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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revision1d82a210d19beb73a3dfc1ccec0b6a9311dabfa9 (tree)
Time2014-08-26 12:49:29
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Modify and Add tutorial data of Tomography

Modify: support to mrcImageCorrelation's(-corInfo) version up.
modified: Tomography/Tomography4/Makefile
modified: Tomography/Tomography5/Makefile
modified: Tomography/Tomography6/Makefile
Modify: Initial Angle data.
modified: Tomography/Tomography6/DataB_0XX.tiltangle
Add Sample of using Radon Transform.
new file: Tomography/Tomography7/0000-d.roilst
new file: Tomography/Tomography7/DataA_0XX-0000.roi
new file: Tomography/Tomography7/DataB_0XX-0000.roi
new file: Tomography/Tomography7/Makefile

Change Summary

Incremental Difference

--- a/Tomography/Tomography4/Makefile
+++ b/Tomography/Tomography4/Makefile
@@ -210,7 +210,7 @@ $(ORIBASE).roiinfo-coarse:
210210
211211 .orimrccentre.oricorinfo:
212212 echo "orimrccentre -> oricorinfo: SHIFT:= current.orimrccentre for prev.oirmrccentre"
213- mrcImageCorrelation -i $*.orimrccentre -r $*.oriref -c $*.oricorinfo
213+ mrcImageCorrelation -i $*.orimrccentre -r $*.oriref -corInfo $*.oricorinfo
214214
215215 .oricorinfo.roiinfo-coarse:
216216 TOTALX=`awk '/TotalPrev:/ { print $$2 }' $*.oricorinfo`; \
@@ -281,7 +281,7 @@ CleanBoxCreate::
281281 touch $*.roiallref
282282
283283 .roi.corinfo:
284- mrcImageCorrelation -i $*.roi -r $*.ref -c $*.corinfo
284+ mrcImageCorrelation -i $*.roi -r $*.ref -corInfo $*.corinfo
285285
286286 .roiinforef.roiinfo:
287287 # Extract ROIs using roiinfo of previous image (roiinforef)
--- a/Tomography/Tomography5/Makefile
+++ b/Tomography/Tomography5/Makefile
@@ -573,7 +573,7 @@ $(ORIFILE2)_0$(ZEROTILTNUM).roiinfo-coarse:
573573 ### Calculate Correlation between primrccentre and oriref
574574 .orimrccentre.oricorinfo:
575575 echo "orimrccentre -> oricorinfo: SHIFT:= current.orimrccentre for prev.oirmrccentre"
576- mrcImageCorrelation -i $*.orimrccentre -r $*.oriref -c $*.oricorinfo -o $*.oricormap -m $(CORMODE) -s $*.orishift
576+ mrcImageCorrelation -i $*.orimrccentre -r $*.oriref -corInfo $*.oricorinfo -o $*.oricormap -m $(CORMODE) -s $*.orishift
577577
578578 ### Create roiinfo for ROI(centre)
579579 .oricorinfo.roiinfo-coarse:
@@ -715,7 +715,7 @@ CleanRoiDisplay::
715715
716716 .roi.corinfo:
717717 mrcImageWindowing -i $*.ref -o $*.refwin -W 0.35 0.2 0.35 0.2 -m 18
718- mrcImageCorrelation -i $*.roi -r $*.refwin -c $*.corinfo -m $(CORMODE)
718+ mrcImageCorrelation -i $*.roi -r $*.refwin -corInfo $*.corinfo -m $(CORMODE)
719719
720720 .roiinforef.roiinfo:
721721 # Extract ROIs using roiinfo of previous image (roiinforef)
--- a/Tomography/Tomography6/DataB_000.tiltangle
+++ b/Tomography/Tomography6/DataB_000.tiltangle
@@ -1 +1 @@
1-0
1+-60
--- a/Tomography/Tomography6/DataB_001.tiltangle
+++ b/Tomography/Tomography6/DataB_001.tiltangle
@@ -1 +1 @@
1-0
1+-50
--- a/Tomography/Tomography6/DataB_002.tiltangle
+++ b/Tomography/Tomography6/DataB_002.tiltangle
@@ -1 +1 @@
1-0
1+-40
--- a/Tomography/Tomography6/DataB_003.tiltangle
+++ b/Tomography/Tomography6/DataB_003.tiltangle
@@ -1 +1 @@
1-0
1+-30
--- a/Tomography/Tomography6/DataB_004.tiltangle
+++ b/Tomography/Tomography6/DataB_004.tiltangle
@@ -1 +1 @@
1-0
1+-20
--- a/Tomography/Tomography6/DataB_005.tiltangle
+++ b/Tomography/Tomography6/DataB_005.tiltangle
@@ -1 +1 @@
1-0
1+-10
--- a/Tomography/Tomography6/DataB_007.tiltangle
+++ b/Tomography/Tomography6/DataB_007.tiltangle
@@ -1 +1 @@
1-0
1+10
--- a/Tomography/Tomography6/DataB_008.tiltangle
+++ b/Tomography/Tomography6/DataB_008.tiltangle
@@ -1 +1 @@
1-0
1+20
--- a/Tomography/Tomography6/DataB_009.tiltangle
+++ b/Tomography/Tomography6/DataB_009.tiltangle
@@ -1 +1 @@
1-0
1+30
--- a/Tomography/Tomography6/DataB_010.tiltangle
+++ b/Tomography/Tomography6/DataB_010.tiltangle
@@ -1 +1 @@
1-0
1+40
--- a/Tomography/Tomography6/DataB_011.tiltangle
+++ b/Tomography/Tomography6/DataB_011.tiltangle
@@ -1 +1 @@
1-0
1+50
--- a/Tomography/Tomography6/DataB_012.tiltangle
+++ b/Tomography/Tomography6/DataB_012.tiltangle
@@ -1 +1 @@
1-0
1+60
--- a/Tomography/Tomography6/Makefile
+++ b/Tomography/Tomography6/Makefile
@@ -573,7 +573,7 @@ $(ORIFILE2)_0$(ZEROTILTNUM).roiinfo-coarse:
573573 ### Calculate Correlation between primrccentre and oriref
574574 .orimrccentre.oricorinfo:
575575 echo "orimrccentre -> oricorinfo: SHIFT:= current.orimrccentre for prev.oirmrccentre"
576- mrcImageCorrelation -i $*.orimrccentre -r $*.oriref -c $*.oricorinfo -o $*.oricormap -m $(CORMODE) -s $*.orishift
576+ mrcImageCorrelation -i $*.orimrccentre -r $*.oriref -corInfo $*.oricorinfo -o $*.oricormap -m $(CORMODE) -s $*.orishift
577577
578578 ### Create roiinfo for ROI(centre)
579579 .oricorinfo.roiinfo-coarse:
@@ -715,7 +715,7 @@ CleanRoiDisplay::
715715
716716 .roi.corinfo:
717717 mrcImageWindowing -i $*.ref -o $*.refwin -W 0.35 0.2 0.35 0.2 -m 18
718- mrcImageCorrelation -i $*.roi -r $*.refwin -c $*.corinfo -m $(CORMODE)
718+ mrcImageCorrelation -i $*.roi -r $*.refwin -corInfo $*.corinfo -m $(CORMODE)
719719
720720 .roiinforef.roiinfo:
721721 # Extract ROIs using roiinfo of previous image (roiinforef)
--- /dev/null
+++ b/Tomography/Tomography7/0000-d.roilst
@@ -0,0 +1,25 @@
1+DataA_000-0000.roi ZEYS -0.000000 -60.000000 0.000000
2+DataA_001-0000.roi ZEYS -0.000000 -50.000000 0.000000
3+DataA_002-0000.roi ZEYS -0.000000 -40.000000 0.000000
4+DataA_003-0000.roi ZEYS -0.000000 -30.000000 0.000000
5+DataA_004-0000.roi ZEYS -0.000000 -20.000000 0.000000
6+DataA_005-0000.roi ZEYS -0.000000 -10.000000 0.000000
7+DataA_006-0000.roi ZEYS -0.000000 0.000000 0.000000
8+DataA_007-0000.roi ZEYS -0.000000 10.000000 0.000000
9+DataA_008-0000.roi ZEYS -0.000000 20.000000 0.000000
10+DataA_009-0000.roi ZEYS -0.000000 30.000000 0.000000
11+DataA_010-0000.roi ZEYS -0.000000 40.000000 0.000000
12+DataA_011-0000.roi ZEYS -0.000000 50.000000 0.000000
13+DataA_012-0000.roi ZEYS -0.000000 60.000000 0.000000
14+DataB_000-0000.roi ZEYS -0.000000 0.000000 -60.000000
15+DataB_001-0000.roi ZEYS -0.000000 0.000000 -50.000000
16+DataB_002-0000.roi ZEYS -0.000000 0.000000 -40.000000
17+DataB_003-0000.roi ZEYS -0.000000 0.000000 -30.000000
18+DataB_004-0000.roi ZEYS -0.000000 0.000000 -20.000000
19+DataB_005-0000.roi ZEYS -0.000000 0.000000 -10.000000
20+DataB_007-0000.roi ZEYS -0.000000 0.000000 10.000000
21+DataB_008-0000.roi ZEYS -0.000000 0.000000 20.000000
22+DataB_009-0000.roi ZEYS -0.000000 0.000000 30.000000
23+DataB_010-0000.roi ZEYS -0.000000 0.000000 40.000000
24+DataB_011-0000.roi ZEYS -0.000000 0.000000 50.000000
25+DataB_012-0000.roi ZEYS -0.000000 0.000000 60.000000
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--- /dev/null
+++ b/Tomography/Tomography7/Makefile
@@ -0,0 +1,348 @@
1+#
2+# This is a sample Makefile for electron tomography.
3+#
4+
5+#### Input extention and listname ####
6+# For mrcImageCorrelation
7+IN_CORR_EXT=mask
8+
9+# For mrc2tiff
10+IN_TIFF_EXT=fit
11+
12+# For mrcImageNoiseAdd
13+IN_NOISE_EXT=roi
14+
15+# For mrcImageWindowing
16+IN_MASK_EXT=nroi
17+
18+# For mrcImageTiltAxisSearch
19+IN_TILT_EXT=roi
20+
21+# For Reconstruction
22+#IN_3D_EXT=fit
23+IN_3D_EXT=roi
24+IN_LIST_EXT=roilst
25+
26+#### INCLUDE ####
27+.SUFFIXES: .roi .nroi .mask .tiff .3dlst .3d .fit .tiltinfo .sino .sinolst .3dradon .$(IN_TIFF_EXT) .$(IN_CORR_EXT) .$(IN_NOISE_EXT) .$(IN_MASK_EXT) .$(IN_TILT_EXT) .$(IN_TILT_EXT)tmp .$(IN_3D_EXT)
28+
29+SHELL=/bin/bash
30+
31+-include IN_NOISE_LIST
32+-include IN_MASK_LIST
33+-include IN_CORR_LIST_plus
34+-include IN_CORR_LIST_minus
35+-include IN_3D_LIST
36+-include IN_TIFF_LIST
37+
38+#### Definition ####
39+
40+# Initial Reference Model
41+#INITIAL=Initial
42+INITIAL=1WDC-shift1
43+#INITIAL=1WDC-9Set
44+# Target structure name
45+TARGET=0000-d
46+
47+### For mrc3Dto2D
48+# RotMode
49+ROTMODE=YOYR
50+#ROTMODE=ZOYS
51+# Rot1
52+ROT1MIN=0
53+ROT1MAX=0
54+ROT1D=10
55+ROT1N=`expr \( $(ROT1MAX) - $(ROT1MIN) \) / $(ROT1D) + 1`
56+# Rot2
57+ROT2MIN=-60
58+ROT2MAX=60
59+ROT2D=10
60+ROT2N=`expr \( $(ROT2MAX) - $(ROT2MIN) \) / $(ROT2D) + 1`
61+# Rot3
62+ROT3MIN=-60
63+ROT3MAX=60
64+ROT3D=10
65+ROT3N=`expr \( $(ROT3MAX) - $(ROT3MIN) \) / $(ROT3D) + 1`
66+# Expansion mode
67+# 0:Mercator 1:Mollweide
68+EX_MODE=1
69+# Interpolation mode : Common with mrc2Dto3D
70+IN_MODE=2
71+
72+### For mrcImageMove
73+SHIFT2MAX=5
74+SHIFT3MAX=10
75+
76+### For mrcImageNoiseAdd
77+SNRATIO=3
78+
79+# For mrcImageWindowing
80+MASK_X=0.2
81+MASK_X_MAX=0.2
82+MASK_Y=0.1
83+MASK_Y_MAX=0.1
84+MASK_MODE=18
85+
86+### For mrcImageCorrelation
87+# mode
88+COR_MODE=18
89+# Reference angle: Rot2, 3 is Usually 0
90+ROT1REF=$(ROT1MIN)
91+ROT2REF=0
92+ROT3REF=0
93+
94+### For mrcImageTiltAxisSearch
95+TILTMIN=-10
96+TILTMAX=10
97+TILTN=10
98+TILTITER=100
99+TILTSCALE=5
100+
101+### For mrc2Dto3D
102+# mode
103+# 0:Simple Back Projection 1:Filter Back Projection
104+PRJ_MODE=1
105+# single (Tilt Axis)
106+# 0:X-axis 1:Y-axis
107+AXIS1=1
108+
109+### RadonTransform
110+PD=2.5
111+PHID=10
112+THETAD=10
113+RBP_MODE=1
114+#RBP_OPTION=-Rmin 0.05 -Rmax 0.1
115+
116+#### For Works ####
117+JOP_NUM=-j 3
118+
119+nroi:$(IN_NOISE_LIST:.$(IN_NOISE_EXT)=.nroi)
120+mask:$(IN_MASK_LIST:.$(IN_MASK_EXT)=.mask)
121+fit_plus:$(IN_CORR_LIST_plus:.$(IN_CORR_EXT)=.fit)
122+fit_minus:$(IN_CORR_LIST_minus:.$(IN_CORR_EXT)=.fit)
123+sino:$(IN_3D_LIST:.$(IN_3D_EXT)=.sino)
124+tiff:$(IN_TIFF_LIST:.$(IN_TIFF_EXT)=.tiff)
125+
126+IN_NOISE_LIST::
127+ touch IN_NOISE_LIST
128+ echo "IN_NOISE_LIST=\\" > IN_NOISE_LIST
129+ ls -1 *.$(IN_NOISE_EXT) | sed s/$(IN_NOISE_EXT)/$(IN_NOISE_EXT)\\\\/ >> IN_NOISE_LIST
130+ echo "" >> IN_NOISE_LIST
131+
132+IN_MASK_LIST::
133+ touch IN_MASK_LIST
134+ echo "IN_MASK_LIST=\\" > IN_MASK_LIST
135+ ls -1 *.$(IN_MASK_EXT) | sed s/$(IN_MASK_EXT)/$(IN_MASK_EXT)\\\\/ >> IN_MASK_LIST
136+ echo "" >> IN_MASK_LIST
137+
138+IN_TILT_LIST::
139+ touch IN_TILT_LIST
140+ rm IN_TILT_LIST
141+ ls -1 *.$(IN_TILT_EXT) >> IN_TILT_LIST
142+
143+IN_3D_LIST::
144+ touch IN_3D_LIST
145+ echo "IN_3D_LIST=\\" > IN_3D_LIST
146+ ls -1 *.$(IN_3D_EXT) | sed s/$(IN_3D_EXT)/$(IN_3D_EXT)\\\\/ >> IN_3D_LIST
147+ echo "" >> IN_3D_LIST
148+
149+IN_TIFF_LIST::
150+ touch IN_TIFF_LIST
151+ echo "IN_TIFF_LIST=\\" > IN_TIFF_LIST
152+ ls -1 *.$(IN_TIFF_EXT) | sed s/$(IN_TIFF_EXT)/$(IN_TIFF_EXT)\\\\/ >> IN_TIFF_LIST
153+ echo "" >> IN_TIFF_LIST
154+
155+#### Commands ####
156+Help::
157+ @echo "This is a sample Makefile for electron tomography."
158+
159+TestData::
160+ @for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D) )) \
161+ do \
162+ for (( rot2 = $(ROT2MIN), shift2 = -$(SHIFT2MAX); rot2 <= $(ROT2MAX); rot2 += $(ROT2D), shift2 = ( ( $$rot2 + $(ROT2D) ) * $(SHIFT2MAX) ) / ( $(ROT2MAX) + 1 ) )) \
163+ do \
164+ for (( rot3 = $(ROT3MIN), shift3 = -$(SHIFT3MAX); rot3 <= $(ROT3MAX); rot3 += $(ROT3D), shift3 = ( ( $$rot3 + $(ROT3D) ) * $(SHIFT3MAX) ) / ( $(ROT3MAX) + 1 ) )) \
165+ do \
166+ echo $$rot1, $$rot2, $$rot3, $$shift2, $$shift3; \
167+ mrc3Dto2D -i $(INITIAL).3d -o $(TARGET)-$$rot1-$$rot2-$$rot3.roitmp \
168+ -InterpolationMode $(IN_MODE) -EulerMode $(ROTMODE) \
169+ -Rot1 $$rot1 $$rot1 1 \
170+ -Rot2 $$rot2 $$rot2 1 \
171+ -Rot3 $$rot3 $$rot3 1 ; \
172+ mrcImageMove -i $(TARGET)-$$rot1-$$rot2-$$rot3.roitmp -o $(TARGET)-$$rot1-$$rot2-$$rot3.roi \
173+ -x $$shift2 \
174+ -y $$shift3; \
175+ rm $(TARGET)-$$rot1-$$rot2-$$rot3.roitmp; \
176+ done \
177+ done \
178+ done
179+
180+NoiseAdd::
181+ make IN_NOISE_LIST;
182+ make $(JOP_NUM) nroi;
183+
184+All::
185+ make Windowing;
186+ make CorFit1;
187+ make CorFit2;
188+# make TiltFit;
189+ make 3D;
190+ make Radon3D;
191+
192+Windowing::
193+ make IN_MASK_LIST;
194+ make $(JOP_NUM) mask;
195+
196+CorFit1::
197+ cp $(TARGET)-$(ROT1REF)-$(ROT2REF)-$(ROT3REF).$(IN_CORR_EXT) $(TARGET)-$(ROT1REF)-$(ROT2REF)-$(ROT3REF).fit
198+ cp $(TARGET)-$(ROT1REF)-$(ROT2REF)-$(ROT3REF).$(IN_CORR_EXT) $(TARGET).tmp;
199+ make IN_CORR_LIST1;
200+ make fit_plus;
201+ make fit_minus;
202+ rm $(TARGET).tmp;
203+
204+IN_CORR_LIST1::
205+ touch IN_CORR_LIST_plus;
206+ rm IN_CORR_LIST_plus;
207+ echo "IN_CORR_LIST_plus=\\" > IN_CORR_LIST_plus;
208+ @for (( rot2 = $(ROT2REF) + $(ROT2D) ; rot2 <= $(ROT2MAX); rot2 += $(ROT2D) )) \
209+ do \
210+ echo $(TARGET)-$(ROT1REF)-$$rot2-$(ROT3REF).$(IN_CORR_EXT) | sed s/$(IN_CORR_EXT)/$(IN_CORR_EXT)\\\\/ >> IN_CORR_LIST_plus; \
211+ done
212+ echo "" >> IN_CORR_LIST_plus;
213+
214+ touch IN_CORR_LIST_minus;
215+ rm IN_CORR_LIST_minus;
216+ echo "IN_CORR_LIST_minus=\\" > IN_CORR_LIST_minus;
217+ @for (( rot2 = $(ROT2REF) - $(ROT2D) ; rot2 >= $(ROT2MIN); rot2 -= $(ROT2D) )) \
218+ do \
219+ echo $(TARGET)-$(ROT1REF)-$$rot2-$(ROT3REF).$(IN_CORR_EXT) | sed s/$(IN_CORR_EXT)/$(IN_CORR_EXT)\\\\/ >> IN_CORR_LIST_minus; \
220+ done
221+ echo "" >> IN_CORR_LIST_minus;
222+
223+CorFit2::
224+ @for (( rot2 = $(ROT2MIN) ; rot2 <= $(ROT2MAX); rot2 += $(ROT2D) )) \
225+ do \
226+ export rot2; \
227+ make IN_CORR_LIST2; \
228+ cp $(TARGET)-$(ROT1REF)-$$rot2-$(ROT3REF).fit $(TARGET).tmp; \
229+ make fit_plus; \
230+ make fit_minus; \
231+ done
232+ rm $(TARGET).tmp;
233+
234+IN_CORR_LIST2::
235+ touch IN_CORR_LIST_plus;
236+ rm IN_CORR_LIST_plus;
237+ echo "IN_CORR_LIST_plus=\\" > IN_CORR_LIST_plus;
238+ @for (( rot3 = $(ROT3REF) + $(ROT3D) ; rot3 <= $(ROT3MAX); rot3 += $(ROT3D) )) \
239+ do \
240+ echo $(TARGET)-$(ROT1REF)-$(rot2)-$$rot3.$(IN_CORR_EXT) | sed s/$(IN_CORR_EXT)/$(IN_CORR_EXT)\\\\/ >> IN_CORR_LIST_plus; \
241+ done
242+ echo "" >> IN_CORR_LIST_plus
243+
244+ touch IN_CORR_LIST_minus;
245+ rm IN_CORR_LIST_minus;
246+ echo "IN_CORR_LIST_minus=\\" > IN_CORR_LIST_minus;
247+ @for (( rot3 = $(ROT3REF) - $(ROT3D) ; rot3 >= $(ROT3MIN); rot3 -= $(ROT3D) )) \
248+ do \
249+ echo $(TARGET)-$(ROT1REF)-$(rot2)-$$rot3.$(IN_CORR_EXT) | sed s/$(IN_CORR_EXT)/$(IN_CORR_EXT)\\\\/ >> IN_CORR_LIST_minus; \
250+ done
251+ echo "" >> IN_CORR_LIST_minus;
252+
253+TiltFit::
254+ make IN_TILT_LIST;
255+ @cp $(TARGET)-$(ROT1REF)-$(ROT2REF)-$(ROT3REF).$(IN_TILT_EXT) $(TARGET).$(IN_TILT_EXT)tmp;
256+ make $(TARGET).tiltinfo;
257+
258+3D::
259+ make 3DList;
260+ make $(TARGET).3d;
261+
262+3DList::
263+ touch $(TARGET).3dlst;
264+ touch $(TARGET).tiltinfo;
265+ rm $(TARGET).3dlst;
266+ @for (( rot1 = $(ROT1MIN); rot1 <= $(ROT1MAX); rot1 += $(ROT1D) )) \
267+ do \
268+ for (( rot2 = $(ROT2MIN); rot2 <= $(ROT2MAX); rot2 += $(ROT2D) )) \
269+ do \
270+ for (( rot3 = $(ROT3MIN); rot3 <= $(ROT3MAX); rot3 += $(ROT3D) )) \
271+ do \
272+ echo $(TARGET)-$$rot1-$$rot2-$$rot3.$(IN_3D_EXT) $(ROTMODE) `cat $(TARGET).tiltinfo`0 $$rot2 $$rot3 >> $(TARGET).3dlst; \
273+ done \
274+ done \
275+ done
276+
277+Radon3D::
278+ make RadonList;
279+ make $(JOP_NUM) sino;
280+ make $(TARGET).3dradon;
281+ make $(TARGET).3d;
282+
283+RadonList::
284+ touch IN_3D_LIST;
285+ echo "IN_3D_LIST=\\" > IN_3D_LIST;
286+ awk '{printf("%s\n"), $$1}' $(TARGET).$(IN_LIST_EXT) | sed -e s/.$(IN_3D_EXT)/.$(IN_3D_EXT)\\\\/ >> IN_3D_LIST;
287+ echo "" >> IN_3D_LIST;
288+ sed -e s/.$(IN_3D_EXT)/.sino/ $(TARGET).$(IN_LIST_EXT) > $(TARGET).sinolst;
289+
290+Tiff::
291+ make IN_TIFF_LIST;
292+ make $(JOP_NUM) tiff;
293+
294+3DTiff::
295+ make $(TARGET).tiff
296+
297+Test::
298+ make Radon3D;
299+
300+
301+##### Commands(Input to Output) #####
302+.$(IN_NOISE_EXT).nroi:
303+ mrcImageNoiseAdd -i $*.$(IN_NOISE_EXT) -o $*.nroi -SN $(SNRATIO);
304+
305+.$(IN_MASK_EXT).mask:
306+ mrcImageWindowing -i $*.$(IN_MASK_EXT) -o $*.mask -m $(MASK_MODE) -W $(MASK_X) $(MASK_X_MAX) $(MASK_Y) $(MASK_Y_MAX) 2> /dev/null;
307+
308+.$(IN_CORR_EXT).fit:
309+ mrcImageCorrelation -i $*.$(IN_CORR_EXT) -r $(TARGET).tmp -s $*.fit 2> /dev/null;
310+ cp $*.fit $(TARGET).tmp
311+
312+.$(IN_TILT_EXT)tmp.tiltinfo:
313+ @tiltmax=`expr "scale=$(TILTSCALE); $(TILTMAX)" | bc -l`; \
314+ tiltmin=`expr "scale=$(TILTSCALE); $(TILTMIN)" | bc -l`; \
315+ tiltw=`expr "scale=$(TILTSCALE); $$tiltmax - $$tiltmin" | bc -l`; \
316+ for (( iter = 1; iter <= $(TILTITER); iter += 1 )) \
317+ do \
318+ tiltd=`expr "scale=$(TILTSCALE); $$tiltw / $(TILTN)" | bc -l`; \
319+ mrcImageTiltAxisSearch -I IN_TILT_LIST -r $(TARGET).$(IN_TILT_EXT)tmp -o $(TARGET).tilt -O $(TARGET).tiltinfo -range $$tiltmin $$tiltmax $$tiltd 2> /dev/null; \
320+ tmp_p=`cat $(TARGET).tiltinfo`; \
321+ echo $$tmp_p; \
322+ tiltmin=`expr "scale=$(TILTSCALE); $$tmp_p - ( $$tiltw / 2 )" | bc -l`; \
323+ tiltmax=`expr "scale=$(TILTSCALE); $$tmp_p + ( $$tiltw / 2 )" | bc -l`; \
324+ done;
325+
326+.3dlst.3d:
327+ mrc2Dto3D -I $*.3dlst -o $*.3d -InterpolationMode $(IN_MODE) -m $(PRJ_MODE) -single $(AXIS1);
328+# mrc2Dto3D -I $*.3dlst -o $*.3d -InterpolationMode $(IN_MODE) -m $(PRJ_MODE) -Double;
329+
330+.$(IN_3D_EXT).sino:
331+ mrcImageSinogramCreate -i $*.$(IN_3D_EXT) -o $*.sino -dphi $(PHID);
332+
333+.sinolst.3dradon:
334+ mrcRadon2Dto3D -I $*.sinolst -o $*.3dradon -ow $*.3dradonw -dp $(PD) -dtheta $(THETAD) -dphi $(PHID) -InterpolationMode $(IN_MODE);
335+
336+.3dradon.3d:
337+ mrcImageInverseRadonTransform -i $*.3dradon -o $*.3d -bpm $(RBP_MODE) $(RBP_OPTION);
338+
339+.$(IN_TIFF_EXT).tiff:
340+ mrc2tiff -i $*.$(IN_TIFF_EXT) -o $*.tiff 2> /dev/null;
341+
342+.3d.tiff:
343+ @for (( loop_num = 0; loop_num <= 2; loop_num += 1 )) \
344+ do \
345+ mrcImageProjection -i $(TARGET).3d -o $(TARGET).tmp -m $$loop_num; \
346+ mrc2tiff -i $(TARGET).tmp -o $(TARGET)$$loop_num.tiff; \
347+ done;
348+ rm $(TARGET).tmp;
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