17 count_max="${1:?"provide count max"}"
21 local count="${1:?"provide count"}"
22 local message="${2:?"provide message"}"
23 local percent=$(echo "100*${count}/${count_max}" | bc)
24 #printf "[%03d/%03d] %3d%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
25 printf "[%03d/%03d] %3d%% %-80.80s\n" ${count} ${count_max} ${percent} "${message}"
33 rootMerger="clitkMergeRootFiles"
34 test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
39 echo " ${indent}entering root merger"
40 echo " ${indent}merger is ${rootMerger}"
41 echo " ${indent}creating ${merged}"
43 local arguments=" -o ${merged}"
49 local arguments=" -i ${partial} ${arguments}"
51 ${rootMerger} ${arguments} > /dev/null || { warning "error while calling ${rootMerger}" && return; }
52 echo " ${indent}merged ${count} files"
55 statMerger="mergeStatFile.py"
56 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
57 test -x "./mergeStatFile.py" && statMerger="./mergeStatFile.py"
62 echo " ${indent}entering stat merger"
63 echo " ${indent}merger is ${statMerger}"
64 echo " ${indent}creating ${merged}"
73 if test ! -f "${merged}"
75 update_bar ${count} "copying first partial result ${partial}"
76 cp "${partial}" "${merged}"
80 update_bar ${count} "adding ${partial}"
81 ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || { warning "error while calling ${statMerger}" && return; }
84 echo " ${indent}merged ${count} files"
87 txtImageMerger="clitkMergeAsciiDoseActor"
88 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
90 function merge_txt_image {
93 echo " ${indent}entering text image merger"
94 echo " ${indent}merger is ${txtImageMerger}"
95 echo " ${indent}creating ${merged}"
104 if test ! -f "${merged}"
106 update_bar ${count} "copying first partial result ${partial}"
107 cp "${partial}" "${merged}"
111 update_bar ${count} "adding ${partial}"
112 local header="$(cat "${merged}" | head -n 6)"
113 local tmp="$(mktemp)"
114 ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || { warning "error while calling ${txtImageMerger}" && return; }
115 echo "${header}" > "${merged}"
116 grep -v '## Merge' "${tmp}" >> "${merged}"
120 echo " ${indent}merged ${count} files"
123 hdrImageMerger="clitkImageArithm"
124 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
126 function merge_hdr_image {
128 local merged_bin="${merged%.*}.img"
130 echo " ${indent}entering hdr image merger"
131 echo " ${indent}merger is ${hdrImageMerger}"
132 echo " ${indent}creating ${merged}"
138 local partial_bin="${partial%.*}.img"
142 if test ! -f "${merged}"
144 update_bar ${count} "copying first partial result ${partial}"
145 cp "${partial}" "${merged}"
146 cp "${partial_bin}" "${merged_bin}"
150 update_bar ${count} "adding ${partial}"
151 ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || { warning "error while calling ${hdrImageMerger}" && return; }
154 echo " ${indent}merged ${count} files"
157 function merge_dispatcher {
159 local outputfile="${1:?"provide output filename"}"
160 echo "merging ${outputfile}"
162 local partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
163 local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
164 if test ${nboutputdirs} -ne ${nboutputfiles}
166 warning "missing files"
170 local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
171 local firstpartialoutputextension="${firstpartialoutputfile##*.}"
172 echo "${indent}testing file type on ${firstpartialoutputfile}"
174 if test "${firstpartialoutputextension}" == "hdr"
176 echo "${indent}this is a analyse image"
177 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
178 merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
182 if test "${firstpartialoutputextension}" == "root"
184 echo "${indent}this is a root file"
185 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
186 merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
190 if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
192 echo "${indent}this is a stat file"
193 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
194 merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
198 if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
200 local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
201 local resolx="$(echo "${resol}" | cut -d',' -f1)"
202 local resoly="$(echo "${resol}" | cut -d',' -f2)"
203 local resolz="$(echo "${resol}" | cut -d',' -f3)"
204 if test "${resol}" == "1,1,1"
206 echo "${indent}this is a txt integral value"
207 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
208 merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
211 if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
213 echo "${indent}this is a txt profile"
214 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
215 merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
220 warning "unknown file type"
223 rundir="${1?"provide run dir"}"
224 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
226 test ${nboutputdirs} -gt 0 || error "no output dir found"
227 echo "found ${nboutputdirs} partial output dirs"
230 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
232 outputdir="results.${rundir##*.}"
234 outputdir="$(basename "${outputdir}")"
235 echo "output dir is ${outputdir}"
236 test -d "${outputdir}" && rm -r "${outputdir}"
239 for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(hdr|root|txt)' | awk -F '/' '{ print $NF }' | sort | uniq)
241 merge_dispatcher "${outputfile}"
244 echo "these was ${warning_count} warning(s)"