+++ /dev/null
-#! /bin/bash +x
-
-source `dirname $0`/midp_common.sh
-
-
-############# main
-
-if echo $* | grep "\-h"; then
- echo Usage: calculate_motion_amplitude.sh { REFERENCE_IMAGE RTSTRUCT_FILE [ RTSTRUCT_ROI | --gui ] } | --gui
- 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 " --gui: use GUI to select files"
- exit 0
-fi
-
-
-rtstruct_roi=
-
-if echo $* | grep "\-\-gui" > /dev/null 2>&1; then
- gui_mode=1
- if [ $# = 1 ]; then
- rtstruct_ref_image=`zenity --file-selection --title="Select Reference Image."`
- rtstruct_file=`zenity --file-selection --title="Select RT Struct file."`
- select_roi
- elif [ $# = 3 ]; then
- rtstruct_ref_image=$1
- rtstruct_file=$2
- select_roi
- else
- echo Invalid arguments. Type \'`basename $0` -h\' for help
- exit -1
- fi
-
-else
- gui_mode=0
- rtstruct_ref_image=$1
- rtstruct_file=$2
- if [ $# = 2 ]; then
- select_roi
- elif [ $# = 3 ]; then
- rtstruct_roi=$3
- rtstruct_roi_name=$rtstruct_roi
- else
- echo Invalid arguments. Type \'`basename $0` -h\' for help
- exit -1
- fi
-
-fi
-
-
-#echo "Processing \"${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 > /tmp/result.txt
-
-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/result.txt