#### Create Makefile in Tools
cd ${ToolClassHome}
rm -f ./Makefile
- ln -s ${ToolHomeTemplate}/Makefile ./Makefile
+ #ln -s ${ToolHomeTemplate}/Makefile ./Makefile
+ cp ${ToolHomeTemplate}/Makefile ./Makefile
#### Create Config in Tools
cd ${ToolClassHome}
if [ -d ./Config ]
WORLDNAME=Tools
WORLDNAME=Tools
WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
mrcImage2DBackProjection \
mrcImage2DProjection \
mrcImage2pdb \
+mrcImage3DCTFObservation \
mrcImage3DHighResoEmphasis \
mrcImage3DPad \
mrcImage3DPad2 \
mrcFFTBandPassFilter \
mrcFFTCTFCompensation \
mrcFFTCentralSection \
+mrcFFTCentralSectionCompare \
mrcFFTDigitize \
mrcFFTExpression \
mrcFFTFibreDiagram \
--- /dev/null
+OBJECTNAME = mrcImage3DCTFObservation
+EXTRA_LIB =
+EXTRA_CCOPTS =
+EXTRA_INC =
--- /dev/null
+# OptionControlFile
+# FileFormat
+"-i","-i[nput]","Input:3D","Essential","1","1","In","inFile::mrcImage","NULL"
+"-o","-o[utput]","Output:2D","Essential","1","1","Out","outFile::mrcImage","NULL"
+"-info","-info[rmation]","Input:ctfInfo","Essential","1","1","In","inFile::ASCII","NULL"
+"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
+"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
--- /dev/null
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+ cd src; make all; cd ..
+
+install:
+ cd src; make install; cd ..
+
+
+putSF:
+ if [ -f private ] ; \
+ then \
+ echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+ else \
+ cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+ fi
+
+put:
+ cd src; make put; cd ..
+
+clean:
+ cd src; make clean; cd ..
+
+depend:
+ cd src; make depend; cd ..
+
+check:
+ @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+ echo making directory; \
+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+ fi
+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
+ @$(RM) src/Makefile
+ @echo "New src/Makefile"
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+ @cd src; touch $(OSTYPE)/.Depend; make depend
+
+update:
+ @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+ echo making directory; \
+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+ fi
+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
+ @$(RM) src/Makefile
+ @echo "New src/Makefile"
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+ @cd src; touch $(OSTYPE)/.Depend; echo "Y" | make update
+
+cvsupdate::
+ cvs -d $(EOS_CVSROOT) update -d
+
+cvscommit::
+ cvs -d $(EOS_CVSROOT) commit
+
+backup:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+distribute:
+ cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+distribute-all:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+ ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./
+
+include Config/Target.inc
--- /dev/null
+install:
+ cd ../src; make install-doc; cd ../doc
--- /dev/null
+#ifndef CONFIG_H
+#define CONFIG_H
+
+#include "../inc/mrcImage3DCTFObservation.h"
+
+#endif /* CONFIG_H */
--- /dev/null
+#ifndef MRCIMAGE3DCTFOBSERVATION_H
+#define MRCIMAGE3DCTFOBSERVATION_H
+#include <stdio.h>
+#include <stdlib.h>
+
+#define OPTION_FLAG '-'
+#define OPTION_FLAG_POS (0)
+#define OPTION_POS (1)
+
+
+
+
+typedef struct mrcImage3DCTFObservationInfo {
+ long flagRedirect;
+
+ long flagIn;
+ char* In;
+ FILE* fptIn;
+
+ long flagOut;
+ char* Out;
+ FILE* fptOut;
+
+ long flagIn;
+ char* In;
+ FILE* fptIn;
+
+ long flagconfigFile;
+ char* configFile;
+ FILE* fptconfigFile;
+
+ long flagmode;
+ long mode;
+
+} mrcImage3DCTFObservationInfo;
+#ifdef __cplusplus
+extern "C" {
+#endif
+extern void argCheck(mrcImage3DCTFObservationInfo* info, int argc, char* avgv[]);
+extern void khorosInit(int argc, char* avgv[]);
+extern void init0(mrcImage3DCTFObservationInfo* info);
+extern void init1(mrcImage3DCTFObservationInfo* info);
+extern void usage(char* usage);
+extern void additionalUsage(void);
+extern void htmlBeforeUsage(char* usage);
+extern void htmlAfterUsage(char* usage);
+#ifdef __cplusplus
+};
+#endif
+#endif /* MRCIMAGE3DCTFOBSERVATION_H */
--- /dev/null
+include ../Config/Define.inc
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+
+EOSHOME=../../../../../
+DSTDIR=$(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/mrcImage3DCTFObservation/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(mrcImage3DCTFObservationInfo* 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->In = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagIn++;
+ } 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("info") {
+ if(i+1<argc) {
+ info->In = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagIn++;
+ } 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(mrcImage3DCTFObservationInfo* info)
+{
+ info->fptIn = NULL; info->flagIn = 0;
+ info->fptOut = NULL; info->flagOut = 0;
+ info->fptIn = NULL; info->flagIn = 0;
+ info->fptconfigFile = NULL; info->flagconfigFile = 0;
+ info->mode = 0; info->flagmode = 0;
+}
+
+void
+init1(mrcImage3DCTFObservationInfo* info)
+{
+ char s[1024];
+ int i;
+ if(!info->flagIn) {
+ stringGetFromFile(s, "In", stdin, stdout, 0);
+ info->In = stringGetNthWord(s, 1, " ,\t");
+ info->flagIn++;
+ }
+ if(info->flagIn) {
+ info->fptIn = fileOpen(info->In, "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->flagIn) {
+ stringGetFromFile(s, "In", stdin, stdout, 0);
+ info->In = stringGetNthWord(s, 1, " ,\t");
+ info->flagIn++;
+ }
+ if(info->flagIn) {
+ info->fptIn = fileOpen(info->In, "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/mrcImage3DCTFObservation/src/mrcImage3DCTFObservation.pane", eospath);
+ khoros_initialize(argc, argv, "EOS");
+ fpt = fopen(panepath, "r"); if(NULL!=fpt) {
+ fclose(fpt);
+ kclui_initialize(panepath, KGEN_NONE, "EOS", "mrcImage3DCTFObservation",
+ func_usage_additions,
+ func_get_args,
+ func_free_args);
+ }
+}
+#endif /* KHOROS */
--- /dev/null
+/*
+# mrcImage3DCTFObservation : $Revision$
+# $Date$
+# Created by $Author$
+# Usage : mrcImage3DCTFObservation
+# 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 "ctfInfo.h"
+
+typedef struct lmrcImage3DCTFObservationInfo {
+ float a;
+ int b;
+} lmrcImage3DCTFObservationInfo;
+
+/*
+typedef enum lmrcImage3DCTFObservationMode {
+ a=0,
+ b=1
+} lmrcImage3DCTFObservationMode;
+*/
+
+int
+main(int argc, char* argv[])
+{
+ mrcImage3DCTFObservationInfo info;
+ mrcImage in;
+ mrcImage out;
+ ctfInfo ctf;
+
+ init0(&info);
+ argCheck(&info, argc, argv);
+ init1(&info);
+
+ DEBUGPRINT("Program Start\n");
+ mrcFileRead(&in, in.In, "in main", 0);
+ memoryClear(&ctf, sizeof(ctf), (char)0);
+ ctfInfoRead(info.fptIn, &ctf, "", 0);
+
+
+ mrcFileRead(&in, in.In, "in main", 0);
+
+
+
+ mrcFileWrite(&out, in.Out, "in main", 0);
+ exit(EXIT_SUCCESS);
+}
+
+void
+additionalUsage()
+{
+ fprintf(stderr, "----- Additional Usage -----\n");
+}
--- /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 ' ' mrcImage3DCTFObservation
+ -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/mrcImage3DCTFObservation
+ -H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImage3DCTFObservation/doc/mrcImage3DCTFObservation.doc help
+ -Q 1 0 5.25x1+47+0 'Close'
+ -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input:3D' i
+ -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'Output:2D' o
+ -I 1 0 1 1 0 1 -1x1+1+4.500000 ' ' 'In' 'Input:ctfInfo' info
+ -I 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'configFile' 'ConfigurationFile' c
+ -i 1 0 1 0 0 -1x1+1+7.500000 0 0 0 0 0 'mode' 'Mode' m
+ -E
+ -E
+-E
--- /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 (NULL ).as(inFile::mrcImage ) ] :Essential :Input:3D\n");
+ fprintf(stderr, " [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:2D\n");
+ fprintf(stderr, " [-info[rmation] In (NULL ).as(inFile::ASCII ) ] :Essential :Input:ctfInfo\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"
+
# OptionControlFile
# FileFormat
-"-i","-i[nput]","InputFile","Essential","1","1","In","inFile","stdin"
-"-o","-o[utput]","OutputDataFile","Essential","1","1","Out","outFile","stdout"
+"-i","-i[nput]","Input:2D","Essential","1","1","In","inFile::mrcImage","stdin"
+"-o","-o[utput]","Output:2D","Essential","1","1","Out","outFile::mrcImage","stdout"
+"-ctf","-ctf","Input:ctfInfo","Essential","1","1","CTF","inFile::ASCII","stdin"
"-kV","-kV","AccVol[kV]","Optional","1","1","kV","Real","200"
"-Cs","-Cs","Cs[mm]","Optional","1","1","Cs","Real","2.1"
"-df","-df","Defocus [A]:under(+)","Optional","1","1","Defocus","Real","27000"
char* Out;
FILE* fptOut;
+ long flagCTF;
+ char* CTF;
+ FILE* fptCTF;
+
long flagkV;
float kV;
}
SBREAK;
}
+ SCASE("ctf") {
+ if(i+1<argc) {
+ info->CTF = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagCTF++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
SCASE("kV") {
if(i+1<argc) {
info->kV = stringGetNthRealData(argv[i+1], 1, " ,");
{
info->fptIn = stdin; info->flagIn = 0;
info->fptOut = stdout; info->flagOut = 0;
+ info->fptCTF = stdin; info->flagCTF = 0;
info->kV = 200; info->flagkV = 0;
info->Cs = 2.1; info->flagCs = 0;
info->Defocus = 27000; info->flagDefocus = 0;
info->fptOut = fileOpen(info->Out, "w");
}
+ if(!info->flagCTF) {
+ stringGetFromFile(s, "CTF", stdin, stdout, 0);
+ info->CTF = stringGetNthWord(s, 1, " ,\t");
+ info->flagCTF++;
+ }
+ if(info->flagCTF) {
+ info->fptCTF = fileOpen(info->CTF, "r");
+ }
+
if(info->flagkV) {
}
init1(&info);
memoryClear(&CTFInfo, sizeof(CTFInfo), (char)0);
- CTFInfo.Cs = info.Cs;
- CTFInfo.defocus = info.Defocus;
- CTFInfo.kV = info.kV;
- CTFInfo.mode = info.ctfMode;
- CTFInfo.ratioOfAmpToPhase = info.AoverP;
- CTFInfo.Ain = info.Ain;
+ if(info.flagCTF) {
+ ctfInfoRead(info.fptCTF, &CTFInfo, "", 0);
+ if(info.flagCs ) CTFInfo.Cs = info.Cs;
+ if(info.flagDefocus) CTFInfo.defocus = info.Defocus;
+ if(info.flagkV ) CTFInfo.kV = info.kV;
+ if(info.flagctfMode) CTFInfo.mode = info.ctfMode;
+ if(info.flagAoverP ) CTFInfo.ratioOfAmpToPhase = info.AoverP;
+ if(info.flagAoverP ) CTFInfo.Ain = info.Ain;
+ } else {
+ CTFInfo.Cs = info.Cs;
+ CTFInfo.defocus = info.Defocus;
+ CTFInfo.kV = info.kV;
+ CTFInfo.mode = info.ctfMode;
+ CTFInfo.ratioOfAmpToPhase = info.AoverP;
+ CTFInfo.Ain = info.Ain;
+ }
if(info.flagSinWinRmin && info.flagSinWinRmax) {
CTFInfo.flagWin = 1;
CTFInfo.CutLow = info.SinWinRmin;
<PRE>
Usage: mrcImageCTFObservation
Options:
- [-i[nput] In (stdin ).as(inFile ) ] :Essential :InputFile
- [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile
+ [-i[nput] In (stdin ).as(inFile::mrcImage ) ] :Essential :Input:2D
+ [-o[utput] Out (stdout ).as(outFile::mrcImage ) ] :Essential :Output:2D
+ [-ctf CTF (stdin ).as(inFile::ASCII ) ] :Essential :Input:ctfInfo
[-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
[-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
[-df Defocus (27000 ).as(Real ) ] :Optional :Defocus [A]:under(+)
-R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrcImageCTFObservation
-H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImageCTFObservation/doc/mrcImageCTFObservation.doc help
-Q 1 0 5.25x1+47+0 'Close'
- -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'InputFile' i
- -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'OutputDataFile' o
- -f 1 0 1 0 0 -1x1+1+4.500000 0 0 200.000000 0 0 0 'kV' 'AccVol[kV]' kV
- -f 1 0 1 0 0 -1x1+1+6.000000 0 0 2.100000 0 0 0 'Cs' 'Cs[mm]' Cs
- -f 1 0 1 0 0 -1x1+1+7.500000 0 0 27000.000000 0 0 0 'Defocus' 'Defocus [A]:under(+)' df
- -f 1 0 1 0 0 -1x1+1+9.000000 0 0 0.000000 0 0 0 'AoverP' 'AmplitudeContrast/PhaseContrast' A
- -f 1 0 1 0 0 -1x1+1+10.500000 0 0 0.000000 0 0 0 'Ain' 'IlluminationAperture[mrad]' Ain
- -f 1 0 1 0 0 -1x1+1+12.000000 0 0 1.000000 0 0 0 'WhiteNoise' 'WhiteNoise(N/S)' white
- -I 1 0 0 1 0 1 -1x1+1+13 ' ' '0.1' 'SinWinRmin' Windowing by sine function from Rmin[A] to Rmax[A]
- -i 1 0 1 0 0 -1x1+1+15.000000 0 0 0 0 0 'ctfMode' 'CTFMode' ctfMode
- -I 1 0 0 1 0 1 -1x1+1+16 ' ' '0' 'dfMin' With Atigmatism
- -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
+ -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input:2D' i
+ -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'Output:2D' o
+ -I 1 0 1 1 0 1 -1x1+1+4.500000 ' ' 'CTF' 'Input:ctfInfo' ctf
+ -f 1 0 1 0 0 -1x1+1+6.000000 0 0 200.000000 0 0 0 'kV' 'AccVol[kV]' kV
+ -f 1 0 1 0 0 -1x1+1+7.500000 0 0 2.100000 0 0 0 'Cs' 'Cs[mm]' Cs
+ -f 1 0 1 0 0 -1x1+1+9.000000 0 0 27000.000000 0 0 0 'Defocus' 'Defocus [A]:under(+)' df
+ -f 1 0 1 0 0 -1x1+1+10.500000 0 0 0.000000 0 0 0 'AoverP' 'AmplitudeContrast/PhaseContrast' A
+ -f 1 0 1 0 0 -1x1+1+12.000000 0 0 0.000000 0 0 0 'Ain' 'IlluminationAperture[mrad]' Ain
+ -f 1 0 1 0 0 -1x1+1+13.500000 0 0 1.000000 0 0 0 'WhiteNoise' 'WhiteNoise(N/S)' white
+ -I 1 0 0 1 0 1 -1x1+1+15 ' ' '0.1' 'SinWinRmin' Windowing by sine function from Rmin[A] to Rmax[A]
+ -i 1 0 1 0 0 -1x1+1+16.500000 0 0 0 0 0 'ctfMode' 'CTFMode' ctfMode
+ -I 1 0 0 1 0 1 -1x1+1+18 ' ' '0' 'dfMin' With Atigmatism
+ -I 1 0 1 0 0 1 -1x1+1+19.500000 ' ' 'configFile' 'ConfigurationFile' c
+ -i 1 0 1 0 0 -1x1+1+21.000000 0 0 0 0 0 'mode' 'Mode' m
-E
-E
-E
{
fprintf(stderr, "Usage: %s\n", thisProgram);
fprintf(stderr, "Options:\n");
- fprintf(stderr, " [-i[nput] In (stdin ).as(inFile ) ] :Essential :InputFile\n");
- fprintf(stderr, " [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile\n");
+ fprintf(stderr, " [-i[nput] In (stdin ).as(inFile::mrcImage ) ] :Essential :Input:2D\n");
+ fprintf(stderr, " [-o[utput] Out (stdout ).as(outFile::mrcImage ) ] :Essential :Output:2D\n");
+ fprintf(stderr, " [-ctf CTF (stdin ).as(inFile::ASCII ) ] :Essential :Input:ctfInfo\n");
fprintf(stderr, " [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]\n");
fprintf(stderr, " [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]\n");
fprintf(stderr, " [-df Defocus (27000 ).as(Real ) ] :Optional :Defocus [A]:under(+)\n");
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