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Bug fixed:
authorTakuo Yasunaga <yasunaga@bio.kyutech.ac.jp>
Sat, 9 Aug 2014 20:53:07 +0000 (05:53 +0900)
committerTakuo Yasunaga <yasunaga@bio.kyutech.ac.jp>
Sat, 9 Aug 2014 20:53:07 +0000 (05:53 +0900)
  mrcImageShapePCA
  When -C was not defined, wrong processing.

12 files changed:
hostdepend/X86MAC64/bin/X86MAC64/mrcImageShapePCA patch | blob | history
hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA patch | blob | history
src/Tools/Config/Define.inc patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/Makefile [changed from file to symlink] patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/doc/Makefile patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/argCheck.c patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html [changed mode: 0644->0755] patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/test/Makefile [changed mode: 0644->0755] patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/usage.c patch | blob | history

diff --git a/hostdepend/X86MAC64/bin/X86MAC64/mrcImageShapePCA b/hostdepend/X86MAC64/bin/X86MAC64/mrcImageShapePCA
index 7910f69..6907151 100755 (executable)
Binary files a/hostdepend/X86MAC64/bin/X86MAC64/mrcImageShapePCA and b/hostdepend/X86MAC64/bin/X86MAC64/mrcImageShapePCA differ
diff --git a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA
index 7910f69..6907151 100755 (executable)
Binary files a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA and b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageShapePCA/src/X86MAC64/mrcImageShapePCA differ
diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index f731d9e..c29d9c7 100755 (executable)
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -152,3 +152,5 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile
index 82b460b..a64a77e 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile
+++ b/src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile
@@ -1,7 +1,7 @@
 # OptionControlFile
 # FileFormat
-"-i","-i[nput]","Input: mrcImage","Essential","1","1","In","inFile","NULL"
-"-o","-o[utput]","Output: ASCII","Optional","1","1","Out","outFile","stdout"
+"-i","-i[nput]","Input: mrcImage","Essential","1","1","In","inFile::mrcImage","NULL"
+"-o","-o[utput]","Output: ASCII","Optional","1","1","Out","outFile::ASCII","stdout"
 "-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
 "-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
-"-C","-C[ontour]","Contour","Variable","1","1","Contour","Real","0.0"
+"-C","-C[ontour]","Contour","Variable","1","1","Contour","Real","1.0"
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/Makefile b/src/Tools/mrcImage/mrcImageShapePCA/Makefile
deleted file mode 100755 (executable)
index 4dbb018acae5475bce203b3db2365124accfa24b..0000000000000000000000000000000000000000
--- a/src/Tools/mrcImage/mrcImageShapePCA/Makefile
+++ /dev/null
@@ -1,104 +0,0 @@
-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
-
-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
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/Makefile b/src/Tools/mrcImage/mrcImageShapePCA/Makefile
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..ef1f6300ba0b84da4931ed574ccec31fc5b88177
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageShapePCA/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/mrcImageShapePCA/doc/Makefile b/src/Tools/mrcImage/mrcImageShapePCA/doc/Makefile
index e35804f..d75d753 120000 (symlink)
--- a/src/Tools/mrcImage/mrcImageShapePCA/doc/Makefile
+++ b/src/Tools/mrcImage/mrcImageShapePCA/doc/Makefile
@@ -1 +1 @@
-/home/people/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/doc/Makefile
\ No newline at end of file
+/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/doc/Makefile
\ No newline at end of file
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/argCheck.c b/src/Tools/mrcImage/mrcImageShapePCA/src/argCheck.c
index 59cac18..cdab52d 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/argCheck.c
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/argCheck.c
@@ -12,7 +12,7 @@
 void
 argCheck(mrcImageShapePCAInfo* info, int argc, char* argv[])
 {
-    long i, j, nv;
+    long i;
     char s[1024];
     FILE* fpt;
     
@@ -74,13 +74,20 @@ argCheck(mrcImageShapePCAInfo* info, int argc, char* argv[])
                 }
                 SCASE("C") {
                     if(i+1<argc) {
-                        nv = argc - i - 1;
-                        info->Contour = (float*)memoryAllocate(sizeof(float)*nv, "in argCheck");
-                        for(j=0; j<nv; j++) {
-                            info->Contour[j] = stringGetNthRealData(argv[i+j+1], 1, " ,");
+                        {
+                        int j, nv, check, count, nitem;
+                        nv    = argc - i - 1;
+                        nitem = 1 ;
+                        check = nv%nitem ;
+                        count = nv/nitem ;
+                        if(0!=check) { fprintf(stderr, "Variable Number is strange. The number must be %d-times. nv: %d i\n", nitem, nv); usage(argv[0]); exit(EXIT_FAILURE);} 
+                        info->Contour = (float*)memoryAllocate(sizeof(float)*count, "in argCheck");
+                        for(j=0; j<count; j++) {
+                            info->Contour[j] = stringGetNthRealData(argv[i+j*nitem+1], 1, " ,");
+                        }
+                        i++;
+                        info->flagContour=count;
                         }
-                        info->flagContour=nv;
-                        i+=nv;
                     } else {
                         usage(argv[0]);
                         exit(EXIT_FAILURE);
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c
index a2c9980..e7415af 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c
@@ -37,11 +37,12 @@ main(int argc, char* argv[])
        if(0<linfo.nLevel) {
                linfo.Level  = info.Contour;
        } else {
-               if(NULL!=(linfo.Level=(float*)malloc(sizeof(float)*1))) {
+               if(NULL==(linfo.Level=(float*)malloc(sizeof(float)*1))) {
                        fprintf(stderr, "Not allocated \n");
                        exit(EXIT_FAILURE);
                }
-               linfo.Level[0] = 1;
+               linfo.Level[0] = 0.0; // Cannot get this value from OptionControlFile 
+               linfo.nLevel = 1;
        }
 
 
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html
old mode 100644 (file)
new mode 100755 (executable)
index f8df478..3bd6a0e
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageShapePCA
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: ASCII
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-C[ontour]          Contour             (0.0       )... ] :Variable  :Contour
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: ASCII
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-C[ontour]          Contour             (1.0       ).as(Real                ) ... ] :Variable  :Contour
 ----- Additional Usage -----
 -C : ContourLevels
    e.g. -C  20  30  40 
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane
index 78f12fd..3a3e0e7 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane
@@ -11,7 +11,7 @@
         -O 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'Out' 'Output: ASCII' o
         -I 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'configFile' 'ConfigurationFile' c
         -i 1 0 1 0 0 -1x1+1+6.000000 0 0 0 0 0 'mode' 'Mode' m
-        -f 1 0 1 0 0 -1x1+1+7.500000 0 0 0.000000 0 0 0 'Contour' 'Contour' C
+        -f 1 0 1 0 0 -1x1+1+7.500000 0 0 1.000000 0 0 0 'Contour' 'Contour' C
     -E
   -E
 -E
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/usage.c b/src/Tools/mrcImage/mrcImageShapePCA/src/usage.c
index acf3005..b6a5b59 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/usage.c
@@ -7,11 +7,11 @@ usage(char* thisProgram)
 {
     fprintf(stderr, "Usage: %s\n", thisProgram);
     fprintf(stderr, "Options:\n");
-    fprintf(stderr, "    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage\n");
-    fprintf(stderr, "    [-o[utput]           Out                 (stdout    )] :Optional  :Output: ASCII\n");
-    fprintf(stderr, "    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile\n");
-    fprintf(stderr, "    [-m[ode]             mode                (0         )] :Optional  :Mode\n");
-    fprintf(stderr, "    [-C[ontour]          Contour             (0.0       )... ] :Variable  :Contour\n");
+    fprintf(stderr, "    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage\n");
+    fprintf(stderr, "    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: ASCII\n");
+    fprintf(stderr, "    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile\n");
+    fprintf(stderr, "    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode\n");
+    fprintf(stderr, "    [-C[ontour]          Contour             (1.0       ).as(Real                ) ... ] :Variable  :Contour\n");
     additionalUsage();
 }
 
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