--- /dev/null
+../sbin/MachineIndependent
\ No newline at end of file
--- /dev/null
+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
--- /dev/null
+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
--- /dev/null
+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64
\ No newline at end of file
} 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;
int flagXshiftOnly;
int flagNoShift;
+/* Output */
+ float max; //
+ float maxTheta; //
+ mrcImageParaTypeRealCoord maxP;
+ mrcImageInformation corInfo;
+ lmrcImageSSDAInfo SSDAInfo;
+ float EuclidDistance;
+ float LinearCorrelation;
+
} lmrcImageAutoRotationCorrelationInfo;
typedef struct lmrcImageCorrelationRefinementInfo {
} 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;
int flagXshiftOnly;
int flagNoShift;
+/* Output */
+ float max; //
+ float maxTheta; //
+ mrcImageParaTypeRealCoord maxP;
+ mrcImageInformation corInfo;
+ lmrcImageSSDAInfo SSDAInfo;
+ float EuclidDistance;
+ float LinearCorrelation;
+
} lmrcImageAutoRotationCorrelationInfo;
typedef struct lmrcImageCorrelationRefinementInfo {
WORLDNAME=Tools
WORLDNAME=Tools
WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
mrcImageAutoCorrelationWithWindowing \
mrcImageAutoFilamentExtract \
mrcImageAutoFilamentExtractResultAnalysis \
+mrcImageAutoRotationAverage \
mrcImageAutoRotationCorrelation \
mrcImageAutoRotationCorrelation3D \
mrcImageAutoRotationCorrelationResultPrint \
--- /dev/null
+OBJECTNAME = mrcImageAutoRotationAverage
+EXTRA_LIB =
+EXTRA_CCOPTS =
+EXTRA_INC =
--- /dev/null
+# 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"
--- /dev/null
+/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file
--- /dev/null
+/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/doc/Makefile
\ No newline at end of file
--- /dev/null
+#ifndef CONFIG_H
+#define CONFIG_H
+
+#include "../inc/mrcImageAutoRotationAverage.h"
+
+#endif /* CONFIG_H */
--- /dev/null
+#ifndef MRCIMAGEAUTOROTATIONAVERAGE_H
+#define MRCIMAGEAUTOROTATIONAVERAGE_H
+#include <stdio.h>
+#include <stdlib.h>
+
+#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 */
--- /dev/null
+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
--- /dev/null
+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64
\ No newline at end of file
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#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; i<argc; i++) {
+ fprintf(fpt, "%s ", argv[i]);
+ }
+ fprintf(fpt, "\n");
+ fclose(fpt);
+ }
+ for(i=1; i<argc; i++) {
+ if(OPTION_FLAG==argv[i][OPTION_FLAG_POS]) {
+ SSWITCH(argv[i]+OPTION_POS)
+ SCASE("i") {
+ if(i+1<argc) {
+ info->InList = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagIn++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("r") {
+ if(i+1<argc) {
+ info->Ref = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagRef++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("o") {
+ if(i+1<argc) {
+ info->Out = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagOut++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("range") {
+ if(i+4<argc) {
+ info->Min = 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+1<argc) {
+ info->iter = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagiter++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("M") {
+ if(i+1<argc) {
+ info->CorMode = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagCorMode++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("Method") {
+ if(i+1<argc) {
+ info->Method = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagMethod++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("Periodic") {
+ if(i+0<argc) {
+ info->Periodic++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("maxIter") {
+ if(i+1<argc) {
+ info->maxIter = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagmaxIter++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("rmsd") {
+ if(i+1<argc) {
+ info->rmsd = stringGetNthRealData(argv[i+1], 1, " ,");
+ i++;
+ info->flagrmsd++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("log") {
+ if(i+1<argc) {
+ info->Log = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagLog++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("c") {
+ if(i+1<argc) {
+ info->configFile = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagconfigFile++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("m") {
+ if(i+1<argc) {
+ info->mode = 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;
+ }
+ }
+}
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#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 <stdio.h>
+#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 */
--- /dev/null
+/*
+# mrcImageAutoRotationAverage : $Revision$
+# $Date$
+# Created by $Author$
+# Usage : mrcImageAutoRotationAverage
+# Attention
+# $Loccker$
+# $State$
+#
+*/
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#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<info.flagIn; i++) {
+ mrcFileRead(&(in[i]), info.In[i], "in main", 0);
+ }
+ if(info.flagRef) {
+ mrcFileRead(&ref, info.Ref, "in main", 0);
+ } else {
+ fprintf(stderr, "FileImage(%s) is used as a reference.\n", info.In[0]);
+ mrcFileRead(&ref, info.In[0], "in main", 0);
+ }
+
+ // linfo
+ for(i=0; i<info.flagIn; i++) {
+ linfo[i].iter = info.iter;
+ linfo[i].nRot = (int)((info.Max - info.Min)/info.Delta)+1;
+ linfo[i].Method = info.Method;
+ linfo[i].flagRestrictionArea = 1;
+ linfo[i].thetaMin = info.Min*RADIAN;
+ linfo[i].thetaMax = info.Max*RADIAN;
+ }
+
+ for(k=0; k<info.maxIter; k++) {
+ for(i=0; i<info.flagIn; i++) {
+ DEBUGPRINT2("%d: %d\n", k, i);
+ lmrcImageAutoRotationCorrelation(&(fit[i]), &(cor[i]), &(in[i]), &ref, &(linfo[i]), info.CorMode);
+ }
+ }
+
+ lmrcImageAverage(&out, fit, info.flagIn, info.mode);
+
+ mrcFileWrite(&out, info.Out, "in main", 0);
+
+ for(i=0; i<info.flagIn; i++) {
+ fprintf(info.fptLog, "%d %f %f %f %f\n", i, linfo[i].max, linfo[i].maxTheta*DEGREE, linfo[i].maxP.x, linfo[i].maxP.y);
+ }
+ exit(EXIT_SUCCESS);
+}
+
+void
+additionalUsage()
+{
+ fprintf(stderr, "----- Additional Usage -----\n");
+ fprintf(stderr, "----- -Mode -----\n");
+ lmrcImageCorrelationModePrint(stderr);
+
+}
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoRotationAverage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoRotationAverage</H1>
+<H2>Usage</H2>
+<PRE>
+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| )
+</PRE>
+</BODY>
+</HTML>
--- /dev/null
+-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' $EOS/src/Tools/mrcImage/mrcImageAutoRotationAverage/doc/mrcImageAutoRotationAverage.doc help
+ -Q 1 0 5.25x1+47+0 'Close'
+ -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input: Ins' i
+ -I 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'Ref' 'Input: Ref' r
+ -O 1 0 1 1 0 1 -1x1+1+4.500000 ' ' 'Out' 'Output:Average' o
+ -I 1 0 0 1 0 1 -1x1+1+6 ' ' '0.0' 'Min' Mode
+ -i 1 0 1 0 0 -1x1+1+7.500000 0 0 2 0 0 'iter' 'iteration for rotation' iter
+ -i 1 0 1 0 0 -1x1+1+9.000000 0 0 16 0 0 'CorMode' 'Mode: Correlation' M
+ -i 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'Method' 'Method: Correlation' Method
+ -t 1 0 1 0 0 6x1+1+12 'Periodic' 'Periodic' Periodic
+ -i 1 0 1 0 0 -1x1+1+13.500000 0 0 10 0 0 'maxIter' 'MaxIteration' maxIter
+ -f 1 0 1 0 0 -1x1+1+15.000000 0 0 0.010000 0 0 0 'rmsd' 'rmsd' rmsd
+ -I 1 0 1 0 0 1 -1x1+1+16.500000 ' ' 'Log' 'logFile' log
+ -I 1 0 1 0 0 1 -1x1+1+18.000000 ' ' 'configFile' 'ConfigurationFile' c
+ -i 1 0 1 0 0 -1x1+1+19.500000 0 0 0 0 0 'mode' 'Mode' m
+ -E
+ -E
+-E
--- /dev/null
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+include ../../../../../Config/Define.inc
+
+all: help exec
+
+help:
+ @echo "----- Help Message Check -----"
+ @../$(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:
--- /dev/null
+../../../../../..//data/mrcImageAutoRotationAverage
\ No newline at end of file
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#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, "<HTML>\n");
+ fprintf(stderr, "<HEAD>\n");
+ fprintf(stderr, "<TITLE>%s</TITLE>\n", thisProgram);
+ fprintf(stderr, "</HEAD>\n");
+ fprintf(stderr, "<BODY>\n");
+ fprintf(stderr, "<H1>%s</H1>\n", thisProgram);
+ fprintf(stderr, "<H2>Usage</H2>\n");
+ fprintf(stderr, "<PRE>\n");
+}
+
+void
+htmlAfterUsage(char* thisProgram)
+{
+ fprintf(stderr, "</PRE>\n");
+ fprintf(stderr, "</BODY>\n");
+ fprintf(stderr, "</HTML>\n");
+}
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+