--- /dev/null
+# For GroupingPoint
+param $filename := "121p-shift2"
+param $ROT2 := (0.upto(3)) * 45
+param $divide := 4
+
+Rule Main
+ input '*.padsortlst'
+ input '{$I[1][1]}.treeinfo'
+ output '{$I[1][1]}.groupinfo'
+Action
+ cp {$I[1]} 1.lst
+ cp {$I[2]} 1.tree
+ for (( i=2; i<={$divide}; i++ ))
+ do
+ max=0
+ for data in $(ls *.lst)
+ do
+ num=$(wc -l ${data} | awk '{printf $1}')
+ if [ ${num} -gt ${max} ] ; then
+ max=${num}
+ maxlist="${data}"
+ fi
+ done
+ maxtree="$(basename ${maxlist} '.lst').tree"
+ root=$(head -1 ${maxtree} | awk '{printf("%d", $1)}')
+ rootname=$(basename $(awk -v val=${root} '$2==val {printf("%s", $1)}' ${maxlist}) ".pad")
+ cp ${maxlist} ${rootname}.avglst
+ maxpos=$(awk -v val=${root} '$2==val {printf("%f", $3)}' ${maxlist})
+ line=$(awk -v val=${root} '$2==val {print NR}' ${maxlist})
+ head -$((${line} - 1)) ${maxlist} > ${i}.lst
+ tail -$(($(wc -l ${maxlist} | awk '{print $1}') - ${line} + 1)) ${maxlist} > tmp
+ cp tmp ${maxlist}
+
+ max_t=$(wc -l ${maxtree} | awk '{printf $1}')
+ max_l=$(wc -l ${maxlist} | awk '{printf $1}')
+ line_t=$(awk -v val=${root} '$1==val {print NR}' ${maxtree})
+ head -$((${max_l} + ${line_t} - 1)) ${maxtree} | tail -$((${max_l} - 1)) > tmp
+ tail -$((${max_t} - ${max_l})) ${maxtree} > ${i}.tree
+ cp tmp ${maxtree}
+ done
+
+ array_rot2=( {$ROT2} )
+
+ total=0
+ element_total=0
+ for lst in $(ls *.lst)
+ do
+ num=$(basename ${lst} ".lst")
+ element_num=$(wc -l ${num}.lst | awk '{print $1}')
+ element_total=$(( ${element_total} + ${element_num} ))
+ data=$(head -1 ${num}.tree)
+ root_i=$(echo ${data} | awk '{print $1}')
+ root_name=$(basename $(awk -v i=${root_i} '$2==i {print $1}' ${num}.lst) ".pad")
+
+ max=0
+ max_i=0
+ i=0
+ include_max_rot2=${array_rot2[0]}
+ for rot2 in ${array_rot2[@]}
+ do
+ include_num=$(grep "{$filename}-0-${rot2}-" ${num}.lst | wc -l | awk '{print $1}')
+ if [ ${include_num} -gt ${max} ] ; then
+ max=${include_num}
+ include_max_rot2=${rot2}
+ max_i=${i}
+ fi
+ i=$(( ${i} + 1 ))
+ done
+
+ echo "group${root_i}: match: ${max} owner: ${include_max_rot2}" >> {$O[1]}
+ total=$(( ${total} + ${max} ))
+
+ unset array_rot2[${max_i}]
+ array_rot2=("${array_rot2[@]}")
+ done
+ echo " total: ${total}" >> {$O[1]}
+ echo "${total} ${element_total}" | awk '{printf("parcentage: %f\n", $1 / $2)}' >> {$O[1]}
+End
-param $task := 2
-param $divide := 2
-param $refine := 5
+param $task := 4
+param $divide := 4
+param $refine := 0#5
# Cluster Name
param $CLUSTER := "all"
param $PADMODE := 13
# LOWPASS
param $LowPassMode := 4
-param $LowPassResolution := 0.1
+param $LowPassResolution := 0.085
# Clustering
param $ClusterCorrelationMode := 19
("TreeScaleY":$TreeScaleY) |
("TreeOffset":$TreeOffset)
+# For GroupingPoint
+param $filename := "121p-shift2"
+param $ROT2 := (0.upto(3)) * 45
+
Rule Main
input '*.roi'.all
input 'Makefile'
+ output '*.pad'.all
output '*.avg'.all
output '*.tiff'.all
- output 'all.logps'
- output 'all.treeinfo'
- output 'all.avgsortlst'
+ output '{$CLUSTER}.logps'
+ output '{$CLUSTER}.treeinfo'
+ output '{$CLUSTER}.padsortlst'
+ output '{$CLUSTER}.avgsortlst'
+ output '*.avg*'.all
+ output '*.groupinfo'.all
Flow
rule SetParam
rule Preprocess {filelist:$I[1].all, num:1.upto($task), length:$I[1].length()}
rule Process
- rule Refinement {num:1.upto($divide)}
+ rule Refinement {num:1.upto($divide)} >>> GroupingPoint
rule RefinementRoot
rule MontageAverage
End
input '*.pad'.all
input 'Makefile'
input 'Makefile.config'
- output 'all.padsortlst'
- output 'all.treeinfo'
- output 'all.avgsortlst'
+ output '{$CLUSTER}.padsortlst'
+ output '{$CLUSTER}.treeinfo'
+ output '{$CLUSTER}.avgsortlst'
output ((1.upto($divide).str())+".lst").d().all()
output ((1.upto($divide).str())+".tree").d().all()
output ("*.pad"+(1.upto($divide).str())).d().all()
output ("*.avg"+(0.upto($divide).str())).d().all()
output '*.avglst'.all
- output 'all.padsortmon.tiff'
- output 'all.avgsortmon.tiff'
- output 'all.logps'
+ output '{$CLUSTER}.padsortmon.tiff'
+ output '{$CLUSTER}.avgsortmon.tiff'
+ output '{$CLUSTER}.logps'
Action
- ls -1 *.pad > all.padlst
+ ls -1 *.pad > {$CLUSTER}.padlst
make Log
make LogPS
- mrc2tiff -i all.padsortmon -o all.padsortmon.tiff
- mrc2tiff -i all.avgsortmon -o all.avgsortmon.tiff
+ mrc2tiff -i {$CLUSTER}.padsortmon -o {$CLUSTER}.padsortmon.tiff
+ mrc2tiff -i {$CLUSTER}.avgsortmon -o {$CLUSTER}.avgsortmon.tiff
cp {$O[1]} 1.lst
cp {$O[2]} 1.tree
Action
max=$(wc -l {$num}.tree | awk '{printf $1}')
data=$(head -1 {$num}.tree)
- i=$(echo ${data} | awk '{print $1}')
- name=$(basename $(awk -v i=${i} '$2==i {print $1}' {$num}.lst) ".pad")
- cp {$num}.lst ${name}.avglst
- cp {$num}.tree ${name}.tree
+ root_i=$(echo ${data} | awk '{print $1}')
+ root_name=$(basename $(awk -v i=${root_i} '$2==i {print $1}' {$num}.lst) ".pad")
+ cp {$num}.lst ${root_name}.avglst
+ cp {$num}.tree ${root_name}.tree
for (( k=1; k<=max ; k++ ))
do
mrcImageAverage -i ${name}.fitlst -o ${name}.pad.avg
done
+
mrc2tiff -i ${name}.pad.avg -o ${name}.pad.avg.tiff
mrc2tiff -i ${name}.pad.avg{$num} -o ${name}.pad.avg{$num}.tiff
done
ClusterRotationRangePartitionNumber=$(awk '$1=="ClusterRotationRangePartitionNumber" {print $2}' Makefile.config.tmp)
ClusterRotationIterationNumber=$(awk '$1=="ClusterRotationIterationNumber" {print $2}' Makefile.config.tmp)
ClusterRotationCorrelationMode=$(awk '$1=="ClusterRotationCorrelationMode" {print $2}' Makefile.config.tmp)
-
+
for data in $(ls *.avglst)
do
name=$(basename ${data} ".avglst")
mrcImageAverage -i ${name}.fitlst -o ${name}.pad.avg
done
+
mrc2tiff -i ${name}.pad.avg -o ${name}.pad.avg.tiff
mrc2tiff -i ${name}.pad.avg0 -o ${name}.pad.avg0.tiff
done
End
+Rule GroupingPoint
+ input '*.lst'.all
+ input '*.tree'.all
+ output '{$CLUSTER}.groupinfo'
+Action
+ array_rot2=( {$ROT2} )
+
+ total=0
+ element_total=0
+ for num in {$I[1][1]}
+ do
+ element_num=$(wc -l ${num}.lst | awk '{print $1}')
+ element_total=$(( ${element_total} + ${element_num} ))
+ data=$(head -1 ${num}.tree)
+ root_i=$(echo ${data} | awk '{print $1}')
+ root_name=$(basename $(awk -v i=${root_i} '$2==i {print $1}' ${num}.lst) ".pad")
+
+ max=0
+ max_i=0
+ i=0
+ include_max_rot2=${array_rot2[0]}
+ for rot2 in ${array_rot2[@]}
+ do
+ include_num=$(grep "{$filename}-0-${rot2}-" ${num}.lst | wc -l | awk '{print $1}')
+ if [ ${include_num} -gt ${max} ] ; then
+ max=${include_num}
+ include_max_rot2=${rot2}
+ max_i=${i}
+ fi
+ i=$(( ${i} + 1 ))
+ done
+
+ echo "group${root_i}: match: ${max} owner: ${include_max_rot2}" >> {$O[1]}
+ total=$(( ${total} + ${max} ))
+
+ unset array_rot2[${max_i}]
+ array_rot2=("${array_rot2[@]}")
+ done
+ echo " total: ${total}" >> {$O[1]}
+ echo "${total} ${element_total}" | awk '{printf("parcentage: %f\n", $1 / $2)}' >> {$O[1]}
+End
+
Rule MontageAverage
- input 'all.avgsortlst'
- input 'all.treeinfo'
+ input '{$CLUSTER}.avgsortlst'
+ input '{$CLUSTER}.treeinfo'
input '*.pad.avg'.all
- output 'all.avgrefinemon'
- output 'all.avgrefinemon.tiff'
+ output '{$CLUSTER}.avgrefinemon'
+ output '{$CLUSTER}.avgrefinemon.tiff'
Action
root=$(head -1 {$I[2]} | awk '{print $1}')
root_file=$(awk -v val=${root} '$2==val {print $1}' {$I[1]})
--- /dev/null
+Rule Main
+ input '*.ref3d'
+ output '*.roi'.all
+ output '*.tiff'.all
+ param $X_SIZE := 32
+ param $Y_SIZE := 32
+ param $ROI_ROT_MODE := "XEYS"
+ param $ROI_ROT1_MIN := 0
+ param $ROI_ROT1_MAX := 0
+ param $ROI_ROT1_DELTA := 45
+ $ROI_ROT1 := (((0.upto(($ROI_ROT1_MAX - $ROI_ROT1_MIN) / $ROI_ROT1_DELTA)) * $ROI_ROT1_DELTA) + $ROI_ROT1_MIN).all
+ param $ROI_ROT2_MIN := 0
+ param $ROI_ROT2_MAX := 135
+ param $ROI_ROT2_DELTA := 45
+ $ROI_ROT2 := (((0.upto(($ROI_ROT2_MAX - $ROI_ROT2_MIN) / $ROI_ROT2_DELTA)) * $ROI_ROT2_DELTA) + $ROI_ROT2_MIN).all
+ param $ROI_ROT3_MIN := 0
+ param $ROI_ROT3_MAX := 270
+ param $ROI_ROT3_DELTA := 30
+ $ROI_ROT3 := (((0.upto(($ROI_ROT3_MAX - $ROI_ROT3_MIN) / $ROI_ROT3_DELTA)) * $ROI_ROT3_DELTA) + $ROI_ROT3_MIN).all
+ param $ROI_SN := 0.9
+Action
+ data=$(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} ${sampling_length}
+
+ for rot1 in {$ROI_ROT1}
+ do
+ for rot2 in {$ROI_ROT2}
+ do
+ for rot3 in {$ROI_ROT3}
+ do
+ mrc3Dto2D -i {$I[1][1]}.sample3d -o {$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 {$ROI_SN}
+ mrc2tiff -i {$I[1][1]}-${rot1}-${rot2}-${rot3}-{$ROI_SN}.roi -o {$I[1][1]}-${rot1}-${rot2}-${rot3}-{$ROI_SN}.tiff
+ done
+ done
+ done
+End
input '*.ref3d'
output '*.roi'.all
output '*.tiff'.all
- param $X_SIZE := 32
- param $Y_SIZE := 32
+ #output '*.ref2d'.all
+ param $X_SIZE := 64#32
+ param $Y_SIZE := 64#32
param $ROI_ROT_MODE := "XEYS"
- param $ROI_ROT1_NUM := 3
- param $ROI_ROT2_NUM := 3
- param $ROI_ROT3_NUM := 3
- param $ROI_SHIFT_NUM := 2
- param $ROI_SN := 1
+ param $ROI_ROT1_NUM := 1#3
+ param $ROI_ROT2_NUM := 4#3
+ param $ROI_ROT3_NUM := 10
+ param $ROI_SHIFT_NUM := 1#2
+ param $ROI_SN := 0.3
param $ROI_NOISE_NUM := 1
Action
data=$(mrcInfo -i {$I[1]} | head -1)
done
done
done
+ #mrc3Dto2D -i {$I[1][1]}.sample3d -o all.ref2d -InterpolationMode 2 -EulerMode {$ROI_ROT_MODE} \
+ # -Rot1 ${rot1} ${rot1} 1 \
+ # -Rot2 ${rot2} ${rot2} 1 \
+ # -Rot3 0 0 1
done
done
End
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