X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=scripts%2Fcreate_midP_masks-2.0.sh;h=6fa7476ffb156b0ab53dd1cd03518502e90abf35;hb=5e63914651ec58eebb2a08537c94a00e9e861d35;hp=6023df578f5e32c6c7e439589b584af911fcda16;hpb=34af28a29bf9c7816747f8507c4a9985354811f8;p=clitk.git

diff --git a/scripts/create_midP_masks-2.0.sh b/scripts/create_midP_masks-2.0.sh
index 6023df5..6fa7476 100755
--- a/scripts/create_midP_masks-2.0.sh
+++ b/scripts/create_midP_masks-2.0.sh
@@ -1,5 +1,5 @@
 #! /bin/bash -x
-
+  
 ###############################################################################
 #
 # FILE: create_midP-2.0.sh
@@ -15,13 +15,16 @@
 #
 ###############################################################################
 
-source `dirname $0`/common.sh
+source `dirname $0`/midp_common.sh
 
 extract_patient()
 {
   echo "$phase_file -> Extracting patient..."
   clitkExtractPatient -i $phase_file -o $mask_dir_tmp/patient_mask_$phase_nb.mhd --noAutoCrop -a $afdb_file $ExtractPatientExtra
+#   abort_on_error clitkExtractPatient $?
+
   clitkSetBackground -i $phase_file -o $mask_dir_tmp/patient_$phase_nb.mhd --mask $mask_dir_tmp/patient_mask_$phase_nb.mhd --outsideValue -1000
+#   abort_on_error clitkSetBackground $?
 }
 
 extract_bones()
@@ -39,16 +42,19 @@ extract_bones()
 
 extract_lungs()
 {
-  echo "$phase_file -> Extracting lungs..."
-  clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop
+  echo "$phase_file -> Extracting lungs..."  
+  clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs --type 1
 }
 
+
+
 resample()
 {
   echo "$phase_file -> Resampling..."
   clitkResampleImage -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/patient_$phase_nb.mhd --spacing $resample_spacing --interp $resample_algo
-
+  clitkResampleImage -i $mask_dir_tmp/patient_mask_$phase_nb.mhd -o $mask_dir_tmp/patient_mask_$phase_nb.mhd --spacing $resample_spacing --interp $resample_algo
   clitkResampleImage -i $mask_dir_tmp/lungs_$phase_nb.mhd -o $mask_dir_tmp/lungs_$phase_nb.mhd --like $mask_dir_tmp/patient_$phase_nb.mhd
+  clitkResampleImage -i $mask_dir_tmp/bones_$phase_nb.mhd -o $mask_dir_tmp/bones_$phase_nb.mhd --like $mask_dir_tmp/patient_$phase_nb.mhd
 }
 
 compute_motion_mask()
@@ -60,7 +66,8 @@ compute_motion_mask()
     FillingLevel=94
   fi
 
-  clitkMotionMask -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/mm_$phase_nb.mhd --featureLungs $mask_dir_tmp/lungs_$phase_nb.mhd --upperThresholdLungs -400 --fillingLevel $FillingLevel --offsetDetect 0,-5,0 --pad --writeFeature=$mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra 
+  #clitkMotionMask -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/mm_$phase_nb.mhd --featureLungs $mask_dir_tmp/lungs_$phase_nb.mhd --upperThresholdLungs -400 --fillingLevel $FillingLevel --offsetDetect $MotionMaskOffsetDetect --pad --writeFeature=$mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra
+  clitkMotionMask -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/mm_$phase_nb.mhd --featureLungs $mask_dir_tmp/lungs_$phase_nb.mhd --upperThresholdLungs -400 --featureBones $mask_dir_tmp/bones_$phase_nb.mhd --fillingLevel $FillingLevel --offsetDetect $MotionMaskOffsetDetect --pad --writeFeature $mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra  
   #--monitor=$mask_dir_tmp/monitor_$phase_nb.mhd
 }
 
@@ -91,8 +98,8 @@ create_banded_mask()
   clitkImageArithm -i $input_mask -j $input_dir/band1_$input_base -o $output_mask -t 0
   clitkImageArithm -i $output_mask -j $input_dir/band2_$input_base -o $output_mask -t 0
   # combine bands with image
-  clitkCombineImage -i $input_dir/short_band1_$input_base -j $input -m $input_dir/band1_$input_base -o $output
-  clitkCombineImage -i $input_dir/short_band2_$input_base -j $output -m $input_dir/band2_$input_base -o $output
+  combine_image $input_dir/short_band1_$input_base $input $output $input_dir/band1_$input_base
+  combine_image $input_dir/short_band2_$input_base $output $output $input_dir/band2_$input_base
 
   # clean-up
   rm `echo $input_dir/extra?_$input_base | sed 's:.mhd:.*:g'`
@@ -102,7 +109,30 @@ create_banded_mask()
 
 create_registration_masks()
 {
-  # extract inside and outside lung regions from the patient image, 
+  # extract inside and outside regions from the patient image, 
+  # using the motion mask computed previously
+  echo "$phase_file -> Setting Background..."
+  clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/inside_$phase_nb.mhd --mask $mask_dir_tmp/${mask_type}_$phase_nb.mhd --outsideValue -1200
+  clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/outside_$phase_nb.mhd --mask $mask_dir_tmp/${mask_type}_$phase_nb.mhd --outsideValue -1200 --fg
+
+  # the registration masks for inside (and outside) region correspond
+  # to the motion mask (and its complement) plus extra grey value bands,
+  # obtained with morphological dilations.
+  # 
+  echo "$phase_file -> Creating registration masks..."
+  # inside
+  clitkMorphoMath -i $mask_dir_tmp/${mask_type}_$phase_nb.mhd -o $mask_dir_tmp/mask_inside_$phase_nb.mhd --type 1 --radius 8
+  create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/${mask_type}_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$phase_nb.mhd 4
+  # outside 
+  clitkBinarizeImage -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd -l -999 -u 4000 --mode both 
+  #clitkExtractPatient -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd --noAutoCrop
+  clitkMorphoMath -i $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd -o $mask_dir_tmp/mask_outside_$phase_nb.mhd --type 1 --radius 8
+  create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
+}
+
+create_registration_motion_masks()
+{
+  # extract inside and outside regions from the patient image, 
   # using the motion mask computed previously
   echo "$phase_file -> Setting Background..."
   clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/inside_$phase_nb.mhd --mask $mask_dir_tmp/mm_$phase_nb.mhd --outsideValue -1200
@@ -114,43 +144,178 @@ create_registration_masks()
   # 
   echo "$phase_file -> Creating registration masks..."
   # inside
-  create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/mm_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/mask_inside_$phase_nb.mhd 4
+  clitkMorphoMath -i $mask_dir_tmp/mm_$phase_nb.mhd -o $mask_dir_tmp/mask_inside_$phase_nb.mhd --type 1 --radius 8
+  create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/mm_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$phase_nb.mhd 4
   # outside 
   clitkExtractPatient -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/mm_outside_$phase_nb.mhd --noAutoCrop
-  create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/mm_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/mask_outside_$phase_nb.mhd 4
+  clitkMorphoMath -i $mask_dir_tmp/mm_outside_$phase_nb.mhd -o $mask_dir_tmp/mask_outside_$phase_nb.mhd --type 1 --radius 8
+  create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/mm_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
+}
+
+create_registration_lung_masks()
+{
+  # extract inside and outside lung regions from the patient image, 
+  # using the motion mask computed previously
+  echo "$phase_file -> Setting Background..."
+  clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/inside_$phase_nb.mhd --mask $mask_dir_tmp/lungs_$phase_nb.mhd --outsideValue -1200
+  clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/outside_$phase_nb.mhd --mask $mask_dir_tmp/lungs_$phase_nb.mhd --outsideValue -1200 --fg
+
+  # the registration masks for inside (and outside) region correspond
+  # to the motion mask (and its complement) plus extra grey value bands,
+  # obtained with morphological dilations.
+  # 
+  echo "$phase_file -> Creating registration masks..."
+  # inside
+  clitkMorphoMath -i $mask_dir_tmp/lungs_$phase_nb.mhd -o $mask_dir_tmp/mask_inside_$phase_nb.mhd --type 1 --radius 8
+  create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/lungs_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$phase_nb.mhd 4
+  # outside 
+  clitkBinarizeImage -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/lungs_outside_$phase_nb.mhd -l -999 -u 4000 --mode both 
+  clitkMorphoMath -i $mask_dir_tmp/lungs_outside_$phase_nb.mhd -o $mask_dir_tmp/mask_outside_$phase_nb.mhd --type 1 --radius 8
+  create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/lungs_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
 }
 
 mm_preprocessing()
 {
   extract_patient
-  # extract_bones
+  extract_bones
   extract_lungs
   # remove_tmp_masks 1
-  resample
+  if [ $resample_spacing -ne 0 ] ; then 
+    resample
+  fi
 }
 
 mm_postprocessing()
 {
   # remove_tmp_masks 2
   # remove_tmp_masks 3
+
   create_registration_masks
+#   if [ "$mask_type" == "mm" ]; then
+#     create_registration_motion_masks
+#   elif [ "$mask_type" == "lungs" ]; then
+#     create_registration_lung_masks
+#   fi
+}
+
+wait_mm_creation()
+{
+  # the motion masks are first created in a tmp directory. this directory is 
+  # later going to be renamed to the final motion mask directory. concurrent
+  # executions trying to create the same set of masks will be blocked until
+  # the first execution finishes. naturally, these other executions will not
+  # recreate the masks. so first we try to create the tmp directory. 
+  # if the creation fails, it means that another execution is
+  # already creating the masks, so this execution will be blocked. the
+  # execution is unblocked only when the creation of masks is finished and
+  # the mask directory is renamed.
+  #
+  do_mm=1
+  if [ -e $mask_dir ]; then
+    # check that the final mask dir exists and that it contains all files it needs.
+    # the check assumes that the inside and outside masks are the key files to exist.
+    do_mm=0
+    nb_phases=${#phase_nbs[@]}
+    if [ "$mask_type" == "patient" ]; then
+      nb_masks=`ls $mask_dir/lungs_*.mhd | wc -l`
+      if [ $nb_masks != $nb_phases ]; then
+        # if the mask dir is invalid, remove it and recreate all masks, just in case.
+        rm -fr $mask_dir 2> /dev/null
+        do_mm=1
+      fi
+    else
+      nb_mm_masks=`ls $mask_dir/${mask_type}_outside*.mhd | wc -l`
+      nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
+      nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
+      if [ $nb_mm_masks != $nb_phases -o $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
+        # if the mask dir is invalid, remove it and recreate all masks, just in case.
+        rm -fr $mask_dir 2> /dev/null
+        do_mm=1
+      fi
+    fi
+#     elif [ "$mask_type" == "lungs" ]; then
+#       nb_mm_masks=`ls $mask_dir/lungs_outside*.mhd | wc -l`
+#       nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
+#       nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
+#       if [ $nb_mm_masks != $nb_phases -o $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
+#         # if the mask dir is invalid, remove it and recreate all masks, just in case.
+#         rm -fr $mask_dir 2> /dev/null
+#         do_mm=1
+#       fi
+#     elif [ "$mask_type" == "mm" ]; then
+#       nb_mm_masks=`ls $mask_dir/mm_outside*.mhd | wc -l`
+#       nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
+#       nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
+#       if [ $nb_mm_masks != $nb_phases -o $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
+#         # if the mask dir is invalid, remove it and recreate all masks, just in case.
+#         rm -fr $mask_dir 2> /dev/null
+#         do_mm=1
+#       fi
+#     fi
+  fi
+  
+  if [ $do_mm = 1 ]; then
+    if ! mkdir $mask_dir_tmp 2> /dev/null; then
+      if [ ! -e $mask_dir_tmp ]; then
+        # if the temp dir couldn't be created, but it doesn't exist, abort
+        abort_on_error wait_mm_creation $? clean_up_masks
+      else
+        # assumes another process is creating the maks in the temp dir.
+        # now we need to wait until the masks are complete or until the
+        # time limit is reached. 
+        interval=10
+        sleeping=0
+        max_wait=3600 # one hour
+        nb_files0=`ls $mask_dir_tmp/* | wc -l`
+        while [ ! -e $mask_dir -a $sleeping -le $max_wait ]; do
+          echo "waiting creation of motion masks..."
+          sleep $interval
+          sleeping=$(( $sleeping + $interval ))
+          nb_files1=`ls $mask_dir_tmp/* | wc -l`
+          if [ $nb_files1 != $nb_files0 ]; then
+            nb_files0=$nb_files1
+            sleeping=0
+          fi  
+        done
+
+        if [ $sleeping -gt $max_wait ]; then
+          abort_on_error wait_mm_creation -1 clean_up_masks
+        else
+          echo "finished waiting"
+          do_mm=0
+        fi
+      fi
+    fi  
+  fi
 }
 
 motion_mask()
 {
   #set cmd line variables
-  mhd4d=$1
-  resample_spacing=$2
-  resample_algo=$3
-
-  # import variables specific to each patient
-  source variables
+  local mhd4d=`basename $1`
+  mask_type=$2
+  if [ $# -eq 4 ] ; then
+    resample_spacing=$3
+    resample_algo=$4
+  else
+    resample_spacing=0
+    resample_algo=0
+  fi
 
   dir=`dirname $1`
   cd $dir
     
+  # import variables specific to each patient
+  if test -e ./variables; then
+    source ./variables
+  fi
+
   #set other global variables
-  mask_dir="MASK-${resample_spacing}mm-$resample_algo"
+  if [ $resample_spacing -ne 0 ] ; then
+    mask_dir="MASK-${resample_spacing}mm-$resample_algo"
+  else
+    mask_dir="MASK"
+  fi
   mask_dir_tmp="tmp.$mask_dir"
   extract_4d_phases $mhd4d
 
@@ -160,35 +325,8 @@ motion_mask()
   echo "start: $start"
   echo
 
-  # the motion masks are first created in a tmp directory. this directory is 
-  # later going to be renamed to the final motion mask directory. concurrent
-  # executions trying to create the same set of masks will be blocked until
-  # the first execution finishes. naturally, these other executions will not
-  # recreate the masks. so first we try to create the tmp directory. 
-  # if the creation fails, it means that another execution is
-  # already creating the masks, so this execution will be blocked. the
-  # execution is unblocked only when the creation of masks is finished and
-  # the mask directory is renamed.
-  #
-  # ATTENTION: RP - 08/02/2011
-  # robustness issue: tmp directory may exist but may be empty or 
-  # incomplete. the solution is to check per file, but I'll leave it like 
-  # this for the moment.
-  do_mm=0
-  if [ $(ls -d $mask_dir 2> /dev/null | wc -l) -eq 0 ]; then
-    mkdir $mask_dir_tmp 2> /dev/null
-    return_mkdir=$?
-    if [ $return_mkdir == 0 ]; then
-      do_mm=1 
-    else
-      while [[ $(ls -d $mask_dir 2> /dev/null | wc -l) -eq 0 ]]; do
-        echo "waiting creation of motion masks..."
-        sleep 2
-      done
-      echo "finished waiting"
-    fi  
-  fi
-  
+  wait_mm_creation
+
 #   do_mm=1
 #   mask_dir_tmp=$mask_dir
   if [ $do_mm == 1 ]; then
@@ -196,6 +334,7 @@ motion_mask()
     mkdir -p $mask_log_dir
 
     # multi-threaded pre-processing for motion mask calcs
+    pids=( )
     for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
       phase_nb=${phase_nbs[$i]}
       phase_file=${phase_files[$i]}
@@ -203,26 +342,44 @@ motion_mask()
 
       check_threads $MAX_THREADS
       mm_preprocessing &
+      pids=( "${pids[@]}" "$!" )
     done
 
-    # single-threaded motion mask calc
-    for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
-      phase_nb=${phase_nbs[$i]}
-      phase_file=${phase_files[$i]}
-
-      check_threads 1
-      echo "$phase_file -> Computing motion mask..."
-      compute_motion_mask > $mask_log_dir/motion_mask_$phase_file.log
+    wait_pids ${pids[@]}
+    for ret in $ret_codes; do
+      abort_on_error mm_preprocessing $ret clean_up_masks
     done
 
-    # multi-threaded post-processing of motion mask calcs
-    for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
-      phase_nb=${phase_nbs[$i]}
-      phase_file=${phase_files[$i]}
+    if [ "$mask_type" == "mm" ]; then
+      # single-threaded motion mask calc
+      for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+        phase_nb=${phase_nbs[$i]}
+        phase_file=${phase_files[$i]}
 
-      check_threads $MAX_THREADS 
-      mm_postprocessing &
-    done
+        check_threads 1
+        echo "$phase_file -> Computing motion mask..."
+        compute_motion_mask > $mask_log_dir/motion_mask_$phase_file.log
+        abort_on_error compute_motion_mask $? clean_up_masks
+      done
+    fi
+
+    # multi-threaded post-processing of motion mask calcs
+    if [ "$mask_type" != "patient" ]; then
+      pids=( )
+      for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+        phase_nb=${phase_nbs[$i]}
+        phase_file=${phase_files[$i]}
+
+        check_threads $MAX_THREADS 
+        mm_postprocessing &
+        pids=( "${pids[@]}" "$!" )
+      done
+    
+      wait_pids ${pids[@]}
+      for ret in $ret_codes; do
+        abort_on_error mm_postprocessing $ret clean_up_masks
+      done
+    fi
 
     # rename tmp mask directory after mask creation
     check_threads 1
@@ -242,8 +399,9 @@ motion_mask()
 # main  #
 #################
 
-if [ $# != 3 ]; then
-  echo "Usage: $0 CT_4D RESAMPLE_SPACING RESAMPLE_ALGORITHM"
+if [ $# -ne 4 -a $# -ne 2 -a $# -ne 1 ]; then
+  echo "Usage: $0 CT_4D TYPE [RESAMPLE_SPACING RESAMPLE_ALGORITHM]"
+  echo "  TYPE: \"motion\" (traditional motion masks); \"lungs\" (lung masks); \"patient\" (patient mask only)"
   exit -1
 fi
 
@@ -254,5 +412,11 @@ fi
 #
 
 if [ $1 != "using-as-lib" ]; then
-  motion_mask $1 $2 $3
+  if [ $# -eq 4 ] ; then
+    motion_mask $1 $2 $3 $4
+  elif [ $# -eq 2 ] ; then
+    motion_mask $1 $2
+  else
+    motion_mask $1 all
+  fi
 fi