#! /bin/bash -x
-MAX_THREADS=2
-
-check_threads()
-{
- while [[ $(jobs -p | wc -l) -ge $1 ]]; do
- jobs
- sleep 10
- done
-}
+source `dirname $0`/midp_common.sh
extract_patient()
{
if [ x = x$ExtractBonesLower1 ]; then
ExtractBonesLower1=120
fi
+ if [ x = x$ExtractBonesLower2 ]; then
+ ExtractBonesLower2=80
+ fi
echo "$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
+ clitkExtractBones -i $mask_dir_tmp/float_$image_name -o $mask_dir_tmp/bones_$image_name -a $afdb_name --lower1 $ExtractBonesLower1 --upper1 2000 --lower2 $ExtractBonesLower2 --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
}
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_$image_name
+ if [ x = x$FillingLevel ]; then
+ FillingLevel=94
+ 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 $FillingLevel --offsetDetect 0,-5,0 --pad --writeFeature=$mask_dir_tmp/feature_$image_name $MotionMaskExtra --monitor=$mask_dir_tmp/monitor_$image_name
}
set_background()
dir=`dirname $1`
cd $dir
+ # import variables specific to each patient
+ source variables
+
resample_spacing=$2
resample_algo=$3
#
# variables exported in this scope
#
-# mask_dir: directory where all mask are kept
+# mask_dir: directory where all masks 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