-#! /bin/sh +x
+#! /bin/sh -x
###############################################################################
#
#
###############################################################################
+#
+# check return value passed and abort if it represents an error (ie, ret != 0)
+# optionally, a function can be passed as a 3rd parameter, to be called just
+# before exiting. this is useful for cleaning up, for example.
+#
+abort_on_error()
+{
+ if [ $2 != 0 ]; then
+ echo Aborted at $1 with code $2
+ #if [ $# = 3 ]; then
+ # eval $3
+ #fi
+
+ exit $2
+ fi
+}
+
+#
+# wait for all processes in the list and return their exit codes
+# in the ret_codes variable.
+#
+# OBS: this function must always be called in the same shell
+# that launched the processes.
+#
+wait_pids()
+{
+ local pids=$*
+ local ret=
+ local rets=
+# echo PIDS: $pids
+ for p in $pids; do
+# echo waiting $p
+ wait $p > /dev/null 2> /dev/null
+ ret=$?
+ if [ ret != 127 ]; then
+ rets=$rets" "$ret
+ else
+ rets=$rets" "0
+ fi
+
+ done
+
+ ret_codes=$rets
+}
+#
+# clean-up functions for maks, registration, and midp
+#
+clean_up_masks()
+{
+ rm -fr $mask_dir_tmp
+}
+
+clean_up_midp()
+{
+ rm -fr $midp_dir
+}
+
+clean_up_registration()
+{
+ rm -fr $vf_dir
+ rm -fr $output_dir
+}
+
+
+#
# block execution untill the number of threads (jobs) launched by the
# current process is below the given number of threads.
MAX_THREADS=2
nb_phases=${#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
fi
done
}
+
+#
+# replacement for clitkCombineImage
+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 $tmp1.mhd -m $4
+ clitkSetBackground -i $2 -o $tmp2.mhd -m $4 --fg
+
+ clitkImageArithm -i $tmp1.mhd -j $tmp2.mhd -o $3
+ rm $tmp1.* $tmp2.*
+}
+
+#
+# replacement for clitkAverageTemporalDimension
+average_temporal_dimension()
+{
+ # eg: -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ local tmp=$RANDOM
+ local tot=$tmp.mhd
+
+ local dir=`dirname $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 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 $tmp.*
+}
+
+select_contour_gui()
+{
+ local roi_list=$@
+ 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