X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=scripts%2Fcreate_midP.sh;fp=scripts%2Fcreate_midP.sh;h=0000000000000000000000000000000000000000;hb=b0a5bad2f1ac4991b4d2bdb1c015275128441635;hp=7591efb8004e2c7ad51b384377f4e62893c6abb9;hpb=ee568ccc2ae2be4d9d60967e522e2d81cb148d95;p=clitk.git

diff --git a/scripts/create_midP.sh b/scripts/create_midP.sh
deleted file mode 100755
index 7591efb..0000000
--- a/scripts/create_midP.sh
+++ /dev/null
@@ -1,535 +0,0 @@
-#!/bin/sh -x
-
-#################################################################
-# create_MidP 	arguments : CT_4D.mhd ref_phase spacing 	#
-#################################################################
-source `dirname $0`/midp_common.sh
-
-extract_patient()
-{
-  echo "$image_name -> Extracting patient..."
-  $CLITK/clitkExtractPatient -i $image_name -o MASK/patient_$image_name --noAutoCrop
-  $CLITK/clitkBinarizeImage -i MASK/patient_$image_name -o MASK/patient_$image_name -l 1 -u 1 --mode=BG
-  $CLITK/clitkSetBackground -i $image_name -o MASK/patient_only_$image_name --mask MASK/patient_$image_name --outsideValue -1000
-}
-
-extract_bones()
-{
-  echo "$image_name -> Extracting bones..."
-  $CLITK/clitkImageConvert -i $image_name -o MASK/float_$image_name -t float
-  $CLITK/clitkExtractBones -i MASK/float_$image_name -o MASK/bones_$image_name --lower1 120 --upper1 2000 --lower2 70 --upper2 2000 --smooth --time 0.0625 --noAutoCrop
-  $CLITK/clitkMorphoMath -i MASK/bones_$image_name -o MASK/bones_$image_name --type 2 --radius 4,4,2
-}
-
-resample()
-{
-  echo "$image_name -> Resampling..."
-  $CLITK/clitkResampleImage -i MASK/patient_$image_name -o MASK/patient_$image_name --spacing $spacing
-  $CLITK/clitkResampleImage -i MASK/patient_only_$image_name -o MASK/patient_only_$image_name --spacing $spacing
-  #$CLITK/clitkResampleImage -i MASK/bones_$image_name -o MASK/bones_$image_name --like MASK/patient_only_$image_name
-}
-
-compute_motion_mask()
-{
-#   $CLITK/clitkMotionMask -i MASK/patient_only_$image_name -o MASK/mm_$image_name --featureBones=MASK/bones_$image_name --upperThresholdLungs -400 --fillingLevel 94 --offsetDetect 0,-5,0 --pad --writeFeature=MASK/feature_$image_name --writeEllips=MASK/inital_ellipse_$image_name --writeGrownEllips=MASK/growing_ellipse_$image_name;
-$CLITK/clitkMotionMask -i MASK/patient_only_$image_name -o MASK/mm_$image_name --upperThresholdLungs -400 --fillingLevel 94 --offsetDetect 0,-5,0 --pad --writeFeature=MASK/feature_$image_name --writeEllips=MASK/inital_ellipse_$image_name --writeGrownEllips=MASK/growing_ellipse_$image_name;
-}
-
-set_background()
-{
-  echo "$image_name -> Setting Background..."
-  $CLITK/clitkSetBackground -i MASK/patient_only_$image_name -o MASK/inside_$image_name --mask MASK/mm_$image_name --outsideValue -1200
-  $CLITK/clitkSetBackground -i MASK/patient_only_$image_name -o MASK/outside_$image_name --mask MASK/mm_$image_name --outsideValue -1200 --fg
-}
-
-create_registration_masks()
-{
-  echo "$image_name -> Creating registration masks..."
-  $CLITK/clitkMorphoMath -i MASK/mm_$image_name -o MASK/regmask_in_$image_name --type 1 --radius 8
-  $CLITK/clitkExtractPatient -i MASK/outside_$image_name -o MASK/regmask_out_$image_name --noAutoCrop
-  $CLITK/clitkMorphoMath -i MASK/regmask_out_$image_name -o MASK/regmask_out_$image_name --type 1 --radius 8
-}
-
-remove_files()
-{
-  echo "Removing temporary files..."
-  image_name_base=`echo $image_name | sed 's/mhd//'`
-  case $1 in
-    1)
-      rm MASK/float_$image_name_base*;;
-    2)
-      rm MASK/bones_$image_name_base*;;
-    3)
-      rm MASK/patient_only_$image_name_base*;;
-    4)
-      #rm MASK/patient_$image_name_base*
-      #rm MASK/mm_$image_name_base*
-      rm -f $vf_dir/vf_tmp_in_${ref}_${phase}.*
-      rm -f $vf_dir/vf_tmp_out_${ref}_${phase}.*
-      #rm MASK/regmask_in_$image_name_base*
-      #rm MASK/regmask_out_$image_name_base*
-      ;;
-    5)
-#       rm -f coeff_*
-      #rm $vf_dir/vf_in_*
-      #rm $vf_dir/vf_out_*
-#       rm MASK/regmask_*
-#       rm MASK/mm_*
-      ;;
-    6)
-      ;;
-      #rm -f $vf_dir/_4D.*
-      #rm -f $vf_dir/vf_MIDP_${ref}.*
-      #rm -f $vf_dir/vf_${ref}_MIDP.*;;
-    7)
-      ;; #rm $vf_dir/vf_MIDP_${phase}.*;;
-    8)
-      rm $vf_dir/*.txt
-      rm $vf_dir/*.log
-  esac
-}
-
-mm_preprocessing()
-{
-  extract_patient
-  #extract_bones
-  remove_files 1
-  resample
-}
-
-mm_postprocessing()
-{
-  remove_files 2
-  set_background
-  remove_files 3
-  create_registration_masks
-}
-
-# mm_workflow()
-# {
-#   extract_patient
-#   extract_bones
-#   remove_files 1
-#   resample
-#   echo "$image_name -> Computing motion mask..."
-#   compute_motion_mask >> LOG/motion_mask_$image_name.log
-#   remove_files 2
-#   set_background
-#   remove_files 3
-#   create_registration_masks
-# }
-
-motion_mask()
-{
-  echo
-  echo "------------ Motion mask ------------"
-  start=`date`
-  echo "start: $start"
-  echo
-  mkdir -p "MASK"
-  rm -f "LOG/motion_mask*.log"
-  regmask_in_list=""
-  regmask_out_list=""
-  reg_in_list=""
-  reg_out_list=""
-
-  # multi-threaded pre-processing for motion mask calcs
-  for phase in $phase_list
-  do
-    image_name=`echo $phase | sed 's/raw/mhd/'`
-    check_threads $MAX_THREADS
-    #mm_preprocessing &
-  done
-
-  # single-threaded motion mask calc
-  check_threads 1
-  for phase in $phase_list
-  do
-    image_name=`echo $phase | sed 's/raw/mhd/'`
-
-    echo "$image_name -> Computing motion mask..."
-    #compute_motion_mask >> LOG/motion_mask_$image_name.log
-  done
-
-  # multi-threaded post-processing of motion mask calcs
-  for phase in $phase_list
-  do
-    image_name=`echo $phase | sed 's/raw/mhd/'`
-    check_threads $MAX_THREADS 
-    #mm_postprocessing &
-    regmask_in_list="$regmask_in_list regmask_in_$image_name"
-    regmask_out_list="$regmask_out_list regmask_out_$image_name"
-    reg_in_list="$reg_in_list inside_$image_name"
-    reg_out_list="$reg_out_list outside_$image_name"
-  done
-
-  wait
-  echo
-  echo "-------- Motion mask done ! ---------"
-  end=`date`
-  echo "start: $start"
-  echo "end: $end"
-  echo
-}
-
-compute_BLUTDIR()
-{
-  ########## register in ##########
-  for reg_in in $reg_in_list
-  do
-    if [ ! -z `echo $reg_in | grep "$phase"` ]
-    then
-      target_in=$reg_in
-    fi
-  done
-  echo "Computing BLUTDIR $reference_in -> $target_in ..."
-  #$CLITK/clitkBLUTDIR --reference="MASK/$reference_in" --target="MASK/$target_in" --output="MASK/reg_$target_in" --referenceMask="MASK/$reference_mask_in" --vf="$vf_dir/vf_in_${ref}_${phase}.mhd" $coeff_in_ini --coeff="$coeff_dir/coeff_in_${ref}_${phase}.mhd" $registration_parameters_BLUTDIR >> LOG/registration_${ref}_${phase}.log
-  $CLITK/clitkBLUTDIR --reference="MASK/$reference_in" --target="MASK/$target_in" --output="MASK/reg_$target_in" --referenceMask="MASK/$reference_mask_in" --vf="$vf_dir/vf_in_${ref}_${phase}.mhd" --coeff="$coeff_dir/coeff_in_${ref}_${phase}.mhd" $registration_parameters_BLUTDIR >> LOG/registration_${ref}_${phase}.log
-  coeff_in_ini="--initCoeff=$coeff_dir/coeff_in_${ref}_${phase}.mhd"
-  ########## register out ##########
-  for reg_out in $reg_out_list
-  do
-    if [ ! -z `echo $reg_out | grep "$phase"` ]
-    then
-      target_out=$reg_out
-    fi
-  done
-  echo "Computing BLUTDIR $reference_out -> $target_out ..."
-  #$CLITK/clitkBLUTDIR --reference="MASK/$reference_out" --target="MASK/$target_out" --output="MASK/reg_$target_out" --referenceMask="MASK/$reference_mask_out" --vf="$vf_dir/vf_out_${ref}_${phase}.mhd" $coeff_out_ini --coeff="$coeff_dir/coeff_out_${ref}_${phase}.mhd" $registration_parameters_BLUTDIR >> LOG/registration_${ref}_${phase}.log
-  $CLITK/clitkBLUTDIR --reference="MASK/$reference_out" --target="MASK/$target_out" --output="MASK/reg_$target_out" --referenceMask="MASK/$reference_mask_out" --vf="$vf_dir/vf_out_${ref}_${phase}.mhd" --coeff="$coeff_dir/coeff_out_${ref}_${phase}.mhd" $registration_parameters_BLUTDIR >> LOG/registration_${ref}_${phase}.log
-  coeff_out_ini="--initCoeff=$coeff_dir/coeff_out_${ref}_${phase}.mhd"
-  ##################################
-  $CLITK/clitkCombineImage -i $vf_dir/vf_in_${ref}_${phase}.mhd -j $vf_dir/vf_out_${ref}_${phase}.mhd -m MASK/mm_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
-  $CLITK/clitkZeroVF -i $vf_dir/vf_${ref}_${phase}.mhd -o $vf_dir/vf_${ref}_${ref}.mhd
-  $CLITK/clitkCombineImage -i $vf_dir/vf_${ref}_${phase}.mhd -j $vf_dir/vf_${ref}_${ref}.mhd -m MASK/patient_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
-  remove_files 4
-}
-
-compute_DEMONSDIR()
-{
-  ########## register in ##########
-  for reg_in in $reg_in_list
-  do
-    if [ ! -z `echo $reg_in | grep "_$phase"` ]
-    then
-      target_in=$reg_in
-    fi
-  done
-  echo "Computing DEMONSDIR $reference_in -> $target_in ..."
-  $CLITK/clitkDemonsDeformableRegistration --reference="MASK/$reference_in" --target="MASK/$target_in" --output="MASK/reg_$target_in" --vf="$vf_dir/vf_in_${ref}_${phase}.mhd" $vf_in_ini $registration_parameters_DEMONSDIR #&>> LOG/registration_${ref}_${phase}.log
-  vf_in_ini="--init=$vf_dir/vf_in_${ref}_${phase}.mhd"
-  ########## register out ##########
-  for reg_out in $reg_out_list
-  do
-    if [ ! -z `echo $reg_out | grep "_$phase"` ]
-    then
-      target_out=$reg_out
-    fi
-  done
-  echo "Computing DEMONSDIR $reference_out -> $target_out ..."
-  $CLITK/clitkDemonsDeformableRegistration --reference="MASK/$reference_out" --target="MASK/$target_out" --output="MASK/reg_$target_out" --vf="$vf_dir/vf_out_${ref}_${phase}.mhd" $vf_out_ini $registration_parameters_DEMONSDIR #&>> LOG/registration_${ref}_${phase}.log
-  vf_out_ini="--init=$vf_dir/vf_out_${ref}_${phase}.mhd"
-  ##################################
-  $CLITK/clitkCombineImage -i $vf_dir/vf_in_${ref}_${phase}.mhd -j $vf_dir/vf_out_${ref}_${phase}.mhd -m MASK/mm_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
-  $CLITK/clitkZeroVF -i $vf_dir/vf_${ref}_${phase}.mhd -o $vf_dir/vf_${ref}_${ref}.mhd
-  $CLITK/clitkCombineImage -i $vf_dir/vf_${ref}_${phase}.mhd -j $vf_dir/vf_${ref}_${ref}.mhd -m MASK/patient_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
-  remove_files 4
-}
-
-compute_ELASTIX()
-{
-  ########## register in ##########
-  for reg_in in $reg_in_list
-  do
-    if [ ! -z `echo $reg_in | grep "_$phase"` ]
-    then
-      target_in=$reg_in
-    fi
-  done
-  echo "Computing ELASTIX $reference_in -> $target_in ..."
-  exec_dir=`which elastix`
-  exec_dir=`dirname $exec_dir`
-  cat $exec_dir/params_BSpline.txt | sed -e "s+<NbIterations>+500+" \
-                              -e "s+<LabelsFile>++" \
-                              -e "s+<HistBins>+25+" \
-                              -e "s+<Levels>+3+" \
-                              -e "s+<NbSamples>+2000+" \
-                              -e "s+<SamplerType>+Random+" \
-                              -e "s+<Spacing>+32+" > params_BSpline.txt 
-  elastix -f "MASK/$reference_in" -m "MASK/$target_in" -fMask "MASK/$reference_mask_in" -out $vf_dir -p params_BSpline.txt > /dev/null
-  transformix -tp $vf_dir/TransformParameters.0.txt -out $vf_dir -def all > /dev/null  
-  mv $vf_dir/deformationField.mhd $vf_dir/vf_in_${ref}_${phase}.mhd
-  mv $vf_dir/deformationField.raw $vf_dir/vf_in_${ref}_${phase}.raw
-  sed -i "s:deformationField:vf_in_${ref}_${phase}:" $vf_dir/vf_in_${ref}_${phase}.mhd
-  mv $vf_dir/result.0.mhd MASK/reg_$target_in
-  targetraw=`echo reg_$target_in | sed 's:mhd:raw:'`
-  sed -i "s:result.0.mhd:$targetraw" MASK/reg_$target_in
-  mv $vf_dir/result.0.raw MASK/$targetraw
-  remove_files 8
-
-  ########## register out ##########
-  for reg_out in $reg_out_list
-  do
-    if [ ! -z `echo $reg_out | grep "_$phase"` ]
-    then
-      target_out=$reg_out
-    fi
-  done
-  echo "Computing ELASTIX $reference_out -> $target_out ..."
-  elastix -f "MASK/$reference_out" -m "MASK/$target_out" -fMask "MASK/$reference_mask_out" -out $vf_dir -p params_BSpline.txt > /dev/null
-  transformix -tp $vf_dir/TransformParameters.0.txt -out $vf_dir -def all > /dev/null  
-  mv $vf_dir/deformationField.mhd $vf_dir/vf_out_${ref}_${phase}.mhd
-  mv $vf_dir/deformationField.raw $vf_dir/vf_out_${ref}_${phase}.raw
-  sed -i "s:deformationField:vf_out_${ref}_${phase}:" $vf_dir/vf_out_${ref}_${phase}.mhd
-  mv $vf_dir/result.0.mhd MASK/reg_$target_out
-  targetraw=`echo reg_$target_out | sed 's:mhd:raw:'`
-  sed -i "s:result.0.mhd:$targetraw" MASK/reg_$target_out
-  mv $vf_dir/result.0.raw MASK/$targetraw
-  remove_files 8
-
-  ##################################
-  $CLITK/clitkCombineImage -i $vf_dir/vf_in_${ref}_${phase}.mhd -j $vf_dir/vf_out_${ref}_${phase}.mhd -m MASK/mm_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
-  $CLITK/clitkZeroVF -i $vf_dir/vf_${ref}_${phase}.mhd -o $vf_dir/vf_${ref}_${ref}.mhd
-  $CLITK/clitkCombineImage -i $vf_dir/vf_${ref}_${phase}.mhd -j $vf_dir/vf_${ref}_${ref}.mhd -m MASK/patient_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
-  remove_files 4
-}
-
-registration()
-{
-  echo
-  echo "----------- Registration ------------"
-  start=`date`
-  echo "start: $start"
-  echo
-
-  rm -f "LOG/registration*.log"
-
-  # wait any unfinished threads
-  check_threads 1
-
-  for reg_in in $reg_in_list
-  do
-    if [ ! -z `echo $reg_in | grep "$ref"` ]
-    then
-      reference_in=$reg_in
-    fi
-  done
-  for reg_out in $reg_out_list
-  do
-    if [ ! -z `echo $reg_out | grep "$ref"` ]
-    then
-      reference_out=$reg_out
-    fi
-  done
-  for regmask_in in $regmask_in_list
-  do
-    if [ ! -z `echo $regmask_in | grep "$ref"` ]
-    then
-      reference_mask_in=$regmask_in
-    fi
-  done
-  for regmask_out in $regmask_out_list
-  do
-    if [ ! -z `echo $regmask_out | grep "$ref"` ]
-    then
-      reference_mask_out=$regmask_out
-    fi
-  done
-
-  registration_parameters_BLUTDIR="--spacing=32,32,32 --interp=2 --metric=11 --bins=25 --samples=1 --levels=3 --verbose " #--coeffEveryN 5"
-  registration_parameters_DEMONSDIR="--demons=3 --levels=1"
-  registration_parameters_ELASTIX="--demons=3 --levels=1"
-
-  coeff_in_ini=""
-  coeff_out_ini=""
-  vf_in_ini=""
-  vf_out_ini=""
-  
-  for phase in $list_phases
-  do
-    for img in $phase_list
-    do
-      if [ ! -z `echo $img | grep "$phase" | grep -v "[0-9]$phase"` ]
-      then
-	image_name=`echo $img | sed 's/raw/mhd/'`
-      fi
-    done
-    if [ $method = 1 ]
-    then
-      compute_BLUTDIR
-    elif [ $method = 2 ]
-    then
-      compute_DEMONSDIR
-    elif [ $method = 3 ]
-    then
-      compute_ELASTIX
-    fi
-  done
-  remove_files 5
-
-  echo
-  echo "-------- Registration done ! --------"
-  end=`date`
-  echo "start: $start"
-  echo "end: $end"
-  echo
-}
-
-calculate_vf_MIDP_REF()
-{
-  echo "Calculating vf_REF_MIDP.mhd..."
-  remove_files 6
-  create_mhd_4D.sh $vf_dir #"vf_4D.mhd"
-  $CLITK/clitkAverageTemporalDimension -i $vf_dir/_4D.mhd -o $vf_dir/vf_${ref}_MIDP.mhd
-  $CLITK/clitkInvertVF -i $vf_dir/vf_${ref}_MIDP.mhd -o $vf_dir/vf_MIDP_${ref}.mhd
-}
-
-calculate_CT_MIDP_REF()
-{
-  reference=`ls *.mhd | grep $ref #| grep -v "[0-9]$ref.mhd"`
-  echo "Calculating CT_MIDP_REF.mhd '$reference'..."
-  $CLITK/clitkWarpImage -i $reference -o CT_MIDP_REF.mhd --vf=$vf_dir/vf_MIDP_${ref}.mhd -s 1
-}
-
-calculate_CT_MIDP_PHASE()
-{
-  echo "Calculating CT_MIDP_${phase}.mhd..."
-  $CLITK/clitkComposeVF -i $vf_dir/vf_MIDP_${ref}.mhd -j $vf_dir/vf_${ref}_${phase}.mhd -o $vf_dir/vf_MIDP_${phase}.mhd
-  phase_img=`ls *.mhd | grep "${phase}" # | grep -v "[0-9]$ref.mhd"`
-  $CLITK/clitkWarpImage -i $phase_img -o MIDP/CT_MIDP_${phase}.mhd --vf=$vf_dir/vf_MIDP_${phase}.mhd -s 1
-  $CLITK/clitkImageConvert -i MIDP/CT_MIDP_${phase}.mhd -o MIDP/CT_MIDP_${phase}.mhd -t float
-  remove_files 7
-}
-
-prepare_MIDP_images()
-{
-  echo "Preparing MIDP images..."
-  cp CT_MIDP_REF.mhd MIDP/CT_MIDP_${ref}.mhd
-  cp CT_MIDP_REF.raw MIDP/CT_MIDP_${ref}.raw
-  cat MIDP/CT_MIDP_${ref}.mhd | sed "s/ElementDataFile = .*/ElementDataFile = CT\_MIDP\_${ref}\.raw/" > MIDP/CT_MIDP_${ref}_tmp.mhd
-  rm MIDP/CT_MIDP_${ref}.mhd
-  mv MIDP/CT_MIDP_${ref}_tmp.mhd MIDP/CT_MIDP_${ref}.mhd
-  $CLITK/clitkImageConvert -i MIDP/CT_MIDP_${ref}.mhd -o MIDP/CT_MIDP_${ref}.mhd -t float
-  create_mhd_4D.sh MIDP #"CT_MIDP_4D.mhd"
-}
-
-calculate_CT_MIDP_MOY()
-{
-  echo "Calculating CT_MIDP_MOY.mhd..."
-  $CLITK/clitkAverageTemporalDimension -i MIDP/_4D.mhd -o CT_MIDP_MOY.mhd
-}
-
-calculate_CT_MIDP_MED()
-{
-  echo "Calculating CT_MIDP_MED.mhd..."
-  $CLITK/clitkMedianTemporalDimension -i MIDP/_4D.mhd -o CT_MIDP_MED.mhd
-}
-
-calculate_CT_MIDP_MIP()
-{
-  echo "Calculating CT_MIDP_MIP.mhd..."
-  $CLITK/clitkMIP -i MIDP/_4D.mhd -o CT_MIDP_MIP.mhd -d 3
-}
-
-mid_position()
-{
-  echo
-  echo "----------- Mid-position ------------"
-  start=`date`
-  echo "start: $start"
-  echo
-  
-  mkdir -p "MIDP"
-
-  calculate_vf_MIDP_REF
-  calculate_CT_MIDP_REF
-  for phase in $list_phases
-  do  
-    check_threads $MAX_THREADS
-    calculate_CT_MIDP_PHASE &
-  done
-  wait
-  prepare_MIDP_images
-  calculate_CT_MIDP_MED &
-  calculate_CT_MIDP_MIP &
-  calculate_CT_MIDP_MOY &
-  wait
-      
-  echo
-  echo "-------- Mid-position done ! --------"
-  end=`date`
-  echo "start: $start"
-  echo "end: $end"
-  echo
-}
-
-#################
-#	main	#
-#################
-
-if [ $# -lt 1 ]
-then
-    echo "Usage: create_midP.sh CT_4D.mhd ref_phase computation_spacing(mm) method(1:BSPLINE, 2:DEMONS)"
-    exit 1
-fi
-CLITK=~/creatis/clitk3/build/bin
-CT_4D_path=$1
-CT_4D=`basename $CT_4D_path`
-work_dir=`dirname $CT_4D_path`
-cd $work_dir
-ref=$2
-spacing=$3
-method=$4
-
-vf_dir="VF"
-coeff_dir="$vf_dir/coeff"
-
-mkdir -p $vf_dir
-mkdir -p $coeff_dir
-
-echo
-echo "--------------- START ---------------"
-begining=`date`
-echo "start: $begining"
-echo
-
-mkdir -p "LOG"
-phase_list=`grep ".raw" $CT_4D`
-echo "phases -> " $phase_list
-nb_phases=`grep ".raw" $CT_4D | wc -l`
-gt_ref=""
-lt_ref=""
-
-phase_files=( `cat $CT_4D | grep ".raw" | sed 's:.raw:.mhd:'` )
-echo "Phase files are ${phase_files[@]}"
-
-phase_nbs=( `echo ${phase_files[@]} | grep -o '[[:alpha:][:punct:]][0-9]\{1,2\}[[:punct:]]' | grep -o '[0-9]\{1,2\}'` )
-#phase_nbs=( `echo ${phase_files[@]} | grep -o '[0-9]\{1,2\}'` )  
-echo "Phase numbers are ${phase_nbs[@]}"
-
-
-for ph in $phase_list
-do
-  #ph_nb=`echo $ph | grep -o "[0-9][0-9]*\.raw" | sed -e 's/\.raw//'`
-  ph_nb=`echo $ph | grep -o "[0-9][0-9]"`  
-  if [ $ph_nb -gt $ref ]
-  then
-    gt_ref="$gt_ref $ph_nb"
-  elif [ $ph_nb -lt $ref ]
-  then
-    lt_ref="$lt_ref $ph_nb"
-  fi
-done
-list_phases="$gt_ref $lt_ref"
-echo list_phases $list_phases
-
-motion_mask
-registration
-mid_position
-
-echo
-echo "---------------- END ----------------"
-terminating=`date`
-echo "start: $begining"
-echo "end: $terminating"
-echo