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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revisionb8e7f1ce27e58418b8ee3dac224a27922deba547 (tree)
Time2015-02-05 14:24:02
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Add: PIONE tutorial Advanced4 new version.
modified: SampleCode/PIONE/Advanced4/Anotation.pione
modified: SampleCode/PIONE/Advanced4/Create_3d.pione
modified: SampleCode/PIONE/Advanced4/Create_3d4s.pione
deleted: SampleCode/PIONE/Advanced4/Create_3d4slst.pione
deleted: SampleCode/PIONE/Advanced4/Create_3dlst.pione
modified: SampleCode/PIONE/Advanced4/Create_3dwhole.pione
deleted: SampleCode/PIONE/Advanced4/Create_3dwholelst.pione
deleted: SampleCode/PIONE/Advanced4/Create_fit.pione
new file: SampleCode/PIONE/Advanced4/Create_fit_3d_all.pione
new file: SampleCode/PIONE/Advanced4/Create_fit_each.pione
modified: SampleCode/PIONE/Advanced4/Create_stack.pione
modified: SampleCode/PIONE/Advanced4/Main.pione
modified: SampleCode/PIONE/Advanced4/Parameter.pione
modified: SampleCode/PIONE/Advanced4/Preprocess.pione

Modify: Bug fixed: Basic7
modified: SampleCode/PIONE/Basic7/ForDebug.pione

Change Summary

Incremental Difference

--- a/SampleCode/PIONE/Advanced4/Anotation.pione
+++ b/SampleCode/PIONE/Advanced4/Anotation.pione
@@ -1,5 +1,5 @@
11 .@ PackageName :: "SingleParticle_3DReconstruction"
22 .@ Editor :: "Kinoshita"
3-.@ Tag :: "v0.1.1"
3+.@ Tag :: "v0.2.0"
44 # Ref: Makefile in Eos v2.1.16p0093
55 # $EOS_HOME/Integration/SingleParticle/Makefile-fromKanae
\ No newline at end of file
--- a/SampleCode/PIONE/Advanced4/Create_3d.pione
+++ b/SampleCode/PIONE/Advanced4/Create_3d.pione
@@ -1,28 +1,19 @@
11 Rule Create_3d
2- input '*.3dlst'
2+ input '*.3dinfo'.all
33 input '*.fit'.all
4- output '{$I[1][1]}.3d'
5- output '{$I[1][1]}.3dcounter'
6- output '{$I[1][1]}.ds6'
7-Flow
8- rule Reconstruct_3dlst_3d
9- rule Convert_3d_ds6
10-End
11-
12-#.3dlst.3d:
13-Rule Reconstruct_3dlst_3d
14- input '*.3dlst'
15- input '*.fit'.all
16- output '{$I[1][1]}.3d'
17- output '{$I[1][1]}.3dcounter'
4+ output '{$filename}.3d'
5+ output '{$filename}.ds6'
6+ param $filename
187 Action
19- mrc2Dto3D -I {$I[1]} -o {$O[1]} -InterpolationMode 2 -Double -DoubleCounter {$O[2]} -CounterThreshold 0.5 -m 1 -WeightMode 6
20-End
8+ # Sum_3dinfo_3dlst
9+ for info in {$I[1]}
10+ do
11+ cat $info >> {$filename}.3dlst
12+ done
2113
22-#.3d.ds6:
23-Rule Convert_3d_ds6
24- input '*.3d'
25- output '{$I[1][1]}.ds6'
26-Action
27- mrc2map -i {$I[1]} -o {$O[1]} -m 3
14+ # Reconstruct_3dlst_3d
15+ mrc2Dto3D -I {$filename}.3dlst -o {$O[1]} -InterpolationMode 2 -Double -DoubleCounter {$filename}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 6
16+
17+ # Convert_3d_ds6
18+ mrc2map -i {$O[1]} -o {$O[2]} -m 3
2819 End
\ No newline at end of file
--- a/SampleCode/PIONE/Advanced4/Create_3d4s.pione
+++ b/SampleCode/PIONE/Advanced4/Create_3d4s.pione
@@ -1,31 +1,19 @@
11 Rule Create_3d4s
2- input '*.3d4slst'
2+ input '*.3d4sinfo'.all
33 input '*.4shift'.all
4- output '{$I[1][1]}.3d4s'
5- output '{$I[1][1]}.3d4scounter'
6- output '{$I[1][1]}.4sds6'
7- output '{$I[1][1]}.4s.ds6'
8-Flow
9- rule Reconstruct_3d4slst_3d4s
10- rule Convert_3d4s_4sds6
11-End
12-
13-#.3d4sinfolst.3d4s:
14-Rule Reconstruct_3d4slst_3d4s
15- input '*.3d4slst'
16- input '*.4shift'.all
17- output '{$I[1][1]}.3d4s'
18- output '{$I[1][1]}.3d4scounter'
4+ output '{$filename}.3d4s'
5+ output '{$filename}.4s.ds6'
6+ param $filename
197 Action
20- mrc2Dto3D -I {$I[1]} -o {$O[1]} -InterpolationMode 2 -Double -DoubleCounter {$O[2]} -CounterThreshold 0.5 -m 1 -WeightMode 6
21-End
8+ # Sum_3d4sinfo_3d4slst
9+ for info in {$I[1]}
10+ do
11+ cat $info >> {$filename}.3d4slst
12+ done
2213
23-#.3d4s.4sds6:
24-Rule Convert_3d4s_4sds6
25- input '*.3d4s'
26- output '{$I[1][1]}.4sds6'
27- output '{$I[1][1]}.4s.ds6'
28-Action
29- mrc2map -i {$I[1]} -o {$O[1]} -m 3
30- ln -sf {$O[1]} {$O[2]}
14+ # Reconstruct_3d4slst_3d4s
15+ mrc2Dto3D -I {$filename}.3d4slst -o {$O[1]} -InterpolationMode 2 -Double -DoubleCounter {$filename}.3d4scounter -CounterThreshold 0.5 -m 1 -WeightMode 6
16+
17+ # Convert_3d4s_4sds6
18+ mrc2map -i {$O[1]} -o {$O[2]} -m 3
3119 End
--- a/SampleCode/PIONE/Advanced4/Create_3d4slst.pione
+++ /dev/null
@@ -1,43 +0,0 @@
1-Rule Create_3d4slst
2- input '*.roi'.all
3- input '*.corinfo'.all
4- output '{$filename}.3d4slst'
5- output '*.4shift'.all
6- param $filename
7-Flow
8- rule fit_3d4sinfo
9- rule Sum_3d4sinfo_3d4slst {filename: $filename}
10-End
11-
12-#.fit.3d4sinfo:
13-Rule fit_3d4sinfo
14- input '*.corinfo'
15- input '{$I[1][1]}.roi'
16- output '{$I[1][1]}.3d4sinfolst'
17- output '{$I[1][1]}.3d4sinfo'
18- output '{$I[1][1]}.4shrink'
19- output '{$I[1][1]}.4spad'
20- output '{$I[1][1]}.4shift'
21-Action
22- awk '/Cor/ { print $18,$16,$2,$3,$4,$9,$11,$12}' {$I[1]} | sort -r | sed -e s/pad/4shift/ > {$O[1]}
23- head -n 1 {$O[1]} | awk ' {print $2,$3,$4,$5,$6,$7,$8,$1'} > {$O[2]}
24- X=`awk '{print -{$SHRINK4S}*$6; }' {$O[2]}`; \
25- Y=`awk '{print -{$SHRINK4S}*$7; }' {$O[2]}`; \
26- echo $X,$Y;
27- mrcImageShrink -i {$I[2]} -o {$O[3]} -S {$SHRINK4S}
28- width=`expr {$X_SIZE} / {$SHRINK4S}`
29- height=`expr {$Y_SIZE} / {$SHRINK4S}`
30- mrcImagePad -i {$O[3]} -o {$O[4]} -W ${width} -H ${height}
31- mrcImageShift -i {$O[4]} -o {$O[5]} -x $X -y $Y -z 0
32-End
33-
34-Rule Sum_3d4sinfo_3d4slst
35- input '*.3d4sinfo'.all
36- output '{$filename}.3d4slst'
37- param $filename
38-Action
39- for info in {$I[1].join()}
40- do
41- cat $info >> {$O[1]}
42- done
43-End
--- a/SampleCode/PIONE/Advanced4/Create_3dlst.pione
+++ /dev/null
@@ -1,29 +0,0 @@
1-Rule Create_3dlst
2- input '*.corinfo'.all
3- output '{$filename}.3dlst'
4- param $filename
5-Flow
6- rule fit_3dinfo
7- rule Sum_3dinfo_3dlst {filename: $filename}
8-End
9-
10-# .fit.3dinfo:
11-Rule fit_3dinfo
12- input '*.corinfo'
13- output '{$I[1][1]}.3dinfolst'
14- output '{$I[1][1]}.3dinfo'
15-Action
16- awk '/Cor/ { print $18,$16,$2,$3,$4,"0.0"}' {$I[1]} | sort -r | sed -e s/pad/fit/ > {$O[1]}
17- head -n 1 {$O[1]} | awk ' {print $2,$3,$4,$5,$6,$1'} > {$O[2]}
18-End
19-
20-Rule Sum_3dinfo_3dlst
21- input '*.3dinfo'.all
22- output '{$filename}.3dlst'
23- param $filename
24-Action
25- for info in {$I[1].join()}
26- do
27- cat $info >> {$O[1]}
28- done
29-End
--- a/SampleCode/PIONE/Advanced4/Create_3dwhole.pione
+++ b/SampleCode/PIONE/Advanced4/Create_3dwhole.pione
@@ -1,31 +1,19 @@
11 Rule Create_3dwhole
2- input '*.3dwholelst'
2+ input '*.3dwholeinfo'.all
33 input '*.shift'.all
4- output '{$I[1][1]}.3dwhole'
5- output '{$I[1][1]}.3dwholecounter'
6- output '{$I[1][1]}.wholeds6'
7- output '{$I[1][1]}.whole.ds6'
8-Flow
9- rule Reconstruct_3dwholelst_3dwhole
10- rule Convert_3dwhole_wholeds6
11-End
12-
13-#.3dwholelst.3dwhole:
14-Rule Reconstruct_3dwholelst_3dwhole
15- input '*.3dwholelst'
16- input '*.shift'.all
17- output '{$I[1][1]}.3dwhole'
18- output '{$I[1][1]}.3dwholecounter'
19-Action
20- mrc2Dto3D -I {$I[1]} -o {$O[1]} -InterpolationMode 2 -Double -DoubleCounter {$O[2]} -CounterThreshold 0.5 -m 1 -WeightMode 6
21-End
22-
23-#.3dwhole.3dwholelst:
24-Rule Convert_3dwhole_wholeds6
25- input '*.3dwhole'
26- output '{$I[1][1]}.wholeds6'
27- output '{$I[1][1]}.whole.ds6'
4+ output '{$filename}.3dwhole'
5+ output '{$filename}.whole.ds6'
6+ param $filename
287 Action
29- mrc2map -i {$I[1]} -o {$O[1]} -m 3
30- ln -sf {$O[1]} {$O[2]}
8+ # Sum_3dwholeinfo_3dwholelst
9+ for info in {$I[1]}
10+ do
11+ cat $info >> {$filename}.3dwholelst
12+ done
13+
14+ # Reconstruct_3dwholelst_3dwhole
15+ mrc2Dto3D -I {$filename}.3dwholelst -o {$O[1]} -InterpolationMode 2 -Double -DoubleCounter {$filename}.3dwholecounter -CounterThreshold 0.5 -m 1 -WeightMode 6
16+
17+ # Convert_3dwhole_wholeds6
18+ mrc2map -i {$O[1]} -o {$O[2]} -m 3
3119 End
--- a/SampleCode/PIONE/Advanced4/Create_3dwholelst.pione
+++ /dev/null
@@ -1,36 +0,0 @@
1-Rule Create_3dwholelst
2- input '*.roi'.all
3- input '*.corinfo'.all
4- output '{$filename}.3dwholelst'
5- output '*.shift'.all
6- param $filename
7-Flow
8- rule fit_3dwholeinfo
9- rule Sum_3dwholeinfo_3dwholelst {filename: $filename}
10-End
11-
12-#.fit.3dwholeinfo:
13-Rule fit_3dwholeinfo
14- input '*.roi'
15- input '{$I[1][1]}.corinfo'
16- output '{$I[1][1]}.3dwholeinfolst'
17- output '{$I[1][1]}.3dwholeinfo'
18- output '{$I[1][1]}.shift'
19-Action
20- awk '/Cor/ { print $18,$16,$2,$3,$4,$9,$11,$12}' {$I[2]} | sort -r | sed -e s/pad/shift/ > {$O[1]}
21- head -n 1 {$O[1]} | awk ' {print $2,$3,$4,$5,$6,$7,$8,$1'} > {$O[2]}
22- X=`awk '{print -{$SHRINK}*$6; }' {$O[2]}`;
23- Y=`awk '{print -{$SHRINK}*$7; }' {$O[2]}`;
24- echo $X,$Y; mrcImageShift -i {$I[1]} -o {$O[3]} -x $X -y $Y -z 0
25-End
26-
27-Rule Sum_3dwholeinfo_3dwholelst
28- input '*.3dwholeinfo'.all
29- output '{$filename}.3dwholelst'
30- param $filename
31-Action
32- for info in {$I[1].join()}
33- do
34- cat $info >> {$O[1]}
35- done
36-End
\ No newline at end of file
--- a/SampleCode/PIONE/Advanced4/Create_fit.pione
+++ /dev/null
@@ -1,23 +0,0 @@
1-#.pad.fit:
2-Rule Create_fit_each
3- input '*.pad'
4- input '*.stack'
5- output '{$I[1][1]}.fit'
6- output '{$I[1][1]}.corinfo'
7-Action
8- mrcImageAutoRotationCorrelation -i {$I[1]} -r {$I[2]} -fit {$O[1]} -O {$O[2]} \
9- -n {$N_ROT} -m 18 -nRot1 {$N_ROT1} -nRot2 {$N_ROT2} -nRot3 {$N_ROT3} > /dev/null
10-End
11-
12-Rule Create_fit_all
13- input '*.pad'.all
14- input '*.stack'
15- output '*.fit'.all
16- output '*.corinfo'.all
17-Action
18- for data in {$I[1][1]}
19- do
20- mrcImageAutoRotationCorrelation -i ${data}.pad -r {$I[2]} -fit ${data}.fit -O ${data}.corinfo \
21- -n {$N_ROT} -m 18 -nRot1 {$N_ROT1} -nRot2 {$N_ROT2} -nRot3 {$N_ROT3} > /dev/null
22- done
23-End
\ No newline at end of file
--- /dev/null
+++ b/SampleCode/PIONE/Advanced4/Create_fit_3d_all.pione
@@ -0,0 +1,89 @@
1+Rule Create_fit_3d_all
2+ input '*.pad'.all
3+ input '*.stack'
4+if ($Flag_3DWhole or $Flag_3D4S)
5+ input '*.roi'.all
6+end
7+if $Flag_3D
8+ output '{$filename}.3d'
9+ output '{$filename}.ds6'
10+end
11+if $Flag_3DWhole
12+ output '{$filename}.3dwhole'
13+ output '{$filename}.whole.ds6'
14+end
15+if $Flag_3D4S
16+ output '{$filename}.3d4s'
17+ output '{$filename}.4s.ds6'
18+end
19+ param $filename
20+Action
21+ for data in {$I[1][1]}
22+ do
23+ # Create_fit
24+ mrcImageAutoRotationCorrelation -i ${data}.pad -r {$I[2]} -fit ${data}.fit -O ${data}.corinfo \
25+ -n {$N_ROT} -m 18 -nRot1 {$N_ROT1} -nRot2 {$N_ROT2} -nRot3 {$N_ROT3} > /dev/null
26+
27+ if {$Flag_3D} ; then
28+ # fit_3dinfo
29+ awk '/Cor/ { print $18,$16,$2,$3,$4,"0.0"}' ${data}.corinfo | sort -r | sed -e s/pad/fit/ > ${data}.3dinfolst
30+ head -n 1 ${data}.3dinfolst | awk ' {print $2,$3,$4,$5,$6,$1'} > ${data}.3dinfo
31+
32+ # Sum_3dinfo_3dlst
33+ cat ${data}.3dinfo >> {$filename}.3dlst
34+ fi
35+
36+ if {$Flag_3DWhole} ; then
37+ # fit_3dwholeinfo
38+ awk '/Cor/ { print $18,$16,$2,$3,$4,$9,$11,$12}' ${data}.corinfo | sort -r | sed -e s/pad/4shift/ > ${data}.3d4sinfolst
39+ head -n 1 ${data}.3d4sinfolst | awk ' {print $2,$3,$4,$5,$6,$7,$8,$1'} > ${data}.3d4sinfo
40+ X=`awk '{print -{$SHRINK4S}*$6; }' ${data}.3d4sinfo`;
41+ Y=`awk '{print -{$SHRINK4S}*$7; }' ${data}.3d4sinfo`;
42+ echo $X,$Y;
43+ mrcImageShrink -i ${data}.roi -o ${data}.4shrink -S {$SHRINK4S}
44+ width=`expr {$X_SIZE} / {$SHRINK4S}`
45+ height=`expr {$Y_SIZE} / {$SHRINK4S}`
46+ mrcImagePad -i ${data}.4shrink -o ${data}.4spad -W ${width} -H ${height}
47+ mrcImageShift -i ${data}.4spad -o ${data}.4shift -x $X -y $Y -z 0
48+
49+ # Sum_3dwholeinfo_3dwholelst
50+ ${data}.3d4sinfo >> {$filename}.3dwholelst
51+ fi
52+
53+ if {$Flag_3D4S} ; then
54+ # fit_3d4sinfo
55+ awk '/Cor/ { print $18,$16,$2,$3,$4,$9,$11,$12}' ${data}.corinfo | sort -r | sed -e s/pad/shift/ > ${data}.3dwholeinfolst
56+ head -n 1 ${data}.3dwholeinfolst | awk ' {print $2,$3,$4,$5,$6,$7,$8,$1'} > ${data}.3dwholeinfo
57+ X=`awk '{print -{$SHRINK}*$6; }' ${data}.3dwholeinfo`;
58+ Y=`awk '{print -{$SHRINK}*$7; }' ${data}.3dwholeinfo`;
59+ echo $X,$Y; mrcImageShift -i ${data}.roi -o ${data}.shift -x $X -y $Y -z 0
60+
61+ # Sum_3d4sinfo_3d4slst
62+ ${data}.3dwholeinfo >> {$filename}.3d4slst
63+ fi
64+ done
65+
66+ if {$Flag_3D} ; then
67+ # Reconstruct_3dlst_3d
68+ mrc2Dto3D -I {$filename}.3dlst -o {$filename}.3d -InterpolationMode 2 -Double -DoubleCounter {$filename}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 6
69+
70+ # Convert_3d_ds6
71+ mrc2map -i {$filename}.3d -o {$filename}.ds6 -m 3
72+ fi
73+
74+ if {$Flag_3DWhole} ; then
75+ # Reconstruct_3dwholelst_3dwhole
76+ mrc2Dto3D -I {$filename}.3dwholelst -o {$filename}.3dwhole -InterpolationMode 2 -Double -DoubleCounter {$filename}.3dwholecounter -CounterThreshold 0.5 -m 1 -WeightMode 6
77+
78+ # Convert_3dwhole_wholeds6
79+ mrc2map -i {$filename}.3dwhole -o {$filename}.whole.ds6 -m 3
80+ fi
81+
82+ if {$Flag_3D4S} ; then
83+ # Reconstruct_3d4slst_3d4s
84+ mrc2Dto3D -I {$filename}.3d4slst -o {$filename}.3d4s -InterpolationMode 2 -Double -DoubleCounter {$filename}.3d4scounter -CounterThreshold 0.5 -m 1 -WeightMode 6
85+
86+ # Convert_3d4s_4sds6
87+ mrc2map -i {$filename}.3d4s -o {$filename}.4s.ds6 -m 3
88+ fi
89+End
--- /dev/null
+++ b/SampleCode/PIONE/Advanced4/Create_fit_each.pione
@@ -0,0 +1,52 @@
1+Rule Create_fit_each
2+ input '*.pad'
3+ input '*.stack'
4+if ($Flag_3DWhole or $Flag_3D4S)
5+ input '{$I[1][1]}.roi'
6+end
7+if $Flag_3D
8+ output '{$I[1][1]}.fit'
9+ output '{$I[1][1]}.3dinfo'
10+end
11+if $Flag_3DWhole
12+ output '{$I[1][1]}.shift'
13+ output '{$I[1][1]}.3dwholeinfo'
14+end
15+if $Flag_3D4S
16+ output '{$I[1][1]}.4shift'
17+ output '{$I[1][1]}.3d4sinfo'
18+end
19+Action
20+ # Create_fit
21+ mrcImageAutoRotationCorrelation -i {$I[1]} -r {$I[2]} -fit {$I[1][1]}.fit -O {$I[1][1]}.corinfo \
22+ -n {$N_ROT} -m 18 -nRot1 {$N_ROT1} -nRot2 {$N_ROT2} -nRot3 {$N_ROT3} > /dev/null
23+
24+ # fit_3dinfo
25+ if {$Flag_3D} ; then
26+ awk '/Cor/ { print $18,$16,$2,$3,$4,"0.0"}' {$I[1][1]}.corinfo | sort -r | sed -e s/pad/fit/ > {$I[1][1]}.3dinfolst
27+ head -n 1 {$I[1][1]}.3dinfolst | awk ' {print $2,$3,$4,$5,$6,$1'} > {$I[1][1]}.3dinfo
28+ fi
29+
30+ # fit_3dwholeinfo
31+ if {$Flag_3DWhole} ; then
32+ awk '/Cor/ { print $18,$16,$2,$3,$4,$9,$11,$12}' {$I[1][1]}.corinfo | sort -r | sed -e s/pad/shift/ > {$I[1][1]}.3dwholeinfolst
33+ head -n 1 {$I[1][1]}.3dwholeinfolst | awk ' {print $2,$3,$4,$5,$6,$7,$8,$1'} > {$I[1][1]}.3dwholeinfo
34+ X=`awk '{print -{$SHRINK}*$6; }' {$I[1][1]}.3dwholeinfo`;
35+ Y=`awk '{print -{$SHRINK}*$7; }' {$I[1][1]}.3dwholeinfo`;
36+ echo $X,$Y; mrcImageShift -i {$I[1][1]}.roi -o {$I[1][1]}.shift -x $X -y $Y -z 0
37+ fi
38+
39+ # fit_3d4sinfo
40+ if {$Flag_3D4S} ; then
41+ awk '/Cor/ { print $18,$16,$2,$3,$4,$9,$11,$12}' {$I[1][1]}.corinfo | sort -r | sed -e s/pad/4shift/ > {$I[1][1]}.3d4sinfolst
42+ head -n 1 {$I[1][1]}.3d4sinfolst | awk ' {print $2,$3,$4,$5,$6,$7,$8,$1'} > {$I[1][1]}.3d4sinfo
43+ X=`awk '{print -{$SHRINK4S}*$6; }' {$I[1][1]}.3d4sinfo`;
44+ Y=`awk '{print -{$SHRINK4S}*$7; }' {$I[1][1]}.3d4sinfo`;
45+ echo $X,$Y;
46+ mrcImageShrink -i {$I[1][1]}.roi -o {$I[1][1]}.4shrink -S {$SHRINK4S}
47+ width=`expr {$X_SIZE} / {$SHRINK4S}`
48+ height=`expr {$Y_SIZE} / {$SHRINK4S}`
49+ mrcImagePad -i {$I[1][1]}.4shrink -o {$I[1][1]}.4spad -W ${width} -H ${height}
50+ mrcImageShift -i {$I[1][1]}.4spad -o {$I[1][1]}.4shift -x $X -y $Y -z 0
51+ fi
52+End
--- a/SampleCode/PIONE/Advanced4/Create_stack.pione
+++ b/SampleCode/PIONE/Advanced4/Create_stack.pione
@@ -27,8 +27,8 @@ Action
2727
2828 image_size={$X_SIZE}
2929
30- if [ ${image_size} -lt ${Y_SIZE} ] ; then \
31- image_size=${Y_SIZE}
30+ if [ ${image_size} -lt {$Y_SIZE} ] ; then \
31+ image_size={$Y_SIZE}
3232 fi
3333
3434 sampling_length=$(echo "scale=15.7; ${length} * {$SHRINK} * ${ref_size} / ${image_size}" | bc)
--- a/SampleCode/PIONE/Advanced4/Main.pione
+++ b/SampleCode/PIONE/Advanced4/Main.pione
@@ -12,22 +12,17 @@ Rule Main
1212 end
1313
1414 if $Flag_3D
15- output '{$I[1][1]}.3dlst'
1615 output '{$I[1][1]}.3d'
1716 output '{$I[1][1]}.ds6'
1817 end
1918
2019 if $Flag_3DWhole
21- output '{$I[1][1]}.3dwholelst'
2220 output '{$I[1][1]}.3dwhole'
23- output '{$I[1][1]}.wholeds6'
2421 output '{$I[1][1]}.whole.ds6'
2522 end
2623
2724 if $Flag_3D4S
28- output '{$I[1][1]}.3d4slst'
2925 output '{$I[1][1]}.3d4s'
30- output '{$I[1][1]}.4sds6'
3126 output '{$I[1][1]}.4s.ds6'
3227 end
3328
@@ -54,26 +49,23 @@ Flow
5449
5550 rule Preprocess
5651
57- case $Mode_Cor
52+ case $Mode_3D
5853 when 1
5954 rule Create_fit_each
60- when 2
61- rule Create_fit_all
62- end
55+
56+ if $Flag_3D
57+ rule Create_3d {filename: $I[1][1].str()}
58+ end
6359
64- if $Flag_3D
65- rule Create_3dlst {filename: $I[1][1].str()}
66- rule Create_3d
67- end
60+ if $Flag_3DWhole
61+ rule Create_3dwhole {filename: $I[1][1].str()}
62+ end
6863
69- if $Flag_3DWhole
70- rule Create_3dwholelst {filename: $I[1][1].str()}
71- rule Create_3dwhole
72- end
73-
74- if $Flag_3D4S
75- rule Create_3d4slst {filename: $I[1][1].str()}
76- rule Create_3d4s
64+ if $Flag_3D4S
65+ rule Create_3d4s {filename: $I[1][1].str()}
66+ end
67+ when 2
68+ rule Create_fit_3d_all {filename: $I[1][1].str()}
7769 end
7870
7971 if $Flag_Projection
--- a/SampleCode/PIONE/Advanced4/Parameter.pione
+++ b/SampleCode/PIONE/Advanced4/Parameter.pione
@@ -1,7 +1,7 @@
11 # basic param
22 ## For Size
3-param $X_SIZE := 80
4-param $Y_SIZE := 80
3+param $X_SIZE := 256 #80
4+param $Y_SIZE := 256 #80
55 param $SHRINK := 8
66 param $SHRINK4S := 4
77
@@ -27,11 +27,11 @@ param $REF_ROT3_DELTA := 15
2727 param $ROI_ROT_MODE := "XOYS"
2828 param $ROI_ROT1_START := 0
2929 param $ROI_ROT1_END := 359
30-param $ROI_ROT1_DELTA := 30
30+param $ROI_ROT1_DELTA := 60 #30
3131 $roi_rot1_loop := ($ROI_ROT1_END - $ROI_ROT1_START) / $ROI_ROT1_DELTA
3232 param $ROI_ROT2_START := 0
3333 param $ROI_ROT2_END := 359
34-param $ROI_ROT2_DELTA := 30
34+param $ROI_ROT2_DELTA := 60 #30
3535 $roi_rot2_loop := ($ROI_ROT2_END - $ROI_ROT2_START) / $ROI_ROT2_DELTA
3636 param $ROI_ROT3_START := 0
3737 param $ROI_ROT3_END := 0
@@ -41,11 +41,11 @@ param $ROI_SN := 1
4141
4242 # advanced param
4343 ## Mode 0: do not, 1: each, 2: all
44-advanced param $Mode_ROI := 1
45-advanced param $Mode_Ref := 1
46-advanced param $Mode_Cor := 1
44+advanced param $Mode_ROI := 0
45+advanced param $Mode_Ref := 0
46+advanced param $Mode_3D := 1
4747 ## Flag true: do, false: do not
4848 advanced param $Flag_3D := true
49-advanced param $Flag_3DWhole := true
50-advanced param $Flag_3D4S := true
51-advanced param $Flag_Projection := true
49+advanced param $Flag_3DWhole := false
50+advanced param $Flag_3D4S := false
51+advanced param $Flag_Projection := false
--- a/SampleCode/PIONE/Advanced4/Preprocess.pione
+++ b/SampleCode/PIONE/Advanced4/Preprocess.pione
@@ -1,35 +1,15 @@
1-# .lst.padlst:
21 Rule Preprocess
32 input '*.roi'
43 output '{$I[1][1]}.pad'
5-Flow
6- rule roi_smooth;
7- rule smooth_shrink;
8- rule shrink_pad;
9-End
10-
11-#.roi.smooth:
12-Rule roi_smooth
13- input '*.roi'
14- output '{$I[1][1]}.smooth'
15-Action
16- mrcImageSmoothing -i {$I[1]} -o {$O[1]} -m 1 -r 4
17-End
18-
19-#.smooth.shrink:
20-Rule smooth_shrink
21- input '*.smooth'
22- output '{$I[1][1]}.shrink'
23-Action
24- mrcImageShrink -i {$I[1]} -o {$O[1]} -S {$SHRINK}
25-End
26-
27-#.shrink.pad:
28-Rule shrink_pad
29- input '*.shrink'
30- output '{$I[1][1]}.pad'
314 Action
5+ # roi_smooth
6+ mrcImageSmoothing -i {$I[1]} -o {$I[1][1]}.smooth -m 1 -r 4
7+
8+ # smooth_shrink
9+ mrcImageShrink -i {$I[1][1]}.smooth -o {$I[1][1]}.shrink -S {$SHRINK}
10+
11+ # shrink_pad
3212 width=`expr {$X_SIZE} / {$SHRINK}`
3313 height=`expr {$Y_SIZE} / {$SHRINK}`
34- mrcImagePad -i {$I[1]} -o {$O[1]} -W ${width} -H ${height}
35-End
14+ mrcImagePad -i {$I[1][1]}.shrink -o {$O[1]} -W ${width} -H ${height}
15+End
\ No newline at end of file
--- a/SampleCode/PIONE/Basic7/ForDebug.pione
+++ b/SampleCode/PIONE/Basic7/ForDebug.pione
@@ -38,6 +38,6 @@ Rule Sub3
3838 Action
3939 touch {$O[1]}
4040 if [ {$LogFlag} ] ; then
41- wc {$I[1]} > {$O[2]}
41+ wc {$I[1]} > {$LogFile}
4242 fi
4343 End
\ No newline at end of file
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