+++ /dev/null
-#=========================================================
-# Install scripts when running make install
-SET(SCRIPTS
- ${CLITK_SOURCE_DIR}/scripts/calculate_motion_amplitude.sh
- ${CLITK_SOURCE_DIR}/scripts/calculate_contour_stats.sh
- ${CLITK_SOURCE_DIR}/scripts/midp_common.sh
- ${CLITK_SOURCE_DIR}/scripts/registration.sh
- ${CLITK_SOURCE_DIR}/scripts/compress_mhd.sh
- ${CLITK_SOURCE_DIR}/scripts/create_midP.sh
- ${CLITK_SOURCE_DIR}/scripts/create_midP-2.0.sh
- ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D.sh
- ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D_pattern.sh
- ${CLITK_SOURCE_DIR}/scripts/create_midP_masks.sh
- ${CLITK_SOURCE_DIR}/scripts/create_midP_masks-2.0.sh
- ${CLITK_SOURCE_DIR}/scripts/pts_to_landmarks.sh
- ${CLITK_SOURCE_DIR}/scripts/create_mhd_3D.sh
- ${CLITK_SOURCE_DIR}/scripts/dicom_info.sh
-)
-
-INSTALL (FILES ${SCRIPTS} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
+++ /dev/null
-#! /bin/bash +x
-
-source `dirname $0`/midp_common.sh
-
-
-############# main
-
-if echo $* | grep "\-h"; then
- echo Usage: calculate_motion_amplitude.sh { REFERENCE_IMAGE RTSTRUCT_FILE [ RTSTRUCT_ROI | --gui ] } | --gui
- echo " RTSTRUCT_REF_IMAGE: mhd of the reference image used in the contour delineation"
- echo " RTSTRUCT_FILE: dicom with contours"
- echo " RTSTRUCT_ROI: number of the contour whose motion to analyze"
- echo " --gui: use GUI to select files"
- exit 0
-fi
-
-
-rtstruct_roi=
-
-if echo $* | grep "\-\-gui" > /dev/null 2>&1; then
- gui_mode=1
- if [ $# = 1 ]; then
- rtstruct_ref_image=`zenity --file-selection --title="Select Reference Image."`
- rtstruct_file=`zenity --file-selection --title="Select RT Struct file."`
- select_roi
- elif [ $# = 3 ]; then
- rtstruct_ref_image=$1
- rtstruct_file=$2
- select_roi
- else
- echo Invalid arguments. Type \'`basename $0` -h\' for help
- exit -1
- fi
-
-else
- gui_mode=0
- rtstruct_ref_image=$1
- rtstruct_file=$2
- if [ $# = 2 ]; then
- select_roi
- elif [ $# = 3 ]; then
- rtstruct_roi=$3
- rtstruct_roi_name=$rtstruct_roi
- else
- echo Invalid arguments. Type \'`basename $0` -h\' for help
- exit -1
- fi
-
-fi
-
-
-#echo "Processing \"${rtstruct_roi_list[$roi_struct]}\"..."
-# create ROI mask from rtstruct
-roi_mask=roi_${rtstruct_roi_name}.mhd
-clitkDicomRTStruct2Image -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
-if cat /tmp/err.txt | grep -q "No ROI"; then
- echo Invalid contour number.
- exit -3
-fi
-
-# guarantees the same sampling for roi mask and vector image
-roi_mask2=resampled_${roi_mask}
-clitkResampleImage -i ${roi_mask} -o ${roi_mask2} --like ${rtstruct_ref_image}
-
-# calculate stats
-clitkImageStatistics -i ${rtstruct_ref_image} -m ${roi_mask2} --verbose 2> /dev/null | tail -n 8 > /tmp/result.txt
-
-if [ $gui_mode = 1 ]; then
- cat /tmp/result.txt | zenity --text-info --title "Restuls for \"${rtstruct_roi_name}\""
-else
- echo "Restuls for \"${rtstruct_roi_name}\""
- cat /tmp/result.txt
-fi
-
-rm `basename $roi_mask .mhd`.{mhd,raw}
-rm `basename $roi_mask2 .mhd`.{mhd,raw}
-rm /tmp/err.txt
-rm /tmp/result.txt
+++ /dev/null
-#! /bin/bash +x
-
-source `dirname $0`/midp_common.sh
-
-
-calculate_motion()
-{
- # calculate motion amplitudes along the 3 image axes
- rm /tmp/result.txt 2> /dev/null
- dir=( "\"left-right\"" "\"anterior-posterior\"" "\"cranio-caudal\"" )
- pct=( 0 33 67 )
- for i in 0 1 2; do
- if [ $gui_mode = 1 ]; then
- echo "${pct[$i]}"; echo "# Calculating motion along ${dir[$i]} direction.."
- else
- echo "Calculating motion along ${dir[$i]} direction.."
- fi
-
- echo "Motion along ${dir[$i]} direction" >> /tmp/result.txt
- clitkImageStatistics -i ${vector_file} -m ${roi_mask2} -c $i --verbose 2> /dev/null | tail -n 8 | head -n 6 >> /tmp/result.txt
- min=`tail -n 2 /tmp/result.txt | head -n 1 | cut -f 2 -d ':'`
- max=`tail -n 1 /tmp/result.txt | cut -f 2 -d ':'`
- amp=`echo $max-$min | bc`
-
- echo "Amplitude: $amp" >> /tmp/result.txt
- echo "" >> /tmp/result.txt
- done
-}
-
-############# main
-
-if echo $* | grep "\-h"; then
- echo "Usage: calculate_motion_amplitude.sh { VECTOR_FILE RTSTRUCT_REF_IMAGE RTSTRUCT_FILE [ RTSTRUCT_ROI_NUMBER | --gui ] } | --gui "
- echo " VECTOR_FILE: mhd of the vector field from where to extract motion information (may also be 4D)"
- echo " RTSTRUCT_REF_IMAGE: mhd of the reference image used in the contour delineation"
- echo " RTSTRUCT_FILE: dicom with contours"
- echo " RTSTRUCT_ROI: number of the contour whose motion to analyze"
- echo " --gui: use GUI to select files"
- exit 0
-fi
-
-if echo $* | grep "\-\-gui" > /dev/null 2>&1; then
- gui_mode=1
- if [ $# = 1 ]; then
- vector_file=`zenity --file-selection --title="Select 4D Vector Field file."`
- rtstruct_ref_image=`zenity --file-selection --title="Select Reference Image."`
- rtstruct_file=`zenity --file-selection --title="Select RT Struct file."`
- select_roi
- elif [ $# = 4 ]; then
- vector_file=$1
- rtstruct_ref_image=$2
- rtstruct_file=$3
- select_roi
- else
- echo Invalid arguments. Type \'`basename $0` -h\' for help
- exit -1
- fi
-else
- gui_mode=0
- vector_file=$1
- rtstruct_ref_image=$2
- rtstruct_file=$3
- if [ $# = 4 ]; then
- rtstruct_roi=$4
- rtstruct_roi_name=$rtstruct_roi
- elif [ $# = 3 ]; then
- select_roi
- else
- echo Invalid arguments. Type \'`basename $0` -h\' for help
- exit -1
- fi
-fi
-
-if ! cat $vector_file | grep -q "Channels = 3"; then
- echo Vector file must have 3 channels.
- exit -2
-fi
-
-# create ROI mask from rtstruct
-roi_mask=roi_${rtstruct_roi}.mhd
-clitkDicomRTStruct2Image -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
-if cat /tmp/err.txt | grep -q "No ROI"; then
- echo Invalid contour number.
- exit -3
-fi
-
-# guarantees the same sampling for roi mask and vector image
-roi_mask2=resampled_${roi_mask}
-clitkResampleImage -i ${roi_mask} -o ${roi_mask2} --like ${vector_file}
-
-if [ $gui_mode = 1 ]; then
- calculate_motion | zenity --progress --auto-close --percentage=0 --text=""
-else
- calculate_motion
-fi
-
-if [ $gui_mode = 1 ]; then
- cat /tmp/result.txt | zenity --text-info --title "Restuls for \"${rtstruct_roi_name}\""
-else
- echo "Restuls for \"${rtstruct_roi_name}\""
- cat /tmp/result.txt
-fi
-
-rm `basename $roi_mask .mhd`.{mhd,raw}
-rm `basename $roi_mask2 .mhd`.{mhd,raw}
-rm /tmp/err.txt
-rm /tmp/result.txt
+++ /dev/null
-#! /bin/bash
-
-compress_file()
-{
- local f=$1
- if [ "$verbose" = "1" ]; then
- echo "Compressing $f..."
- fi
-
- local msg=`clitkImageConvert -i $f -o $f -c`
- if [ -z "$msg" ]; then
- raw=`echo $f | sed 's/\.mhd/\.raw/'`
- if test -e $raw; then
- rm $raw
- fi
- fi
-}
-
-compress_directory()
-{
- local input=$1
-
- files=$(find $input -name "*.mhd" | sort)
- for f in $files; do
- if ! grep -iq 'LIST' $f; then
- # process all except 4D files
- compress_file $f
- else
- # process only 4D files (just update pointers to new zraw files)
- # assumes each .RAW in the list has a corresponding .MHD, which
- # must be compressed separately
- sed -i 's/\.raw/\.zraw/g' $f
- if grep -q "CompressedData" $f; then
- sed -i 's/CompressedData.*/CompressedData = True/' $f
- else
- tmp=/tmp/$RANDOM.mhd
- echo "CompressedData = True" > $tmp
- cat $f >> $tmp
- mv $tmp $f
- fi
- fi
- done
-}
-
-# main program
-
-if [ $# -lt 1 -o $# -gt 2 ]; then
- echo "Invalid params. `basename $0` [-h | --help] for help" 1>&2
- exit -1
-fi
-
-if [ -n "`echo $@ | grep '\-h\|--help'`" ]; then
- echo "Usage: `basename $0` {FILE | DIRECTORY | -h | --help | -v}"
- exit 0
-fi
-
-if [ -n "`echo $@ | grep '\-v'`" ]; then
- echo Verbose mode : ON
- verbose=1
-fi
-
-input=$1
-if test -d $input; then
- compress_directory $input
-elif test -f $input; then
- compress_file $input
-else
- echo "Unknow input file type." 1>&2
-fi
+++ /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
-
-
-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
- ph=`basename $ph`
- echo "$ph" >> "$1/$file_name_4D"
- done
- echo $1/$file_name_4D
-}
-
-#################################################
-# create_mhd_4D argument : repertoire #
-#################################################
-if [ $# -lt 1 ]
-then
- echo "Usage: create_mhd_4D.sh DIRECTORY"
- exit 1
-fi
-
-nb_phase_file=`find $1 -maxdepth 1 -iname "*[0-9]*.mhd" | wc -l`
-if [ $nb_phase_file = 0 ]
-then
- echo "No phase found in $1"
- exit 1
-fi
-
-
-list_prefix=""
-list_phase_file=`find $1 -maxdepth 1 -iname "*[0-9]*.mhd"`
-for phase_file in $list_phase_file
-do
- if grep -q "NDims = 4" $phase_file 2> /dev/null
- then
- #echo $phase_file is 4D
- continue;
- fi;
-
- phase_file_name=`basename $phase_file .mhd`
-# if [[ ! -z `echo "$phase_file_name" | grep "__[0-9]"` ]]
-# then
-# prefix=`echo $phase_file_name | sed "s/__[0-9].*/__/"`
-# else
-# if [[ ! -z `echo "$phase_file_name" | grep "[0-9]-.*\]"` ]]
-# then
-# if [[ ! -z `echo "$phase_file_name" | grep "[0-9][0-9]-.*\]"` ]]
-# then
-# prefix=`echo $phase_file_name | sed "s/[0-9][0-9]-.*//"`
-# else
-# prefix=`echo $phase_file_name | sed "s/[0-9]-.*//"`
-# fi
-# else
-# prefix="NONE"
-# fi
-# fi
-
- # preffix: grep sequence of characters followed by sequence of numbers and remove sequence of numbers
- # prefix=`echo $phase_file_name | grep -o "\(^[[:alpha:][:punct:]]*\)\([[:digit:]\.\_\-]\+\)" | sed 's/\(^[[:alpha:][:punct:]]*\)\([[:digit:]\.\_\-]\+\)/\1/'`
- prefix=`echo $phase_file_name | grep -o "\(^[[:alpha:][:punct:]]*\)\([[:digit:]]\+\)\([\.\_\-]*\)"`
- prefix=`echo $prefix | sed 's/^\-\+//' | sed 's/\(^[[:alpha:][:punct:]]*\)\([[:digit:]]\+\)\([\.\_\-]*\)/\1/'`
- if [[ -z $prefix ]]
- then
- prefix="NONE"
- fi
-
- # register new preffix if not yet done
- if [[ -z `echo "$list_prefix" | grep -w -- "$prefix"` ]]
- then
- list_prefix="$list_prefix $prefix"
- fi
-done
-
-
-for prefix in $list_prefix
-do
- if [ "$prefix" = "NONE" ]
- then
- prefix=""
- fi
-
- list_suffix=""
- list_phase_file_prefix=`find $1 -maxdepth 1 -iname "${prefix}[0-9]*.mhd"`
- for phase_file_prefix in $list_phase_file_prefix
- do
- if grep -q "NDims = 4" $phase_file_prefix 2> /dev/null
- then
- #echo $phase_file_prefix is 4D
- continue;
- fi;
- phase_file_prefix_name=`basename $phase_file_prefix .mhd`
-# if [[ ! -z `echo "$phase_file_prefix_name" | grep "__[0-9]"` ]]
-# then
-# suffix="NONE"
-# else
-# if [[ ! -z `echo "$phase_file_prefix_name" | grep "[0-9]-.*\]"` ]]
-# then
-# suffix=`echo $phase_file_prefix_name | sed "s/.*[0-9]-//;s/_\.mhd//;s/\.mhd//"`
-# else
-# suffix="NONE"
-# fi
-# fi
-#
-
- # suffix: grep sequence of numbers followed by sequence of characters and remove sequence of numbers
- # suffix=`echo $phase_file_prefix_name | grep -o "\([[:digit:]\.\_\-]\+\)\([[:alpha:][:punct:]]*$\)" | sed 's/\([[:digit:]\.\_\-]\+\)\([[:alpha:][:punct:]]*$\)/\2/'`
- suffix=`echo $phase_file_prefix_name | grep -o "\([\.\_\-]*\)\([[:digit:]]\+\)\([[:alpha:][:punct:]]*$\)"`
- if ! echo $suffix | grep -qo "^\-\+"; then
- suffix=`echo $suffix | sed 's/\([\.\_\-]*\)\([[:digit:]]\+\)\([[:alpha:][:punct:]]*$\)/\3/'`
- fi
- suffix=`echo $suffix | sed 's/[\.\_\-]\+$//'`
- if [[ -z $suffix ]]
- then
- suffix="NONE"
- fi
-
- # register new suffix if not yet done
- if [[ -z `echo "$list_suffix" | grep -w -- "$suffix"` ]]
- then
- list_suffix="$list_suffix $suffix"
- fi
- done
-
-
- for suffix in $list_suffix
- do
- if [ "$suffix" = "NONE" ]
- then
- suffix=""
- fi
- orig=`find $1 -maxdepth 1 -iname "${prefix}[0-9]*${suffix}*.mhd" | grep "${prefix}[[:digit:][:punct:]]\+${suffix}[\.\_\-]*.mhd" | sort | head -n 1`
- listph=( `find $1 -maxdepth 1 -iname "${prefix}[0-9]*${suffix}*.*raw" | grep "${prefix}[[:digit:][:punct:]]\+${suffix}[\.\_\-]*.z*raw" | sort` )
- nbph=${#listph[@]}
-
- # only create 4D file if potential number of phases is > 1
- if [ $nbph -gt 1 ]; then
- file_name_4D="${prefix}4D${suffix}.mhd"
- write_mhd_4D $1
- fi
-
- done
-
-done
-
+++ /dev/null
-#!/bin/sh
-
-###############################################################################
-#
-# 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/.*/& $nbph/
- s/ElementDataFile = .*/ElementDataFile = LIST/" > "$dirname/$file_name_4D"
-
- for ph in $listph
- do
- phase=`basename $ph`
- echo "$phase" >> "$dirname/$file_name_4D"
- done
-}
-
-#################################################
-# create_mhd_4D argument : repertoire #
-#################################################
-if [ $# -lt 1 ]
-then
- echo "Usage: $0 PREFIX [SUFFIX]"
- exit 1
-fi
-
-dirname=`dirname $1`
-prefix=`basename $1`
-suffix=$2
-
-nbph=0
-list_phase_file=`ls -1 $dirname/$prefix*[0-9]*$suffix.mhd`
-for ph in $list_phase_file
-do
- if [ -e `echo $ph | sed 's/mhd/raw/'` ]
- then
- listph="$listph $ph"
- nbph=$(( nbph + 1 ))
- fi
-done
-
-nb_phase_file=`ls -1 $dirname/$prefix*[0-9]*$suffix.mhd | wc -l`
-if [ $nb_phase_file = 0 ]
-then
- echo "Error: no phase found"
- exit 1
-fi
-
-orig=`echo $list_phase_file | cut -f 1 -d ' '`
-listph=`echo $listph | sed 's:\.mhd:\.raw:g'`
-
-file_name_4D=`echo "${prefix}4D${suffix}.mhd"`
-
-write_mhd_4D
-echo "$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
-source `dirname $0`/registration.sh
-source `dirname $0`/midp_common.sh
-
-registration()
-{
- echo
- echo "----------- Registration ------------"
- start=`date`
- echo "start: $start"
- echo
-
- mkdir -p $vf_dir
- mkdir -p $output_dir
-
- # banded images may be created as separate files,
- # with the specified preffix, which is interesting for debugging.
- # if blank, it means that the original images (those without bands)
- # will be used (see create_midP_masks-2.0.sh for details).
- banded=""
-
- # params read from conf file
- use_coeffs=1
- params="$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
- if [ $use_coeffs = 1 ]; then
- init_coeff_in=$coeff_in # empty at first iteration
- coeff_in=$vf_dir/coeff_inside_${ref_phase_nb}_$phase_nb.mhd
- fi
-
- # outside params
- reference_out=$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
- if [ $use_coeffs = 1 ]; then
- init_coeff_out=$coeff_out # empty at first iteration
- coeff_out=$vf_dir/coeff_outside_${ref_phase_nb}_$phase_nb.mhd
- fi
-
- # registration
- if [ "$method" == "blutdir" ]; then
- registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in
- registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out
- elif [ "$method" == "elastix" ]; then
- registration_elastix $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in
- registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out
- fi
-
- motion_mask=$mask_dir/${mask_type}_$phase_nb.mhd
-
- # combine in and out results
- out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
- # clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
- combine_image $result_in $result_out $out_result $motion_mask
- abort_on_error registration $? clean_up_registration
-
- # combine in and out vf
- vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
- #clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
- combine_image $vf_in $vf_out $vf_result $motion_mask
- abort_on_error registration $? clean_up_registration
-
- clitkZeroVF -i $vf_in -o vf_zero.mhd
- abort_on_error registration $? clean_up_registration
-
- patient_mask=$mask_dir/patient_mask_$phase_nb.mhd
- #clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
- combine_image $vf_result vf_zero.mhd $vf_result $patient_mask
- abort_on_error registration $? clean_up_registration
-
- rm vf_zero.*
-
- # save for later...
- vf_ref=$vf_in
- fi
- done
-
- # create (zero) vf from reference to reference and associated images
- vf_in=$vf_dir/vf_inside_${ref_phase_nb}_${ref_phase_nb}.mhd
- vf_out=$vf_dir/vf_outside_${ref_phase_nb}_${ref_phase_nb}.mhd
- clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
- clitkZeroVF -i $vf_ref -o $vf_in
- clitkZeroVF -i $vf_ref -o $vf_out
- abort_on_error registration $? clean_up_registration
-
- motion_mask=$mask_dir/${mask_type}_${ref_phase_nb}.mhd
- reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd
- reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
- out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd
- #clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
- combine_image $reference_in $reference_out $out_result $motion_mask
- abort_on_error registration $? clean_up_registration
-
- # create 4D vf
- create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
- create_mhd_4D_pattern.sh $vf_dir/vf_inside_${ref_phase_nb}_
- create_mhd_4D_pattern.sh $vf_dir/vf_outside_${ref_phase_nb}_
-
- # create 4D coeffs
- create_mhd_4D_pattern.sh $vf_dir/coeff_inside_${ref_phase_nb}_ _0
- create_mhd_4D_pattern.sh $vf_dir/coeff_outside_${ref_phase_nb}_ _0
-
- # create 4D result image
- create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
- create_mhd_4D_pattern.sh $output_dir/result_outside_${ref_phase_nb}_
- create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
-
- echo
- echo "-------- Registration done ! --------"
- end=`date`
- echo "start: $start"
- echo "end: $end"
- echo
-}
-
-registration_no_motion_mask()
-{
- echo
- echo "----------- Registration Without Motion Masks ------------"
- start=`date`
- echo "start: $start"
- echo
-
- mkdir -p $vf_dir
- mkdir -p $output_dir
-
- # banded images may be created as separate files,
- # with the specified preffix, which is interesting for debugging.
- # if blank, it means that the original images (those without bands)
- # will be used (see create_midP_masks-2.0.sh for details).
- banded=""
-
- # params read from conf file
- use_coeffs=1
- params="$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
- # params
- reference=$mask_dir/patient_$ref_phase_nb.mhd
- target=$mask_dir/patient_$phase_nb.mhd
- mask_ref=$mask_dir/patient_mask_$ref_phase_nb.mhd
- mask_targ=$mask_dir/patient_mask_$phase_nb.mhd
- vf=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
- result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
- log=$log_dir/log_${ref_phase_nb}_$phase_nb.log
- if [ $use_coeffs = 1 ]; then
- init_coeff=$coeff_in # empty at first iteration
- coeff=$vf_dir/coeff_${ref_phase_nb}_$phase_nb.mhd
- fi
-
- # registration
- if [ "$method" == "blutdir" ]; then
- registration_blutdir $reference $target $mask_ref $mask_targ $vf $result $params $log $coeff
- elif [ "$method" == "elastix" ]; then
- registration_elastix $reference $target $mask_ref $mask_targ $vf $result $params $log
- fi
-
- # save for later...
- vf_ref=$vf
- fi
- done
-
- 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}_
-
- # create 4D coeffs
- create_mhd_4D_pattern.sh $vf_dir/coeff_${ref_phase_nb}_ _0
-
- # create 4D result image
- create_mhd_4D_pattern.sh $output_dir/result_${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_midp_$phase_nb.mhd
- midp=$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
- average_temporal_dimension $vf_dir/vf_${ref_phase_nb}_4D.mhd $vf_midp
- abort_on_error midp $? clean_up_midp
-
- # invert the vf (why?)
- clitkInvertVF -i $vf_midp -o $vf_midp
- abort_on_error midp $? clean_up_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
- abort_on_error midp $? clean_up_midp
-
- ref_vf_midp=$vf_midp
- ref_midp=$midp
- clitkImageConvert -i $ref_midp -o $ref_midp -t float
- abort_on_error midp $? clean_up_midp
-
- ########### 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=$midp_dir/vf_midp_$phase_nb.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
- abort_on_error midp $? clean_up_midp
-
- clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
- abort_on_error midp $? clean_up_midp
-
- clitkImageConvert -i $midp -o $midp -t float
- abort_on_error midp $? clean_up_midp
- fi
- done
-
- # create 4D midp
- create_mhd_4D_pattern.sh $midp_dir/midp_
- create_mhd_4D_pattern.sh $midp_dir/vf_midp_
-
- echo "Calculating midp_avg.mhd..."
- #clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
- average_temporal_dimension $midp_dir/midp_4D.mhd $midp_dir/midp_avg.mhd
- abort_on_error midp $? clean_up_midp
-
- echo "Calculating midp_med.mhd..."
- clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
- abort_on_error midp $? clean_up_midp
-
- # clean-up
- #rm $midp_dir/vf_*
-
- echo
- echo "-------- Mid-position done ! --------"
- end=`date`
- echo "start: $start"
- echo "end: $end"
- echo
-}
-
-midp_in_out()
-{
- 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
- phase_file=$ref_phase_file
- echo "Calculating midp_$phase_nb.mhd..."
- vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
- vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
- coeff_midp_in=$midp_dir/coeff_inside_midp_$phase_nb.mhd
- coeff_midp_out=$midp_dir/coeff_outside_midp_$phase_nb.mhd
- # average the vf's from reference phase to phase
- average_temporal_dimension $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd $coeff_midp_in
- abort_on_error midp $? clean_up_midp
- average_temporal_dimension $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd $coeff_midp_out
- abort_on_error midp $? clean_up_midp
-
- # invert the vf
- clitkInvertVF -i $coeff_midp_in -o $vf_midp_in --type 1 --like $ref_phase_file
- abort_on_error midp $? clean_up_midp
- clitkInvertVF -i $coeff_midp_out -o $vf_midp_out --type 1 --like $ref_phase_file
- abort_on_error midp $? clean_up_midp
-
- # combine in and out VF's
- ref_vf_midp_in=$vf_midp_in
- ref_vf_midp_out=$vf_midp_out
- vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
- combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/${mask_type}_$phase_nb.mhd
- clitkZeroVF -i $vf_midp -o vf_zero.mhd
- combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd
-
- # create the midp by warping the reference phase with the reference vf
- midp=$midp_dir/midp_$phase_nb.mhd
- clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
- abort_on_error midp $? clean_up_midp
-
- clitkImageConvert -i $midp -o $midp -t float
- abort_on_error midp $? clean_up_midp
-
- ########### 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_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
- vf_midp_out=$midp_dir/vf_outside_midp_$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_in -j $vf_dir/vf_inside_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp_in
- abort_on_error midp $? clean_up_midp
- clitkComposeVF -i $ref_vf_midp_out -j $vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp_out
- abort_on_error midp $? clean_up_midp
-
- # combine in and out VF's
- vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
- combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/${mask_type}_$phase_nb.mhd
- clitkZeroVF -i $vf_midp -o vf_zero.mhd
- combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd
-
- midp=$midp_dir/midp_$phase_nb.mhd
- clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
- abort_on_error midp $? clean_up_midp
-
- clitkImageConvert -i $midp -o $midp -t float
- abort_on_error midp $? clean_up_midp
- fi
- done
-
- rm vf_zero.*
-
- # create 4D midp
- create_mhd_4D_pattern.sh $midp_dir/midp_
- create_mhd_4D_pattern.sh $midp_dir/vf_midp_
- create_mhd_4D_pattern.sh $midp_dir/vf_inside_midp_
- create_mhd_4D_pattern.sh $midp_dir/vf_outside_midp_
-
- echo "Calculating midp_avg.mhd..."
- average_temporal_dimension $midp_dir/midp_4D.mhd $midp_dir/midp_avg.mhd
- abort_on_error midp $? clean_up_midp
-
- echo "Calculating midp_med.mhd..."
- clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
- abort_on_error midp $? clean_up_midp
-
- 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
-
-cd `dirname $mhd4d`
-
-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_type $mask_interpolation_spacing $mask_interpolation_algorithm
-fi
-
-if [ "$step" == "registration" -o "$step" == "all" ]; then
- if [ "$mask_type" == "mm" ]; then
- registration
- elif [ "$mask_type" == "lungs" ]; then
- registration
- elif [ "$mask_type" == "patient" ]; then
- registration_no_motion_mask
- midp_combined_vf=1
- fi
-fi
-
-if [ "$step" == "midp" -o "$step" == "all" ]; then
- if [ $midp_combined_vf = 0 ]; then
- midp_in_out
- else
- midp
- fi
-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 $0`/midp_common.sh
-
-extract_patient()
-{
- echo "$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 $0`/midp_common.sh
-
-extract_patient()
-{
- echo "$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
+++ /dev/null
-#! /bin/bash -x
-
-source `dirname $0`/midp_common.sh
-
-extract_patient()
-{
- echo "$image_name -> Extracting patient..."
- clitkExtractPatient -i $image_name -o $mask_dir_tmp/patient_$image_name --noAutoCrop -a $afdb_name $ExtractPatientExtra
- clitkBinarizeImage -i $mask_dir_tmp/patient_$image_name -o $mask_dir_tmp/patient_$image_name -l 1 -u 1 --mode=BG
- clitkSetBackground -i $image_name -o $mask_dir_tmp/patient_only_$image_name --mask $mask_dir_tmp/patient_$image_name --outsideValue -1000
-}
-
-extract_bones()
-{
- 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 $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
-}
-
-extract_lungs()
-{
- echo "$image_name -> Extracting lungs..."
- clitkExtractLung -i $image_name -o $mask_dir_tmp/lungs_$image_name -a $afdb_name --noAutoCrop
-}
-
-resample()
-{
- echo "$image_name -> Resampling..."
- clitkResampleImage -i $mask_dir_tmp/patient_$image_name -o $mask_dir_tmp/patient_$image_name --spacing $resample_spacing --interp $resample_algo
- clitkResampleImage -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/patient_only_$image_name --spacing $resample_spacing --interp $resample_algo
- clitkResampleImage -i $mask_dir_tmp/bones_$image_name -o $mask_dir_tmp/bones_$image_name --like $mask_dir_tmp/patient_only_$image_name --interp $resample_algo
- clitkResampleImage -i $mask_dir_tmp/lungs_$image_name -o $mask_dir_tmp/lungs_$image_name --like $mask_dir_tmp/patient_only_$image_name
-}
-
-compute_motion_mask()
-{
- if [ x = x$MotionMaskOffsetDetect ]; then
- MotionMaskOffsetDetect="0,-5,0"
- fi
- if [ x = x$FillingLevel ]; then
- FillingLevel=94
- fi
- clitkMotionMask -i $mask_dir_tmp/patient_only_$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_$image_name
-}
-
-set_background()
-{
- echo "$image_name -> Setting Background..."
- clitkSetBackground -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/inside_$image_name --mask $mask_dir_tmp/mm_$image_name --outsideValue -1200
- clitkSetBackground -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/outside_$image_name --mask $mask_dir_tmp/mm_$image_name --outsideValue -1200 --fg
-}
-
-create_registration_masks()
-{
- echo "$image_name -> Creating registration masks..."
- clitkMorphoMath -i $mask_dir_tmp/mm_$image_name -o $mask_dir_tmp/regmask_in_$image_name --type 1 --radius 8
- clitkExtractPatient -i $mask_dir_tmp/outside_$image_name -o $mask_dir_tmp/regmask_out_$image_name --noAutoCrop
- clitkMorphoMath -i $mask_dir_tmp/regmask_out_$image_name -o $mask_dir_tmp/regmask_out_$image_name --type 1 --radius 8
-}
-
-remove_tmp_masks()
-{
- echo "Removing temporary files..."
- image_name_base=`echo $image_name | sed 's/mhd//'`
- case $1 in
- 1)
- #rm $mask_dir_tmp/float_$image_name_base*
- ;;
- 2)
- #rm $mask_dir_tmp/bones_$image_name_base*
- ;;
- 3)
- #rm $mask_dir_tmp/patient_only_$image_name_base*
- ;;
- esac
-}
-
-mm_preprocessing()
-{
- extract_patient
- extract_bones
- extract_lungs
- remove_tmp_masks 1
- resample
-}
-
-mm_postprocessing()
-{
- remove_tmp_masks 2
- set_background
- remove_tmp_masks 3
- create_registration_masks
-}
-
-mm_workflow()
-{
- extract_patient
- extract_bones
- remove_tmp_masks 1
- resample
- echo "$image_name -> Computing motion mask..."
- compute_motion_mask >> $mask_log_dir/motion_mask_$image_name.log
- remove_tmp_masks 2
- set_background
- remove_tmp_masks 3
- create_registration_masks
-}
-
-motion_mask()
-{
- #set cmd line variables
- echo "4D CT -> "$1
- phases=`grep ".raw" $1`
- echo "mask phases -> " $phases
-
- dir=`dirname $1`
- cd $dir
-
- # import variables specific to each patient
- source variables
-
- resample_spacing=$2
- resample_algo=$3
-
-
- #set other global variables
- mask_dir="MASK-$resample_spacing""mm""-$resample_algo"
- mask_dir_tmp="tmp."$mask_dir
-
- 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
-
- regmask_in_list=""
- regmask_out_list=""
- reg_in_list=""
- reg_out_list=""
-
- # multi-threaded pre-processing for motion mask calcs
- if [ $do_mm == 1 ]; then
- mask_log_dir=$mask_dir_tmp/LOG
- mkdir -p $mask_log_dir
-
- for phase in $phases
- do
- image_name=`echo $phase | sed 's/raw/mhd/'`
- afdb_name=`echo $phase | sed 's/raw/afdb/'`
- check_threads $MAX_THREADS
- mm_preprocessing &
- done
-
- # single-threaded motion mask calc
- for phase in $phases
- do
- image_name=`echo $phase | sed 's/raw/mhd/'`
-
- check_threads 1
- echo "$image_name -> Computing motion mask..."
- compute_motion_mask >> $mask_log_dir/motion_mask_$image_name.log
- done
- fi
-
- # multi-threaded post-processing of motion mask calcs
- for phase in $phases
- do
- image_name=`echo $phase | sed 's/raw/mhd/'`
- if [ $do_mm = 1 ]; then
- check_threads $MAX_THREADS
- mm_postprocessing &
- fi
-
- regmask_in_list="$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
-
- # rename tmp mask directory after mask creation
- check_threads 1
- mv $mask_dir_tmp $mask_dir
-
- wait
-
- echo
- echo "-------- Motion mask done ! ---------"
- end=`date`
- echo "start: $start"
- echo "end: $end"
- echo
-}
-
-
-#################
-# main #
-#################
-
-if [ $# != 3 ]; then
- echo "Usage: create_midP_masks.sh 4D_CT.mhd resample_spacing resample_algorithm"
- exit -1
-fi
-
-#
-# variables exported in this scope
-#
-# 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)
-#
-
-if [ $1 != "using-as-lib" ]; then
- motion_mask $1 $2 $3
-fi
+++ /dev/null
-#!/bin/bash
-#Get info about the first dicom image in the directory
-find . -iname "*.dcm" -type f | head -n1 | xargs clitkDicomInfo | less
+++ /dev/null
-#! /bin/sh -x
-
-###############################################################################
-#
-# FILE: midp_common.sh
-# AUTHOR: Rômulo Pinho 05/08/2011
-#
-# Helper file with many functions used in the midP scripts.
-#
-###############################################################################
-
-bin=`dirname $0`
-source $bin/tools.sh
-
-#
-# check return value passed and abort if it represents an error (ie, ret != 0)
-# optionally, a function can be passed as a 3rd parameter, to be called just
-# before exiting. this is useful for cleaning up, for example.
-#
-abort_on_error()
-{
- if [ $2 != 0 ]; then
- echo Aborted at $1 with code $2
- #if [ $# = 3 ]; then
- # eval $3
- #fi
-
- exit $2
- fi
-}
-
-#
-# wait for all processes in the list and return their exit codes
-# in the ret_codes variable.
-#
-# OBS: this function must always be called in the same shell
-# that launched the processes.
-#
-wait_pids()
-{
- local pids=$*
- local ret=
- local rets=
-# echo PIDS: $pids
- for p in $pids; do
-# echo waiting $p
- wait $p > /dev/null 2> /dev/null
- ret=$?
- if [ ret != 127 ]; then
- rets=$rets" "$ret
- else
- rets=$rets" "0
- fi
-
- done
-
- ret_codes=$rets
-}
-
-#
-# clean-up functions for maks, registration, and midp
-#
-clean_up_masks()
-{
- rm -fr $mask_dir_tmp
-}
-
-clean_up_midp()
-{
- rm -fr $midp_dir
-}
-
-clean_up_registration()
-{
- rm -fr $vf_dir
- rm -fr $output_dir
-}
-
-
-#
-# 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()
-{
- 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 $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "[^0-9[:punct:]]*" | sort -u > /tmp/patterns.txt
-
- # find which patterns have the phases connected to it
- patterns=`cat /tmp/patterns.txt`
- if [ -z "$patterns" ]; then
- phase_nbs=( `cat $mhd4d | grep ".z*raw" | sed 's:.z*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 $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "$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 $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "$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 $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | sort -u | wc -l`
- if [ $nb_phases_found == $nb_phases ]; then
- # keep only what identifies the phase number
- phase_nbs=( `cat $mhd4d | grep ".z*raw" | sed 's:.z*raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$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 ".z*raw" | sed 's:.z*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 ".z*raw" | sed 's:.z*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
-}
-
-#
-# replacement for clitkCombineImage
-combine_image()
-{
-# eg: -i $result_in -j $result_out -o $out_result -m $motion_mask
- local tmp1=$RANDOM
- local tmp2=$RANDOM
-
- clitkSetBackground -i $1 -o $tmp1.mhd -m $4
- clitkSetBackground -i $2 -o $tmp2.mhd -m $4 --fg
-
- clitkImageArithm -i $tmp1.mhd -j $tmp2.mhd -o $3
- rm $tmp1.* $tmp2.*
-}
-
-#
-# replacement for clitkAverageTemporalDimension
-average_temporal_dimension()
-{
- # eg: -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
- local tmp=$RANDOM
- local tot=$tmp.mhd
-
- local dir=`dirname $1`
- local first=`grep z*raw $1 | sed 's/z*raw/mhd/g' | head -n 1`
- clitkImageArithm -i $dir/$first -o $tot -t 1 -s 0
-
- local nbphases=`grep z*raw $1 | sed 's/z*raw/mhd/g' | wc -l`
- for i in $(grep z*raw $1 | sed 's/z*raw/mhd/g'); do
- clitkImageArithm -i $dir/$i -j $tot -o $tot
- done
-
- clitkImageArithm -i $tot -o $2 -t 11 -s $nbphases
- rm $tmp.*
-}
-
-select_contour_gui()
-{
- local roi_list=$@
- roi=`zenity --list --title="Available Contours" --column="Please choose a contour:" $roi_list`
- case $? in
- 0)
- if [ -z $roi ]
- then
- zenity --warning --text="You must choose one contour."
- select_contour_gui $roi_list
- else
- rtstruct_roi_name=$roi
- fi;;
- 1)
- if zenity --question --text="Do you really wish to quit?"
- then
- exit
- else
- select_contour_gui $roi_list
- fi;;
- -1)
- zenity --error --text="Unexpected error. Please relaunch the application."
- exit;;
- esac
-}
-
-select_contour()
-{
- local roi_list=$@
- echo "Available Contours:"
- for r in $roi_list; do
- echo $r
- done
-
- echo "Please choose a contour number:"
- read rtstruct_roi_index
- let i=0
- for r in $roi_list; do
- if [ $rtstruct_roi_index = `echo $r | cut -d ':' -f 1` ]; then
- rtstruct_roi_index=$i
- break;
- fi
- let i=i+1
- done
-
-}
-
-select_roi()
-{
- rtstruct_roi_name_list=( `get_dicom_field_value "3006|0026" ${rtstruct_file} all | sed 's/ /_/g'` )
- rtstruct_roi_number_list=( `get_dicom_field_value "3006|0022" ${rtstruct_file} all | sed 's/ //g'` )
- rtstruct_roi_list=( )
- for i in $(seq 0 1 $(( ${#rtstruct_roi_name_list[@]} - 1 ))); do
- rtstruct_roi_list[$i]=${rtstruct_roi_number_list[$i]}:${rtstruct_roi_name_list[$i]}
- done
-
- if [ $gui_mode = 1 ]; then
- select_contour_gui ${rtstruct_roi_list[@]}
- rtstruct_roi=`echo ${rtstruct_roi_name} | cut -d ':' -f 1`
- rtstruct_roi_name=`echo ${rtstruct_roi_name} | cut -d ':' -f 2`
- else
- select_contour ${rtstruct_roi_list[@]}
- rtstruct_roi=${rtstruct_roi_number_list[$(( $rtstruct_roi_index ))]}
- rtstruct_roi_name=${rtstruct_roi_name_list[$(( $rtstruct_roi_index ))]}
- fi
-}
+++ /dev/null
-###############################################################################
-#
-# FILE: midp_template.conf
-# AUTHOR: Rômulo Pinho 05/08/2011
-#
-# Template configuration file for create_midP-2.0.sh. Values between <> must be
-# changed according to the methods.
-#
-###############################################################################
-
-# output directories
-vf_dir="<VFDIR>"
-midp_dir="<MIDPDIR>"
-output_dir="<OUTDIR>"
-log_dir="<LOGDIR>"
-
-# script step to be executed (mask, registration, midp, all)
-# midp depends on registration, which depends on mask
-step="all"
-
-# indicate if midp images are computed with the in and out
-# VFs combined
-midp_combined_vf=0
-
-# indicate which masks are used in the registration (mm, lungs, patient). if
-# "patient", only the patient mask is used, and midp_combined_vf is
-# set to 1.
-mask_type="<TYPE>"
-
-# mask parameters
-#
-# interpolation algorithm for resampling (see clitkResampleImage)
-mask_interpolation_algorithm="<MASK_INTERPOLATION_ALGORITHM>"
-# interpolation spacing (in mm)
-mask_interpolation_spacing=<MASK_INTERPOLATION_SPACING>
-
-# registration method (blut, elastix)
-method="<METHOD>"
-
-# registration parameters (depend on registration method - see descriptions)
-#
-
-# b-spline spacing (blut, elastix)
-bspline_spacing=<BSPLINE_SPACING>
-
-# multi-resolution levels
-nb_levels=<NB_LEVELS>
-
-# number of histogram bins (blut, elastix)
-nb_hist_bins=<NB_HIST_BINS>
-
-# number of points (samples) to calculate metric
-# (blut: percentage of image size; elastix: absolute number)
-nb_samples=<NBSAMPLES>
-
-# algorithm used to sample points for the metric
-# (elastix: see docs)
-sampling_algo="<SAMPLING_ALGO>"
-
-# number of iterations (blut, elastix)
-nb_iter=<NB_ITER>
-
-# tolerance (stop condition for the metric) (blut)
-tolerance=<TOLERANCE>
-
-# metric used in the registration
-# (blut: see clitkBLUTDIR; elastix: see docs)
-metric="<METRIC>"
-
-# interpolation type
-# (blut: see clitkBLUTDIR; elastix: see docs)
-interpolator="<INTERPOLATOR>"
-
-# optmizer
-# (blut: see clitkBLUTDIR; elastix: see docs)
-optimizer="<OPTIMIZER>"
+++ /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
- exit 1
-fi
-
-to_append=`mktemp`
-to_prepend=`mktemp`
-pts_file_spaced=`mktemp`
-
-for i in $(seq 0 $((`cat $1 | wc -l` - 1)));
-do
- echo "0 0" >> $to_append
- echo $i >> $to_prepend
-done
-
-echo "LANDMARKS1" > $2
-cat $1 | sed -e 's/\s/ /g' >> $pts_file_spaced
-paste -d ' ' $to_prepend $pts_file_spaced $to_append >> $2
-
-rm $to_append $to_prepend $pts_file_spaced
+++ /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.
-#
-###############################################################################
-
-source `dirname $0`/midp_common.sh
-
-
-################# BLUTDIR #####################
-registration_blutdir()
-{
- local reference=$1
- local target=$2
- local mask_ref=$3
- local mask_targ=$4
- local vf=$5
- local result=$6
- local nb_iter=$7
- local nb_samples=$8
- local sampling_algo=$9
- local hist_bins=${10}
- local nb_levels=${11}
- local spacing=${12}
- local metric=${13}
- local optimizer=${14}
- local interpolator=${15}
- local log=${16}
- local coeff=${17}
- local init_coeff=${18}
-
- 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 $interpolator --centre --verbose"
-
- if [ -n "$coeff" ]; then
- coeff="--coeff $coeff"
- fi
-
- if [ -n "$init_coeff" ]; then
- init_coeff="--initCoeff $init_coeff"
- fi
-
- cmd="clitkBLUTDIR -r $reference -t $target -m $mask_ref --targetMask $mask_targ --vf $vf $coeff $init_coeff -o $result $blutdir_params"
- $cmd > $log
-
- abort_on_error registration_blutdir $? clean_up_registration
-}
-
-################# ELASTIX #####################
-registration_elastix()
-{
- local reference=$1
- local target=$2
- local mask_ref=$3
- local mask_targ=$4
- local vf=$5
- local result=$6
- local nb_iter=$7
- local nb_samples=$8
- local sampling_algo=$9
- local hist_bins=${10}
- local nb_levels=${11}
- local spacing=${12}
- local metric=${13}
- local optimizer=${14}
- local interpolator=${15}
- local log=${16}
- local coeff=${17}
- local init_coeff=${18}
-
-# RP 25/06/2012: unused variables (for now at elast)
-# local log=${16}
-# local coeff=${17}
-# local init_coeff=${18}
-
- ########## 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 $exec_dir`
- suffix=${nb_samples}_${nb_iter}_${nb_levels}
- cat $exec_dir/params_elastix_template.txt | sed -e "s+<NbIterations>+$nb_iter+" \
- -e "s+<HistBins>+$hist_bins+" \
- -e "s+<Levels>+$nb_levels+" \
- -e "s+<PctSamples>+$nb_samples+" \
- -e "s+<SamplerType>+$sampling_algo+" \
- -e "s+<Metric>+$metric+" \
- -e "s+<Optimizer>+$optimizer+" \
- -e "s+<Interpolator>+$interpolator+" \
- -e "s+<Spacing>+$spacing+" > params_elastix_${suffix}.txt
-
- # set elastix to write out the coefficient images and corresponding DVFs
- echo "(WriteCoefficientImage \"true\")" >> params_elastix_${suffix}.txt
- echo "(WriteDVFFromCoeff \"true\")" >> params_elastix_${suffix}.txt
-
- vf_dir=`dirname $vf`
- vf_base=`basename $vf .mhd`
- coeff_dir=`dirname $coeff`
- coeff_base=`basename $coeff .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 $result_dir -p params_elastix_${suffix}.txt"
- $cmd > /dev/null
- abort_on_error registration_elastix $? clean_up_registration
-
- # generate vector field
- # cmd="transformix -tp $result_dir/TransformParameters.0.txt -out $vf_dir -def all"
- # $cmd > /dev/null
- # abort_on_error registration_elastix $? clean_up_registration
-
- # post-processing
- local level=$(($nb_levels - 1))
- mv $result_dir/dvf.0.R$level.mhd $vf
- mv $result_dir/dvf.0.R$level.raw `echo $vf | sed 's/mhd/raw/'`
- sed -i "s+dvf.0.R$level+$vf_base+" $vf
-
- mv $result_dir/coeff.0.R$level.mhd $coeff_dir/${coeff_base}_0.mhd
- mv $result_dir/coeff.0.R$level.raw $coeff_dir/${coeff_base}_0.raw
- sed -i "s+coeff.0.R$level+$coeff_base+" $coeff_dir/${coeff_base}_0.mhd
-
- 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/elastix.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