15 count_max="${1:?"provide count max"}"
19 local count="${1:?"provide count"}"
20 local message="${2:?"provide message"}"
21 local percent=$(echo "100*${count}/${count_max}" | bc)
22 printf "[%03d/%03d] %3d%% %-80s\r" ${count} ${count_max} ${percent} "${message}"
30 rootMerger="clitkMergeRootFiles"
31 test -f "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
36 echo " ${indent}entering root merger"
37 echo " ${indent}merger is ${rootMerger}"
38 echo " ${indent}creating ${merged}"
40 local arguments=" -o ${merged}"
46 local arguments=" -i ${partial} ${arguments}"
48 ${rootMerger} ${arguments} 2> /dev/null > /dev/null || error "error while calling ${rootMerger}"
49 echo " ${indent}merged ${count} files"
52 statMerger="mergeStatFile.py"
53 test -f "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
58 echo " ${indent}entering stat merger"
59 echo " ${indent}merger is ${statMerger}"
60 echo " ${indent}creating ${merged}"
69 if test ! -f "${merged}"
71 update_bar ${count} "copying first partial result ${partial}"
72 cp "${partial}" "${merged}"
76 update_bar ${count} "adding ${partial}"
77 ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" > /dev/null || error "error while calling ${statMerger}"
80 echo " ${indent}merged ${count} files"
83 txtImageMerger="clitkMergeAsciiDoseActor"
84 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
86 function merge_txt_image {
89 echo " ${indent}entering text image merger"
90 echo " ${indent}merger is ${txtImageMerger}"
91 echo " ${indent}creating ${merged}"
100 if test ! -f "${merged}"
102 update_bar ${count} "copying first partial result ${partial}"
103 cp "${partial}" "${merged}"
107 update_bar ${count} "adding ${partial}"
108 local header="$(cat "${merged}" | head -n 6)"
109 local tmp="$(mktemp)"
110 ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" > /dev/null || error "error while calling ${txtImageMerger}"
111 echo "${header}" > "${merged}"
112 grep -v '## Merge' "${tmp}" >> "${merged}"
116 echo " ${indent}merged ${count} files"
119 hdrImageMerger="clitkImageArithm"
120 test -f "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
122 function merge_hdr_image {
124 local merged_bin="${merged%.*}.img"
126 echo " ${indent}entering hdr image merger"
127 echo " ${indent}merger is ${hdrImageMerger}"
128 echo " ${indent}creating ${merged}"
134 local partial_bin="${partial%.*}.img"
138 if test ! -f "${merged}"
140 update_bar ${count} "copying first partial result ${partial}"
141 cp "${partial}" "${merged}"
142 cp "${partial_bin}" "${merged_bin}"
146 update_bar ${count} "adding ${partial}"
147 ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || error "error while calling ${hdrImageMerger}"
150 echo " ${indent}merged ${count} files"
153 rundir="${1?"provide run dir"}"
154 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
156 test ${nboutputdirs} -gt 0 || error "no output dir found"
157 echo "found ${nboutputdirs} partial output dirs"
160 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
162 outputdir="results.${rundir##*.}"
164 outputdir="$(basename "${outputdir}")"
165 echo "output dir is ${outputdir}"
166 test -d "${outputdir}" && rm -r "${outputdir}"
169 for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(hdr|root|txt)' | awk -F '/' '{ print $NF }' | sort | uniq)
172 echo "merging ${outputfile}"
174 partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
175 nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
176 if test ${nboutputdirs} -ne ${nboutputfiles}
178 warning "missing files"
182 firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
183 firstpartialoutputextension="${firstpartialoutputfile##*.}"
184 echo "${indent}testing file type on ${firstpartialoutputfile}"
186 if test "${firstpartialoutputextension}" == "hdr"
188 echo "${indent}this is a analyse image"
189 mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
190 merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
194 if test "${firstpartialoutputextension}" == "root"
196 echo "${indent}this is a root file"
197 mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
198 merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
202 if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
204 echo "${indent}this is a stat file"
205 mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
206 merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
210 if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
212 resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
213 resolx="$(echo "${resol}" | cut -d',' -f1)"
214 resoly="$(echo "${resol}" | cut -d',' -f2)"
215 resolz="$(echo "${resol}" | cut -d',' -f3)"
216 if test "${resol}" == "1,1,1"
218 echo "${indent}this is a txt integral value"
219 mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
220 merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
223 if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
225 echo "${indent}this is a txt profile"
226 mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
227 merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
233 warning "unknown file type"