 0.0,"Bad norm_curve: %f\n", norm_curve); //MyDebugPrint("(CtffindCurveObjectiveFunction) D1 = %6.2f , PhaseShift = %6.3f , Low freq = %f /pxl, High freq = %f/pxl Score = %g\n",array_of_values[0], array_of_values[1], my_ctf.GetLowestFrequencyForFitting(),my_ctf.GetHighestFrequencyForFitting(), - cross_product / sqrtf(norm_ctf * norm_curve)); // Note, we are not properly normalizing the cross correlation coefficient. For our // purposes this should be OK, since the average power of the theoretical CTF should not // change much with defocus. At least I hope so. return - cross_product / sqrtf(norm_ctf * norm_curve); } //#pragma GCC pop_options float FindRotationalAlignmentBetweenTwoStacksOfImages(Image *self, Image *other_image, int number_of_images, float search_half_range, float search_step_size, float minimum_radius, float maximum_radius); void ComputeImagesWithNumberOfExtremaAndCTFValues(CTF *ctf, Image *number_of_extrema, Image *ctf_values); int ReturnSpectrumBinNumber(int number_of_bins, float number_of_extrema_profile[], Image *number_of_extrema, long address, Image *ctf_values, float ctf_values_profile[]); bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]); void ComputeEquiPhaseAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Curve *epa_pre_max, Curve *epa_post_max); void OverlayCTF( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins_in_1d_spectra, double spatial_frequency[], double rotational_average_astig[], float number_of_extrema_profile[], float ctf_values_profile[], Curve *equiphase_average_pre_max, Curve *equiphase_average_post_max); void ComputeFRCBetween1DSpectrumAndFit( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[], double frc[], double frc_sigma[], int first_fit_bin); bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ); void Renormalize1DSpectrumForFRC( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[]); float ReturnAzimuthToUseFor1DPlots(CTF *ctf); IMPLEMENT_APP(CtffindApp) // override the DoInteractiveUserInput void CtffindApp::DoInteractiveUserInput() { float lowest_allowed_minimum_resolution = 50.0; std::string input_filename = "/dev/null"; bool input_is_a_movie = false; int number_of_frames_to_average = 0; std::string output_diagnostic_filename = "/dev/null"; float pixel_size = 0.0; float acceleration_voltage = 0.0; float spherical_aberration = 0.0; float amplitude_contrast = 0.0; int box_size = 0; float minimum_resolution = 0.0; float maximum_resolution = 0.0; float minimum_defocus = 0.0; float maximum_defocus = 0.0; float defocus_search_step = 0.0; bool astigmatism_is_known = false; float known_astigmatism = 0.0; float known_astigmatism_angle = 0.0; bool slower_search = false; bool should_restrain_astigmatism = false; float astigmatism_tolerance = 0.0; bool find_additional_phase_shift = false; float minimum_additional_phase_shift = 0.0; float maximum_additional_phase_shift = 0.0; float additional_phase_shift_search_step = 0.0; bool give_expert_options = false; bool resample_if_pixel_too_small = false; bool movie_is_gain_corrected = false; wxString gain_filename = "/dev/null"; bool correct_movie_mag_distortion = false; float movie_mag_distortion_angle = 0.0; float movie_mag_distortion_major_scale = 1.0; float movie_mag_distortion_minor_scale = 1.0; bool defocus_is_known = false; float known_defocus_1 = 0.0; float known_defocus_2 = 0.0; float known_phase_shift = 0.0; int desired_number_of_threads = 1; // Things we need for old school input double temp_double = -1.0; long temp_long = -1; float xmag = -1; float dstep = -1.0; int token_counter = -1; const bool old_school_input = command_line_parser.FoundSwitch("old-school-input"); const bool old_school_input_ctffind4 = command_line_parser.FoundSwitch("old-school-input-ctffind4"); if (old_school_input || old_school_input_ctffind4) { astigmatism_is_known = false; known_astigmatism = 0.0; known_astigmatism_angle = 0.0; resample_if_pixel_too_small = true; movie_is_gain_corrected = true; gain_filename = ""; char buf[4096]; wxString my_string; // Line 1 std::cin.getline(buf,4096); input_filename = buf; // Line 2 std::cin.getline(buf,4096); output_diagnostic_filename = buf; // Line 3 std::cin.getline(buf,4096); my_string = buf; wxStringTokenizer tokenizer(my_string,","); if (tokenizer.CountTokens() != 5) { SendError(wxString::Format("Bad number of arguments (%i, expected %i) in line 3 of input\n",tokenizer.CountTokens(),5)); exit(-1); } token_counter = -1; while (tokenizer.HasMoreTokens()) { token_counter ++; tokenizer.GetNextToken().ToDouble(&temp_double); switch (token_counter) { case 0: spherical_aberration = float(temp_double); break; case 1: acceleration_voltage = float(temp_double); break; case 2: amplitude_contrast = float(temp_double); break; case 3: xmag = float(temp_double); break; case 4: dstep = float(temp_double); break; default: wxPrintf("Ooops - bad token number: %li\n",tokenizer.GetPosition()); MyDebugAssertTrue(false,"oops\n"); } } pixel_size = dstep * 10000.0 / xmag; // Line 4 std::cin.getline(buf,4096); my_string = buf; tokenizer.SetString(my_string,","); if (tokenizer.CountTokens() != 7) { SendError(wxString::Format("Bad number of arguments (%i, expected %i) in line 4 of input\n",tokenizer.CountTokens(),7)); exit(-1); } token_counter = -1; while (tokenizer.HasMoreTokens()) { token_counter ++; switch (token_counter) { case 0: tokenizer.GetNextToken().ToLong(&temp_long); box_size = int(temp_long); break; case 1: tokenizer.GetNextToken().ToDouble(&temp_double); minimum_resolution = float(temp_double); break; case 2: tokenizer.GetNextToken().ToDouble(&temp_double); maximum_resolution = float(temp_double); break; case 3: tokenizer.GetNextToken().ToDouble(&temp_double); minimum_defocus= float(temp_double); break; case 4: tokenizer.GetNextToken().ToDouble(&temp_double); maximum_defocus = float(temp_double); break; case 5: tokenizer.GetNextToken().ToDouble(&temp_double); defocus_search_step = float(temp_double); break; case 6: tokenizer.GetNextToken().ToDouble(&temp_double); astigmatism_tolerance = float(temp_double); break; } } // If we are getting dAst = 0.0, which is the default in Relion, the user probably // expects the ctffind3 behaviour, which is no restraint on astigmatism if (astigmatism_tolerance == 0.0) astigmatism_tolerance = -100.0; // Output for old-school users if (is_running_locally) { wxPrintf("\n CS[mm], HT[kV], AmpCnst, XMAG, DStep[um]\n"); wxPrintf("%5.1f%9.1f%8.2f%10.1f%9.3f\n\n",spherical_aberration,acceleration_voltage,amplitude_contrast,xmag,dstep); } // Extra lines of input if (old_school_input_ctffind4) { // Line 5 std::cin.getline(buf,4096); my_string = buf; tokenizer.SetString(my_string,","); if (tokenizer.CountTokens() != 2) { SendError(wxString::Format("Bad number of arguments (%i, expected %i) in line 5 of input\n",tokenizer.CountTokens(),2)); exit(-1); } while (tokenizer.HasMoreTokens()) { switch (tokenizer.GetPosition()) { case 0: tokenizer.GetNextToken().ToDouble(&temp_double); if (int(temp_double) != 0) { input_is_a_movie = true; } else { input_is_a_movie = false; } break; case 1: tokenizer.GetNextToken().ToDouble(&temp_double); number_of_frames_to_average = 1; if (input_is_a_movie) { number_of_frames_to_average = int(temp_double); } break; } } // Line 6 std::cin.getline(buf,4096); my_string = buf; tokenizer.SetString(my_string,","); if (tokenizer.CountTokens() != 4) { SendError(wxString::Format("Bad number of arguments (%i, expected %i) in line 6 of input\n",tokenizer.CountTokens(),4)); exit(-1); } while (tokenizer.HasMoreTokens()) { switch (tokenizer.GetPosition()) { case 0: tokenizer.GetNextToken().ToDouble(&temp_double); if (int(temp_double) != 0) { find_additional_phase_shift = true; } else { find_additional_phase_shift = false; } break; case 1: tokenizer.GetNextToken().ToDouble(&temp_double); minimum_additional_phase_shift = 0.0; if (find_additional_phase_shift) { minimum_additional_phase_shift = float(temp_double); } break; case 2: tokenizer.GetNextToken().ToDouble(&temp_double); maximum_additional_phase_shift = 0.0; if (find_additional_phase_shift) { maximum_additional_phase_shift = float(temp_double); } break; case 3: tokenizer.GetNextToken().ToDouble(&temp_double); additional_phase_shift_search_step = 0.0; if (find_additional_phase_shift) { additional_phase_shift_search_step = float(temp_double); } break; } } } // end of old school ctffind4 input else { input_is_a_movie = false; find_additional_phase_shift = false; minimum_additional_phase_shift = 0.0; maximum_additional_phase_shift = 0.0; additional_phase_shift_search_step = 0.0; number_of_frames_to_average = 1; } // Do some argument checking on movie processing option MRCFile input_file(input_filename,false); if (input_is_a_movie) { if (input_file.ReturnZSize() < number_of_frames_to_average) { SendError(wxString::Format("Input stack has %i images, so you cannot average %i frames together\n",input_file.ReturnZSize(),number_of_frames_to_average)); ExitMainLoop(); } } else { // We're not doing movie processing if (input_file.ReturnZSize() > 1) { SendError("Input stacks are only supported --old-school-input-ctffind4 if doing movie processing\n"); ExitMainLoop(); } } if (find_additional_phase_shift) { if (minimum_additional_phase_shift > maximum_additional_phase_shift) { SendError(wxString::Format("Minimum phase shift (%f) cannot be greater than maximum phase shift (%f)\n",minimum_additional_phase_shift,maximum_additional_phase_shift)); ExitMainLoop(); } } desired_number_of_threads = 1; } // end of test for old-school-input or old-school-input-ctffind4 else { UserInput *my_input = new UserInput("Ctffind", ctffind_version); input_filename = my_input->GetFilenameFromUser("Input image file name", "Filename of input image", "input.mrc", true ); ImageFile input_file(input_filename,false); if (input_file.ReturnZSize() > 1) { input_is_a_movie = my_input->GetYesNoFromUser("Input is a movie (stack of frames)","Answer yes if the input file is a stack of frames from a dose-fractionated movie. If not, each image will be processed separately","no"); } else { input_is_a_movie = false; } if (input_is_a_movie) { number_of_frames_to_average = my_input->GetIntFromUser("Number of frames to average together","If the number of electrons per frame is too low, there may be strong artefacts in the estimated power spectrum. This can be alleviated by averaging frames with each other in real space before computing their Fourier transforms","1"); } else { number_of_frames_to_average = 1; } output_diagnostic_filename = my_input->GetFilenameFromUser("Output diagnostic image file name","Will contain the experimental power spectrum and the best CTF fit","diagnostic_output.mrc",false); pixel_size = my_input->GetFloatFromUser("Pixel size","In Angstroms","1.0",0.0); acceleration_voltage = my_input->GetFloatFromUser("Acceleration voltage","in kV","300.0",0.0); spherical_aberration = my_input->GetFloatFromUser("Spherical aberration","in mm","2.70",0.0); amplitude_contrast = my_input->GetFloatFromUser("Amplitude contrast","Fraction of amplitude contrast","0.07",0.0,1.0); box_size = my_input->GetIntFromUser("Size of amplitude spectrum to compute","in pixels","512",128); minimum_resolution = my_input->GetFloatFromUser("Minimum resolution","Lowest resolution used for fitting CTF (Angstroms)","30.0",0.0,lowest_allowed_minimum_resolution); maximum_resolution = my_input->GetFloatFromUser("Maximum resolution","Highest resolution used for fitting CTF (Angstroms)","5.0",0.0,minimum_resolution); minimum_defocus = my_input->GetFloatFromUser("Minimum defocus","Positive values for underfocus. Lowest value to search over (Angstroms)","5000.0"); maximum_defocus = my_input->GetFloatFromUser("Maximum defocus","Positive values for underfocus. Highest value to search over (Angstroms)","50000.0",minimum_defocus); defocus_search_step = my_input->GetFloatFromUser("Defocus search step","Step size for defocus search (Angstroms)","100.0",1.0); astigmatism_is_known = my_input->GetYesNoFromUser("Do you know what astigmatism is present?","Answer yes if you already know how much astigmatism was present. If you answer no, the program will search for the astigmatism and astigmatism angle","no"); if (astigmatism_is_known) { slower_search = my_input->GetYesNoFromUser("Slower, more exhaustive search?","Answer yes to use a slower exhaustive search against 2D spectra (rather than 1D radial averages) for the initial search","no");; should_restrain_astigmatism = false; astigmatism_tolerance = -100.0; known_astigmatism = my_input->GetFloatFromUser("Known astigmatism", "In Angstroms, the amount of astigmatism, defined as the difference between the defocus along the major and minor axes","0.0",0.0); known_astigmatism_angle = my_input->GetFloatFromUser("Known astigmatism angle", "In degrees, the angle of astigmatism","0.0"); } else { slower_search = my_input->GetYesNoFromUser("Slower, more exhaustive search?","Answer yes if you expect very high astigmatism (say, greater than 1000A) or in tricky cases. In that case, a slower exhaustive search against 2D spectra (rather than 1D radial averages) will be used for the initial search","no"); should_restrain_astigmatism = my_input->GetYesNoFromUser("Use a restraint on astigmatism?","If you answer yes, the CTF parameter search and refinement will penalise large astigmatism. You will specify the astigmatism tolerance in the next question. If you answer no, no such restraint will apply","no"); if (should_restrain_astigmatism) { astigmatism_tolerance = my_input->GetFloatFromUser("Expected (tolerated) astigmatism","Astigmatism values much larger than this will be penalised (Angstroms). Give a negative value to turn off this restraint.","200.0"); } else { astigmatism_tolerance = -100.0; // a negative value here signals that we don't want any restraint on astigmatism } } find_additional_phase_shift = my_input->GetYesNoFromUser("Find additional phase shift?","Input micrograph was recorded using a phase plate with variable phase shift, which you want to find","no"); if (find_additional_phase_shift) { minimum_additional_phase_shift = my_input->GetFloatFromUser("Minimum phase shift (rad)","Lower bound of the search for additional phase shift. Phase shift is of scattered electrons relative to unscattered electrons. In radians","0.0",-3.15,3.15); maximum_additional_phase_shift = my_input->GetFloatFromUser("Maximum phase shift (rad)","Upper bound of the search for additional phase shift. Phase shift is of scattered electrons relative to unscattered electrons. In radians","3.15",minimum_additional_phase_shift,3.15); additional_phase_shift_search_step = my_input->GetFloatFromUser("Phase shift search step","Step size for phase shift search (radians)","0.5",0.0,maximum_additional_phase_shift-minimum_additional_phase_shift); } else { minimum_additional_phase_shift = 0.0; maximum_additional_phase_shift = 0.0; additional_phase_shift_search_step = 0.0; } give_expert_options = my_input->GetYesNoFromUser("Do you want to set expert options?","There are options which normally not changed, but can be accessed by answering yes here","no"); if (give_expert_options) { resample_if_pixel_too_small = my_input->GetYesNoFromUser("Resample micrograph if pixel size too small?","When the pixel is too small, Thon rings appear very thin and near the origin of the spectrum, which can lead to suboptimal fitting. This options resamples micrographs to a more reasonable pixel size if needed","yes"); if (input_is_a_movie) { movie_is_gain_corrected = my_input->GetYesNoFromUser("Movie is gain-corrected?", "If the movie is not gain-corrected, you will need to provide a gain reference image", "yes"); if (movie_is_gain_corrected) { gain_filename = ""; } else { gain_filename = my_input->GetFilenameFromUser("Gain image filename", "The filename of the gain reference image for the detector/camera", "gain.dm4", true); } correct_movie_mag_distortion = my_input->GetYesNoFromUser("Correct Movie Mag. Distortion?", "If the movie has a mag distortion you can specify the parameters to correct it prior to estimation", "no"); if (correct_movie_mag_distortion == true) { movie_mag_distortion_angle = my_input->GetFloatFromUser("Mag. distortion angle","The angle of the distortion","0.0"); movie_mag_distortion_major_scale = my_input->GetFloatFromUser("Mag. distortion major scale","The scale factor along the major axis","1.0"); movie_mag_distortion_minor_scale = my_input->GetFloatFromUser("Mag. distortion minor scale","The scale factor along the minor axis","1.0");; } else { movie_mag_distortion_angle = 0.0; movie_mag_distortion_major_scale = 1.0; movie_mag_distortion_minor_scale = 1.0; } } else { movie_is_gain_corrected = true; } defocus_is_known = my_input->GetYesNoFromUser("Do you already know the defocus?","Answer yes if you already know the defocus and you just want to know the score or fit resolution. If you answer yes, the known astigmatism parameter specified eariler will be ignored","no"); if (defocus_is_known) { /* * Right now, we don't support phase plate data for this. The proper way to do this would be to also ask whether phase shift is known. * Another acceptable solution might be to say that if you know the defocus you must also know the phase shift (in other words, this would * only be used to test the ctffind scoring function / diagnostics using given defocus parameters). Neither are implemented right now, * because I don't need either. */ known_defocus_1 = my_input->GetFloatFromUser("Known defocus 1", "In Angstroms, the defocus along the first axis","0.0"); known_defocus_2 = my_input->GetFloatFromUser("Known defocus 2", "In Angstroms, the defocus along the second axis","0.0"); known_astigmatism_angle = my_input->GetFloatFromUser("Known astigmatism angle", "In degrees, the angle of astigmatism","0.0"); if (find_additional_phase_shift) { known_phase_shift = my_input->GetFloatFromUser("Known phase shift (radians)", "In radians, the phase shift (from a phase plate presumably)","0.0"); } } else { known_defocus_1 = 0.0; known_defocus_2 = 0.0; known_astigmatism_angle = 0.0; known_phase_shift = 0.0; } desired_number_of_threads = my_input->GetIntFromUser("Desired number of parallel threads","The command-line option -j will override this","1",1); } else // expert options not supplied by user { resample_if_pixel_too_small = true; movie_is_gain_corrected = true; defocus_is_known = false; desired_number_of_threads = 1; } delete my_input; } my_current_job.Reset(35); my_current_job.ManualSetArguments("tbitffffifffffbfbfffbffbbsbfffbfffi",input_filename.c_str(), //1 input_is_a_movie, number_of_frames_to_average, output_diagnostic_filename.c_str(), pixel_size, acceleration_voltage, spherical_aberration, amplitude_contrast, box_size, minimum_resolution, //10 maximum_resolution, minimum_defocus, maximum_defocus, defocus_search_step, slower_search, astigmatism_tolerance, find_additional_phase_shift, minimum_additional_phase_shift, maximum_additional_phase_shift, additional_phase_shift_search_step, //20 astigmatism_is_known, known_astigmatism, known_astigmatism_angle, resample_if_pixel_too_small, movie_is_gain_corrected, gain_filename.ToStdString().c_str(), correct_movie_mag_distortion, movie_mag_distortion_angle, movie_mag_distortion_major_scale, movie_mag_distortion_minor_scale, defocus_is_known, known_defocus_1, known_defocus_2, known_phase_shift, desired_number_of_threads); } // Optional command-line stuff void CtffindApp::AddCommandLineOptions() { command_line_parser.AddLongSwitch("old-school-input","Pretend this is ctffind3 (for compatibility with old scripts and programs)"); command_line_parser.AddLongSwitch("old-school-input-ctffind4","Accept parameters from stdin, like ctffind3, but with extra lines for ctffind4-specific options (movie processing and phase shift estimation"); command_line_parser.AddLongSwitch("amplitude-spectrum-input","The input image is an amplitude spectrum, not a real-space image"); command_line_parser.AddLongSwitch("filtered-amplitude-spectrum-input","The input image is filtered (background-subtracted) amplitude spectrum"); command_line_parser.AddLongSwitch("fast","Skip computation of fit statistics as well as spectrum contrast enhancement"); command_line_parser.AddOption("j","","Desired number of threads. Overrides interactive user input. Is overriden by env var OMP_NUM_THREADS",wxCMD_LINE_VAL_NUMBER); } // override the do calculation method which will be what is actually run.. bool CtffindApp::DoCalculation() { wxDateTime time_start = wxDateTime::Now(); // Arguments for this job const std::string input_filename = my_current_job.arguments[0].ReturnStringArgument(); const bool input_is_a_movie = my_current_job.arguments[1].ReturnBoolArgument(); const int number_of_frames_to_average = my_current_job.arguments[2].ReturnIntegerArgument(); const std::string output_diagnostic_filename = my_current_job.arguments[3].ReturnStringArgument(); float pixel_size_of_input_image = my_current_job.arguments[4].ReturnFloatArgument(); // no longer const, as the mag distortion can change it. const float acceleration_voltage = my_current_job.arguments[5].ReturnFloatArgument(); const float spherical_aberration = my_current_job.arguments[6].ReturnFloatArgument(); const float amplitude_contrast = my_current_job.arguments[7].ReturnFloatArgument(); const int box_size = my_current_job.arguments[8].ReturnIntegerArgument(); const float minimum_resolution = my_current_job.arguments[9].ReturnFloatArgument(); const float maximum_resolution = my_current_job.arguments[10].ReturnFloatArgument(); const float minimum_defocus = my_current_job.arguments[11].ReturnFloatArgument(); const float maximum_defocus = my_current_job.arguments[12].ReturnFloatArgument(); const float defocus_search_step = my_current_job.arguments[13].ReturnFloatArgument(); const bool slower_search = my_current_job.arguments[14].ReturnBoolArgument(); const float astigmatism_tolerance = my_current_job.arguments[15].ReturnFloatArgument(); const bool find_additional_phase_shift = my_current_job.arguments[16].ReturnBoolArgument(); const float minimum_additional_phase_shift = my_current_job.arguments[17].ReturnFloatArgument(); const float maximum_additional_phase_shift = my_current_job.arguments[18].ReturnFloatArgument(); const float additional_phase_shift_search_step = my_current_job.arguments[19].ReturnFloatArgument(); const bool astigmatism_is_known = my_current_job.arguments[20].ReturnBoolArgument(); const float known_astigmatism = my_current_job.arguments[21].ReturnFloatArgument(); const float known_astigmatism_angle = my_current_job.arguments[22].ReturnFloatArgument(); const bool resample_if_pixel_too_small = my_current_job.arguments[23].ReturnBoolArgument(); const bool movie_is_gain_corrected = my_current_job.arguments[24].ReturnBoolArgument(); const wxString gain_filename = my_current_job.arguments[25].ReturnStringArgument(); const bool correct_movie_mag_distortion = my_current_job.arguments[26].ReturnBoolArgument(); const float movie_mag_distortion_angle = my_current_job.arguments[27].ReturnFloatArgument(); const float movie_mag_distortion_major_scale = my_current_job.arguments[28].ReturnFloatArgument(); const float movie_mag_distortion_minor_scale = my_current_job.arguments[29].ReturnFloatArgument(); const bool defocus_is_known = my_current_job.arguments[30].ReturnBoolArgument(); const float known_defocus_1 = my_current_job.arguments[31].ReturnFloatArgument(); const float known_defocus_2 = my_current_job.arguments[32].ReturnFloatArgument(); const float known_phase_shift = my_current_job.arguments[33].ReturnFloatArgument(); int desired_number_of_threads = my_current_job.arguments[34].ReturnIntegerArgument(); // if we are applying a mag distortion, it can change the pixel size, so do that here to make sure it is used forever onwards.. if (input_is_a_movie && correct_movie_mag_distortion) { pixel_size_of_input_image = ReturnMagDistortionCorrectedPixelSize(pixel_size_of_input_image, movie_mag_distortion_major_scale, movie_mag_distortion_minor_scale); } // These variables will be set by command-line options const bool old_school_input = command_line_parser.FoundSwitch("old-school-input") || command_line_parser.FoundSwitch("old-school-input-ctffind4"); const bool amplitude_spectrum_input = command_line_parser.FoundSwitch("amplitude-spectrum-input"); const bool filtered_amplitude_spectrum_input = command_line_parser.FoundSwitch("filtered-amplitude-spectrum-input"); const bool compute_extra_stats = ! command_line_parser.FoundSwitch("fast"); const bool boost_ring_contrast = ! command_line_parser.FoundSwitch("fast"); long command_line_desired_number_of_threads; if (command_line_parser.Found("j", &command_line_desired_number_of_threads)) { // Command-line argument overrides desired_number_of_threads = command_line_desired_number_of_threads; } // Resampling of input images to ensure that the pixel size isn't too small const float target_nyquist_after_resampling = 2.8; // Angstroms const float target_pixel_size_after_resampling = 0.5 * target_nyquist_after_resampling; float pixel_size_for_fitting = pixel_size_of_input_image; int temporary_box_size; // Maybe the user wants to hold the phase shift value (which they can do by giving the same value for min and max) const bool fixed_additional_phase_shift = fabs(maximum_additional_phase_shift - minimum_additional_phase_shift) < 0.01; // This could become a user-supplied parameter later - for now only for developers / expert users const bool follow_1d_search_with_local_2D_brute_force = false; // Initial search should be done only using up to that resolution, to improve radius of convergence const float maximum_resolution_for_initial_search = 5.0; // Debugging const bool dump_debug_files = false; /* * Scoring function */ float MyFunction(float []); // Other variables int number_of_movie_frames; int number_of_micrographs; ImageFile input_file(input_filename,false); Image *average_spectrum = new Image(); Image *average_spectrum_masked = new Image(); wxString output_text_fn; ProgressBar *my_progress_bar; NumericTextFile *output_text; NumericTextFile *output_text_avrot; int current_micrograph_number; int number_of_tiles_used; Image *current_power_spectrum = new Image(); int current_first_frame_within_average; int current_frame_within_average; int current_input_location; Image *current_input_image = new Image(); Image *current_input_image_square = new Image(); int micrograph_square_dimension; Image *temp_image = new Image(); Image *sum_image = new Image(); Image *resampled_power_spectrum = new Image(); bool resampling_is_necessary; CTF *current_ctf = new CTF(); float average, sigma; int convolution_box_size; ImageCTFComparison *comparison_object_2D; CurveCTFComparison comparison_object_1D; float estimated_astigmatism_angle; float bf_halfrange[4]; float bf_midpoint[4]; float bf_stepsize[4]; float cg_starting_point[4]; float cg_accuracy[4]; int number_of_search_dimensions; BruteForceSearch *brute_force_search; int counter; ConjugateGradient *conjugate_gradient_minimizer; int current_output_location; int number_of_bins_in_1d_spectra; Curve *number_of_averaged_pixels = new Curve(); Curve *rotational_average = new Curve(); Image *number_of_extrema_image = new Image(); Image *ctf_values_image = new Image(); double *rotational_average_astig = NULL; double *rotational_average_astig_renormalized = NULL; double *spatial_frequency = NULL; double *spatial_frequency_in_reciprocal_angstroms = NULL; double *rotational_average_astig_fit = NULL; float *number_of_extrema_profile = NULL; float *ctf_values_profile = NULL; double *fit_frc = NULL; double *fit_frc_sigma = NULL; MRCFile output_diagnostic_file(output_diagnostic_filename,true); int last_bin_with_good_fit; double *values_to_write_out = new double[7]; float best_score_after_initial_phase; int last_bin_without_aliasing; ImageFile gain_file; Image *gain = new Image(); float final_score; // Timings variables wxDateTime time_before_spectrum_computation; wxDateTime time_after_spectrum_computation; wxDateTime time_before_diagnostics; wxDateTime time_finish; // Some argument checking if (minimum_resolution < maximum_resolution) { SendError(wxString::Format("Error: Minimum resolution (%f) higher than maximum resolution (%f). Terminating.", minimum_resolution,maximum_resolution)); ExitMainLoop(); } if (minimum_defocus > maximum_defocus) { SendError(wxString::Format("Minimum defocus must be less than maximum defocus. Terminating.")); ExitMainLoop(); } // How many micrographs are we dealing with if (input_is_a_movie) { // We only support 1 movie per file number_of_movie_frames = input_file.ReturnZSize(); number_of_micrographs = 1; } else { number_of_movie_frames = 1; number_of_micrographs = input_file.ReturnZSize(); } if (is_running_locally) { // Print out information about input file input_file.PrintInfo(); } // Prepare the output text file output_text_fn = FilenameReplaceExtension(output_diagnostic_filename,"txt"); if (is_running_locally) { output_text = new NumericTextFile(output_text_fn,OPEN_TO_WRITE,7); // Print header to the output text file output_text->WriteCommentLine("# Output from CTFFind version %s, run on %s\n",ctffind_version.c_str(),wxDateTime::Now().FormatISOCombined(' ').ToStdString().c_str()); output_text->WriteCommentLine("# Input file: %s ; Number of micrographs: %i\n",input_filename.c_str(),number_of_micrographs); output_text->WriteCommentLine("# Pixel size: %0.3f Angstroms ; acceleration voltage: %0.1f keV ; spherical aberration: %0.2f mm ; amplitude contrast: %0.2f\n",pixel_size_of_input_image,acceleration_voltage,spherical_aberration,amplitude_contrast); output_text->WriteCommentLine("# Box size: %i pixels ; min. res.: %0.1f Angstroms ; max. res.: %0.1f Angstroms ; min. def.: %0.1f um; max. def. %0.1f um\n",box_size,minimum_resolution,maximum_resolution,minimum_defocus,maximum_defocus); output_text->WriteCommentLine("# Columns: #1 - micrograph number; #2 - defocus 1 [Angstroms]; #3 - defocus 2; #4 - azimuth of astigmatism; #5 - additional phase shift [radians]; #6 - cross correlation; #7 - spacing (in Angstroms) up to which CTF rings were fit successfully\n"); } // Prepare a text file with 1D rotational average spectra output_text_fn = FilenameAddSuffix(output_text_fn.ToStdString(),"_avrot"); if (! old_school_input && number_of_micrographs > 1 && is_running_locally) { wxPrintf("Will estimate the CTF parameters for %i micrographs.\n",number_of_micrographs); wxPrintf("Results will be written to this file: %s\n",output_text->ReturnFilename()); wxPrintf("\nEstimating CTF parameters...\n\n"); my_progress_bar = new ProgressBar(number_of_micrographs); } // time_before_spectrum_computation = wxDateTime::Now(); // Prepare the gain_reference if (input_is_a_movie && ! movie_is_gain_corrected) { gain_file.OpenFile(gain_filename.ToStdString(), false); gain->ReadSlice(&gain_file,1); } // Prepare the average spectrum image average_spectrum->Allocate(box_size,box_size,true); // Loop over micrographs for (current_micrograph_number=1; current_micrograph_number <= number_of_micrographs; current_micrograph_number++) { if (is_running_locally && (old_school_input || number_of_micrographs == 1)) wxPrintf("Working on micrograph %i of %i\n", current_micrograph_number, number_of_micrographs); number_of_tiles_used = 0; average_spectrum->SetToConstant(0.0); average_spectrum->is_in_real_space = true; if (amplitude_spectrum_input || filtered_amplitude_spectrum_input) { current_power_spectrum->ReadSlice(&input_file,current_micrograph_number); current_power_spectrum->ForwardFFT(); average_spectrum->Allocate(box_size,box_size,1,false); current_power_spectrum->ClipInto(average_spectrum); average_spectrum->BackwardFFT(); average_spectrum_masked->CopyFrom(average_spectrum); } else { for (current_first_frame_within_average = 1; current_first_frame_within_average <= number_of_movie_frames; current_first_frame_within_average += number_of_frames_to_average) { for (current_frame_within_average = 1; current_frame_within_average <= number_of_frames_to_average; current_frame_within_average++) { current_input_location = current_first_frame_within_average + number_of_movie_frames * (current_micrograph_number-1) + (current_frame_within_average-1); if (current_input_location > number_of_movie_frames * current_micrograph_number) continue; // Read the image in current_input_image->ReadSlice(&input_file,current_input_location); if (current_input_image->IsConstant()) { if (is_running_locally == false) { // don't crash, as this will lead to the gui job never finishing, instead send a blank result.. SendError(wxString::Format("Error: location %i of input file %s is blank, defocus parameters will be set to 0",current_input_location, input_filename)); float results_array[7]; results_array[0] = 0.0; // Defocus 1 (Angstroms) results_array[1] = 0.0; // Defocus 2 (Angstroms) results_array[2] = 0.0; // Astigmatism angle (degrees) results_array[3] = 0.0; // Additional phase shift (e.g. from phase plate) (radians) results_array[4] = 0.0; // CTFFIND score results_array[5] = 0.0; results_array[6] = 0.0; my_result.SetResult(7,results_array); delete average_spectrum; delete average_spectrum_masked; delete current_power_spectrum; delete current_input_image; delete current_input_image_square; delete temp_image; delete sum_image; delete resampled_power_spectrum; delete number_of_extrema_image; delete ctf_values_image; delete gain; delete [] values_to_write_out; return true; } else { SendError(wxString::Format("Error: location %i of input file %s is blank",current_input_location, input_filename)); ExitMainLoop(); } } // Apply gain reference if (input_is_a_movie && ! movie_is_gain_corrected) { if (! current_input_image->HasSameDimensionsAs(gain)) { SendError(wxString::Format("Error: location %i of input file %s does not have same dimensions as the gain image",current_input_location,input_filename)); ExitMainLoop(); } current_input_image->MultiplyPixelWise(*gain); } // correct for mag distortion if (input_is_a_movie && correct_movie_mag_distortion) { current_input_image->CorrectMagnificationDistortion(movie_mag_distortion_angle, movie_mag_distortion_major_scale, movie_mag_distortion_minor_scale); } // Make the image square micrograph_square_dimension = std::max(current_input_image->logical_x_dimension,current_input_image->logical_y_dimension); if (IsOdd((micrograph_square_dimension))) micrograph_square_dimension++; if (current_input_image->logical_x_dimension != micrograph_square_dimension || current_input_image->logical_y_dimension != micrograph_square_dimension) { current_input_image_square->Allocate(micrograph_square_dimension,micrograph_square_dimension,true); //current_input_image->ClipInto(current_input_image_square,current_input_image->ReturnAverageOfRealValues()); current_input_image->ClipIntoLargerRealSpace2D(current_input_image_square,current_input_image->ReturnAverageOfRealValues()); current_input_image->Consume(current_input_image_square); } // if (current_frame_within_average == 1) { sum_image->Allocate(current_input_image->logical_x_dimension,current_input_image->logical_y_dimension,true); sum_image->SetToConstant(0.0); } sum_image->AddImage(current_input_image); } // end of loop over frames to average together current_input_image->Consume(sum_image); // Taper the edges of the micrograph in real space, to lessen Gibbs artefacts // Introduces an artefact of its own, so it's not clear on balance whether tapering helps, especially with modern micrographs from good detectors //current_input_image->TaperEdges(); number_of_tiles_used++; // Compute the amplitude spectrum current_power_spectrum->Allocate(current_input_image->logical_x_dimension,current_input_image->logical_y_dimension,true); current_input_image->ForwardFFT(false); current_input_image->ComputeAmplitudeSpectrumFull2D(current_power_spectrum); //current_power_spectrum->QuickAndDirtyWriteSlice("dbg_spec_before_resampling.mrc",1); // Set origin of amplitude spectrum to 0.0 current_power_spectrum->real_values[current_power_spectrum->ReturnReal1DAddressFromPhysicalCoord(current_power_spectrum->physical_address_of_box_center_x,current_power_spectrum->physical_address_of_box_center_y,current_power_spectrum->physical_address_of_box_center_z)] = 0.0; // Resample the amplitude spectrum if (resample_if_pixel_too_small && pixel_size_of_input_image < target_pixel_size_after_resampling) { // The input pixel was too small, so let's resample the amplitude spectrum into a large temporary box, before clipping the center out for fitting temporary_box_size = round(float(box_size) / pixel_size_of_input_image * target_pixel_size_after_resampling); if (IsOdd(temporary_box_size)) temporary_box_size++; resampling_is_necessary = current_power_spectrum->logical_x_dimension != box_size || current_power_spectrum->logical_y_dimension != box_size; if (resampling_is_necessary) { current_power_spectrum->ForwardFFT(false); resampled_power_spectrum->Allocate(temporary_box_size,temporary_box_size,1,false); current_power_spectrum->ClipInto(resampled_power_spectrum); resampled_power_spectrum->BackwardFFT(); temp_image->Allocate(box_size,box_size,1,true); temp_image->SetToConstant(0.0); // To avoid valgrind uninitialised errors, but maybe this is a waste? resampled_power_spectrum->ClipInto(temp_image); resampled_power_spectrum->Consume(temp_image); } else { resampled_power_spectrum->CopyFrom(current_power_spectrum); } pixel_size_for_fitting = pixel_size_of_input_image * float(temporary_box_size) / float(box_size); } else { // The regular way (the input pixel size was large enough) resampling_is_necessary = current_power_spectrum->logical_x_dimension != box_size || current_power_spectrum->logical_y_dimension != box_size; if (resampling_is_necessary) { current_power_spectrum->ForwardFFT(false); resampled_power_spectrum->Allocate(box_size,box_size,1,false); current_power_spectrum->ClipInto(resampled_power_spectrum); resampled_power_spectrum->BackwardFFT(); } else { resampled_power_spectrum->CopyFrom(current_power_spectrum); } } average_spectrum->AddImage(resampled_power_spectrum); } // end of loop over movie frames // We need to take care of the scaling of the FFTs, as well as the averaging of tiles if (resampling_is_necessary) { average_spectrum->MultiplyByConstant(1.0 / ( float(number_of_tiles_used) * current_input_image->logical_x_dimension * current_input_image->logical_y_dimension * current_power_spectrum->logical_x_dimension * current_power_spectrum->logical_y_dimension ) ); } else { average_spectrum->MultiplyByConstant(1.0 / ( float(number_of_tiles_used) * current_input_image->logical_x_dimension * current_input_image->logical_y_dimension ) ); } } // end of test of whether we were given amplitude spectra on input //average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_before_bg_sub.mrc",1); // Filter the amplitude spectrum, remove background if (! filtered_amplitude_spectrum_input) { // Try to weaken cross artefacts average_spectrum->ComputeAverageAndSigmaOfValuesInSpectrum(float(average_spectrum->logical_x_dimension)*pixel_size_for_fitting/minimum_resolution,float(average_spectrum->logical_x_dimension),average,sigma,12); average_spectrum->DivideByConstant(sigma); average_spectrum->SetMaximumValueOnCentralCross(average/sigma+10.0); // average_spectrum_masked->CopyFrom(average_spectrum); //average_spectrum->QuickAndDirtyWriteSlice("dbg_average_spectrum_before_conv.mrc",1); // Compute low-pass filtered version of the spectrum convolution_box_size = int( float(average_spectrum->logical_x_dimension) * pixel_size_for_fitting / minimum_resolution * sqrt(2.0) ); if (IsEven(convolution_box_size)) convolution_box_size++; current_power_spectrum->Allocate(average_spectrum->logical_x_dimension,average_spectrum->logical_y_dimension,true); current_power_spectrum->SetToConstant(0.0); // According to valgrind, this avoid potential problems later on. average_spectrum->SpectrumBoxConvolution(current_power_spectrum,convolution_box_size,float(average_spectrum->logical_x_dimension)*pixel_size_for_fitting/minimum_resolution); //current_power_spectrum->QuickAndDirtyWriteSlice("dbg_spec_convoluted.mrc",1); // Subtract low-pass-filtered spectrum from the spectrum. This should remove the background slope. average_spectrum->SubtractImage(current_power_spectrum); // average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_before_thresh.mrc",1); // Threshold high values average_spectrum->SetMaximumValue(average_spectrum->ReturnMaximumValue(3,3)); // convolution_box_size = int( float(average_spectrum->logical_x_dimension) * pixel_size_for_fitting / minimum_resolution / sqrt(2.0) ); // if (IsEven(convolution_box_size)) convolution_box_size++; // current_power_spectrum->SetToConstant(0.0); // According to valgrind, this avoid potential problems later on. // average_spectrum_masked->SpectrumBoxConvolution(current_power_spectrum,convolution_box_size,float(average_spectrum_masked->logical_x_dimension)*pixel_size_for_fitting/minimum_resolution); // average_spectrum_masked->SubtractImage(current_power_spectrum); // average_spectrum_masked->SetMaximumValue(average_spectrum_masked->ReturnMaximumValue(3,3)); average_spectrum_masked->CopyFrom(average_spectrum); average_spectrum_masked->CosineMask(float(average_spectrum_masked->logical_x_dimension)*pixel_size_for_fitting/std::max(maximum_resolution, 8.0f),float(average_spectrum_masked->logical_x_dimension)*pixel_size_for_fitting/std::max(maximum_resolution, 4.0f), true); // average_spectrum_masked->QuickAndDirtyWriteSlice("dbg_spec_before_thresh.mrc",1); // average_spectrum_masked->CorrectSinc(); // average_spectrum_masked->CorrectSinc(float(average_spectrum_masked->logical_x_dimension)*pixel_size_for_fitting/std::max(maximum_resolution, 8.0f), 0.5, true, 0.0); } /* * * * We now have a spectrum which we can use to fit CTFs * * */ time_after_spectrum_computation = wxDateTime::Now(); if (dump_debug_files) average_spectrum->WriteSlicesAndFillHeader("dbg_spectrum_for_fitting.mrc",pixel_size_for_fitting); #ifdef threshold_spectrum wxPrintf("DEBUG: thresholding spectrum\n"); for (counter = 0; counter < average_spectrum->real_memory_allocated; counter ++ ) { average_spectrum->real_values[counter] = std::max(average_spectrum->real_values[counter], -0.0f); average_spectrum->real_values[counter] = std::min(average_spectrum->real_values[counter], 1.0f); } average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_thr.mrc",1); #endif // Set up the CTF object current_ctf->Init(acceleration_voltage,spherical_aberration,amplitude_contrast,minimum_defocus,minimum_defocus,0.0,1.0/minimum_resolution,1.0/std::max(maximum_resolution,maximum_resolution_for_initial_search),astigmatism_tolerance,pixel_size_for_fitting,minimum_additional_phase_shift); current_ctf->SetDefocus(minimum_defocus/pixel_size_for_fitting,minimum_defocus/pixel_size_for_fitting,0.0); current_ctf->SetAdditionalPhaseShift(minimum_additional_phase_shift); // Set up the comparison object comparison_object_2D = new ImageCTFComparison(1,*current_ctf,pixel_size_for_fitting,find_additional_phase_shift && ! fixed_additional_phase_shift, astigmatism_is_known, known_astigmatism / pixel_size_for_fitting, known_astigmatism_angle / 180.0 * PIf, false); comparison_object_2D->SetImage(0,average_spectrum_masked); comparison_object_2D->SetupQuickCorrelation(); if (defocus_is_known) { current_ctf->SetDefocus(known_defocus_1/pixel_size_for_fitting,known_defocus_2/pixel_size_for_fitting,known_astigmatism_angle / 180.0 * PIf); current_ctf->SetAdditionalPhaseShift(known_phase_shift); current_ctf->SetHighestFrequencyForFitting(pixel_size_for_fitting/maximum_resolution); comparison_object_2D->SetCTF(*current_ctf); comparison_object_2D->SetupQuickCorrelation(); final_score = 0.0; final_score = comparison_object_2D->img[0].QuickCorrelationWithCTF(*current_ctf, comparison_object_2D->number_to_correlate, comparison_object_2D->norm_image, comparison_object_2D->image_mean, comparison_object_2D->addresses, comparison_object_2D->spatial_frequency_squared, comparison_object_2D->azimuths); } else { if (is_running_locally && old_school_input) { wxPrintf("\nSEARCHING CTF PARAMETERS...\n"); } // Let's look for the astigmatism angle first if (astigmatism_is_known) { estimated_astigmatism_angle = known_astigmatism_angle; } else { temp_image->CopyFrom(average_spectrum); temp_image->ApplyMirrorAlongY(); //temp_image.QuickAndDirtyWriteSlice("dbg_spec_y.mrc",1); estimated_astigmatism_angle = 0.5 * FindRotationalAlignmentBetweenTwoStacksOfImages(average_spectrum,temp_image,1,90.0,5.0,pixel_size_for_fitting/minimum_resolution,pixel_size_for_fitting/std::max(maximum_resolution,maximum_resolution_for_initial_search)); } //MyDebugPrint ("Estimated astigmatism angle = %f degrees\n", estimated_astigmatism_angle); /* * Initial brute-force search, in 1D (fast, but not as accurate) */ if (!slower_search) { // 1D rotational average number_of_bins_in_1d_spectra = int(ceil(average_spectrum_masked->ReturnMaximumDiagonalRadius())); rotational_average->SetupXAxis(0.0,float(number_of_bins_in_1d_spectra) * average_spectrum_masked->fourier_voxel_size_x,number_of_bins_in_1d_spectra); number_of_averaged_pixels->CopyFrom(rotational_average); average_spectrum_masked->Compute1DRotationalAverage(*rotational_average,*number_of_averaged_pixels,true); comparison_object_1D.ctf = *current_ctf; comparison_object_1D.curve = new float[number_of_bins_in_1d_spectra]; for (counter=0; counter < number_of_bins_in_1d_spectra; counter++) { comparison_object_1D.curve[counter] = rotational_average->data_y[counter]; } comparison_object_1D.find_phase_shift = find_additional_phase_shift && ! fixed_additional_phase_shift; comparison_object_1D.number_of_bins = number_of_bins_in_1d_spectra; comparison_object_1D.reciprocal_pixel_size = average_spectrum_masked->fourier_voxel_size_x; // We can now look for the defocus value bf_halfrange[0] = 0.5 * (maximum_defocus - minimum_defocus) / pixel_size_for_fitting; bf_halfrange[1] = 0.5 * (maximum_additional_phase_shift - minimum_additional_phase_shift); bf_midpoint[0] = minimum_defocus / pixel_size_for_fitting + bf_halfrange[0]; bf_midpoint[1] = minimum_additional_phase_shift + bf_halfrange[1]; bf_stepsize[0] = defocus_search_step / pixel_size_for_fitting; bf_stepsize[1] = additional_phase_shift_search_step; if (find_additional_phase_shift && ! fixed_additional_phase_shift) { number_of_search_dimensions = 2; } else { number_of_search_dimensions = 1; } // DNM: Do one-time set of phase shift for fixed value if (find_additional_phase_shift && fixed_additional_phase_shift) { current_ctf->SetAdditionalPhaseShift(minimum_additional_phase_shift); } // Actually run the BF search brute_force_search = new BruteForceSearch(); brute_force_search->Init(&CtffindCurveObjectiveFunction,&comparison_object_1D,number_of_search_dimensions,bf_midpoint,bf_halfrange,bf_stepsize,false,false,desired_number_of_threads); brute_force_search->Run(); /* wxPrintf("After 1D brute\n"); wxPrintf(" DFMID1 DFMID2 ANGAST CC\n"); wxPrintf("%12.2f%12.2f%12.2f%12.5f\n",brute_force_search->GetBestValue(0),brute_force_search->GetBestValue(0),0.0,brute_force_search->GetBestScore()); wxPrintf("%12.2f%12.2f%12.2f%12.5f\n",brute_force_search->GetBestValue(0)*pixel_size_for_fitting,brute_force_search->GetBestValue(0)*pixel_size_for_fitting,0.0,brute_force_search->GetBestScore()); */ /* * We can now do a local optimization. * The end point of the BF search is the beginning of the CG search, but we will want to use * the full resolution range */ current_ctf->SetHighestFrequencyForFitting(pixel_size_for_fitting/maximum_resolution); comparison_object_1D.ctf = *current_ctf; for (counter=0;counterGetBestValue(counter); } cg_accuracy[0] = 100.0; cg_accuracy[1] = 0.05; conjugate_gradient_minimizer = new ConjugateGradient(); conjugate_gradient_minimizer->Init(&CtffindCurveObjectiveFunction,&comparison_object_1D,number_of_search_dimensions,cg_starting_point,cg_accuracy); conjugate_gradient_minimizer->Run(); for (counter=0;counterGetBestValue(counter); } current_ctf->SetDefocus(cg_starting_point[0], cg_starting_point[0],estimated_astigmatism_angle / 180.0 * PIf); if (find_additional_phase_shift) { if (fixed_additional_phase_shift) { current_ctf->SetAdditionalPhaseShift(minimum_additional_phase_shift); } else { current_ctf->SetAdditionalPhaseShift(cg_starting_point[1]); } } // Remember the best score so far best_score_after_initial_phase = - conjugate_gradient_minimizer->GetBestScore(); // Cleanup delete conjugate_gradient_minimizer; delete brute_force_search; delete [] comparison_object_1D.curve; } // end of the fast search over the 1D function /* * Brute-force search over the 2D scoring function. * This is either the first search we are doing, or just a refinement * starting from the result of the 1D search */ if (slower_search || (!slower_search && follow_1d_search_with_local_2D_brute_force)) { // Setup the parameters for the brute force search if (slower_search) // This is the first search we are doing - scan the entire range the user specified { if (astigmatism_is_known) { bf_halfrange[0] = 0.5 * (maximum_defocus-minimum_defocus)/pixel_size_for_fitting; bf_halfrange[1] = 0.5 * (maximum_additional_phase_shift-minimum_additional_phase_shift); bf_midpoint[0] = minimum_defocus/pixel_size_for_fitting + bf_halfrange[0]; bf_midpoint[1] = minimum_additional_phase_shift + bf_halfrange[3]; bf_stepsize[0] = defocus_search_step/pixel_size_for_fitting; bf_stepsize[1] = additional_phase_shift_search_step; if (find_additional_phase_shift && ! fixed_additional_phase_shift) { number_of_search_dimensions = 2; } else { number_of_search_dimensions = 1; } } else { bf_halfrange[0] = 0.5 * (maximum_defocus-minimum_defocus)/pixel_size_for_fitting; bf_halfrange[1] = bf_halfrange[0]; bf_halfrange[2] = 0.0; bf_halfrange[3] = 0.5 * (maximum_additional_phase_shift-minimum_additional_phase_shift); bf_midpoint[0] = minimum_defocus/pixel_size_for_fitting + bf_halfrange[0]; bf_midpoint[1] = bf_midpoint[0]; bf_midpoint[2] = estimated_astigmatism_angle / 180.0 * PIf; bf_midpoint[3] = minimum_additional_phase_shift + bf_halfrange[3]; bf_stepsize[0] = defocus_search_step/pixel_size_for_fitting; bf_stepsize[1] = bf_stepsize[0]; bf_stepsize[2] = 0.0; bf_stepsize[3] = additional_phase_shift_search_step; if (find_additional_phase_shift && ! fixed_additional_phase_shift) { number_of_search_dimensions = 4; } else { number_of_search_dimensions = 3; } } } else // we will do a brute-force search near the result of the search over the 1D objective function { if (astigmatism_is_known) { bf_midpoint[0] = current_ctf->GetDefocus1(); bf_midpoint[1] = current_ctf->GetAdditionalPhaseShift(); bf_stepsize[0] = defocus_search_step/pixel_size_for_fitting; bf_stepsize[1] = additional_phase_shift_search_step; bf_halfrange[0] = 2.0 * defocus_search_step/pixel_size_for_fitting + 0.1; bf_halfrange[1] = 2.0 * additional_phase_shift_search_step + 0.01; if (find_additional_phase_shift && ! fixed_additional_phase_shift) { number_of_search_dimensions = 2; } else { number_of_search_dimensions = 1; } } else { bf_midpoint[0] = current_ctf->GetDefocus1(); bf_midpoint[1] = current_ctf->GetDefocus2(); bf_midpoint[2] = current_ctf->GetAstigmatismAzimuth(); bf_midpoint[3] = minimum_additional_phase_shift + bf_halfrange[3]; bf_stepsize[0] = defocus_search_step/pixel_size_for_fitting; bf_stepsize[1] = bf_stepsize[0]; bf_stepsize[2] = 0.0; bf_stepsize[3] = additional_phase_shift_search_step; if (astigmatism_tolerance > 0) { bf_halfrange[0] = 2.0 * astigmatism_tolerance/pixel_size_for_fitting + 0.1; } else { bf_halfrange[0] = 2.0 * defocus_search_step/pixel_size_for_fitting + 0.1; } bf_halfrange[1] = bf_halfrange[0]; bf_halfrange[2] = 0.0; bf_halfrange[3] = 2.0 * additional_phase_shift_search_step + 0.01; if (find_additional_phase_shift && ! fixed_additional_phase_shift) { number_of_search_dimensions = 4; } else { number_of_search_dimensions = 3; } } } // Actually run the BF search (we run a local minimizer at every grid point only if this is a refinement search following 1D search (otherwise the full brute-force search would get too long) brute_force_search = new BruteForceSearch(); brute_force_search->Init(&CtffindObjectiveFunction,comparison_object_2D,number_of_search_dimensions,bf_midpoint,bf_halfrange,bf_stepsize,!slower_search,is_running_locally,desired_number_of_threads); brute_force_search->Run(); // The end point of the BF search is the beginning of the CG search for (counter=0;counterGetBestValue(counter); } // if (astigmatism_is_known) { current_ctf->SetDefocus(cg_starting_point[0],cg_starting_point[0] - known_astigmatism / pixel_size_for_fitting, known_astigmatism_angle / 180.0 * PIf); if (find_additional_phase_shift) { if (fixed_additional_phase_shift) { current_ctf->SetAdditionalPhaseShift(minimum_additional_phase_shift); } else { current_ctf->SetAdditionalPhaseShift(cg_starting_point[1]); } } } else { current_ctf->SetDefocus(cg_starting_point[0],cg_starting_point[1],cg_starting_point[2]); if (find_additional_phase_shift) { if (fixed_additional_phase_shift) { current_ctf->SetAdditionalPhaseShift(minimum_additional_phase_shift); } else { current_ctf->SetAdditionalPhaseShift(cg_starting_point[3]); } } } current_ctf->EnforceConvention(); // Remember the best score so far best_score_after_initial_phase = - brute_force_search->GetBestScore(); delete brute_force_search; } // Print out the results of brute force search //if (is_running_locally && old_school_input) { wxPrintf(" DFMID1 DFMID2 ANGAST CC\n"); wxPrintf("%12.2f%12.2f%12.2f%12.5f\n",current_ctf->GetDefocus1()*pixel_size_for_fitting,current_ctf->GetDefocus2()*pixel_size_for_fitting,current_ctf->GetAstigmatismAzimuth()*180.0/PIf,best_score_after_initial_phase); } // Now we refine in the neighbourhood by using Powell's conjugate gradient algorithm if (is_running_locally && old_school_input) { wxPrintf("\nREFINING CTF PARAMETERS...\n"); wxPrintf(" DFMID1 DFMID2 ANGAST CC\n"); } /* * Set up the conjugate gradient minimization of the 2D scoring function */ if (astigmatism_is_known) { cg_starting_point[0] = current_ctf->GetDefocus1(); if (find_additional_phase_shift) cg_starting_point[1] = current_ctf->GetAdditionalPhaseShift(); if (find_additional_phase_shift && ! fixed_additional_phase_shift) { number_of_search_dimensions = 2; } else { number_of_search_dimensions = 1; } cg_accuracy[0] = 100.0; cg_accuracy[1] = 0.05; } else { cg_accuracy[0] = 100.0; //TODO: try defocus_search_step / pix_size_for_fitting / 10.0 cg_accuracy[1] = 100.0; cg_accuracy[2] = 0.025; cg_accuracy[3] = 0.05; cg_starting_point[0] = current_ctf->GetDefocus1(); cg_starting_point[1] = current_ctf->GetDefocus2(); if (slower_search || (!slower_search && follow_1d_search_with_local_2D_brute_force)) { // we did a search against the 2D power spectrum so we have a better estimate // of the astigmatism angle in the CTF object cg_starting_point[2] = current_ctf->GetAstigmatismAzimuth(); } else { // all we have right now is the guessed astigmatism angle from the mirror // trick before any CTF fitting was even tried cg_starting_point[2] = estimated_astigmatism_angle / 180.0 * PIf; } if (find_additional_phase_shift) cg_starting_point[3] = current_ctf->GetAdditionalPhaseShift(); if (find_additional_phase_shift && ! fixed_additional_phase_shift) { number_of_search_dimensions = 4; } else { number_of_search_dimensions = 3; } } // CG minimization comparison_object_2D->SetCTF(*current_ctf); conjugate_gradient_minimizer = new ConjugateGradient(); conjugate_gradient_minimizer->Init(&CtffindObjectiveFunction,comparison_object_2D,number_of_search_dimensions,cg_starting_point,cg_accuracy); conjugate_gradient_minimizer->Run(); // Remember the results of the refinement for (counter=0;counterGetBestValue(counter); } if (astigmatism_is_known) { current_ctf->SetDefocus(cg_starting_point[0],cg_starting_point[0] - known_astigmatism / pixel_size_for_fitting, known_astigmatism_angle / 180.0 * PIf); if (find_additional_phase_shift) { if (fixed_additional_phase_shift) { current_ctf->SetAdditionalPhaseShift(minimum_additional_phase_shift); } else { current_ctf->SetAdditionalPhaseShift(cg_starting_point[1]); } } } else { current_ctf->SetDefocus(cg_starting_point[0],cg_starting_point[1],cg_starting_point[2]); if (find_additional_phase_shift) { if (fixed_additional_phase_shift) { current_ctf->SetAdditionalPhaseShift(minimum_additional_phase_shift); } else { current_ctf->SetAdditionalPhaseShift(cg_starting_point[3]); } } } current_ctf->EnforceConvention(); // Print results to the terminal if (is_running_locally && old_school_input) { wxPrintf("%12.2f%12.2f%12.2f%12.5f Final Values\n",current_ctf->GetDefocus1()*pixel_size_for_fitting,current_ctf->GetDefocus2()*pixel_size_for_fitting,current_ctf->GetAstigmatismAzimuth()*180.0/PIf,-conjugate_gradient_minimizer->GetBestScore()); if (find_additional_phase_shift) { wxPrintf("Final phase shift = %0.3f radians\n",current_ctf->GetAdditionalPhaseShift()); } } final_score = -conjugate_gradient_minimizer->GetBestScore(); } // End of test for defocus_is_known /* * We're all done with our search & refinement of defocus and phase shift parameter values. * Now onto diagnostics. */ time_before_diagnostics = wxDateTime::Now(); // Generate diagnostic image if (dump_debug_files) average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_diag_start.mrc",1); current_output_location = current_micrograph_number; average_spectrum->AddConstant(-1.0 * average_spectrum->ReturnAverageOfRealValuesOnEdges()); /* * Attempt some renormalisations - we want to do this over a range not affected by the central peak or strong Thon rings, * so as to emphasize the "regular" Thon rings */ float start_zero = sqrtf(current_ctf->ReturnSquaredSpatialFrequencyOfAZero(3,current_ctf->GetAstigmatismAzimuth(),true)); float finish_zero = sqrtf(current_ctf->ReturnSquaredSpatialFrequencyOfAZero(4,current_ctf->GetAstigmatismAzimuth(),true)); float normalization_radius_min = start_zero * average_spectrum->logical_x_dimension; float normalization_radius_max = finish_zero * average_spectrum->logical_x_dimension; if (start_zero > current_ctf->GetHighestFrequencyForFitting() || start_zero < current_ctf->GetLowestFrequencyForFitting() || finish_zero > current_ctf->GetHighestFrequencyForFitting() || finish_zero < current_ctf->GetLowestFrequencyForFitting()) { normalization_radius_max = current_ctf->GetHighestFrequencyForFitting() * average_spectrum->logical_x_dimension; normalization_radius_min = std::max(0.5f * normalization_radius_max, current_ctf->GetLowestFrequencyForFitting() * average_spectrum->logical_x_dimension); } MyDebugAssertTrue(normalization_radius_max > normalization_radius_min,"Bad values for min (%f) and max (%f) normalization radii\n"); if (normalization_radius_max - normalization_radius_min > 2.0) { average_spectrum->ComputeAverageAndSigmaOfValuesInSpectrum( normalization_radius_min, normalization_radius_max, average,sigma); average_spectrum->CircleMask(5.0,true); average_spectrum->SetMaximumValueOnCentralCross(average); average_spectrum->SetMinimumAndMaximumValues(average - 4.0 * sigma, average + 4.0 * sigma); average_spectrum->ComputeAverageAndSigmaOfValuesInSpectrum( normalization_radius_min, normalization_radius_max, average,sigma); average_spectrum->AddConstant(-1.0 * average); average_spectrum->MultiplyByConstant(1.0 / sigma); average_spectrum->AddConstant(average); } if (dump_debug_files) average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_diag_1.mrc",1); // 1D rotational average number_of_bins_in_1d_spectra = int(ceil(average_spectrum->ReturnMaximumDiagonalRadius())); rotational_average->SetupXAxis(0.0,float(number_of_bins_in_1d_spectra) * average_spectrum->fourier_voxel_size_x ,number_of_bins_in_1d_spectra); rotational_average->ZeroYData(); //number_of_averaged_pixels.ZeroYData(); number_of_averaged_pixels->CopyFrom(rotational_average); average_spectrum->Compute1DRotationalAverage(*rotational_average,*number_of_averaged_pixels,true); // Rotational average, taking astigmatism into account Curve equiphase_average_pre_max; Curve equiphase_average_post_max; if (compute_extra_stats) { number_of_extrema_image->Allocate(average_spectrum->logical_x_dimension,average_spectrum->logical_y_dimension,true); ctf_values_image->Allocate(average_spectrum->logical_x_dimension,average_spectrum->logical_y_dimension,true); spatial_frequency = new double[number_of_bins_in_1d_spectra]; rotational_average_astig = new double[number_of_bins_in_1d_spectra]; rotational_average_astig_renormalized = new double[number_of_bins_in_1d_spectra]; rotational_average_astig_fit = new double[number_of_bins_in_1d_spectra]; number_of_extrema_profile = new float[number_of_bins_in_1d_spectra]; ctf_values_profile = new float[number_of_bins_in_1d_spectra]; fit_frc = new double[number_of_bins_in_1d_spectra]; fit_frc_sigma = new double[number_of_bins_in_1d_spectra]; ComputeImagesWithNumberOfExtremaAndCTFValues(current_ctf, number_of_extrema_image, ctf_values_image); //ctf_values_image.QuickAndDirtyWriteSlice("dbg_ctf_values.mrc",1); if (dump_debug_files) { average_spectrum->QuickAndDirtyWriteSlice("dbg_spectrum_before_1dave.mrc",1); number_of_extrema_image->QuickAndDirtyWriteSlice("dbg_num_extrema.mrc",1); } ComputeRotationalAverageOfPowerSpectrum(average_spectrum, current_ctf, number_of_extrema_image, ctf_values_image, number_of_bins_in_1d_spectra, spatial_frequency, rotational_average_astig, rotational_average_astig_fit, rotational_average_astig_renormalized, number_of_extrema_profile, ctf_values_profile); #ifdef use_epa_rather_than_zero_counting ComputeEquiPhaseAverageOfPowerSpectrum(average_spectrum, current_ctf, &equiphase_average_pre_max, &equiphase_average_post_max); // Replace the old curve with EPA values { float current_sq_sf; float azimuth_for_1d_plots = ReturnAzimuthToUseFor1DPlots(current_ctf); float defocus_for_1d_plots = current_ctf->DefocusGivenAzimuth(azimuth_for_1d_plots); float sq_sf_of_phase_shift_maximum = current_ctf->ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(defocus_for_1d_plots); for (counter=1;counterPhaseShiftGivenSquaredSpatialFrequencyAndDefocus(current_sq_sf,defocus_for_1d_plots)); } else { rotational_average_astig[counter] = equiphase_average_post_max.ReturnLinearInterpolationFromX(current_ctf->PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(current_sq_sf,defocus_for_1d_plots)); } rotational_average_astig_renormalized[counter] = rotational_average_astig[counter]; } Renormalize1DSpectrumForFRC(number_of_bins_in_1d_spectra,rotational_average_astig_renormalized,rotational_average_astig_fit,number_of_extrema_profile); } #endif // Here, do FRC int first_fit_bin = 0; for (int bin_counter = number_of_bins_in_1d_spectra - 1; bin_counter >= 0; bin_counter -- ) { if (spatial_frequency[bin_counter] >= current_ctf->GetLowestFrequencyForFitting()) first_fit_bin = bin_counter; } ComputeFRCBetween1DSpectrumAndFit(number_of_bins_in_1d_spectra,rotational_average_astig_renormalized,rotational_average_astig_fit,number_of_extrema_profile,fit_frc,fit_frc_sigma,first_fit_bin); // At what bin does CTF aliasing become problematic? last_bin_without_aliasing = 0; int location_of_previous_extremum = 0; for (counter=1;counter= 0.9) { // We just reached a new extremum if (counter-location_of_previous_extremum < 4) { last_bin_without_aliasing = location_of_previous_extremum; break; } location_of_previous_extremum = counter; } } if (is_running_locally && old_school_input && last_bin_without_aliasing != 0) { wxPrintf("CTF aliasing apparent from %0.1f Angstroms\n",pixel_size_for_fitting / spatial_frequency[last_bin_without_aliasing]); } } if (dump_debug_files) average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_diag_2.mrc",1); // Until what frequency were CTF rings detected? if (compute_extra_stats) { static float low_threshold = 0.1; static float frc_significance_threshold = 0.5; // In analogy to the usual criterion when comparing experimental results to the atomic model static float high_threshold = 0.66; bool at_last_bin_with_good_fit; int number_of_bins_above_low_threshold = 0; int number_of_bins_above_significance_threshold = 0; int number_of_bins_above_high_threshold = 0; int first_bin_to_check = 0.1 * number_of_bins_in_1d_spectra; MyDebugAssertTrue(first_bin_to_check >= 0 && first_bin_to_check < number_of_bins_in_1d_spectra,"Bad first bin to check\n"); //wxPrintf("Will only check from bin %i of %i onwards\n", first_bin_to_check, number_of_bins_in_1d_spectra); last_bin_with_good_fit = -1; for (counter=first_bin_to_check;counter 3) && ( fit_frc[counter] < low_threshold) ) || ( (number_of_bins_above_high_threshold > 3) && ( fit_frc[counter] < frc_significance_threshold) ); if (at_last_bin_with_good_fit) { last_bin_with_good_fit = counter; break; } // Count number of bins above given thresholds if (fit_frc[counter] > low_threshold) number_of_bins_above_low_threshold++; if (fit_frc[counter] > frc_significance_threshold) number_of_bins_above_significance_threshold++; if (fit_frc[counter] > high_threshold) number_of_bins_above_high_threshold++; } //wxPrintf("%i bins out of %i checked were above significance threshold\n",number_of_bins_above_significance_threshold,number_of_bins_in_1d_spectra-first_bin_to_check); if ( number_of_bins_above_significance_threshold == number_of_bins_in_1d_spectra-first_bin_to_check) last_bin_with_good_fit = number_of_bins_in_1d_spectra - 1; if ( number_of_bins_above_significance_threshold == 0 ) last_bin_with_good_fit = 1; last_bin_with_good_fit = std::min(last_bin_with_good_fit,number_of_bins_in_1d_spectra); } else { last_bin_with_good_fit = 1; } #ifdef DEBUG //MyDebugAssertTrue(last_bin_with_good_fit >= 0 && last_bin_with_good_fit < number_of_bins_in_1d_spectra,"Did not find last bin with good fit: %i", last_bin_with_good_fit); if (! (last_bin_with_good_fit >= 0 && last_bin_with_good_fit < number_of_bins_in_1d_spectra) ) { wxPrintf("WARNING: Did not find last bin with good fit: %i\n", last_bin_with_good_fit); } #else if (last_bin_with_good_fit < 1 && last_bin_with_good_fit >= number_of_bins_in_1d_spectra) { last_bin_with_good_fit = 1; } #endif // Prepare output diagnostic image //average_spectrum->AddConstant(- average_spectrum->ReturnAverageOfRealValuesOnEdges()); // this used to be done in OverlayCTF / CTFOperation in the Fortran code //average_spectrum.QuickAndDirtyWriteSlice("dbg_spec_diag_3.mrc",1); if (dump_debug_files) average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_before_rescaling.mrc",1); if (compute_extra_stats) { RescaleSpectrumAndRotationalAverage(average_spectrum,number_of_extrema_image,ctf_values_image,number_of_bins_in_1d_spectra,spatial_frequency,rotational_average_astig,rotational_average_astig_fit,number_of_extrema_profile,ctf_values_profile,last_bin_without_aliasing,last_bin_with_good_fit); } //average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_before_thresholding.mrc",1); normalization_radius_max = std::max(normalization_radius_max,float(average_spectrum->logical_x_dimension * spatial_frequency[last_bin_with_good_fit])); average_spectrum->ComputeAverageAndSigmaOfValuesInSpectrum( normalization_radius_min, normalization_radius_max, average,sigma); average_spectrum->SetMinimumAndMaximumValues(average - sigma, average + 2.0 * sigma ); //average_spectrum->QuickAndDirtyWriteSlice("dbg_spec_before_overlay.mrc",1); OverlayCTF(average_spectrum, current_ctf, number_of_extrema_image, ctf_values_image,number_of_bins_in_1d_spectra,spatial_frequency,rotational_average_astig,number_of_extrema_profile,ctf_values_profile, &equiphase_average_pre_max, &equiphase_average_post_max); average_spectrum->WriteSlice(&output_diagnostic_file,current_output_location); output_diagnostic_file.SetDensityStatistics(average_spectrum->ReturnMinimumValue(), average_spectrum->ReturnMaximumValue(), average_spectrum->ReturnAverageOfRealValues(), 0.1); // Keep track of time time_finish = wxDateTime::Now(); // Print more detailed results to terminal if (is_running_locally && number_of_micrographs == 1) { wxPrintf("\nTimings\n"); wxTimeSpan time_to_initialize = time_before_spectrum_computation.Subtract(time_start); wxTimeSpan time_to_compute_spectrum = time_after_spectrum_computation.Subtract(time_before_spectrum_computation); wxTimeSpan time_to_fit = time_before_diagnostics.Subtract(time_after_spectrum_computation); wxTimeSpan time_to_diagnose = time_finish.Subtract(time_before_diagnostics); wxTimeSpan time_total = time_finish.Subtract(time_start); wxPrintf(" Initialization : %s\n",time_to_initialize.Format()); wxPrintf(" Spectrum computation : %s\n",time_to_compute_spectrum.Format()); wxPrintf(" Parameter search : %s\n",time_to_fit.Format()); wxPrintf(" Diagnosis : %s\n",time_to_diagnose.Format()); wxPrintf(" Total : %s\n",time_total.Format()); wxPrintf("\n\nEstimated defocus values : %0.2f , %0.2f Angstroms\nEstimated azimuth of astigmatism: %0.2f degrees\n",current_ctf->GetDefocus1()*pixel_size_for_fitting,current_ctf->GetDefocus2()*pixel_size_for_fitting,current_ctf->GetAstigmatismAzimuth() / PIf * 180.0); if (find_additional_phase_shift) { wxPrintf("Additional phase shift : %0.3f degrees (%0.3f radians) (%0.3f PIf)\n",current_ctf->GetAdditionalPhaseShift() / PIf * 180.0, current_ctf->GetAdditionalPhaseShift(),current_ctf->GetAdditionalPhaseShift() / PIf); } wxPrintf("Score : %0.5f\n", final_score); wxPrintf("Pixel size for fitting : %0.3f Angstroms\n",pixel_size_for_fitting); if (compute_extra_stats) { wxPrintf("Thon rings with good fit up to : %0.1f Angstroms\n",pixel_size_for_fitting / spatial_frequency[last_bin_with_good_fit]); if (last_bin_without_aliasing != 0) { wxPrintf("CTF aliasing apparent from : %0.1f Angstroms\n", pixel_size_for_fitting / spatial_frequency[last_bin_without_aliasing]); } else { wxPrintf("Did not detect CTF aliasing\n"); } } } // Warn the user if significant aliasing occurred within the fit range if (compute_extra_stats && last_bin_without_aliasing != 0 && spatial_frequency[last_bin_without_aliasing] < current_ctf->GetHighestFrequencyForFitting()) { if (is_running_locally && number_of_micrographs == 1) { MyPrintfRed("Warning: CTF aliasing occurred within your CTF fitting range. Consider computing a larger spectrum (current size = %i).\n",box_size); } else { //SendInfo(wxString::Format("Warning: for image %s (location %i of %i), CTF aliasing occurred within the CTF fitting range. Consider computing a larger spectrum (current size = %i)\n",input_filename,current_micrograph_number, number_of_micrographs,box_size)); } } if (is_running_locally) { // Write out results to a summary file values_to_write_out[0] = current_micrograph_number; values_to_write_out[1] = current_ctf->GetDefocus1() * pixel_size_for_fitting; values_to_write_out[2] = current_ctf->GetDefocus2() * pixel_size_for_fitting; values_to_write_out[3] = current_ctf->GetAstigmatismAzimuth() * 180.0 / PIf; values_to_write_out[4] = current_ctf->GetAdditionalPhaseShift(); values_to_write_out[5] = final_score; if (compute_extra_stats) { values_to_write_out[6] = pixel_size_for_fitting / spatial_frequency[last_bin_with_good_fit]; } else { values_to_write_out[6] = 0.0; } output_text->WriteLine(values_to_write_out); if ( (!old_school_input) && number_of_micrographs > 1 && is_running_locally) my_progress_bar->Update(current_micrograph_number); } // Write out avrot // TODO: add to the output a line with non-normalized avrot, so that users can check for things like ice crystal reflections if (compute_extra_stats) { if (current_micrograph_number == 1) { output_text_avrot = new NumericTextFile(output_text_fn,OPEN_TO_WRITE,number_of_bins_in_1d_spectra); output_text_avrot->WriteCommentLine("# Output from CTFFind version %s, run on %s\n",ctffind_version.c_str(),wxDateTime::Now().FormatISOCombined(' ').ToUTF8().data()); output_text_avrot->WriteCommentLine("# Input file: %s ; Number of micrographs: %i\n",input_filename.c_str(),number_of_micrographs); output_text_avrot->WriteCommentLine("# Pixel size: %0.3f Angstroms ; acceleration voltage: %0.1f keV ; spherical aberration: %0.2f mm ; amplitude contrast: %0.2f\n",pixel_size_of_input_image,acceleration_voltage,spherical_aberration,amplitude_contrast); output_text_avrot->WriteCommentLine("# Box size: %i pixels ; min. res.: %0.1f Angstroms ; max. res.: %0.1f Angstroms ; min. def.: %0.1f um; max. def. %0.1f um; num. frames averaged: %i\n",box_size,minimum_resolution,maximum_resolution,minimum_defocus,maximum_defocus,number_of_frames_to_average); output_text_avrot->WriteCommentLine("# 6 lines per micrograph: #1 - spatial frequency (1/Angstroms); #2 - 1D rotational average of spectrum (assuming no astigmatism); #3 - 1D rotational average of spectrum; #4 - CTF fit; #5 - cross-correlation between spectrum and CTF fit; #6 - 2sigma of expected cross correlation of noise\n"); } spatial_frequency_in_reciprocal_angstroms = new double[number_of_bins_in_1d_spectra]; for (counter=0; counterWriteLine(spatial_frequency_in_reciprocal_angstroms); output_text_avrot->WriteLine(rotational_average->data_y); output_text_avrot->WriteLine(rotational_average_astig); output_text_avrot->WriteLine(rotational_average_astig_fit); output_text_avrot->WriteLine(fit_frc); output_text_avrot->WriteLine(fit_frc_sigma); delete [] spatial_frequency_in_reciprocal_angstroms; } delete comparison_object_2D; } // End of loop over micrographs if (is_running_locally && (! old_school_input) && number_of_micrographs > 1) { delete my_progress_bar; wxPrintf("\n"); } // Tell the user where the outputs are if (is_running_locally) { wxPrintf("\n\nSummary of results : %s\n", output_text->ReturnFilename()); wxPrintf( "Diagnostic images : %s\n", output_diagnostic_filename); if (compute_extra_stats) { wxPrintf("Detailed results, including 1D fit profiles : %s\n",output_text_avrot->ReturnFilename()); wxPrintf("Use this command to plot 1D fit profiles : ctffind_plot_results.sh %s\n",output_text_avrot->ReturnFilename()); } wxPrintf("\n\n"); } // Send results back float results_array[8]; results_array[0] = current_ctf->GetDefocus1() * pixel_size_for_fitting; // Defocus 1 (Angstroms) results_array[1] = current_ctf->GetDefocus2() * pixel_size_for_fitting; // Defocus 2 (Angstroms) results_array[2] = current_ctf->GetAstigmatismAzimuth() * 180.0 / PIf; // Astigmatism angle (degrees) results_array[3] = current_ctf->GetAdditionalPhaseShift(); // Additional phase shift (e.g. from phase plate) (radians) results_array[4] = final_score; // CTFFIND score if (last_bin_with_good_fit == 0) { results_array[5] = 0.0; // A value of 0.0 indicates that the calculation to determine the goodness of fit failed for some reason } else { results_array[5] = pixel_size_for_fitting / spatial_frequency[last_bin_with_good_fit]; // The resolution (Angstroms) up to which Thon rings are well fit by the CTF } if (last_bin_without_aliasing == 0) { results_array[6] = 0.0; // A value of 0.0 indicates that no aliasing was detected } else { results_array[6] = pixel_size_for_fitting / spatial_frequency[last_bin_without_aliasing]; // The resolution (Angstroms) at which aliasing was just detected } results_array[7] = average_spectrum->ReturnIcinessOfSpectrum(pixel_size_for_fitting); my_result.SetResult(8,results_array); // Cleanup delete current_ctf; delete average_spectrum; delete average_spectrum_masked; delete current_power_spectrum; delete current_input_image; delete current_input_image_square; delete temp_image; delete sum_image; delete resampled_power_spectrum; delete number_of_extrema_image; delete ctf_values_image; delete gain; delete [] values_to_write_out; if (is_running_locally) delete output_text; if (compute_extra_stats) { delete [] spatial_frequency; delete [] rotational_average_astig; delete [] rotational_average_astig_renormalized; delete [] rotational_average_astig_fit; delete [] number_of_extrema_profile; delete [] ctf_values_profile; delete [] fit_frc; delete [] fit_frc_sigma; delete output_text_avrot; } if (! defocus_is_known) delete conjugate_gradient_minimizer; delete number_of_averaged_pixels; delete rotational_average; // Return return true; } /* * Go from an experimental radial average with decaying Thon rings to a function between 0.0 and 1.0 for every oscillation. * This is done by treating each interval between a zero and an extremum of the CTF separately, and for each of them, * sorting and ranking the values in the radial average. * Each value is then replaced by its rank, modified to make it looks like a |CTF| signal. * This makes sense as a preparation for evaluating the quality of fit of a CTF when we want to ignore the amplitude of the Thon * rings and just focus on whether the fit agrees in terms of the positions of the zeros and extrema. * Without this, a very good fit doesn't always have a great FRC for regions where the experimental radial average is decaying rapidly. */ void Renormalize1DSpectrumForFRC( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[]) { int bin_counter; int bin_of_previous_extremum; int bin_of_current_extremum; int i; int bin_of_zero; std::vector temp_vector; std::vector temp_ranks; float number_of_extrema_delta; // bin_of_previous_extremum = 0; bin_of_current_extremum = 0; for (bin_counter = 1; bin_counter < number_of_bins; bin_counter ++ ) { number_of_extrema_delta = number_of_extrema_profile[bin_counter]-number_of_extrema_profile[bin_counter-1]; if (number_of_extrema_delta >= 0.9 && number_of_extrema_delta <= 1.9) // if the CTF is oscillating too quickly, let's not do anything { // We just passed an extremum, at bin_counter-1 // (number_of_extrema_profile keeps track of the count of extrema before the spatial frequency corresponding to this bin) bin_of_current_extremum = bin_counter - 1; if (bin_of_previous_extremum > 0) { if ((bin_of_current_extremum - bin_of_previous_extremum >= 4 && false) || (number_of_extrema_profile[bin_counter] < 7)) { // Loop from the previous extremum to the one we just found // (there is a zero in between, let's find it) // TODO: redefine the zero as the lowest point between the two extrema? bin_of_zero = (bin_of_current_extremum - bin_of_previous_extremum)/2 + bin_of_previous_extremum; for (i=bin_of_previous_extremum;i max_value) max_value = average[i]; if (average[i] < min_value) min_value = average[i]; } for (i=bin_of_previous_extremum;i 0.0001) average[i] /= (max_value - min_value); //wxPrintf(" with %f\n",average[i]); } } } bin_of_previous_extremum = bin_of_current_extremum; } MyDebugAssertFalse(std::isnan(average[bin_counter]),"Average is NaN for bin %i\n",bin_counter); } } // void ComputeFRCBetween1DSpectrumAndFit( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[], double frc[], double frc_sigma[], int first_fit_bin) { MyDebugAssertTrue(first_fit_bin >= 0,"Bad first fit bin on entry: %i", first_fit_bin); int bin_counter; int half_window_width[number_of_bins]; int bin_of_previous_extremum; int i; int first_bin, last_bin; double spectrum_mean, fit_mean; double spectrum_sigma, fit_sigma; double cross_product; float number_of_bins_in_window; const int minimum_window_half_width = number_of_bins / 40; // First, work out the size of the window over which we'll compute the FRC value bin_of_previous_extremum = 0; for (bin_counter=1; bin_counter < number_of_bins; bin_counter++) { if (number_of_extrema_profile[bin_counter] != number_of_extrema_profile[bin_counter-1]) { for (i=bin_of_previous_extremum;i= number_of_bins) { last_bin = number_of_bins - 1; first_bin = last_bin - 2 * half_window_width[bin_counter] - 1; } MyDebugAssertTrue(first_bin >=0 && first_bin < number_of_bins,"Bad first_bin: %i",first_bin); MyDebugAssertTrue(last_bin >=0 && last_bin < number_of_bins,"Bad last_bin: %i",last_bin); // First pass for (i=first_bin;i<=last_bin;i++) { spectrum_mean += average[i]; fit_mean += fit[i]; } number_of_bins_in_window = float(2 * half_window_width[bin_counter] + 1); //wxPrintf("bin %03i, number of extrema: %f, number of bins in window: %f , spectrum_sum = %f\n", bin_counter, number_of_extrema_profile[bin_counter], number_of_bins_in_window,spectrum_mean); spectrum_mean /= number_of_bins_in_window; fit_mean /= number_of_bins_in_window; // Second pass for (i=first_bin;i<=last_bin;i++) { cross_product += (average[i] - spectrum_mean) * (fit[i] - fit_mean); spectrum_sigma += pow(average[i] - spectrum_mean,2); fit_sigma += pow(fit[i] - fit_mean,2); } MyDebugAssertTrue(spectrum_sigma > 0.0 && spectrum_sigma < 10000.0,"Bad spectrum_sigma: %f\n",spectrum_sigma); MyDebugAssertTrue(fit_sigma > 0.0 && fit_sigma < 10000.0,"Bad fit sigma: %f\n",fit_sigma); if (spectrum_sigma > 0.0 && fit_sigma > 0.0) { frc[bin_counter] = cross_product / (sqrtf(spectrum_sigma/number_of_bins_in_window) * sqrtf(fit_sigma/number_of_bins_in_window)) / number_of_bins_in_window; } else { frc[bin_counter] = 0.0; } frc_sigma[bin_counter] = 2.0 / sqrtf(number_of_bins_in_window); } //wxPrintf("First fit bin: %i\n", first_fit_bin); MyDebugAssertTrue(frc[bin_counter] > -1.01 && frc[bin_counter] < 1.01, "Bad FRC value: %f", frc[bin_counter]); } } // void OverlayCTF( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins_in_1d_spectra, double spatial_frequency[], double rotational_average_astig[], float number_of_extrema_profile[], float ctf_values_profile[], Curve *epa_pre_max, Curve *epa_post_max) { MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); // EmpiricalDistribution values_in_rings; EmpiricalDistribution values_in_fitting_range; int i; int j; long address; float i_logi, i_logi_sq; float j_logi, j_logi_sq; float current_spatial_frequency_squared; float current_azimuth; float current_defocus; float current_phase_aberration; float sq_sf_of_phase_aberration_maximum; const float lowest_freq = pow(ctf->GetLowestFrequencyForFitting(),2); const float highest_freq = pow(ctf->GetHighestFrequencyForFitting(),2); float current_ctf_value; float target_sigma; int chosen_bin; //spectrum->QuickAndDirtyWriteSlice("dbg_spec_overlay_entry.mrc",1); // address = 0; for (j=0;j < spectrum->logical_y_dimension;j++) { j_logi = float(j-spectrum->physical_address_of_box_center_y) * spectrum->fourier_voxel_size_y; j_logi_sq = powf(j_logi,2); for (i=0 ;i < spectrum->logical_x_dimension; i++) { i_logi = float(i-spectrum->physical_address_of_box_center_x) * spectrum->fourier_voxel_size_x; i_logi_sq = powf(i_logi,2); // current_spatial_frequency_squared = j_logi_sq + i_logi_sq; current_azimuth = atan2(j_logi,i_logi); current_defocus = ctf->DefocusGivenAzimuth(current_azimuth); current_phase_aberration = ctf->PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(current_spatial_frequency_squared,current_defocus); // sq_sf_of_phase_aberration_maximum = ctf->ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(current_defocus); if (j < spectrum->physical_address_of_box_center_y && i >= spectrum->physical_address_of_box_center_x) { // Experimental 1D average #ifdef use_epa_rather_than_zero_counting if (current_spatial_frequency_squared <= sq_sf_of_phase_aberration_maximum) { spectrum->real_values[address] = epa_pre_max->ReturnLinearInterpolationFromX(current_phase_aberration); } else { spectrum->real_values[address] = epa_post_max->ReturnLinearInterpolationFromX(current_phase_aberration); } #else // Work out which bin in the astig rot average this pixel corresponds to chosen_bin = ReturnSpectrumBinNumber(number_of_bins_in_1d_spectra,number_of_extrema_profile,number_of_extrema, address, ctf_values, ctf_values_profile); spectrum->real_values[address] = rotational_average_astig[chosen_bin]; #endif } // if (current_spatial_frequency_squared > lowest_freq && current_spatial_frequency_squared <= highest_freq) { current_azimuth = atan2(j_logi,i_logi); current_ctf_value = fabs(ctf->Evaluate(current_spatial_frequency_squared,current_azimuth)); if (current_ctf_value > 0.5) values_in_rings.AddSampleValue(spectrum->real_values[address]); values_in_fitting_range.AddSampleValue(spectrum->real_values[address]); //if (current_azimuth <= ctf->GetAstigmatismAzimuth() && current_azimuth >= ctf->GetAstigmatismAzimuth() - 3.1415*0.5) spectrum->real_values[address] = current_ctf_value; if (j < spectrum->physical_address_of_box_center_y && i < spectrum->physical_address_of_box_center_x) spectrum->real_values[address] = current_ctf_value; } if (current_spatial_frequency_squared <= lowest_freq) { spectrum->real_values[address] = 0.0; } // address++; } address += spectrum->padding_jump_value; } //spectrum->QuickAndDirtyWriteSlice("dbg_spec_overlay_1.mrc",1); /* // We will renormalize the experimental part of the diagnostic image target_sigma = sqrtf(values_in_rings.GetSampleVariance()) ; if (target_sigma > 0.0) { address = 0; for (j=0;j < spectrum->logical_y_dimension;j++) { j_logi = float(j-spectrum->physical_address_of_box_center_y) * spectrum->fourier_voxel_size_y; j_logi_sq = powf(j_logi,2); for (i=0 ;i < spectrum->logical_x_dimension; i++) { i_logi = float(i-spectrum->physical_address_of_box_center_x) * spectrum->fourier_voxel_size_x; i_logi_sq = powf(i_logi,2); // current_spatial_frequency_squared = j_logi_sq + i_logi_sq; // Normalize the experimental part of the diagnostic image if (i > spectrum->physical_address_of_box_center_x || j > spectrum->physical_address_of_box_center_y) { spectrum->real_values[address] /= target_sigma; } else { // Normalize the outside of the theoretical part of the diagnostic image if (current_spatial_frequency_squared > highest_freq) spectrum->real_values[address] /= target_sigma; } address++; } address += spectrum->padding_jump_value; } } */ //spectrum->QuickAndDirtyWriteSlice("dbg_spec_overlay_final.mrc",1); } // Rescale the spectrum and its 1D rotational avereage so that the peaks and troughs are at 0.0 and 1.0. The location of peaks and troughs are worked out // by parsing the suppilied 1D average_fit array bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ) { MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); MyDebugAssertTrue(number_of_bins > 1,"Bad number of bins: %i\n",number_of_bins); // const bool spectrum_is_blank = spectrum->IsConstant(); const int rescale_based_on_maximum_number = 2; // This peak will be used as a renormalization. const int sg_width = 7; const int sg_order = 2; const bool rescale_peaks = false; // if this is false, only the background will be subtracted, the Thon rings "heights" will be unaffected float background[number_of_bins]; float peak[number_of_bins]; int bin_counter; bool at_a_maximum, at_a_minimum, maximum_at_previous_bin, minimum_at_previous_bin; int location_of_previous_maximum, location_of_previous_minimum; int current_maximum_number = 0; int normalisation_bin_number; int i; int j; bool actually_do_rescaling; int chosen_bin; long address; int last_bin_to_rescale; float min_scale_factor; float scale_factor; float rescale_peaks_to; Curve *minima_curve = new Curve; Curve *maxima_curve = new Curve; // Initialise arrays and variables for (bin_counter=0; bin_counter < number_of_bins; bin_counter++) { background[bin_counter] = 0.0; peak[bin_counter] = 0.0; } location_of_previous_maximum = 0; location_of_previous_minimum = 0; current_maximum_number = 0; at_a_maximum = false; at_a_minimum = true; // Note, this may not be true if we have the perfect phase plate // if ( ! spectrum_is_blank ) { for (bin_counter=1; bin_counter < number_of_bins - 1; bin_counter ++) { // Remember where we were before - minimum, maximum or neither maximum_at_previous_bin = at_a_maximum; minimum_at_previous_bin = at_a_minimum; // Are we at a CTF min or max? at_a_minimum = (average_fit[bin_counter] <= average_fit[bin_counter-1]) && (average_fit[bin_counter] <= average_fit[bin_counter+1]); at_a_maximum = (average_fit[bin_counter] >= average_fit[bin_counter-1]) && (average_fit[bin_counter] >= average_fit[bin_counter+1]); // It could be that the CTF is constant in this region, in which case we stay at a minimum if we were there if (at_a_maximum && at_a_minimum) { at_a_minimum = minimum_at_previous_bin; at_a_maximum = maximum_at_previous_bin; } // Fill in values for the background or peak by linear interpolation if (at_a_minimum) { for (i=location_of_previous_minimum+1;i<=bin_counter;i++) { // Linear interpolation of average values at the peaks and troughs of the CTF background[i] = average[location_of_previous_minimum] * float(bin_counter-i) / float(bin_counter-location_of_previous_minimum) + average[bin_counter] * float(i-location_of_previous_minimum) / float(bin_counter-location_of_previous_minimum); } location_of_previous_minimum = bin_counter; minima_curve->AddPoint(spatial_frequency[bin_counter],average[bin_counter]); } if (at_a_maximum) { if ((! maximum_at_previous_bin) && (average_fit[bin_counter] > 0.7)) current_maximum_number = current_maximum_number + 1; for (i=location_of_previous_maximum+1;i<=bin_counter;i++) { // Linear interpolation of average values at the peaks and troughs of the CTF peak[i] = average[location_of_previous_maximum] * float(bin_counter-i) / float(bin_counter-location_of_previous_maximum) + average[bin_counter] * float(i-location_of_previous_maximum) / float(bin_counter-location_of_previous_maximum); // if (current_maximum_number == rescale_based_on_maximum_number) normalisation_bin_number = bin_counter; } location_of_previous_maximum = bin_counter; maxima_curve->AddPoint(spatial_frequency[bin_counter],average[bin_counter]); } if (at_a_maximum && at_a_minimum) { MyPrintfRed("Rescale spectrum: Error. At a minimum and a maximum simultaneously."); //TODO: return false instead DEBUG_ABORT; } } // Fit the minima and maximum curves using Savitzky-Golay smoothing if (maxima_curve->number_of_points > sg_width) maxima_curve->FitSavitzkyGolayToData(sg_width, sg_order); if (minima_curve->number_of_points > sg_width) minima_curve->FitSavitzkyGolayToData(sg_width, sg_order); // Replace the background and peak envelopes with the smooth min/max curves for (bin_counter=0;bin_counternumber_of_points > sg_width) background[bin_counter] = minima_curve->ReturnSavitzkyGolayInterpolationFromX(spatial_frequency[bin_counter]); if (maxima_curve->number_of_points > sg_width) peak[bin_counter] = maxima_curve->ReturnSavitzkyGolayInterpolationFromX(spatial_frequency[bin_counter]); } // Now that we have worked out a background and a peak envelope, let's do the actual rescaling actually_do_rescaling = (peak[normalisation_bin_number] - background[normalisation_bin_number]) > 0.0; if (last_bin_without_aliasing != 0) { last_bin_to_rescale = std::min(last_bin_with_good_fit,last_bin_without_aliasing); } else { last_bin_to_rescale = last_bin_with_good_fit; } if (actually_do_rescaling) { min_scale_factor = 0.2; rescale_peaks_to = 0.75; address = 0; for (j=0;jlogical_y_dimension;j++) { for (i=0;ilogical_x_dimension;i++) { chosen_bin = ReturnSpectrumBinNumber(number_of_bins,number_of_extrema_profile,number_of_extrema, address, ctf_values, ctf_values_profile); if (chosen_bin >= 0) { if (chosen_bin <= last_bin_to_rescale) { spectrum->real_values[address] -= background[chosen_bin]; // This alone makes the spectrum look very nice already if (rescale_peaks) spectrum->real_values[address] /= std::min(1.0f,std::max(min_scale_factor,peak[chosen_bin]-background[chosen_bin])) / rescale_peaks_to; // This is supposed to help "boost" weak Thon rings } else { spectrum->real_values[address] -= background[last_bin_to_rescale]; if (rescale_peaks) spectrum->real_values[address] /= std::min(1.0f,std::max(min_scale_factor,peak[last_bin_to_rescale]-background[last_bin_to_rescale])) / rescale_peaks_to; } } else { //TODO: return false } // address++; } address += spectrum->padding_jump_value; } } else { MyDebugPrint("(RescaleSpectrumAndRotationalAverage) Warning: bad peak/background detection"); } // Rescale the 1D average if (peak[normalisation_bin_number] > background[normalisation_bin_number]) { for (bin_counter=0;bin_counter 0.000001) && bin_counter <= last_bin_without_aliasing) { average[bin_counter] = average[bin_counter] / (peak[bin_counter]-background[bin_counter]) * ( peak[normalisation_bin_number] - background[normalisation_bin_number] ) * 0.1; } } } else { MyDebugPrint("(RescaleSpectrumAndRotationalAverage): unable to rescale 1D average experimental spectrum\n"); } } // end of test of spectrum_is_blank // Cleanup delete minima_curve; delete maxima_curve; } /* * Compute average value in power spectrum as a function of wave function aberration. This allows for averaging even when * there is significant astigmatism. * This should be nicer than counting zeros and looking for nearest CTF value as described in the original ctffind4 manuscript. * Inspired by gctf and others, but I think more robust because it takes into account that the aberration decreases again at * very high spatial frequencies, when Cs takes over from defocus. */ void ComputeEquiPhaseAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Curve *epa_pre_max, Curve *epa_post_max) { MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); const bool spectrum_is_blank = spectrum->IsConstant(); const int curve_oversampling_factor = 3; const bool curve_x_is_linear = true; /* * Initialize the curve objects. One keeps track of EPA pre phase aberration maximum (before Cs term takes over), the other post. * In the case where we are overfocus (negative defocus value), the phase aberration starts at 0.0 at the origin * and just gets more and more negative * * This is one of the messiest parts of the code. I really need to come up with a cleaner way to decide how many points * to give each curve. This is a goldilocks problem: too few or too many both give worse curves and FRCs. */ if (curve_x_is_linear) { float maximum_aberration_in_ctf = ctf->ReturnPhaseAberrationMaximum(); float maximum_sq_freq_in_spectrum= powf(spectrum->fourier_voxel_size_x * spectrum->logical_lower_bound_complex_x,2)+powf(spectrum->fourier_voxel_size_y * spectrum->logical_lower_bound_complex_y,2); float lowest_sq_freq_of_ctf_aberration_max = std::min( fabs(ctf->ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(ctf->GetDefocus1())), fabs(ctf->ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(ctf->GetDefocus2()))); float maximum_abs_aberration_in_spectrum = std::max( fabs(ctf->PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(maximum_sq_freq_in_spectrum,ctf->GetDefocus1())), fabs(ctf->PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(maximum_sq_freq_in_spectrum,ctf->GetDefocus2()))); /* * Minimum phase aberration might be 0.0 + additional_phase_shift (at the origin), or if the phase aberration function * peaks before Nyquist, it might be at the edge of the spectrum */ float minimum_aberration_in_ctf_at_edges = std::min(ctf->PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(maximum_sq_freq_in_spectrum,ctf->GetDefocus1()), ctf->PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(maximum_sq_freq_in_spectrum,ctf->GetDefocus2())); // Watch out: messy heuristics int number_of_points_pre_max = std::max(2,myroundint(spectrum->ReturnMaximumDiagonalRadius() * curve_oversampling_factor * maximum_aberration_in_ctf / maximum_abs_aberration_in_spectrum)); int number_of_points_post_max = std::max(2,myroundint(spectrum->ReturnMaximumDiagonalRadius() * curve_oversampling_factor)); epa_pre_max->SetupXAxis(ctf->GetAdditionalPhaseShift(),maximum_aberration_in_ctf,number_of_points_pre_max); epa_post_max->SetupXAxis(std::min(maximum_aberration_in_ctf,minimum_aberration_in_ctf_at_edges-0.5f*fabsf(minimum_aberration_in_ctf_at_edges)),maximum_aberration_in_ctf,number_of_points_post_max); } else { MyDebugAssertTrue(false,"Not implemented"); } epa_pre_max->SetYToConstant(0.0); epa_post_max->SetYToConstant(0.0); /* * We'll also need to keep track of the number of values */ Curve * count_pre_max = new Curve; Curve * count_post_max = new Curve; count_pre_max->CopyFrom(epa_pre_max); count_post_max->CopyFrom(epa_post_max); if (!spectrum_is_blank) { long address = 0; int i,j; float i_logi,j_logi; float i_logi_sq,j_logi_sq; float current_spatial_frequency_squared; float current_azimuth; float current_phase_aberration; float sq_sf_of_phase_aberration_maximum; float current_defocus; for (j=0;j < spectrum->logical_y_dimension;j++) { j_logi = float(j-spectrum->physical_address_of_box_center_y) * spectrum->fourier_voxel_size_y; j_logi_sq = powf(j_logi,2); for (i=0 ;i < spectrum->logical_x_dimension; i++) { i_logi = float(i-spectrum->physical_address_of_box_center_x) * spectrum->fourier_voxel_size_x; i_logi_sq = powf(i_logi,2); // current_spatial_frequency_squared = j_logi_sq + i_logi_sq; current_azimuth = atan2(j_logi,i_logi); current_defocus = ctf->DefocusGivenAzimuth(current_azimuth); current_phase_aberration = ctf->PhaseShiftGivenSquaredSpatialFrequencyAndDefocus(current_spatial_frequency_squared,current_defocus); // sq_sf_of_phase_aberration_maximum = ctf->ReturnSquaredSpatialFrequencyOfPhaseShiftExtremumGivenDefocus(current_defocus); // if (current_spatial_frequency_squared <= sq_sf_of_phase_aberration_maximum) { // Add to pre-max epa_pre_max->AddValueAtXUsingLinearInterpolation(current_phase_aberration,spectrum->real_values[address],curve_x_is_linear); count_pre_max->AddValueAtXUsingLinearInterpolation(current_phase_aberration,1.0,curve_x_is_linear); } else { /* * We are after the maximum phase aberration (i.e. the Cs term has taken over, phase aberration is decreasing as a function of sf) */ // Add to post-max epa_post_max->AddValueAtXUsingLinearInterpolation(current_phase_aberration,spectrum->real_values[address],curve_x_is_linear); count_post_max->AddValueAtXUsingLinearInterpolation(current_phase_aberration,1.0,curve_x_is_linear); } // address++; } address += spectrum->padding_jump_value; } /* * Do the averaging */ epa_pre_max->DivideBy(count_pre_max); epa_post_max->DivideBy(count_post_max); } delete count_pre_max; delete count_post_max; } float ReturnAzimuthToUseFor1DPlots(CTF *ctf) { const float min_angular_distances_from_axes_radians = 10.0 / 180.0 * PIf; float azimuth_of_mid_defocus; float angular_distance_from_axes; // We choose the azimuth to be mid way between the two defoci of the astigmatic CTF azimuth_of_mid_defocus = ctf->GetAstigmatismAzimuth() + PIf * 0.25f; // We don't want the azimuth too close to the axes, which may have been blanked by the central-cross-artefact-suppression-system (tm) angular_distance_from_axes = fmod(azimuth_of_mid_defocus,PIf * 0.5f); if(fabs(angular_distance_from_axes) < min_angular_distances_from_axes_radians) { if (angular_distance_from_axes > 0.0f) { azimuth_of_mid_defocus = min_angular_distances_from_axes_radians; } else { azimuth_of_mid_defocus = - min_angular_distances_from_axes_radians; } } if (fabs(angular_distance_from_axes) > 0.5f * PIf - min_angular_distances_from_axes_radians) { if (angular_distance_from_axes > 0.0) { azimuth_of_mid_defocus = PIf * 0.5f - min_angular_distances_from_axes_radians; } else { azimuth_of_mid_defocus = - PIf * 0.5f + min_angular_distances_from_axes_radians; } } return azimuth_of_mid_defocus; } // bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[]) { MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); MyDebugAssertTrue(number_of_extrema->is_in_memory,"Number of extrema image not allocated"); MyDebugAssertTrue(ctf_values->is_in_memory,"CTF values image not allocated"); MyDebugAssertTrue(spectrum->HasSameDimensionsAs(number_of_extrema),"Spectrum and number of extrema images do not have same dimensions"); MyDebugAssertTrue(spectrum->HasSameDimensionsAs(ctf_values),"Spectrum and CTF values images do not have same dimensions"); // const bool spectrum_is_blank = spectrum->IsConstant(); int counter; float azimuth_of_mid_defocus; float current_spatial_frequency_squared; int number_of_values[number_of_bins]; int i, j; long address; float ctf_diff_from_current_bin; int chosen_bin; // Initialise the output arrays for (counter=0; counterfourier_voxel_size_y, 2); spatial_frequency[counter] = sqrt(current_spatial_frequency_squared); ctf_values_profile[counter] = ctf->Evaluate(current_spatial_frequency_squared,azimuth_of_mid_defocus); number_of_extrema_profile[counter] = ctf->ReturnNumberOfExtremaBeforeSquaredSpatialFrequency(current_spatial_frequency_squared,azimuth_of_mid_defocus); //wxPrintf("bin %i: phase shift= %f, number of extrema = %f\n",counter,ctf->PhaseShiftGivenSquaredSpatialFrequencyAndAzimuth(current_spatial_frequency_squared,azimuth_of_mid_defocus),number_of_extrema_profile[counter]); } // Now we can loop over the spectrum again and decide to which bin to add each component address = 0; for (j=0; jlogical_y_dimension; j++) { for (i=0; i < spectrum->logical_x_dimension; i++) { ctf_diff_from_current_bin = std::numeric_limits::max(); chosen_bin = ReturnSpectrumBinNumber(number_of_bins,number_of_extrema_profile,number_of_extrema, address, ctf_values, ctf_values_profile); if (chosen_bin >= 0) { average[chosen_bin] += spectrum->real_values[address]; number_of_values[chosen_bin]++; } else { //TODO: return false } // address++; } address += spectrum->padding_jump_value; } // Do the actual averaging for (counter = 0; counter < number_of_bins; counter++) { if (number_of_values[counter] > 0) { average[counter] = average[counter] / float(number_of_values[counter]); MyDebugAssertFalse(std::isnan(average[counter]),"Average is NaN for bin %i\n",counter); } else { average[counter] = 0.0; } average_fit[counter] = fabs(ctf_values_profile[counter]); } } // Compute the rank version of the rotational average for (counter = 0; counter < number_of_bins; counter ++ ) { average_rank[counter] = average[counter]; } Renormalize1DSpectrumForFRC(number_of_bins,average_rank,average_fit,number_of_extrema_profile); for (counter = 0; counter < number_of_bins; counter ++ ) { MyDebugAssertFalse(std::isnan(average[counter]),"Average is NaN for bin %i\n",counter); MyDebugAssertFalse(std::isnan(average_rank[counter]),"AverageRank is NaN for bin %i\n",counter); } } int ReturnSpectrumBinNumber(int number_of_bins, float number_of_extrema_profile[], Image *number_of_extrema, long address, Image *ctf_values, float ctf_values_profile[]) { int current_bin; float diff_number_of_extrema; float diff_number_of_extrema_previous; float diff_number_of_extrema_next; float ctf_diff_from_current_bin; float ctf_diff_from_current_bin_old; int chosen_bin; // //MyDebugPrint("address: %li - number of extrema: %f - ctf_value: %f\n", address, number_of_extrema->real_values[address], ctf_values->real_values[address]); MyDebugAssertTrue(address < number_of_extrema->real_memory_allocated,"Oops, bad address: %li\n",address); // Let's find the bin which has the same number of preceding extrema and the most similar ctf value ctf_diff_from_current_bin = std::numeric_limits::max(); chosen_bin = -1; for (current_bin=0; current_bin < number_of_bins; current_bin++) { diff_number_of_extrema = fabs(number_of_extrema->real_values[address] - number_of_extrema_profile[current_bin]); if (current_bin > 0) { diff_number_of_extrema_previous = fabs(number_of_extrema->real_values[address]- number_of_extrema_profile[current_bin-1]); } else { diff_number_of_extrema_previous = std::numeric_limits::max(); } if (current_bin < number_of_bins - 1) { diff_number_of_extrema_next = fabs(number_of_extrema->real_values[address] - number_of_extrema_profile[current_bin+1]); } else { diff_number_of_extrema_next = std::numeric_limits::max(); } // if (number_of_extrema->real_values[address] > number_of_extrema_profile[number_of_bins-1]) { chosen_bin = number_of_bins - 1; } else { if ( diff_number_of_extrema <= 0.01 || ( diff_number_of_extrema < diff_number_of_extrema_previous && diff_number_of_extrema <= diff_number_of_extrema_next && number_of_extrema_profile[std::max(current_bin-1,0)] != number_of_extrema_profile[std::min(current_bin+1,number_of_bins-1)] ) ) { // We're nearly there // Let's look for the position for the nearest CTF value ctf_diff_from_current_bin_old = ctf_diff_from_current_bin; ctf_diff_from_current_bin = fabs(ctf_values->real_values[address] - ctf_values_profile[current_bin]); if (ctf_diff_from_current_bin < ctf_diff_from_current_bin_old) { //MyDebugPrint("new chosen bin: %i\n",current_bin); chosen_bin = current_bin; } } } } if (chosen_bin == -1) { //TODO: return false #ifdef DEBUG MyPrintfRed("Could not find bin\n"); DEBUG_ABORT; #endif } else { //MyDebugAssertTrue(chosen_bin > 0 && chosen_bin < number_of_bins,"Oops, bad chosen bin number: %i (number of bins = %i)\n",chosen_bin,number_of_bins); //MyDebugPrint("final chosen bin = %i\n", chosen_bin); return chosen_bin; } } /* integer function ComputePowerSpectrumBinNumber(number_of_bins,number_of_extrema_profile,number_of_extrema, & i,j,ctf_values,ctf_values_profile) result(chosen_bin) integer, intent(in) :: number_of_bins real, intent(in) :: number_of_extrema_profile(:) type(Image), intent(in) :: number_of_extrema integer, intent(in) :: i,j !< Physical memory address type(Image), intent(in) :: ctf_values real, intent(in) :: ctf_values_profile(:) ! private variables integer :: current_bin real :: diff_number_of_extrema, diff_number_of_extrema_previous, diff_number_of_extrema_next real :: ctf_diff_from_current_bin real :: ctf_diff_from_current_bin_old ! Let's find the bin which has the same number of preceding extrema and the most similar ctf value ctf_diff_from_current_bin = huge(1.0e0) chosen_bin = 0 do current_bin=1,number_of_bins diff_number_of_extrema = abs(number_of_extrema%real_values(i,j,1) - number_of_extrema_profile(current_bin)) if (current_bin .gt. 1) then diff_number_of_extrema_previous = abs(number_of_extrema%real_values(i,j,1) & - number_of_extrema_profile(current_bin-1)) else diff_number_of_extrema_previous = huge(1.0e0) endif if (current_bin .lt. number_of_bins) then diff_number_of_extrema_next = abs(number_of_extrema%real_values(i,j,1) & - number_of_extrema_profile(current_bin+1)) else diff_number_of_extrema_next = huge(1.0e0) endif if (number_of_extrema%real_values(i,j,1) .gt. number_of_extrema_profile(number_of_bins)) then chosen_bin = number_of_bins else if ( diff_number_of_extrema .le. 0.01 & .or. ( diff_number_of_extrema .lt. diff_number_of_extrema_previous & .and. diff_number_of_extrema .le. diff_number_of_extrema_next & .and. number_of_extrema_profile(max(current_bin-1,1)) & .ne. number_of_extrema_profile(min(current_bin+1,number_of_bins))) & ) then ! We're nearly there ! Let's look for the position of the nearest CTF value ctf_diff_from_current_bin_old = ctf_diff_from_current_bin ctf_diff_from_current_bin = abs(ctf_values%real_values(i,j,1) - ctf_values_profile(current_bin)) if (ctf_diff_from_current_bin .lt. ctf_diff_from_current_bin_old) then chosen_bin = current_bin endif endif endif enddo if (chosen_bin .eq. 0) then print *, number_of_extrema_profile print *, i, j, number_of_extrema%real_values(i,j,1), ctf_values%real_values(i,j,1) print *, diff_number_of_extrema, diff_number_of_extrema_previous, diff_number_of_extrema_next call this_program%TerminateWithFatalError('ComputeRotationalAverageOfPowerSpectrum','Could not find bin') endif end function ComputePowerSpectrumBinNumber */ // Compute an image where each pixel stores the number of preceding CTF extrema. This is described as image "E" in Rohou & Grigorieff 2015 (see Fig 3) void ComputeImagesWithNumberOfExtremaAndCTFValues(CTF *ctf, Image *number_of_extrema, Image *ctf_values) { MyDebugAssertTrue(number_of_extrema->is_in_memory,"Memory not allocated"); MyDebugAssertTrue(ctf_values->is_in_memory,"Memory not allocated"); MyDebugAssertTrue(ctf_values->HasSameDimensionsAs(number_of_extrema),"Images do not have same dimensions"); int i, j; float i_logi, i_logi_sq; float j_logi, j_logi_sq; float current_spatial_frequency_squared; float current_azimuth; long address; address = 0; for (j=0;jlogical_y_dimension;j++) { j_logi = float(j - number_of_extrema->physical_address_of_box_center_y) * number_of_extrema->fourier_voxel_size_y; j_logi_sq = pow(j_logi,2); for (i=0;ilogical_x_dimension;i++) { i_logi = float(i - number_of_extrema->physical_address_of_box_center_x) * number_of_extrema->fourier_voxel_size_x; i_logi_sq = pow(i_logi,2); // Where are we? current_spatial_frequency_squared = j_logi_sq + i_logi_sq; if (current_spatial_frequency_squared > 0.0) { current_azimuth = atan2(j_logi,i_logi); } else { current_azimuth = 0.0; } // ctf_values->real_values[address] = ctf->Evaluate(current_spatial_frequency_squared,current_azimuth); number_of_extrema->real_values[address] = ctf->ReturnNumberOfExtremaBeforeSquaredSpatialFrequency(current_spatial_frequency_squared,current_azimuth); // address++; } address += number_of_extrema->padding_jump_value; } number_of_extrema->is_in_real_space = true; ctf_values->is_in_real_space = true; } // Align rotationally a (stack) of image(s) against another image. Return the rotation angle that gives the best normalised cross-correlation. float FindRotationalAlignmentBetweenTwoStacksOfImages(Image *self, Image *other_image, int number_of_images, float search_half_range, float search_step_size, float minimum_radius, float maximum_radius) { MyDebugAssertTrue(self[0].is_in_memory, "Memory not allocated"); MyDebugAssertTrue(self[0].is_in_real_space, "Not in real space"); MyDebugAssertTrue(self[0].logical_z_dimension == 1, "Meant for images, not volumes"); MyDebugAssertTrue(other_image[0].is_in_memory, "Memory not allocated - other_image"); MyDebugAssertTrue(other_image[0].is_in_real_space, "Not in real space - other_image"); MyDebugAssertTrue(other_image[0].logical_z_dimension == 1, "Meant for images, not volumes - other_image"); MyDebugAssertTrue(self[0].HasSameDimensionsAs(&other_image[0]),"Images and reference images do not have same dimensions."); // Local variables const float minimum_radius_sq = pow(minimum_radius,2); const float maximum_radius_sq = pow(maximum_radius,2); const float inverse_logical_x_dimension = 1.0 / float(self[0].logical_x_dimension); const float inverse_logical_y_dimension = 1.0 / float(self[0].logical_y_dimension); float best_cc = - std::numeric_limits::max(); float best_rotation = - std::numeric_limits::max(); float current_rotation = - search_half_range; float current_rotation_rad; EmpiricalDistribution cc_numerator_dist; EmpiricalDistribution cc_denom_self_dist; EmpiricalDistribution cc_denom_other_dist; int current_image; int i, i_logi; float i_logi_frac, ii_phys; int j, j_logi; float j_logi_frac, jj_phys; float current_interpolated_value; long address_in_other_image; float current_cc; // Loop over possible rotations while ( current_rotation < search_half_range + search_step_size ) { current_rotation_rad = current_rotation / 180.0 * PIf; cc_numerator_dist.Reset(); cc_denom_self_dist.Reset(); cc_denom_other_dist.Reset(); // Loop over the array of images for (current_image=0; current_image < number_of_images; current_image++) { // Loop over the other (reference) image address_in_other_image = 0; for (j=0; j < other_image[0].logical_y_dimension; j++) { j_logi = j - other_image[0].physical_address_of_box_center_y; j_logi_frac = pow(j_logi * inverse_logical_y_dimension,2); for (i=0; i < other_image[0].logical_x_dimension; i++) { i_logi = i - other_image[0].physical_address_of_box_center_x; i_logi_frac = pow(i_logi * inverse_logical_x_dimension,2) + j_logi_frac; if (i_logi_frac >= minimum_radius_sq && i_logi_frac <= maximum_radius_sq) { // We do ccw rotation to go from other_image (reference) to self (input image) ii_phys = i_logi * cos(current_rotation_rad) - j_logi * sin(current_rotation_rad) + self[0].physical_address_of_box_center_x ; jj_phys = i_logi * sin(current_rotation_rad) + j_logi * cos(current_rotation_rad) + self[0].physical_address_of_box_center_y ; // if (int(ii_phys) > 0 && int(ii_phys)+1 < self[0].logical_x_dimension && int(jj_phys) > 0 && int(jj_phys)+1 < self[0].logical_y_dimension ) // potential optimization: we have to compute the floor and ceiling in the interpolation routine. Is it not worth doing the bounds checking in the interpolation routine somehow? { self[0].GetRealValueByLinearInterpolationNoBoundsCheckImage(ii_phys,jj_phys,current_interpolated_value); //MyDebugPrint("%g %g\n",current_interpolated_value,other_image[0].real_values[address_in_other_image]); cc_numerator_dist.AddSampleValue(current_interpolated_value * other_image[current_image].real_values[address_in_other_image]); cc_denom_other_dist.AddSampleValue(pow(other_image[0].real_values[address_in_other_image],2)); // potential optimization: since other_image is not being rotated, we should only need to compute this quantity once, not for every potential rotation cc_denom_self_dist.AddSampleValue(pow(current_interpolated_value,2)); } } address_in_other_image++; } // i address_in_other_image += other_image[0].padding_jump_value; } // end of loop over other (reference) image } // end of loop over array of images current_cc = cc_numerator_dist.GetSampleSum() / sqrt(cc_denom_other_dist.GetSampleSum()*cc_denom_self_dist.GetSampleSum()); if (current_cc > best_cc) { best_cc = current_cc; best_rotation = current_rotation; } // Increment the rotation current_rotation += search_step_size; } // end of loop over rotations return best_rotation; }