motion masks with and without bands

[clitk.git] / scripts / create_midP_masks-2.0.sh

diff --git a/scripts/create_midP_masks-2.0.sh b/scripts/create_midP_masks-2.0.sh
index 68560cae1c76750fbe9319f95dc224d53c5fa6eb..5bd0c9fa0c554798eef7e6998420886deb1d8fbc 100755 (executable)
--- a/scripts/create_midP_masks-2.0.sh
+++ b/scripts/create_midP_masks-2.0.sh
@@ -1,5 +1,5 @@
-#! /bin/bash -x
-
+#! /bin/bash 
+  
 ###############################################################################
 #
 # FILE: create_midP-2.0.sh
@@ -21,7 +21,10 @@ 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()
@@ -39,15 +42,17 @@ 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
 }
 
@@ -60,7 +65,7 @@ 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 $MotionMaskExtra 
   #--monitor=$mask_dir_tmp/monitor_$phase_nb.mhd
 }
 
@@ -114,10 +119,12 @@ 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
 }
 
 mm_preprocessing()
@@ -126,7 +133,9 @@ mm_preprocessing()
   # extract_bones
   extract_lungs
   # remove_tmp_masks 1
-  resample
+  if [ $resample_spacing -ne 0 ] ; then 
+    resample
+  fi
 }
 
 mm_postprocessing()
@@ -139,18 +148,29 @@ mm_postprocessing()
 motion_mask()
 {
   #set cmd line variables
-  mhd4d=$1
-  resample_spacing=$2
-  resample_algo=$3
-
-  # import variables specific to each patient
-  source variables
+  mhd4d=`basename $1`
+  if [ $# -eq 3 ] ; then
+    resample_spacing=$2
+    resample_algo=$3
+  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
 
@@ -196,6 +216,7 @@ 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]}
@@ -203,6 +224,12 @@ motion_mask()
 
       check_threads $MAX_THREADS
       mm_preprocessing &
+      pids=( "${pids[@]}" "$!" )
+    done
+
+    wait_pids ${pids[@]}
+    for ret in $ret_codes; do
+      abort_on_error mm_preprocessing $ret clean_up_masks
     done
 
     # single-threaded motion mask calc
@@ -213,17 +240,26 @@ motion_mask()
       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
 
     # multi-threaded post-processing of motion mask calcs
+    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
 
+
     # rename tmp mask directory after mask creation
     check_threads 1
     mv -f $mask_dir_tmp $mask_dir
@@ -242,8 +278,8 @@ motion_mask()
 # main  #
 #################
 
-if [ $# != 3 ]; then
-  echo "Usage: $0 CT_4D RESAMPLE_SPACING RESAMPLE_ALGORITHM"
+if [ $# -ne 3 -a $# -ne 1 ]; then
+  echo "Usage: $0 CT_4D [RESAMPLE_SPACING RESAMPLE_ALGORITHM]"
   exit -1
 fi
 
@@ -254,5 +290,9 @@ fi
 #
 
 if [ $1 != "using-as-lib" ]; then
-  motion_mask $1 $2 $3
+  if [ $# -eq 3 ] ; then
+    motion_mask $1 $2 $3
+  else
+    motion_mask $1
+  fi
 fi