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 bbf44f0fa9a857da69581133681ddb046f715905..5bd0c9fa0c554798eef7e6998420886deb1d8fbc 100755 (executable)
--- a/scripts/create_midP_masks-2.0.sh
+++ b/scripts/create_midP_masks-2.0.sh
@@ -43,7 +43,7 @@ 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 --doNotSeparateLungs
+  clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs --type 1
 }
 
 
@@ -52,6 +52,7 @@ 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
 }
 
@@ -118,10 +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()
@@ -130,7 +133,9 @@ mm_preprocessing()
   # extract_bones
   extract_lungs
   # remove_tmp_masks 1
-  resample
+  if [ $resample_spacing -ne 0 ] ; then 
+    resample
+  fi
 }
 
 mm_postprocessing()
@@ -143,9 +148,14 @@ mm_postprocessing()
 motion_mask()
 {
   #set cmd line variables
-  mhd4d=$1
-  resample_spacing=$2
-  resample_algo=$3
+  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
@@ -156,7 +166,11 @@ motion_mask()
   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
 
@@ -264,8 +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
 
@@ -276,5 +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