From: Takuo Yasunaga Date: Wed, 1 Oct 2014 11:09:10 +0000 (+0900) Subject: Create a new tool of mrcImageAutoRotationAverage: X-Git-Tag: v2.3.65p0294~215 X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=refs%2Ftags%2Fv2.1.4p0034;p=eos%2Fbase.git Create a new tool of mrcImageAutoRotationAverage: new file: mrcImageAutoRotationAverage modified: src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h Input/Output separation of struct --- diff --git a/bin/mrcImageAutoRotationAverage b/bin/mrcImageAutoRotationAverage new file mode 120000 index 0000000000..eddb95508d --- /dev/null +++ b/bin/mrcImageAutoRotationAverage @@ -0,0 +1 @@ +../sbin/MachineIndependent \ No newline at end of file diff --git a/hostdepend/X86MAC64/bin/X86MAC64/mrcImageAutoRotationAverage b/hostdepend/X86MAC64/bin/X86MAC64/mrcImageAutoRotationAverage new file mode 100755 index 0000000000..118a26d5d3 Binary files /dev/null and b/hostdepend/X86MAC64/bin/X86MAC64/mrcImageAutoRotationAverage differ diff --git a/hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a b/hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a index 11ef85ac3b..cb38151712 100644 Binary files a/hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a and b/hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a differ diff --git a/hostdepend/X86MAC64/lib/X86MAC64/libmrcImage.a b/hostdepend/X86MAC64/lib/X86MAC64/libmrcImage.a index 0ed16adb0c..c2352ef7ed 100644 Binary files a/hostdepend/X86MAC64/lib/X86MAC64/libmrcImage.a and b/hostdepend/X86MAC64/lib/X86MAC64/libmrcImage.a differ diff --git a/hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageCorrelation.sharedo b/hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageCorrelation.sharedo index 0bd2bd0629..3d97882221 100644 Binary files a/hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageCorrelation.sharedo and b/hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageCorrelation.sharedo differ diff --git a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a index 0ed16adb0c..c2352ef7ed 100644 Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a differ diff --git a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a index 66680d7d84..9d3240c282 100644 Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a differ diff --git a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelation.sharedo b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelation.sharedo index 0bd2bd0629..3d97882221 100644 Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelation.sharedo and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelation.sharedo differ diff --git a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/.Depend b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/.Depend new file mode 100644 index 0000000000..bb569f8698 --- /dev/null +++ b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/.Depend @@ -0,0 +1,209 @@ +argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \ + /usr/include/sys/_symbol_aliasing.h \ + /usr/include/sys/_posix_availability.h /usr/include/Availability.h \ + /usr/include/AvailabilityInternal.h /usr/include/_types.h \ + /usr/include/sys/_types.h /usr/include/machine/_types.h \ + /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \ + /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \ + /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \ + /usr/include/secure/_stdio.h /usr/include/secure/_common.h \ + /usr/include/stdlib.h /usr/include/sys/wait.h \ + /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \ + /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \ + /usr/include/machine/signal.h /usr/include/i386/signal.h \ + /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \ + /usr/include/mach/i386/_structs.h \ + /usr/include/sys/_types/_sigaltstack.h \ + /usr/include/sys/_types/_ucontext.h \ + /usr/include/sys/_types/_pthread_attr_t.h \ + /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \ + /usr/include/sys/resource.h \ + /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \ + /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \ + /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \ + /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \ + /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \ + /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \ + /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \ + /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \ + /usr/include/machine/endian.h /usr/include/i386/endian.h \ + /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \ + /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \ + /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \ + /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \ + /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \ + /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \ + /Users/tacyas/Eos/include/string.h /usr/include/math.h ../inc/config.h \ + ../inc/../inc/mrcImageAutoRotationAverage.h \ + /Users/tacyas/Eos/include/genUtil.h /Users/tacyas/Eos/include/File.h \ + /Users/tacyas/Eos/include/Memory.h \ + /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/limits.h \ + /usr/include/limits.h /usr/include/machine/limits.h \ + /usr/include/i386/limits.h /usr/include/i386/_limits.h \ + /usr/include/sys/syslimits.h +init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \ + /usr/include/sys/_symbol_aliasing.h \ + /usr/include/sys/_posix_availability.h /usr/include/Availability.h \ + /usr/include/AvailabilityInternal.h /usr/include/_types.h \ + /usr/include/sys/_types.h /usr/include/machine/_types.h \ + /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \ + /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \ + /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \ + /usr/include/secure/_stdio.h /usr/include/secure/_common.h \ + /usr/include/stdlib.h /usr/include/sys/wait.h \ + /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \ + /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \ + /usr/include/machine/signal.h /usr/include/i386/signal.h \ + /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \ + /usr/include/mach/i386/_structs.h \ + /usr/include/sys/_types/_sigaltstack.h \ + /usr/include/sys/_types/_ucontext.h \ + /usr/include/sys/_types/_pthread_attr_t.h \ + /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \ + /usr/include/sys/resource.h \ + /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \ + /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \ + /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \ + /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \ + /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \ + /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \ + /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \ + /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \ + /usr/include/machine/endian.h /usr/include/i386/endian.h \ + /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \ + /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \ + /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \ + /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \ + /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \ + /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \ + /Users/tacyas/Eos/include/string.h /usr/include/math.h ../inc/config.h \ + ../inc/../inc/mrcImageAutoRotationAverage.h \ + /Users/tacyas/Eos/include/genUtil.h /Users/tacyas/Eos/include/File.h \ + /Users/tacyas/Eos/include/Memory.h \ + /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/limits.h \ + /usr/include/limits.h /usr/include/machine/limits.h \ + /usr/include/i386/limits.h /usr/include/i386/_limits.h \ + /usr/include/sys/syslimits.h +mrcImageAutoRotationAverage.o: mrcImageAutoRotationAverage.c \ + /usr/include/stdio.h /usr/include/sys/cdefs.h \ + /usr/include/sys/_symbol_aliasing.h \ + /usr/include/sys/_posix_availability.h /usr/include/Availability.h \ + /usr/include/AvailabilityInternal.h /usr/include/_types.h \ + /usr/include/sys/_types.h /usr/include/machine/_types.h \ + /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \ + /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \ + /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \ + /usr/include/secure/_stdio.h /usr/include/secure/_common.h \ + /usr/include/stdlib.h /usr/include/sys/wait.h \ + /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \ + /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \ + /usr/include/machine/signal.h /usr/include/i386/signal.h \ + /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \ + /usr/include/mach/i386/_structs.h \ + /usr/include/sys/_types/_sigaltstack.h \ + /usr/include/sys/_types/_ucontext.h \ + /usr/include/sys/_types/_pthread_attr_t.h \ + /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \ + /usr/include/sys/resource.h \ + /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \ + /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \ + /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \ + /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \ + /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \ + /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \ + /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \ + /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \ + /usr/include/machine/endian.h /usr/include/i386/endian.h \ + /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \ + /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \ + /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \ + /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \ + /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \ + /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \ + /Users/tacyas/Eos/include/string.h /usr/include/math.h ../inc/config.h \ + ../inc/../inc/mrcImageAutoRotationAverage.h \ + /Users/tacyas/Eos/include/genUtil.h \ + /Users/tacyas/Eos/include/mrcImage.h \ + /Users/tacyas/Eos/include/Matrix3D.h \ + /Users/tacyas/Eos/include/Vector.h /Users/tacyas/Eos/include/Array.h \ + /Users/tacyas/Eos/include/ctfInfo.h /Users/tacyas/Eos/include/Memory.h \ + /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/limits.h \ + /usr/include/limits.h /usr/include/machine/limits.h \ + /usr/include/i386/limits.h /usr/include/i386/_limits.h \ + /usr/include/sys/syslimits.h \ + /Users/tacyas/Eos/include/lmrcImageAverage.h \ + /Users/tacyas/Eos/include/lmrcImageCorrelation.h \ + /Users/tacyas/Eos/include/PVM.h \ + /Users/tacyas/Eos/include/lmrcImageSSDA.h +usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \ + /usr/include/sys/_symbol_aliasing.h \ + /usr/include/sys/_posix_availability.h /usr/include/Availability.h \ + /usr/include/AvailabilityInternal.h /usr/include/_types.h \ + /usr/include/sys/_types.h /usr/include/machine/_types.h \ + /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \ + /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \ + /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \ + /usr/include/secure/_stdio.h /usr/include/secure/_common.h \ + /usr/include/stdlib.h /usr/include/sys/wait.h \ + /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \ + /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \ + /usr/include/machine/signal.h /usr/include/i386/signal.h \ + /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \ + /usr/include/mach/i386/_structs.h \ + /usr/include/sys/_types/_sigaltstack.h \ + /usr/include/sys/_types/_ucontext.h \ + /usr/include/sys/_types/_pthread_attr_t.h \ + /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \ + /usr/include/sys/resource.h \ + /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \ + /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \ + /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \ + /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \ + /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \ + /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \ + /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \ + /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \ + /usr/include/machine/endian.h /usr/include/i386/endian.h \ + /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \ + /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \ + /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \ + /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \ + /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \ + /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \ + ../inc/config.h ../inc/../inc/mrcImageAutoRotationAverage.h +util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \ + /usr/include/sys/_symbol_aliasing.h \ + /usr/include/sys/_posix_availability.h /usr/include/Availability.h \ + /usr/include/AvailabilityInternal.h /usr/include/_types.h \ + /usr/include/sys/_types.h /usr/include/machine/_types.h \ + /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \ + /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \ + /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \ + /usr/include/secure/_stdio.h /usr/include/secure/_common.h \ + /usr/include/stdlib.h /usr/include/sys/wait.h \ + /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \ + /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \ + /usr/include/machine/signal.h /usr/include/i386/signal.h \ + /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \ + /usr/include/mach/i386/_structs.h \ + /usr/include/sys/_types/_sigaltstack.h \ + /usr/include/sys/_types/_ucontext.h \ + /usr/include/sys/_types/_pthread_attr_t.h \ + /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \ + /usr/include/sys/resource.h \ + /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \ + /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \ + /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \ + /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \ + /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \ + /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \ + /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \ + /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \ + /usr/include/machine/endian.h /usr/include/i386/endian.h \ + /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \ + /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \ + /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \ + /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \ + /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \ + /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \ + ../inc/config.h ../inc/../inc/mrcImageAutoRotationAverage.h diff --git a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/Makefile b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/Makefile new file mode 100755 index 0000000000..ec6124702f --- /dev/null +++ b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/Makefile @@ -0,0 +1,114 @@ +include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc +include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc +include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc +include $(EOS_HOME)/src/Config/DefineTool.inc + +LIBFILES = \ + $(LIBPREFIX)EosObjects$(LIBSUFFIX) + +LIBFILESDEBUG = \ + $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) + +SRCC = \ + $(OBJECTNAME).c \ + init.c \ + argCheck.c \ + usage.c \ + util.c + +SRCCXX = \ + $(OBJECTNAME).cc \ + init.cc \ + argCheck.cc \ + usage.cc \ + util.cc + +MODULES = \ + $(OBJECTNAME).o \ + init.o \ + argCheck.o \ + usage.o \ + util.o + +REALMODULES = \ + $(OSTYPE)/$(OBJECTNAME).o \ + $(OSTYPE)/init.o \ + $(OSTYPE)/argCheck.o \ + $(OSTYPE)/usage.o \ + $(OSTYPE)/util.o + +MODULESDEBUG = \ + $(OBJECTNAME).debugo \ + init.debugo \ + argCheck.debugo \ + usage.debugo \ + util.debugo + +MODULESCUDAGDB = \ + $(OBJECTNAME).cudagdb.o \ + init.cudagdb.o \ + argCheck.cudagdb.o \ + usage.cudagdb.o \ + util.cudagdb.o + +REALMODULESDEBUG = \ + $(OSTYPE)/$(OBJECTNAME).debugo \ + $(OSTYPE)/init.debugo \ + $(OSTYPE)/argCheck.debugo \ + $(OSTYPE)/usage.debugo \ + $(OSTYPE)/util.debugo + + +$(OBJECTNAME): $(MODULES) $(LIBFILES) + @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \ + then \ + echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + fi + @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \ + then \ + echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + fi + @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \ + then \ + echo "MICO"; \ + echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + fi + @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \ + then \ + echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ; \ + $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ; \ + fi + + +$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG) + @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \ + then \ + echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + fi + @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \ + then \ + echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + fi + @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \ + then \ + echo "MICO"; \ + echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + fi + @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \ + then \ + echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \ + fi + +$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG) + echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@" + $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ + +include ./.Depend +include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc diff --git a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/X86MAC64 b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/X86MAC64 new file mode 120000 index 0000000000..d7e4682e53 --- /dev/null +++ b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/X86MAC64 @@ -0,0 +1 @@ +../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64 \ No newline at end of file diff --git a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/mrcImageAutoRotationAverage b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/mrcImageAutoRotationAverage new file mode 100755 index 0000000000..118a26d5d3 Binary files /dev/null and b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/mrcImageAutoRotationAverage differ diff --git a/include/lmrcImageCorrelation.h b/include/lmrcImageCorrelation.h index 37db234a95..c62cbddc74 100644 --- a/include/lmrcImageCorrelation.h +++ b/include/lmrcImageCorrelation.h @@ -26,19 +26,12 @@ typedef enum lmrcImageAutoRotationCorrelationMethod { } lmrcImageAutoRotationCorrelationMethod; typedef struct lmrcImageAutoRotationCorrelationInfo { +/* Input */ int iter; /* iteration */ int nRot; /* Rotation */ - lmrcImageAutoRotationCorrelationMethod Method; - float max; - float maxTheta; - mrcImageParaTypeRealCoord maxP; - mrcImageInformation corInfo; - lmrcImageSSDAInfo SSDAInfo; - float EuclidDistance; - float LinearCorrelation; + lmrcImageAutoRotationCorrelationMethod Method; /* Correlation Method */ - /* Restriction Rotation Area */ - int flagRestrictionArea; + int flagRestrictionArea; float thetaMin; float thetaMax; @@ -51,6 +44,15 @@ typedef struct lmrcImageAutoRotationCorrelationInfo { int flagXshiftOnly; int flagNoShift; +/* Output */ + float max; // + float maxTheta; // + mrcImageParaTypeRealCoord maxP; + mrcImageInformation corInfo; + lmrcImageSSDAInfo SSDAInfo; + float EuclidDistance; + float LinearCorrelation; + } lmrcImageAutoRotationCorrelationInfo; typedef struct lmrcImageCorrelationRefinementInfo { diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h b/src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h index 37db234a95..c62cbddc74 100755 --- a/src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h +++ b/src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h @@ -26,19 +26,12 @@ typedef enum lmrcImageAutoRotationCorrelationMethod { } lmrcImageAutoRotationCorrelationMethod; typedef struct lmrcImageAutoRotationCorrelationInfo { +/* Input */ int iter; /* iteration */ int nRot; /* Rotation */ - lmrcImageAutoRotationCorrelationMethod Method; - float max; - float maxTheta; - mrcImageParaTypeRealCoord maxP; - mrcImageInformation corInfo; - lmrcImageSSDAInfo SSDAInfo; - float EuclidDistance; - float LinearCorrelation; + lmrcImageAutoRotationCorrelationMethod Method; /* Correlation Method */ - /* Restriction Rotation Area */ - int flagRestrictionArea; + int flagRestrictionArea; float thetaMin; float thetaMax; @@ -51,6 +44,15 @@ typedef struct lmrcImageAutoRotationCorrelationInfo { int flagXshiftOnly; int flagNoShift; +/* Output */ + float max; // + float maxTheta; // + mrcImageParaTypeRealCoord maxP; + mrcImageInformation corInfo; + lmrcImageSSDAInfo SSDAInfo; + float EuclidDistance; + float LinearCorrelation; + } lmrcImageAutoRotationCorrelationInfo; typedef struct lmrcImageCorrelationRefinementInfo { diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc index 9ee0144a02..813c136431 100755 --- a/src/Tools/Config/Define.inc +++ b/src/Tools/Config/Define.inc @@ -172,3 +172,11 @@ WORLDNAME=Tools WORLDNAME=Tools WORLDNAME=Tools WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools diff --git a/src/Tools/mrcImage/.Source b/src/Tools/mrcImage/.Source index 0345ee2265..e57dfba544 100644 --- a/src/Tools/mrcImage/.Source +++ b/src/Tools/mrcImage/.Source @@ -47,6 +47,7 @@ mrcImageAssignedToTFofPDB \ mrcImageAutoCorrelationWithWindowing \ mrcImageAutoFilamentExtract \ mrcImageAutoFilamentExtractResultAnalysis \ +mrcImageAutoRotationAverage \ mrcImageAutoRotationCorrelation \ mrcImageAutoRotationCorrelation3D \ mrcImageAutoRotationCorrelationResultPrint \ diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/Define.inc b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/Define.inc new file mode 100755 index 0000000000..4b49b86400 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/Define.inc @@ -0,0 +1,4 @@ +OBJECTNAME = mrcImageAutoRotationAverage +EXTRA_LIB = +EXTRA_CCOPTS = +EXTRA_INC = diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/OptionControlFile new file mode 100755 index 0000000000..f95befe0a5 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/OptionControlFile @@ -0,0 +1,15 @@ +# OptionControlFile +# FileFormat +"-i","-i[nput]","Input: Ins","Essential","1","1","In","inFileList::mrcImage","stdin" +"-r","-r[eferenc]","Input: Ref","Optional","1","1","Ref","inFile::mrcImage","NULL" +"-o","-o[utput]","Output:Average","Essential","1","1","Out","outFile::mrcImage","NULL" +"-range","-range","Mode","Optional","4","1","Min","Real","0.0","2","Max","Real","360.0","3","Delta","Real","5.0","4","Iter","Integer","2" +"-iter","-iter","iteration for rotation","Optional","1","1","iter","Integer","2" +"-M","-M[odeCorrelation]","Mode: Correlation","Optional","1","1","CorMode","Integer","16" +"-Method","-Method[Correlation]","Method: Correlation","Optional","1","1","Method","Integer","0" +"-Periodic","-Periodic","Periodic","Optional","0" +"-maxIter","-maxIter[aration]","MaxIteration","Optional","1","1","maxIter","Integer","10" +"-rmsd","-rmsd","rmsd","Optional","1","1","rmsd","Real","1e-2" +"-log","-log","logFile","Optional","1","1","Log","inFile::ASCII","stdout" +"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL" +"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0" diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/Target.inc b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/Target.inc new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/Makefile b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Makefile new file mode 120000 index 0000000000..ef1f6300ba --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Makefile @@ -0,0 +1 @@ +/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile \ No newline at end of file diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/doc/Makefile b/src/Tools/mrcImage/mrcImageAutoRotationAverage/doc/Makefile new file mode 120000 index 0000000000..d75d7539e2 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/doc/Makefile @@ -0,0 +1 @@ +/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/doc/Makefile \ No newline at end of file diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/inc/config.h b/src/Tools/mrcImage/mrcImageAutoRotationAverage/inc/config.h new file mode 100755 index 0000000000..e2427e90ac --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/inc/config.h @@ -0,0 +1,6 @@ +#ifndef CONFIG_H +#define CONFIG_H + +#include "../inc/mrcImageAutoRotationAverage.h" + +#endif /* CONFIG_H */ diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/inc/mrcImageAutoRotationAverage.h b/src/Tools/mrcImage/mrcImageAutoRotationAverage/inc/mrcImageAutoRotationAverage.h new file mode 100755 index 0000000000..17b6be22c6 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/inc/mrcImageAutoRotationAverage.h @@ -0,0 +1,85 @@ +#ifndef MRCIMAGEAUTOROTATIONAVERAGE_H +#define MRCIMAGEAUTOROTATIONAVERAGE_H +#include +#include + +#define OPTION_FLAG '-' +#define OPTION_FLAG_POS (0) +#define OPTION_POS (1) + + + + +typedef struct mrcImageAutoRotationAverageInfo { + long flagRedirect; + + long flagIn; + char** In; + char* InList; + FILE** fptIn; + FILE* fptInList; + + long flagRef; + char* Ref; + FILE* fptRef; + + long flagOut; + char* Out; + FILE* fptOut; + + long flagMin; + float Min; + + long flagMax; + float Max; + + long flagDelta; + float Delta; + + long flagIter; + long Iter; + + long flagiter; + long iter; + + long flagCorMode; + long CorMode; + + long flagMethod; + long Method; + + long Periodic; + + long flagmaxIter; + long maxIter; + + long flagrmsd; + float rmsd; + + long flagLog; + char* Log; + FILE* fptLog; + + long flagconfigFile; + char* configFile; + FILE* fptconfigFile; + + long flagmode; + long mode; + +} mrcImageAutoRotationAverageInfo; +#ifdef __cplusplus +extern "C" { +#endif +extern void argCheck(mrcImageAutoRotationAverageInfo* info, int argc, char* avgv[]); +extern void khorosInit(int argc, char* avgv[]); +extern void init0(mrcImageAutoRotationAverageInfo* info); +extern void init1(mrcImageAutoRotationAverageInfo* info); +extern void usage(char* usage); +extern void additionalUsage(void); +extern void htmlBeforeUsage(char* usage); +extern void htmlAfterUsage(char* usage); +#ifdef __cplusplus +}; +#endif +#endif /* MRCIMAGEAUTOROTATIONAVERAGE_H */ diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/.Depend b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/.Depend new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/.Source b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/.Source new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/Makefile b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/Makefile new file mode 100755 index 0000000000..7beb110976 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/Makefile @@ -0,0 +1,427 @@ +include ../Config/Define.inc +include ../../Config/Define.inc +include ../../../Config/Define.inc +include ../../../../Config/Define.inc + +EOSHOME=../../../../../ +DSTDIR=$(EOSHOME)/bin +DSTDOC=$(EOSHOME)/doc +DSTTAR=$(EOSHOME)/tar + +INCFILES = + +LIBFILES = \ + $(LIBPREFIX)EosObjects$(LIBSUFFIX) + +LIBFILESDEBUG = \ + $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) + +SRCC = \ + $(OBJECTNAME).c \ + init.c \ + argCheck.c \ + usage.c \ + util.c \ + +SRCCXX = \ + $(OBJECTNAME).cc \ + init.cc \ + argCheck.cc \ + usage.cc \ + util.cc \ + +MODULES = \ + $(OBJECTNAME).o \ + init.o \ + argCheck.o \ + usage.o \ + util.o \ + +REALMODULES = \ + $(OSTYPE)/$(OBJECTNAME).o \ + $(OSTYPE)/init.o \ + $(OSTYPE)/argCheck.o \ + $(OSTYPE)/usage.o \ + $(OSTYPE)/util.o + +MODULESDEBUG = \ + $(OBJECTNAME).debugo \ + init.debugo \ + argCheck.debugo \ + usage.debugo \ + util.debugo \ + +REALMODULESDEBUG = \ + $(OSTYPE)/$(OBJECTNAME).debugo \ + $(OSTYPE)/init.debugo \ + $(OSTYPE)/argCheck.debugo \ + $(OSTYPE)/usage.debugo \ + $(OSTYPE)/util.debugo + + +all: $(OSTYPE)/$(OBJECTNAME) + if [ ! -L $(OSTYPE) ] ; then \ + moveHostdependent; \ + fi + +debug: $(OSTYPE)/$(OBJECTNAME).debug + +cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb + + +$(OSTYPE)/$(OBJECTNAME):: + @$(RM) -f $(OSTYPE)/Makefile ; \ + $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \ + cd $(OSTYPE); \ + $(MAKE) $(OBJECTNAME) WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) + +$(OSTYPE)/$(OBJECTNAME).debug:: + @$(RM) -f $(OSTYPE)/Makefile ; \ + $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \ + cd $(OSTYPE); \ + $(MAKE) $(OBJECTNAME).debug WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) + +$(OSTYPE)/$(OBJECTNAME).cudagdb:: + @$(RM) -f $(OSTYPE)/Makefile ; \ + $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \ + cd $(OSTYPE); \ + $(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) + +cvsupdate:: + cvs -d $(EOS_CVSROOT) update -d + +cvscommit:: + cvs -d $(EOS_CVSROOT) commit + +edit: + @if [ -r $(OBJECTNAME).c ]; \ + then \ + sccsEdit $(OBJECTNAME).c; \ + else \ + echo "Source files are already editable"; \ + fi + @if [ -r wish/$(OBJECTNAME).wish ]; \ + then \ + cd wish; sccsEdit $(OBJECTNAME).wish; \ + else \ + echo "Source files (wish) are already editable."; \ + fi + @if [ -r ruby/$(OBJECTNAME).rb ]; \ + then \ + cd ruby; sccsEdit $(OBJECTNAME).rb; \ + else \ + echo "Source files (ruby) are already editable."; \ + fi + @if [ -r perl/$(OBJECTNAME).pl ]; \ + then \ + cd perl; sccsEdit $(OBJECTNAME).pl ; \ + else \ + echo "Source files (perl) are already editable."; \ + fi + @if [ -r ../Config/OptionControlFile ]; \ + then \ + cd ../Config; sccsEdit OptionControlFile; \ + else \ + echo "OptionControlFile are already editable."; \ + fi + +unedit: + @if [ -w $(OBJECTNAME).c ]; \ + then \ + sccsUnedit $(OBJECTNAME).c; \ + else \ + echo "Source files are not editable"; \ + fi + @if [ -w wish/$(OBJECTNAME).wish ]; \ + then \ + cd wish; sccsUnedit $(OBJECTNAME).wish; \ + else \ + echo "Source files (wish) are not editable."; \ + fi + @if [ -w ruby/$(OBJECTNAME).rb]; \ + then \ + cd ruby; sccsUnedit $(OBJECTNAME).rb; \ + else \ + echo "Source files (ruby) are not editable."; \ + fi + @if [ -w perl/$(OBJECTNAME).pl ]; \ + then \ + cd perl; sccsUnedit $(OBJECTNAME).pl ; \ + else \ + echo "Source files (ruby) are not editable."; \ + fi + @if [ -w ../Config/OptionControlFile ]; \ + then \ + cd ../Config; sccsUnedit OptionControlFile; \ + else \ + echo "OptionControlFile are not editable."; \ + fi + +report: + @if [ -r $(OBJECTNAME).c ]; \ + then \ + sccsReport $(OBJECTNAME).c; \ + else \ + echo "Source files are already editable"; \ + fi + @if [ -r wish/$(OBJECTNAME).wish ]; \ + then \ + cd wish; sccsReport $(OBJECTNAME).wish; \ + else \ + echo "Source files (wish) are already editable."; \ + fi + @if [ -r ruby/$(OBJECTNAME).rb ]; \ + then \ + cd ruby; sccsReport $(OBJECTNAME).rb; \ + else \ + echo "Source files (ruby) are already editable."; \ + fi + @if [ -r perl/$(OBJECTNAME).pl ] ; \ + then \ + cd perl; sccsReport $(OBJECTNAME).pl ; \ + else \ + echo "Source files (perl) are already editable."; \ + fi + @if [ -r ../Config/OptionControlFile ]; \ + then \ + cd ../Config; sccsReport OptionControlFile; \ + else \ + echo "OptionControlFile are already editable."; \ + fi + +clean : + rm -f *.debugo $(OSTYPE)/*.debugo *.cudagdbo $(OSTYPE)/*.cudagdbo *.o $(OSTYPE)/*.o *.linkinfo $(OSTYPE)/*.linkinfo \ + $(OSTYPE)/$(OBJECTNAME) $(OSTYPE)/*.$(OSTYPE) \ + $(OSTYPE)/$(OBJECTNAME).debug $(OSTYPE)/*.$(OSTYPE).debug \ + $(OSTYPE)/$(OBJECTNAME).cudagdb $(OSTYPE)/*.$(OSTYPE).cudagdb \ + $(OSTYPE)/$(OBJECTNAME).linkinfo $(OSTYPE)/*.$(OSTYPE).linkinfo \ + *.bak *.$(OSTYPE) core + +install: install-bin install-doc install-wish install-ruby install-shell install-perl + @if [ dummy$(KHOROS_KENGOBJ) != dummy ] ; \ + then \ + if [ -x $(KHOROS_KGENOBJ) ] ; \ + then \ + make install-khoros ; \ + fi; \ + fi + +install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) + +$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME) + @echo ---- Installing to bin + @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) + @if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \ + then \ + mkdir $(DSTDIR)/$(OSTYPE); \ + fi + @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \ + then \ + echo "Compilation is complete"; \ + $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \ + $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \ + $(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \ + else \ + echo "Compilation is incomplete. $(OBJECTNAME)"; \ + fi + @echo ---- end of bin + +install-wish: + @if [ -d wish ]; \ + then \ + echo "---- Tcl/Tk file Install"; \ + if [ ! -d $(DSTDIR)/wish/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/wish/$(OBJECTNAME) ; \ + fi ; \ + $(CP) -f wish/* $(DSTDIR)/wish/$(OBJECTNAME); \ + $(CHMOD) 555 $(DSTDIR)/wish/$(OBJECTNAME)/* ;\ + touch $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\ + $(CHMOD) 666 $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\ + echo "---- Tcl/Tk file Installed";\ + fi + +install-ruby: + @if [ -d ruby ]; \ + then \ + echo "---- Ruby/Tk file Install"; \ + if [ ! -d $(DSTDIR)/ruby/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/ruby/$(OBJECTNAME) ; \ + fi ; \ + $(CP) -f ruby/* $(DSTDIR)/ruby/$(OBJECTNAME); \ + $(CHMOD) 555 $(DSTDIR)/ruby/$(OBJECTNAME)/* ; \ + echo "---- Ruby/Tk file Installed"; \ + fi + +install-perl: + @if [ -d perl ]; \ + then \ + echo "---- Perl/Tk file Install"; \ + if [ ! -d $(DSTDIR)/perl/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/perl/$(OBJECTNAME) ; \ + fi; \ + $(CP) -f perl/* $(DSTDIR)/perl/$(OBJECTNAME); \ + $(CHMOD) 555 $(DSTDIR)/perl/$(OBJECTNAME)/* ; \ + echo "---- Perl/Tk file Installed"; \ + fi + +install-shell: + @if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \ + fi + @if [ -d shell ]; \ + then \ + echo "---- Shell file Install"; \ + if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \ + fi ; \ + $(CP) -f shell/* $(DSTDIR)/shell/$(OBJECTNAME); \ + $(CHMOD) 555 $(DSTDIR)/shell/$(OBJECTNAME)/*; \ + echo "---- Shell file Installed"; \ + fi + +install-khoros: + @echo Installing to khoros + @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KGENOBJ) ]; \ + then \ + echo kgenobj;\ + $(KHOROS_KGENOBJ) -tb Eos -oname $(OBJECTNAME) -type script -pane -cantata true -cat Eos -subcat $(CLASSNAME) -description $(OBJECTNAME) -bname $(OBJECTNAME) -form -lang ksh ; \ + fi + @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \ + then \ + $(KHOROS_KSET) -tb Eos -oname $(OBJECTNAME) -icon $(OBJECTNAME) ; \ + fi + @if [ -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \ + then \ + $(CHMOD) -R 775 ../../../../../objects/script/$(OBJECTNAME) ; \ + if [ $? ] ; \ + then \ + echo "-- setting khoros ---" ; \ + if [ -d ../../../../../objects/script/$(OBJECTNAME)/uis/ ] ; \ + then \ + $(CD) ../../../../../objects/script/$(OBJECTNAME)/uis/ ; \ + $(RM) -f $(OBJECTNAME).pane ; \ + $(LN) -s ../../../../src/Tools/$(CLASSNAME)/$(OBJECTNAME)/src/$(OBJECTNAME).pane $(OBJECTNAME).pane; \ + $(CD) ../../ ; \ + $(CHMOD) -R 555 $(OBJECTNAME); \ + else \ + echo "../../../../../objects/script/$(OBJECTNAME)/uis/ does not exist."; \ + fi ; \ + else \ + echo "Failed !!: Cannot chage mode in installing $(OBJECTNAME) to khoros system"; \ + fi ; \ + echo "-- end of khoros-installing"; \ + fi + +install-doc: html + @if [ ! -d $(DSTDOC)/SmallTools ]; \ + then \ + mkdir $(DSTDOC)/SmallTools ;\ + fi + @if [ -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ]; \ + then \ + $(RM) -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ;\ + fi + @$(CP) $(OBJECTNAME).html $(DSTDOC)/SmallTools/$(OBJECTNAME).html + @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html + @if [ -f ../doc/*.html ]; \ + then \ + $(CP) ../doc/*.html $(DSTDOC)/SmallTools/ ;\ + fi + @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html + @if [ -f $(DSTDOC)/SmallTools/Makefile ]; \ + then \ + cd $(DSTDOC)/SmallTools; $(MAKE); \ + fi + +html: $(OBJECTNAME).html + +configFileRead: + @ctrl2configFileRead $(CLASSNAME) $(OBJECTNAME) ../Config/OptionControlFile + +$(OBJECTNAME).html: $(OSTYPE)/$(OBJECTNAME) + @echo creating html + @$(OSTYPE)/$(OBJECTNAME) -html 2> $(OBJECTNAME).html.tmp + @sed -e s/$(OSTYPE)\\/// $(OBJECTNAME).html.tmp > $(OBJECTNAME).html + @$(RM) $(OBJECTNAME).html.tmp + +$(DSTDIR)/$(OBJECTNAME): $(OSTYPE)/$(OBJECTNAME) + @ln -s -f ../sbin/MachineIndependent $@ + +depend:: + @echo dependency checking now + @if [ ! -L $(OSTYPE) ] ; then \ + moveHostdependent; \ + fi + rm -f $(OSTYPE)/.Depend + #echo C + @if [ -f $(OBJECTNAME).c ] ; \ + then \ + echo "dependency: *.c"; \ + echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c ; \ + $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c >> $(OSTYPE)/.Depend ; \ + fi + #echo CC + @if [ -f $(OBJECTNAME).cc ] ; \ + then \ + echo "dependency: *.cc"; \ + echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc ; \ + $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc >> $(OSTYPE)/.Depend ; \ + fi + @if [ -f $(OBJECTNAME).ccm ] ; \ + then \ + echo "dependency: *.ccm"; \ + echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm ; \ + $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm >> $(OSTYPE)/.Depend ; \ + fi + @if [ -f $(OBJECTNAME).cu ] ; \ + then \ + echo "dependency: *.cu"; \ + echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu ; \ + $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu >> $(OSTYPE)/.Depend ; \ + fi + +update:../Config/OptionControlFile + maketool $(CLASSNAME) $(OBJECTNAME) update + +changeName:: + +Test:$(OSTYPE)/$(OBJECTNAME) TestDir + @if [ -f test/Makefile ] ; \ + then \ + cd test; make ; \ + else \ + echo "No test Makefile"; \ + fi + +TestDir:: + @if [ ! -d test ] ; \ + then \ + echo "Creating test dir"; \ + mkdir test; \ + fi + @if [ ! -f test/Makefile ] ; \ + then \ + echo "Creating Makefile"; \ + cd test; \ + protoTestMakefileCreate; \ + fi + @if [ ! -d test/data ]; \ + then \ + mkdir $(EOSHOME)/data/$(OBJECTNAME); \ + cd test; \ + ln -sf ../$(EOSHOME)/data/$(OBJECTNAME) data; \ + fi + +tar:: + cd $(DSTTAR); tar cvf Tools.$(CLASSNAME).$(OBJECTNAME).tar ../bin/$(OBJECTNAME) \ + ../bin/*/$(OBJECTNAME).* \ + ../src/Tools/$(CLASSNAME)/$(OBJECTNAME) \ + ; gzip Tools.$(CLASSNAME).$(OBJECTNAME).tar + +-include $(OSTYPE)/.Depend +-include ../Config/Target.inc diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64 b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64 new file mode 120000 index 0000000000..d7e4682e53 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64 @@ -0,0 +1 @@ +../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64 \ No newline at end of file diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/argCheck.c b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/argCheck.c new file mode 100755 index 0000000000..8372ed38bd --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/argCheck.c @@ -0,0 +1,202 @@ +#include +#include +#include +#include +#include "../inc/config.h" +#include "genUtil.h" +#include "String.h" +#include "File.h" +#include "Memory.h" + + +void +argCheck(mrcImageAutoRotationAverageInfo* info, int argc, char* argv[]) +{ + long i; + char s[1024]; + FILE* fpt; + + if(NULL==(fpt=fopen(".EosLog", "a+"))) { + + } else { + for(i=0; iInList = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagIn++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("r") { + if(i+1Ref = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagRef++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("o") { + if(i+1Out = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagOut++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("range") { + if(i+4Min = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagMin++; + info->Max = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagMax++; + info->Delta = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagDelta++; + info->Iter = stringGetNthIntegerData(argv[i+1], 1, " ,"); + i++; + info->flagIter++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("iter") { + if(i+1iter = stringGetNthIntegerData(argv[i+1], 1, " ,"); + i++; + info->flagiter++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("M") { + if(i+1CorMode = stringGetNthIntegerData(argv[i+1], 1, " ,"); + i++; + info->flagCorMode++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("Method") { + if(i+1Method = stringGetNthIntegerData(argv[i+1], 1, " ,"); + i++; + info->flagMethod++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("Periodic") { + if(i+0Periodic++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("maxIter") { + if(i+1maxIter = stringGetNthIntegerData(argv[i+1], 1, " ,"); + i++; + info->flagmaxIter++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("rmsd") { + if(i+1rmsd = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagrmsd++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("log") { + if(i+1Log = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagLog++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("c") { + if(i+1configFile = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagconfigFile++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("m") { + if(i+1mode = stringGetNthIntegerData(argv[i+1], 1, " ,"); + i++; + info->flagmode++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("h") { + usage(argv[0]); + exit(EXIT_SUCCESS); + break; + } + SCASE("html") { + htmlBeforeUsage(argv[0]); + usage(argv[0]); + htmlAfterUsage(argv[0]); + exit(EXIT_SUCCESS); + break; + } + SDEFAULT { + fprintf(stderr, "Not Supported Options: :%s\n", argv[i]); + usage(argv[0]); + exit(EXIT_FAILURE); + break; + } + SSWITCHEND; + } + } +} diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/init.c b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/init.c new file mode 100755 index 0000000000..fb5d3be44f --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/init.c @@ -0,0 +1,153 @@ +#include +#include +#include +#include +#include "../inc/config.h" +#include "genUtil.h" +#include "String.h" +#include "File.h" +#include "Memory.h" + + +void +init0(mrcImageAutoRotationAverageInfo* info) +{ + info->fptIn = stdin; info->fptInList = stdin; info->flagIn = 0; + info->fptRef = NULL; info->flagRef = 0; + info->fptOut = NULL; info->flagOut = 0; + info->Min = 0.0; info->flagMin = 0; + info->Max = 360.0; info->flagMax = 0; + info->Delta = 5.0; info->flagDelta = 0; + info->Iter = 2; info->flagIter = 0; + info->iter = 2; info->flagiter = 0; + info->CorMode = 16; info->flagCorMode = 0; + info->Method = 0; info->flagMethod = 0; + info->Periodic=0; + info->maxIter = 10; info->flagmaxIter = 0; + info->rmsd = 1e-2; info->flagrmsd = 0; + info->fptLog = stdout; info->flagLog = 0; + info->fptconfigFile = NULL; info->flagconfigFile = 0; + info->mode = 0; info->flagmode = 0; +} + +void +init1(mrcImageAutoRotationAverageInfo* info) +{ + char s[1024]; + int i; + if(!info->flagIn) { + stringGetFromFile(s, "In", stdin, stdout, 0); + info->InList = stringGetNthWord(s, 1, " ,\t"); + info->flagIn++; + } + if(info->flagIn) { + info->fptInList = fileOpen(info->InList, "r"); + fseek(info->fptInList, 0L, SEEK_SET); + i=0; + while(NULL!=stringGetFromFile(s, "", info->fptInList, stdout, 1)) { + i++; + } + info->fptIn = (FILE**)memoryAllocate(i*sizeof(FILE*), "in init1"); + info->In = (char**)memoryAllocate(i*sizeof(char*), "in init1"); + info->flagIn = i; + fseek(info->fptInList, 0L, SEEK_SET); + i=0; + while(NULL!=stringGetFromFile(s, "", info->fptInList, stdout, 1)) { + info->In[i] = stringGetNthWord(s, 1, " ,\t"); + info->fptIn[i] = fileOpen(info->In[i],"r"); + i++; + } + } + + if(info->flagRef) { + info->fptRef = fileOpen(info->Ref, "r"); + } + + if(!info->flagOut) { + stringGetFromFile(s, "Out", stdin, stdout, 0); + info->Out = stringGetNthWord(s, 1, " ,\t"); + info->flagOut++; + } + if(info->flagOut) { + info->fptOut = fileOpen(info->Out, "w"); + } + + if(info->flagMin) { + } + + if(info->flagMax) { + } + + if(info->flagDelta) { + } + + if(info->flagIter) { + } + + if(info->flagiter) { + } + + if(info->flagCorMode) { + } + + if(info->flagMethod) { + } + + if(info->flagmaxIter) { + } + + if(info->flagrmsd) { + } + + if(info->flagLog) { + info->fptLog = fileOpen(info->Log, "r"); + } + + if(info->flagconfigFile) { + info->fptconfigFile = fileOpen(info->configFile, "r"); + } + + if(info->flagmode) { + } + +} +#ifdef KHOROS +#include +#include "bootstrap.h" +#include "dataserv.h" +#include "datamanip.h" +extern void func_usage_additions(void); +extern void func_free_args(kexit_status status, kaddr client_data); +extern void func_get_args(kform* pane); + +void +func_usage_additions(void) +{ +} +void +func_free_args(kexit_status status, kaddr client_data) +{ +} +void +func_get_args(kform* pane) +{ +} +void +khorosInit(int argc, char* argv[]) +{ + char* eospath; + char panepath[1024]; + FILE* fpt; + + eospath = getenv("EOS_HOME"); + sprintf(panepath, "%s/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.pane", eospath); + khoros_initialize(argc, argv, "EOS"); + fpt = fopen(panepath, "r"); if(NULL!=fpt) { + fclose(fpt); + kclui_initialize(panepath, KGEN_NONE, "EOS", "mrcImageAutoRotationAverage", + func_usage_additions, + func_get_args, + func_free_args); + } +} +#endif /* KHOROS */ diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.c b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.c new file mode 100755 index 0000000000..fe4963728c --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.c @@ -0,0 +1,103 @@ +/* +# mrcImageAutoRotationAverage : $Revision$ +# $Date$ +# Created by $Author$ +# Usage : mrcImageAutoRotationAverage +# Attention +# $Loccker$ +# $State$ +# +*/ +#include +#include +#include +#include +#define GLOBAL_DECLARATION +#include "../inc/config.h" + +#define DEBUG +#include "genUtil.h" +#include "mrcImage.h" +#include "Memory.h" +#include "lmrcImageAverage.h" +#include "lmrcImageCorrelation.h" + +/* +Example: +typedef struct lmrcImageAutoRotationAverageInfo { + float a; + int b; +} lmrcImageAutoRotationAverageInfo; + +typedef enum lmrcImageAutoRotationAverageMode { + a=0, + b=1 +} lmrcImageAutoRotationAverageMode; +*/ + +int +main(int argc, char* argv[]) +{ + mrcImage* in; + mrcImage ref; + mrcImage* fit; + mrcImage* cor; + mrcImage out; + mrcImageAutoRotationAverageInfo info; + lmrcImageAutoRotationCorrelationInfo* linfo; + int i, k; + + init0(&info); + argCheck(&info, argc, argv); + init1(&info); + + DEBUGPRINT("Program Start\n"); + in = (mrcImage*)memoryAllocate(sizeof(mrcImage)*info.flagIn, "in main"); + fit = (mrcImage*)memoryAllocate(sizeof(mrcImage)*info.flagIn, "in main"); + cor = (mrcImage*)memoryAllocate(sizeof(mrcImage)*info.flagIn, "in main"); + linfo = (lmrcImageAutoRotationCorrelationInfo*)memoryAllocate(sizeof(lmrcImageAutoRotationCorrelationInfo)*info.flagIn, "in main"); + for(i=0; i + +mrcImageAutoRotationAverage + + +

mrcImageAutoRotationAverage

+

Usage

+
+Usage: mrcImageAutoRotationAverage
+Options:
+    [-i[nput]            In                  (stdin     ).as(inFileList::mrcImage) ] :Essential :Input: Ins
+    [-r[eferenc]         Ref                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input: Ref
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output:Average
+    [-range              Min                 (0.0       ).as(Real                ) 
+                         Max                 (360.0     ).as(Real                ) 
+                         Delta               (5.0       ).as(Real                ) 
+                         Iter                (2         ).as(Integer             ) ] :Optional  :Mode
+    [-iter               iter                (2         ).as(Integer             ) ] :Optional  :iteration for rotation
+    [-M[odeCorrelation]  CorMode             (16        ).as(Integer             ) ] :Optional  :Mode: Correlation
+    [-Method[Correlation]Method              (0         ).as(Integer             ) ] :Optional  :Method: Correlation
+    [-Periodic                                                                     ] :Optional  :Periodic
+    [-maxIter[aration]   maxIter             (10        ).as(Integer             ) ] :Optional  :MaxIteration
+    [-rmsd               rmsd                (1e-2      ).as(Real                ) ] :Optional  :rmsd
+    [-log                Log                 (stdout    ).as(inFile::ASCII       ) ] :Optional  :logFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+----- -Mode -----
+0: Normal Correlation FxG*
+1: Phase  Correlation FxG*/     |FxG*|
+2: Phase  Correlation FxG*/sqrt(|FxG*|)
+3: Normalized Normal Correlation FxG*/|F||G|)
+16: (0,0) = 0 
+Refinement Correlation Map
+0: sqrt(Sum |Fi-Gi|^2                 / Sum |Gi|^2)
+1:      Sum |Gi||phaseFi - phaseGi|   / Sum |Gi|  
+2: sqrt(Sum |Gi||phaseFi - phaseGi|^2 / Sum |Gi|  )
+
+ + diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.pane b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.pane new file mode 100755 index 0000000000..5bd0200166 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.pane @@ -0,0 +1,25 @@ +-F 4.3 1 0 52x1+0+0 +0+0 'Cantata' cantata + -M 1 1 52x1+0+0 +1+0 ' ' subform + -P 1 0 52x1+0+1 +0+0 ' ' mrcImageAutoRotationAverage + -D 1 0 9x1+0+0 'Options' _gui_options + -H 1 6x1+0+0 'License' 'license' $BOOTSTRAP/repos/license/License license + -E + -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrcImageAutoRotationAverage + -H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImageAutoRotationAverage/doc/mrcImageAutoRotationAverage.doc help + -Q 1 0 5.25x1+47+0 'Close' + -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input: Ins' i + -I 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'Ref' 'Input: Ref' r + -O 1 0 1 1 0 1 -1x1+1+4.500000 ' ' 'Out' 'Output:Average' o + -I 1 0 0 1 0 1 -1x1+1+6 ' ' '0.0' 'Min' Mode + -i 1 0 1 0 0 -1x1+1+7.500000 0 0 2 0 0 'iter' 'iteration for rotation' iter + -i 1 0 1 0 0 -1x1+1+9.000000 0 0 16 0 0 'CorMode' 'Mode: Correlation' M + -i 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'Method' 'Method: Correlation' Method + -t 1 0 1 0 0 6x1+1+12 'Periodic' 'Periodic' Periodic + -i 1 0 1 0 0 -1x1+1+13.500000 0 0 10 0 0 'maxIter' 'MaxIteration' maxIter + -f 1 0 1 0 0 -1x1+1+15.000000 0 0 0.010000 0 0 0 'rmsd' 'rmsd' rmsd + -I 1 0 1 0 0 1 -1x1+1+16.500000 ' ' 'Log' 'logFile' log + -I 1 0 1 0 0 1 -1x1+1+18.000000 ' ' 'configFile' 'ConfigurationFile' c + -i 1 0 1 0 0 -1x1+1+19.500000 0 0 0 0 0 'mode' 'Mode' m + -E + -E +-E diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/test/Makefile b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/test/Makefile new file mode 100755 index 0000000000..364e680d62 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/test/Makefile @@ -0,0 +1,25 @@ +include ../../Config/Define.inc +include ../../../Config/Define.inc +include ../../../../Config/Define.inc +include ../../../../../Config/Define.inc + +all: help exec + +help: + @echo "----- Help Message Check -----" + @../$(OSTYPE)/$(OBJECTNAME) -h + +exec: + @echo "----- Execution Check -----" + ../$(OSTYPE)/$(OBJECTNAME) -i data/in.lst -r data/test-000.mrc -o data/test.avg -Periodic -range 0 360 5 -M 18 -m 0 -maxIter 10 -iter 4; + @echo "----- Calc check -----" + +init: + pdb2mrc2d -i data/121p-GC.pdb -o data/test-000.mrc -d 2.5 2.5 -s -40 -40 -n 32 32 -sig 2.0 -w 1.0 + echo "data/test-000.mrc" > data/in.lst + for i in 030 060 090 120 150 180 ; do \ + mrcImageRotation -i data/test-000.mrc -o data/test-$$i.mrc -a $$i -Periodic; \ + echo "data/test-$$i.mrc" >> data/in.lst; \ + done + +clean: diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/test/data b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/test/data new file mode 120000 index 0000000000..1879600136 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/test/data @@ -0,0 +1 @@ +../../../../../..//data/mrcImageAutoRotationAverage \ No newline at end of file diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/usage.c b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/usage.c new file mode 100755 index 0000000000..17c5cfe2d5 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/usage.c @@ -0,0 +1,45 @@ +#include +#include +#include "../inc/config.h" + +void +usage(char* thisProgram) +{ + fprintf(stderr, "Usage: %s\n", thisProgram); + fprintf(stderr, "Options:\n"); + fprintf(stderr, " [-i[nput] In (stdin ).as(inFileList::mrcImage) ] :Essential :Input: Ins\n"); + fprintf(stderr, " [-r[eferenc] Ref (NULL ).as(inFile::mrcImage ) ] :Optional :Input: Ref\n"); + fprintf(stderr, " [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:Average\n"); + fprintf(stderr, " [-range Min (0.0 ).as(Real ) \n Max (360.0 ).as(Real ) \n Delta (5.0 ).as(Real ) \n Iter (2 ).as(Integer ) ] :Optional :Mode\n"); + fprintf(stderr, " [-iter iter (2 ).as(Integer ) ] :Optional :iteration for rotation\n"); + fprintf(stderr, " [-M[odeCorrelation] CorMode (16 ).as(Integer ) ] :Optional :Mode: Correlation\n"); + fprintf(stderr, " [-Method[Correlation]Method (0 ).as(Integer ) ] :Optional :Method: Correlation\n"); + fprintf(stderr, " [-Periodic ] :Optional :Periodic\n"); + fprintf(stderr, " [-maxIter[aration] maxIter (10 ).as(Integer ) ] :Optional :MaxIteration\n"); + fprintf(stderr, " [-rmsd rmsd (1e-2 ).as(Real ) ] :Optional :rmsd\n"); + fprintf(stderr, " [-log Log (stdout ).as(inFile::ASCII ) ] :Optional :logFile\n"); + fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n"); + fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n"); + additionalUsage(); +} + +void +htmlBeforeUsage(char* thisProgram) +{ + fprintf(stderr, "\n"); + fprintf(stderr, "\n"); + fprintf(stderr, "%s\n", thisProgram); + fprintf(stderr, "\n"); + fprintf(stderr, "\n"); + fprintf(stderr, "

%s

\n", thisProgram); + fprintf(stderr, "

Usage

\n"); + fprintf(stderr, "
\n");
+}
+
+void
+htmlAfterUsage(char* thisProgram)
+{
+    fprintf(stderr, "
\n"); + fprintf(stderr, "\n"); + fprintf(stderr, "\n"); +} diff --git a/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/util.c b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/util.c new file mode 100755 index 0000000000..ee5e5f2324 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/util.c @@ -0,0 +1,4 @@ +#include +#include +#include "../inc/config.h" +