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== Eosによる実現方法 ==
 
== Eosによる実現方法 ==
−
　演習では、Eosをつかった３次元再構成法の一例を示しています。Makefileの形でまとめています。
+
　演習では、Eosをつかった３次元再構成法の一例を示しています。下記に利用したMakefileを示します。
 +
 
 +
<pre>
 +
#
 +
# Eos for 3D reconstrucion from 2D rois using 3D initail reference
 +
#
 +
 
 +
.SUFFIXES: .3d .ref3d .ref2d .pad .padtmp .mask .maskfit .fit .fitmask .roi .corinfo .3dinfo .3dlst .3d .3dsm .3dsmCenter .ds6 .3dsmds6 .corinfo2 .corinfolst .cormap .parcorinfolst .parcorinfolstsort .gnuplotcorinfolst .3dlstselect .monlst .mon
 +
 
 +
SHELL=/bin/bash
 +
 
 +
-include ROIs
 +
-include CORINFOs
 +
-include PADs
 +
-include 3DINFOs
 +
-include 3DLIST
 +
-include CORINFO2s
 +
 
 +
#
 +
# Initial Reference Model
 +
INITIAL=initial
 +
# Target structure name
 +
TARGET=all
 +
 
 +
# Simultaneous Jobs for AutoRotaionCorrelation
 +
JOP_NUM=-j 3
 +
 
 +
#
 +
# Search Area for 3D
 +
#
 +
ROTMODE=YOYS
 +
# Rot1
 +
ROT1MIN=0
 +
ROT1MAX=359
 +
ROT1D=30
 +
nRot1=12
 +
#
 +
ROT2MIN=0
 +
ROT2MAX=359
 +
ROT2D=30
 +
nRot2=12
 +
# Rot3
 +
ROT3MIN=0
 +
ROT3MAX=0
 +
ROT3D=30
 +
nRot3=1
 +
# For 2D
 +
STEP=12
 +
ROTMIN=0
 +
ROTMAX=359
 +
nROT=`echo "" | awk 'BEGIN {printf 360 / $(STEP)}'`
 +
 
 +
# Seletion Step
 +
COR_THRESHOLD=0.4
 +
Y_SHIFT_THRESHOLD=20
 +
 
 +
# Pad size for 2D
 +
PAD_W=64
 +
PAD_H=64
 +
 
 +
###
 +
### Initial model from PDB
 +
###
 +
REFSOURCE=121p-shift
 +
DELTA=2.5
 +
SIZE_X=64
 +
SIZE_Y=64
 +
SIZE_Z=64
 +
START_X=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_X)/2}'`
 +
START_Y=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_Y)/2}'`
 +
START_Z=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_Z)/2}'`
 +
SNRATIO=3
 +
###############################
 +
 
 +
Help::
 +
@echo "----- Makefile for Single Particle with Reference"
 +
@echo "1. Prepare files from EM images, which has a suffix of roi "
 +
@echo "2. Prepare an initial model as $(INITIAL).3d "
 +
@echo "3. make First"
 +
@echo "4. make All"
 +
@echo "If you want to repeat refinement again, "
 +
@echo "  1. make Again"
 +
@echo "  2. make All"
 +
@echo ""
 +
@echo "--- If you want to create an initail model from PDB ---"
 +
@echo " make InitialModel"
 +
@echo ""
 +
@echo "--- If you want to create an test from the initial model ---"
 +
@echo " make TestData"
 +
 
 +
pad:$(ROIs:.roi=.pad)
 +
corinfo:$(PADs:.pad=.corinfo)
 +
3dinfo:$(CORINFOs:.corinfo=.3dinfo)
 +
fit:$(ROIs:.roi=.fit)
 +
3dlst:$(3DINFOs:.3dinfo=.3dlst)
 +
3d:$(3DLIST:.3dlst=.3d)
 +
corinfo2:$(CORINFOs:.corinfo=.corinfo2)
 +
parcorinfolst:$(CORINFO2s:.corinfo2=.parcorinfolst)
 +
 
 +
#
 +
#
 +
#
 +
InitialModel::
 +
pdb2mrc -i $(REFSOURCE).pdb -o $(INITIAL).3d -nx $(SIZE_X) -ny $(SIZE_Y) -nz $(SIZE_Z) -Sx $(START_X) -Sy $(START_Y) -Sz $(START_Z) -dx $(DELTA) -dy $(DELTA) -dz $(DELTA) -m 1
 +
 
 +
TestData::
 +
@for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D)*2 )) \
 +
do \
 +
for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D)*2 )) \
 +
do \
 +
for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D)*2 )) \
 +
do \
 +
echo $$rot1, $$rot2, $$rot3; \
 +
mrc3Dto2D -i $(INITIAL).3d -o $(REFSOURCE)-$$rot1-$$rot2-$$rot3.roi \
 +
  -InterpolationMode 2 -EulerMode $(ROTMODE) \
 +
  -Rot1 $$rot1 $$rot1 1 \
 +
  -Rot2 $$rot2 $$rot2 1 \
 +
  -Rot3 $$rot3 $$rot3 1 ; \
 +
done \
 +
done \
 +
done
 +
 
 +
TestDataNoise::
 +
@for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D)*2 )) \
 +
do \
 +
for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D)*2 )) \
 +
do \
 +
for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D)*2 )) \
 +
do \
 +
echo $$rot1, $$rot2, $$rot3; \
 +
name="$(REFSOURCE)-noise-$$rot1-$$rot2-$$rot3.roi"; \
 +
mrc3Dto2D -i $(INITIAL).3d -o $$name.noNoise \
 +
  -InterpolationMode 2 -EulerMode $(ROTMODE) \
 +
  -Rot1 $$rot1 $$rot1 1 \
 +
  -Rot2 $$rot2 $$rot2 1 \
 +
  -Rot3 $$rot3 $$rot3 1 ; \
 +
mrcImageNoiseAdd -i $$name.noNoise -o $$name -SN $(SNRATIO) ; \
 +
rm $$name.noNoise ; \
 +
done \
 +
done \
 +
done
 +
 
 +
##############
 +
ROIs::
 +
touch ROIs
 +
echo "ROIs=\\" > ROIs
 +
#find -name "*.roi" -type f | sed s/..// | xargs ls -1 | sed s/roi/roi\\\\/ >> ROIs
 +
ls -1 *.roi |  sed s/roi/roi\\\\/ >> ROIs
 +
echo "" >> ROIs
 +
 
 +
CORINFOs::
 +
touch CORINFOs
 +
echo "CORINFOs=\\" > CORINFOs
 +
#find -name "*.corinfo" -type f | sed s/..// | xargs ls -1 | sed s/corinfo/corinfo\\\\/ >> CORINFOs
 +
ls -1 *.corinfo |  sed s/corinfo/corinfo\\\\/ >> CORINFOs
 +
echo "" >> CORINFOs
 +
 
 +
PADs::
 +
touch PADs
 +
echo "PADs=\\" > PADs
 +
#find -name "*.pad" -type f | sed s/..// | xargs ls -1 | sed s/pad/pad\\\\/ >> PADs
 +
ls -1 *.pad |  sed s/pad/pad\\\\/ >> PADs
 +
echo "" >> PADs
 +
 
 +
3DINFOs::
 +
touch 3DINFOs
 +
echo "3DINFOs=\\" > 3DINFOs
 +
#find -name "*.3dinfo" -type f | sed s/..// | xargs ls -1 | sed s/3dinfo/3dinfo\\\\/ >> 3DINFOs
 +
ls -1 *.3dinfo | sed s/3dinfo/3dinfo\\\\/ >> 3DINFOs
 +
echo "" >> 3DINFOs
 +
 
 +
3DLIST::
 +
touch 3DLIST
 +
echo "3DLIST=\\" > 3DLIST
 +
#find -name "*.3dlst" -type f | sed s/..// | xargs ls -1 | sed s/3dlst/3dlst\\\\/ >> 3DLIST
 +
ls -1 *.3dlst |  sed s/3dlst/3dlst\\\\/ >> 3DLIST
 +
echo "" >> 3DLIST
 +
 
 +
CORINFO2s::
 +
touch CORINFO2s
 +
echo "CORINFO2s=\\" > CORINFO2s
 +
#find -name "*.corinfo2" -type f | sed s/..// | xargs ls -1 | sed s/corinfo2/corinfo2\\\\/ >> CORINFO2s
 +
ls -1 *.corinfo2 | sed s/corinfo2/corinfo2\\\\/ >> CORINFO2s
 +
echo "" >> CORINFO2s
 +
 
 +
##############
 +
First::
 +
cp $(INITIAL).3d $(TARGET).ref3d
 +
touch *.roi
 +
 
 +
All::
 +
make $(TARGET).ref2d;
 +
make ROIs;
 +
make $(JOP_NUM) pad;
 +
make PADs;
 +
make $(JOP_NUM) corinfo;
 +
make CORINFOs;
 +
make $(JOP_NUM) 3dinfo;
 +
make 3DINFOs;
 +
make $(JOP_NUM) 3dlst;
 +
make 3DLIST;
 +
make $(TARGET).3d;
 +
 
 +
Again::
 +
touch *.pad
 +
cp $(TARGET).3d $(TARGET).ref3d;
 +
TMPNAME=`date +%y%m%d%H%M%S`; \
 +
mv $(TARGET).3dlst  $(TARGET).3dlst.$$TMPNAME; \
 +
mv $(TARGET).3d      $(TARGET).3d.$$TMPNAME; \
 +
mv $(TARGET).3dsm    $(TARGET).3dsm.$$TMPNAME; \
 +
mv $(TARGET).ds6    $(TARGET).ds6.$$TMPNAME; \
 +
mv $(TARGET).3dsmds6 $(TARGET).3dsmds6.$$TMPNAME;
 +
 +
 
 +
#### Prepare Reference ####
 +
 
 +
.ref3d.ref2d:
 +
mrc3Dto2D -i $(TARGET).ref3d -o $(TARGET).ref2d -EulerMode $(ROTMODE) -InterpolationMode 2 -Rot2 $(ROT2MIN) $(ROT2MAX) $(ROT2D) -Rot1 $(ROT1MIN) $(ROT1MAX) $(ROT1D) -Rot3 $(ROT3MIN) $(ROT3MAX) $(ROT3D) -m 0
 +
 
 +
.roi.pad:
 +
mrcImageWindowing -i $*.roi -o $*.mask -W 0.1 0.0 0.05 0.0 -m 18
 +
mrcImagePad -i $*.mask -o $*.padtmp -W $(PAD_W) -H $(PAD_H) -m 3
 +
mrcImageWindowing -i $*.padtmp -o $*.pad -W 0.1 0.0 0.1 0.0 -m 2
 +
 
 +
.pad.corinfo:
 +
mrcImageAutoRotationCorrelation -i $*.pad -r $(TARGET).ref2d -O $*.corinfo -fit $*.fit -cor $*.cormap -n $(nRot) -m 18 -range $(ROTMIN) $(ROTMAX) -Iter 2 -nRot2 $(nRot2) -nRot1 $(nRot1) -nRot3 $(nRot3) 2> /dev/null
 +
 
 +
##############################################################################
 +
 
 +
 
 +
.corinfo.3dinfo:
 +
awk '/Cor/ { print $$7,$$16,$$2,$$3,$$4,$$5,$$9,$$11,$$12}' $*.corinfo | sort -r | sed -e s/.pad/.fit/ > $*.3dinfolst
 +
head -n 1 $*.3dinfolst | awk '{print $$2,$$3,$$4,$$5,$$6,$$1}' > $*.3dinfo
 +
##  ##18 -> ##7  ##
 +
 
 +
.3dinfo.3dlst:
 +
cat $*.3dinfo >> $(TARGET).3dlst
 +
 +
.3dlst.3d:
 +
mrc2Dto3D -I $(TARGET).3dlst -o $(TARGET).3d -InterpolationMode 2 -Double -DoubleCounter $(TARGET).3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2
 +
 
 +
.3d.3dsm:
 +
mrcImageSmoothing -i $(TARGET).3d -o $(TARGET).3dsm -m 1 -M 1 -r 3
 +
 
 +
.3dsm.3dsmCenter:
 +
mrcImageCenterGet -i $(TARGET).3dsm -o $(TARGET).3dsmCenter -Nx 128 -Ny 128 -Nz 128
 +
 
 +
.3dsmCenter.ds6:
 +
mrc2map -i $(TARGET).3dsmCenter -o $(TARGET).ds6 -m 3
 +
 
 +
.3d.ds6:
 +
mrc2map -i $*.3d -o $*.ds6 -m 0
 +
 
 +
#####Select Particles#####
 +
 
 +
.corinfo.corinfo2:
 +
awk '/Cor/ { print $$18,$$16,$$2,$$3,$$4,$$5,$$9,$$11,$$12}' $*.corinfo | sort -r | sed -e 's/.roi/.fit/' > $*.corinfolst
 +
head -n 1 $*.corinfolst | awk '{if($(PAD_W)-$$8>=$$8&&$(PAD_H)-$$9>=$$9) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,0+$$8,0+$$9;else if($(PAD_W)-$$8>=$$8) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,0+$$8,$(PAD_H)-$$9;else if($(PAD_H)-$$9>=$$9) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$(PAD_W)-$$8,0+$$9;else print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$(PAD_W)-$$8,$(PAD_H)-$$9}' > $*.corinfo2
 +
 
 +
.corinfo2.parcorinfolst:
 +
cat $*.corinfo2 >> $(TARGET).parcorinfolst
 +
 
 +
CorinfoSort::
 +
awk '{ print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$$8,$$9}' $(TARGET).parcorinfolst | sort -r > $(TARGET).parcorinfolstsort
 +
 
 +
SelectParticle::
 +
awk '$$1 >= $(COR_THRESHOLD) || $$9 <= $(Y_SHIFT_THRESHOLD){print $$2,$$3,$$4,$$5,$$6,$$1}' $(TARGET).parcorinfolstsort > $(TARGET).3dlstselect
 +
 
 +
 
 +
#####Check alignment#####
 +
 
 +
GnuplotCorinfo::
 +
awk '{ print $$1,$$9}' $(TARGET).parcorinfolst | sort -r > $(TARGET).gnuplotcorinfolst
 +
####################################################
 +
##gnuplot
 +
##set out "Corinfo.ps"
 +
##plot "$(TARGET).gnuplotcorinfolst"
 +
###################################################
 +
 
 +
GnuplotAngle::
 +
awk '{ print $$4,$$5}' $(TARGET).parcorinfolst > $(TARGET).gnuplotanglelst
 +
######################################################
 +
##gnuplot
 +
##set out "Angle.ps"
 +
##plot "$(TARGET).gnuplotanglelst"
 +
######################################################
 +
 
 +
GnuplotShift::
 +
awk '{ print $$4,$$5}' $(TARGET).parcorinfolst > $(TARGET).gnuplotshiftlst
 +
######################################################
 +
##gnuplot
 +
##set out "Shift.ps"
 +
##plot "$(TARGET).gnuplotshiftlst"
 +
###################################################### 
 +
 
 +
MontageList::
 +
awk '{ print $$1}' $(TARGET).3dlst > $(TARGET).monlst
 +
mrcImageMontageCreate -i $(TARGET).monlst -o $(TARGET).mon -nx 15 -ny 10
 +
 
 +
</pre>

2012年9月28日 (金) 20:25時点における版

　参照付投影角度の決定のためには、参照像が必要です。手順を下記に述べます。

１．参照像（３次元）を準備する

２．参照像（２次元）を３次元像から参照投影像として作成する。それぞれの参照投影像は角度が決定されています。

３．切り出した２次元投影画像と２で作成した参照投影像とを比較して、一番似ている参照投影像を選択し、それぞれの２次元画像の投影角として推定します。その際、参照画像に一番適合した位置、回転方向に投影像を回転及び移動し、３次元再構成のための投影像のセットを手に入れいます。

４．推定した投影角を用いて、３次元再構成のための投影像のセットから３次元再構成を行います。

似ている画像の決定方法

　最も利用されるのは、相関関数を用いた方法です。この相関関数の前処理等を行い、ノイズによる影響を抑えることで、よりよい相関を得るように工夫が必要です。 　相関関数そのものも今後更に検討が必要だと思います。

Eosによる実現方法

　演習では、Eosをつかった３次元再構成法の一例を示しています。下記に利用したMakefileを示します。 

#
# Eos for 3D reconstrucion from 2D rois using 3D initail reference 
#

.SUFFIXES: .3d .ref3d .ref2d .pad .padtmp .mask .maskfit .fit .fitmask .roi .corinfo .3dinfo .3dlst .3d .3dsm .3dsmCenter .ds6 .3dsmds6 .corinfo2 .corinfolst .cormap .parcorinfolst .parcorinfolstsort .gnuplotcorinfolst .3dlstselect .monlst .mon

SHELL=/bin/bash

-include ROIs
-include CORINFOs
-include PADs
-include 3DINFOs
-include 3DLIST
-include CORINFO2s

#
# Initial Reference Model 
INITIAL=initial
# Target structure name 
TARGET=all

# Simultaneous Jobs for AutoRotaionCorrelation
JOP_NUM=-j 3

#
# Search Area for 3D
#
ROTMODE=YOYS
# Rot1
ROT1MIN=0
ROT1MAX=359
ROT1D=30
nRot1=12
#
ROT2MIN=0
ROT2MAX=359
ROT2D=30
nRot2=12
# Rot3
ROT3MIN=0
ROT3MAX=0
ROT3D=30
nRot3=1
# For 2D 
STEP=12
ROTMIN=0
ROTMAX=359
nROT=`echo "" | awk 'BEGIN {printf 360 / $(STEP)}'`

# Seletion Step 
COR_THRESHOLD=0.4
Y_SHIFT_THRESHOLD=20

# Pad size for 2D 
PAD_W=64
PAD_H=64

###
### Initial model from PDB
###
REFSOURCE=121p-shift
DELTA=2.5
SIZE_X=64
SIZE_Y=64
SIZE_Z=64
START_X=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_X)/2}'`
START_Y=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_Y)/2}'`
START_Z=`awk 'BEGIN { print -1*$(DELTA)*$(SIZE_Z)/2}'`
SNRATIO=3
###############################

Help::
	@echo "----- Makefile for Single Particle with Reference"
	@echo "1. Prepare files from EM images, which has a suffix of roi "
	@echo "2. Prepare an initial model as $(INITIAL).3d "
	@echo "3. make First"
	@echo "4. make All"
	@echo "If you want to repeat refinement again, "
	@echo "  1. make Again"
	@echo "  2. make All"
	@echo ""
	@echo "--- If you want to create an initail model from PDB ---"
	@echo " make InitialModel"
	@echo ""
	@echo "--- If you want to create an test from the initial model ---"
	@echo " make TestData"

pad:$(ROIs:.roi=.pad)
corinfo:$(PADs:.pad=.corinfo)
3dinfo:$(CORINFOs:.corinfo=.3dinfo)
fit:$(ROIs:.roi=.fit)
3dlst:$(3DINFOs:.3dinfo=.3dlst)
3d:$(3DLIST:.3dlst=.3d)
corinfo2:$(CORINFOs:.corinfo=.corinfo2)
parcorinfolst:$(CORINFO2s:.corinfo2=.parcorinfolst)

#
#
#
InitialModel::
	pdb2mrc -i $(REFSOURCE).pdb -o $(INITIAL).3d -nx $(SIZE_X) -ny $(SIZE_Y) -nz $(SIZE_Z) -Sx $(START_X) -Sy $(START_Y) -Sz $(START_Z) -dx $(DELTA) -dy $(DELTA) -dz $(DELTA) -m 1

TestData::
	@for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D)*2 )) \
	do \
	for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D)*2 )) \
	do \
	for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D)*2 )) \
	do \
		echo $$rot1, $$rot2, $$rot3; \
		mrc3Dto2D -i $(INITIAL).3d -o $(REFSOURCE)-$$rot1-$$rot2-$$rot3.roi \
				  -InterpolationMode 2 -EulerMode $(ROTMODE) \
				  -Rot1 $$rot1 $$rot1 1 \
				  -Rot2 $$rot2 $$rot2 1 \
				  -Rot3 $$rot3 $$rot3 1 ; \
	done \
	done \
	done

TestDataNoise::
	@for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D)*2 )) \
	do \
	for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D)*2 )) \
	do \
	for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D)*2 )) \
	do \
		echo $$rot1, $$rot2, $$rot3; \
		name="$(REFSOURCE)-noise-$$rot1-$$rot2-$$rot3.roi"; \
		mrc3Dto2D -i $(INITIAL).3d -o $$name.noNoise \
				  -InterpolationMode 2 -EulerMode $(ROTMODE) \
				  -Rot1 $$rot1 $$rot1 1 \
				  -Rot2 $$rot2 $$rot2 1 \
				  -Rot3 $$rot3 $$rot3 1 ; \
		mrcImageNoiseAdd -i $$name.noNoise -o $$name -SN $(SNRATIO) ; \
		rm $$name.noNoise ; \
	done \
	done \
	done

##############
ROIs::
	touch ROIs
	echo "ROIs=\\" > ROIs
	#find -name "*.roi" -type f | sed s/..// | xargs ls -1 | sed s/roi/roi\\\\/ >> ROIs
	ls -1 *.roi |  sed s/roi/roi\\\\/ >> ROIs
	echo "" >> ROIs

CORINFOs::
	touch CORINFOs
	echo "CORINFOs=\\" > CORINFOs
	#find -name "*.corinfo" -type f | sed s/..// | xargs ls -1 | sed s/corinfo/corinfo\\\\/ >> CORINFOs
	ls -1 *.corinfo |  sed s/corinfo/corinfo\\\\/ >> CORINFOs
	echo "" >> CORINFOs

PADs::
	touch PADs
	echo "PADs=\\" > PADs
	#find -name "*.pad" -type f | sed s/..// | xargs ls -1 | sed s/pad/pad\\\\/ >> PADs
	ls -1 *.pad |  sed s/pad/pad\\\\/ >> PADs
	echo "" >> PADs

3DINFOs::
	touch 3DINFOs
	echo "3DINFOs=\\" > 3DINFOs
	#find -name "*.3dinfo" -type f | sed s/..// | xargs ls -1 | sed s/3dinfo/3dinfo\\\\/ >> 3DINFOs
	ls -1 *.3dinfo | sed s/3dinfo/3dinfo\\\\/ >> 3DINFOs
	echo "" >> 3DINFOs

3DLIST::
	touch 3DLIST
	echo "3DLIST=\\" > 3DLIST
	#find -name "*.3dlst" -type f | sed s/..// | xargs ls -1 | sed s/3dlst/3dlst\\\\/ >> 3DLIST
	ls -1 *.3dlst |  sed s/3dlst/3dlst\\\\/ >> 3DLIST
	echo "" >> 3DLIST

CORINFO2s::
	touch CORINFO2s
	echo "CORINFO2s=\\" > CORINFO2s
	#find -name "*.corinfo2" -type f | sed s/..// | xargs ls -1 | sed s/corinfo2/corinfo2\\\\/ >> CORINFO2s
	ls -1 *.corinfo2 | sed s/corinfo2/corinfo2\\\\/ >> CORINFO2s
	echo "" >> CORINFO2s

##############
First::
	cp $(INITIAL).3d $(TARGET).ref3d
	touch *.roi

All::
	make $(TARGET).ref2d;
	make ROIs;
	make $(JOP_NUM) pad;
	make PADs;
	make $(JOP_NUM) corinfo;
	make CORINFOs;
	make $(JOP_NUM) 3dinfo;
	make 3DINFOs;
	make $(JOP_NUM) 3dlst;
	make 3DLIST;
	make $(TARGET).3d;

Again::
	touch *.pad
	cp $(TARGET).3d $(TARGET).ref3d;
	TMPNAME=`date +%y%m%d%H%M%S`;	\
	mv $(TARGET).3dlst   $(TARGET).3dlst.$$TMPNAME;	\
	mv $(TARGET).3d      $(TARGET).3d.$$TMPNAME;	\
	mv $(TARGET).3dsm    $(TARGET).3dsm.$$TMPNAME;	\
	mv $(TARGET).ds6     $(TARGET).ds6.$$TMPNAME;	\
	mv $(TARGET).3dsmds6 $(TARGET).3dsmds6.$$TMPNAME;	
	

#### Prepare Reference ####

.ref3d.ref2d:
	mrc3Dto2D -i $(TARGET).ref3d -o $(TARGET).ref2d -EulerMode $(ROTMODE) -InterpolationMode 2 -Rot2 $(ROT2MIN) $(ROT2MAX) $(ROT2D) -Rot1 $(ROT1MIN) $(ROT1MAX) $(ROT1D) -Rot3 $(ROT3MIN) $(ROT3MAX) $(ROT3D) -m 0

.roi.pad:
	mrcImageWindowing -i $*.roi -o $*.mask -W 0.1 0.0 0.05 0.0 -m 18
	mrcImagePad -i $*.mask -o $*.padtmp -W $(PAD_W) -H $(PAD_H) -m 3
	mrcImageWindowing -i $*.padtmp -o $*.pad -W 0.1 0.0 0.1 0.0 -m 2 

.pad.corinfo:
	mrcImageAutoRotationCorrelation -i $*.pad -r $(TARGET).ref2d -O $*.corinfo -fit $*.fit -cor $*.cormap -n $(nRot) -m 18 -range $(ROTMIN) $(ROTMAX) -Iter 2 -nRot2 $(nRot2) -nRot1 $(nRot1) -nRot3 $(nRot3) 2> /dev/null

##############################################################################


.corinfo.3dinfo:
	awk '/Cor/ { print $$7,$$16,$$2,$$3,$$4,$$5,$$9,$$11,$$12}' $*.corinfo | sort -r | sed -e s/.pad/.fit/ > $*.3dinfolst
	head -n 1 $*.3dinfolst | awk '{print $$2,$$3,$$4,$$5,$$6,$$1}' > $*.3dinfo
##   ##18 -> ##7  ##

.3dinfo.3dlst:
	cat $*.3dinfo >> $(TARGET).3dlst		
	
.3dlst.3d:
	mrc2Dto3D -I $(TARGET).3dlst -o $(TARGET).3d -InterpolationMode 2 -Double -DoubleCounter $(TARGET).3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2

.3d.3dsm:
	mrcImageSmoothing -i $(TARGET).3d -o $(TARGET).3dsm -m 1 -M 1 -r 3

.3dsm.3dsmCenter:
	mrcImageCenterGet -i $(TARGET).3dsm -o $(TARGET).3dsmCenter -Nx 128 -Ny 128 -Nz 128

.3dsmCenter.ds6:
	mrc2map -i $(TARGET).3dsmCenter -o $(TARGET).ds6 -m 3

.3d.ds6:
	mrc2map -i $*.3d -o $*.ds6 -m 0 

#####Select Particles#####

.corinfo.corinfo2:
	awk '/Cor/ { print $$18,$$16,$$2,$$3,$$4,$$5,$$9,$$11,$$12}' $*.corinfo | sort -r | sed -e 's/.roi/.fit/' > $*.corinfolst
	head -n 1 $*.corinfolst | awk '{if($(PAD_W)-$$8>=$$8&&$(PAD_H)-$$9>=$$9) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,0+$$8,0+$$9;else if($(PAD_W)-$$8>=$$8) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,0+$$8,$(PAD_H)-$$9;else if($(PAD_H)-$$9>=$$9) print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$(PAD_W)-$$8,0+$$9;else print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$(PAD_W)-$$8,$(PAD_H)-$$9}' > $*.corinfo2

.corinfo2.parcorinfolst:
	cat $*.corinfo2 >> $(TARGET).parcorinfolst

CorinfoSort::
	awk '{ print $$1,$$2,$$3,$$4,$$5,$$6,$$7,$$8,$$9}' $(TARGET).parcorinfolst | sort -r > $(TARGET).parcorinfolstsort

SelectParticle::
	awk '$$1 >= $(COR_THRESHOLD) || $$9 <= $(Y_SHIFT_THRESHOLD){print $$2,$$3,$$4,$$5,$$6,$$1}' $(TARGET).parcorinfolstsort > $(TARGET).3dlstselect


#####Check alignment#####

GnuplotCorinfo::
	awk '{ print $$1,$$9}' $(TARGET).parcorinfolst | sort -r > $(TARGET).gnuplotcorinfolst
####################################################
	##gnuplot 
	##set out "Corinfo.ps" 
	##plot "$(TARGET).gnuplotcorinfolst"
###################################################

GnuplotAngle::
	awk '{ print $$4,$$5}' $(TARGET).parcorinfolst > $(TARGET).gnuplotanglelst
######################################################
	##gnuplot
	##set out "Angle.ps"
	##plot "$(TARGET).gnuplotanglelst"
######################################################	

GnuplotShift::
	awk '{ print $$4,$$5}' $(TARGET).parcorinfolst > $(TARGET).gnuplotshiftlst
######################################################
	##gnuplot
	##set out "Shift.ps"
	##plot "$(TARGET).gnuplotshiftlst"
######################################################  

MontageList::
	awk '{ print $$1}' $(TARGET).3dlst > $(TARGET).monlst
	mrcImageMontageCreate -i $(TARGET).monlst -o $(TARGET).mon -nx 15 -ny 10

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