--- /dev/null
+#! /bin/bash -x
+
+###############################################################################
+#
+# FILE: create_midP-2.0.sh
+# AUTHOR: Rômulo Pinho 05/08/2011
+#
+# Version 2.0 of the create_midP_masks.sh script. The most relevant changes are:
+# * creation of bands around input and output image regions to try to improve
+# the registration along lung boundaries (naturally, it depends on the quality
+# of motion mask generation).
+# * some steps are now in different modules, to facilitate re-use (see "includes" section).
+# * minor modifications on output file names.
+# * attempt to simplify the code a bit.
+#
+###############################################################################
+
+source `dirname $0`/common.sh
+
+extract_patient()
+{
+ echo "$phase_file -> Extracting patient..."
+ clitkExtractPatient -i $phase_file -o $mask_dir_tmp/patient_mask_$phase_nb.mhd --noAutoCrop -a $afdb_file $ExtractPatientExtra
+ clitkSetBackground -i $phase_file -o $mask_dir_tmp/patient_$phase_nb.mhd --mask $mask_dir_tmp/patient_mask_$phase_nb.mhd --outsideValue -1000
+}
+
+extract_bones()
+{
+ if [ x = x$ExtractBonesLower1 ]; then
+ ExtractBonesLower1=120
+ fi
+ if [ x = x$ExtractBonesLower2 ]; then
+ ExtractBonesLower2=80
+ fi
+ echo "$phase_file -> Extracting bones..."
+ clitkImageConvert -i $phase_file -o $mask_dir_tmp/float_$phase_nb.mhd -t float
+ clitkExtractBones -i $mask_dir_tmp/float_$phase_nb.mhd -o $mask_dir_tmp/bones_$phase_nb.mhd -a $afdb_file --lower1 $ExtractBonesLower1 --upper1 2000 --lower2 $ExtractBonesLower2 --upper2 2000 --smooth --time 0.0625 --noAutoCrop
+}
+
+extract_lungs()
+{
+ echo "$phase_file -> Extracting lungs..."
+ clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop
+}
+
+resample()
+{
+ echo "$phase_file -> Resampling..."
+ clitkResampleImage -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/patient_$phase_nb.mhd --spacing $resample_spacing --interp $resample_algo
+
+ clitkResampleImage -i $mask_dir_tmp/lungs_$phase_nb.mhd -o $mask_dir_tmp/lungs_$phase_nb.mhd --like $mask_dir_tmp/patient_$phase_nb.mhd
+}
+
+compute_motion_mask()
+{
+ if [ x = x$MotionMaskOffsetDetect ]; then
+ MotionMaskOffsetDetect="0,-5,0"
+ fi
+ if [ x = x$FillingLevel ]; then
+ FillingLevel=94
+ fi
+
+ clitkMotionMask -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/mm_$phase_nb.mhd --featureLungs $mask_dir_tmp/lungs_$phase_nb.mhd --upperThresholdLungs -400 --fillingLevel $FillingLevel --offsetDetect 0,-5,0 --pad --writeFeature=$mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra
+ #--monitor=$mask_dir_tmp/monitor_$phase_nb.mhd
+}
+
+create_banded_mask()
+{
+ input=$1
+ input_mask=$2
+ output=$3
+ output_mask=$4
+ radius=$5
+
+ input_dir=`dirname $input`
+ input_base=`basename $input`
+
+ # first band
+ clitkMorphoMath -i $input_mask -o $input_dir/extra1_$input_base --type 1 --radius $radius
+ clitkImageArithm -i $input_dir/extra1_$input_base -j $input_mask -o $input_dir/band1_$input_base -t 7
+ clitkBinarizeImage -i $input_dir/band1_$input_base -o $input_dir/band1_$input_base -l 1 -u 1 --fg 100 --mode both
+ clitkImageConvert -i $input_dir/band1_$input_base -o $input_dir/short_band1_$input_base -t short
+
+ # second band
+ clitkMorphoMath -i $input_dir/extra1_$input_base -o $input_dir/extra2_$input_base --type 1 --radius $radius
+ clitkImageArithm -i $input_dir/extra2_$input_base -j $input_dir/extra1_$input_base -o $input_dir/band2_$input_base -t 7
+ clitkBinarizeImage -i $input_dir/band2_$input_base -o $input_dir/band2_$input_base -l 1 -u 1 --fg 200 --mode both
+ clitkImageConvert -i $input_dir/band2_$input_base -o $input_dir/short_band2_$input_base -t short
+
+ # combine bands with masks
+ clitkImageArithm -i $input_mask -j $input_dir/band1_$input_base -o $output_mask -t 0
+ clitkImageArithm -i $output_mask -j $input_dir/band2_$input_base -o $output_mask -t 0
+ # combine bands with image
+ clitkCombineImage -i $input_dir/short_band1_$input_base -j $input -m $input_dir/band1_$input_base -o $output
+ clitkCombineImage -i $input_dir/short_band2_$input_base -j $output -m $input_dir/band2_$input_base -o $output
+
+ # clean-up
+ rm `echo $input_dir/extra?_$input_base | sed 's:.mhd:.*:g'`
+ rm `echo $input_dir/band?_$input_base | sed 's:.mhd:.*:g'`
+ rm `echo $input_dir/short_band?_$input_base | sed 's:.mhd:.*:g'`
+}
+
+create_registration_masks()
+{
+ # extract inside and outside lung regions from the patient image,
+ # using the motion mask computed previously
+ echo "$phase_file -> Setting Background..."
+ clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/inside_$phase_nb.mhd --mask $mask_dir_tmp/mm_$phase_nb.mhd --outsideValue -1200
+ clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/outside_$phase_nb.mhd --mask $mask_dir_tmp/mm_$phase_nb.mhd --outsideValue -1200 --fg
+
+ # the registration masks for inside (and outside) region correspond
+ # to the motion mask (and its complement) plus extra grey value bands,
+ # obtained with morphological dilations.
+ #
+ echo "$phase_file -> Creating registration masks..."
+ # inside
+ create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/mm_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/mask_inside_$phase_nb.mhd 4
+ # outside
+ clitkExtractPatient -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/mm_outside_$phase_nb.mhd --noAutoCrop
+ create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/mm_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/mask_outside_$phase_nb.mhd 4
+}
+
+mm_preprocessing()
+{
+ extract_patient
+ # extract_bones
+ extract_lungs
+ # remove_tmp_masks 1
+ resample
+}
+
+mm_postprocessing()
+{
+ # remove_tmp_masks 2
+ # remove_tmp_masks 3
+ create_registration_masks
+}
+
+motion_mask()
+{
+ #set cmd line variables
+ mhd4d=$1
+ resample_spacing=$2
+ resample_algo=$3
+
+ # import variables specific to each patient
+ source variables
+
+ dir=`dirname $1`
+ cd $dir
+
+ #set other global variables
+ mask_dir="MASK-${resample_spacing}mm-$resample_algo"
+ mask_dir_tmp="tmp.$mask_dir"
+ extract_4d_phases $mhd4d
+
+ 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 $mask_dir 2> /dev/null | wc -l) -eq 0 ]]; do
+ echo "waiting creation of motion masks..."
+ sleep 2
+ done
+ echo "finished waiting"
+ fi
+ fi
+
+# do_mm=1
+# mask_dir_tmp=$mask_dir
+ if [ $do_mm == 1 ]; then
+ mask_log_dir=$mask_dir_tmp/LOG
+ mkdir -p $mask_log_dir
+
+ # multi-threaded pre-processing for motion mask calcs
+ for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+ phase_nb=${phase_nbs[$i]}
+ phase_file=${phase_files[$i]}
+ afdb_file=`echo $phase_file | sed 's/mhd/afdb/'`
+
+ check_threads $MAX_THREADS
+ mm_preprocessing &
+ done
+
+ # single-threaded motion mask calc
+ for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+ phase_nb=${phase_nbs[$i]}
+ phase_file=${phase_files[$i]}
+
+ check_threads 1
+ echo "$phase_file -> Computing motion mask..."
+ compute_motion_mask > $mask_log_dir/motion_mask_$phase_file.log
+ done
+
+ # multi-threaded post-processing of motion mask calcs
+ for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+ phase_nb=${phase_nbs[$i]}
+ phase_file=${phase_files[$i]}
+
+ check_threads $MAX_THREADS
+ mm_postprocessing &
+ done
+
+ # rename tmp mask directory after mask creation
+ check_threads 1
+ mv -f $mask_dir_tmp $mask_dir
+ fi
+
+ echo
+ echo "-------- Motion mask done ! ---------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
+
+
+#################
+# main #
+#################
+
+if [ $# != 3 ]; then
+ echo "Usage: $0 CT_4D RESAMPLE_SPACING RESAMPLE_ALGORITHM"
+ exit -1
+fi
+
+#
+# variables exported in this scope
+#
+# mask_dir: directory where all masks are kept
+#
+
+if [ $1 != "using-as-lib" ]; then
+ motion_mask $1 $2 $3
+fi
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff