Rule Create_3d4slst
- input '*.lst'
input '*.roi'.all
input '*.corinfo'.all
- output '{$I[1][1]}.3d4slst'
+ output '{$filename}.3d4slst'
output '*.4shift'.all
+ param $filename
Flow
rule fit_3d4sinfo
- rule Sum_3d4sinfo_3d4slst
+ rule Sum_3d4sinfo_3d4slst {filename: $filename}
End
#.fit.3d4sinfo:
End
Rule Sum_3d4sinfo_3d4slst
- input '*.lst'
input '*.3d4sinfo'.all
- output '{$I[1][1]}.3d4slst'
+ output '{$filename}.3d4slst'
+ param $filename
Action
- for info in {$I[2].join()}
+ for info in {$I[1].join()}
do
cat $info >> {$O[1]}
done
Rule Create_3dlst
- input '*.lst'
input '*.corinfo'.all
- output '{$I[1][1]}.3dlst'
+ output '{$filename}.3dlst'
+ param $filename
Flow
rule fit_3dinfo
- rule Sum_3dinfo_3dlst
+ rule Sum_3dinfo_3dlst {filename: $filename}
End
# .fit.3dinfo:
End
Rule Sum_3dinfo_3dlst
- input '*.lst'
input '*.3dinfo'.all
- output '{$I[1][1]}.3dlst'
+ output '{$filename}.3dlst'
+ param $filename
Action
- for info in {$I[2].join()}
+ for info in {$I[1].join()}
do
cat $info >> {$O[1]}
done
Rule Create_3dwholelst
- input '*.lst'
input '*.roi'.all
input '*.corinfo'.all
- output '{$I[1][1]}.3dwholelst'
+ output '{$filename}.3dwholelst'
output '*.shift'.all
+ param $filename
Flow
rule fit_3dwholeinfo
- rule Sum_3dwholeinfo_3dwholelst
+ rule Sum_3dwholeinfo_3dwholelst {filename: $filename}
End
#.fit.3dwholeinfo:
End
Rule Sum_3dwholeinfo_3dwholelst
- input '*.lst'
input '*.3dwholeinfo'.all
- output '{$I[1][1]}.3dwholelst'
+ output '{$filename}.3dwholelst'
+ param $filename
Action
- for info in {$I[2].join()}
+ for info in {$I[1].join()}
do
cat $info >> {$O[1]}
done
--- /dev/null
+Rule Create_Sample3d
+ input '*.mrc'
+ output '{$I[1][1]}.sample3d'
+Action
+ data=$(mrcInfo -i {$I[1]} | head -1)
+ x_size=$(echo "${data}" | awk '{printf ("%i", $4)}')
+ y_size=$(echo "${data}" | awk '{printf ("%i", $5)}')
+ z_size=$(echo "${data}" | awk '{printf ("%i", $6)}')
+
+ data=$(mrcInfo -i {$I[1]} | head -5 | tail -1)
+ x_length=$(echo "${data}" | awk '{printf ("%f", $4)}')
+ y_length=$(echo "${data}" | awk '{printf ("%f", $5)}')
+ z_length=$(echo "${data}" | awk '{printf ("%f", $6)}')
+
+ ref_size=${x_size}
+ length=${x_length}
+
+ if [ ${ref_size} -lt ${y_size} ] ; then \
+ ref_size=${y_size}
+ length=${y_length}
+ fi
+
+ if [ ${ref_size} -lt ${z_size} ] ; then \
+ ref_size=${z_size}
+ length=${z_length}
+ fi
+
+ image_size={$X_SIZE}
+
+ if [ ${image_size} -lt {$Y_SIZE} ] ; then \
+ image_size={$Y_SIZE}
+ fi
+
+ sampling_length=$(echo "scale=7; ${length} * ${ref_size} / ${image_size}" | bc)
+
+ mrcImageSamplingUnitChange -i {$I[1]} -o {$I[1][1]}.sample3d -m 2 -S ${sampling_length} ${sampling_length} ${sampling_length}
+End
-Rule Create_SampleROI
- input '*.mrc'
- output '{$I[1][1]}.lst'
+Rule Create_SampleROI_each
+ input '*.sample3d'
+ output '{$I[1][1]}-{$rot1}-{$rot2}-{$rot3}.roi'
+ output '{$I[1][1]}-{$rot1}-{$rot2}-{$rot3}.tiff'
+ param $rot1
+ param $rot2
+ param $rot3
+Action
+ mrc3Dto2D -i {$I[1]} -o {$I[1][1]}-{$rot1}-{$rot2}-{$rot3}.data2d -InterpolationMode 2 -EulerMode {$ROI_ROT_MODE} \
+ -Rot1 {$rot1} {$rot1} 1 \
+ -Rot2 {$rot2} {$rot2} 1 \
+ -Rot3 {$rot3} {$rot3} 1
+ mrcImageNoiseAdd -i {$I[1][1]}-{$rot1}-{$rot2}-{$rot3}.data2d -o {$O[1]} -SN {$ROI_SN}
+ mrc2tiff -i {$O[1]} -o {$O[2]}
+End
+
+Rule Create_SampleROI_all
+ input '*.sample3d'
output '{$I[1][1]}-*.roi'.all
output '{$I[1][1]}-*.tiff'.all
Action
- data=$(mrcInfo -i {$I[1]} | head -1)
- x_size=$(echo "${data}" | awk '{printf ("%i", $4)}')
- y_size=$(echo "${data}" | awk '{printf ("%i", $5)}')
- z_size=$(echo "${data}" | awk '{printf ("%i", $6)}')
-
- data=$(mrcInfo -i {$I[1]} | head -5 | tail -1)
- x_length=$(echo "${data}" | awk '{printf ("%f", $4)}')
- y_length=$(echo "${data}" | awk '{printf ("%f", $5)}')
- z_length=$(echo "${data}" | awk '{printf ("%f", $6)}')
-
- ref_size=${x_size}
- length=${x_length}
-
- if [ ${ref_size} -lt ${y_size} ] ; then \
- ref_size=${y_size}
- length=${y_length}
- fi
-
- if [ ${ref_size} -lt ${z_size} ] ; then \
- ref_size=${z_size}
- length=${z_length}
- fi
-
- image_size={$X_SIZE}
-
- if [ ${image_size} -lt {$Y_SIZE} ] ; then \
- image_size={$Y_SIZE}
- fi
-
- sampling_length=$(echo "scale=7; ${length} * ${ref_size} / ${image_size}" | bc)
-
- mrcImageSamplingUnitChange -i {$I[1]} -o {$I[1][1]}.data3d -m 2 -S ${sampling_length} ${sampling_length} ${sampling_length}
-
for (( rot1 = {$ROI_ROT1_START}; rot1 <= {$ROI_ROT1_END}; rot1 += {$ROI_ROT1_DELTA} ))
do
for (( rot2 = {$ROI_ROT2_START}; rot2 <= {$ROI_ROT2_END}; rot2 += {$ROI_ROT2_DELTA} ))
do
for (( rot3 = {$ROI_ROT3_START}; rot3 <= {$ROI_ROT3_END}; rot3 += {$ROI_ROT3_DELTA} ))
do
- mrc3Dto2D -i {$I[1][1]}.data3d -o {$I[1][1]}-${rot1}-${rot2}-${rot3}.data2d -InterpolationMode 2 -EulerMode {$ROI_ROT_MODE} \
- -Rot1 ${rot1} ${rot1} 1 \
- -Rot2 ${rot2} ${rot2} 1 \
- -Rot3 ${rot3} ${rot3} 1
+ mrc3Dto2D -i {$I[1]} -o {$I[1][1]}-${rot1}-${rot2}-${rot3}.data2d -InterpolationMode 2 -EulerMode {$ROI_ROT_MODE} \
+ -Rot1 ${rot1} ${rot1} 1 \
+ -Rot2 ${rot2} ${rot2} 1 \
+ -Rot3 ${rot3} ${rot3} 1
mrcImageNoiseAdd -i {$I[1][1]}-${rot1}-${rot2}-${rot3}.data2d -o {$I[1][1]}-${rot1}-${rot2}-${rot3}.roi -SN {$ROI_SN}
mrc2tiff -i {$I[1][1]}-${rot1}-${rot2}-${rot3}.roi -o {$I[1][1]}-${rot1}-${rot2}-${rot3}.tiff
done
done
done
-
- ls *.roi > {$O[1]}
End
#.pad.fit:
-Rule Create_fit
+Rule Create_fit_each
input '*.pad'
input '*.stack'
output '{$I[1][1]}.fit'
Action
mrcImageAutoRotationCorrelation -i {$I[1]} -r {$I[2]} -fit {$O[1]} -O {$O[2]} \
-n {$N_ROT} -m 18 -nRot1 {$N_ROT1} -nRot2 {$N_ROT2} -nRot3 {$N_ROT3} > /dev/null
+End
+
+Rule Create_fit_all
+ input '*.pad'.all
+ input '*.stack'
+ output '*.fit'.all
+ output '*.corinfo'.all
+Action
+ for data in {$I[1][1]}
+ do
+ mrcImageAutoRotationCorrelation -i ${data}.pad -r {$I[2]} -fit ${data}.fit -O ${data}.corinfo \
+ -n {$N_ROT} -m 18 -nRot1 {$N_ROT1} -nRot2 {$N_ROT2} -nRot3 {$N_ROT3} > /dev/null
+ done
End
\ No newline at end of file
Rule Main
- if $Flag_ROI or $Flag_Ref
+ if ($Mode_ROI + $Mode_Ref) != 0
input '*.mrc'
end
- if $Flag_ROI.not()
- input '*.lst'
- input '*.roi'.all
+ if $Mode_Ref == 0
+ input '*.stack'
end
- if $Flag_Ref.not()
- input '*.stack'
+ if $Mode_ROI == 0
+ input '*.roi'.all
end
if $Flag_3D
output '{$I[1][1]}.4s.ds6'
end
- if $Flag_ROI
+ if $Mode_ROI != 0
output '*.tiff'.all
end
- output '*.gif'.all
-
+ if $Flag_Projection
+ output '*.gif'.all
+ end
Flow
-
- if $Flag_ROI
- rule Create_SampleROI
+ case $Mode_ROI
+ when 1
+ rule Create_Sample3d
+ rule Create_SampleROI_each {rot1: (0.upto($roi_rot1_loop))*$ROI_ROT1_DELTA, rot2: (0.upto($roi_rot2_loop))*$ROI_ROT2_DELTA, rot3: (0.upto($roi_rot3_loop))*$ROI_ROT3_DELTA}
+ when 2
+ rule Create_Sample3d
+ rule Create_SampleROI_all
end
- if $Flag_Ref
+ if $Mode_Ref != 0
rule Create_stack
end
rule Preprocess
- rule Create_fit
+
+ case $Mode_Cor
+ when 1
+ rule Create_fit_each
+ when 2
+ rule Create_fit_all
+ end
if $Flag_3D
- rule Create_3dlst
+ rule Create_3dlst {filename: $I[1][1].str()}
rule Create_3d
end
if $Flag_3DWhole
- rule Create_3dwholelst
+ rule Create_3dwholelst {filename: $I[1][1].str()}
rule Create_3dwhole
end
if $Flag_3D4S
- rule Create_3d4slst
+ rule Create_3d4slst {filename: $I[1][1].str()}
rule Create_3d4s
end
- rule Projection_3d
+ if $Flag_Projection
+ rule Projection_3d
+ end
End
param $ROI_ROT1_START := 0
param $ROI_ROT1_END := 359
param $ROI_ROT1_DELTA := 30
+$roi_rot1_loop := ($ROI_ROT1_END - $ROI_ROT1_START) / $ROI_ROT1_DELTA
param $ROI_ROT2_START := 0
param $ROI_ROT2_END := 359
param $ROI_ROT2_DELTA := 30
+$roi_rot2_loop := ($ROI_ROT2_END - $ROI_ROT2_START) / $ROI_ROT2_DELTA
param $ROI_ROT3_START := 0
param $ROI_ROT3_END := 0
param $ROI_ROT3_DELTA := 30
+$roi_rot3_loop := ($ROI_ROT3_END - $ROI_ROT3_START) / $ROI_ROT3_DELTA
param $ROI_SN := 1
# advanced param
-advanced param $Flag_ROI := true
-advanced param $Flag_Ref := true
+## Mode 0: do not, 1: each, 2: all
+advanced param $Mode_ROI := 1
+advanced param $Mode_Ref := 1
+advanced param $Mode_Cor := 1
+## Flag true: do, false: do not
advanced param $Flag_3D := true
advanced param $Flag_3DWhole := true
advanced param $Flag_3D4S := true
+advanced param $Flag_Projection := true
# .lst.padlst:
Rule Preprocess
- input '*.lst'
- input '*.roi'.all
- output '*.pad'.all
- output '{$I[1][1]}.padlst'
+ input '*.roi'
+ output '{$I[1][1]}.pad'
Flow
rule roi_smooth;
rule smooth_shrink;
rule shrink_pad;
- rule pad_padlst;
End
#.roi.smooth:
height=`expr {$Y_SIZE} / {$SHRINK}`
mrcImagePad -i {$I[1]} -o {$O[1]} -W ${width} -H ${height}
End
-
-Rule pad_padlst
- input '*.lst'
- input '*.pad'.all
- output '{$I[1][1]}.padlst'
-Action
- echo "{$I[2].join("\\n")}" > {$O[1]}
-End
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