#!/usr/bin/env bash
-set -u
+set -u
function error {
-echo "ERROR: $1"
-exit 1
+ echo "ERROR: $1"
+ exit 1
}
+warning_count=0
function warning {
-echo "WARNING: $1"
+ let "warning_count++"
+ echo "MERGE_WARNING: $1"
}
function start_bar {
-count_max="${1:?"provide count max"}"
+ 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}"
+ 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'
+ 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}"
-local count=0
-local arguments=" -o ${merged}"
-while test $# -gt 0
-do
- local partial="$1"
+ local merged="$1"
shift
- let count++
- local arguments=" -i ${partial} ${arguments}"
-done
-${rootMerger} ${arguments} > /dev/null || warning "error while calling ${rootMerger}"
-echo " ${indent}merged ${count} files"
+ 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"
+ local merged="$1"
shift
- let count++
+ 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}" "${merged}"
+ continue
+ fi
- if test ! -f "${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"
+}
- 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="mergeDosePerEnergyFile.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"
+}
+
+doseMerger="mergeDoseByRegions.sh"
+test -x "./mergeDoseByRegions.sh" && doseMerger="./mergeDoseByRegions.sh"
+
+function merge_doseByRegions {
+ local merged="$1"
+ shift
+ echo " ${indent}entering dose merger"
+ echo " ${indent}merger is ${doseMerger}"
+ echo " ${indent}creating ${merged}"
+ local count=0
+ start_bar $#
+ source ${doseMerger}
+ 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}" "${merged}"
+ copyFirstPartialResult -i "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+ continue
+ fi
+
+ update_bar ${count} "adding ${partial}"
+ addToPartialResult -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+ done
+ divideUncertaintyResult -i "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+ 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"
+ local merged="$1"
shift
- let count++
-
- if test ! -f "${merged}"
- then
- update_bar ${count} "copying first partial result ${partial}"
- cp "${partial}" "${merged}"
- continue
- fi
+ 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"
+ 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"
+ local merged="$1"
+ local merged_bin="${merged%.*}.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
+ 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"
+ 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 ${count} files"
}
-rundir="${1?"provide run dir"}"
-nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
+mhdImageMerger="clitkImageArithm"
+test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
-test ${nboutputdirs} -gt 0 || error "no output dir found"
-echo "found ${nboutputdirs} partial output dirs"
+function merge_mhd_image {
+ local merged="$1"
+ local merged_bin="${merged%.*}.raw"
+ local last_character=${merged#${merged%?}}
+ 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}" "${merged}"
+ if test "$last_character" = "d"
+ then
+ cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+ fi
+ continue
+ fi
-outputdir="results"
-if [ "${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}"
+ update_bar ${count} "adding ${partial}"
+ ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
+ if test "$last_character" = "d" && test "${merged_bin}" != "${merged_bin%.*}.${partial_bin##*.}"
+ then
+ mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+ sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
+ fi
+ done
+ end_bar
+ echo " ${indent}merged ${count} files"
+}
-for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(hdr|root|txt)' | awk -F '/' '{ print $NF }' | sort | uniq)
-do
- indent=" ** "
+function merge_dispatcher {
+ local indent=" ** "
+ local outputfile="${1:?"provide output filename"}"
echo "merging ${outputfile}"
- partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
- nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
+ local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
+ local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
if test ${nboutputdirs} -ne ${nboutputfiles}
then
warning "missing files"
- continue
+ if ! test "${2}" == "--force"
+ then
+ return
+ fi
fi
- firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
- firstpartialoutputextension="${firstpartialoutputfile##*.}"
+ local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
+ local firstpartialoutputextension="${firstpartialoutputfile##*.}"
echo "${indent}testing file type on ${firstpartialoutputfile}"
+ if test "${firstpartialoutputextension}" == "hdr" && test grep -qs 'INTERFILE' "${firstpartialoutputfile}"
+ then
+ echo "${indent}this is an 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"
- mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ echo "${indent}this is an analyse image"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
- continue
+ return
+ fi
+
+ if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
+ then
+ echo "${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 "${indent}this is a root file"
- mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
- continue
+ return
fi
- if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
+ if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
then
echo "${indent}this is a stat file"
- mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
- continue
+ return
+ fi
+
+ if test "${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 'Resol' "${firstpartialoutputfile}" > /dev/null
+
+
+ if test "${firstpartialoutputextension}" == "txt" && grep -qs 'Resol' "${firstpartialoutputfile}"
then
- resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
- resolx="$(echo "${resol}" | cut -d',' -f1)"
- resoly="$(echo "${resol}" | cut -d',' -f2)"
- resolz="$(echo "${resol}" | cut -d',' -f3)"
+ 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"
- mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
- continue
+ return
fi
if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
then
echo "${indent}this is a txt profile"
- mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
- continue
+ return
+ fi
+ fi
+
+ if test "${firstpartialoutputextension}" == "txt" && grep -qs 'vol(mm3)' "${firstpartialoutputfile}"
+ then
+ echo "${indent}this is a DoseByRegions file"
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ merge_doseByRegions "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+ return
+ fi
+
+
+ if test "${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}" "${mergedfile}" || error "error while merging"
+ return
+ fi
+ fi
+
+ error "unknown file type"
+}
+
+function merge_dispatcher_uncertainty {
+ local indent=" ** "
+ local outputfile="${1:?"provide output filename"}"
+
+ local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
+ local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
+ if test ${nboutputdirs} -ne ${nboutputfiles}
+ then
+ warning "missing files"
+ if ! test "${2}" == "--force"
+ then
+ return
+ fi
+ fi
+
+ local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
+ local firstpartialoutputextension="${firstpartialoutputfile##*.}"
+
+ if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
+ then
+ if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
+ then
+ echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
+ ## search for sum
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ summed_merged_file=${mergedfile//-Uncertainty/}
+ if [ ! -f ${summed_merged_file} ];
+ then
+ warning "${summed_merged_file} does not exist. Error, no uncertainty computed"
+ return;
+ fi
+ echo "${indent}${summed_merged_file} found"
+ ## search for Squared
+ squared_merged_file=${mergedfile//-Uncertainty/-Squared}
+ if [ ! -f ${squared_merged_file} ];
+ then
+ warning "${squared_merged_file} does not exist. Error, no uncertainty computed"
+ return;
+ fi
+ echo "${indent}${squared_merged_file} found"
+ ## search for NumberOfEvent
+ totalEvents=0;
+ unamestr=`uname`
+ if [[ "$unamestr" == 'Darwin' ]]; then
+ files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
+ else
+ files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+ fi
+ echo $files
+ for outputfile in ${files}
+ do
+ #echo $outputfile
+ if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
+ then
+ totalEvents="$(grep "NumberOfEvents" "${outputdir}/${outputfile}" | cut -d' ' -f4)"
+ echo "${indent}Find the NumberOfEvent in $outputfile: ${totalEvents}"
+ fi
+ done
+
+ if test ${totalEvents} -gt 0
+ then
+ uncerImageMerger="clitkImageUncertainty"
+ test -x "./clitkImageUncertainty" && uncerImageMerger="./clitkImageUncertainty"
+ ${uncerImageMerger} -i ${summed_merged_file} -s ${squared_merged_file} -o ${mergedfile} -n ${totalEvents}
+ else
+ warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
+ return;
+ fi
+ else
+ error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
fi
fi
+}
+
+echo "!!!! this is $0 v0.3k !!!!"
+echo "Usage: gate_power_merge.sh run.dir [--force]"
+echo " where --force allows to merge files even if the file is missing in some output directories"
+
+rundir="${1?"provide run dir"}"
+force=${2:-""}
+rundir="$(echo "${rundir}" | sed 's|/*$||')"
+nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' -o -type l -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}"
- warning "unknown file type"
+unamestr=`uname`
+if [[ "$unamestr" == 'Darwin' ]]; then
+ files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
+else
+ files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+fi
+echo files $files
+for outputfile in ${files}
+do
+ merge_dispatcher "${outputfile}" "${force}"
+done
+
+echo ""
+echo "Merging done. Special case for statistical uncertainty"
+
+unamestr=`uname`
+if [[ "$unamestr" == 'Darwin' ]]; then
+ files=$(find -L "${outputdir}" -type f -regex ".*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
+else
+ files=$(find -L "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+fi
+echo files = $files
+for outputfile in ${files}
+do
+ merge_dispatcher_uncertainty "${outputfile}" "${force}"
done
+echo "compute job statistics"
+python computeEnlapsedTime.py ${rundir} gate
+mv "statJobs.txt" "${outputdir}/statJobs.txt"
+
+
+if [ -f "${rundir}/params.txt" ]
+then
+ echo "copying params file"
+ cp "${rundir}/params.txt" "${outputdir}/params.txt"
+fi
+
+if [ -d "${rundir}/mac" ]
+then
+ echo "copying mac folder"
+ cp -r "${rundir}/mac" "${outputdir}/mac"
+fi
+
+echo "these was ${warning_count} warning(s)"
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff