Commit: e2e49dc4bd4327c897d866888f985af01c36e57e - Eos (git)

Commit MetaInfo

• Revisión: e2e49dc4bd4327c897d866888f985af01c36e57e (tree)
• Tiempo: 2014-11-04 04:39:28
• Autor: Takuo Yasunaga <yasunaga@bio....>
• Commiter: Takuo Yasunaga

Log Message

Bug fixed:
Eos_env
install-eos.sh

Cambiar Resumen

• delete: bin/wish/Visualmake/Makefile
• delete: bin/wish/Visualmake/Makefile.tmp
• delete: bin/wish/Visualmake/a.hoge
• delete: bin/wish/Visualmake/a.hogehoge
• delete: bin/wish/Visualmake/handmake.lst
• delete: bin/wish/Visualmake/tclIndex
• modified: env/Eos_env
• modified: env/install-eos.sh

Diferencia incremental

--- a/bin/wish/Visualmake/Makefile
+++ /dev/null
@@ -1,498 +0,0 @@
-.SUFFIXES: .tif .dat .prectf .fft .ctf .ctfinfoauto .ctfinfo .mrc .divideroi .divideroiinfo \
-	.box .roi \
-	.roiinfo-coarse .roiall-coarse .roiinforef-coarse .roiallref-coarse  .roiinfoprev-coarse \
-	.roiinfo        .roiall        .roiinforef        .roiallref         .roiinfoprev \
-	.box2roiinfo .roiinfo2box .corinfo .divideroiinfo \
-	.roilst0 .roilst .mrc3d .ds6 .mrc3dcentremed .mrc3dcentre .mrc3dcentremedpad .orimrccentre .oricorinfo .coarroi .coarroiinfo .roi2 .pad .mul
-
-
-#comment#Forall
-TILTAXISNUMBER=2
-ORIFILE1=a
-ORIFILE2=b
-ZEROTILTNUM=60
-MINTILTNUM=0
-MAXTILTNUM=120
-STEPTILTNUM=4
-T=43
-
-#comment#Fordata2mrc
-RESOLUTION=1.7
-
-#comment#For2ndAxisRotate
-ROTATIONANGLE=-90
-
-#comment#ForCOARCreate
-ORISIZEX=2048
-ORISIZEY=2048
-CORMODE=16
-ORINX=1024
-ORINY=1024
-ORINZ=1
-
-#comment#Forroiinfo
-ORIBASE=$(ORIFILE1)0$(ZEROTILTNUM)
-
-#comment#ForPadAndMul
-TILTAXISANGLE=0
-IMAGEPADm=15
-IMAGEPADV=0
-IMAGEMULTIPLYINGv=-1
-
-#comment#ForroilstCreate
-EULARANGLE=ZENS
-MINTILTANGLE=-60
-STEPTILTANGLE=4
-
-#comment#Fords6Create
-MRC2MAPmul=1
-SMOOTHr=5
-SMOOTHm=1
-SMOOTHM=1
-CENTERNX=200
-CENTERNY=200
-CENTERNZ=200
-
-all: data2mrc Smoothing 2ndAxisRotate COARCreate $(ORIBASE).roiinfo BoxCreate PadAndMul roilstCreate ds6Create
-data2mrc::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-			else \
-				orifile=$(ORIFILE2); \
-			fi ; \
-			for (( i=0 ; $$i <= $(MAXTILTNUM) ; i=$$(($$i + $(STEPTILTNUM))))) \
-				do \
-					ori=`printf "%s%03d" $$orifile $$i`; \
-					make $$ori.prectf; \
-					make $$ori.divideroiinfo; \
-					awk '{ printf("%s\n", $$1); }' $$ori.divideroiinfo >> dvdroilst ; \
-					for divideroivaliable in `ls -1 $$ori*.divideroi` ; do \
-						dividefilename=`basename $$divideroivaliable .divideroi`; \
-						make $$dividefilename.fft; \
-						make $$dividefilename.ctfinfo; \
-						make $$dividefilename.ctf; \
-					done ; \
-					make $$ori.mrc ; \
-				done ; \
-		done 
-
-.dat.prectf:
-	emData2mrc -i $*.dat -o $*.prectf
-
-.tif.prectf:
-	tiff2mrc -i $*.tif -o $*.prectf -m 1 -r $(RESOLUTION)
-
-.prectf.divideroiinfo:
-	mrcImageDivideInfoForTomography -i $*.prectf -o $*.divideroiinfo -m 1 -d 4
-	sed 's/roi/divideroi/' $*.divideroiinfo >> $*.tmproiinfo
-	mv $*.tmproiinfo $*.divideroiinfo
-	mrcImageROIs -i $*.prectf -o $*.mon -I $*.divideroiinfo -S 1
-
-.divideroi.fft:
-	mrcImagePad -i $*.divideroi -o $*.dividepad -W 1024 -H 1024 -m 3 ; \
-	mrcImageAbnormalValueRemove -i $*.dividepad -o $*.prectfab -m 1 ; \
-	mrcImageFFT -i $*.prectfab -o $*.fft ; \
-
-.fft.ctfinfo:
-	ctfDetermine -i $*.fft -o $*.ctfinfo -D 10000 -m 128 -CutLow 0.05 -CutHigh 0.2 -Ac 200 -d 3 -Cc 0.7 -Cs 1.7 -ratio 0.2 | grep defocus > CTFD ; \
-	awk -v BASE=$* '{ printf("%s %s\n", BASE, $$2); }' CTFD >> $*.defocuslst ; \
-
-.fft.ctf:
-	mrcImageCTFCompensation -i $*.fft -o $*.ctf -info2 $*.ctfinfo -m 1 ; \
-	mrcImageCenterGet -i $*.ctf -o $*.ctfcentre -Nx 512 -Ny 512 ; \
-
-.prectf.mrc:
-	cat $*.divideroiinfo | sed s/divideroi/ctfcentre/g > $*.divideroiinfo2
-	mrcImageCTFCompensationForTiltImage -i $*.prectf -I $*.divideroiinfo2 -o $*.mrc
-
-#.fft.ctfinfoauto:
-#	ctfDetermine -i $*.fft -o $*.ctfinfoauto -D 50000 -m 163 -CutLow 0.04 -CutHigh 0.15 -Ac 200 -d 3 -Cc 0.7 -Cs 2.1	
-##	awk '/^[^:]/ {print $$0};' $*.ctfinfoauto > $*.ctfinfo
-##	Display2 -i $*.fft -H 1e7
-
-#.ctfinfoauto.ctfinfo:
-#	if [ ! -f $*.ctfinfo ] ; then \
-		if [ -f default.ctfinfo ] ; then \
-			cat default.ctfinfo >> $*.ctfinfo ; \
-		else \
-			cat $*.ctfinfoauto >> $*.ctfinfo ; \
-		fi \
-	fi 
-#	ctfDisplay -i $*.fft
-#	mv $@ $@.tmp
-#	grep .: $@.tmp > $@
-#	cp $@ default.ctfinfo
-
-#.ctfinfo.mrc:
-#	mv $*.ctfinfo $*.ctfinfotmp
-#	awk '/^[^:]/ {print $$0};' $*.ctfinfotmp > $*.ctfinfo
-#	mrcImageCTFCompensation -i $*.fft -o $*.mrc -info2 $*.ctfinfo -m 1	
-#	Display2 -i $*.mrc -geometry 1024x1024+0+0 -Zoom 0.5 &
-
-mrcImageSmoothing::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-			else \
-				orifile=$(ORIFILE2); \
-			fi ; \
-			for (( i=0 ; $$i <= $(MAXTILTNUM) ; i=$$(($$i + $(STEPTILTNUM))))) \
-				do \
-					ori=`printf "%s%03d" $$orifile $$i`; \
-					mrcImageSmoothing -i $$ori.mrc -o $$ori.smth -sx 5 -sy 5 -m 1 ; \
-					mv $$ori.smth $$ori.mrc ; \
-				done ; \
-		done
-
-mrcImageWindowing::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-			else \
-				orifile=$(ORIFILE2); \
-			fi ; \
-			for (( i=0 ; $$i <= $(MAXTILTNUM) ; i=$$(($$i + $(STEPTILTNUM))))) \
-				do \
-					ori=`printf "%s%03d" $$orifile $$i`; \
-					mrcImageWindowing -i $$ori.mrc -o $$ori.wnd ; \
-					mv $$ori.wnd $$ori.mrc ; \
-				done ; \
-		done
-
-2ndAxisRotate::
-	for (( i=0 ; $$i <= $(MAXTILTNUM) ; i=$$(( $$i + $(STEPTILTNUM) )) )) \
-		do \
-			ori=`printf "%s%03d" $(ORIFILE2) $$i`; \
-			mrcImageRotation -i $$ori.mrc -o $$ori.mrc2 -a $(ROTATIONANGLE) ; \
-			mv $$ori.mrc2 $$ori.mrc ; \
-		done
-
-##sep
-
-COARCreate::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-				oribase=$(ORIFILE1)0$(ZEROTILTNUM); \
-			else \
-				orifile=$(ORIFILE2); \
-			fi ; \
-			ORIZEROFILE=$$oribase.mrc; \
-			previous=$$oribase ; \
-			echo "Create the zero-tilt Image ROI (same as mrc, just copy)"; \
-			make $$oribase.roiinfo-coarse; echo "$$oribase.roi will be created."; \
-			make $$oribase.roiall-coarse ; echo "$$oribase.roi was created." ;  \
-			make $$oribase.orimrccentre  ; echo "The centre of $$oribase.roi was created." ;  \
-		for delta in +$(STEPTILTNUM) -$(STEPTILTNUM) ;  do \
-			echo "$$delta"; \
-			previous=$$oribase; \
-			TOTALX=0 ; \
-			TOTALY=0 ; \
-			echo "Total: $$TOTALX $$TOTALY" > $$previous.oricorinfo; \
-			for (( i=$$(($(ZEROTILTNUM) + $$delta )) ; (( $(MINTILTNUM) <= $$i && $$i <= $(MAXTILTNUM)  )) ; i=$$(($$i + $$delta)) )) \
-				do \
-					ori=`printf "%s%03d" $$orifile $$i`; \
-					echo $$i, $(MAXTILTNUM), $(MINTILTNUM); \
-					echo $$previous > $$ori.prevname ; \
-					ln -sf $$previous.roiinfo-coarse $$ori.roiinfoprev-coarse ; make $$ori.roiinforef-coarse ; \
-					make $$ori.roiallref-coarse ; \
-					make $$ori.orimrccentre ;     \
-					TOTALX=`awk '/Total:/ { print $$2 }' $$previous.oricorinfo`; \
-					TOTALY=`awk '/Total:/ { print $$3 }' $$previous.oricorinfo`; \
-					ln -sf $$previous.orimrccentre $$ori.oriref ; make $$ori.oricorinfo ; \
-					echo "TotalPrev: $$TOTALX $$TOTALY" >> $$ori.oricorinfo; \
-					make $$ori.roiinfo-coarse; \
-					make $$ori.roiall-coarse; \
-					make $$ori.orimrccentre ; sleep 1; \
-					touch $$ori.oricorinfo   ; sleep 1; \
-					touch $$ori.roiinfo-coarse; sleep 1; \
-					touch $$ori.roiall-coarse; sleep 1; \
-					previous=$$ori; \
-				done ; \
-			echo $$i; \
-			done ; \
-		done
-
-CleanCOARCreate::
-	rm *.roiinfo-coarse
-
-$(ORIFILE1)0$(ZEROTILTNUM).roiinfo-coarse:
-	printf "%s%03d.roi Rect2 %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f\n" $(ORIFILE1) $(ZEROTILTNUM) $$(($(ORISIZEX)/2)) $$(($(ORISIZEY)/2)) $(ORISIZEX) $(ORISIZEY) > $(ORIFILE1)0$(ZEROTILTNUM).roiinfo-coarse 
-
-$(ORIFILE2)0$(ZEROTILTNUM).roiinfo-coarse:
-	printf "%s%03d.roi Rect2 %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f\n" $(ORIFILE2) $(ZEROTILTNUM) $$(($(ORISIZEX)/2)) $$(($(ORISIZEY)/2)) $(ORISIZEX) $(ORISIZEY) > $(ORIFILE2)0$(ZEROTILTNUM).roiinfo-coarse 
-
-.orimrccentre.oricorinfo:
-	echo "orimrccentre -> oricorinfo: SHIFT:= current.orimrccentre for prev.oirmrccentre"
-	mrcImageCorrelation -i $*.orimrccentre -r $*.oriref -c $*.oricorinfo -o $*.oricormap -m $(CORMODE) -s $*.orishift
-
-.oricorinfo.roiinfo-coarse:
-	TOTALX=`awk '/TotalPrev:/ { print $$2 }' $*.oricorinfo`; \
-	TOTALY=`awk '/TotalPrev:/ { print $$3 }' $*.oricorinfo`; \
-	SHIFTX=`awk '/Shift:/ { print $$2 }' $*.oricorinfo`; \
-	SHIFTY=`awk '/Shift:/ { print $$3 }' $*.oricorinfo`; \
-	echo "$$SHIFTX,$$SHIFTY"; \
-	if [ $$(($(ORINX)/2)) -lt $$SHIFTX ]; then  \
-		SHIFTX=$$(($$SHIFTX - $(ORINX))) ; \
-	fi ; \
-	if [ $$(($(ORINY)/2)) -lt $$SHIFTY ]; then  \
-		SHIFTY=$$(($$SHIFTY - $(ORINY))) ; \
-	fi ; \
-	TOTALX=$$(($$TOTALX + $$SHIFTX)) ; \
-	TOTALY=$$(($$TOTALY + $$SHIFTY)) ; \
-	echo "Total: $$TOTALX $$TOTALY" >> $*.oricorinfo; \
-	printf "%s.roi Rect2 %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f\n" $* $$(($(ORISIZEX)/2+$$TOTALX)) $$(($(ORISIZEY)/2+$$TOTALY)) $(ORISIZEX) $(ORISIZEY) $$TOTALX $$TOTALY > $*.roiinfo-coarse ;
-
-.roiinfo-coarse.roiall-coarse:
-	make $*.mrc
-	mrcImageROIs -i $*.mrc -I $*.roiinfo-coarse 
-	touch $*.roiall-coarse 
-
-.roiinforef-coarse.roiallref-coarse:
-	mrcImageROIs -i $*.mrc -I $*.roiinforef-coarse
-	touch $*.roiallref-coarse
-
-.roiinfoprev-coarse.roiinforef-coarse:
-	previous=`cat $*.prevname`; \
-	sed -s s/$$previous/$*/ $*.roiinfoprev-coarse  > $*.roiinforef-coarse
-
-.roi.orimrccentre:
-	echo "roi -> orimrccentre"
-	mrcImageCenterGet -i $*.roi -o $*.orimrccentre -Nx $(ORINX) -Ny $(ORINY) -Nz $(ORINZ)
-	mrcImageWindowing -i $*.orimrccentre -o $*.wnd -m 16
-	mv $*.wnd $*.orimrccentre
-
-$(ORIBASE).roiinfo:
-	Display2 -i $*.mrc ;
-#	if [ $(TILTAXISNUMBER) -eq 2 ]; then \
-#		Display2 -i $(ORIFILE2)0$(ZEROTILTNUM).mrc ;\
-#	fi; \
-		
-##sep
-
-BoxCreate::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-				oribase=$(ORIFILE1)0$(ZEROTILTNUM); \
-			else \
-				orifile=$(ORIFILE2); \
-			fi ; \
-			BASE=$$oribase; \
-			make $$BASE.roiall ; \
-			for delta in +$(STEPTILTNUM) -$(STEPTILTNUM) ; \
-				do \
-					echo $$delta,$$BASE ;  \
-					previous=$$BASE	; \
-					for (( i=$$(($(ZEROTILTNUM)+$$delta)) ; (( $(MINTILTNUM) <= $$i && $$i <= $(MAXTILTNUM) )) ; i=$$(($$i + $$delta)) )) \
-						do  \
-							name=`printf "%s%03d" $$orifile $$i`; \
-							echo ">>>> $$name $$i start: $(ZEROTILTNUM) $$(($(ZEROTILTNUM)+$$delta))"; \
-							echo $$previous > $$name.prevname; \
-							ln -sf $$previous.roiinfo $$name.roiinfoprev ; make $$name.roiinforef ; \
-							make $$name.roiinfo ; \
-							make $$name.roiall ; \
-							previous=$$name ; \
-						done  ; \
-				done ; \
-		done
-
-CleanBoxCreate::
-	rm *.roiall *.roiinfoprev *.roiinforef
-
-.roiinfo.roiall:
-	make $*.roi
-	mrcImageROIs -i $*.roi -I $*.roiinfo
-	touch $*.roiall
-
-.roiinforef.roiallref:
-	mrcImageROIs -i $*.roi -I $*.roiinforef
-	touch $*.roiallref
-
-.roi.corinfo:
-	mrcImageCorrelation -i $*.roi -r $*.ref -c $*.corinfo 
-
-.roiinforef.roiinfo:
-	# Extract ROIs using roiinfo of previous image (roiinforef)
-	previous=`cat $*.prevname`; \
-	echo $$previous; \
-	echo "start initial ROI"; \
-	make $*.roiallref ; \
-	ROINUM=`wc -l $*.roiinforef | awk '{print $$1}'` ; \
-	echo $$ROINUM ; \
-	rm -f $*.roiinfo ; \
-	for (( j=0 ; $$j < $$ROINUM ; j=$$(($$j+1)))) \
-	do  \
-		input=`printf "%s-%04d" $*         $$j`; \
-		refer=`printf "%s-%04d" $$previous $$j`; \
-		echo $$input, $$refer ; \
-		ln -sf $$refer.roi $$input.ref ; make $$input.corinfo ; \
-		SHIFTX=`awk '/Shift:/ { print $$2 }' $$input.corinfo`; \
-		SHIFTY=`awk '/Shift:/ { print $$3 }' $$input.corinfo`; \
-		echo "$$SHIFTX,$$SHIFTY,$$input"; \
-		awk -v SHIFTXAWK0=$$SHIFTX -v SHIFTYAWK0=$$SHIFTY -v NAMEAWK=$$input -v BASEAWK=$* \
-		 ' /'"$$input"'/ { \
-			SizeX = int(sqrt(($$5-$$3)*($$5-$$3)+( $$6-$$4)*( $$6-$$4))+0.5)+1; \
-			SizeY = int(sqrt(($$9-$$3)*($$9-$$3)+($$10-$$4)*($$10-$$4))+0.5)+1; \
-		 	if(SizeX/2<SHIFTXAWK0) { \
-				SHIFTXAWK0 -= SizeX ; \
-			} \
-			if(SizeY/2<SHIFTYAWK0) { \
-				SHIFTYAWK0 -= SizeY ; \
-			} \
-			Angle = atan2($$6-$$4, $$5-$$3) ; \
-			SHIFTXAWK = +1*( SHIFTXAWK0*cos(Angle) - SHIFTYAWK0*sin(Angle)); \
-			SHIFTYAWK = +1*( SHIFTXAWK0*sin(Angle) + SHIFTYAWK0*cos(Angle)); \
-			printf("%s-%04d.roi Rect %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f\n", BASEAWK, FNR-1, $$3+SHIFTXAWK, $$4+SHIFTYAWK, $$5+SHIFTXAWK, $$6+SHIFTYAWK, $$7+SHIFTXAWK, $$8+SHIFTYAWK, $$9+SHIFTXAWK, $$10+SHIFTYAWK, SHIFTXAWK, SHIFTYAWK, Angle*180/3.141592653589793238, SizeX, SizeY);}' \
-		 $*.roiinforef | tee -a $*.roiinfo ; \
-	done ; 
-
-.roiinfoprev.roiinforef:
-	previous=`cat $*.prevname`; \
-	sed -s s/$$previous/$*/ $*.roiinfoprev  > $*.roiinforef
-
-##sep
-
-PadAndMul::
-	for (( k=1 ; $$k <= $(TILTAXISNUMBER) ; k=$$(($$k + 1 )))) \
-		do \
-			if [ $$k -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-				oribase=$(ORIFILE1)0$(ZEROTILTNUM); \
-			else \
-				orifile=$(ORIFILE2); \
-				oribase=$(ORIFILE2)0$(ZEROTILTNUM); \
-			fi ; \
-			roiNum=`wc -l  $$oribase.roiinfo | awk '{print $$1}' `; \
-			for ((i=$(MINTILTNUM);i<=$(MAXTILTNUM);i=$$(($$i+$(STEPTILTNUM))) )) \
-				do \
-					for((j=0 ; j < $$roiNum ; j = $$(($$j+1)))) \
-						do \
-							name=`printf "%s%03d-%04d" $$orifile $$i $$j` ; \
-							echo $$(($$i-$(ZEROTILTNUM))) > $$name.tilt ; \
-							ln -sf $$name.roi $$name.roi2 ; make $$name.pad ; \
-							make $$name.mul ; \
-						done ; \
-				done ; \
-		done
-
-CleanPadAndMul::
-	rm *.pad
-
-.roi2.pad:
-	tilt=`cat $*.tilt` ; \
-	echo $$tilt ; \
-	mrcImagePad -i $*.roi2 -o $*.pad -Tilt $(TILTAXISANGLE) $$tilt -m $(IMAGEPADm) -V $(IMAGEPADV)
-
-.pad.mul:
-	mrcImageMultiplying -i $*.pad -o $*.mul -v $(IMAGEMULTIPLYINGv)
-
-roilstCreate::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-				oribase=$(ORIFILE1)0$(ZEROTILTNUM); \
-				echo "$(ORIFILE1)" > roilstorifile.txt; \
-			else \
-				orifile=$(ORIFILE2); \
-				oribase=$(ORIFILE2)0$(ZEROTILTNUM); \
-				echo "$(ORIFILE2)" > roilstorifile.txt; \
-			fi ; \
-			roiNum=`wc -l  $$oribase.roiinfo | awk '{print $$1}' `;\
-			echo $$roiNum; \
-			for (( i=0 ; $$i < $$roiNum ; i=$$(($$i + 1)))) \
-				do \
-					tiltnum=`printf "%s%04d" $$orifile $$i`; \
-					echo "$$i" > $$tiltnum.roilst0; \
-					make $$tiltnum.roilst ; \
-				done ; \
-		done ; \
-		roiNum=`wc -l  $$oribase.roiinfo | awk '{print $$1}' `;\
-		echo $$roiNum; \
-		for (( i=0 ; $$i < $$roiNum ; i=$$(($$i + 1)))) \
-			do \
-				tiltnum=`printf "%04d" $$i`; \
-				echo "$$i" > $$tiltnum.roilst0; \
-				cat $(ORIFILE1)$$tiltnum.roilst >> $$tiltnum-d.roilst ; \
-				cat $(ORIFILE2)$$tiltnum.roilst >> $$tiltnum-d.roilst ; \
-			done
-
-Cleanroilst::
-	rm *.roilst
-
-.roilst0.roilst:
-		i=`cat $*.roilst0`; \
-		orifile=`cat roilstorifile.txt`; \
-		oribase=`printf "%s%03d" $$orifile $(ZEROTILTNUM)`; \
-		num=`printf "%04d" $$i`; \
-		roiname=`printf "%s-%04d" $$oribase $$i`; \
-		echo "$$roiname in $$oribase.roiinfo"; \
-		if [ $$orifile = a ]; then \
-			echo "$*.roilst creating" ; \
-			ls -1 $$orifile*-$$num.mul | awk -v eularangle=$(EULARANGLE) ' BEGIN {angle=$(MINTILTANGLE)} {printf("%s %s %f %f %f\n",$$1, eularangle, 0, angle, 0); angle+=$(STEPTILTANGLE); if (angle == 0 ) { angle+=$(STEPTILTANGLE)} }' > $*.roilst ; \
-		else \
-			echo "$*.roilst creating" ; \
-			ls -1 $$orifile*-$$num.mul | awk -v eularangle=$(EULARANGLE) ' BEGIN {angle=$(MINTILTANGLE)} {printf("%s %s %f %f %f\n",$$1, eularangle, angle, 0, 0); angle+=$(STEPTILTANGLE); if (angle == 0 ){ angle+=$(STEPTILTANGLE)} }' > $*.roilst ; \
-		fi
-##sep
-
-ds6Create::
-	roiNum=`ls -1 *-d.roilst | wc -l `; \
-	echo $$roiNum; \
-	for (( i=0 ; $$i < $$roiNum ; i=$$(($$i + 1)) )) \
-	do \
-		tiltnum=`printf "%04d-d" $$i`; \
-		make $$tiltnum.mrc3d ; \
-		make $$tiltnum.mrc3dcentre ; \
-		make $$tiltnum.mrc3dcentremed ; \
-		make $$tiltnum.mrc3dcentremedpad ; \
-		make $$tiltnum.ds6 ; \
-	done ;
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-			else \
-				orifile=$(ORIFILE2); \
-			fi ; \
-	roiNum=`ls -1 $$orifile*.roilst | wc -l `; \
-	echo $$roiNum; \
-	for (( i=0 ; $$i < $$roiNum ; i=$$(($$i + 1)) )) \
-		do \
-			tiltnum=`printf "%s%04d" $$orifile $$i`; \
-			make $$tiltnum.mrc3d ; \
-			make $$tiltnum.mrc3dcentre ; \
-			make $$tiltnum.mrc3dcentremed ; \
-			make $$tiltnum.mrc3dcentremedpad ; \
-			make $$tiltnum.ds6 ; \
-		done ; \
-	done
-
-Cleands6::
-	rm *.mrc3d
-
-.roilst.mrc3d:
-	mrc2Dto3D -I $*.roilst -o $*.mrc3d -single 0 -InterpolationMode 2 -m 1 
-	
-.mrc3dcentremedpad.ds6:
-	mrc2map -i $*.mrc3d -o $*.ds6 -mul $(MRC2MAPmul)
-	mrc2map -i $*.mrc3dcentre -o $*.centre.ds6 -mul $(MRC2MAPmul)
-	mrc2map -i $*.mrc3dcentremed -o $*.centremed.ds6 -mul $(MRC2MAPmul)
-	mrc2map -i $*.mrc3dcentremedpad -o $*.centremedpad.ds6 -mul $(MRC2MAPmul)
-
-.mrc3dcentre.mrc3dcentremed:
-	mrcImageSmoothing -i $*.mrc3dcentre -o $*.mrc3dcentremed -r $(SMOOTHr) -m $(SMOOTHm) -M $(SMOOTHM)
-
-.mrc3d.mrc3dcentre:
-	mrcImageCenterGet -i $*.mrc3d -o $*.mrc3dcentre -Nx $(CENTERNX) -Ny $(CENTERNY) -Nz $(CENTERNZ)
-
-.mrc3dcentremed.mrc3dcentremedpad:
-	 mrcImage3DPad -i $*.mrc3dcentremed -o $*.mrc3dcentremedpad -r 90 -m 1 -M 1 -v 0
-

--- a/bin/wish/Visualmake/Makefile.tmp
+++ /dev/null
@@ -1,377 +0,0 @@
-.SUFFIXES: .tif .dat .prectf .fft .ctfinfo .mrc \
-	.box .roi \
-	.roiinfo-coarse .roiall-coarse .roiinforef-coarse .roiallref-coarse  .roiinfoprev-coarse \
-	.roiinfo        .roiall        .roiinforef        .roiallref         .roiinfoprev \
-	.box2roiinfo .roiinfo2box .corinfo \
-	.roilst0 .roilst .mrc3d .ds6 .mrc3dmed .mrc3dmedcentre .orimrccentre .oricorinfo .coarroi .coarroiinfo .roi2 .pad .mul
-
-RESOLUTION=2.0
-ORIFILE1=a
-ORIFILE2=b
-EULARANGLE1=XOYS
-EULARANGLE2=YOYS
-ZEROTILTNUM=60
-ORIBASE=$(ORIFILE1)0$(ZEROTILTNUM)
-MINTILTNUM=0
-MAXTILTNUM=121
-STEPTILTNUM=4
-MINTILTANGLE=-60
-STEPTILTANGLE=4
-TILTAXISNUMBER=2
-
-SMOOTHr=5
-SMOOTHm=1
-SMOOTHM=1
-CENTERNX=100
-CENTERNY=100
-CENTERNZ=100
-
-ORINX=1024
-ORINY=1024
-
-ORINZ=1
-ORISIZEX=2048
-ORISIZEY=2048
-TILTAXISANGLE=0
-IMAGEPADm=15
-IMAGEPADV=0
-IMAGEMULTIPLYINGv=-1
-MRC2MAPmul=1
-
-all: data2mrc COARCreate $(ORIBASE).roiinfo BoxCreate PadAndMul roilstCreate ds6Create
-
-data2mrc::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-			else \
-				orifile=$(ORIFILE2); \
-			fi ; \
-			for (( i=0 ; $$i <= $(MAXTILTNUM) ; i=$$(($$i + $(STEPTILTNUM))))) \
-				do \
-					ori=`printf "%s%03d" $$orifile $$i`; \
-					make $$ori.prectf; \
-					make $$ori.fft; \
-					make $$ori.ctfinfo; \
-					make $$ori.mrc ; \
-				done ; \
-		done 
-
-.dat.prectf:
-	emData2mrc -i $*.dat -o $*.prectf
-
-.tif.prectf:
-	tiff2mrc -i $*.tif -o $*.prectf -m 1 -r $(RESOLUTION)
-
-.prectf.fft:
-	mrcImageFFT -i $*.prectf -o $*.fft	
-
-.fft.ctfinfo:
-	ctfDetermine -i $*.fft -o $*.ctfinfoauto -D 50000 -m 163 -CutLow 0.07 -CutHigh 0.15 -Ac 200 -d 3 -Cc 0.7 -Cs 2.1	
-	awk '/^[^:]/ {print $$0};' $*.ctfinfoauto > $*.ctfinfo
-	Display2 -i $*.fft -H 1e7
-
-.ctfinfo.mrc:
-	mv $*.ctfinfo $*.ctfinfotmp
-	awk '/^[^:]/ {print $$0};' $*.ctfinfotmp > $*.ctfinfo
-	mrcImageCTFCompensation -i $*.fft -o $*.mrc -info2 $*.ctfinfo -m 1	
-	Display2 -i $*.mrc -geometry 1024x1024+0+0 -Zoom 0.5 &
-
-##sep
-
-COARCreate::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-				oribase=$(ORIFILE1)0$(ZEROTILTNUM); \
-			else \
-				orifile=$(ORIFILE2); \
-				oribase=$(ORIFILE2)0$(ZEROTILTNUM); \
-			fi ; \
-			ORIZEROFILE=$$oribase.mrc; \
-			previous=$$oribase ; \
-			echo "Create the zero-tilt Image ROI (same as mrc, just copy)"; \
-			make $$oribase.roiinfo-coarse; echo "$$oribase.roi will be created."; \
-			make $$oribase.roiall-coarse ; echo "$$oribase.roi was created." ;  \
-			make $$oribase.orimrccentre  ; echo "The centre of $$oribase.roi was created." ;  \
-		for delta in -$(STEPTILTNUM) +$(STEPTILTNUM) ;  do \
-			echo "$$delta"; \
-			previous=$$oribase; \
-			TOTALX=0 ; \
-			TOTALY=0 ; \
-			echo "Total: $$TOTALX $$TOTALY" > $$previous.oricorinfo; \
-			for (( i=$$(($(ZEROTILTNUM) + $$delta )) ; (( $(MINTILTNUM) <= $$i && $$i <= $(MAXTILTNUM)  )) ; i=$$(($$i + $$delta)) )) \
-				do \
-					ori=`printf "%s%03d" $$orifile $$i`; \
-					echo $$i, $(MAXTILTNUM), $(MINTILTNUM); \
-					echo $$previous > $$ori.prevname ; \
-					ln -sf $$previous.roiinfo-coarse $$ori.roiinfoprev-coarse ; make $$ori.roiinforef-coarse ; \
-					make $$ori.roiallref-coarse ; \
-					make $$ori.orimrccentre ;     \
-					TOTALX=`awk '/Total:/ { print $$2 }' $$previous.oricorinfo`; \
-					TOTALY=`awk '/Total:/ { print $$3 }' $$previous.oricorinfo`; \
-					ln -sf $$previous.orimrccentre $$ori.oriref ; make $$ori.oricorinfo ; \
-					echo "TotalPrev: $$TOTALX $$TOTALY" >> $$ori.oricorinfo; \
-					make $$ori.roiinfo-coarse; \
-					make $$ori.roiall-coarse; \
-					touch $$ori.orimrccentre ; sleep 1; \
-					touch $$ori.oricorinfo   ; sleep 1; \
-					touch $$ori.roiinfo-coarse; sleep 1; \
-					touch $$ori.roiall-coarse; sleep 1; \
-					previous=$$ori; \
-				done ; \
-			echo $$i; \
-			done ; \
-		done
-
-CleanCOARCreate::
-	rm *.roiinfo-coarse
-
-$(ORIFILE1)0$(ZEROTILTNUM).roiinfo-coarse:
-	printf "%s%03d.roi Rect2 %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f\n" $(ORIFILE1) $(ZEROTILTNUM) $$(($(ORISIZEX)/2)) $$(($(ORISIZEY)/2)) $(ORISIZEX) $(ORISIZEY) > $(ORIFILE1)0$(ZEROTILTNUM).roiinfo-coarse 
-
-$(ORIFILE2)0$(ZEROTILTNUM).roiinfo-coarse:
-	printf "%s%03d.roi Rect2 %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f\n" $(ORIFILE2) $(ZEROTILTNUM) $$(($(ORISIZEX)/2)) $$(($(ORISIZEY)/2)) $(ORISIZEX) $(ORISIZEY) > $(ORIFILE2)0$(ZEROTILTNUM).roiinfo-coarse 
-
-.orimrccentre.oricorinfo:
-	echo "orimrccentre -> oricorinfo: SHIFT:= current.orimrccentre for prev.oirmrccentre"
-	mrcImageCorrelation -i $*.orimrccentre -r $*.oriref -c $*.oricorinfo
-
-.oricorinfo.roiinfo-coarse:
-	TOTALX=`awk '/TotalPrev:/ { print $$2 }' $*.oricorinfo`; \
-	TOTALY=`awk '/TotalPrev:/ { print $$3 }' $*.oricorinfo`; \
-	SHIFTX=`awk '/Shift:/ { print $$2 }' $*.oricorinfo`; \
-	SHIFTY=`awk '/Shift:/ { print $$3 }' $*.oricorinfo`; \
-	echo "$$SHIFTX,$$SHIFTY"; \
-	if [ $$(($(ORINX)/2)) -lt $$SHIFTX ]; then  \
-		SHIFTX=$$(($$SHIFTX - $(ORINX))) ; \
-	fi ; \
-	if [ $$(($(ORINY)/2)) -lt $$SHIFTY ]; then  \
-		SHIFTY=$$(($$SHIFTY - $(ORINY))) ; \
-	fi ; \
-	TOTALX=$$(($$TOTALX + $$SHIFTX)) ; \
-	TOTALY=$$(($$TOTALY + $$SHIFTY)) ; \
-	echo "Total: $$TOTALX $$TOTALY" >> $*.oricorinfo; \
-	printf "%s.roi Rect2 %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f\n" $* $$(($(ORISIZEX)/2+$$TOTALX)) $$(($(ORISIZEY)/2+$$TOTALY)) $(ORISIZEX) $(ORISIZEY) $$TOTALX $$TOTALY > $*.roiinfo-coarse ;
-
-.roiinfo-coarse.roiall-coarse:
-	make $*.mrc
-	mrcImageROIs -i $*.mrc -I $*.roiinfo-coarse 
-	touch $*.roiall-coarse 
-
-.roiinforef-coarse.roiallref-coarse:
-	mrcImageROIs -i $*.mrc -I $*.roiinforef-coarse
-	touch $*.roiallref-coarse
-
-.roiinfoprev-coarse.roiinforef-coarse:
-	previous=`cat $*.prevname`; \
-	sed -s s/$$previous/$*/ $*.roiinfoprev-coarse  > $*.roiinforef-coarse
-
-.roi.orimrccentre:
-	echo "roi -> orimrccentre"
-	mrcImageCenterGet -i $*.roi -o $*.orimrccentre -Nx $(ORINX) -Ny $(ORINY) -Nz $(ORINZ)
-
-
-$(ORIBASE).roiinfo:
-	Display2 -i $*.mrc ; \
-	if [ $(TILTAXISNUMBER) -eq 2 ]; then \
-		Display2 -i $(ORIFILE2)0$(ZEROTILTNUM).mrc ;\
-	fi; \
-		
-##sep
-
-BoxCreate::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-				oribase=$(ORIFILE1)0$(ZEROTILTNUM); \
-			else \
-				orifile=$(ORIFILE2); \
-				oribase=$(ORIFILE2)0$(ZEROTILTNUM); \
-			fi ; \
-			BASE=$$oribase; \
-			make $$BASE.roiall ; \
-			for delta in +$(STEPTILTNUM) -$(STEPTILTNUM) ; \
-				do \
-					echo $$delta,$$BASE ;  \
-					previous=$$BASE	; \
-					for (( i=$$(($(ZEROTILTNUM)+$$delta)) ; (( $(MINTILTNUM) <= $$i && $$i <= $(MAXTILTNUM) )) ; i=$$(($$i + $$delta)) )) \
-						do  \
-							name=`printf "%s%03d" $$orifile $$i`; \
-							echo ">>>> $$name $$i start: $(ZEROTILTNUM) $$(($(ZEROTILTNUM)+$$delta))"; \
-							echo $$previous > $$name.prevname; \
-							ln -sf $$previous.roiinfo $$name.roiinfoprev ; make $$name.roiinforef ; \
-							make $$name.roiinfo ; \
-							make $$name.roiall ; \
-							previous=$$name ; \
-						done  ; \
-				done ; \
-		done
-
-CleanBoxCreate::
-	rm *.roiall *.roiinfoprev *.roiinforef
-
-.roiinfo.roiall:
-	make $*.roi
-	mrcImageROIs -i $*.roi -I $*.roiinfo
-	touch $*.roiall
-
-.roiinforef.roiallref:
-	mrcImageROIs -i $*.roi -I $*.roiinforef
-	touch $*.roiallref
-
-.roi.corinfo:
-	mrcImageCorrelation -i $*.roi -r $*.ref -c $*.corinfo 
-
-.roiinforef.roiinfo:
-	# Extract ROIs using roiinfo of previous image (roiinforef)
-	previous=`cat $*.prevname`; \
-	echo $$previous; \
-	echo "start initial ROI"; \
-	make $*.roiallref ; \
-	ROINUM=`wc -l $*.roiinforef | awk '{print $$1}'` ; \
-	echo $$ROINUM ; \
-	rm -f $*.roiinfo ; \
-	for (( j=0 ; $$j < $$ROINUM ; j=$$(($$j+1)))) \
-	do  \
-		input=`printf "%s-%04d" $*         $$j`; \
-		refer=`printf "%s-%04d" $$previous $$j`; \
-		echo $$input, $$refer ; \
-		ln -sf $$refer.roi $$input.ref ; make $$input.corinfo ; \
-		SHIFTX=`awk '/Shift:/ { print $$2 }' $$input.corinfo`; \
-		SHIFTY=`awk '/Shift:/ { print $$3 }' $$input.corinfo`; \
-		echo "$$SHIFTX,$$SHIFTY,$$input"; \
-		awk -v SHIFTXAWK0=$$SHIFTX -v SHIFTYAWK0=$$SHIFTY -v NAMEAWK=$$input -v BASEAWK=$* \
-		 ' /'"$$input"'/ { \
-			SizeX = int(sqrt(($$5-$$3)*($$5-$$3)+( $$6-$$4)*( $$6-$$4))+0.5)+1; \
-			SizeY = int(sqrt(($$9-$$3)*($$9-$$3)+($$10-$$4)*($$10-$$4))+0.5)+1; \
-		 	if(SizeX/2<SHIFTXAWK0) { \
-				SHIFTXAWK0 -= SizeX ; \
-			} \
-			if(SizeY/2<SHIFTYAWK0) { \
-				SHIFTYAWK0 -= SizeY ; \
-			} \
-			Angle = atan2($$6-$$4, $$5-$$3) ; \
-			SHIFTXAWK = +1*( SHIFTXAWK0*cos(Angle) - SHIFTYAWK0*sin(Angle)); \
-			SHIFTYAWK = +1*( SHIFTXAWK0*sin(Angle) + SHIFTYAWK0*cos(Angle)); \
-			printf("%s-%04d.roi Rect %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f %15.6f\n", BASEAWK, FNR-1, $$3+SHIFTXAWK, $$4+SHIFTYAWK, $$5+SHIFTXAWK, $$6+SHIFTYAWK, $$7+SHIFTXAWK, $$8+SHIFTYAWK, $$9+SHIFTXAWK, $$10+SHIFTYAWK, SHIFTXAWK, SHIFTYAWK, Angle*180/3.141592653589793238, SizeX, SizeY);}' \
-		 $*.roiinforef | tee -a $*.roiinfo ; \
-	done ; 
-
-.roiinfoprev.roiinforef:
-	previous=`cat $*.prevname`; \
-	sed -s s/$$previous/$*/ $*.roiinfoprev  > $*.roiinforef
-
-PadAndMul::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-				oribase=$(ORIFILE1)0$(ZEROTILTNUM); \
-			else \
-				orifile=$(ORIFILE2); \
-				oribase=$(ORIFILE2)0$(ZEROTILTNUM); \
-			fi ; \
-			roiNum=`wc -l  $$oribase.roiinfo | awk '{print $$1}' `; \
-			for ((i=$(MINTILTNUM);i<=$(MAXTILTNUM);i=$$(($$i+$(STEPTILTNUM))) )) \
-				do \
-					for((j=0;j<$$roiNum;j=$$(($$j+1)))) \
-						do \
-							name=`printf "%s%03d-%04d" $$orifile $$i $$j` ; \
-							echo $$(($$i-$(ZEROTILTNUM))) > $$name.tilt ; \
-							ln -sf $$name.roi $$name.roi2 ; make $$name.pad ; \
-							make $$name.mul ; \
-						done ; \
-				done ; \
-		done
-
-CleanPadAndMul::
-	rm *.pad
-
-.roi2.pad:
-	tilt=`cat $*.tilt` ; \
-	echo $$tilt ; \
-	mrcImagePad -i $*.roi2 -o $*.pad -Tilt $(TILTAXISANGLE) $$tilt -m $(IMAGEPADm) -V $(IMAGEPADV)
-
-.pad.mul:
-	mrcImageMultiplying -i $*.pad -o $*.mul -v $(IMAGEMULTIPLYINGv)
-
-roilstCreate::
-	for (( j=1 ; $$j <= $(TILTAXISNUMBER) ; j=$$(($$j + 1 )))) \
-		do \
-			if [ $$j -eq 1 ]; then \
-				orifile=$(ORIFILE1); \
-				oribase=$(ORIFILE1)0$(ZEROTILTNUM); \
-				echo "$(ORIFILE1)" > roilstorifile.txt; \
-			else \
-				orifile=$(ORIFILE2); \
-				oribase=$(ORIFILE2)0$(ZEROTILTNUM); \
-				echo "$(ORIFILE2)" > roilstorifile.txt; \
-			fi ; \
-			roiNum=`wc -l  $$oribase.roiinfo | awk '{print $$1}' `; \
-			echo $$roiNum; \
-			for (( i=0 ; $$i < $$roiNum ; i=$$(($$i + 1)))) \
-				do \
-					tiltnum=`printf "%s%04d" $$orifile $$i`; \
-					echo "$$i" > $$tiltnum.roilst0; \
-					make $$tiltnum.roilst ; \
-				done ; \
-		done
-
-Cleanroilst::
-	rm *.roilst
-
-.roilst0.roilst:
-		i=`cat $*.roilst0`; \
-		orifile=`cat roilstorifile.txt`; \
-		oribase=`printf "%s%03d" $$orifile $(ZEROTILTNUM)`; \
-		num=`printf "%04d" $$i`; \
-		roiname=`printf "%s-%04d" $$oribase $$i`; \
-		echo "$$roiname in $$oribase.roiinfo"; \
-		tiltangle=`awk -v ORIBASE=$$oribase '/'"$$roiname"'/ { printf("%15.6f", atan2($$6-$$4, $$5-$$3)*180/3.141592653589793238); }' ORIBASE.roiinfo`; \
-		if [ $orifile = a ]; then \
-			eularangle=$(EULARANGLE1); \
-		else \
-			eularangle=$(EULARANGLE2); \
-		fi ; \	
-		echo "$*.roilst creating" ; \
-		ls -1 *-$$num.mul | awk ' BEGIN {angle=$(MINTILTANGLE)} {printf("%s %s %f %f %f\n",$$1, '"$$eularangle"', -1*angle, -1*'"$$tiltangle"', 0); angle+=$(STEPTILTANGLE)}' > $*.roilst ; \
-
-##sep
-
-##noshow
-ds6Create::
-	roiNum=`ls -1 *.roilst | wc -l `; \
-	echo $$roiNum; \
-	for (( i=0 ; $$i < $$roiNum ; i=$$(($$i + 1)) )) \
-	do \
-		tiltnum=`printf "%s-%04d" $(ORIFILE) $$i`; \
-		make $$tiltnum.mrc3d ; \
-		make $$tiltnum.mrc3dmed ; \
-		make $$tiltnum.mrc3dmedcentre ; \
-		make $$tiltnum.ds6 ; \
-	done ;
-
-##noshow
-
-Cleands6::
-	rm *.mrc3d
-
-.roilst.mrc3d:
-	mrc2Dto3D -I $*.roilst -o $*.mrc3d -single 0 -InterpolationMode 2 -m 1 
-	
-.mrc3dmedcentre.ds6:
-	mrc2map -i $*.mrc3d -o $*.ds6 -mul $(MRC2MAPmul)
-	mrc2map -i $*.mrc3dmed -o $*.med.ds6 -mul $(MRC2MAPmul)
-	mrc2map -i $*.mrc3dmedcentre -o $*.medcentre.ds6 -mul $(MRC2MAPmul)
-
-.mrc3d.mrc3dmed:
-	mrcImageSmoothing -i $*.mrc3d -o $*.mrc3dmed -r $(SMOOTHr) -m $(SMOOTHm) -M $(SMOOTHM)
-
-.mrc3dmed.mrc3dmedcentre:
-	mrcImageCenterGet -i $*.mrc3dmed -o $*.mrc3dmedcentre -Nx $(CENTERNX) -Ny $(CENTERNY) -Nz $(CENTERNZ)
-	
-	

--- a/bin/wish/Visualmake/a.hoge
+++ /dev/null
@@ -1 +0,0 @@
-test

--- a/bin/wish/Visualmake/a.hogehoge
+++ /dev/null
@@ -1 +0,0 @@
-test

--- a/bin/wish/Visualmake/handmake.lst
+++ /dev/null
@@ -1,6 +0,0 @@
-data2mrc
-COARCreate
-roilstCreate
-mrcImagePadAndMultiplying
-ds6Create
-

--- a/env/Eos_env
+++ b/env/Eos_env
@@ -347,10 +347,11 @@ then
 		source $ATISTREAMROOT/.bash_profile
 	fi
 else
-    OIFS=$IFS
-    IFS=":"
-    read k v < <(echo "$LD_LIBRARY_PATH" | egrep "$ATISTREAMSDKROOT" )
-    IFS=$OIFS
+#    OIFS=$IFS
+#    IFS=":"
+#    read k v < <(echo "$LD_LIBRARY_PATH" | egrep "$ATISTREAMSDKROOT" )
+    k=`echo "$LD_LIBRARY_PATH" | egrep "$ATISTREAMSDKROOT"` 
+#    IFS=$OIFS
 #	echo "()k=$k"
 #	echo "v=$v"
 	if [ -z "$k" ];
@@ -385,10 +386,11 @@ then
 		done
 	fi
 else
-    OIFS=$IFS
-    IFS=":"
-    read k v < <(echo "$LD_LIBRARY_PATH" | egrep "$LD_LIBGFORTRAN" )
-    IFS=$OIFS
+#    OIFS=$IFS
+#    IFS=":"
+#    read k v < <(echo "$LD_LIBRARY_PATH" | egrep "$LD_LIBGFORTRAN" )
+    k=`echo "$LD_LIBRARY_PATH" | egrep "$LD_LIBGFORTRAN`
+#    IFS=$OIFS
 #	echo "()k=$k"
 #	echo "v=$v"
 	if [ -z "$k" ];

--- a/env/install-eos.sh
+++ b/env/install-eos.sh
@@ -16,7 +16,9 @@ if [ ! -d $EOS_HOME0 ] ; then
 	mkdir $EOS_HOME0
 fi
 
-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
+#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