--- /dev/null
+
+
+VV, a 4D image viewer, see : http://vv.creatis.insa-lyon.fr
+
--- /dev/null
+
+set -u
+
+# print error message and exit immediately
+programname="$(basename ${0})"
+function error {
+ echo "${programname} **ERROR** $1"
+ exit 1
+}
+
+# ensure a valid proxy is present for at least one hour
+# if no proxy is found, try to create a new one
+# return 0 if a valid proxy is found or created
+# else return voms-proxy-init error code
+function ensure_proxy {
+ voms-proxy-info --exists -valid 1:0 > /dev/null && return 0
+ voms-proxy-init --voms biomed -valid 24:00 || exit 1
+}
+
+# print prompt to ensure that the user want to continue further
+# the user has to answer with 'y' to continue
+function check_user {
+ prompt="${1:-is that correct?}"
+ read -p "${prompt} [y/n] " answer
+ test "${answer}" == "y" && return 0
+ test "${answer}" == "n" && return 1
+ check_user "${prompt}"
+}
+
+# checks if the lfn file exists
+function file_exists {
+ lfnfile="${1:?"provide lfn to file"}"
+ lfc-ls ${lfnfile} 2>&1 > /dev/null
+}
+
+
+# upload file to grid storage element
+# source can be a relative or an absolute path to the source file
+# dest must be the lfn to the target **file** (not the directory)
+# if dest already exists, it prompts the user for overwritting
+function upload_file {
+ sourcefile=${1:?"provide source file"}
+ destlfn=${2:?"provide destination file lfn"}
+ sourcefile="$(readlink -f "${sourcefile}")" # convert to absolute path
+ test -f "${sourcefile}" || error "can't find ${sourcefile}"
+ echo "uploading ${sourcefile} to ${destlfn}"
+ if file_exists "${destlfn}"; then
+ check_user "${destlfn} already exists. overwrite it?" || return 2
+ lcg-del -a "lfn:${destlfn}" || error "lcg-del error"
+ fi
+ echo "lets roll"
+
+ local pending_ses=${SES}
+ local registered=false
+ while [ "x${pending_ses}" != "x" ]
+ do
+ #select a se from list
+ local S=`echo ${pending_ses} | awk '{print $1}'`
+ #update list of SEs
+ local new_list=""
+ for i in `echo ${pending_ses}`
+ do
+ if [ "$i" != "${S}" ]
+ then
+ new_list="${new_list} ${i}"
+ fi
+ done
+ pending_ses=${new_list}
+ local TEMP=`mktemp lcg-XXXXX`
+ if [ "${registered}" = "false" ]
+ then
+ echo -n "Registering release to ${S}..."
+ lcg-cr -v -d ${S} -l "lfn:${destlfn}" "file:${sourcefile}" &>${TEMP}
+ if [ $? != 0 ]
+ then
+ echo -e "\t [\033[31m FAILED \033[0m]"
+ cat ${TEMP}
+ \rm ${TEMP}
+ else
+ echo -e "\t [\033[32m OK \033[0m]"
+ registered=true
+ \rm ${TEMP}
+ fi
+ else
+ echo -n "Replicating release to ${S}..."
+ lcg-rep -v -d ${S} "lfn:${destlfn}" &>${TEMP}
+ if [ $? != 0 ]
+ then
+ echo -e "\t [\033[31m FAILED \033[0m]"
+ cat ${TEMP}
+ \rm ${TEMP}
+ else
+ echo -e "\t [\033[32m OK \033[0m]"
+ \rm ${TEMP}
+ fi
+ fi
+ done
+}
+
+
+# common path used
+lfnbase="/grid/biomed/creatis/fgate/"
+lfnrelease="/grid/biomed/creatis/vip/data/groups/GateLab/releases/"
+lfnworkflow="${lfnbase}workflow/"
+lfngasw="${lfnbase}gasw/"
+lfnscript="${lfnbase}bin/"
+
+#list of SEs used for storage. Don't modify this list unless you know
+# what you're doing. Replicating the release in a bad place (e.g. on a
+# remote continent) can dramatically slow down the transfers
+SES="ccsrm02.in2p3.fr sbgse1.in2p3.fr marsedpm.in2p3.fr"
+
+# define the prefix for uploaded file
+# default to local machine username
+prefix="${USER:?"USER must be set"}_"
--- /dev/null
+#!/bin/bash
+#
+# MACRODIR
+# MACROFILE
+# RELEASEDIR
+# OUTPUTDIR
+# INDEX
+# INDEXMAX
+# PARAM
+#
+#PBS -r n
+#PBS -l walltime=100:00:00
+#PBS -j oe
+
+#env
+#pwd
+#exit 1
+
+
+function error {
+echo "ERROR: $1"
+exit 1
+}
+
+function warning {
+echo "WARNING: $1"
+}
+
+test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
+set -u
+
+echo "Checking"
+uname -a
+echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
+echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
+echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
+echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
+echo "PBS_JOBID=${PBS_JOBID}"
+echo "INDEX=${INDEX}"
+echo "INDEXMAX=${INDEX}"
+echo "PARAM=${PARAM}"
+
+if test "$RELEASEDIR" = "NONE"
+then
+ echo Using $(which Gate)
+ ldd $(which Gate)
+else
+ test -d "${RELEASEDIR}" || error "can't find release"
+ md5sum ${RELEASEDIR}/Gate
+ test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
+
+ echo "Finding libraries"
+ ROOTLIBS="${RELEASEDIR}/libCore.so:${RELEASEDIR}/libCint.so:${RELEASEDIR}/libRIO.so:${RELEASEDIR}/libNet.so:${RELEASEDIR}/libHist.so:${RELEASEDIR}/libGraf.so:${RELEASEDIR}/libGraf3d.so:${RELEASEDIR}/libGpad.so:${RELEASEDIR}/libTree.so:${RELEASEDIR}/libRint.so:${RELEASEDIR}/libPostscript.so:${RELEASEDIR}/libMatrix.so:${RELEASEDIR}/libPhysics.so:${RELEASEDIR}/libMathCore.so:${RELEASEDIR}/libThread.so:"
+ echo "ROOTLIBS=${ROOTLIBS}"
+ G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
+ echo "G4LIBS=${G4LIBS}"
+ CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
+ echo "CLHEPLIBS=${CLHEPLIBS}"
+ GATELIBS=""
+ test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
+ echo "GATELIBS=${GATELIBS}"
+fi
+test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
+
+
+echo "Copying inputs"
+LOCALMACRODIR=$(mktemp -d)
+trap "mv output ${OUTPUTDIR}/output.${PBS_JOBID%%.*} ; rm -r ${LOCALMACRODIR} ; exit 1" 1 2 3 15
+cd ${LOCALMACRODIR}
+cp -r -L "${MACRODIR}"/{data,mac} .
+mkdir output
+
+# Enforce one thread
+ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+
+echo "Lauching macro"
+date
+if test "$RELEASEDIR" = "NONE"
+then
+ Gate ${PARAM} ${MACROFILE} || error "gate failed"
+else
+ LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
+ G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
+ G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
+ G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
+ G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
+ G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
+ G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
+ G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
+ G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
+ /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
+ ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
+ || error "gate failed"
+fi
+
+echo "Copying data back"
+mv output "${OUTPUTDIR}/output.${PBS_JOBID%%.*}"
+
+echo "Cleanup"
+rm -r ${LOCALMACRODIR}
+
+echo "Success!!!"
--- /dev/null
+#!/bin/bash
+
+function usage {
+ echo "ERROR: $1"
+ echo "$(basename $0) [name]"
+ exit 1
+}
+
+GATENAME="${1:-Gate}"
+which "${GATENAME}" > /dev/null || usage "cant locate ${GATENAME} binary"
+GATEBIN="$(which ${GATENAME})"
+echo "${GATENAME} executable is ${GATEBIN}"
+
+test -d "${G4NEUTRONHPDATA}" || usage "can't locate neutron data. please set G4NEUTRONHPDATA"
+echo "neutron data is ${G4NEUTRONHPDATA}"
+test -d "${G4LEVELGAMMADATA}" || usage "can't locate gamma data. please set G4LEVELGAMMADATA"
+echo "gamma data is ${G4LEVELGAMMADATA}"
+test -d "${G4RADIOACTIVEDATA}" || usage "can't locate radioactivity data. please set G4RADIOACTIVEDATA"
+echo "radioactivity data is ${G4RADIOACTIVEDATA}"
+test -d "${G4ABLADATA}" || usage "can't locate abla data. please set G4ABLADATA"
+echo "abla data is ${G4ABLADATA}"
+test -d "${G4LEDATA}" || usage "can't locate em data. please set G4LEDATA"
+echo "em data is ${G4LEDATA}"
+test -d "${G4REALSURFACEDATA}" || usage "can't locate surface data. please set G4REALSURFACEDATA"
+echo "surface data is ${G4REALSURFACEDATA}"
+test -d "${G4NEUTRONXSDATA}" || usage "can't locate neutron xs data. please set G4NEUTRONXSDATA"
+echo "neutron xs data is ${G4NEUTRONXSDATA}"
+test -d "${G4PIIDATA}" || usage "can't locate pii data. please set G4PIIDATA"
+echo "pii data is ${G4PIIDATA}"
+
+echo "Cleaning previous build"
+rm -fr $(basename ${G4NEUTRONHPDATA})
+rm -fr $(basename ${G4LEVELGAMMADATA})
+rm -fr $(basename ${G4RADIOACTIVEDATA})
+rm -fr $(basename ${G4ABLADATA})
+rm -fr $(basename ${G4LEDATA})
+rm -fr $(basename ${G4REALSURFACEDATA})
+rm -fr test_libs gate_shared_libs.tar.gz gate_release.tar.gz
+
+echo "Copying libraries"
+function get_deps {
+ ldd $1 | while read library; do
+ libfile="$(echo ${library} | awk -F' ' '/=> \// {print $3}')"
+ test $libfile || continue # didn't macht regex
+ test -f "test_libs/$(basename ${libfile})" && continue # already exists
+ echo "${libfile}"
+ cp "${libfile}" "test_libs/$(basename ${libfile})"
+ get_deps "${libfile}"
+ done
+}
+
+mkdir test_libs
+get_deps "${GATEBIN}"
+
+echo "Removing unused libraries"
+rm -f test_libs/libdl.so*
+rm -f test_libs/libm.so*
+rm -f test_libs/libstdc++.so*
+rm -f test_libs/libgcc_s.so*
+rm -f test_libs/libpthread.so*
+rm -f test_libs/libc.so*
+
+echo "Zipping libraries"
+(
+ cd test_libs
+ tar -czvf ../gate_shared_libs.tar.gz **
+) || usage "can't create libraries tar"
+
+echo "Copying binary"
+cp "${GATEBIN}" .
+
+echo "Copying data"
+cp -r "${G4NEUTRONHPDATA}" .
+cp -r "${G4LEVELGAMMADATA}" .
+cp -r "${G4RADIOACTIVEDATA}" .
+cp -r "${G4ABLADATA}" .
+cp -r "${G4LEDATA}" .
+cp -r "${G4REALSURFACEDATA}" .
+cp -r "${G4NEUTRONXSDATA}" .
+cp -r "${G4PIIDATA}" .
+
+echo "Making release"
+tar -czvf gate_release.tar.gz \
+ ${GATENAME} gate_shared_libs.tar.gz \
+ $(basename ${G4NEUTRONHPDATA}) \
+ $(basename ${G4LEVELGAMMADATA}) \
+ $(basename ${G4RADIOACTIVEDATA}) \
+ $(basename ${G4ABLADATA}) \
+ $(basename ${G4LEDATA}) \
+ $(basename ${G4REALSURFACEDATA}) \
+ $(basename ${G4NEUTRONXSDATA}) \
+ $(basename ${G4PIIDATA}) \
+ || usage "can't create release zip"
+
+chmod -w gate_release.tar.gz
+
+
--- /dev/null
+#!/usr/bin/env bash
+
+set -u
+
+function error {
+echo "ERROR: $1"
+exit 1
+}
+
+warning_count=0
+function warning {
+let "warning_count++"
+echo "MERGE_WARNING: $1"
+}
+
+function start_bar {
+count_max="${1:?"provide count max"}"
+}
+
+function update_bar {
+local count="${1:?"provide count"}"
+local message="${2:?"provide message"}"
+local percent=$(echo "100*${count}/${count_max}" | bc)
+#printf "[%03d/%03d] %3d%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
+printf "[%03d/%03d] %3d%% %-80.80s\n" ${count} ${count_max} ${percent} "${message}"
+}
+
+function end_bar {
+unset count_max
+#echo -ne '\n'
+}
+
+function check_interfile {
+local input_interfile="${1:?"provide input interfile"}"
+
+grep -qs '!INTERFILE :=' "${input_interfile}" || return 1
+
+local header_byte_size=$(awk -F' ' '
+BEGIN { zsize = 0; }
+/matrix size/ && $3 == "[1]" { xsize = $5; }
+/matrix size/ && $3 == "[2]" { ysize = $5; }
+/number of projections/ { zsize += $5; }
+/number of bytes per pixel/ { byte_per_pixel = $7; }
+END { print xsize * ysize * zsize * byte_per_pixel; }' "${input_interfile}")
+
+local raw_interfile="$(dirname "${input_interfile}")/$(awk -F' := ' '/name of data file/ { print $2; }' "${input_interfile}")"
+
+test -f "${raw_interfile}" || return 1
+test $(stat -c%s "${raw_interfile}") -eq ${header_byte_size} || return 1
+}
+
+function write_mhd_header {
+local input_interfile="${1:?"provide input interfile"}"
+local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
+
+check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
+
+local header_start='ObjectType = Image
+NDims = 3
+AcquisitionDate = none
+BinaryData = True
+BinaryDataByteOrderMSB = False
+CompressedData = False
+TransformMatrix = 1 0 0 0 1 0 0 0 1
+Offset = 0 0 0
+CenterOfRotation = 0 0 0
+DistanceUnits = mm
+AnatomicalOrientation = RIP'
+
+echo "${header_start}" > "${output_mhd}"
+
+awk -F' ' '
+/scaling factor/ && $4 == "[1]" { xspacing = $6; }
+/scaling factor/ && $4 == "[2]" { yspacing = $6; }
+END { print "ElementSpacing = " xspacing " " yspacing " 1"; }' "${input_interfile}" >> "${output_mhd}"
+
+awk -F' ' '
+BEGIN { zsize = 0; }
+/matrix size/ && $3 == "[1]" { xsize = $5; }
+/matrix size/ && $3 == "[2]" { ysize = $5; }
+/number of projections/ { zsize += $5; }
+END { print "DimSize = " xsize " " ysize " " zsize; }' "${input_interfile}" >> "${output_mhd}"
+
+awk -F' := ' '
+/number format/ { format = $2; }
+/number of bytes per pixel/ { byte_per_pixel = $2 }
+END {
+if (format == "unsigned integer" && byte_per_pixel == 8) { print "ElementType = MET_ULONG"; exit };
+if (format == "unsigned integer" && byte_per_pixel == 4) { print "ElementType = MET_UINT"; exit };
+if (format == "unsigned integer" && byte_per_pixel == 2) { print "ElementType = MET_USHORT"; exit };
+if (format == "unsigned integer" && byte_per_pixel == 1) { print "ElementType = MET_UCHAR"; exit };
+if (format == "integer" && byte_per_pixel == 8) { print "ElementType = MET_LONG"; exit };
+if (format == "integer" && byte_per_pixel == 4) { print "ElementType = MET_INT"; exit };
+if (format == "integer" && byte_per_pixel == 2) { print "ElementType = MET_SHORT"; exit };
+if (format == "integer" && byte_per_pixel == 1) { print "ElementType = MET_CHAR"; exit };
+if (format == "float" && byte_per_pixel == 8) { print "ElementType = MET_FLOAT"; exit };
+if (format == "float" && byte_per_pixel == 4) { print "ElementType = MET_DOUBLE"; exit };
+print "ElementType = MET_INT";
+}' "${input_interfile}" >> "${output_mhd}"
+
+awk -F' := ' '
+/name of data file/ { print "ElementDataFile = " $2; }' "${input_interfile}" >> "${output_mhd}"
+}
+
+rootMerger="clitkMergeRootFiles"
+test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
+
+function merge_root {
+local merged="$1"
+shift
+echo " ${indent}entering root merger"
+echo " ${indent}merger is ${rootMerger}"
+echo " ${indent}creating ${merged}"
+#echo "######## $#"
+#echo "######## $*"
+
+if test $# -eq 1
+then
+ echo " ${indent}just one partial file => just copy it"
+ cp "$1" "${merged}"
+ return
+fi
+
+local count=0
+local arguments=" -o ${merged}"
+while test $# -gt 0
+do
+ local partial="$1"
+ shift
+ let count++
+ local arguments=" -i ${partial} ${arguments}"
+done
+${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
+echo " ${indent}merged ${count} files"
+}
+
+statMerger="mergeStatFile.py"
+test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
+
+function merge_stat {
+local merged="$1"
+shift
+echo " ${indent}entering stat merger"
+echo " ${indent}merger is ${statMerger}"
+echo " ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+ local partial="$1"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ continue
+ fi
+
+ update_bar ${count} "adding ${partial}"
+ ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
+done
+end_bar
+echo " ${indent}merged ${count} files"
+}
+
+doseMerger="mergeDosePerEnegryFile.sh"
+test -x "./mergeDosePerEnergyFile.sh" && doseMerger="./mergeDosePerEnergyFile.sh"
+
+function merge_dose {
+local merged="$1"
+shift
+echo " ${indent}entering dose merger"
+echo " ${indent}merger is ${doseMerger}"
+echo " ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+ local partial="$1"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ continue
+ fi
+
+ update_bar ${count} "adding ${partial}"
+ ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+done
+end_bar
+echo " ${indent}merged ${count} files"
+}
+
+txtImageMerger="clitkMergeAsciiDoseActor"
+test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
+
+function merge_txt_image {
+local merged="$1"
+shift
+echo " ${indent}entering text image merger"
+echo " ${indent}merger is ${txtImageMerger}"
+echo " ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+ local partial="$1"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ continue
+ fi
+
+ update_bar ${count} "adding ${partial}"
+ local header="$(cat "${merged}" | head -n 6)"
+ local tmp="$(mktemp)"
+ ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
+ echo "${header}" > "${merged}"
+ grep -v '## Merge' "${tmp}" >> "${merged}"
+ rm "${tmp}"
+done
+end_bar
+echo " ${indent}merged ${count} files"
+}
+
+hdrImageMerger="clitkImageArithm"
+test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
+
+function merge_hdr_image {
+local merged="$1"
+local merged_bin="${merged%.*}.img"
+shift
+echo " ${indent}entering hdr image merger"
+echo " ${indent}merger is ${hdrImageMerger}"
+echo " ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+ local partial="$1"
+ local partial_bin="${partial%.*}.img"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ cp "${partial_bin}" "${merged_bin}"
+ continue
+ fi
+
+ update_bar ${count} "adding ${partial}"
+ ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
+done
+end_bar
+echo " ${indent}merged ${count} files"
+}
+
+mhdImageMerger="clitkImageArithm"
+test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
+
+function merge_mhd_image {
+local merged="$1"
+local merged_bin="${merged%.*}.raw"
+shift
+echo " ${indent}entering mhd image merger"
+echo " ${indent}merger is ${mhdImageMerger}"
+echo " ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+ local partial="$1"
+ local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+ continue
+ fi
+
+ update_bar ${count} "adding ${partial}"
+ ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
+ mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+ sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
+done
+end_bar
+echo " ${indent}merged ${count} files"
+}
+
+function merge_dispatcher {
+ local indent=" ** "
+ local outputfile="${1:?"provide output filename"}"
+ echo "merging ${outputfile}"
+
+ local partialoutputfiles="$(find "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
+ local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
+ if test ${nboutputdirs} -ne ${nboutputfiles}
+ then
+ warning "missing files"
+ return
+ fi
+
+ local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
+ local firstpartialoutputextension="${firstpartialoutputfile##*.}"
+ echo "${indent}testing file type on ${firstpartialoutputfile}"
+
+ if test "${firstpartialoutputextension}" == "hdr" && grep -qs 'INTERFILE' "${firstpartialoutputfile}"
+ then
+ echo "${indent}this is a interfile image"
+ echo "${indent}creating mhd headers"
+ for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
+ local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
+ local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
+ merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
+ echo "${indent}cleaning mhd headers"
+ for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done
+ rm "${mhd_mergedfile}"
+ echo "${indent}copy interfile header"
+ cp "${firstpartialoutputfile}" "${outputdir}"
+ return
+ fi
+
+ if test "${firstpartialoutputextension}" == "hdr"
+ then
+ echo "${indent}this is a analyse image"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+ return
+ fi
+
+ if test "${firstpartialoutputextension}" == "mhd"
+ then
+ echo "${indent}this is a mhd image"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+ return
+ fi
+
+ if test "${firstpartialoutputextension}" == "root"
+ then
+ echo "${indent}this is a root file"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+ return
+ fi
+
+ if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
+ then
+ echo "${indent}this is a stat file"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+ return
+ fi
+
+ if test "${firstpartialoutputextension}" == "txt" && grep -qs 'energydose' "${firstpartialoutputfile}"
+ then
+ echo "${indent}this is a dose file"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ merge_dose "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+ return
+ fi
+
+
+
+ if test "${firstpartialoutputextension}" == "txt" && grep -qs 'Resol' "${firstpartialoutputfile}"
+ then
+ local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
+ local resolx="$(echo "${resol}" | cut -d',' -f1)"
+ local resoly="$(echo "${resol}" | cut -d',' -f2)"
+ local resolz="$(echo "${resol}" | cut -d',' -f3)"
+ if test "${resol}" == "1,1,1"
+ then
+ echo "${indent}this is a txt integral value"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+ return
+ fi
+ if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
+ then
+ echo "${indent}this is a txt profile"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+ return
+ fi
+ fi
+
+ if test "${firstpartialoutputextension}" == "txt"
+ then
+ echo "${indent}this is a non specific txt output"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ local nbdifferent="$(md5sum ${partialoutputfiles} | awk '{ print $1; }' | sort | uniq | wc -l)"
+ echo " ${indent}${nbdifferent} different files"
+ if test ${nbdifferent} -gt 1
+ then
+ echo " ${indent}catting to ${mergedfile}"
+ cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
+ return
+ else
+ echo " ${indent}moving to ${mergedfile}"
+ cp "${firstpartialoutputfile}" "${mergedfile}" || error "error while merging"
+ return
+ fi
+ fi
+
+ error "unknown file type"
+}
+
+echo "!!!! this is $0 v0.3k !!!!"
+
+rundir="${1?"provide run dir"}"
+rundir="$(echo "${rundir}" | sed 's|/*$||')"
+nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
+
+test ${nboutputdirs} -gt 0 || error "no output dir found"
+echo "found ${nboutputdirs} partial output dirs"
+
+outputdir="results"
+if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
+then
+ outputdir="results.${rundir##*.}"
+fi
+outputdir="$(basename "${outputdir}")"
+echo "output dir is ${outputdir}"
+test -d "${outputdir}" && rm -r "${outputdir}"
+mkdir "${outputdir}"
+
+for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+do
+ merge_dispatcher "${outputfile}"
+done
+
+if [ -f "${rundir}/params.txt" ]
+then
+ echo "copying params file"
+ cp "${rundir}/params.txt" "${outputdir}/params.txt"
+fi
+
+echo "these was ${warning_count} warning(s)"
--- /dev/null
+#!/usr/bin/env bash
+
+set -u
+SCRIPTNAME="$(basename "${0}")"
+
+# -------------------------------------------------
+function error {
+ echo "ERROR: $1"
+ usage
+ exit 1
+}
+# -------------------------------------------------
+
+DEFAULTRELEASESUFFIX="NONE"
+DEFAULTNUMBEROFJOBS="10"
+
+# -------------------------------------------------
+function usage {
+ echo "${SCRIPTNAME} mac/main.mac njobs releasesuffix paramtogate"
+ echo "default njobs = ${DEFAULTNUMBEROFJOBS}"
+ echo "default releasesuffix = ${DEFAULTRELEASESUFFIX} (NONE means use Gate in PATH)"
+}
+# -------------------------------------------------
+
+test $# -eq 0 && usage && exit 0
+
+SCRIPTDIR="${HOME}/git/gate-tests/bin"
+RELEASESUFFIX=${3:-"${DEFAULTRELEASESUFFIX}"}
+RELEASEDIR="${HOME}/releases/grid_release${RELEASESUFFIX}"
+JOBFILE="$(dirname $0)/gate_job_cluster.job"
+
+echo "Checking stuff"
+test -f ${JOBFILE} || error "can't find job file ${JOBFILE}"
+if test "${RELEASESUFFIX}" = "${DEFAULTRELEASESUFFIX}"
+then
+ RELEASEDIR="NONE"
+ which Gate 2>&1 >/dev/null || error "there is no Gate in the PATH"
+else
+ test -d ${RELEASEDIR} || error "invalid release dir ${RELEASEDIR}"
+fi
+MACRODIR=$(pwd)
+test -d ${MACRODIR}/mac && test -d ${MACRODIR}/data || error "invalid path"
+MACROFILE=${1:?"provide relative macro path"}
+test -f ${MACRODIR}/${MACROFILE} || error "invalid macro"
+OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+test -d ${OUTPUTDIR} || error "can't locate output dir"
+RUNID=${OUTPUTDIR##*.}
+NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"}
+NJOBSMAX=${NJOBS}
+PARAM="${4:-""}"
+
+echo "Lets roll!!"
+echo "runid is ${RUNID}"
+
+QSUB=$(which qsub 2> /dev/null)
+# echo "qsub is $(which qsub)"
+test -z "${QSUB}" && QSUB="noqsub"
+if test "${QSUB}" = "noqsub"
+then
+ echo "qsub is not found. Simply run Gate on multiple cores."
+fi
+
+test -z "${PARAM}" && echo "no param" || echo "param is ${PARAM}"
+if test "$RELEASESUFFIX" = "$DEFAULTRELEASESUFFIX"
+then
+ echo "Gate is $(which Gate)"
+else
+ echo "Gate release is $(basename ${RELEASEDIR})"
+fi
+echo "submitting ${NJOBS} jobs"
+
+PARAMFILE="${OUTPUTDIR}/params.txt"
+echo "njobs = ${NJOBS}" >> "${PARAMFILE}"
+echo "macro = ${MACROFILE}" >> "${PARAMFILE}"
+test -z "${PARAM}" || echo "param = ${PARAM}" >> "${PARAMFILE}"
+
+while test $NJOBS -gt 0; do
+
+ if test "${QSUB}" = "noqsub"
+ then
+ echo "Launching Gate log in ${OUTPUTDIR}/gate_${NJOBS}.log"
+ PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} SCRIPTDIR=${SCRIPTDIR} OUTPUTDIR=${OUTPUTDIR} RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
+ else
+ qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
+ -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},SCRIPTDIR=${SCRIPTDIR},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+ "${JOBFILE}" || error "submission error"
+ fi
+
+ let NJOBS--
+done
+
+echo "runid is ${RUNID}"
--- /dev/null
+#!/bin/bash
+
+. gate_common.sh
+
+releasearchive="${1:?"provide path to release archive"}"
+test -f ${releasearchive} || error "file ${releasearchive} doesn't exist"
+releasename="${prefix}$(basename "${releasearchive}")"
+
+ensure_proxy || error "no valid proxy"
+
+echo "releasearchive=${releasearchive}"
+echo "releasename=${releasename}"
+echo "lfnrelease=${lfnrelease}"
+check_user || exit 2
+
+upload_file "${releasearchive}" "${lfnrelease}${releasename}" && echo "success" || echo "failed"
--- /dev/null
+#!/bin/bash
+set -u
+
+function usage {
+ echo "$0 -i <file1> -j <file2> -o <result>"
+ exit 1
+}
+
+if [ $# != 6 ]
+then
+ usage
+fi
+
+IN1=$2
+IN2=$4
+RESULT=$6
+
+test -f ${IN1} && test -f ${IN2} || usage
+
+TMP="$(mktemp)"
+echo "merging dose file"
+for PARAM in `awk '$1 == "#" {print $3}' ${IN1}`
+do
+ echo "merging ${PARAM}"
+ V1=`awk -v P=${PARAM} '$3 == P {print $4}' ${IN1} `
+ V2=`awk -v P=${PARAM} '$3 == P {print $4}' ${IN2} `
+ V1=`echo ${V1} | sed -e 's/[eE]+*/\*10\^/'`
+ V2=`echo ${V2} | sed -e 's/[eE]+*/\*10\^/'`
+ R=`echo "scale=30; ${V1} + ${V2}" | bc -l`
+ test -z "${R}" && continue
+ echo "# energydose ${PARAM} ${R}" >> ${TMP}
+done
+mv -f ${TMP} ${RESULT}
--- /dev/null
+#!/usr/bin/env python
+# coding: utf-8
+
+import sys
+import re
+import datetime
+
+linere = re.compile(r'''^#\s+([a-zA-Z]+)\s+=\s(.*)$''')
+mergedlines = ['NumberOfRun', 'NumberOfEvents', 'NumberOfTracks', 'NumberOfSteps', 'NumberOfGeometricalSteps', 'NumberOfPhysicalSteps', 'ElapsedTimeWoInit', 'ElapsedTime', 'StartDate', 'EndDate']
+
+assert(len(sys.argv)==7)
+assert(sys.argv[1]=="-i")
+assert(sys.argv[3]=="-j")
+assert(sys.argv[5]=="-o")
+
+def total_seconds(deltat):
+ try:
+ return float(deltat.total_seconds())
+ except AttributeError: # total_seconds defined in 2.7
+ total = 0.
+ total += deltat.seconds
+ total += deltat.microseconds*1e-6
+ total += deltat.days*3600.*24.
+ return total
+
+def parse_stat_file(filename):
+ keys = {}
+ for line in open(filename,"r").readlines():
+ match = linere.match(line)
+ assert(match is not None)
+ groups = match.groups()
+ if groups[0] not in mergedlines:
+ continue
+ keys[groups[0]]=groups[1]
+ return keys
+
+def merge_keys(ikeys,jkeys):
+ mindate = None
+ maxdate = None
+ keys = {}
+ for line in mergedlines:
+ value = None
+
+ if value is None:
+ try:
+ ivalue = int(ikeys[line])
+ jvalue = int(jkeys[line])
+ value = ivalue + jvalue
+ value = str(value)
+ except ValueError:
+ pass
+
+ if value is None:
+ try:
+ ivalue = float(ikeys[line])
+ jvalue = float(jkeys[line])
+ value = ivalue + jvalue
+ value = str(value)
+ except ValueError:
+ pass
+
+ if value is None:
+ ivalue = datetime.datetime.strptime(ikeys[line],"%a %b %d %H:%M:%S %Y")
+ jvalue = datetime.datetime.strptime(jkeys[line],"%a %b %d %H:%M:%S %Y")
+ if line=="StartDate":
+ value = min(ivalue,jvalue)
+ mindate = value
+ if line=="EndDate":
+ value = max(ivalue,jvalue)
+ maxdate = value
+ value = value.strftime("%a %b %d %H:%M:%S %Y")
+
+ assert(value is not None)
+ keys[line] = value
+ if mindate is not None and maxdate is not None:
+ speedup = float(keys["ElapsedTime"])/total_seconds(maxdate-mindate)
+ keys["Speedup"] = str(speedup)
+ return keys
+
+def format_keys(keys):
+ output = "\n".join("# %s = %s" % (line,keys[line]) for line in mergedlines)
+ if "Speedup" in keys:
+ output += "\n# Speedup = %s" % keys["Speedup"]
+ return output
+
+ikeys = parse_stat_file(sys.argv[2])
+jkeys = parse_stat_file(sys.argv[4])
+keys = merge_keys(ikeys,jkeys)
+output = format_keys(keys)
+open(sys.argv[6],"w").write(output)
+
--- /dev/null
+#!/bin/bash
+set -u
+
+function usage {
+ echo "$0 -i <file1> -j <file2> -o <result>"
+ exit 1
+}
+
+if [ $# != 6 ]
+then
+ usage
+fi
+
+IN1=$2
+IN2=$4
+RESULT=$6
+
+
+test -f ${IN1} && test -f ${IN2} || usage
+
+TMP="$(mktemp)"
+echo "merging stat file"
+for PARAM in `awk '$1 == "#" {print $2}' ${IN1}`
+do
+ echo "merging ${PARAM}"
+ V1=`awk -v P=${PARAM} '$2 == P {print $4}' ${IN1} `
+ V2=`awk -v P=${PARAM} '$2 == P {print $4}' ${IN2} `
+ R=`echo "${V1} + ${V2}" | bc`
+ test -z "${R}" && continue
+ echo "# ${PARAM} = ${R}" >> ${TMP}
+done
+mv -f ${TMP} ${RESULT}
IF (CLITK_USE_SYSTEM_GDCM)
FIND_PACKAGE(GDCM REQUIRED)
include(${GDCM_USE_FILE})
- TARGET_LINK_LIBRARIES(clitkCommon vtkgdcm)
- # gdcmDICT gdcmMSFF)
+ TARGET_LINK_LIBRARIES(clitkCommon vtkgdcm gdcmDICT gdcmMSFF gdcmMEXD)
ENDIF()
#=========================================================
//mColor = //FIXME !!
+ // gdcm::Attribute<0x3006,0x002a> color = {};
+
+ // const gdcm::DataSet & nestedds = mItemContour->GetNestedDataSet();
+ // color.SetFromDataSet( nestedds );
+ // assert( color.GetNumberOfValues() == 3 );
+ // mColor[0] = color.GetValue(0);
+ // mColor[1] = color.GetValue(1);
+ // mColor[2] = color.GetValue(2);
+
+
SetDicomUptodateFlag(true);
// Get the contour
mMesh = reader->GetOutput(roiindex);
typedef typename clitk::DicomRT_StructureSet::Pointer DicomRTStructPointer;
// Set inputs
- itkSetMacro(Input, ImagePointer);
- itkGetConstMacro(Input, ImagePointer);
+ itkSetMacro(InputFilenames, std::vector<std::string> );
itkSetMacro(StructureSetFilename, std::string);
itkSetMacro(DicomFolder, std::string);
itkSetMacro(OutputFilename, std::string);
- void SetROIName(std::string name, std::string type);
+ void SetROIType(std::string type);
itkSetMacro(ThresholdValue, PixelType);
+ itkSetMacro(SkipInitialStructuresFlag, bool);
// Run filter
void Update();
protected:
- ImagePointer m_Input;
std::string m_StructureSetFilename;
std::string m_DicomFolder;
std::string m_OutputFilename;
- std::string m_ROIName;
std::string m_ROIType;
PixelType m_ThresholdValue;
+ std::vector<std::string> m_InputFilenames;
+ bool m_SkipInitialStructuresFlag;
};
//--------------------------------------------------------------------
#include "vtkCamera.h"
#include "vtkProperty.h"
#include "vtkProperty2D.h"
+#include <vtksys/SystemTools.hxx>
// itk
#include <itkImage.h>
m_DicomFolder = "";
m_OutputFilename = "default-output.dcm";
m_ThresholdValue = 0.5;
+ m_SkipInitialStructuresFlag = false;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class PixelType>
void
-clitk::Image2DicomRTStructFilter<PixelType>::SetROIName(std::string name, std::string type)
+clitk::Image2DicomRTStructFilter<PixelType>::SetROIType(std::string type)
{
- m_ROIName = name;
m_ROIType = type;
}
//--------------------------------------------------------------------
<< p->GetNumberOfStructureSetROIs() << std::endl;
}
+
+ // number of additional contours
+ int m = m_InputFilenames.size();
+
// Init writer
vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
- int numMasks = reader->GetNumberOfOutputPorts() + 1;//add one more
+ int numMasks = reader->GetNumberOfOutputPorts() + m;
+
+ if (m_SkipInitialStructuresFlag) {
+ numMasks = m;
+ }
+
writer->SetNumberOfInputPorts(numMasks);
writer->SetFileName(m_OutputFilename.c_str());
writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
roiTypes->SetNumberOfValues(numMasks);
// Convert the image into a mesh
- typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
- typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
- convert->SetThresholdValue(m_ThresholdValue);
- convert->SetInput(m_Input);
- convert->Update();
- vtkPolyData* mesh = convert->GetOutputMesh();
- if (GetVerboseFlag()) {
- std::cout << "Mesh has " << mesh->GetNumberOfLines() << " lines." << std::endl;
+ std::vector<vtkSmartPointer<vtkPolyData> > meshes;
+ std::vector<std::string> m_ROINames;
+ meshes.resize(m);
+ m_ROINames.resize(m);
+ for(unsigned int i=0; i<m; i++) {
+
+ // read image
+ // typedef float PixelType;
+ //typedef itk::Image<PixelType, 3> ImageType;
+ ImagePointer input = clitk::readImage<ImageType>(m_InputFilenames[i], false);
+
+ std::ostringstream oss;
+ oss << vtksys::SystemTools::
+ GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(m_InputFilenames[i]));
+ std::string name = oss.str();
+ m_ROINames[i] = name;
+
+ // convert to mesh
+ typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
+ typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
+ convert->SetThresholdValue(m_ThresholdValue);
+ convert->SetInput(input);
+ convert->Update();
+ meshes[i] = convert->GetOutputMesh();
+ if (GetVerboseFlag()) {
+ std::cout << "Mesh has " << meshes[i]->GetNumberOfLines() << " lines." << std::endl;
+ }
+
+ /*
+ // debug mesh write FIXME
+ vtkSmartPointer<vtkPolyDataWriter> wr = vtkSmartPointer<vtkPolyDataWriter>::New();
+ wr->SetInputConnection(convert->GetOutputPort()); //psurface->GetOutputPort()
+ wr->SetFileName("bidon.obj");
+ wr->Update();
+ wr->Write();
+ */
}
-
+
// Copy previous contours
- for (unsigned int i = 0; i < numMasks-1; ++i) {
+ for (unsigned int i = 0; i < numMasks-m; ++i) {
writer->SetInput(i, reader->GetOutput(i));
std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
roiNames->InsertValue(i, theString);
roiTypes->InsertValue(i, theString);
}
- // Add new one
- int last = numMasks-1;
- writer->SetInput(last, mesh);
- roiNames->InsertValue(last, m_ROIName);
- roiAlgorithms->InsertValue(last, "CLITK_CREATED");
- roiTypes->InsertValue(last, m_ROIType);
-
+ // Add new ones
+ for (unsigned int i = numMasks-m; i < numMasks; ++i) {
+ writer->SetInput(i, meshes[i-numMasks+m]);
+ roiNames->InsertValue(i, m_ROINames[i-numMasks+m]);
+ roiAlgorithms->InsertValue(i, "CLITK_CREATED");
+ roiTypes->InsertValue(i, m_ROIType);
+ }
+
/*
// Visu DEBUG
vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
return GetRotationMatrix3D(rotationParameters);
}
+//--------------------------------------------------------------------
+itk::Matrix<double, 4, 4> ReadMatrix3D(std::string fileName)
+{
+ // read input matrix
+ std::ifstream is;
+ openFileForReading(is, fileName);
+ std::vector<double> nb;
+ double x;
+ skipComment(is);
+ is >> x;
+ while (is && !is.eof()) {
+ nb.push_back(x);
+ skipComment(is);
+ is >> x;
+ }
+
+ if(nb.size() != 16)
+ itkGenericExceptionMacro(<< "Could not read 4x4 matrix in " << fileName);
+
+ //copy it to the matrix
+ itk::Matrix<double, 4, 4> matrix;
+ unsigned int index=0;
+ for (unsigned int i=0;i<4;i++)
+ for (unsigned int j=0;j<4;j++)
+ matrix[i][j]=nb[index++];
+ return matrix;
+}
+
}
return matrix;
}
- inline itk::Matrix<double, 4, 4> ReadMatrix3D(std::string fileName)
- {
- // read input matrix
- std::ifstream is;
- openFileForReading(is, fileName);
- std::vector<double> nb;
- double x;
- skipComment(is);
- is >> x;
- while (!is.eof()) {
- nb.push_back(x);
- skipComment(is);
- is >> x;
- }
-
- //copy it to the matrix
- itk::Matrix<double, 4, 4> matrix;
- unsigned int index=0;
- for (unsigned int i=0;i<4;i++)
- for (unsigned int j=0;j<4;j++)
- matrix[i][j]=nb[index++];
- return matrix;
- }
+ itk::Matrix<double, 4, 4> ReadMatrix3D(std::string fileName);
inline vtkMatrix4x4* ReadVTKMatrix3D(std::string fileName) {
// read input matrix
if(f.is_open()) {
f.close();
- itk::Matrix<double, 4, 4> itkMat = clitk::ReadMatrix3D(filename);
+ itk::Matrix<double, 4, 4> itkMat;
+ itkMat.SetIdentity();
+ try {
+ itkMat = clitk::ReadMatrix3D(filename);
+ }
+ catch (itk::ExceptionObject & err) {
+ itkWarningMacro(<< "Found " << filename
+ << " but this is not a 4x4 matrix so it is ignored.");
+ }
vtkSmartPointer<vtkMatrix4x4> matrix = vtkSmartPointer<vtkMatrix4x4>::New();
matrix->Identity();
UpdateWithDimAndOutputPixelType<unsigned char,VImageDimension>();
} else if (OutputPixelType == "int") {
UpdateWithDimAndOutputPixelType<int,VImageDimension>();
+ } else if (OutputPixelType == "unsigned_int") {
+ UpdateWithDimAndOutputPixelType<unsigned int,VImageDimension>();
} else if (OutputPixelType == "double") {
UpdateWithDimAndOutputPixelType<double,VImageDimension>();
} else if (OutputPixelType == "float") {
option "upperThresholdForTrachea" - "0: Initial upper threshold for trachea" double no default="-900"
option "multiplierForTrachea" - "0: Multiplier for the region growing" double no default="5"
option "thresholdStepSizeForTrachea" - "0: Threshold step size" int no default="64"
-option "seed" - "0,1: Index of the trachea seed point (in pixel, not in mm)" int no multiple
+option "seed" - "0,1: Index of the trachea seed point (in mm NOT IN PIXELS)" float no multiple
option "doNotCheckTracheaVolume" - "0,1: If set, do not check the trachea volume" flag off
option "verboseRG" - "0,1: Verbose RegionGrowing" flag off
option "maxElongation" - "1: Maximum allowed elongation of candidate regions for the trachea" float no default="0.5"
section "Step 6 : fill holes"
option "doNotFillHoles" - "Do not fill holes if set" flag on
-option "dir" d "Directions (axes) to perform filling (defaults to 2,1,0)" int multiple no
+#option "dir" d "Directions (axes) to perform filling (defaults to 2,1,0)" int multiple no
section "Step 7 : lung separation (labelling)"
option "doNotSeparateLungs" - "Do not separate lungs if set" flag off
itkSetMacro(SeedPreProcessingThreshold, int);
itkGetConstMacro(SeedPreProcessingThreshold, int);
- void AddSeed(InternalIndexType s);
+ void AddSeedInPixels(InternalIndexType s);
+ void AddSeed(InputImagePointType s);
std::vector<InternalIndexType> & GetSeeds() { return m_Seeds; }
itkSetMacro(TracheaVolumeMustBeCheckedFlag, bool);
InputImagePixelType m_ThresholdStepSizeForTrachea;
double m_MultiplierForTrachea;
std::vector<InternalIndexType> m_Seeds;
+ std::vector<InputImagePointType> m_SeedsInMM;
int m_NumberOfSlicesToSkipBeforeSearchingSeed;
bool m_TracheaVolumeMustBeCheckedFlag;
bool m_VerboseRegionGrowingFlag;
TracheaVolumeMustBeCheckedFlagOn();
SetNumSlices(50);
SetMaxElongation(0.5);
- SetSeedPreProcessingThreshold(-400);
-
+ SetSeedPreProcessingThreshold(-400);
// Step 3 default values
SetNumberOfHistogramBins(500);
template <class ImageType>
void
clitk::ExtractLungFilter<ImageType>::
-AddSeed(InternalIndexType s)
+//AddSeed(InternalIndexType s)
+AddSeed(InputImagePointType s)
+{
+ m_SeedsInMM.push_back(s);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLungFilter<ImageType>::
+AddSeedInPixels(InternalIndexType s)
{
m_Seeds.push_back(s);
}
// smalest one (sometimes appends with the stomach
if (initialNumberOfLabels >1) {
if (GetRemoveSmallLabelBeforeSeparationFlag()) {
- DD(GetRemoveSmallLabelBeforeSeparationFlag());
typedef itk::RelabelComponentImageFilter<MaskImageType, MaskImageType> RelabelFilterType;
typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
relabelFilter->SetInput(working_mask);
it.GoToBegin();
while (!it.IsAtEnd()) {
if(it.Get() < GetUpperThresholdForTrachea() ) {
- AddSeed(it.GetIndex());
+ AddSeedInPixels(it.GetIndex());
// DD(it.GetIndex());
}
++it;
f->SetVerbose(GetVerboseRegionGrowingFlag());
for(unsigned int i=0; i<m_Seeds.size();i++) {
f->AddSeed(m_Seeds[i]);
- // DD(m_Seeds[i]);
+ //DD(m_Seeds[i]);
}
f->Update();
PrintMemory(GetVerboseMemoryFlag(), "After RG update");
// compute trachea volume
// if volume not plausible -> skip more slices and restart
+ // If initial seed, convert from mm to pixels
+ if (m_SeedsInMM.size() > 0) {
+ for(unsigned int i=0; i<m_SeedsInMM.size(); i++) {
+ InputImageIndexType index;
+ working_input->TransformPhysicalPointToIndex(m_SeedsInMM[i], index);
+ m_Seeds.push_back(index);
+ }
+ }
+
bool has_seed;
bool stop = false;
double volume = 0.0;
f->SetMaxElongation(mArgsInfo.maxElongation_arg);
f->SetSeedPreProcessingThreshold(mArgsInfo.seedPreProcessingThreshold_arg);
- typename FilterType::InputImageIndexType s;
+ typename FilterType::InputImagePointType s;
if (mArgsInfo.seed_given) {
ConvertOptionMacro(mArgsInfo.seed, s, 3, false);
- f->AddSeed(s);
+ f->AddSeed(s);
}
f->SetMinimalComponentSize(mArgsInfo.minSize_arg);
TARGET_LINK_LIBRARIES(clitkAffineTransform clitkCommon )
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAffineTransform)
+ WRAP_GGO(clitkElastixTransformToMatrix_GGO_C clitkElastixTransformToMatrix.ggo)
+ ADD_EXECUTABLE(clitkElastixTransformToMatrix clitkElastixTransformToMatrix.cxx ${clitkElastixTransformToMatrix_GGO_C})
+ TARGET_LINK_LIBRARIES(clitkElastixTransformToMatrix clitkCommon )
+ SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkElastixTransformToMatrix)
+
+
WRAP_GGO(clitkSetBackground_GGO_C clitkSetBackground.ggo)
ADD_EXECUTABLE(clitkSetBackground clitkSetBackground.cxx clitkSetBackgroundGenericFilter.cxx ${clitkSetBackground_GGO_C})
TARGET_LINK_LIBRARIES(clitkSetBackground clitkCommon)
IF(CLITK_EXPERIMENTAL)
WRAP_GGO(clitkBinaryImageToMesh_GGO_C clitkBinaryImageToMesh.ggo)
ADD_EXECUTABLE(clitkBinaryImageToMesh clitkBinaryImageToMesh.cxx ${clitkBinaryImageToMesh_GGO_C})
- TARGET_LINK_LIBRARIES(clitkBinaryImageToMesh itksys ${ITK_LIBRARIES} ${VTK_LIBRARIES})
+ TARGET_LINK_LIBRARIES(clitkBinaryImageToMesh clitkCommon)
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBinaryImageToMesh)
WRAP_GGO(clitkMeshToBinaryImage_GGO_C clitkMeshToBinaryImage.ggo)
WRAP_GGO(clitkMeshViewer_GGO_C clitkMeshViewer.ggo)
ADD_EXECUTABLE(clitkMeshViewer clitkMeshViewer.cxx ${clitkMeshViewer_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMeshViewer ${ITK_LIBRARIES} ${VTK_LIBRARIES})
+ TARGET_LINK_LIBRARIES(clitkMeshViewer clitkCommon)
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshViewer)
ENDIF(CLITK_EXPERIMENTAL)
//----------------------------------------
void Update();
+ template<unsigned int Dimension, class PixelType>
+ static
+ typename itk::Matrix<double, Dimension+1, Dimension+1>
+ createMatrixFromElastixFile(std::vector<std::string> & filename, bool verbose=true);
+
protected:
//----------------------------------------
template <unsigned int Dimension, class PixelType> void UpdateWithDimAndPixelType();
template <unsigned int Dimension, class PixelType> void UpdateWithDimAndVectorType();
- template<unsigned int Dimension, class PixelType>
- typename itk::Matrix<double, Dimension+1, Dimension+1>
- createMatrixFromElastixFile(std::vector<std::string> & filename);
-
- bool GetElastixValueFromTag(std::ifstream & is, std::string tag, std::string & value);
- void GetValuesFromValue(const std::string & s,
- std::vector<std::string> & values);
+ static bool GetElastixValueFromTag(std::ifstream & is, std::string tag, std::string & value);
+ static void GetValuesFromValue(const std::string & s,
+ std::vector<std::string> & values);
//----------------------------------------
// Data members
if (m_ArgsInfo.elastix_given) {
std::vector<std::string> s;
for(uint i=0; i<m_ArgsInfo.elastix_given; i++) s.push_back(m_ArgsInfo.elastix_arg[i]);
- matrix = createMatrixFromElastixFile<Dimension,PixelType>(s);
+ matrix = createMatrixFromElastixFile<Dimension,PixelType>(s, m_Verbose);
}
else
matrix.SetIdentity();
template<class args_info_type>
template<unsigned int Dimension, class PixelType>
typename itk::Matrix<double, Dimension+1, Dimension+1>
- AffineTransformGenericFilter<args_info_type>::createMatrixFromElastixFile(std::vector<std::string> & filename)
+ AffineTransformGenericFilter<args_info_type>::createMatrixFromElastixFile(std::vector<std::string> & filename, bool verbose)
{
if (Dimension != 3) {
FATAL("Only 3D yet" << std::endl);
for(uint j=0; j<filename.size(); j++) {
// Open file
- if (m_Verbose) std::cout << "Read elastix parameters in " << filename[j] << std::endl;
+ if (verbose) std::cout << "Read elastix parameters in " << filename[j] << std::endl;
std::ifstream is;
clitk::openFileForReading(is, filename[j]);
p[i+6] = atof(results[i+3].c_str()); // Translation
mat->SetParameters(p);
- if (m_Verbose) {
+ if (verbose) {
std::cout << "Rotation (deg) : " << rad2deg(p[0]) << " " << rad2deg(p[1]) << " " << rad2deg(p[2]) << std::endl;
std::cout << "Center of rot (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
std::cout << "Translation (phy) : " << p[6] << " " << p[7] << " " << p[8] << std::endl;
// Compose with previous if needed
if (j!=0) {
mat->Compose(previous);
- if (m_Verbose) {
+ if (verbose) {
std::cout << "Composed rotation (deg) : " << rad2deg(mat->GetAngleX()) << " " << rad2deg(mat->GetAngleY()) << " " << rad2deg(mat->GetAngleZ()) << std::endl;
std::cout << "Composed center of rot (phy) : " << mat->GetCenter() << std::endl;
std::cout << "Compsoed translation (phy) : " << mat->GetTranslation() << std::endl;
gdcm::Attribute<0x28, 0x100> pixel_size;
pixel_size.SetFromDataSet(ds);
- if (pixel_size.GetValue() != 16)
- {
- std::cerr << "Pixel type 2 bytes ! " << std::endl;
- std::cerr << "In file " << input_files[i] << std::endl;
- exit(0);
- }
+ /* if (pixel_size.GetValue() != 16)
+ {
+ std::cerr << "Pixel type not 2 bytes ! " << std::endl;
+ std::cerr << "In file " << input_files[i] << std::endl;
+ exit(0);
+ }
+ */
#else
if (args_info.verbose_flag)
std::cout << "Not using GDCM-2.x" << std::endl;
theorigin[series_number][2] = header->GetZOrigin();
sliceLocations[series_number].push_back(theorigin[series_number][2]);
seriesFiles[series_number].push_back(input_files[i]);
- if (header->GetPixelSize() != 2) {
+ /*if (header->GetPixelSize() != 2) {
std::cerr << "Pixel type 2 bytes ! " << std::endl;
std::cerr << "In file " << input_files[i] << std::endl;
exit(0);
}
+ */
#endif
}
// itk (gdcm) include
#include "gdcmFile.h"
#if GDCM_MAJOR_VERSION == 2
- #include "gdcmReader.h"
- #include "gdcmPrinter.h"
+#include "gdcmReader.h"
+#include "gdcmPrinter.h"
+#include "gdcmDict.h"
+#include "gdcmStringFilter.h"
#endif
//--------------------------------------------------------------------
// check arg
if (args_info.inputs_num == 0) return 0;
+ // Study ID
+ #if GDCM_MAJOR_VERSION == 2
+ if (args_info.studyID_flag) {
+ std::set<std::string> l;
+ for(unsigned int i=0; i<args_info.inputs_num; i++) {
+ gdcm::Reader reader;
+ reader.SetFileName(args_info.inputs[i]);
+ std::set<gdcm::Tag> tags;
+ gdcm::Tag StudyInstanceUIDTag(0x0020, 0x000d);
+ gdcm::Tag SeriesDateTag(0x0008, 0x0021);
+ tags.insert(StudyInstanceUIDTag);
+ tags.insert(SeriesDateTag);
+ if (reader.ReadSelectedTags(tags)) {
+ gdcm::StringFilter sf;
+ sf.SetFile(reader.GetFile());
+ std::pair<std::string, std::string> p = sf.ToStringPair(StudyInstanceUIDTag);
+ std::pair<std::string, std::string> d = sf.ToStringPair(SeriesDateTag);
+ if (args_info.uniq_flag) {
+ if (l.insert(p.second).second == true) {
+ if (args_info.filename_flag)
+ std::cout << args_info.inputs[i] << " " << p.second << " " << d.second << std::endl;
+ else
+ std::cout << p.second << std::endl;
+ }
+ }
+ else {
+ if (args_info.filename_flag)
+ std::cout << args_info.inputs[i] << " " << p.second << " " << d.second << std::endl;
+ else
+ std::cout << p.second << std::endl;
+ }
+ } // tag not found
+ }
+ }
+#endif
+
// Loop files
+ if (!args_info.studyID_flag)
for(unsigned int i=0; i<args_info.inputs_num; i++) {
+ if (args_info.filename_flag) std::cout << args_info.inputs[i] << std::endl;
#if GDCM_MAJOR_VERSION == 2
gdcm::Reader reader;
reader.SetFileName(args_info.inputs[i]);
version "read and print Dicom header"
option "config" - "Config file" string no
+option "studyID" s "Only display Study UID" flag off
+option "uniq" u "Do not display if same study UID" flag off
+option "filename" f "Display filename" flag off
option "verboseFile" - "Verbose file content" flag off
option "input" i "Input Dicom file" string yes
option "image" j "Used to read image info (spacing, origin)" string yes
-option "output" o "Output image filename" string yes
+option "output" o "Output image base filename (roi number and extension will be append)" string yes
defgroup "ROIoption" groupdesc="an option of this group is required"
groupoption "roi" r "ROI to binarize (if -1 = all roi)" int no default="-1" group="ROIoption"
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+// clitk
+#include "clitkElastixTransformToMatrix_ggo.h"
+#include "clitkAffineTransformGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkElastixTransformToMatrix, args_info);
+ CLITK_INIT;
+
+ // Use static fct of AffineTransformGenericFilter
+ typedef clitk::AffineTransformGenericFilter<args_info_clitkElastixTransformToMatrix> FilterType;
+ std::vector<std::string> l;
+ l.push_back(args_info.input_arg);
+ itk::Matrix<double, 4, 4> m =
+ FilterType::createMatrixFromElastixFile<3, int>(l, args_info.verbose_flag);
+
+ // Print matrix
+ std::ofstream os;
+ clitk::openFileForWriting(os, args_info.output_arg);
+ for(unsigned int i=0; i<4; i++) {
+ for(unsigned int j=0; j<4; j++)
+ os << m[i][j] << " ";
+ os << std::endl;
+ }
+ os.close();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkElastixTransformToMatrix.ggo
+package "clitkElastixTransformToMatrix"
+version "1.0"
+purpose ""
+
+option "config" - "Config file" string optional
+option "verbose" v "Verbose" flag off
+option "input" i "Input elastix filename" string required
+option "output" o "Output matrix filename" string required
// Init command line
GGO(clitkImage2DicomRTStruct, args_info);
- // Read initial 3D image
- typedef float PixelType;
- typedef itk::Image<PixelType, 3> ImageType;
- ImageType::Pointer input = clitk::readImage<ImageType>(args_info.input_arg, args_info.verbose_flag);
+ // Set initial 3D image filenames
+ std::vector<std::string> filenames;
+ for(unsigned int i=0; i< args_info.input_given; i++)
+ filenames.push_back(args_info.input_arg[i]);
// Create a filter to convert image into dicomRTStruct and write to disk
+ typedef float PixelType;
clitk::Image2DicomRTStructFilter<PixelType> filter;
filter.SetVerboseFlag(args_info.verbose_flag);
- filter.SetInput(input);
+ filter.SetInputFilenames(filenames);
filter.SetDicomFolder(args_info.dicom_arg);
filter.SetStructureSetFilename(args_info.rtstruct_arg);
filter.SetOutputFilename(args_info.output_arg);
- filter.SetROIName(args_info.roiname_arg, args_info.roitype_arg);
+ filter.SetROIType(args_info.roitype_arg);
filter.SetThresholdValue(args_info.threshold_arg);
+ filter.SetSkipInitialStructuresFlag(args_info.skip_flag);
filter.Update();
// This is the end my friend
option "config" - "Config file" string no
option "verbose" v "Verbose" flag off
-option "input" i "Input image file (binary image) to be converted into contours" string yes
+option "input" i "Input image file (binary image) to be converted into contours" string multiple yes
option "rtstruct" r "Input rt struct" string yes
option "dicom" d "Input folder where the initial dicom ct is" string yes
option "output" o "Output DicomRT filename" string yes
option "threshold" t "Threshold for binary image" float no default = "0.5"
-option "roiname" - "Name of the roi added into the rt-struct" string yes
+option "skip" s "Do not write in output the structures that was in input" flag off
option "roitype" - "Name of the type of roi added into the rt-struct" string no default = "ORGAN"
if (Components==3)
{
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and 3D float..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
+ if (PixelType == "unsigned_char")
+ UpdateWithDimAndPixelType<Dimension, itk::Vector<unsigned char, 3> >();
+ else
+ {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and 3D float..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
+ }
}
else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
}
#define __vvPacsSettingsDialog_H
#include "ui_vvPacsSettingsDialog.h"
#include <QFileDialog>
-#include <QTGUI/QWidget>
+#include <QWidget>
class vvPacsSettingsDialog : public QDialog
{
void accept();
};
-#endif //__vvPacsSettingsDialog_H
\ No newline at end of file
+#endif //__vvPacsSettingsDialog_H
#ifndef __vvQPacsConnection_h_INCLUDED__
#define __vvQPacsConnection_h_INCLUDED__
-#include <QTGUI/QWidget>
+#include <QWidget>
#include "ui_vvPacsConnection.h"
#include "gdcmCompositeNetworkFunctions.h"
-#include <QtGui/QStandardItemModel.h>
-#include <QtGui/QStringListModel.h>
+#include <QStandardItemModel>
+#include <QStringListModel>
#include <QFileDialog>
#include "vvDicomServerQueryFactory.h"
- class vvQPacsConnection : public QDialog
- {
+class vvQPacsConnection : public QDialog
+{
Q_OBJECT
- public:
+public:
//vvQPacsConnection(){}
vvQPacsConnection(QWidget *parent=0);
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff