echo " ${indent}merged ${count} files"
}
-doseMerger="mergeDosePerEnegryFile.sh"
+doseMerger="mergeDosePerEnergyFile.sh"
test -x "./mergeDosePerEnergyFile.sh" && doseMerger="./mergeDosePerEnergyFile.sh"
function merge_dose {
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 ${partial}"
+ addWithoutPartialResult -i "${partial}" -o "${merged}"
+ 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}" -j "${count}" -o "${merged}"
+ end_bar
+ echo " ${indent}merged ${count} files"
+}
+
txtImageMerger="clitkMergeAsciiDoseActor"
test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
then
update_bar ${count} "copying first partial result ${partial}"
cp "${partial}" "${merged}"
- if test "$last_character" = "d"
+ if test "$last_character" = "d"
then
cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
fi
update_bar ${count} "adding ${partial}"
${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
- if test "$last_character" = "d"
+ 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##*.}")/" "${merged}"
local outputfile="${1:?"provide output filename"}"
echo "merging ${outputfile}"
- local partialoutputfiles="$(find "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
+ local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
if test ${nboutputdirs} -ne ${nboutputfiles}
then
warning "missing files"
- return
+ if ! test "${2}" == "--force"
+ then
+ return
+ fi
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' "${firstpartialoutputfile}"
+ if test "${firstpartialoutputextension}" == "hdr" && test grep -qs 'INTERFILE' "${firstpartialoutputfile}"
then
- echo "${indent}this is a interfile image"
+ 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)"
if test "${firstpartialoutputextension}" == "hdr"
then
- echo "${indent}this is a analyse image"
+ echo "${indent}this is an analyse image"
local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
return
fi
fi
+ if test "${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 "${indent}this is a non specific txt output"
local indent=" ** "
local outputfile="${1:?"provide output filename"}"
- local partialoutputfiles="$(find "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
+ local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
if test ${nboutputdirs} -ne ${nboutputfiles}
then
warning "missing files"
- return
+ if ! test "${2}" == "--force"
+ then
+ return
+ fi
fi
local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
then
- if test "${firstpartialoutputextension}" == "mhd"
+ if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
then
echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
## search for sum
echo "${indent}${squared_merged_file} found"
## search for NumberOfEvent
totalEvents=0;
- for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+ unamestr=`uname`
+ if [[ "$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}/${outputfile}"
warning "${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*' | wc -l)"
+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 ${nboutputdirs} partial output dirs"
test -d "${outputdir}" && rm -r "${outputdir}"
mkdir "${outputdir}"
-for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+unamestr=`uname`
+if [[ "$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}"
+ merge_dispatcher "${outputfile}" "${force}"
done
echo ""
echo "Merging done. Special case for statistical uncertainty"
-for outputfile in $(find "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+
+unamestr=`uname`
+if [[ "$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}"
+ 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