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tutorial: Commit

This repository is for tutorials of Eos.

Commit MetaInfo

Revisión	00b17156a869ad17ac439f1dc40f7707b02d8ef7 (tree)
Tiempo	2015-02-16 10:59:47
Autor	kinoshita-eos <kinoshita@yasu...>
Commiter	kinoshita-eos

Log Message

Add: PIONE tutorial to repeat for Single Particle Makefile.
modified: SampleCode/PIONE/Advanced4/Anotation.pione
modified: SampleCode/PIONE/Advanced4/Create_3d.pione
modified: SampleCode/PIONE/Advanced4/Create_SampleROI.pione
modified: 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
new file: SampleCode/PIONE/Advanced4/Repeat_3d.pione

Cambiar Resumen

modified: SampleCode/PIONE/Advanced4/Anotation.pione (diff)
modified: SampleCode/PIONE/Advanced4/Create_3d.pione (diff)
modified: SampleCode/PIONE/Advanced4/Create_SampleROI.pione (diff)
modified: SampleCode/PIONE/Advanced4/Create_fit_each.pione (diff)
modified: SampleCode/PIONE/Advanced4/Create_stack.pione (diff)
modified: SampleCode/PIONE/Advanced4/Main.pione (diff)
modified: SampleCode/PIONE/Advanced4/Parameter.pione (diff)
add: SampleCode/PIONE/Advanced4/Repeat_3d.pione (diff)

Diferencia incremental

--- a/SampleCode/PIONE/Advanced4/Anotation.pione

+++ b/SampleCode/PIONE/Advanced4/Anotation.pione

		@@ -1,5 +1,5 @@
1	1	.@ PackageName :: "SingleParticle_3DReconstruction"
2	2	.@ Editor :: "Kinoshita"
3		-.@ Tag :: "v0.2.0"
	3	+.@ Tag :: "v0.3.0"
4	4	# Ref: Makefile in Eos v2.1.16p0093
5	5	# $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

		@@ -1,18 +1,19 @@
1	1	Rule Create_3d
2		- input '*.3dinfo'.all
3		- input '*.fit'.all
4		- output '{$filename}.3d'
5		- output '{$filename}.ds6'
	2	+ input '*.3dinfo-{$count}'.all
	3	+ input '*.fit-{$count}'.all
	4	+ output '{$filename}-{$count}.3d'
	5	+ output '{$filename}-{$count}.ds6'
6	6	param $filename
	7	+ param $count
7	8	Action
8	9	# Sum_3dinfo_3dlst
9	10	for info in {$I[1]}
10	11	do
11		- cat $info >> {$filename}.3dlst
	12	+ cat $info >> {$filename}-{$count}.3dlst
12	13	done
13	14
14	15	# Reconstruct_3dlst_3d
15		- mrc2Dto3D -I {$filename}.3dlst -o {$O[1]} -InterpolationMode 2 -Double -DoubleCounter {$filename}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 6
	16	+ mrc2Dto3D -I {$filename}-{$count}.3dlst -o {$O[1]} -InterpolationMode 2 -Double -DoubleCounter {$filename}-{$count}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 6
16	17
17	18	# Convert_3d_ds6
18	19	mrc2map -i {$O[1]} -o {$O[2]} -m 3

--- a/SampleCode/PIONE/Advanced4/Create_SampleROI.pione

+++ b/SampleCode/PIONE/Advanced4/Create_SampleROI.pione

		@@ -35,3 +35,15 @@ Action
35	35	done
36	36	done
37	37	End
	38	+
	39	+Rule Cutout_ROI
	40	+ input '*.mrc'
	41	+ output '*.roi'.all
	42	+ output '*.tiff'.all
	43	+Action
	44	+ Display2 -i {$I[1]}
	45	+ for data in $(ls *.roi)
	46	+ do
	47	+ mrc2tiff -i ${data} -o ${data}.tiff
	48	+ done
	49	+End
		\ No newline at end of file

--- a/SampleCode/PIONE/Advanced4/Create_fit_each.pione

+++ b/SampleCode/PIONE/Advanced4/Create_fit_each.pione

		@@ -1,52 +1,52 @@
1	1	Rule Create_fit_each
2	2	input '*.pad'
3		- input '*.stack'
	3	+ input '-.stack'
4	4	if ($Flag_3DWhole or $Flag_3D4S)
5	5	input '{$I[1][1]}.roi'
6	6	end
7	7	if $Flag_3D
8		- output '{$I[1][1]}.fit'
9		- output '{$I[1][1]}.3dinfo'
	8	+ output '{$I[1][1]}.fit-{$I[2][2]}'
	9	+ output '{$I[1][1]}.3dinfo-{$I[2][2]}'
10	10	end
11	11	if $Flag_3DWhole
12		- output '{$I[1][1]}.shift'
13		- output '{$I[1][1]}.3dwholeinfo'
	12	+ output '{$I[1][1]}.shift-{$I[2][2]}'
	13	+ output '{$I[1][1]}.3dwholeinfo-{$I[2][2]}'
14	14	end
15	15	if $Flag_3D4S
16		- output '{$I[1][1]}.4shift'
17		- output '{$I[1][1]}.3d4sinfo'
	16	+ output '{$I[1][1]}.4shift-{$I[2][2]}'
	17	+ output '{$I[1][1]}.3d4sinfo-{$I[2][2]}'
18	18	end
19	19	Action
20	20	# Create_fit
21		- mrcImageAutoRotationCorrelation -i {$I[1]} -r {$I[2]} -fit {$I[1][1]}.fit -O {$I[1][1]}.corinfo \
	21	+ mrcImageAutoRotationCorrelation -i {$I[1]} -r {$I[2]} -fit {$I[1][1]}.fit-{$I[2][2]} -O {$I[1][1]}.corinfo-{$I[2][2]} \
22	22	-n {$N_ROT} -m 18 -nRot1 {$N_ROT1} -nRot2 {$N_ROT2} -nRot3 {$N_ROT3} > /dev/null
23	23
24	24	# fit_3dinfo
25	25	if {$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
	26	+ awk '/Cor/ { print $18,$16,$2,$3,$4,"0.0"}' {$I[1][1]}.corinfo-{$I[2][2]} \| sort -r \| sed -e s/pad/fit-{$I[2][2]}/ > {$I[1][1]}.3dinfolst-{$I[2][2]}
	27	+ head -n 1 {$I[1][1]}.3dinfolst-{$I[2][2]} \| awk ' {print $2,$3,$4,$5,$6,$1'} > {$I[1][1]}.3dinfo-{$I[2][2]}
28	28	fi
29	29
30	30	# fit_3dwholeinfo
31	31	if {$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
	32	+ awk '/Cor/ { print $18,$16,$2,$3,$4,$9,$11,$12}' {$I[1][1]}.corinfo-{$I[2][2]} \| sort -r \| sed -e s/pad/shift-{$I[2][2]}/ > {$I[1][1]}.3dwholeinfolst-{$I[2][2]}
	33	+ head -n 1 {$I[1][1]}.3dwholeinfolst-{$I[2][2]} \| awk ' {print $2,$3,$4,$5,$6,$7,$8,$1'} > {$I[1][1]}.3dwholeinfo-{$I[2][2]}
	34	+ X=`awk '{print -{$SHRINK}*$6; }' {$I[1][1]}.3dwholeinfo-{$I[2][2]}`;
	35	+ Y=`awk '{print -{$SHRINK}*$7; }' {$I[1][1]}.3dwholeinfo-{$I[2][2]}`;
	36	+ echo $X,$Y; mrcImageShift -i {$I[1][1]}.roi -o {$I[1][1]}.shift-{$I[2][2]} -x $X -y $Y -z 0
37	37	fi
38	38
39	39	# fit_3d4sinfo
40	40	if {$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`;
	41	+ awk '/Cor/ { print $18,$16,$2,$3,$4,$9,$11,$12}' {$I[1][1]}.corinfo-{$I[2][2]} \| sort -r \| sed -e s/pad/4shift-{$I[2][2]}/ > {$I[1][1]}.3d4sinfolst-{$I[2][2]}
	42	+ head -n 1 {$I[1][1]}.3d4sinfolst-{$I[2][2]} \| awk ' {print $2,$3,$4,$5,$6,$7,$8,$1'} > {$I[1][1]}.3d4sinfo-{$I[2][2]}
	43	+ X=`awk '{print -{$SHRINK4S}*$6; }' {$I[1][1]}.3d4sinfo-{$I[2][2]}`;
	44	+ Y=`awk '{print -{$SHRINK4S}*$7; }' {$I[1][1]}.3d4sinfo-{$I[2][2]}`;
45	45	echo $X,$Y;
46		- mrcImageShrink -i {$I[1][1]}.roi -o {$I[1][1]}.4shrink -S {$SHRINK4S}
	46	+ mrcImageShrink -i {$I[1][1]}.roi -o {$I[1][1]}.4shrink-{$I[2][2]} -S {$SHRINK4S}
47	47	width=`expr {$X_SIZE} / {$SHRINK4S}`
48	48	height=`expr {$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 $Y -z 0
	49	+ mrcImagePad -i {$I[1][1]}.4shrink-{$I[2][2]} -o {$I[1][1]}.4spad-{$I[2][2]} -W ${width} -H ${height}
	50	+ mrcImageShift -i {$I[1][1]}.4spad-{$I[2][2]} -o {$I[1][1]}.4shift-{$I[2][2]} -x $X -y $Y -z 0
51	51	fi
52	52	End

--- a/SampleCode/PIONE/Advanced4/Create_stack.pione

+++ b/SampleCode/PIONE/Advanced4/Create_stack.pione

		@@ -1,6 +1,6 @@
1	1	Rule Create_stack
2	2	input '*.mrc'
3		- output '{$I[1][1]}.stack'
	3	+ output '{$I[1][1]}-1.stack'
4	4	Action
5	5	data=$(mrcInfo -i {$I[1]} \| head -1)
6	6	x_size=$(echo "${data}" \| awk '{printf ("%i", $4)}')

--- a/SampleCode/PIONE/Advanced4/Main.pione

+++ b/SampleCode/PIONE/Advanced4/Main.pione

		@@ -1,9 +1,9 @@
1	1	Rule Main
2		- if ($Mode_ROI + $Mode_Ref) != 0
	2	+ if (($Mode_ROI != 0) or $Flag_Ref)
3	3	input '*.mrc'
4	4	end
5	5
6		- if $Mode_Ref == 0
	6	+ if $Flag_Ref.not()
7	7	input '*.stack'
8	8	end
9	9

		@@ -12,18 +12,18 @@ Rule Main
12	12	end
13	13
14	14	if $Flag_3D
15		- output '{$I[1][1]}.3d'
16		- output '{$I[1][1]}.ds6'
	15	+ output '{$I[1][1]}-{$Repeat_Count}.3d'.all
	16	+ output '{$I[1][1]}-{$Repeat_Count}.ds6'.all
17	17	end
18	18
19	19	if $Flag_3DWhole
20		- output '{$I[1][1]}.3dwhole'
21		- output '{$I[1][1]}.whole.ds6'
	20	+ output '{$I[1][1]}-{$Repeat_Count}.3dwhole'
	21	+ output '{$I[1][1]}-{$Repeat_Count}.whole.ds6'
22	22	end
23	23
24	24	if $Flag_3D4S
25		- output '{$I[1][1]}.3d4s'
26		- output '{$I[1][1]}.4s.ds6'
	25	+ output '{$I[1][1]}-{$Repeat_Count}.3d4s'
	26	+ output '{$I[1][1]}-{$Repeat_Count}.4s.ds6'
27	27	end
28	28
29	29	if $Mode_ROI != 0

		@@ -41,9 +41,11 @@ Flow
41	41	when 2
42	42	rule Create_Sample3d
43	43	rule Create_SampleROI_all
	44	+ when 3
	45	+ rule Cutout_ROI
44	46	end
45	47
46		- if $Mode_Ref != 0
	48	+ if $Flag_Ref
47	49	rule Create_stack
48	50	end
49	51

		@@ -54,7 +56,8 @@ Flow
54	56	rule Create_fit_each
55	57
56	58	if $Flag_3D
57		- rule Create_3d {filename: $I[1][1].str()}
	59	+ rule Create_3d {filename: $I[1][1].str(), count: 1.upto($Repeat_Count)}
	60	+ rule Repeat_3d {count: 1.upto($Repeat_Count - 1)}
58	61	end
59	62
60	63	if $Flag_3DWhole

--- a/SampleCode/PIONE/Advanced4/Parameter.pione

+++ b/SampleCode/PIONE/Advanced4/Parameter.pione

		@@ -39,13 +39,17 @@ param $ROI_ROT3_DELTA := 30
39	39	$roi_rot3_loop := ($ROI_ROT3_END - $ROI_ROT3_START) / $ROI_ROT3_DELTA
40	40	param $ROI_SN := 1
41	41
	42	+## For repeat count
	43	+param $Repeat_Count := 2
	44	+
42	45	# advanced param
	46	+## Mode 0: do not, 1: each, 2: all, 3: use Display2
	47	+advanced param $Mode_ROI := 1
43	48	## Mode 0: do not, 1: each, 2: all
44		-advanced param $Mode_ROI := 0
45		-advanced param $Mode_Ref := 0
46	49	advanced param $Mode_3D := 1
47	50	## Flag true: do, false: do not
	51	+advanced param $Flag_Ref := true
48	52	advanced param $Flag_3D := true
49	53	advanced param $Flag_3DWhole := false
50	54	advanced param $Flag_3D4S := false
51		-advanced param $Flag_Projection := false
	55	+advanced param $Flag_Projection := true

--- /dev/null

+++ b/SampleCode/PIONE/Advanced4/Repeat_3d.pione

		@@ -0,0 +1,10 @@
	1	+Rule Repeat_3d
	2	+ input '*-{$count}.3d'
	3	+ output '{$I[1][1]}-{$count + 1}.stack'
	4	+ param $count
	5	+Action
	6	+ mrc3Dto2D -i {$I[1]} -o {$O[1]} -m 1 -InterpolationMode 2 -EulerMode {$REF_ROT_MODE} \
	7	+ -Rot1 {$REF_ROT1_START} {$REF_ROT1_END} {$REF_ROT1_DELTA} \
	8	+ -Rot2 {$REF_ROT2_START} {$REF_ROT2_END} {$REF_ROT2_DELTA} \
	9	+ -Rot3 {$REF_ROT3_START} {$REF_ROT3_END} {$REF_ROT3_DELTA}
	10	+End

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