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}"
then
update_bar ${count} "copying first partial result ${partial}"
cp "${partial}" "${merged}"
- cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+ if test "$last_character" = "d"
+ then
+ cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+ fi
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}"
+ 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 ${count} files"
local outputfile="${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}" ${partialoutputfiles} || error "error while merging"
return
fi
- if test "${firstpartialoutputextension}" == "mhd"
+ if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
then
echo "${indent}this is a mhd image"
local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
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*' | 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 ${nboutputdirs} partial output dirs"
fi
outputdir="$(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 $NF; }' | sort | uniq)
+unamestr=`uname`
+if [[ "$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"
+
+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}" "${force}"
done
if [ -f "${rundir}/params.txt" ]
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