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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revisionc4ed58dcc525b27a55bce9b63f0f0d811457c429 (tree)
Time2014-09-19 16:31:00
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Modify: to be usable at other makefile(include Makefile.config)
modified: CTFCorrection/CTFCorrection1/Makefile
modified: CTFCorrection/CTFCorrection2/Makefile
renamed: CTFCorrection/CTFCorrection2/Makefile -> CTFCorrection/CTFCorrection2/Makefile.config
modified: CTFCorrection/CTFCorrection3/Makefile
renamed: CTFCorrection/CTFCorrection3/Makefile -> CTFCorrection/CTFCorrection3/Makefile.config
new file: CTFCorrection/CTFCorrection4/Input.inimrc
modified: CTFCorrection/CTFCorrection4/Makefile
new file: CTFCorrection/CTFCorrection4/Makefile.config

Change Summary

Incremental Difference

--- a/CTFCorrection/CTFCorrection1/Makefile
+++ b/CTFCorrection/CTFCorrection1/Makefile
@@ -126,7 +126,8 @@ DispCEN:
126126 cat $*.ctfinfoauto >> $*.ctfinfo ; \
127127 fi \
128128 fi
129- ctfDisplay -i $*.fft
129+ $(SHELL_PATH)exe/__old.sh "make TIF2CTF"
130+ $(ENV_SWITCH) ctfDisplay -i $*.fft
130131 mv $@ $@.tmp
131132 grep .: $@.tmp > $@
132133 awk '!/.ctfinfo/ {print $$0}' $@ > default.ctfinfo
--- a/CTFCorrection/CTFCorrection2/Makefile
+++ b/CTFCorrection/CTFCorrection2/Makefile
@@ -4,11 +4,7 @@
44
55 #### Input extention ####
66 # These extensions must all be different.
7-INI_PDB_EXT=pdb
87 INI_MRC_EXT=inimrc
9-FIL_PDB_EXT=filpdb
10-FIL_MRC_EXT=filmrc
11-INPUT_3D_EXT=3d
128 INPUT_2D_EXT=2d
139 CTF_2D_EXT=prectf
1410 FFT_2D_EXT=fft
@@ -16,18 +12,9 @@ CTF_INFO_EXT=ctfinfo
1612 OUT_CTF_EXT=ctf
1713
1814 #### Suffixes rule ####
19-.SUFFIXES: .$(INI_PDB_EXT) .$(INI_MRC_EXT) .$(FIL_PDB_EXT) .$(FIL_MRC_EXT) .$(INPUT_3D_EXT) .$(INPUT_2D_EXT) \
20- .$(CTF_2D_EXT) .$(FFT_2D_EXT) .$(CTF_INFO_EXT) .$(OUT_CTF_EXT) .tiff
2115
2216 #### INCLUDE ####
23-SHELL=/bin/bash
24-
25--include ../CTFCorrection1/Makefile
26-#-include Makefile.common
27--include INPUT_2D_LIST
28--include CTF_2D_LIST
29--include FFT_2D_LIST
30--include CTF_INFO_LIST
17+-include Makefile.config
3118
3219 #### Definition ####
3320 CCD=14.0
@@ -35,34 +22,7 @@ CCD=14.0
3522 # Input FileName
3623 INPUT=Input
3724
38-### For pdbHelix
39-HELIX_DELTA_PHI=165
40-HELIX_DELTA_Z=5
41-HELIX_NUM_MOL=840
42-HELIX_PIXEL_X=2000
43-HELIX_PIXEL_Y=2000
44-HELIX_PIXEL_Z=2000
45-HELIX_START_X=-1000
46-HELIX_START_Y=-1000
47-HELIX_START_Z=-1000
48-HELIX_LENGTH_X=1
49-HELIX_LENGTH_Y=1
50-HELIX_LENGTH_Z=1
51-
52-### For pdb2mrc2d(Projection Angle of Filament)
53-PROJECTION_ANGLE_TYPE=YOYS
54-PROJECTION_ANGLE_1=60
55-PROJECTION_ANGLE_2=60
56-PROJECTION_ANGLE_3=0
57-PROJECTION_PIXEL_X=$(HELIX_PIXEL_Z)
58-PROJECTION_PIXEL_Y=$(HELIX_PIXEL_Z)
59-PROJECTION_START_X=`expr $(PROJECTION_PIXEL_X) / 10`
60-PROJECTION_START_Y=-`expr $(PROJECTION_PIXEL_Y) / 4`
61-#PROJECTION_START_X=0
62-#PROJECTION_START_Y=0
63-
6425 ### For mrcImageNoiseAdd
65-SNRATIO=1
6626 NSRATIO=0
6727
6828 ### For mrcImageSiemensStar
@@ -80,67 +40,20 @@ JOP_NUM=-j 3
8040
8141
8242 #### Rules of the list created ####
83-$(CTF_2D_EXT):$(INPUT_2D_LIST:.$(INPUT_2D_EXT)=.$(CTF_2D_EXT))
8443
8544
8645 ##### Commands #####
87-all::
88-# make InitialCTFDataFromPDB;
89- make InitialSiemensStar;
90-# make InitialCTFDataFromMRC;
46+all2::
47+ make InitialCTFDataFromMRC;
9148 make ProcessForInput;
9249 make TIF2CTF;
9350 make $(INPUT).tiff
9451
95-InitialCTFDataFromPDB::
96- make $(INPUT).$(FIL_PDB_EXT);
97- make $(INPUT).$(INPUT_2D_EXT);
98-
99-InitialCTFDataFromMRC::
100- cp $(INPUT).$(INI_MRC_EXT) $(INPUT).$(INPUT_2D_EXT);
101-
102-InitialSiemensStar::
103- mrcImageSiemensStar -o $(INPUT).$(INPUT_2D_EXT)tmp -m 2 -Shape $(SSTAR_SHAPE);
104- mrcImageNoiseAdd -i $(INPUT).$(INPUT_2D_EXT)tmp -o $(INPUT).$(INPUT_2D_EXT) -NS $(NSRATIO) -SD 1;
105- rm $(INPUT).$(INPUT_2D_EXT)tmp;
106-
107-ProcessForInput::
108- make $(INPUT).$(CTF_2D_EXT);
109- ln -s $(INPUT).$(CTF_2D_EXT) $(INPUT).mrc;
110- mrc2tiff -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)_org.tiff;
111- mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT)_i.tiff -I;
112- mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT).tif;
113-
114-
115-Test::
116- mrcInfo -i Input.mrc -o INFO;
117- NX=$$(head -1 INFO | awk '{printf("%d\n", $$4);}'); \
118- NY=$$(head -1 INFO | awk '{printf("%d\n", $$5);}'); \
119- echo $$NX $$NY;
120-
52+all2S::
53+ make InitialSiemensStar;
54+ make ProcessForInput;
55+ make TIF2CTF;
56+ make $(INPUT).tiff
12157
12258 ##### Commands(Input to Output) #####
123-.$(INI_PDB_EXT).$(FIL_PDB_EXT):
124- pdbHelix -i $*.$(INI_PDB_EXT) -o $*.$(FIL_PDB_EXT) -p $(HELIX_DELTA_PHI) -z $(HELIX_DELTA_Z) -n $(HELIX_NUM_MOL) \
125- -nx $(HELIX_PIXEL_X) -ny $(HELIX_PIXEL_Y) -nz $(HELIX_PIXEL_Z) \
126- -Sx $(HELIX_START_X) -Sy $(HELIX_START_Y) -Sz $(HELIX_START_Z) \
127- -dx $(HELIX_LENGTH_X) -dy $(HELIX_LENGTH_Y) -dz $(HELIX_LENGTH_Z)
128-
129-.$(FIL_PDB_EXT).$(INPUT_3D_EXT):
130- pdb2mrc -i $*.$(FIL_PDB_EXT) -o $*.$(INPUT_3D_EXT) -m 1
131-
132-.$(FIL_PDB_EXT).$(INPUT_2D_EXT):
133- pdb2mrc2d -i $*.$(FIL_PDB_EXT) -o $*.$(INPUT_2D_EXT)tmp -w 100 -sig 1 -Rot 1 1 \
134- -d $(HELIX_LENGTH_X) $(HELIX_LENGTH_Y) -n $(PROJECTION_PIXEL_X) $(PROJECTION_PIXEL_Y) -s $(PROJECTION_START_X) $(PROJECTION_START_Y) \
135- -startEA $(PROJECTION_ANGLE_TYPE) $(PROJECTION_ANGLE_1) $(PROJECTION_ANGLE_2) $(PROJECTION_ANGLE_3);
136-
137- mrcImageNoiseAdd -i $*.$(INPUT_2D_EXT)tmp -o $*.$(INPUT_2D_EXT) -SN $(SNRATIO);
138- rm $*.$(INPUT_2D_EXT)tmp
139-
140-.$(INPUT_2D_EXT).$(CTF_2D_EXT):
141- mrcImageCTFObservation -i $*.$(INPUT_2D_EXT) -o $*.$(CTF_2D_EXT) -ctfMode $(CTF_MODE) \
142- -kV $(CTF_KV) -Cs $(CTF_CS) -df $(CTF_DEFOCUS) -Ain $(CTF_AIN);
143-
144-.$(OUT_CTF_EXT).tiff:
145- mrc2tiff -i $*.$(OUT_CTF_EXT) -o $*_ctf.tiff
14659
\ No newline at end of file
--- /dev/null
+++ b/CTFCorrection/CTFCorrection2/Makefile.config
@@ -0,0 +1,111 @@
1+#
2+# This is Makefile for CTF Correction Demo.
3+#
4+
5+#### Input extention ####
6+# These extensions must all be different.
7+INI_PDB_EXT=pdb
8+FIL_PDB_EXT=filpdb
9+FIL_MRC_EXT=filmrc
10+INPUT_3D_EXT=3d
11+
12+#### Suffixes rule ####
13+.SUFFIXES: .$(INI_PDB_EXT) .$(INI_MRC_EXT) .$(FIL_PDB_EXT) .$(FIL_MRC_EXT) .$(INPUT_3D_EXT) .$(INPUT_2D_EXT) \
14+ .$(CTF_2D_EXT) .$(FFT_2D_EXT) .$(CTF_INFO_EXT) .$(OUT_CTF_EXT) .tiff
15+
16+#### INCLUDE ####
17+-include ../CTFCorrection1/Makefile
18+-include INPUT_2D_LIST
19+-include CTF_2D_LIST
20+-include FFT_2D_LIST
21+-include CTF_INFO_LIST
22+
23+#### Definition ####
24+
25+### For pdbHelix
26+HELIX_DELTA_PHI=165
27+HELIX_DELTA_Z=5
28+HELIX_NUM_MOL=840
29+HELIX_PIXEL_X=2000
30+HELIX_PIXEL_Y=2000
31+HELIX_PIXEL_Z=2000
32+HELIX_START_X=-1000
33+HELIX_START_Y=-1000
34+HELIX_START_Z=-1000
35+HELIX_LENGTH_X=1
36+HELIX_LENGTH_Y=1
37+HELIX_LENGTH_Z=1
38+
39+### For pdb2mrc2d(Projection Angle of Filament)
40+PROJECTION_ANGLE_TYPE=YOYS
41+PROJECTION_ANGLE_1=60
42+PROJECTION_ANGLE_2=60
43+PROJECTION_ANGLE_3=0
44+PROJECTION_PIXEL_X=$(HELIX_PIXEL_Z)
45+PROJECTION_PIXEL_Y=$(HELIX_PIXEL_Z)
46+PROJECTION_START_X=`expr $(PROJECTION_PIXEL_X) / 10`
47+PROJECTION_START_Y=-`expr $(PROJECTION_PIXEL_Y) / 4`
48+#PROJECTION_START_X=0
49+#PROJECTION_START_Y=0
50+
51+### For mrcImageNoiseAdd
52+SNRATIO=1
53+
54+
55+#### Rules of the list created ####
56+$(CTF_2D_EXT):$(INPUT_2D_LIST:.$(INPUT_2D_EXT)=.$(CTF_2D_EXT))
57+
58+
59+##### Commands #####
60+InitialCTFDataFromPDB::
61+ make $(INPUT).$(FIL_PDB_EXT);
62+ make $(INPUT).$(INPUT_2D_EXT);
63+
64+InitialCTFDataFromMRC::
65+ cp $(INPUT).$(INI_MRC_EXT) $(INPUT).$(INPUT_2D_EXT);
66+
67+InitialSiemensStar::
68+ mrcImageSiemensStar -o $(INPUT).$(INPUT_2D_EXT)tmp -m 2 -Shape $(SSTAR_SHAPE);
69+ mrcImageNoiseAdd -i $(INPUT).$(INPUT_2D_EXT)tmp -o $(INPUT).$(INPUT_2D_EXT) -NS $(NSRATIO) -SD 1;
70+ rm $(INPUT).$(INPUT_2D_EXT)tmp;
71+
72+ProcessForInput::
73+ make $(INPUT).$(CTF_2D_EXT);
74+ ln -s $(INPUT).$(CTF_2D_EXT) $(INPUT).mrc;
75+ mrc2tiff -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)_org.tiff;
76+ mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT)_i.tiff -I;
77+ mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT).tif;
78+
79+
80+Test::
81+ mrcInfo -i Input.mrc -o INFO;
82+ NX=$$(head -1 INFO | awk '{printf("%d\n", $$4);}'); \
83+ NY=$$(head -1 INFO | awk '{printf("%d\n", $$5);}'); \
84+ echo $$NX $$NY;
85+
86+
87+##### Commands(Input to Output) #####
88+.$(INI_PDB_EXT).$(FIL_PDB_EXT):
89+ pdbHelix -i $*.$(INI_PDB_EXT) -o $*.$(FIL_PDB_EXT) -p $(HELIX_DELTA_PHI) -z $(HELIX_DELTA_Z) -n $(HELIX_NUM_MOL) \
90+ -nx $(HELIX_PIXEL_X) -ny $(HELIX_PIXEL_Y) -nz $(HELIX_PIXEL_Z) \
91+ -Sx $(HELIX_START_X) -Sy $(HELIX_START_Y) -Sz $(HELIX_START_Z) \
92+ -dx $(HELIX_LENGTH_X) -dy $(HELIX_LENGTH_Y) -dz $(HELIX_LENGTH_Z)
93+
94+.$(FIL_PDB_EXT).$(INPUT_3D_EXT):
95+ pdb2mrc -i $*.$(FIL_PDB_EXT) -o $*.$(INPUT_3D_EXT) -m 1
96+
97+.$(FIL_PDB_EXT).$(INPUT_2D_EXT):
98+ pdb2mrc2d -i $*.$(FIL_PDB_EXT) -o $*.$(INPUT_2D_EXT)tmp -w 100 -sig 1 -Rot 1 1 \
99+ -d $(HELIX_LENGTH_X) $(HELIX_LENGTH_Y) -n $(PROJECTION_PIXEL_X) $(PROJECTION_PIXEL_Y) -s $(PROJECTION_START_X) $(PROJECTION_START_Y) \
100+ -startEA $(PROJECTION_ANGLE_TYPE) $(PROJECTION_ANGLE_1) $(PROJECTION_ANGLE_2) $(PROJECTION_ANGLE_3);
101+
102+ mrcImageNoiseAdd -i $*.$(INPUT_2D_EXT)tmp -o $*.$(INPUT_2D_EXT) -SN $(SNRATIO);
103+ rm $*.$(INPUT_2D_EXT)tmp
104+
105+.$(INPUT_2D_EXT).$(CTF_2D_EXT):
106+ mrcImageCTFObservation -i $*.$(INPUT_2D_EXT) -o $*.$(CTF_2D_EXT) -ctfMode $(CTF_MODE) \
107+ -kV $(CTF_KV) -Cs $(CTF_CS) -df $(CTF_DEFOCUS) -Ain $(CTF_AIN);
108+
109+.$(OUT_CTF_EXT).tiff:
110+ mrc2tiff -i $*.$(OUT_CTF_EXT) -o $*_ctf.tiff
111+
\ No newline at end of file
--- a/CTFCorrection/CTFCorrection3/Makefile
+++ b/CTFCorrection/CTFCorrection3/Makefile
@@ -3,19 +3,38 @@
33 #
44
55 #### Input extention ####
6+# These extensions must all be different.
7+INI_MRC_EXT=inimrc
8+INPUT_2D_EXT=2d
9+CTF_2D_EXT=prectf
10+FFT_2D_EXT=fft
11+CTF_INFO_EXT=ctfinfo
12+OUT_CTF_EXT=ctf
613
714 #### Suffixes rule ####
8-.SUFFIXES: .ctfinfoauto2 .ctfinfo1
915
1016 #### INCLUDE ####
11-#-include ../CTFCorrection1/Makefile
12--include ../CTFCorrection2/Makefile
13-#-include Makefile.common
14-#-include Makefile.common2
15--include CTFAuto2List
16--include CTFInfo1List
17+-include Makefile.config
1718
1819 #### Definition ####
20+CCD=14.0
21+
22+# Input FileName
23+INPUT=Input
24+
25+### For mrcImageNoiseAdd
26+NSRATIO=0
27+
28+### For mrcImageSiemensStar
29+SSTAR_SHAPE=0
30+
31+## For mrcImageCTFObservation
32+CTF_KV=200
33+CTF_CS=2.1
34+CTF_DEFOCUS=27000
35+CTF_AIN=0.3 #need CTF_MODE +32
36+CTF_MODE=0
37+
1938 ## For mrcImageCTFObservation 2
2039 CTF2_KV=200
2140 CTF2_CS=2.1
@@ -23,25 +42,15 @@ CTF2_DEFOCUS=9000
2342 CTF2_AIN=0.3 #need CTF2_MODE +32
2443 CTF2_MODE=0
2544
26-#### Rules of the list created ####
27-ctfinfoauto2: $(FFTS:.fft=.ctfinfoauto2)
28-ctfinfo1: $(CTFAuto2List:.ctfinfoauto2=.ctfinfo1)
45+#### For Works ####
46+JOP_NUM=-j 3
2947
30-CTFAuto2List::
31- echo "CTFAuto2List=\\" > CTFAuto2List
32- ls -1 *.ctfinfoauto2 | sed s/ctfinfoauto2/ctfinfoauto2\\\\/ >> CTFAuto2List
33- echo "" >> CTFAuto2List
3448
35-CTFInfo1List::
36- echo "CTFInfo1List=\\" > CTFInfo1List
37- ls -1 *.ctfinfo1 | sed s/ctfinfo1/ctfinfo1\\\\/ >> CTFInfo1List
38- echo "" >> CTFInfo1List
49+#### Rules of the list created ####
3950
4051 ##### Commands #####
41-all1::
42-# make InitialCTFDataFromPDB;
43- make InitialSiemensStar;
44-# make InitialCTFDataFromMRC;
52+all3::
53+ make InitialCTFDataFromMRC;
4554 make ProcessForInput;
4655 make ProcessForInput2;
4756 make TIF2CTF2;
@@ -49,42 +58,12 @@ all1::
4958 make $(INPUT)-2.tiff
5059 make ImageAverage;
5160
52-ProcessForInput2::
53- mrcImageCTFObservation -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)-2.$(CTF_2D_EXT) -ctfMode $(CTF2_MODE) \
54- -kV $(CTF2_KV) -Cs $(CTF2_CS) -df $(CTF2_DEFOCUS) -Ain $(CTF2_AIN);
55- ln -s $(INPUT)-2.$(CTF_2D_EXT) $(INPUT)-2.mrc;
56- mrc2tiff -i $(INPUT)-2.$(INPUT_2D_EXT) -o $(INPUT)-2_org.tiff;
57- mrc2tiff -i $(INPUT)-2.$(CTF_2D_EXT) -o $(INPUT)-2_i.tiff -I;
58- mrc2tiff -i $(INPUT)-2.$(CTF_2D_EXT) -o $(INPUT)-2.tif;
59-
60-TIF2CTF2::
61- make TIFS; make $(JN) mrc;
62- make MRCS; make $(JN) cen;
63- make CENS; make $(JN) nor;
64- make NORS; make $(JN) fft;
65- make FFTS;
66- make $(JN) ctfinfoauto2;
67- make CTFAutoList; make ctfinfo;
68-# touch $(INPUT).ctfinfo
69-# touch $(INPUT)-2.ctfinfo
70- make CTFInfoList; make $(JN) ctf;
71-# make CTFS;
72-
73-ImageAverage::
74- touch CTF_LIST;
75- rm CTF_LIST;
76- ls -1 *.ctf >> CTF_LIST;
77- mrcImageAverage -i CTF_LIST -o $(INPUT).avg;
78- mrc2tiff -i $(INPUT).avg -o $(INPUT)_avg.tiff;
79-
80-##### Commands(Input to Output) #####
81-.fft.ctfinfoauto2:
82- ctfDetermine -i $*.fft -o $*.ctfinfoauto2 -D 27000 \
83- -CutLow 0.025 -CutHigh 0.15 -d 3 -Cc 0.7 -Cs 2.1 \
84- -BofMTF 1 -Ai 0.14 -Noise 0.2 -I0 1.3;
85- mv $*.ctfinfoauto2 $*.ctfinfoauto;
86-
87-.ctfinfoauto2.ctfinfo1:
88- cat $*.ctfinfoauto2 >> $*.ctfinfo1 ;
89- mv $*.ctfinfo1 $*.ctfinfo;
61+all3S::
62+ make InitialSiemensStar;
63+ make ProcessForInput;
64+ make ProcessForInput2;
65+ make TIF2CTF2;
66+ make $(INPUT).tiff
67+ make $(INPUT)-2.tiff
68+ make ImageAverage;
9069
\ No newline at end of file
--- /dev/null
+++ b/CTFCorrection/CTFCorrection3/Makefile.config
@@ -0,0 +1,70 @@
1+#
2+# This is Makefile for CTF Correction Demo.
3+#
4+
5+#### Input extention ####
6+
7+#### Suffixes rule ####
8+.SUFFIXES: .ctfinfoauto2 .ctfinfo1
9+
10+#### INCLUDE ####
11+-include ../CTFCorrection2/Makefile.config
12+-include CTFAuto2List
13+-include CTFInfo1List
14+
15+#### Definition ####
16+
17+#### Rules of the list created ####
18+ctfinfoauto2: $(FFTS:.fft=.ctfinfoauto2)
19+ctfinfo1: $(CTFAuto2List:.ctfinfoauto2=.ctfinfo1)
20+
21+CTFAuto2List::
22+ echo "CTFAuto2List=\\" > CTFAuto2List
23+ ls -1 *.ctfinfoauto2 | sed s/ctfinfoauto2/ctfinfoauto2\\\\/ >> CTFAuto2List
24+ echo "" >> CTFAuto2List
25+
26+CTFInfo1List::
27+ echo "CTFInfo1List=\\" > CTFInfo1List
28+ ls -1 *.ctfinfo1 | sed s/ctfinfo1/ctfinfo1\\\\/ >> CTFInfo1List
29+ echo "" >> CTFInfo1List
30+
31+##### Commands #####
32+ProcessForInput2::
33+ mrcImageCTFObservation -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)-2.$(CTF_2D_EXT) -ctfMode $(CTF2_MODE) \
34+ -kV $(CTF2_KV) -Cs $(CTF2_CS) -df $(CTF2_DEFOCUS) -Ain $(CTF2_AIN);
35+ ln -s $(INPUT)-2.$(CTF_2D_EXT) $(INPUT)-2.mrc;
36+ mrc2tiff -i $(INPUT)-2.$(INPUT_2D_EXT) -o $(INPUT)-2_org.tiff;
37+ mrc2tiff -i $(INPUT)-2.$(CTF_2D_EXT) -o $(INPUT)-2_i.tiff -I;
38+ mrc2tiff -i $(INPUT)-2.$(CTF_2D_EXT) -o $(INPUT)-2.tif;
39+
40+TIF2CTF2::
41+ make TIFS; make $(JN) mrc;
42+ make MRCS; make $(JN) cen;
43+ make CENS; make $(JN) nor;
44+ make NORS; make $(JN) fft;
45+ make FFTS;
46+ make $(JN) ctfinfoauto2;
47+ make CTFAutoList; make ctfinfo;
48+# touch $(INPUT).ctfinfo
49+# touch $(INPUT)-2.ctfinfo
50+ make CTFInfoList; make $(JN) ctf;
51+# make CTFS;
52+
53+ImageAverage::
54+ touch CTF_LIST;
55+ rm CTF_LIST;
56+ ls -1 *.ctf >> CTF_LIST;
57+ mrcImageAverage -i CTF_LIST -o $(INPUT).avg;
58+ mrc2tiff -i $(INPUT).avg -o $(INPUT)_avg.tiff;
59+
60+##### Commands(Input to Output) #####
61+.fft.ctfinfoauto2:
62+ ctfDetermine -i $*.fft -o $*.ctfinfoauto2 -D 27000 \
63+ -CutLow 0.025 -CutHigh 0.15 -d 3 -Cc 0.7 -Cs 2.1 \
64+ -BofMTF 1 -Ai 0.14 -Noise 0.2 -I0 1.3;
65+ mv $*.ctfinfoauto2 $*.ctfinfoauto;
66+
67+.ctfinfoauto2.ctfinfo1:
68+ cat $*.ctfinfoauto2 >> $*.ctfinfo1 ;
69+ mv $*.ctfinfo1 $*.ctfinfo;
70+
\ No newline at end of file
Binary files /dev/null and b/CTFCorrection/CTFCorrection4/Input.inimrc differ
--- a/CTFCorrection/CTFCorrection4/Makefile
+++ b/CTFCorrection/CTFCorrection4/Makefile
@@ -1,24 +1,58 @@
11 #
2-# This is Makefile for CTF Correction Demo.
2+# This is Main Makefile for CTF Correction Demo.
33 #
44
55
66 #### Input extention ####
7+# These extensions must all be different.
8+INI_MRC_EXT=inimrc
9+INPUT_2D_EXT=2d
10+CTF_2D_EXT=prectf
11+FFT_2D_EXT=fft
712 CTF_INFO_EXT=ctfinfo
13+OUT_CTF_EXT=ctf
814
915 #### Suffixes rule ####
1016
1117 #### INCLUDE ####
12--include ../../TIPS/LoopCommand/Makefile.config
13--include ../CTFCorrection2/Makefile
18+-include Makefile.config
1419
1520 #### Definition ####
16-## For define varioable
21+CCD=14.0
22+
23+# Input FileName
24+INPUT=Input
25+
26+### For mrcImageNoiseAdd
27+NSRATIO=0
28+
29+### For mrcImageSiemensStar
30+SSTAR_SHAPE=0
31+
32+## For mrcImageCTFObservation
33+CTF_KV=200
34+CTF_CS=2.1
35+CTF_DEFOCUS=27000
36+CTF_AIN=0.3 #need CTF_MODE +32
37+CTF_MODE=32
38+
39+#### For Works ####
40+JOP_NUM=-j 3
1741
1842 #### Rules of the list created ####
1943
2044 ##### Commands #####
2145 all4::
46+ make InitialCTFDataFromMRC;
47+ make ProcessForInputLoop;
48+ make ProcessForInfoLoop;
49+ make PRECTF2GIF;
50+ make PRECTF2FFT;
51+ make FFT2GIF;
52+ make FFT2CTF;
53+ make CTF2GIF;
54+
55+all4S::
2256 make InitialSiemensStar;
2357 make ProcessForInputLoop;
2458 make ProcessForInfoLoop;
@@ -48,47 +82,4 @@ ProcessForInfoLoop::
4882 LOOP_DELTA=1000 \
4983 make LoopCommand;
5084
51-PRECTF2FFT::
52- INPUT_EXT=prectf \
53- OUTPUT_EXT=fft \
54- make LoopCommandEachFile;
55-
56-PRECTF2GIF::
57- mkdir -p _PRECTF;
58- INPUT_EXT=prectf \
59- OUTPUT_EXT=prectf.gif \
60- make LoopCommandEachFile;
61-
62-FFT2CTF::
63- INPUT_EXT=fft \
64- OUTPUT_EXT=ctf \
65- make LoopCommandEachFile;
66-
67-FFT2GIF::
68- mkdir -p _FFT;
69- INPUT_EXT=fft \
70- OUTPUT_EXT=fft.gif \
71- make LoopCommandEachFile;
72-
73-CTF2GIF::
74- mkdir -p _CTF;
75- INPUT_EXT=ctf \
76- OUTPUT_EXT=ctf.gif \
77- make LoopCommandEachFile;
78-
7985 ##### Commands(Input to Output) #####
80-.prectf.fft:
81- mrcImageFFT -i $*.prectf -o $*.fft
82-
83-.fft.ctf:
84- mrcImageCTFCompensation -i $*.fft -info $*.ctfinfo -o $*.ctf -m 1
85-
86-.prectf.prectf.gif:
87- mrc2gif -i $*.prectf -o _PRECTF/$*.prectf.gif
88-
89-.fft.fft.gif:
90- mrcFFTExpression -i $*.fft -o $*.fftex -m 1;
91- mrc2gif -i $*.fftex -o _FFT/$*.gif
92-
93-.ctf.ctf.gif:
94- mrc2gif -i $*.ctf -o _CTF/$*.ctf.gif
--- /dev/null
+++ b/CTFCorrection/CTFCorrection4/Makefile.config
@@ -0,0 +1,64 @@
1+#
2+# This is Sub Makefile for CTF Correction Demo.
3+#
4+
5+
6+#### Input extention ####
7+# These extensions must all be different.
8+
9+#### Suffixes rule ####
10+
11+#### INCLUDE ####
12+-include ../../TIPS/LoopCommand/Makefile.config
13+-include ../CTFCorrection2/Makefile.config
14+
15+#### Definition ####
16+## For define varioable
17+
18+#### Rules of the list created ####
19+
20+##### Commands #####
21+PRECTF2FFT::
22+ INPUT_EXT=prectf \
23+ OUTPUT_EXT=fft \
24+ make LoopCommandEachFile;
25+
26+PRECTF2GIF::
27+ mkdir -p _PRECTF;
28+ INPUT_EXT=prectf \
29+ OUTPUT_EXT=prectf.gif \
30+ make LoopCommandEachFile;
31+
32+FFT2CTF::
33+ INPUT_EXT=fft \
34+ OUTPUT_EXT=ctf \
35+ make LoopCommandEachFile;
36+
37+FFT2GIF::
38+ mkdir -p _FFT;
39+ INPUT_EXT=fft \
40+ OUTPUT_EXT=fft.gif \
41+ make LoopCommandEachFile;
42+
43+CTF2GIF::
44+ mkdir -p _CTF;
45+ INPUT_EXT=ctf \
46+ OUTPUT_EXT=ctf.gif \
47+ make LoopCommandEachFile;
48+
49+##### Commands(Input to Output) #####
50+.prectf.fft:
51+ mrcImageFFT -i $*.prectf -o $*.fft
52+
53+.fft.ctf:
54+ mrcImageCTFCompensation -i $*.fft -info $*.ctfinfo -o $*.ctf -m 1
55+
56+.prectf.prectf.gif:
57+ mrc2gif -i $*.prectf -o _PRECTF/$*.prectf.gif
58+
59+.fft.fft.gif:
60+ mrcFFTExpression -i $*.fft -o $*.fftex -m 1;
61+ mrc2gif -i $*.fftex -o _FFT/$*.gif
62+
63+.ctf.ctf.gif:
64+ mrc2gif -i $*.ctf -o _CTF/$*.ctf.gif
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