From e2e49dc4bd4327c897d866888f985af01c36e57e Mon Sep 17 00:00:00 2001 From: Takuo Yasunaga Date: Tue, 4 Nov 2014 04:39:28 +0900 Subject: [PATCH] Bug fixed: Eos_env install-eos.sh --- bin/wish/Visualmake/Makefile | 498 --------------------------------------- bin/wish/Visualmake/Makefile.tmp | 377 ----------------------------- bin/wish/Visualmake/a.hoge | 1 - bin/wish/Visualmake/a.hogehoge | 1 - bin/wish/Visualmake/handmake.lst | 6 - bin/wish/Visualmake/tclIndex | 0 env/Eos_env | 18 +- env/install-eos.sh | 4 +- 8 files changed, 13 insertions(+), 892 deletions(-) delete mode 100755 bin/wish/Visualmake/Makefile delete mode 100755 bin/wish/Visualmake/Makefile.tmp delete mode 100755 bin/wish/Visualmake/a.hoge delete mode 100755 bin/wish/Visualmake/a.hogehoge delete mode 100755 bin/wish/Visualmake/handmake.lst delete mode 100644 bin/wish/Visualmake/tclIndex diff --git a/bin/wish/Visualmake/Makefile b/bin/wish/Visualmake/Makefile deleted file mode 100755 index 94e20e779a..0000000000 --- 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-$$4))+0.5)+1; \ - if(SizeX/2 $*.roiinforef - -##sep - -PadAndMul:: - for (( k=1 ; $$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 $$tiltnum.ds6 ; \ - done ; \ - done - -Cleands6:: - rm *.mrc3d - -.roilst.mrc3d: - mrc2Dto3D -I $*.roilst -o $*.mrc3d -single 0 -InterpolationMode 2 -m 1 - -.mrc3dcentremedpad.ds6: - mrc2map -i $*.mrc3d -o $*.ds6 -mul $(MRC2MAPmul) - mrc2map -i $*.mrc3dcentre -o $*.centre.ds6 -mul $(MRC2MAPmul) - mrc2map -i $*.mrc3dcentremed -o $*.centremed.ds6 -mul $(MRC2MAPmul) - mrc2map -i $*.mrc3dcentremedpad -o $*.centremedpad.ds6 -mul $(MRC2MAPmul) - -.mrc3dcentre.mrc3dcentremed: - mrcImageSmoothing -i $*.mrc3dcentre -o $*.mrc3dcentremed -r $(SMOOTHr) -m $(SMOOTHm) -M $(SMOOTHM) - -.mrc3d.mrc3dcentre: - mrcImageCenterGet -i $*.mrc3d -o $*.mrc3dcentre -Nx $(CENTERNX) -Ny $(CENTERNY) -Nz $(CENTERNZ) - -.mrc3dcentremed.mrc3dcentremedpad: - mrcImage3DPad -i $*.mrc3dcentremed -o $*.mrc3dcentremedpad -r 90 -m 1 -M 1 -v 0 - diff --git a/bin/wish/Visualmake/Makefile.tmp b/bin/wish/Visualmake/Makefile.tmp deleted file mode 100755 index 8353e28d8c..0000000000 --- a/bin/wish/Visualmake/Makefile.tmp +++ /dev/null @@ -1,377 +0,0 @@ -.SUFFIXES: .tif .dat .prectf .fft .ctfinfo .mrc \ - .box .roi \ - .roiinfo-coarse .roiall-coarse .roiinforef-coarse .roiallref-coarse .roiinfoprev-coarse \ - .roiinfo .roiall .roiinforef .roiallref .roiinfoprev \ - .box2roiinfo .roiinfo2box .corinfo \ - .roilst0 .roilst .mrc3d .ds6 .mrc3dmed .mrc3dmedcentre .orimrccentre .oricorinfo .coarroi .coarroiinfo .roi2 .pad .mul - -RESOLUTION=2.0 -ORIFILE1=a -ORIFILE2=b -EULARANGLE1=XOYS -EULARANGLE2=YOYS -ZEROTILTNUM=60 -ORIBASE=$(ORIFILE1)0$(ZEROTILTNUM) -MINTILTNUM=0 -MAXTILTNUM=121 -STEPTILTNUM=4 -MINTILTANGLE=-60 -STEPTILTANGLE=4 -TILTAXISNUMBER=2 - -SMOOTHr=5 -SMOOTHm=1 -SMOOTHM=1 -CENTERNX=100 -CENTERNY=100 -CENTERNZ=100 - -ORINX=1024 -ORINY=1024 - -ORINZ=1 -ORISIZEX=2048 -ORISIZEY=2048 -TILTAXISANGLE=0 -IMAGEPADm=15 -IMAGEPADV=0 -IMAGEMULTIPLYINGv=-1 -MRC2MAPmul=1 - -all: data2mrc COARCreate $(ORIBASE).roiinfo BoxCreate PadAndMul roilstCreate ds6Create - -data2mrc:: - for (( j=1 ; $$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-$$4))+0.5)+1; \ - if(SizeX/2 $*.roiinforef - -PadAndMul:: - for (( j=1 ; $$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) - - diff --git a/bin/wish/Visualmake/a.hoge b/bin/wish/Visualmake/a.hoge deleted file mode 100755 index 9daeafb986..0000000000 --- a/bin/wish/Visualmake/a.hoge +++ /dev/null @@ -1 +0,0 @@ -test diff --git a/bin/wish/Visualmake/a.hogehoge b/bin/wish/Visualmake/a.hogehoge deleted file mode 100755 index 9daeafb986..0000000000 --- a/bin/wish/Visualmake/a.hogehoge +++ /dev/null @@ -1 +0,0 @@ -test diff --git a/bin/wish/Visualmake/handmake.lst b/bin/wish/Visualmake/handmake.lst deleted file mode 100755 index 42d3f22a26..0000000000 --- a/bin/wish/Visualmake/handmake.lst +++ /dev/null @@ -1,6 +0,0 @@ -data2mrc -COARCreate -roilstCreate -mrcImagePadAndMultiplying -ds6Create - diff --git a/bin/wish/Visualmake/tclIndex b/bin/wish/Visualmake/tclIndex deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/env/Eos_env b/env/Eos_env index e5bbb0497d..4866636244 100755 --- 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" ]; diff --git a/env/install-eos.sh b/env/install-eos.sh index 829c496358..3e3986606d 100755 --- 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 -- 2.11.0