.SUFFIXES: .tif .mrcraw .mrc .nor .fft .ctf .ctfinfo .ctfshrink .ctfinfo .ctfps .roi .mirrot 

### Default Values
# Pixel interval
RESOLUTION=5
# FILM:1
# CCD:0
TIFF2MRC_MODE=1

## Shinking
# Pre-FFT 
SHRINK=1
# Pre-roi
SHRINK2=1
# Shirnking

## Pad Size 
PADSIZE=1024
PADMODE=3

## CVE Size
CVESIZE=511

###  
-include CONFIG

#
-include TIFS
-include MRCS
-include NORS
-include FFTS
-include CTFInfoList
-include CTFS
-include ALLROIS

help::
	@echo "CTF correction and particle picking"
	@echo ">>> For CTF Correction"
	@echo "$ make ctf-correction"
	@echo ""
	@echo ">>> For CTF Correction of each file"
	@echo "$ make xxxx.ctf"
	@echo ""
	@echo ">>> For CTF-check again"
	@echo "$ make ctfcheck"
	@echo ""
	@echo ">>> For Particle Picking "
	@echo "$ make particle-picking"
	@echo ""
	@echo ">>> For CTF Correction of each file"
	@echo "$ make xxxx.ctf"
	@echo ""
	@echo ">>> For particle picking of each file"
	@echo "$ Display2 -i xxxx.ctf -Inverse &"
	@echo "--- Roi selection and push Extract button"
	@echo ""
	@echo ">>> ctfinfo again"
	@echo "$ touch *.fft"
	@echo ">>> Restart"
	@echo "$ make clean"

ctf-correction::
	make TIFS; make mrcraw ; make mrc
	make MRCS; make nor 
	make NORS; make fft
	make FFTS; make ctfinfo 
	make ctf

particle-picking::
	make CTFS
	make ctfshrink 
	make ROIINFOS
	make -i roi

ctfcheck::
	touch *.fft 
	make ctf-correction

clean::
	rm *.mrcraw *.mrc *.nor *.nortmp *.fft *.ctfinfo *.ctf

mrcraw:$(TIFS:.tif=.mrcraw)
mrc:$(TIFS:.tif=.mrc)
nor:$(MRCS:.mrc=.nor)
fft:$(NORS:.nor=.fft)
ctfinfo:$(FFTS:.fft=.ctfinfo)
ctf:$(FFTS:.fft=.ctf)
ctfshrink:$(CTFS:.ctf=.roi)
roi:$(CTFS:.ctf=.roi)

TIF2FFT::
	make TIFS; make mrc;
	make MRCS; make nor;
	make NORS; make fft;
	make FFTS; 
	make CTFInfoList; make DefaultCTFInfoCreate;
	
TIFS::
	echo "TIFS=\\" > TIFS
	ls -1 *.tif | sed s/tif/tif\\\\/ >> TIFS
	echo "" >> TIFS

MRCS::
	echo "MRCS=\\" > MRCS
	ls -1 *.mrc | sed s/mrc/mrc\\\\/ >> MRCS
	echo "" >> MRCS

NORS::
	echo "NORS=\\" > NORS
	ls -1 *.nor | sed s/nor/nor\\\\/ >> NORS
	echo "" >> NORS

FFTS::
	echo "FFTS=\\" > FFTS
	ls -1 *.fft | sed s/fft/fft\\\\/ >> FFTS
	echo "" >> FFTS

CTFS::
	echo "CTFS=\\" > CTFS
	ls -1 *.ctf | sed s/ctf/ctf\\\\/ >> CTFS
	echo "" >> CTFS

CTFInfoList::
	echo "CTFInfoList=\\" > CTFInfoList ;\
	ls *.fft | sed s/fft/ctfinfo\\\\/ >> CTFInfoList
	echo "" >> CTFInfo

ALLROIS::
	echo "ALLROIS=\\" > ALLROIS
	ls -1 *right*.roi | sed s/roi/roi\\\\/ >> ALLROIS
	ls -1 *MirRot.roi | sed s/roi/roi\\\\/ >>ALLROIS 
	echo "" >> ALLROIS

# tif -> mrc
.tif.mrcraw:
	tiff2mrc -i $*.tif -o $*.mrcraw -r $(RESOLUTION) -m $(TIFF2MRC_MODE) 

# mrc -> shrinking for limitation of computer resources
.mrcraw.mrc:
	if [ $(SHRINK) -eq 1 ] ; then \
		ln -sf $*.mrcraw $*.mrc	; \
	else \
		mrcImageShrink -S $(SHRINK) -i $*.mrcraw -o $*.mrc; \
	fi

# pre-filtering
.mrc.nor:
	mrcImageAbnormalValueRemove -i $*.mrc -o $*.nortmp -m 1
	mrcImagePad -i $*.nortmp -o $*.nor -W $(PADSIZE) -H $(PADSIZE) -m $(PADMODE)
	rm $*.nortmp 

# Fourier Transform
.nor.fft:
	mrcImageFFT -i $*.nor -o $*.fft

# ctf Determine 
.fft.ctfinfo:
	if [ -f  $*.ctfinfo ]; then \
		ctfDisplay -i $*.fft -o $*.ctfinfo ; \
	else \
		ctfDisplay -i $*.fft -o $*.ctfinfo -AutoRange -Log ; \
	fi


.ctfinfo.ctf:
	mrcImageCTFCompensation -i $*.fft -info2 $*.ctfinfo -o $*.ctf -m 1

.ctf.ctfps:
	echo $@
	Mean=`mrcImageInfo -i $*.ctf -I | grep Mean | awk '{print $$2}';` \
	SD=`mrcImageInfo -i $*.ctf   -I | grep SD   | awk '{print $$2}';` \
	DIS2HIGH=`echo "$$Mean + 2*$$SD" | bc `; DIS2LOW=`echo "$$Mean - 2*$$SD" | bc `; \
	echo "$$Mean $$SD $$DIS2LOW $$DIS2HIGH"; \
	mrcImagePrint -i $*.ctf -o $*.ctfps -L $$DIS2HIGH -H $$DIS2LOW -m 17 -S 0.1
	#mrcImagePrint -i $*.ctf -o $*.ctfps -m 17 -S 0.1

.ctf.ctfshrink:
	mrcImageShrink -i $*.ctf -o $*.ctf.shrink -S $(SHRINK2) ; \
	mrcImageSmoothing -i $*.ctf.shrink -o $*.ctf.smooth -r 2 -M 1 -m 1 ; \
	mrcImageCVE -i $*.ctf.smooth -o $*.ctfshrink -sx $(CVESIZE) -sy $(CVESIZE) 
	rm $*.ctf.shrink $*.ctf.smooth 

.ctfshrink.roi:
	Display2 -i $*.ctfshrink -Inverse
	sed s/ctfshrink/ctf/ $*.ctfshrink.roiinfo > $*.ctf.roiinfo
	mrcImageROIs -i $*.ctfshrink -o $*.ctfshrink.mon -I $*.ctfshrink.roiinfo
	mrcImageROIs -i $*.ctf       -o $*.ctf.mon       -I $*.ctf.roiinfo       -S $(SHRINK2) 
	touch $*.roi
	
Disp::
	for i in $(FFTS) ;\
	do \
	   echo $$i ; \
	   Display2 -i $$i ; \
    done

ctfDisp::
	for i in $(FFTS) ;\
	do \
		echo $$i ;\
		ctfDisplay -i $$i ;\
	done

DefaultCTFInfoCreate::
	for i in $(CTFInfoList) ; \
   	do \
      cp .DefCTFInfo $$i ; \
	  echo ".ctfinfo: $$i" >> $$i ; \
	done
	  
DispCTFs::
	for i in $(CTFS) ;\
	do \
      echo $$i ; \
      	 filename=`basename $$i .ctf`.ctfshrink ; \
      	 make $$filename; \
	 Mean=`mrcImageInfo -i $$filename -I | grep Mean | awk '{print $$2}'`; \
	 SD=`mrcImageInfo -i $$filename -I | grep SD | awk '{print $$2}'`; \
	 DIS2HIGH=`echo "$$Mean + 2*$$SD" | bc `; DIS2LOW=`echo "$$Mean - 2*$$SD" | bc `; \
	 echo "$$Mean $$SD $$DIS2LOW $$DIS2HIGH"; \
	 Display2 -i $$filename -L $$DIS2HIGH -H $$DIS2LOW -Zoom 0.5 -geometry 1280x1024+0+0; \
	 echo "$$DIS2LOW $$DIS2HIGH"; \
	done

PrintCTFs::
	for i in $(CTFS) ;\
	do \
		echo $$i ; \
		make $${i}ps; \
	done