IF(BUILD_TESTING)
ADD_SUBDIRECTORY(tests)
ENDIF(BUILD_TESTING)
+
+#=========================================================
+# Install scripts when running make install
+SET(SCRIPTS
+ scripts/common.sh
+ scripts/registration.sh
+ scripts/create_midP.sh
+ scripts/create_midP-2.0.sh
+ scripts/create_mhd_4D.sh
+ scripts/create_mhd_4D_pattern.sh
+ scripts/create_midP_masks.sh
+ scripts/create_midP_masks-2.0.sh
+ scripts/pts_to_landmarks.sh
+)
+
+INSTALL (FILES ${SCRIPTS} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
+
-#! /bin/sh
+#! /bin/sh +x
+###############################################################################
+#
+# FILE: common.sh
+# AUTHOR: Rômulo Pinho 05/08/2011
+#
+# Helper file with many functions used in the midP scripts.
+#
+###############################################################################
-MAX_THREADS=2
+# block execution untill the number of threads (jobs) launched by the
+# current process is below the given number of threads.
+MAX_THREADS=2
check_threads()
{
- while [[ $(jobs -p | wc -l) -ge $1 ]]; do
- jobs
- sleep 10
+ nbth=$1
+ while [[ $(jobs -p | wc -l) -ge $nbth ]]; do
+ jobs
+ sleep 10
+ done
+}
+
+#
+# receive a 4D file and and extract the corresponding phase numbers
+# export the variables containing each of the extracted data
+#
+extract_4d_phase_numbers()
+{
+ mhd4d=$1
+
+ nb_phases=${#phase_files[@]}
+
+ # get everything except numbers and punctuation
+ cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[^0-9[:punct:]]*" | sort -u > /tmp/patterns.txt
+
+ # find which patterns have the phases connected to it
+ patterns=`cat /tmp/patterns.txt`
+ if [ -z "$patterns" ]; then
+ phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep "[0-9]\+"` )
+ else
+ for i in $patterns; do
+
+ # check if the pattern appears before the phase number
+ nb_phases_found=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "$i[0-9[:punct:]]\+" | sort -u | wc -l`
+ if [ $nb_phases_found == $nb_phases ]; then
+ # keep only what identifies the phase number
+ phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "$i[0-9[:punct:]]\+" | grep -o "[^${i}]\+" | grep -o "[0-9]\+[[:punct:]]*[0-9]*" | grep -o "[0-9]*[[:punct:]]*[0-9]\+"` )
+ break
+ fi
+
+ # check if the pattern appears after the phase number
+ nb_phases_found=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | sort -u | wc -l`
+ if [ $nb_phases_found == $nb_phases ]; then
+ # keep only what identifies the phase number
+ phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | grep -o "[^${i}]\+" | grep -o "[0-9]\+[[:punct:]]*[0-9]*" | grep -o "[0-9]*[[:punct:]]*[0-9]\+"` )
+ break
+ fi
+
done
+ fi
+
+ echo "Phase numbers are ${phase_nbs[@]}"
+ rm /tmp/patterns.txt
}
+#
+# receive a 4D file and extract the corresponding phase files,
+# and phase numbers.
+# export the variables containing each of the extracted data
+#
+extract_4d_phases()
+{
+ mhd4d=$1
+
+ echo "4D file is $mhd4d"
+
+ # array of phase files
+ phase_files=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:'` )
+ echo "Phase files are ${phase_files[@]}"
+
+ extract_4d_phase_numbers $mhd4d
+}
+
+#
+# receive a 4D file and the reference phase number as input
+# and extract the corresponding phase files, phase numbers,
+# and reference phase file.
+#
+# export the variables containing each of the extracted data
+#
+extract_4d_phases_ref()
+{
+ extract_4d_phases $1
+
+ # reference phase file
+ ref_phase_file=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | grep $2`
+ echo "Reference phase is $ref_phase_file"
+
+ # reference phase number
+ for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+ ref_phase_nb=`echo ${phase_nbs[$i]} | grep $2`
+ if [ -n "$ref_phase_nb" ]; then
+ echo "Reference phase number is $ref_phase_nb"
+ break
+ fi
+ done
+}
--- /dev/null
+#!/bin/sh
+
+
+#################################################################################
+# create_mhd_3D argument : {image data} raw_image nom_fichier_de_sortie #
+#################################################################################
+if [ $# -lt 1 ]
+then
+ echo "Usage: create_mhd_3D.sh dimx dimy dimz spcx spcy spcz offx offy offz pixel_type raw_image_file output_file"
+ echo "dim*: dimensions of the image"
+ echo "spc*: pixel spacing along each dimension"
+ echo "off*: offset along each dimension"
+ echo "pixel_type: CHAR, UCHAR, SHORT, USHORT, FLOAT"
+ echo "raw_image_file: image to be referenced by the mhd file created"
+ echo "output_file: mhd to be created"
+ exit 1
+fi
+
+# can point to existing raw files
+n=`ls ${11} | wc -l`
+if [ $n -eq 0 ]
+then
+ echo "${11} does not exist. Cannot create mhd file."
+ exit
+fi
+
+# check if the raw file has the "raw" extension
+n=`ls ${11} | grep .raw | wc -l`
+if [ $n -eq 0 ]
+then
+ # change extension to raw
+ raw_base=`echo ${11} | cut -d . -f 1`;
+ raw_file=$raw_base".raw";
+ mv ${11} $raw_file
+else
+ raw_file=${11}
+fi
+
+# create file (with some default values...)
+echo "NDims = 3" > ${12}
+echo "TransformMatrix = 1 0 0 0 1 0 0 0 1" >> ${12}
+echo "Offset = " $7 $8 $9 >> ${12}
+echo "CenterOfRotation = 0 0 0" >> ${12}
+echo "AnatomicalOrientation = RAI" >> ${12}
+echo "ElementSpacing = " $4 $5 $6 >> ${12}
+echo "DimSize = " $1 $2 $3 >> ${12}
+echo "ElementType = MET_"${10} >> ${12}
+echo "ElementDataFile = " $raw_file >> ${12}
+
+
--- /dev/null
+#!/bin/sh +x
+
+
+write_mhd_4D()
+{
+ cat $orig | sed "s/NDims = .*/NDims = 4/
+ s/TransformMatrix = .*/TransformMatrix = 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1/
+ /Offset/ s/.*/& 0/
+ /CenterOfRotation/ s/.*/& 0/
+ s/AnatomicalOrientation = .*/AnatomicalOrientation = ????/
+ /ElementSpacing/ s/.*/& 1/
+ /DimSize/ s/.*/& $nbph/
+ s/ElementDataFile = .*/ElementDataFile = LIST/" > "$1/$file_name_4D"
+
+ for ph in $listph
+ do
+ phase=`basename $ph`
+ echo "$phase" >> "$1/$file_name_4D"
+ done
+}
+
+#################################################
+# create_mhd_4D argument : repertoire #
+#################################################
+if [ $# -lt 1 ]
+then
+ echo "Usage: create_mhd_4D.sh DIRECTORY"
+ exit 1
+fi
+
+dirname=`dirname $1`
+pattern=`basename $1`
+
+list_phase_file=`ls -1 $1*[0-9].mhd`
+nb_phase_file=`ls -1 $1*[0-9].mhd | wc -l`
+if [ $nb_phase_file = 0 ]
+then
+ echo "Error: no phase found"
+ exit 1
+fi
+
+nbph=$nb_phase_file
+orig=`echo $list_phase_file | cut -f 1 -d ' '`
+listph=`echo $list_phase_file | sed 's:\.mhd:\.raw:g'`
+
+file_name_4D=`echo "${pattern}4D.mhd"`
+
+write_mhd_4D $dirname
+echo "$dirname/$file_name_4D"
--- /dev/null
+#!/bin/sh +x
+
+###############################################################################
+#
+# FILE: create_mhd_pattern.sh
+# AUTHOR: Rômulo Pinho 05/08/2011
+#
+# Similar to create_mhd_4D.sh, but receives a pattern as input.
+#
+# Example:
+# create_mhd_pattern.sh "<path>/all_my_phases_start_like_this_"
+#
+###############################################################################
+
+write_mhd_4D()
+{
+ cat $orig | sed "s/NDims = .*/NDims = 4/
+ s/TransformMatrix = .*/TransformMatrix = 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1/
+ /Offset/ s/.*/& 0/
+ /CenterOfRotation/ s/.*/& 0/
+ s/AnatomicalOrientation = .*/AnatomicalOrientation = ????/
+ /ElementSpacing/ s/.*/& 1/
+ /DimSize/ s/.*/& $nbph/
+ s/ElementDataFile = .*/ElementDataFile = LIST/" > "$1/$file_name_4D"
+
+ for ph in $listph
+ do
+ phase=`basename $ph`
+ echo "$phase" >> "$1/$file_name_4D"
+ done
+}
+
+#################################################
+# create_mhd_4D argument : repertoire #
+#################################################
+if [ $# -lt 1 ]
+then
+ echo "Usage: $0 PATTERN"
+ exit 1
+fi
+
+dirname=`dirname $1`
+pattern=`basename $1`
+
+list_phase_file=`ls -1 $1*[0-9].mhd`
+nb_phase_file=`ls -1 $1*[0-9].mhd | wc -l`
+if [ $nb_phase_file = 0 ]
+then
+ echo "Error: no phase found"
+ exit 1
+fi
+
+nbph=$nb_phase_file
+orig=`echo $list_phase_file | cut -f 1 -d ' '`
+listph=`echo $list_phase_file | sed 's:\.mhd:\.raw:g'`
+
+file_name_4D=`echo "${pattern}4D.mhd"`
+
+write_mhd_4D $dirname
+echo "$dirname/$file_name_4D"
--- /dev/null
+#!/bin/sh -x
+
+###############################################################################
+#
+# FILE: create_midP-2.0.sh
+# AUTHOR: Rômulo Pinho 05/08/2011
+#
+# Version 2.0 of the create_midP.sh script. The most relevant changes are:
+# * receives a .conf file as input, with variables related to the registration
+# parameters and to paramters of the script itself (see accompanying midp_template.conf)
+# for details.
+# * separates execution steps: it's now possible to choose which operation to execute
+# (mask, registration, midp, or all).
+# * 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.
+#
+###############################################################################
+
+######################### includes
+
+source `dirname $0`/create_midP_masks-2.0.sh using-as-lib 2 nn
+source `dirname $0`/registration.sh
+source `dirname $0`/common.sh
+
+registration()
+{
+ echo
+ echo "----------- Registration ------------"
+ start=`date`
+ echo "start: $start"
+ echo
+
+ mkdir -p $vf_dir
+ mkdir -p $output_dir
+
+ # banded images may be created as separate files,
+ # with the specified preffix, which is interesting for debugging.
+ # if blank, it means that the original images (those without bands)
+ # will be used (see create_midP_masks-2.0.sh for details).
+ banded="banded_"
+
+ # params read from conf file
+ params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
+
+ # register all phases to the reference
+ for i in $( seq 0 $((${#phase_files[@]} - 1))); do
+ phase_file=${phase_files[$i]}
+ phase_nb=${phase_nbs[$i]}
+
+ if [ "$phase_nb" != "$ref_phase_nb" ]; then
+ # inside params
+ reference_in=$mask_dir/${banded}inside_$ref_phase_nb.mhd
+ target_in=$mask_dir/${banded}inside_$phase_nb.mhd
+ mask_ref_in=$mask_dir/mask_inside_$ref_phase_nb.mhd
+ mask_targ_in=$mask_dir/mask_inside_$phase_nb.mhd
+ vf_in=$vf_dir/vf_inside_${ref_phase_nb}_$phase_nb.mhd
+ result_in=$output_dir/result_inside_${ref_phase_nb}_$phase_nb.mhd
+ log_in=$log_dir/log_inside_${ref_phase_nb}_$phase_nb.log
+
+ # outside params
+ reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
+ target_out=$mask_dir/${banded}outside_$phase_nb.mhd
+ mask_ref_out=$mask_dir/mask_outside_$ref_phase_nb.mhd
+ mask_targ_out=$mask_dir/mask_outside_$phase_nb.mhd
+ vf_out=$vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd
+ result_out=$output_dir/result_outside_$ref_phase_nb\_$phase_nb.mhd
+ log_out=$log_dir/log_outside_${ref_phase_nb}_$phase_nb.log
+
+ # registration
+ if [ "$method" == "blutdir" ]; then
+ registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
+ registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
+ elif [ "$method" == "elastix" ]; then
+ registration_elastix $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
+ registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
+ fi
+
+ # combine in and out vf
+ motion_mask=$mask_dir/mm_$phase_nb.mhd
+ vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
+ clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
+ clitkZeroVF -i $vf_in -o vf_zero.mhd
+ clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
+ rm vf_zero.*
+
+ # save for later...
+ vf_ref=$vf_in
+ fi
+ done
+
+ # create (zero) vf from reference to reference
+ clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
+
+ # create 4D vf
+ create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
+
+ echo
+ echo "-------- Registration done ! --------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
+
+midp()
+{
+ echo
+ echo "----------- Mid-position ------------"
+ start=`date`
+ echo "start: $start"
+ echo
+
+ mkdir -p $midp_dir
+
+ ########### calculate the midp wrt the reference phase
+ phase_nb=$ref_phase_nb
+ echo "Calculating midp_$phase_nb.mhd..."
+ vf_midp=$midp_dir/vf_$phase_nb\_midp.mhd
+ midp=$midp_dir/midp_$phase_nb.mhd
+ # average the vf's from reference phase to phase
+ clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
+ # invert the vf (why?)
+ clitkInvertVF -i $vf_midp -o $vf_midp
+ # create the midp by warping the reference phase with the reference vf
+ clitkWarpImage -i $ref_phase_file -o $midp --vf=$vf_midp -s 1
+
+ ref_vf_midp=$vf_midp
+ ref_midp=$midp
+ clitkImageConvert -i $ref_midp -o $ref_midp -t float
+
+ ########### calculate the midp wrt the other phases
+ for i in $( seq 0 $((${#phase_files[@]} - 1))); do
+ phase_file=${phase_files[$i]}
+ phase_nb=${phase_nbs[$i]}
+ vf_midp=$midp_dir/vf_$phase_nb\_midp.mhd
+ midp=$midp_dir/midp_$phase_nb.mhd
+
+ if [ "$phase_nb" != "$ref_phase_nb" ]; then
+ echo "Calculating midp_$phase_nb.mhd..."
+ # calculate vf from phase to midp, using the vf from reference phase to midp (-i)
+ # and the vf from reference phase to phase (-j)
+ clitkComposeVF -i $ref_vf_midp -j $vf_dir/vf_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp
+ clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
+ clitkImageConvert -i $midp -o $midp -t float
+ fi
+ done
+
+ create_mhd_4D_pattern.sh $midp_dir/midp_
+ echo "Calculating midp_avg.mhd..."
+ clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ echo "Calculating midp_med.mhd..."
+ clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
+
+ # clean-up
+ rm $midp_dir/vf_*
+
+ echo
+ echo "-------- Mid-position done ! --------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
+
+
+
+######################### main
+
+if [ $# != 3 ]; then
+ echo "Usage: create_midP-2.0.sh CT_4D REF_PHASE CONF_FILE"
+ exit -1
+fi
+
+echo
+echo "--------------- START ---------------"
+begining=`date --rfc-3339=seconds`
+# echo "beginning: $begining"
+echo
+
+# variable declarations
+mhd4d=$1
+ref_phase=$2
+conf=$3
+source $conf
+
+mkdir -p $log_dir
+mask_dir="MASK-${mask_interpolation_spacing}mm-$mask_interpolation_algorithm"
+
+extract_4d_phases_ref $mhd4d $ref_phase
+
+if [ "$step" == "mask" -o "$step" == "all" ]; then
+ motion_mask $mhd4d $mask_interpolation_spacing $mask_interpolation_algorithm
+fi
+
+if [ "$step" == "registration" -o "$step" == "all" ]; then
+ registration
+fi
+
+if [ "$step" == "midp" -o "$step" == "all" ]; then
+ midp
+fi
+
+echo
+echo "---------------- END ----------------"
+terminating=`date --rfc-3339=seconds`
+echo "beginning: $begining"
+echo "terminating: $terminating"
+echo
--- /dev/null
+#!/bin/sh -x
+
+#################################################################
+# create_MidP arguments : CT_4D.mhd ref_phase spacing #
+#################################################################
+source `dirname $0`/common.sh
+
+extract_patient()
+{
+ echo "$image_name -> Extracting patient..."
+ $CLITK/clitkExtractPatient -i $image_name -o MASK/patient_$image_name --noAutoCrop
+ $CLITK/clitkBinarizeImage -i MASK/patient_$image_name -o MASK/patient_$image_name -l 1 -u 1 --mode=BG
+ $CLITK/clitkSetBackground -i $image_name -o MASK/patient_only_$image_name --mask MASK/patient_$image_name --outsideValue -1000
+}
+
+extract_bones()
+{
+ echo "$image_name -> Extracting bones..."
+ $CLITK/clitkImageConvert -i $image_name -o MASK/float_$image_name -t float
+ $CLITK/clitkExtractBones -i MASK/float_$image_name -o MASK/bones_$image_name --lower1 120 --upper1 2000 --lower2 70 --upper2 2000 --smooth --time 0.0625 --noAutoCrop
+ $CLITK/clitkMorphoMath -i MASK/bones_$image_name -o MASK/bones_$image_name --type 2 --radius 4,4,2
+}
+
+resample()
+{
+ echo "$image_name -> Resampling..."
+ $CLITK/clitkResampleImage -i MASK/patient_$image_name -o MASK/patient_$image_name --spacing $spacing
+ $CLITK/clitkResampleImage -i MASK/patient_only_$image_name -o MASK/patient_only_$image_name --spacing $spacing
+ #$CLITK/clitkResampleImage -i MASK/bones_$image_name -o MASK/bones_$image_name --like MASK/patient_only_$image_name
+}
+
+compute_motion_mask()
+{
+# $CLITK/clitkMotionMask -i MASK/patient_only_$image_name -o MASK/mm_$image_name --featureBones=MASK/bones_$image_name --upperThresholdLungs -400 --fillingLevel 94 --offsetDetect 0,-5,0 --pad --writeFeature=MASK/feature_$image_name --writeEllips=MASK/inital_ellipse_$image_name --writeGrownEllips=MASK/growing_ellipse_$image_name;
+$CLITK/clitkMotionMask -i MASK/patient_only_$image_name -o MASK/mm_$image_name --upperThresholdLungs -400 --fillingLevel 94 --offsetDetect 0,-5,0 --pad --writeFeature=MASK/feature_$image_name --writeEllips=MASK/inital_ellipse_$image_name --writeGrownEllips=MASK/growing_ellipse_$image_name;
+}
+
+set_background()
+{
+ echo "$image_name -> Setting Background..."
+ $CLITK/clitkSetBackground -i MASK/patient_only_$image_name -o MASK/inside_$image_name --mask MASK/mm_$image_name --outsideValue -1200
+ $CLITK/clitkSetBackground -i MASK/patient_only_$image_name -o MASK/outside_$image_name --mask MASK/mm_$image_name --outsideValue -1200 --fg
+}
+
+create_registration_masks()
+{
+ echo "$image_name -> Creating registration masks..."
+ $CLITK/clitkMorphoMath -i MASK/mm_$image_name -o MASK/regmask_in_$image_name --type 1 --radius 8
+ $CLITK/clitkExtractPatient -i MASK/outside_$image_name -o MASK/regmask_out_$image_name --noAutoCrop
+ $CLITK/clitkMorphoMath -i MASK/regmask_out_$image_name -o MASK/regmask_out_$image_name --type 1 --radius 8
+}
+
+remove_files()
+{
+ echo "Removing temporary files..."
+ image_name_base=`echo $image_name | sed 's/mhd//'`
+ case $1 in
+ 1)
+ rm MASK/float_$image_name_base*;;
+ 2)
+ rm MASK/bones_$image_name_base*;;
+ 3)
+ rm MASK/patient_only_$image_name_base*;;
+ 4)
+ #rm MASK/patient_$image_name_base*
+ #rm MASK/mm_$image_name_base*
+ rm -f $vf_dir/vf_tmp_in_${ref}_${phase}.*
+ rm -f $vf_dir/vf_tmp_out_${ref}_${phase}.*
+ #rm MASK/regmask_in_$image_name_base*
+ #rm MASK/regmask_out_$image_name_base*
+ ;;
+ 5)
+# rm -f coeff_*
+ #rm $vf_dir/vf_in_*
+ #rm $vf_dir/vf_out_*
+# rm MASK/regmask_*
+# rm MASK/mm_*
+ ;;
+ 6)
+ ;;
+ #rm -f $vf_dir/_4D.*
+ #rm -f $vf_dir/vf_MIDP_${ref}.*
+ #rm -f $vf_dir/vf_${ref}_MIDP.*;;
+ 7)
+ ;; #rm $vf_dir/vf_MIDP_${phase}.*;;
+ 8)
+ rm $vf_dir/*.txt
+ rm $vf_dir/*.log
+ esac
+}
+
+mm_preprocessing()
+{
+ extract_patient
+ #extract_bones
+ remove_files 1
+ resample
+}
+
+mm_postprocessing()
+{
+ remove_files 2
+ set_background
+ remove_files 3
+ create_registration_masks
+}
+
+# mm_workflow()
+# {
+# extract_patient
+# extract_bones
+# remove_files 1
+# resample
+# echo "$image_name -> Computing motion mask..."
+# compute_motion_mask >> LOG/motion_mask_$image_name.log
+# remove_files 2
+# set_background
+# remove_files 3
+# create_registration_masks
+# }
+
+motion_mask()
+{
+ echo
+ echo "------------ Motion mask ------------"
+ start=`date`
+ echo "start: $start"
+ echo
+ mkdir -p "MASK"
+ rm -f "LOG/motion_mask*.log"
+ regmask_in_list=""
+ regmask_out_list=""
+ reg_in_list=""
+ reg_out_list=""
+
+ # multi-threaded pre-processing for motion mask calcs
+ for phase in $phase_list
+ do
+ image_name=`echo $phase | sed 's/raw/mhd/'`
+ check_threads $MAX_THREADS
+ #mm_preprocessing &
+ done
+
+ # single-threaded motion mask calc
+ check_threads 1
+ for phase in $phase_list
+ do
+ image_name=`echo $phase | sed 's/raw/mhd/'`
+
+ echo "$image_name -> Computing motion mask..."
+ #compute_motion_mask >> LOG/motion_mask_$image_name.log
+ done
+
+ # multi-threaded post-processing of motion mask calcs
+ for phase in $phase_list
+ do
+ image_name=`echo $phase | sed 's/raw/mhd/'`
+ check_threads $MAX_THREADS
+ #mm_postprocessing &
+ regmask_in_list="$regmask_in_list regmask_in_$image_name"
+ regmask_out_list="$regmask_out_list regmask_out_$image_name"
+ reg_in_list="$reg_in_list inside_$image_name"
+ reg_out_list="$reg_out_list outside_$image_name"
+ done
+
+ wait
+ echo
+ echo "-------- Motion mask done ! ---------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
+
+compute_BLUTDIR()
+{
+ ########## register in ##########
+ for reg_in in $reg_in_list
+ do
+ if [ ! -z `echo $reg_in | grep "$phase"` ]
+ then
+ target_in=$reg_in
+ fi
+ done
+ echo "Computing BLUTDIR $reference_in -> $target_in ..."
+ #$CLITK/clitkBLUTDIR --reference="MASK/$reference_in" --target="MASK/$target_in" --output="MASK/reg_$target_in" --referenceMask="MASK/$reference_mask_in" --vf="$vf_dir/vf_in_${ref}_${phase}.mhd" $coeff_in_ini --coeff="$coeff_dir/coeff_in_${ref}_${phase}.mhd" $registration_parameters_BLUTDIR >> LOG/registration_${ref}_${phase}.log
+ $CLITK/clitkBLUTDIR --reference="MASK/$reference_in" --target="MASK/$target_in" --output="MASK/reg_$target_in" --referenceMask="MASK/$reference_mask_in" --vf="$vf_dir/vf_in_${ref}_${phase}.mhd" --coeff="$coeff_dir/coeff_in_${ref}_${phase}.mhd" $registration_parameters_BLUTDIR >> LOG/registration_${ref}_${phase}.log
+ coeff_in_ini="--initCoeff=$coeff_dir/coeff_in_${ref}_${phase}.mhd"
+ ########## register out ##########
+ for reg_out in $reg_out_list
+ do
+ if [ ! -z `echo $reg_out | grep "$phase"` ]
+ then
+ target_out=$reg_out
+ fi
+ done
+ echo "Computing BLUTDIR $reference_out -> $target_out ..."
+ #$CLITK/clitkBLUTDIR --reference="MASK/$reference_out" --target="MASK/$target_out" --output="MASK/reg_$target_out" --referenceMask="MASK/$reference_mask_out" --vf="$vf_dir/vf_out_${ref}_${phase}.mhd" $coeff_out_ini --coeff="$coeff_dir/coeff_out_${ref}_${phase}.mhd" $registration_parameters_BLUTDIR >> LOG/registration_${ref}_${phase}.log
+ $CLITK/clitkBLUTDIR --reference="MASK/$reference_out" --target="MASK/$target_out" --output="MASK/reg_$target_out" --referenceMask="MASK/$reference_mask_out" --vf="$vf_dir/vf_out_${ref}_${phase}.mhd" --coeff="$coeff_dir/coeff_out_${ref}_${phase}.mhd" $registration_parameters_BLUTDIR >> LOG/registration_${ref}_${phase}.log
+ coeff_out_ini="--initCoeff=$coeff_dir/coeff_out_${ref}_${phase}.mhd"
+ ##################################
+ $CLITK/clitkCombineImage -i $vf_dir/vf_in_${ref}_${phase}.mhd -j $vf_dir/vf_out_${ref}_${phase}.mhd -m MASK/mm_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
+ $CLITK/clitkZeroVF -i $vf_dir/vf_${ref}_${phase}.mhd -o $vf_dir/vf_${ref}_${ref}.mhd
+ $CLITK/clitkCombineImage -i $vf_dir/vf_${ref}_${phase}.mhd -j $vf_dir/vf_${ref}_${ref}.mhd -m MASK/patient_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
+ remove_files 4
+}
+
+compute_DEMONSDIR()
+{
+ ########## register in ##########
+ for reg_in in $reg_in_list
+ do
+ if [ ! -z `echo $reg_in | grep "_$phase"` ]
+ then
+ target_in=$reg_in
+ fi
+ done
+ echo "Computing DEMONSDIR $reference_in -> $target_in ..."
+ $CLITK/clitkDemonsDeformableRegistration --reference="MASK/$reference_in" --target="MASK/$target_in" --output="MASK/reg_$target_in" --vf="$vf_dir/vf_in_${ref}_${phase}.mhd" $vf_in_ini $registration_parameters_DEMONSDIR #&>> LOG/registration_${ref}_${phase}.log
+ vf_in_ini="--init=$vf_dir/vf_in_${ref}_${phase}.mhd"
+ ########## register out ##########
+ for reg_out in $reg_out_list
+ do
+ if [ ! -z `echo $reg_out | grep "_$phase"` ]
+ then
+ target_out=$reg_out
+ fi
+ done
+ echo "Computing DEMONSDIR $reference_out -> $target_out ..."
+ $CLITK/clitkDemonsDeformableRegistration --reference="MASK/$reference_out" --target="MASK/$target_out" --output="MASK/reg_$target_out" --vf="$vf_dir/vf_out_${ref}_${phase}.mhd" $vf_out_ini $registration_parameters_DEMONSDIR #&>> LOG/registration_${ref}_${phase}.log
+ vf_out_ini="--init=$vf_dir/vf_out_${ref}_${phase}.mhd"
+ ##################################
+ $CLITK/clitkCombineImage -i $vf_dir/vf_in_${ref}_${phase}.mhd -j $vf_dir/vf_out_${ref}_${phase}.mhd -m MASK/mm_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
+ $CLITK/clitkZeroVF -i $vf_dir/vf_${ref}_${phase}.mhd -o $vf_dir/vf_${ref}_${ref}.mhd
+ $CLITK/clitkCombineImage -i $vf_dir/vf_${ref}_${phase}.mhd -j $vf_dir/vf_${ref}_${ref}.mhd -m MASK/patient_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
+ remove_files 4
+}
+
+compute_ELASTIX()
+{
+ ########## register in ##########
+ for reg_in in $reg_in_list
+ do
+ if [ ! -z `echo $reg_in | grep "_$phase"` ]
+ then
+ target_in=$reg_in
+ fi
+ done
+ echo "Computing ELASTIX $reference_in -> $target_in ..."
+ exec_dir=`which elastix`
+ exec_dir=`dirname $exec_dir`
+ cat $exec_dir/params_BSpline.txt | sed -e "s+<NbIterations>+500+" \
+ -e "s+<LabelsFile>++" \
+ -e "s+<HistBins>+25+" \
+ -e "s+<Levels>+3+" \
+ -e "s+<NbSamples>+2000+" \
+ -e "s+<SamplerType>+Random+" \
+ -e "s+<Spacing>+32+" > params_BSpline.txt
+ elastix -f "MASK/$reference_in" -m "MASK/$target_in" -fMask "MASK/$reference_mask_in" -out $vf_dir -p params_BSpline.txt > /dev/null
+ transformix -tp $vf_dir/TransformParameters.0.txt -out $vf_dir -def all > /dev/null
+ mv $vf_dir/deformationField.mhd $vf_dir/vf_in_${ref}_${phase}.mhd
+ mv $vf_dir/deformationField.raw $vf_dir/vf_in_${ref}_${phase}.raw
+ sed -i "s:deformationField:vf_in_${ref}_${phase}:" $vf_dir/vf_in_${ref}_${phase}.mhd
+ mv $vf_dir/result.0.mhd MASK/reg_$target_in
+ targetraw=`echo reg_$target_in | sed 's:mhd:raw:'`
+ sed -i "s:result.0.mhd:$targetraw" MASK/reg_$target_in
+ mv $vf_dir/result.0.raw MASK/$targetraw
+ remove_files 8
+
+ ########## register out ##########
+ for reg_out in $reg_out_list
+ do
+ if [ ! -z `echo $reg_out | grep "_$phase"` ]
+ then
+ target_out=$reg_out
+ fi
+ done
+ echo "Computing ELASTIX $reference_out -> $target_out ..."
+ elastix -f "MASK/$reference_out" -m "MASK/$target_out" -fMask "MASK/$reference_mask_out" -out $vf_dir -p params_BSpline.txt > /dev/null
+ transformix -tp $vf_dir/TransformParameters.0.txt -out $vf_dir -def all > /dev/null
+ mv $vf_dir/deformationField.mhd $vf_dir/vf_out_${ref}_${phase}.mhd
+ mv $vf_dir/deformationField.raw $vf_dir/vf_out_${ref}_${phase}.raw
+ sed -i "s:deformationField:vf_out_${ref}_${phase}:" $vf_dir/vf_out_${ref}_${phase}.mhd
+ mv $vf_dir/result.0.mhd MASK/reg_$target_out
+ targetraw=`echo reg_$target_out | sed 's:mhd:raw:'`
+ sed -i "s:result.0.mhd:$targetraw" MASK/reg_$target_out
+ mv $vf_dir/result.0.raw MASK/$targetraw
+ remove_files 8
+
+ ##################################
+ $CLITK/clitkCombineImage -i $vf_dir/vf_in_${ref}_${phase}.mhd -j $vf_dir/vf_out_${ref}_${phase}.mhd -m MASK/mm_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
+ $CLITK/clitkZeroVF -i $vf_dir/vf_${ref}_${phase}.mhd -o $vf_dir/vf_${ref}_${ref}.mhd
+ $CLITK/clitkCombineImage -i $vf_dir/vf_${ref}_${phase}.mhd -j $vf_dir/vf_${ref}_${ref}.mhd -m MASK/patient_$image_name -o $vf_dir/vf_${ref}_${phase}.mhd
+ remove_files 4
+}
+
+registration()
+{
+ echo
+ echo "----------- Registration ------------"
+ start=`date`
+ echo "start: $start"
+ echo
+
+ rm -f "LOG/registration*.log"
+
+ # wait any unfinished threads
+ check_threads 1
+
+ for reg_in in $reg_in_list
+ do
+ if [ ! -z `echo $reg_in | grep "$ref"` ]
+ then
+ reference_in=$reg_in
+ fi
+ done
+ for reg_out in $reg_out_list
+ do
+ if [ ! -z `echo $reg_out | grep "$ref"` ]
+ then
+ reference_out=$reg_out
+ fi
+ done
+ for regmask_in in $regmask_in_list
+ do
+ if [ ! -z `echo $regmask_in | grep "$ref"` ]
+ then
+ reference_mask_in=$regmask_in
+ fi
+ done
+ for regmask_out in $regmask_out_list
+ do
+ if [ ! -z `echo $regmask_out | grep "$ref"` ]
+ then
+ reference_mask_out=$regmask_out
+ fi
+ done
+
+ registration_parameters_BLUTDIR="--spacing=32,32,32 --interp=2 --metric=11 --bins=25 --samples=1 --levels=3 --verbose " #--coeffEveryN 5"
+ registration_parameters_DEMONSDIR="--demons=3 --levels=1"
+ registration_parameters_ELASTIX="--demons=3 --levels=1"
+
+ coeff_in_ini=""
+ coeff_out_ini=""
+ vf_in_ini=""
+ vf_out_ini=""
+
+ for phase in $list_phases
+ do
+ for img in $phase_list
+ do
+ if [ ! -z `echo $img | grep "$phase" | grep -v "[0-9]$phase"` ]
+ then
+ image_name=`echo $img | sed 's/raw/mhd/'`
+ fi
+ done
+ if [ $method = 1 ]
+ then
+ compute_BLUTDIR
+ elif [ $method = 2 ]
+ then
+ compute_DEMONSDIR
+ elif [ $method = 3 ]
+ then
+ compute_ELASTIX
+ fi
+ done
+ remove_files 5
+
+ echo
+ echo "-------- Registration done ! --------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
+
+calculate_vf_MIDP_REF()
+{
+ echo "Calculating vf_REF_MIDP.mhd..."
+ remove_files 6
+ create_mhd_4D.sh $vf_dir #"vf_4D.mhd"
+ $CLITK/clitkAverageTemporalDimension -i $vf_dir/_4D.mhd -o $vf_dir/vf_${ref}_MIDP.mhd
+ $CLITK/clitkInvertVF -i $vf_dir/vf_${ref}_MIDP.mhd -o $vf_dir/vf_MIDP_${ref}.mhd
+}
+
+calculate_CT_MIDP_REF()
+{
+ reference=`ls *.mhd | grep $ref #| grep -v "[0-9]$ref.mhd"`
+ echo "Calculating CT_MIDP_REF.mhd '$reference'..."
+ $CLITK/clitkWarpImage -i $reference -o CT_MIDP_REF.mhd --vf=$vf_dir/vf_MIDP_${ref}.mhd -s 1
+}
+
+calculate_CT_MIDP_PHASE()
+{
+ echo "Calculating CT_MIDP_${phase}.mhd..."
+ $CLITK/clitkComposeVF -i $vf_dir/vf_MIDP_${ref}.mhd -j $vf_dir/vf_${ref}_${phase}.mhd -o $vf_dir/vf_MIDP_${phase}.mhd
+ phase_img=`ls *.mhd | grep "${phase}" # | grep -v "[0-9]$ref.mhd"`
+ $CLITK/clitkWarpImage -i $phase_img -o MIDP/CT_MIDP_${phase}.mhd --vf=$vf_dir/vf_MIDP_${phase}.mhd -s 1
+ $CLITK/clitkImageConvert -i MIDP/CT_MIDP_${phase}.mhd -o MIDP/CT_MIDP_${phase}.mhd -t float
+ remove_files 7
+}
+
+prepare_MIDP_images()
+{
+ echo "Preparing MIDP images..."
+ cp CT_MIDP_REF.mhd MIDP/CT_MIDP_${ref}.mhd
+ cp CT_MIDP_REF.raw MIDP/CT_MIDP_${ref}.raw
+ cat MIDP/CT_MIDP_${ref}.mhd | sed "s/ElementDataFile = .*/ElementDataFile = CT\_MIDP\_${ref}\.raw/" > MIDP/CT_MIDP_${ref}_tmp.mhd
+ rm MIDP/CT_MIDP_${ref}.mhd
+ mv MIDP/CT_MIDP_${ref}_tmp.mhd MIDP/CT_MIDP_${ref}.mhd
+ $CLITK/clitkImageConvert -i MIDP/CT_MIDP_${ref}.mhd -o MIDP/CT_MIDP_${ref}.mhd -t float
+ create_mhd_4D.sh MIDP #"CT_MIDP_4D.mhd"
+}
+
+calculate_CT_MIDP_MOY()
+{
+ echo "Calculating CT_MIDP_MOY.mhd..."
+ $CLITK/clitkAverageTemporalDimension -i MIDP/_4D.mhd -o CT_MIDP_MOY.mhd
+}
+
+calculate_CT_MIDP_MED()
+{
+ echo "Calculating CT_MIDP_MED.mhd..."
+ $CLITK/clitkMedianTemporalDimension -i MIDP/_4D.mhd -o CT_MIDP_MED.mhd
+}
+
+calculate_CT_MIDP_MIP()
+{
+ echo "Calculating CT_MIDP_MIP.mhd..."
+ $CLITK/clitkMIP -i MIDP/_4D.mhd -o CT_MIDP_MIP.mhd -d 3
+}
+
+mid_position()
+{
+ echo
+ echo "----------- Mid-position ------------"
+ start=`date`
+ echo "start: $start"
+ echo
+
+ mkdir -p "MIDP"
+
+ calculate_vf_MIDP_REF
+ calculate_CT_MIDP_REF
+ for phase in $list_phases
+ do
+ check_threads $MAX_THREADS
+ calculate_CT_MIDP_PHASE &
+ done
+ wait
+ prepare_MIDP_images
+ calculate_CT_MIDP_MED &
+ calculate_CT_MIDP_MIP &
+ calculate_CT_MIDP_MOY &
+ wait
+
+ echo
+ echo "-------- Mid-position done ! --------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
+
+#################
+# main #
+#################
+
+if [ $# -lt 1 ]
+then
+ echo "Usage: create_midP.sh CT_4D.mhd ref_phase computation_spacing(mm) method(1:BSPLINE, 2:DEMONS)"
+ exit 1
+fi
+CLITK=~/creatis/clitk3/build/bin
+CT_4D_path=$1
+CT_4D=`basename $CT_4D_path`
+work_dir=`dirname $CT_4D_path`
+cd $work_dir
+ref=$2
+spacing=$3
+method=$4
+
+vf_dir="VF"
+coeff_dir="$vf_dir/coeff"
+
+mkdir -p $vf_dir
+mkdir -p $coeff_dir
+
+echo
+echo "--------------- START ---------------"
+begining=`date`
+echo "start: $begining"
+echo
+
+mkdir -p "LOG"
+phase_list=`grep ".raw" $CT_4D`
+echo "phases -> " $phase_list
+nb_phases=`grep ".raw" $CT_4D | wc -l`
+gt_ref=""
+lt_ref=""
+
+phase_files=( `cat $CT_4D | grep ".raw" | sed 's:.raw:.mhd:'` )
+echo "Phase files are ${phase_files[@]}"
+
+phase_nbs=( `echo ${phase_files[@]} | grep -o '[[:alpha:][:punct:]][0-9]\{1,2\}[[:punct:]]' | grep -o '[0-9]\{1,2\}'` )
+#phase_nbs=( `echo ${phase_files[@]} | grep -o '[0-9]\{1,2\}'` )
+echo "Phase numbers are ${phase_nbs[@]}"
+
+
+for ph in $phase_list
+do
+ #ph_nb=`echo $ph | grep -o "[0-9][0-9]*\.raw" | sed -e 's/\.raw//'`
+ ph_nb=`echo $ph | grep -o "[0-9][0-9]"`
+ if [ $ph_nb -gt $ref ]
+ then
+ gt_ref="$gt_ref $ph_nb"
+ elif [ $ph_nb -lt $ref ]
+ then
+ lt_ref="$lt_ref $ph_nb"
+ fi
+done
+list_phases="$gt_ref $lt_ref"
+echo list_phases $list_phases
+
+motion_mask
+registration
+mid_position
+
+echo
+echo "---------------- END ----------------"
+terminating=`date`
+echo "start: $begining"
+echo "end: $terminating"
+echo
--- /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
#! /bin/bash -x
-. common.sh
+source `dirname $0`/common.sh
extract_patient()
{
#
# 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)
--- /dev/null
+#! /bin/sh
+
+###############################################################################
+#
+# FILE: pts_to_landmarks
+# AUTHOR: Vivien Delmon
+#
+# Conversion from landmarks in the format used in clitkCalculateTRE (.pts)
+# to the format used in VV (.txt).
+#
+###############################################################################
+
+if [ $# -ne 2 ]; then
+ echo "Usage: $0 input.pts output.txt" 1>&2
+fi
+
+to_append=/tmp/$RANDOM
+to_prepend=/tmp/$RANDOM
+
+for i in $(seq 0 $((`cat $1 | wc -l` - 1)));
+do
+ echo 0' '0 >> $to_append
+ echo $i >> $to_prepend
+done
+
+echo "LANDMARKS1" > $2
+paste -d ' ' $to_prepend $1 $to_append >> $2
--- /dev/null
+#! /bin/sh
+
+###############################################################################
+#
+# FILE: registration.sh
+# AUTHOR: Rômulo Pinho 05/08/2011
+#
+# Helper file with registration functions using different methods.
+# Each function receives a set of parameters that overall apply to any
+# registration algorithm, as follows:
+#
+# reference=$1 : reference (fixed) image
+# target=$2 : target (moving) image
+# mask_ref=$3 : mask for the reference image
+# mask_targ=$4 : mask for the moving image
+# vf=$5 : output vector field representing the registration
+# result=$6 : result image after applying the vector field
+# nb_iter=$7 : maximum number of iterations
+# nb_samples=$8 : number of image samples used in the metric calulcation
+# sampling_algo=$9 : algorithm used in the selection of image samples
+# hist_bins=${10} : number of histogram bins used in the metric calculation
+# nb_levels=${11} : number of image resolutions
+# spacing=${12} : spacing of the b-spline grid of the fines resolution
+# metric=${13} : metric algorithm
+# optimizer=${14} : optimizer
+# interpolator=${15} : image interpolator
+# log=${16} : log file
+#
+# New registration functions may be added to this file at any moment,
+# respecting the interface defined above.
+#
+###############################################################################
+
+
+################# BLUTDIR #####################
+registration_blutdir()
+{
+ reference=$1
+ target=$2
+ mask_ref=$3
+ mask_targ=$4
+ vf=$5
+ result=$6
+ nb_iter=$7
+ nb_samples=$8
+ sampling_algo=$9
+ hist_bins=${10}
+ nb_levels=${11}
+ spacing=${12}
+ metric=${13}
+ optimizer=${14}
+ interpolator=${15}
+ log=${16}
+
+ echo "Computing BLUTDIR $reference -> $target ..."
+ blutdir_params="--levels $nb_levels --metric $metric --optimizer $optimizer --samples $nb_samples --spacing $spacing,$spacing,$spacing --bins $hist_bins --maxIt $nb_iter --interp $interpolator --verbose"
+ cmd="clitkBLUTDIR -r $reference -t $target -m $mask_ref --targetMask $mask_targ --vf $vf -o $result $blutdir_params"
+ $cmd > $log
+}
+
+################# ELASTIX #####################
+registration_elastix()
+{
+ reference=$1
+ target=$2
+ mask_ref=$3
+ mask_targ=$4
+ vf=$5
+ result=$6
+ nb_iter=$7
+ nb_samples=$8
+ sampling_algo=$9
+ hist_bins=${10}
+ nb_levels=${11}
+ spacing=${12}
+ metric=${13}
+ optimizer=${14}
+ interpolator=${15}
+
+ ########## register in ##########
+ for reg_in in $reg_in_list
+ do
+ if [ ! -z `echo $reg_in | grep "_$phase"` ]
+ then
+ target_in=$reg_in
+ fi
+ done
+ echo "Computing ELASTIX $reference -> $target ..."
+ exec_dir=`which elastix`
+ exec_dir=`dirname $exec_dir`
+ cat $exec_dir/params_BSpline.txt | sed -e "s+<NbIterations>+$nb_iter+" \
+ -e "s+<LabelsFile>++" \
+ -e "s+<HistBins>+$hist_bins+" \
+ -e "s+<Levels>+$nb_levels+" \
+ -e "s+<NbSamples>+$nb_samples+" \
+ -e "s+<SamplerType>+$sampling_algo+" \
+ -e "s+<Spacing>+$spacing+" > params_BSpline.txt
+
+ vf_dir=`dirname $vf`
+ vf_base=`basename $vf .mhd`
+ result_dir=`dirname $result`
+ result_base=`basename $result .mhd`
+
+ # image registration
+ cmd="elastix -f $reference -m $target -fMask $mask_ref -mMask $mask_targ -out $result_dir -p params_BSpline.txt"
+ $cmd > /dev/null
+
+ # generate vector field
+ cmd="transformix -tp $result_dir/TransformParameters.0.txt -out $vf_dir -def all"
+ $cmd > /dev/null
+
+ # post-processing
+ mv $vf_dir/deformationField.mhd $vf
+ mv $vf_dir/deformationField.raw `echo $vf | sed 's/mhd/raw/'`
+ sed -i "s+deformationField+$vf_base+" $vf
+
+ mv $result_dir/result.0.mhd $result
+ mv $result_dir/result.0.raw `echo $result | sed 's/mhd/raw/'`
+ sed -i "s+result.0+$result_base+" $result
+
+ mv $result_dir/elasitx.log $log
+ mv $result_dir/TransformParameters.0.txt $result_dir/${result_base}_TransformParameters.0.txt
+}
\ No newline at end of file
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff