#! /bin/bash -x
-
+
###############################################################################
#
# FILE: create_midP-2.0.sh
{
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 $?
}
extract_bones()
extract_lungs()
{
- echo "$phase_file -> Extracting lungs..."
- clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop
+ echo "$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
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
+ 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
}
compute_motion_mask()
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 $MotionMaskOffsetDetect --pad --writeFeature=$mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra
+ #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 $MotionMaskOffsetDetect --pad --writeFeature=$mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra
+ 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
}
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
+ 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'`
create_registration_masks()
{
- # extract inside and outside lung regions from the patient image,
+ # 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
+}
+
+create_registration_motion_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 $mask_dir_tmp/mm_$phase_nb.mhd --outsideValue -1200
#
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
+ clitkMorphoMath -i $mask_dir_tmp/mm_$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 $mask_dir_tmp/mm_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$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
+ clitkMorphoMath -i $mask_dir_tmp/mm_outside_$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 $mask_dir_tmp/mm_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
+}
+
+create_registration_lung_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 $mask_dir_tmp/lungs_$phase_nb.mhd --outsideValue -1200
+ clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/outside_$phase_nb.mhd --mask $mask_dir_tmp/lungs_$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 $mask_dir_tmp/lungs_$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 $mask_dir_tmp/lungs_$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 $mask_dir_tmp/lungs_outside_$phase_nb.mhd -l -999 -u 4000 --mode both
+ clitkMorphoMath -i $mask_dir_tmp/lungs_outside_$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 $mask_dir_tmp/lungs_outside_$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
- # extract_bones
+ extract_bones
extract_lungs
# remove_tmp_masks 1
- resample
+ 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 $mask_dir 2> /dev/null
+ do_mm=1
+ fi
+ fi
+# elif [ "$mask_type" == "lungs" ]; then
+# nb_mm_masks=`ls $mask_dir/lungs_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 $mask_dir 2> /dev/null
+# do_mm=1
+# fi
+# elif [ "$mask_type" == "mm" ]; then
+# nb_mm_masks=`ls $mask_dir/mm_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
- mhd4d=$1
- resample_spacing=$2
- resample_algo=$3
+ 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 $dir
# import variables specific to each patient
- source ./variables
+ if test -e ./variables; then
+ source ./variables
+ fi
#set other global variables
- mask_dir="MASK-${resample_spacing}mm-$resample_algo"
+ 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 "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 $mask_dir 2> /dev/null | wc -l) -eq 0 ]]; do
- echo "waiting creation of motion masks..."
- sleep 2
- done
- echo "finished waiting"
- fi
- fi
-
+ wait_mm_creation
+
# do_mm=1
# mask_dir_tmp=$mask_dir
if [ $do_mm == 1 ]; then
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]}
check_threads $MAX_THREADS
mm_preprocessing &
+ pids=( "${pids[@]}" "$!" )
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
+ wait_pids ${pids[@]}
+ for ret in $ret_codes; do
+ abort_on_error mm_preprocessing $ret clean_up_masks
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]}
+ 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 $MAX_THREADS
- mm_postprocessing &
- done
+ check_threads 1
+ echo "$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
# main #
#################
-if [ $# != 3 ]; then
- echo "Usage: $0 CT_4D RESAMPLE_SPACING RESAMPLE_ALGORITHM"
+if [ $# -ne 4 -a $# -ne 2 -a $# -ne 1 ]; then
+ echo "Usage: $0 CT_4D TYPE [RESAMPLE_SPACING RESAMPLE_ALGORITHM]"
+ echo " TYPE: \"motion\" (traditional motion masks); \"lungs\" (lung masks); \"patient\" (patient mask only)"
exit -1
fi
#
if [ $1 != "using-as-lib" ]; then
- motion_mask $1 $2 $3
+ 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