warning_count=0
function warning {
let "warning_count++"
-echo "WARNING: $1"
+echo "MERGE_WARNING: $1"
}
function start_bar {
#echo -ne '\n'
}
+function check_interfile {
+local input_interfile="${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"
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
let count++
local arguments=" -i ${partial} ${arguments}"
done
-${rootMerger} ${arguments} > /dev/null || { warning "error while calling ${rootMerger}" && return; }
+${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
echo " ${indent}merged ${count} files"
}
statMerger="mergeStatFile.py"
test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
-test -x "./mergeStatFile.py" && statMerger="./mergeStatFile.py"
function merge_stat {
local merged="$1"
fi
update_bar ${count} "adding ${partial}"
- ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || { warning "error while calling ${statMerger}" && return; }
+ ${statMerger} -i "${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"
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}" && return; }
+ ${txtImageMerger} -i "${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}"
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}" && return; }
+ ${hdrImageMerger} -t 0 -i "${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 ${count} files"
local outputfile="${1:?"provide output filename"}"
echo "merging ${outputfile}"
- local partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
+ local partialoutputfiles="$(find "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
if test ${nboutputdirs} -ne ${nboutputfiles}
then
local firstpartialoutputextension="${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"
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 "${indent}this is a root file"
return
fi
- if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
+ if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
then
echo "${indent}this is a stat file"
local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
return
fi
- if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
+ if test "${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)"
fi
fi
- warning "unknown file type"
+ 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 ${nboutputdirs} -gt 0 || error "no output dir found"
test -d "${outputdir}" && rm -r "${outputdir}"
mkdir "${outputdir}"
-for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(hdr|root|txt)' | awk -F '/' '{ print $NF }' | sort | uniq)
+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
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff