#
# 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].as_string.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