extract_lungs()
{
echo "$phase_file -> Extracting lungs..."
- clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs
+ clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs --type 1
}
{
echo "$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
}
#
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
}
mm_preprocessing()
create_registration_masks
}
+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[@]}
+ nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
+ nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
+ if [ $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
+
+ 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
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
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff