GUI options for contour statistics scripts

[clitk.git] / scripts / calculate_motion_amplitude.sh

diff --git a/scripts/calculate_motion_amplitude.sh b/scripts/calculate_motion_amplitude.sh
index b40c766997115c960a4ce7a21aab0f8c91b2cbd1..c1128b0ebdec75f3896fd5298bfe6efedf4db8df 100755 (executable)
--- a/scripts/calculate_motion_amplitude.sh
+++ b/scripts/calculate_motion_amplitude.sh
@@ -1,27 +1,76 @@
 #! /bin/bash +x 
 
+source `dirname $0`/midp_common.sh
+
+
+calculate_motion()
+{
+  # calculate motion amplitudes along the 3 image axes
+  rm /tmp/result.txt 2> /dev/null
+  dir=( "\"left-right\"" "\"anterior-posterior\"" "\"cranio-caudal\"" )
+  pct=( 0 33 67 )
+  for i in 0 1 2; do
+    if [ $gui_mode = 1 ]; then
+      echo "${pct[$i]}"; echo "# Calculating motion along ${dir[$i]} direction.."
+    else
+      echo "Calculating motion along ${dir[$i]} direction.."
+    fi
+
+    echo "Motion along ${dir[$i]} direction" >> /tmp/result.txt
+    clitkImageStatistics -i ${vector_file} -m ${roi_mask2} -c $i --verbose 2> /dev/null | tail -n 8 | head -n 6 >> /tmp/result.txt
+    min=`tail -n 2 /tmp/result.txt | head -n 1 | cut -f 2 -d ':'`
+    max=`tail -n 1 /tmp/result.txt | cut -f 2 -d ':'`
+    amp=`echo $max-$min | bc`
+
+    echo "Amplitude: $amp" >> /tmp/result.txt
+    echo "" >> /tmp/result.txt
+  done
+}
+
 ############# main 
 
 if echo $* | grep "\-h"; then
-  echo Usage: calculate_motion_amplitude.sh VECTOR_FILE RTSTRUCT_FILE RTSTRUCT_ROI_NUMBER RTSTRUCT_REF_IMAGE
+  echo "Usage: calculate_motion_amplitude.sh { VECTOR_FILE RTSTRUCT_REF_IMAGE RTSTRUCT_FILE [ RTSTRUCT_ROI_NUMBER | --gui ] } | --gui "
   echo "  VECTOR_FILE: mhd of the vector field from where to extract motion information (may also be 4D)"
+  echo "  RTSTRUCT_REF_IMAGE: mhd of the reference image used in the contour delineation"
   echo "  RTSTRUCT_FILE: dicom with contours"
   echo "  RTSTRUCT_ROI: number of the contour whose motion to analyze"
-  echo "  RTSTRUCT_REF_IMAGE: mhd of the reference image used in the contour delineation"
-
+  echo "  --gui: use GUI to select files"
   exit 0
 fi
 
-if [ $# != 4 ]; then
-  echo Invalid arguments. Type \'`basename $0` -h\' for help
-  exit -1
+if echo $* | grep "\-\-gui" > /dev/null 2>&1; then
+  gui_mode=1
+  if [ $# = 1 ]; then
+    vector_file=`zenity --file-selection --title="Select 4D Vector Field file."`
+    rtstruct_ref_image=`zenity --file-selection --title="Select Reference Image."`
+    rtstruct_file=`zenity --file-selection --title="Select RT Struct file."`
+    select_roi
+  elif [ $# = 4 ]; then
+    vector_file=$1
+    rtstruct_ref_image=$2
+    rtstruct_file=$3
+    select_roi
+  else
+    echo Invalid arguments. Type \'`basename $0` -h\' for help
+    exit -1
+  fi
+else
+  gui_mode=0
+  vector_file=$1
+  rtstruct_ref_image=$2
+  rtstruct_file=$3
+  if [ $# = 4 ]; then
+    rtstruct_roi=$4
+    rtstruct_roi_name=$rtstruct_roi
+  elif [ $# = 3 ]; then
+    select_roi
+  else
+    echo Invalid arguments. Type \'`basename $0` -h\' for help
+    exit -1
+  fi
 fi
 
-vector_file=$1
-rtstruct_file=$2
-rtstruct_roi=$3
-rtstruct_ref_image=$4
-
 if ! cat $vector_file | grep -q "Channels = 3"; then
   echo Vector file must have 3 channels.
   exit -2
@@ -29,7 +78,7 @@ fi
 
 # create ROI mask from rtstruct
 roi_mask=roi_${rtstruct_roi}.mhd
-clitkDicomRTStruct2BinaryImage -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
+clitkDicomRTStruct2Image -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
 if cat /tmp/err.txt | grep -q "No ROI"; then
   echo Invalid contour number.
   exit -3
@@ -39,20 +88,20 @@ fi
 roi_mask2=resampled_${roi_mask}
 clitkResampleImage -i ${roi_mask} -o ${roi_mask2} --like ${vector_file}
 
-# calculate motion amplitudes along the 3 image axes
-dir=( sagittal coronal axial )
-for i in 0 1 2; do
-  echo Motion along ${dir[$i]} direction
-  clitkImageStatistics -i ${vector_file} -m ${roi_mask2} -c $i --verbose 2> /dev/null | tail -n 8 | head -n 6 > /tmp/res.txt
-  min=`tail -n 2 /tmp/res.txt | head -n 1 | cut -f 2 -d ':'`
-  max=`tail -n 1 /tmp/res.txt | cut -f 2 -d ':'`
-  amp=`echo $max-$min | bc`
-  cat /tmp/res.txt
-  echo "Amplitude: $amp"
-  echo
-done
+if [ $gui_mode = 1 ]; then
+  calculate_motion | zenity --progress --auto-close --percentage=0 --text=""
+else
+  calculate_motion
+fi
+
+if [ $gui_mode = 1 ]; then
+  cat /tmp/result.txt | zenity --text-info --title "Restuls for \"${rtstruct_roi_name}\""
+else
+  echo "Restuls for \"${rtstruct_roi_name}\""
+  cat /tmp/result.txt 
+fi
 
 rm `basename $roi_mask .mhd`.{mhd,raw}
 rm `basename $roi_mask2 .mhd`.{mhd,raw}
 rm /tmp/err.txt
-rm /tmp/res.txt
+rm /tmp/result.txt