+++ /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 $0`/midp_common.sh
-
-extract_patient()
-{
- echo "$phase_file -> Extracting patient..."
- clitkExtractPatient -i $phase_file -o $mask_dir_tmp/patient_mask_$phase_nb.mhd --noAutoCrop -a $afdb_file $ExtractPatientExtra
-# abort_on_error clitkExtractPatient $?
-
- clitkSetBackground -i $phase_file -o $mask_dir_tmp/patient_$phase_nb.mhd --mask $mask_dir_tmp/patient_mask_$phase_nb.mhd --outsideValue -1000
-# abort_on_error clitkSetBackground $?
-}
-
-extract_bones()
-{
- if [ x = x$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 $afdb_file --noAutoCrop --doNotSeparateLungs --type 1
-}
-
-
-
-resample()
-{
- echo "$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 $mask_dir_tmp/patient_mask_$phase_nb.mhd -o $mask_dir_tmp/patient_mask_$phase_nb.mhd --spacing $resample_spacing --interp $resample_algo
- if [ "$mask_type" != "patient" ]; then
- 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
- fi
- if [ "$mask_type" == "mm" ]; then
- clitkResampleImage -i $mask_dir_tmp/bones_$phase_nb.mhd -o $mask_dir_tmp/bones_$phase_nb.mhd --like $mask_dir_tmp/patient_$phase_nb.mhd
- fi
-}
-
-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 --featureBones $mask_dir_tmp/bones_$phase_nb.mhd --fillingLevel $FillingLevel --offsetDetect $MotionMaskOffsetDetect --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
- combine_image $input_dir/short_band1_$input_base $input $output $input_dir/band1_$input_base
- combine_image $input_dir/short_band2_$input_base $output $output $input_dir/band2_$input_base
-
- # 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 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 $mask_dir_tmp/${mask_type}_$phase_nb.mhd --outsideValue -1200
- clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/outside_$phase_nb.mhd --mask $mask_dir_tmp/${mask_type}_$phase_nb.mhd --outsideValue -1200 --fg
-
- # the registration masks for inside (and outside) region correspond
- # to the motion mask (and its complement) plus extra grey value bands,
- # obtained with morphological dilations.
- #
- echo "$phase_file -> Creating registration masks..."
- # inside
- clitkMorphoMath -i $mask_dir_tmp/${mask_type}_$phase_nb.mhd -o $mask_dir_tmp/mask_inside_$phase_nb.mhd --type 1 --radius 8
- create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/${mask_type}_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$phase_nb.mhd 4
- # outside
- clitkBinarizeImage -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd -l -999 -u 4000 --mode both
- #clitkExtractPatient -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd --noAutoCrop
- clitkMorphoMath -i $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd -o $mask_dir_tmp/mask_outside_$phase_nb.mhd --type 1 --radius 8
- create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
-}
-
-mm_preprocessing()
-{
- extract_patient
-
- if [ "$mask_type" != "patient" ]; then
- extract_lungs
- fi
-
- if [ "$mask_type" == "mm" ]; then
- extract_bones
- fi
-
- # remove_tmp_masks 1
- if [ $resample_spacing -ne 0 ] ; then
- resample
- fi
-}
-
-mm_postprocessing()
-{
- # remove_tmp_masks 2
- # remove_tmp_masks 3
-
- create_registration_masks
-# if [ "$mask_type" == "mm" ]; then
-# create_registration_motion_masks
-# elif [ "$mask_type" == "lungs" ]; then
-# create_registration_lung_masks
-# fi
-}
-
-wait_mm_creation()
-{
- # 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.
- #
- do_mm=1
- if [ -e $mask_dir ]; then
- # check that the final mask dir exists and that it contains all files it needs.
- # the check assumes that the inside and outside masks are the key files to exist.
- do_mm=0
- nb_phases=${#phase_nbs[@]}
- if [ "$mask_type" == "patient" ]; then
- nb_masks=`ls $mask_dir/lungs_*.mhd | wc -l`
- if [ $nb_masks != $nb_phases ]; then
- # if the mask dir is invalid, remove it and recreate all masks, just in case.
- rm -fr $mask_dir 2> /dev/null
- do_mm=1
- fi
- else
- nb_mm_masks=`ls $mask_dir/${mask_type}_outside*.mhd | wc -l`
- nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
- nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
- if [ $nb_mm_masks != $nb_phases -o $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
- # if the mask dir is invalid, remove it and recreate all masks, just in case.
- rm -fr $mask_dir 2> /dev/null
- do_mm=1
- fi
- fi
- fi
-
- if [ $do_mm = 1 ]; then
- if ! mkdir $mask_dir_tmp 2> /dev/null; then
- if [ ! -e $mask_dir_tmp ]; then
- # if the temp dir couldn't be created, but it doesn't exist, abort
- abort_on_error wait_mm_creation $? clean_up_masks
- else
- # assumes another process is creating the maks in the temp dir.
- # now we need to wait until the masks are complete or until the
- # time limit is reached.
- interval=10
- sleeping=0
- max_wait=3600 # one hour
- nb_files0=`ls $mask_dir_tmp/* | wc -l`
- while [ ! -e $mask_dir -a $sleeping -le $max_wait ]; do
- echo "waiting creation of motion masks..."
- sleep $interval
- sleeping=$(( $sleeping + $interval ))
- nb_files1=`ls $mask_dir_tmp/* | wc -l`
- if [ $nb_files1 != $nb_files0 ]; then
- nb_files0=$nb_files1
- sleeping=0
- fi
- done
-
- if [ $sleeping -gt $max_wait ]; then
- abort_on_error wait_mm_creation -1 clean_up_masks
- else
- echo "finished waiting"
- do_mm=0
- fi
- fi
- fi
- fi
-}
-
-motion_mask()
-{
- #set cmd line variables
- local mhd4d=`basename $1`
- mask_type=$2
- if [ $# -eq 4 ] ; then
- resample_spacing=$3
- resample_algo=$4
- else
- resample_spacing=0
- resample_algo=0
- fi
-
- dir=`dirname $1`
- cd $dir
-
- # import variables specific to each patient
- if test -e ./variables; then
- source ./variables
- fi
-
- #set other global variables
- if [ $resample_spacing -ne 0 ] ; then
- mask_dir="MASK-${resample_spacing}mm-$resample_algo"
- else
- mask_dir="MASK"
- fi
- mask_dir_tmp="tmp.$mask_dir"
- extract_4d_phases $mhd4d
-
- echo
- echo "------------ Motion mask from create_midP_masks.sh ------------"
- start=`date`
- echo "start: $start"
- echo
-
- wait_mm_creation
-
-# do_mm=1
-# mask_dir_tmp=$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
- pids=( )
- 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 $MAX_THREADS
- mm_preprocessing &
- pids=( "${pids[@]}" "$!" )
- done
-
- wait_pids ${pids[@]}
- for ret in $ret_codes; do
- abort_on_error mm_preprocessing $ret clean_up_masks
- done
-
- if [ "$mask_type" == "mm" ]; then
- # 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
- abort_on_error compute_motion_mask $? clean_up_masks
- done
- fi
-
- # multi-threaded post-processing of motion mask calcs
- if [ "$mask_type" != "patient" ]; then
- pids=( )
- for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
- phase_nb=${phase_nbs[$i]}
- phase_file=${phase_files[$i]}
-
- check_threads $MAX_THREADS
- mm_postprocessing &
- pids=( "${pids[@]}" "$!" )
- done
-
- wait_pids ${pids[@]}
- for ret in $ret_codes; do
- abort_on_error mm_postprocessing $ret clean_up_masks
- done
- fi
-
- # 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 [ $# -ne 4 -a $# -ne 2 -a $# -ne 1 ]; then
- echo "Usage: $0 CT_4D TYPE [RESAMPLE_SPACING RESAMPLE_ALGORITHM]"
- echo " TYPE: \"mm\" (traditional motion masks); \"lungs\" (lung masks); \"patient\" (patient mask only)"
- exit -1
-fi
-
-#
-# variables exported in this scope
-#
-# mask_dir: directory where all masks are kept
-#
-
-if [ $1 != "using-as-lib" ]; then
- if [ $# -eq 4 ] ; then
- motion_mask $1 $2 $3 $4
- elif [ $# -eq 2 ] ; then
- motion_mask $1 $2
- else
- motion_mask $1 all
- fi
-fi
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff