pione 0.1.0

data/example/SingleParticlesWithRef/SingleParticlesWithRef.pione

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+#
+# Eos for 3D reconstrucion from 2D rois using 3D initail reference
+#
+
+#
+# Variables
+#
+
+# Target structure name
+$TARGET := "all"
+
+#
+# Search Area for 3D
+#
+
+# Rot1
+$ROT1MIN := 0
+$ROT1MAX := 359
+$ROT1D   := 30
+$nRot1   := 12
+
+# Rot2
+$ROT2MIN := 0
+$ROT2MAX := 359
+$ROT2D   := 30
+$nRot2   := 12
+
+# Rot3
+$ROT3MIN := 0
+$ROT3MAX := 0
+$ROT3D   := 30
+$nRot3   := 1
+
+# For 2D
+$STEP   := 12
+$ROTMIN := 0
+$ROTMAX := 359
+$nROT   := 360 / $STEP
+
+# Pad size for 2D
+$PAD_W := 64
+$PAD_H := 64
+
+#
+# Rules
+#
+
+Rule Main
+  input '*.roi'.all
+  input '{$TARGET}.ref3d'
+  input '{$TARGET}.ref2d'
+  output '{$TARGET}.3d'
+Flow
+  rule Create3dinfo
+  rule Create3dlst
+  rule Create3d
+End
+
+Rule Create3dinfo
+  input '*.roi'
+  input '{$TARGET}.ref2d'
+  output '{$*}.corinfo'
+  output '{$*}.fit'
+  output '{$*}.3dinfo'
+Flow
+  rule ConvertRoiToPad
+  rule ConvertPadToCorinfo
+  rule ConvertCorinfoTo3dinfo
+End
+
+# .roi.pad
+Rule ConvertRoiToPad
+  input '*.roi'
+  output '{$*}.pad'
+Action
+  mrcImageWindowing -i {$*}.roi -o {$*}.mask -W 0.1 0.0 0.05 0.0 -m 18
+  mrcImagePad -i {$*}.mask -o {$*}.padtmp -W {$PAD_W} -H {$PAD_H} -m 3
+  mrcImageWindowing -i {$*}.padtmp -o {$*}.pad -W 0.1 0.0 0.1 0.0 -m 2
+End
+
+# .pad.corinfo
+Rule ConvertPadToCorinfo
+  input '*.pad'
+  input '{$TARGET}.ref2d'
+  output '{$*}.corinfo'
+  output '{$*}.fit'
+Action
+  mrcImageAutoRotationCorrelation -i {$*}.pad -r {$TARGET}.ref2d -O {$*}.corinfo -fit {$*}.fit -cor {$*}.cormap -n {$nROT} -m 18 -range {$ROTMIN} {$ROTMAX} -Iter 2 -nRot2 {$nRot2} -nRot1 {$nRot1} -nRot3 {$nRot3} 2> /dev/null
+End
+
+# .corinfo.3dinfo
+Rule ConvertCorinfoTo3dinfo
+  input '*.corinfo'
+  output '{$*}.3dinfo'
+Action
+  awk '/Cor/ { print $7,$16,$2,$3,$4,$5,$9,$11,$12}' {$*}.corinfo | sort -r | sed -e s/.pad/.fit/ > {$*}.3dinfolst
+  head -n 1 {$*}.3dinfolst | awk '{print $2,$3,$4,$5,$6,$1}' > {$*}.3dinfo
+End
+
+# .3dinfo.3dlst
+Rule Create3dlst
+  input '*.3dinfo'.all
+  output '{$TARGET}.3dlst'
+Action
+  cat {$I[1].join(" ")} | sort > {$TARGET}.3dlst
+End
+
+# .3dlst.3d
+Rule Create3d
+  input '{$TARGET}.3dlst'
+  input '*.fit'.all
+  output '{$TARGET}.3d'
+Action
+  mrc2Dto3D -I {$TARGET}.3dlst -o {$TARGET}.3d -InterpolationMode 2 -Double -DoubleCounter {$TARGET}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2
+End
+

data/example/SingleParticlesWithRef/SingleParticlesWithRefFull.pione

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+#
+# Eos for 3D reconstrucion from 2D rois using 3D initail reference
+#
+
+#
+# Variables
+#
+
+# Initial Reference Model
+$INITIAL := "initial"
+
+# Target structure name
+$TARGET := "all"
+
+#
+# Search Area for 3D
+#
+$ROTMODE := "YOYS"
+
+# Rot1
+$ROT1MIN := 0
+$ROT1MAX := 359
+$ROT1D   := 30
+$nRot1   := 12
+
+# Rot2
+$ROT2MIN := 0
+$ROT2MAX := 359
+$ROT2D   := 30
+$nRot2   := 12
+
+# Rot3
+$ROT3MIN := 0
+$ROT3MAX := 0
+$ROT3D   := 30
+$nRot3   := 1
+
+# For 2D
+$STEP   := 12
+$ROTMIN := 0
+$ROTMAX := 359
+$nROT   := 360 / $STEP
+
+# Seletion Step
+$COR_THRESHOLD     := 0.4
+$Y_SHIFT_THRESHOLD := 20
+
+# Pad size for 2D
+$PAD_W := 64
+$PAD_H := 64
+
+#
+# Initial model from PDB
+#
+$REFSOURCE := "121p-shift"
+$DELTA   := 2.5
+$SIZE_X  := 64.0
+$SIZE_Y  := 64.0
+$SIZE_Z  := 64.0
+$START_X := -1.0 * $DELTA * $SIZE_X / 2.0
+$START_Y := -1.0 * $DELTA * $SIZE_Y / 2.0
+$START_Z := -1.0 * $DELTA * $SIZE_Z / 2.0
+$SNRATIO := 3
+
+#
+# Rules
+#
+
+Rule Main
+  input '{$REFSOURCE}.pdb'
+  output '{$TARGET}.3d'
+  output '{$TARGET}.ds6'
+  output '{$TARGET}.gnuplotcorinfolst'
+  output '{$TARGET}.gnuplotanglelst'
+  output '{$TARGET}.gnuplotshiftlst'
+  output '{$TARGET}.mon'
+Flow
+  rule Init
+  rule First
+  rule All
+End
+
+
+#
+# Init
+#
+
+Rule Init
+  input '{$REFSOURCE}.pdb'
+  output '{$INITIAL}.3d'
+  output '*.roi'.all
+Flow
+  rule CreateInitialModel
+  rule CreateTestData.params({rot1: 0, rot2: 0, rot3: 0})
+End
+
+# InitialModel
+Rule CreateInitialModel
+  input '{$REFSOURCE}.pdb'
+  output '{$INITIAL}.3d'
+Action
+  pdb2mrc -i {$REFSOURCE}.pdb -o {$INITIAL}.3d -nx {$SIZE_X.as_int} -ny {$SIZE_Y.as_int} -nz {$SIZE_Z.as_int} -Sx {$START_X.as_int} -Sy {$START_Y.as_int} -Sz {$START_Z.as_int} -dx {$DELTA} -dy {$DELTA} -dz {$DELTA} -m 1
+End
+
+# TestData
+Rule CreateTestData
+  input '{$INITIAL}.3d'
+  output '*.roi'.all
+  param $rot1
+  param $rot2
+  param $rot3
+Flow
+  if $rot1 <= $ROT1MAX
+    if $rot2 <= $ROT2MAX
+      if $rot3 <= $ROT3MAX
+        if ((($rot1 + $ROT1D*2) > $ROT1MAX) and (($rot2 + $ROT2D*2) > $ROT2MAX)).not
+          rule CreateTestData.params({rot1: $rot1, rot2: $rot2 + $ROT2D*2, rot3: $ROT3MIN})
+        end
+        rule ActionTestData.params({rot1: $rot1, rot2: $rot2, rot3: $rot3})
+        rule ActionTestDataNoise.params({rot1: $rot1, rot2: $rot2, rot3: $rot3})
+      else
+      end
+    else
+      rule CreateTestData.params({rot1: $rot1 + $ROT1D*2, rot2: $ROT2MIN, rot3: $ROT3MIN})
+    end
+  end
+End
+
+Rule ActionTestData
+  input '{$INITIAL}.3d'
+  output '{$REFSOURCE}-{$rot1}-{$rot2}-{$rot3}.roi'
+  param $rot1
+  param $rot2
+  param $rot3
+Action
+  mrc3Dto2D -i {$INITIAL}.3d -o {$REFSOURCE}-{$rot1}-{$rot2}-{$rot3}.roi \
+    -InterpolationMode 2 -EulerMode {$ROTMODE} \
+    -Rot1 {$rot1} {$rot1} 1 -Rot2 {$rot2} {$rot2} 1 -Rot3 {$rot3} {$rot3} 1
+End
+
+Rule ActionTestDataNoise
+  input '{$REFSOURCE}-{$rot1}-{$rot2}-{$rot3}.roi'
+  output '{$REFSOURCE}-noise-{$rot1}-{$rot2}-{$rot3}.roi'
+  param $rot1
+  param $rot2
+  param $rot3
+Action
+  mrcImageNoiseAdd -i {$I[1]} -o {$O[1]} -SN {$SNRATIO};
+End
+
+#
+# First
+#
+
+Rule First
+  input '{$INITIAL}.3d'
+  output '{$TARGET}.ref3d'.all
+  output '{$TARGET}.ref2d'.all
+Flow
+  rule CreateRef3d
+  rule CreateRef2d
+End
+
+Rule CreateRef3d
+  input  '{$INITIAL}.3d'
+  output '{$TARGET}.ref3d'
+Action
+  cp {$INITIAL}.3d {$TARGET}.ref3d
+End
+
+Rule CreateRef2d
+  input  '{$TARGET}.ref3d'
+  output '{$TARGET}.ref2d'
+Action
+  mrc3Dto2D -i {$TARGET}.ref3d -o {$TARGET}.ref2d -EulerMode {$ROTMODE} -InterpolationMode 2 -Rot2 {$ROT2MIN} {$ROT2MAX} {$ROT2D} -Rot1 {$ROT1MIN} {$ROT1MAX} {$ROT1D} -Rot3 {$ROT3MIN} {$ROT3MAX} {$ROT3D} -m 0
+End
+
+#
+# All
+#
+
+Rule All
+  input '*.roi'.all
+  input '{$TARGET}.ref3d'
+  input '{$TARGET}.ref2d'
+  output '{$TARGET}.3d'
+  output '{$TARGET}.ds6'
+  output '{$TARGET}.gnuplotcorinfolst'
+  output '{$TARGET}.gnuplotanglelst'
+  output '{$TARGET}.gnuplotshiftlst'
+  output '{$TARGET}.mon'
+Flow
+  rule Create3dinfo
+  rule Create3dlst
+  rule Create3d
+  rule CreateDs6
+  rule CreateParcorinfoSort
+  rule CreatePlotData
+  rule CreateMontageList
+End
+
+
+#
+# 3dinfo
+#
+
+Rule Create3dinfo
+  input '*.roi'
+  input '{$TARGET}.ref2d'
+  output '{$*}.corinfo'
+  output '{$*}.fit'
+  output '{$*}.3dinfo'
+Flow
+  rule ConvertRoiToPad
+  rule ConvertPadToCorinfo
+  rule ConvertCorinfoTo3dinfo
+End
+
+# .roi.pad
+Rule ConvertRoiToPad
+  input '*.roi'
+  output '{$*}.pad'
+Action
+  mrcImageWindowing -i {$*}.roi -o {$*}.mask -W 0.1 0.0 0.05 0.0 -m 18
+  mrcImagePad -i {$*}.mask -o {$*}.padtmp -W {$PAD_W} -H {$PAD_H} -m 3
+  mrcImageWindowing -i {$*}.padtmp -o {$*}.pad -W 0.1 0.0 0.1 0.0 -m 2
+End
+
+# .pad.corinfo
+Rule ConvertPadToCorinfo
+  input '*.pad'
+  input '{$TARGET}.ref2d'
+  output '{$*}.corinfo'
+  output '{$*}.fit'
+Action
+  mrcImageAutoRotationCorrelation -i {$*}.pad -r {$TARGET}.ref2d -O {$*}.corinfo -fit {$*}.fit -cor {$*}.cormap -n {$nROT} -m 18 -range {$ROTMIN} {$ROTMAX} -Iter 2 -nRot2 {$nRot2} -nRot1 {$nRot1} -nRot3 {$nRot3} 2> /dev/null
+End
+
+# .corinfo.3dinfo
+Rule ConvertCorinfoTo3dinfo
+  input '*.corinfo'
+  output '{$*}.3dinfo'
+Action
+  awk '/Cor/ { print $7,$16,$2,$3,$4,$5,$9,$11,$12}' {$*}.corinfo | sort -r | sed -e s/.pad/.fit/ > {$*}.3dinfolst
+  head -n 1 {$*}.3dinfolst | awk '{print $2,$3,$4,$5,$6,$1}' > {$*}.3dinfo
+End
+
+#
+# 3dlst
+#
+
+# .3dinfo.3dlst
+Rule Create3dlst
+  input '*.3dinfo'.all
+  output '{$TARGET}.3dlst'
+Action
+  cat {$I[1].join(" ")} > {$TARGET}.3dlst
+End
+
+# .3dlst.3d
+Rule Create3d
+  input '{$TARGET}.3dlst'
+  input '*.fit'.all
+  output '{$TARGET}.3d'
+Action
+  mrc2Dto3D -I {$TARGET}.3dlst -o {$TARGET}.3d -InterpolationMode 2 -Double -DoubleCounter {$TARGET}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2
+End
+
+#
+# Ds6
+#
+
+Rule CreateDs6
+  input  '{$TARGET}.3d'
+  output '{$TARGET}.ds6'
+Flow
+  rule Convert3dTo3dsm
+  rule Convert3dsmTo3dsmCenter
+  rule Convert3dsmCenterToDs6
+End
+
+# .3d.3dsm
+Rule Convert3dTo3dsm
+  input  '{$TARGET}.3d'
+  output '{$TARGET}.3dsm'
+Action
+  mrcImageSmoothing -i {$TARGET}.3d -o {$TARGET}.3dsm -m 1 -M 1 -r 3
+End
+
+# .3dsm.3dsmCenter
+Rule Convert3dsmTo3dsmCenter
+  input  '{$TARGET}.3dsm'
+  output '{$TARGET}.3dsmCenter'
+Action
+  mrcImageCenterGet -i {$TARGET}.3dsm -o {$TARGET}.3dsmCenter -Nx 64 -Ny 64 -Nz 64
+End
+
+# .3dsmCenter.ds6
+Rule Convert3dsmCenterToDs6
+  input  '{$TARGET}.3dsmCenter'
+  output '{$TARGET}.ds6'
+Action
+  mrc2map -i {$TARGET}.3dsmCenter -o {$TARGET}.ds6 -m 3
+End
+
+#
+# ParcorinfoSort
+#
+
+Rule CreateParcorinfoSort
+  input '*.corinfo'.all
+  output '{$TARGET}.parcorinfolst'
+Flow
+  rule ConvertCorinfoToCorinfo2
+  rule CreateParcorinfolst
+  rule ConvertParcorinfolstToParcorinfoSort
+  rule ConvertParcorinfolstsortToSelectParticle
+End
+
+# .corinfo.corinfo2
+Rule ConvertCorinfoToCorinfo2
+  input '*.corinfo'
+  output '{$*}.corinfo2'
+Action
+  awk '/Cor/ { print $18,$16,$2,$3,$4,$5,$9,$11,$12}' {$*}.corinfo | sort -r | sed -e 's/.roi/.fit/' > {$*}.corinfolst
+  head -n 1 {$*}.corinfolst | awk '{if({$PAD_W}-$8>=$8&&{$PAD_H}-$9>=$9) print $1,$2,$3,$4,$5,$6,$7,0+$8,0+$9;else if({$PAD_W}-$8>=$8) print $1,$2,$3,$4,$5,$6,$7,0+$8,{$PAD_H}-$9;else if({$PAD_H}-$9>=$9) print $1,$2,$3,$4,$5,$6,$7,{$PAD_W}-$8,0+$9;else print $1,$2,$3,$4,$5,$6,$7,{$PAD_W}-$8,{$PAD_H}-$9}' > {$*}.corinfo2
+End
+
+# .corinfo2.parcorinfolst
+Rule CreateParcorinfolst
+  input '*.corinfo2'.all
+  output '{$TARGET}.parcorinfolst'
+Action
+  cat {$I[1].join(" ")} > {$TARGET}.parcorinfolst
+End
+
+# ConvertParcorinfolstToParcorinfoSort
+Rule ConvertParcorinfolstToParcorinfoSort
+  input '{$TARGET}.parcorinfolst'
+  output '{$TARGET}.parcorinfolstsort'
+Action
+  awk '{ print $1,$2,$3,$4,$5,$6,$7,$8,$9}' {$TARGET}.parcorinfolst | sort -r > {$TARGET}.parcorinfolstsort
+End
+
+# ConvertParcorinfolstsortToSelectParticle
+Rule ConvertParcorinfolstsortToSelectParticle
+  input '{$TARGET}.parcorinfolstsort'
+  output '{$TARGET}.3dlstselect'
+Action
+  awk '$1 >= {$COR_THRESHOLD} || $9 <= {$Y_SHIFT_THRESHOLD}{print $2,$3,$4,$5,$6,$1}' {$TARGET}.parcorinfolstsort > {$TARGET}.3dlstselect
+End
+
+#
+# Plot data
+#
+
+Rule CreatePlotData
+  input '{$TARGET}.parcorinfolst'
+  output '{$TARGET}.gnuplotcorinfolst'
+  output '{$TARGET}.gnuplotanglelst'
+  output '{$TARGET}.gnuplotshiftlst'
+Flow
+  rule CreateGnuplotCorinfo
+  rule CreateGnuplotAngle
+  rule CreateGnuplotShift
+End
+
+Rule CreateGnuplotCorinfo
+  input '{$TARGET}.parcorinfolst'
+  output '{$TARGET}.gnuplotcorinfolst'
+Action
+  awk '{ print $1,$9}' {$TARGET}.parcorinfolst | sort -r > {$TARGET}.gnuplotcorinfolst
+End
+
+Rule CreateGnuplotAngle
+  input '{$TARGET}.parcorinfolst'
+  output '{$TARGET}.gnuplotanglelst'
+Action
+  awk '{ print $4,$5}' {$TARGET}.parcorinfolst > {$TARGET}.gnuplotanglelst
+End
+
+Rule CreateGnuplotShift
+  input '{$TARGET}.parcorinfolst'
+  output '{$TARGET}.gnuplotshiftlst'
+Action
+  awk '{ print $4,$5}' {$TARGET}.parcorinfolst > {$TARGET}.gnuplotshiftlst
+End
+
+#
+# Montage list
+#
+
+Rule CreateMontageList
+  input '{$TARGET}.3dlst'
+  input '*.fit'.all
+  output '{$TARGET}.mon'
+Action
+  awk '{ print $1}' {$TARGET}.3dlst > {$TARGET}.monlst
+  mrcImageMontageCreate -i {$TARGET}.monlst -o {$TARGET}.mon -nx 15 -ny 10
+End