6 roi=`zenity --list --title="Available Contours" --column="Please choose a contour:" $roi_list`
11 zenity --warning --text="You must choose one contour."
12 select_contour $roi_list
14 rtstruct_roi_name=$roi
17 if zenity --question --text="Do you really wish to quit?"
21 select_contour $roi_list
24 zenity --error --text="Unexpected error. Please relaunch the application."
32 echo "Available Contours:"
33 for r in $roi_list; do
37 echo "Please choose a contour number:"
38 read rtstruct_roi_number
43 rtstruct_roi_name_list=( `clitkDicomInfo ${rtstruct_file} | grep "3006|0026" | cut -d '[' -f 4 | sed 's/| V 3006|0026[LO] [ROI Name] \|]//'` )
44 rtstruct_roi_number_list=( `clitkDicomInfo ${rtstruct_file} | grep "3006|0022" | cut -d '[' -f 4 | sed 's/| V 3006|0026[LO] [ROI Number] \|]//'` )
46 for i in $(seq 0 1 $(( ${#rtstruct_roi_name_list[@]} - 1 ))); do
47 rtstruct_roi_list[$i]=${rtstruct_roi_number_list[$i]}:${rtstruct_roi_name_list[$i]}
50 if [ $gui_mode = 1 ]; then
51 select_contour_gui ${rtstruct_roi_list[@]}
52 rtstruct_roi=`echo ${rtstruct_roi_name} | cut -d ':' -f 1`
53 rtstruct_roi_name=`echo ${rtstruct_roi_name} | cut -d ':' -f 2`
55 select_contour ${rtstruct_roi_list[@]}
56 rtstruct_roi=$rtstruct_roi_number
57 rtstruct_roi_name=${rtstruct_roi_name_list[$(( $rtstruct_roi_number - 1))]}
63 if echo $* | grep "\-h"; then
64 echo Usage: calculate_motion_amplitude.sh { RTSTRUCT_FILE REFERENCE_IMAGE | --gui }
72 if echo $* | grep "\-\-gui" > /dev/null 2>&1; then
74 echo Invalid arguments. Type \'`basename $0` -h\' for help
79 rtstruct_file=`zenity --file-selection --title="Select RT Struct file."`
81 rtstruct_ref_image=`zenity --file-selection --title="Select Reference Image."`
84 echo Invalid arguments. Type \'`basename $0` -h\' for help
95 #echo "Processing \"${rtstruct_roi_list[$roi_struct]}\"..."
96 # create ROI mask from rtstruct
97 roi_mask=roi_${rtstruct_roi_name}.mhd
98 clitkDicomRTStruct2Image -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
99 if cat /tmp/err.txt | grep -q "No ROI"; then
100 echo Invalid contour number.
104 # guarantees the same sampling for roi mask and vector image
105 roi_mask2=resampled_${roi_mask}
106 clitkResampleImage -i ${roi_mask} -o ${roi_mask2} --like ${rtstruct_ref_image}
109 clitkImageStatistics -i ${rtstruct_ref_image} -m ${roi_mask2} --verbose 2> /dev/null | tail -n 8 > /tmp/result.txt
111 if [ $gui_mode = 1 ]; then
112 cat /tmp/result.txt | zenity --text-info --title "Restuls for \"${rtstruct_roi_name}\""
114 echo "Restuls for \"${rtstruct_roi_name}\""
118 rm `basename $roi_mask .mhd`.{mhd,raw}
119 rm `basename $roi_mask2 .mhd`.{mhd,raw}