13 echo "MERGE_WARNING: $1"
17 count_max="${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}"
47 echo " ${indent}just one partial file => just copy it"
53 local arguments=" -o ${merged}"
59 local arguments=" -i ${partial} ${arguments}"
61 ${rootMerger} ${arguments} > /dev/null || warning "error while calling ${rootMerger}"
62 echo " ${indent}merged ${count} files"
65 statMerger="mergeStatFile.py"
66 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
71 echo " ${indent}entering stat merger"
72 echo " ${indent}merger is ${statMerger}"
73 echo " ${indent}creating ${merged}"
82 if test ! -f "${merged}"
84 update_bar ${count} "copying first partial result ${partial}"
85 cp "${partial}" "${merged}"
89 update_bar ${count} "adding ${partial}"
90 ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
93 echo " ${indent}merged ${count} files"
96 txtImageMerger="clitkMergeAsciiDoseActor"
97 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
99 function merge_txt_image {
102 echo " ${indent}entering text image merger"
103 echo " ${indent}merger is ${txtImageMerger}"
104 echo " ${indent}creating ${merged}"
113 if test ! -f "${merged}"
115 update_bar ${count} "copying first partial result ${partial}"
116 cp "${partial}" "${merged}"
120 update_bar ${count} "adding ${partial}"
121 local header="$(cat "${merged}" | head -n 6)"
122 local tmp="$(mktemp)"
123 ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
124 echo "${header}" > "${merged}"
125 grep -v '## Merge' "${tmp}" >> "${merged}"
129 echo " ${indent}merged ${count} files"
132 hdrImageMerger="clitkImageArithm"
133 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
135 function merge_hdr_image {
137 local merged_bin="${merged%.*}.img"
139 echo " ${indent}entering hdr image merger"
140 echo " ${indent}merger is ${hdrImageMerger}"
141 echo " ${indent}creating ${merged}"
147 local partial_bin="${partial%.*}.img"
151 if test ! -f "${merged}"
153 update_bar ${count} "copying first partial result ${partial}"
154 cp "${partial}" "${merged}"
155 cp "${partial_bin}" "${merged_bin}"
159 update_bar ${count} "adding ${partial}"
160 ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
163 echo " ${indent}merged ${count} files"
166 mhdImageMerger="clitkImageArithm"
167 test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
169 function merge_mhd_image {
171 local merged_bin="${merged%.*}.img"
173 echo " ${indent}entering mhd image merger"
174 echo " ${indent}merger is ${mhdImageMerger}"
175 echo " ${indent}creating ${merged}"
181 local partial_bin="${partial%.*}.raw"
185 if test ! -f "${merged}"
187 update_bar ${count} "copying first partial result ${partial}"
188 cp "${partial}" "${merged}"
189 cp "${partial_bin}" "${merged_bin}"
193 update_bar ${count} "adding ${partial}"
194 ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
197 echo " ${indent}merged ${count} files"
200 function merge_dispatcher {
202 local outputfile="${1:?"provide output filename"}"
203 echo "merging ${outputfile}"
205 local partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
206 local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
207 if test ${nboutputdirs} -ne ${nboutputfiles}
209 warning "missing files"
213 local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
214 local firstpartialoutputextension="${firstpartialoutputfile##*.}"
215 echo "${indent}testing file type on ${firstpartialoutputfile}"
217 if test "${firstpartialoutputextension}" == "hdr"
219 echo "${indent}this is a analyse image"
220 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
221 merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
225 if test "${firstpartialoutputextension}" == "mhd"
227 echo "${indent}this is a mhd image"
228 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
229 merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
233 if test "${firstpartialoutputextension}" == "root"
235 echo "${indent}this is a root file"
236 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
237 merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
241 if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
243 echo "${indent}this is a stat file"
244 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
245 merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
249 if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
251 local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
252 local resolx="$(echo "${resol}" | cut -d',' -f1)"
253 local resoly="$(echo "${resol}" | cut -d',' -f2)"
254 local resolz="$(echo "${resol}" | cut -d',' -f3)"
255 if test "${resol}" == "1,1,1"
257 echo "${indent}this is a txt integral value"
258 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
259 merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
262 if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
264 echo "${indent}this is a txt profile"
265 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
266 merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
271 if test "${firstpartialoutputextension}" == "txt"
273 echo "${indent}this is a non specific txt output"
274 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
275 echo " ${indent}catting ${mergedfile}"
276 cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
280 warning "unknown file type"
283 echo "!!!! this is $0 v0.3h !!!!"
285 rundir="${1?"provide run dir"}"
286 rundir="$(echo "${rundir}" | sed 's|/*$||')"
287 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
289 test ${nboutputdirs} -gt 0 || error "no output dir found"
290 echo "found ${nboutputdirs} partial output dirs"
293 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
295 outputdir="results.${rundir##*.}"
297 outputdir="$(basename "${outputdir}")"
298 echo "output dir is ${outputdir}"
299 test -d "${outputdir}" && rm -r "${outputdir}"
302 for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
304 merge_dispatcher "${outputfile}"
307 if [ -f "${rundir}/params.txt" ]
309 echo "copying params file"
310 cp "${rundir}/params.txt" "${outputdir}/params.txt"
313 echo "these was ${warning_count} warning(s)"