{
if [ $2 != 0 ]; then
echo Aborted at $1 with code $2
- if [ $# = 3 ]; then
- eval $3
- fi
+ #if [ $# = 3 ]; then
+ # eval $3
+ #fi
exit $2
fi
nb_phases=${#phase_files[@]}
# get everything except numbers and punctuation
- cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[^0-9[:punct:]]*" | sort -u > /tmp/patterns.txt
+ cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "[^0-9[:punct:]]*" | sort -u > /tmp/patterns.txt
# find which patterns have the phases connected to it
patterns=`cat /tmp/patterns.txt`
if [ -z "$patterns" ]; then
- phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep "[0-9]\+"` )
+ phase_nbs=( `cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep "[0-9]\+"` )
else
for i in $patterns; do
# check if the pattern appears before the phase number
- nb_phases_found=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "$i[0-9[:punct:]]\+" | sort -u | wc -l`
+ nb_phases_found=`cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "$i[0-9[:punct:]]\+" | sort -u | wc -l`
if [ $nb_phases_found == $nb_phases ]; then
# keep only what identifies the phase number
- phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "$i[0-9[:punct:]]\+" | grep -o "[^${i}]\+" | grep -o "[0-9]\+[[:punct:]]*[0-9]*" | grep -o "[0-9]*[[:punct:]]*[0-9]\+"` )
+ phase_nbs=( `cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "$i[0-9[:punct:]]\+" | grep -o "[^${i}]\+" | grep -o "[0-9]\+[[:punct:]]*[0-9]*" | grep -o "[0-9]*[[:punct:]]*[0-9]\+"` )
break
fi
# check if the pattern appears after the phase number
- nb_phases_found=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | sort -u | wc -l`
+ nb_phases_found=`cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | sort -u | wc -l`
if [ $nb_phases_found == $nb_phases ]; then
# keep only what identifies the phase number
- phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | grep -o "[^${i}]\+" | grep -o "[0-9]\+[[:punct:]]*[0-9]*" | grep -o "[0-9]*[[:punct:]]*[0-9]\+"` )
+ phase_nbs=( `cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | grep -o "[^${i}]\+" | grep -o "[0-9]\+[[:punct:]]*[0-9]*" | grep -o "[0-9]*[[:punct:]]*[0-9]\+"` )
break
fi
echo "4D file is $mhd4d"
# array of phase files
- phase_files=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:'` )
+ phase_files=( `cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:'` )
echo "Phase files are ${phase_files[@]}"
extract_4d_phase_numbers $mhd4d
extract_4d_phases $1
# reference phase file
- ref_phase_file=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | grep $2`
+ ref_phase_file=`cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | grep $2`
echo "Reference phase is $ref_phase_file"
# reference phase number
combine_image()
{
# eg: -i $result_in -j $result_out -o $out_result -m $motion_mask
+ local tmp1=$RANDOM
+ local tmp2=$RANDOM
- clitkSetBackground -i $1 -o temp1.mhd -m $4
- clitkSetBackground -i $2 -o temp2.mhd -m $4 --fg
+ clitkSetBackground -i $1 -o $tmp1.mhd -m $4
+ clitkSetBackground -i $2 -o $tmp2.mhd -m $4 --fg
- clitkImageArithm -i temp1.mhd -j temp2.mhd -o $3
- rm temp?.*
+ clitkImageArithm -i $tmp1.mhd -j $tmp2.mhd -o $3
+ rm $tmp1.* $tmp2.*
}
#
average_temporal_dimension()
{
# eg: -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
-
- local tot=tot.mhd
+ local tmp=$RANDOM
+ local tot=$tmp.mhd
local dir=`dirname $1`
- local first=`grep raw $1 | sed 's/raw/mhd/g' | head -n 1`
+ local first=`grep z*raw $1 | sed 's/z*raw/mhd/g' | head -n 1`
clitkImageArithm -i $dir/$first -o $tot -t 1 -s 0
- local nbphases=`grep raw $1 | sed 's/raw/mhd/g' | wc -l`
- for i in $(grep raw $1 | sed 's/raw/mhd/g'); do
+ local nbphases=`grep z*raw $1 | sed 's/z*raw/mhd/g' | wc -l`
+ for i in $(grep z*raw $1 | sed 's/z*raw/mhd/g'); do
clitkImageArithm -i $dir/$i -j $tot -o $tot
done
clitkImageArithm -i $tot -o $2 -t 11 -s $nbphases
- rm tot.*
+ rm $tmp.*
+}
+
+select_contour_gui()
+{
+ local roi_list=$@
+ 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 $roi_list
+ fi;;
+ -1)
+ zenity --error --text="Unexpected error. Please relaunch the application."
+ exit;;
+ esac
+}
+
+select_contour()
+{
+ local roi_list=$@
+ echo "Available Contours:"
+ for r in $roi_list; do
+ echo $r
+ done
+
+ echo "Please choose a contour number:"
+ read rtstruct_roi_index
+ let i=0
+ for r in $roi_list; do
+ if [ $rtstruct_roi_index = `echo $r | cut -d ':' -f 1` ]; then
+ rtstruct_roi_index=$i
+ break;
+ fi
+ let i=i+1
+ done
+
}
+
+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
+
+ if [ $gui_mode = 1 ]; then
+ select_contour_gui ${rtstruct_roi_list[@]}
+ rtstruct_roi=`echo ${rtstruct_roi_name} | cut -d ':' -f 1`
+ rtstruct_roi_name=`echo ${rtstruct_roi_name} | cut -d ':' -f 2`
+ else
+ select_contour ${rtstruct_roi_list[@]}
+ rtstruct_roi=${rtstruct_roi_number_list[$(( $rtstruct_roi_index ))]}
+ rtstruct_roi_name=${rtstruct_roi_name_list[$(( $rtstruct_roi_index ))]}
+ fi
+}
\ No newline at end of file
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff