From: Takuo Yasunaga <yasunaga@bio.kyutech.ac.jp>
Date: Sun, 26 Oct 2014 00:21:48 +0000 (+0900)
Subject: 	modified:   env/Eos_env
X-Git-Tag: v2.3.65p0294~185^2~5
X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=70412572a73ddb934dc663c6a85deeaaa5810696;p=eos%2Fbase.git

	modified:   env/Eos_env
	modified:   env/install-eos.sh
---

diff --git a/bin/wish/Display2/tclIndex b/bin/wish/Display2/tclIndex
index 75a715a008..8fd9302e1f 100644
--- a/bin/wish/Display2/tclIndex
+++ b/bin/wish/Display2/tclIndex
@@ -49,6 +49,7 @@ set auto_index(menuMultiRoiOKCommand) [list source [file join $dir Display2MenuR
 set auto_index(menuMultiRoiAllDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
 set auto_index(menuMultiRoiDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
 set auto_index(menuEditCreate) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
 set auto_index(layerLineRecreate) [list source [file join $dir LayerLineUtil.wish]]
 set auto_index(layerLineCreate) [list source [file join $dir LayerLineUtil.wish]]
 set auto_index(layerLineClear) [list source [file join $dir LayerLineUtil.wish]]
@@ -131,4 +132,3 @@ set auto_index(sectionClearAll) [list source [file join $dir SectionUtil.wish]]
 set auto_index(sectionClear) [list source [file join $dir SectionUtil.wish]]
 set auto_index(sectionChange) [list source [file join $dir SectionUtil.wish]]
 set auto_index(unitCellRecreate) [list source [file join $dir UnitCell.wish]]
-set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
diff --git a/env/Eos_env b/env/Eos_env
index b2606e8a16..e5bbb0497d 100755
--- a/env/Eos_env
+++ b/env/Eos_env
@@ -2,15 +2,16 @@
 
 ###### Users may need to modify the below line.
 # Set Eos Home Directory
-export EOS_HOME=$HOME/Eos
-export EOS_MIRROR_SITE=$HOME/EosMirror
-export EOS_GITUSER=$USER
-
-# For Personal(by install-eos.sh)  
-##install##export EOS_HOME=$HOME/Eos
-##install##export EOS_MIRROR_SITE=$HOME/EosMirror
-##install##export EOS_GITUSER=$USER
-
+if [ -z $EOS_HOME0 ] ;  then
+	export EOS_HOME=$HOME/Eos
+	export EOS_MIRROR_SITE=$HOME/EosMirror
+	export EOS_GITUSER=$USER
+else
+	# For Personal(by install-eos.sh)  
+	export EOS_HOME=$EOS_HOME0
+	export EOS_MIRROR_SITE=$EOS_HOME0/EosMirror
+	export EOS_GITUSER=$USER
+fi
 
 #if you want to use the binaries complied by icc, you need set USE_ICC 
 # In most cases, faster but sometimes comannds  cannnot work well.
@@ -299,11 +300,12 @@ then
 		fi
 	fi
 else
-    OIFS=$IFS
-    IFS=":"
-#   read k v << (echo "$LD_LIBRARY_PATH" | egrep "$CUDA_ROOT" )
+#    OIFS=$IFS
+#    IFS=":"
+#   IFS=: read k v << (echo "$LD_LIBRARY_PATH" | egrep "$CUDA_ROOT" )
 	k=$(echo "$LD_LIBRARY_PATH" | egrep "$CUDA_ROOT" )
-    IFS=$OIFS
+#    IFS=$OIFS
+#   read k v << (echo "$LD_LIBRARY_PATH" | egrep "$CUDA_ROOT" )
 #	echo "()k=$k"
 #	echo "v=$v"
 	if [ -z "$k" ];
diff --git a/env/install-eos.sh b/env/install-eos.sh
index 16f7f5fce0..829c496358 100755
--- a/env/install-eos.sh
+++ b/env/install-eos.sh
@@ -16,6 +16,23 @@ if [ ! -d $EOS_HOME0 ] ; then
 	mkdir $EOS_HOME0
 fi
 
-curl -L $ROOT_EOS_SOURCEFORGE/env/Eos_env?export=raw | sh
+curl -L $ROOT_EOS_SOURCEFORGE/env/Eos_env?export=raw | sh; git clone --depth 1 git://git.sourceforge.jp/gitroot/eos/base.git $EOS_HOME0
 
+if [ -z $EOS_HOME0 ] ; then
+	export EOS_HOME0=$HOME/Eos
+fi
+cat >> $HOME/.bashrc << EOF
+
+##
+## Eos_env
+##
+
+if [ ! -z $EOS_HOME0 ] ; then 
+if [ -f $EOS_HOME0/env/Eos_env && ! -f $HOME/.Eos_env ] ; then
+	ln -s $EOS_HOME0/env/Eos_env $HOME/.Eos_env
+fi
+fi
+
+test -r $HOME/.Eos_env  && . $HOME/.Eos_env
 
+EOF
diff --git a/env/test b/env/test
new file mode 100644
index 0000000000..8b13789179
--- /dev/null
+++ b/env/test
@@ -0,0 +1 @@
+
diff --git a/examples b/examples
deleted file mode 120000
index 179e7a9299..0000000000
--- a/examples
+++ /dev/null
@@ -1 +0,0 @@
-data/examples
\ No newline at end of file
diff --git a/hostdepend/X86MAC64/bin/X86MAC64/mrcImageNormalizedSubtraction b/hostdepend/X86MAC64/bin/X86MAC64/mrcImageNormalizedSubtraction
index 2eaf227650..d315bc5824 100755
Binary files a/hostdepend/X86MAC64/bin/X86MAC64/mrcImageNormalizedSubtraction and b/hostdepend/X86MAC64/bin/X86MAC64/mrcImageNormalizedSubtraction differ
diff --git a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/mrcImageNormalizedSubtraction b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/mrcImageNormalizedSubtraction
index 2eaf227650..d315bc5824 100755
Binary files a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/mrcImageNormalizedSubtraction and b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86MAC64/mrcImageNormalizedSubtraction differ
diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index 28733dec3a..87b358533d 100755
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -229,3 +229,4 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools
diff --git a/src/Tools/Makefile b/src/Tools/Makefile
deleted file mode 100755
index ad841104b1..0000000000
--- a/src/Tools/Makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-include Config/Target.inc
diff --git a/src/Tools/Makefile b/src/Tools/Makefile
new file mode 120000
index 0000000000..80a2401a7d
--- /dev/null
+++ b/src/Tools/Makefile
@@ -0,0 +1 @@
+/Users/tacyas/Eos/src/Config/Template/ToolsHomeTemplate.Dir/Makefile
\ No newline at end of file
diff --git a/src/Tools/mrcImage/Makefile b/src/Tools/mrcImage/Makefile
deleted file mode 100755
index dfd525eab5..0000000000
--- a/src/Tools/mrcImage/Makefile
+++ /dev/null
@@ -1,107 +0,0 @@
-include ../../Config/Define.inc
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-all:
-	for dir in ${SOURCE} ; \
-	do \
-		if [ -d $${dir} ] ; then \
-			$(CD) $${dir}; make all; $(CD) ..; \
-		fi \
-	done
-
-install:
-	for dir in ${SOURCE} ; \
-	do \
-		if [ -d $${dir} ] ; then \
-			$(CD) $${dir}; make install; $(CD) ..; \
-		fi \
-	done
-
-put:
-	for dir in ${SOURCE} ; \
-	do \
-		if [ -d $${dir} ] ; then \
-			$(CD) $${dir}; make put; $(CD) ..; \
-		fi \
-	done
-
-putSF:
-	if [ -f private ] ; then \
-		echo "$(WORLDNAME)/$(CLASSNAME) is private " ; \
-	else \
-		for dir in ${SOURCE} ; \
-		do \
-			if [ -d $${dir} ] ; then \
-				$(CD) $${dir}; make putSF; $(CD) ..; \
-			fi \
-		done \
-	fi
-
-clean:
-	for dir in ${SOURCE} ; \
-	do \
-		$(CD) $${dir}; make clean; $(CD) ..; \
-	done
-
-check:
-	@for dir in ${SOURCE} ; do \
-		if [ -d $${dir} ] ; then \
-			$(CD) $${dir}; \
-			echo  $${dir}; \
-			$(RM) Makefile; \
-			$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/Makefile Makefile ; \
-			make check; \
-			$(CD) ..; \
-		fi \
-	done
-
-depend: check
-	@for dir in ${SOURCE} ; \
-	do \
-		$(CD) $${dir}; make depend; $(CD) ..; \
-	done
-
-backup: 
-	cd ../../..; \
-	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
-	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
-	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
-	tar uvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
-	@for dir in ${SOURCE} ; \
-	do \
-		$(CD) $${dir}; make backup; $(CD) ..; \
-	done
-
-backup-all: 
-	cd ../../..; \
-	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
-	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
-	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
-	tar rvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
-	@for dir in ${SOURCE} ; \
-	do \
-		$(CD) $${dir}; make backup; $(CD) ..; \
-	done
-
-distribute: 
-	cd ../../..; \
-	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
-	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
-	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
-	@for dir in ${SOURCE} ; \
-	do \
-		$(CD) $${dir}; make distribute; $(CD) ..; \
-	done
-
-distribute-all: 
-	cd ../../..; \
-	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
-	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
-	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
-	@for dir in ${SOURCE} ; \
-	do \
-		$(CD) $${dir}; make distribute-all; $(CD) ..; \
-	done
-
diff --git a/src/Tools/mrcImage/Makefile b/src/Tools/mrcImage/Makefile
new file mode 120000
index 0000000000..01f58fa4fd
--- /dev/null
+++ b/src/Tools/mrcImage/Makefile
@@ -0,0 +1 @@
+/Users/tacyas/Eos/src/Config/Template/ToolsClassTemplate.Dir/Makefile
\ No newline at end of file
diff --git a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/Makefile b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/Makefile
deleted file mode 100755
index 4dbb018aca..0000000000
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/Makefile
+++ /dev/null
@@ -1,104 +0,0 @@
-include ../../../Config/Define.inc
-include ../../Config/Define.inc
-include ../Config/Define.inc
-include Config/Define.inc
-
-all:
-	cd src; make all; cd ..
-
-install:
-	cd src; make install; cd ..
-
-
-putSF:
-	if [ -f private ] ; \
-	then \
-		echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
-	else \
-		cvs -z4 -d:ext:$$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/mrcImageNormalizedSubtraction/Makefile b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/Makefile
new file mode 120000
index 0000000000..ef1f6300ba
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/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/mrcImageNormalizedSubtraction/doc/Makefile b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/doc/Makefile
index e35804f775..d75d7539e2 120000
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/doc/Makefile
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/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/mrcImageNormalizedSubtraction/src/argCheck.c b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/argCheck.c
index 1486ec5d0b..e56ca8bb4f 100755
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/argCheck.c
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/argCheck.c
@@ -12,7 +12,7 @@
 void
 argCheck(mrcImageNormalizedSubtractionInfo* info, int argc, char* argv[])
 {
-    long i, j, nv;
+    long i;
     char s[1024];
     FILE* fpt;
     
diff --git a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/mrcImageNormalizedSubtraction.c b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/mrcImageNormalizedSubtraction.c
index 52aab470d5..f566164dd2 100755
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/mrcImageNormalizedSubtraction.c
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/mrcImageNormalizedSubtraction.c
@@ -94,7 +94,7 @@ void
 additionalUsage()
 {
   fprintf(stderr, "-- Attention ---\n");
-  fprintf(stderr, "in1(default) -  in2(normalized) : \n");
+  fprintf(stderr, "in1(default:ref) -  in2(normalized:tst) : \n");
   fprintf(stderr, "-- Mode ---\n");
   lmrcImageDensityNormalizationByImageModePrint(stderr);
 }
diff --git a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/mrcImageNormalizedSubtraction.html b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/mrcImageNormalizedSubtraction.html
index 31ee2494e9..0e4f5b21f3 100755
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/mrcImageNormalizedSubtraction.html
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/mrcImageNormalizedSubtraction.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageNormalizedSubtraction
 Options:
-    [-i1[nput]           In1                 (NULL      )] :Essential :InputDataFile
-    [-i2[nput]           In2                 (NULL      )] :Essential :InputDataFile
-    [-nori2[nput]        In2_tmp             (NULL      )] :Optional  :OutDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-rmsd               RMSD                (stdout    )] :Optional  :Output: RMSD
-    [-p[rameter]f[ile]   ParamFile           (stdout    )] :Optional  :ParameterOutputFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i1[nput]           In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i2[nput]           In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-nori2[nput]        In2_tmp             (NULL      ).as(outFile             ) ] :Optional  :OutDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-rmsd               RMSD                (stdout    ).as(outFile             ) ] :Optional  :Output: RMSD
+    [-p[rameter]f[ile]   ParamFile           (stdout    ).as(outFile             ) ] :Optional  :ParameterOutputFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 -- Attention ---
-in1(default) -  in2(normalized) : 
+in1(default:ref) -  in2(normalized:tst) : 
 -- Mode ---
   1: Sigma!=1.0 
   2: Stdout     
diff --git a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/test/Makefile b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/test/Makefile
old mode 100644
new mode 100755
index 323c2db4da..d32b56c432
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/test/Makefile
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/test/Makefile
@@ -11,7 +11,13 @@ help:
 
 exec:
 	@echo "----- Execution Check -----"
-	../$(OSTYPE)/$(OBJECTNAME) 
+	../$(OSTYPE)/$(OBJECTNAME) -i1 data/121p-shift2.mrc2d -i2 data/121p-shift.mrc2d -o data/121p-shift2.fit -pf data/121p-shift2.param  
+	../$(OSTYPE)/$(OBJECTNAME) -i1 data/121p-shift3.mrc2d -i2 data/121p-shift.mrc2d -o data/121p-shift3.fit -pf data/121p-shift3.param  
 	@echo "----- Calc check -----"		
 
+init:
+	pdb2mrc2d -i data/121p-shift.pdb -o data/121p-shift.mrc2d -s -30 -30 -n 30 30 -d 2 2 -m 3 -sig 3
+	mrcImageMultiplying -i data/121p-shift.mrc2d  -o data/121p-shift2.mrc2d -v 2.0
+	mrcImageAddValue    -i data/121p-shift2.mrc2d -o data/121p-shift3.mrc2d -v 3.0 
+
 clean:
diff --git a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/usage.c b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/usage.c
index 316ccb76a6..6139e29ef6 100755
--- a/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/usage.c
@@ -7,13 +7,13 @@ usage(char* thisProgram)
 {
     fprintf(stderr, "Usage: %s\n", thisProgram);
     fprintf(stderr, "Options:\n");
-    fprintf(stderr, "    [-i1[nput]           In1                 (NULL      )] :Essential :InputDataFile\n");
-    fprintf(stderr, "    [-i2[nput]           In2                 (NULL      )] :Essential :InputDataFile\n");
-    fprintf(stderr, "    [-nori2[nput]        In2_tmp             (NULL      )] :Optional  :OutDataFile\n");
-    fprintf(stderr, "    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile\n");
-    fprintf(stderr, "    [-rmsd               RMSD                (stdout    )] :Optional  :Output: RMSD\n");
-    fprintf(stderr, "    [-p[rameter]f[ile]   ParamFile           (stdout    )] :Optional  :ParameterOutputFile\n");
-    fprintf(stderr, "    [-m[ode]             mode                (0         )] :Optional  :Mode\n");
+    fprintf(stderr, "    [-i1[nput]           In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile\n");
+    fprintf(stderr, "    [-i2[nput]           In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile\n");
+    fprintf(stderr, "    [-nori2[nput]        In2_tmp             (NULL      ).as(outFile             ) ] :Optional  :OutDataFile\n");
+    fprintf(stderr, "    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile\n");
+    fprintf(stderr, "    [-rmsd               RMSD                (stdout    ).as(outFile             ) ] :Optional  :Output: RMSD\n");
+    fprintf(stderr, "    [-p[rameter]f[ile]   ParamFile           (stdout    ).as(outFile             ) ] :Optional  :ParameterOutputFile\n");
+    fprintf(stderr, "    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode\n");
     additionalUsage();
 }
 
diff --git a/src/Tools/mrcImage/mrcImageWindowing/src/test/Makefile b/src/Tools/mrcImage/mrcImageWindowing/src/test/Makefile
index 4ab495ff0d..52aa046e9d 100755
--- a/src/Tools/mrcImage/mrcImageWindowing/src/test/Makefile
+++ b/src/Tools/mrcImage/mrcImageWindowing/src/test/Makefile
@@ -18,6 +18,10 @@ exec:
 	time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -o data/test.4.out -m 4 
 	time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -o data/test.5.out -m 5 
 	time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -o data/test.6.out -m 6 
+	time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -o data/test.7.out -m 7 
+	time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -o data/test.8.out -m 8 
+	time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -o data/test.9.out -m 9  -Wx 0.05 -Wy 0.05
+	time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -o data/test.10.out -m 10  -Wx 0.05 -Wy 0.05
 	@echo "----- Calc check -----"		
 
 clean: