X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=scripts%2Fcalculate_contour_stats.sh;fp=scripts%2Fcalculate_contour_stats.sh;h=0000000000000000000000000000000000000000;hb=b0a5bad2f1ac4991b4d2bdb1c015275128441635;hp=be10e9dfc96d7e1c22495070bdbeeb14bf4fa1aa;hpb=ee568ccc2ae2be4d9d60967e522e2d81cb148d95;p=clitk.git

diff --git a/scripts/calculate_contour_stats.sh b/scripts/calculate_contour_stats.sh
deleted file mode 100755
index be10e9d..0000000
--- a/scripts/calculate_contour_stats.sh
+++ /dev/null
@@ -1,78 +0,0 @@
-#! /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