From: Romulo Pinho <romulo.pinho@lyon.unicancer.fr>
Date: Tue, 17 Apr 2012 08:05:08 +0000 (+0200)
Subject: new script to get contour statistics
X-Git-Tag: v1.3.0~52^2~3
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=960bd0fd5ef5a4a10d3425e55a6b16565458200f;p=clitk.git

new script to get contour statistics
---

diff --git a/scripts/calculate_contour_stats.sh b/scripts/calculate_contour_stats.sh
new file mode 100755
index 0000000..e8ad0f2
--- /dev/null
+++ b/scripts/calculate_contour_stats.sh
@@ -0,0 +1,92 @@
+#! /bin/bash +x 
+
+select_contour()
+{
+  local roi_list=$@
+  roi=`zenity --list --title="Available Contours" --column="Please choose a contour:" $roi_list`
+  case $? in
+    0)
+    if [ -z $roi ]
+    then
+      zenity --warning --text="You must choose one contour."
+      select_contour $roi_list
+    else
+      rtstruct_roi_name=$roi
+    fi;;
+    1)
+    if zenity --question --text="Do you really wish to quit?"
+    then
+      exit
+    else
+      select_contour $roi_list
+    fi;;
+    -1)
+      zenity --error --text="Unexpected error. Please relaunch the application."
+      exit;;
+  esac
+}
+
+select_roi()
+{
+  rtstruct_roi_name_list=( `clitkDicomInfo ${rtstruct_file} | grep "3006|0026" | cut -d '[' -f 4 | sed 's/| V 3006|0026[LO] [ROI Name] \|]//'` )
+  rtstruct_roi_number_list=( `clitkDicomInfo ${rtstruct_file} | grep "3006|0022" | cut -d '[' -f 4 | sed 's/| V 3006|0026[LO] [ROI Number] \|]//'` )
+  rtstruct_roi_list=( )
+  for i in $(seq 0 1 $(( ${#rtstruct_roi_name_list[@]} - 1 ))); do
+    rtstruct_roi_list[$i]=${rtstruct_roi_number_list[$i]}:${rtstruct_roi_name_list[$i]}
+  done
+
+  select_contour ${rtstruct_roi_list[@]}
+  rtstruct_roi=`echo ${rtstruct_roi_name} | cut -d ':' -f 1`
+}
+
+############# main 
+
+if echo $* | grep "\-h"; then
+  echo Usage: calculate_motion_amplitude.sh { RTSTRUCT_FILE REFERENCE_IMAGE | --gui }
+
+  exit 0
+fi
+
+
+rtstruct_roi=0
+
+if echo $* | grep "\-\-gui" > /dev/null 2>&1; then
+  if [ $# != 1 ]; then
+    echo Invalid arguments. Type \'`basename $0` -h\' for help
+    exit -1
+  fi
+
+  rtstruct_file=`zenity --file-selection --title="Select RT Struct file."`
+  select_roi
+  rtstruct_ref_image=`zenity --file-selection --title="Select Reference Image."`
+else
+  if [ $# != 2 ]; then
+    echo Invalid arguments. Type \'`basename $0` -h\' for help
+    exit -1
+  fi
+
+  rtstruct_file=$1
+  rtstruct_ref_image=$2
+  select_roi
+fi
+
+
+#echo "Processing \"${rtstruct_roi_list[$roi_struct]}\"..."
+# create ROI mask from rtstruct
+roi_mask=roi_${rtstruct_roi_name}.mhd
+clitkDicomRTStruct2Image -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
+if cat /tmp/err.txt | grep -q "No ROI"; then
+  echo Invalid contour number.
+  exit -3
+fi
+
+# guarantees the same sampling for roi mask and vector image
+roi_mask2=resampled_${roi_mask}
+clitkResampleImage -i ${roi_mask} -o ${roi_mask2} --like ${rtstruct_ref_image}
+
+# calculate stats
+clitkImageStatistics -i ${rtstruct_ref_image} -m ${roi_mask2} --verbose 2> /dev/null | tail -n 8 | zenity --text-info --title "Restuls for \"${rtstruct_roi_name}\""
+
+rm `basename $roi_mask .mhd`.{mhd,raw}
+rm `basename $roi_mask2 .mhd`.{mhd,raw}
+rm /tmp/err.txt