--- /dev/null
+#! /bin/bash -x
+
+# imports
+. common.sh
+
+extract_patient()
+{
+ echo "$image_name -> Extracting patient..."
+ clitkExtractPatient -i $image_name -o $mask_dir_tmp/patient_$image_name --noAutoCrop -a $afdb_name $ExtractPatientExtra
+ clitkBinarizeImage -i $mask_dir_tmp/patient_$image_name -o $mask_dir_tmp/patient_$image_name -l 1 -u 1 --mode=BG
+ clitkSetBackground -i $image_name -o $mask_dir_tmp/patient_only_$image_name --mask $mask_dir_tmp/patient_$image_name --outsideValue -1000
+}
+
+extract_bones()
+{
+ if [ x = x$ExtractBonesLower1 ]; then
+ ExtractBonesLower1=120
+ fi
+ echo "$image_name -> Extracting bones..."
+ clitkImageConvert -i $image_name -o $mask_dir_tmp/float_$image_name -t float
+ #clitkExtractBones -i $mask_dir_tmp/float_$image_name -o $mask_dir_tmp/bones_$image_name --lower1 120 --upper1 2000 --lower2 70 --upper2 2000 --smooth --time 0.0625 --noAutoCrop
+ clitkExtractBones -i $mask_dir_tmp/float_$image_name -o $mask_dir_tmp/bones_$image_name -a $afdb_name --lower1 $ExtractBonesLower1 --upper1 2000 --lower2 80 --upper2 2000 --smooth --time 0.0625 --noAutoCrop
+ #clitkMorphoMath -i $mask_dir_tmp/bones_$image_name -o $mask_dir_tmp/bones_$image_name --type 2 --radius 4,4,2
+}
+
+extract_lungs()
+{
+ echo "$image_name -> Extracting lungs..."
+ clitkExtractLung -i $image_name -o $mask_dir_tmp/lungs_$image_name -a $afdb_name --noAutoCrop
+}
+
+resample()
+{
+ echo "$image_name -> Resampling..."
+ clitkResampleImage -i $mask_dir_tmp/patient_$image_name -o $mask_dir_tmp/patient_$image_name --spacing $resample_spacing --interp $resample_algo
+ clitkResampleImage -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/patient_only_$image_name --spacing $resample_spacing --interp $resample_algo
+ clitkResampleImage -i $mask_dir_tmp/bones_$image_name -o $mask_dir_tmp/bones_$image_name --like $mask_dir_tmp/patient_only_$image_name --interp $resample_algo
+ clitkResampleImage -i $mask_dir_tmp/lungs_$image_name -o $mask_dir_tmp/lungs_$image_name --like $mask_dir_tmp/patient_only_$image_name
+}
+
+compute_motion_mask()
+{
+ if [ x = x$MotionMaskOffsetDetect ]; then
+ MotionMaskOffsetDetect="0,-5,0"
+ fi
+ clitkMotionMask -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/mm_$image_name --featureBones=$mask_dir_tmp/bones_$image_name --featureLungs=$mask_dir_tmp/lungs_$image_name --upperThresholdLungs -400 --fillingLevel 94 --offsetDetect 0,-5,0 --pad --writeFeature=$mask_dir_tmp/feature_$image_name $MotionMaskExtra --monitor=$mask_dir_tmp/monitor_$image_name
+}
+
+set_background()
+{
+ echo "$image_name -> Setting Background..."
+ clitkSetBackground -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/inside_$image_name --mask $mask_dir_tmp/mm_$image_name --outsideValue -1200
+ clitkSetBackground -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/outside_$image_name --mask $mask_dir_tmp/mm_$image_name --outsideValue -1200 --fg
+}
+
+create_registration_masks()
+{
+ echo "$image_name -> Creating registration masks..."
+ clitkMorphoMath -i $mask_dir_tmp/mm_$image_name -o $mask_dir_tmp/regmask_in_$image_name --type 1 --radius 8
+ clitkExtractPatient -i $mask_dir_tmp/outside_$image_name -o $mask_dir_tmp/regmask_out_$image_name --noAutoCrop
+ clitkMorphoMath -i $mask_dir_tmp/regmask_out_$image_name -o $mask_dir_tmp/regmask_out_$image_name --type 1 --radius 8
+}
+
+remove_tmp_masks()
+{
+ echo "Removing temporary files..."
+ image_name_base=`echo $image_name | sed 's/mhd//'`
+ case $1 in
+ 1)
+ #rm $mask_dir_tmp/float_$image_name_base*
+ ;;
+ 2)
+ #rm $mask_dir_tmp/bones_$image_name_base*
+ ;;
+ 3)
+ #rm $mask_dir_tmp/patient_only_$image_name_base*
+ ;;
+ esac
+}
+
+mm_preprocessing()
+{
+ extract_patient
+ extract_bones
+ extract_lungs
+ remove_tmp_masks 1
+ resample
+}
+
+mm_postprocessing()
+{
+ remove_tmp_masks 2
+ set_background
+ remove_tmp_masks 3
+ create_registration_masks
+}
+
+mm_workflow()
+{
+ extract_patient
+ extract_bones
+ remove_tmp_masks 1
+ resample
+ echo "$image_name -> Computing motion mask..."
+ compute_motion_mask >> $mask_log_dir/motion_mask_$image_name.log
+ remove_tmp_masks 2
+ set_background
+ remove_tmp_masks 3
+ create_registration_masks
+}
+
+motion_mask()
+{
+ #set cmd line variables
+ echo "4D CT -> "$1
+ phases=`grep ".raw" $1`
+ echo "mask phases -> " $phases
+
+ dir=`dirname $1`
+ cd $dir
+
+ resample_spacing=$2
+ resample_algo=$3
+
+
+ #set other global variables
+ mask_dir="MASK-$resample_spacing""mm""-$resample_algo"
+ mask_dir_tmp="tmp."$mask_dir
+
+ echo
+ echo "------------ Motion mask from create_midP_masks.sh ------------"
+ start=`date`
+ echo "start: $start"
+ echo
+
+ # the motion masks are first created in a tmp directory. this directory is
+ # later going to be renamed to the final motion mask directory. concurrent
+ # executions trying to create the same set of masks will be blocked until
+ # the first execution finishes. naturally, these other executions will not
+ # recreate the masks. so first we try to create the tmp directory.
+ # if the creation fails, it means that another execution is
+ # already creating the masks, so this execution will be blocked. the
+ # execution is unblocked only when the creation of masks is finished and
+ # the mask directory is renamed.
+ #
+ # ATTENTION: RP - 08/02/2011
+ # robustness issue: tmp directory may exist but may be empty or
+ # incomplete. the solution is to check per file, but I'll leave it like
+ # this for the moment.
+ do_mm=0
+ if [ $(ls -d $mask_dir 2> /dev/null | wc -l) -eq 0 ]; then
+ mkdir $mask_dir_tmp 2> /dev/null
+ return_mkdir=$?
+ if [ $return_mkdir == 0 ]; then
+ do_mm=1
+ else
+ while [[ $(ls -d $mask_dir 2> /dev/null | wc -l) -eq 0 ]]; do
+ echo "waiting creation of motion masks..."
+ sleep 2
+ done
+ echo "finished waiting"
+ fi
+ fi
+
+ regmask_in_list=""
+ regmask_out_list=""
+ reg_in_list=""
+ reg_out_list=""
+
+ # multi-threaded pre-processing for motion mask calcs
+ if [ $do_mm == 1 ]; then
+ mask_log_dir=$mask_dir_tmp/LOG
+ mkdir -p $mask_log_dir
+
+ for phase in $phases
+ do
+ image_name=`echo $phase | sed 's/raw/mhd/'`
+ afdb_name=`echo $phase | sed 's/raw/afdb/'`
+ check_threads $MAX_THREADS
+ mm_preprocessing &
+ done
+
+ # single-threaded motion mask calc
+ for phase in $phases
+ do
+ image_name=`echo $phase | sed 's/raw/mhd/'`
+
+ check_threads 1
+ echo "$image_name -> Computing motion mask..."
+ compute_motion_mask >> $mask_log_dir/motion_mask_$image_name.log
+ done
+ fi
+
+ # multi-threaded post-processing of motion mask calcs
+ for phase in $phases
+ do
+ image_name=`echo $phase | sed 's/raw/mhd/'`
+ if [ $do_mm = 1 ]; then
+ check_threads $MAX_THREADS
+ mm_postprocessing &
+ fi
+
+ regmask_in_list="$regmask_in_list regmask_in_$image_name"
+ regmask_out_list="$regmask_out_list regmask_out_$image_name"
+ reg_in_list="$reg_in_list inside_$image_name"
+ reg_out_list="$reg_out_list outside_$image_name"
+ done
+
+ # rename tmp mask directory after mask creation
+ check_threads 1
+ mv $mask_dir_tmp $mask_dir
+
+ wait
+
+ echo
+ echo "-------- Motion mask done ! ---------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
+
+
+#################
+# main #
+#################
+
+if [ $# != 3 ]; then
+ echo "Usage: create_midP_masks.sh 4D_CT.mhd resample_spacing resample_algorithm"
+ exit -1
+fi
+
+#
+# variables exported in this scope
+#
+# mask_dir: directory where all mask are kept
+# regmask_in_list: list of registration mask files (inside lungs)
+# regmask_out_list: list of registration mask files (outised lungs)
+# reg_in_list: list of registration image files (inside lungs)
+# reg_out_list: list of registration image files (outside lungs)
+#
+
+# import variables specific to each patient
+source variables
+
+if [ $1 != "using-as-lib" ]; then
+ motion_mask $1 $2 $3
+fi
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff