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 function check_interfile {
34 local input_interfile="${1:?"provide input interfile"}"
36 grep -qs '!INTERFILE :=' "${input_interfile}" || return 1
38 local header_byte_size=$(awk -F' ' '
40 /matrix size/ && $3 == "[1]" { xsize = $5; }
41 /matrix size/ && $3 == "[2]" { ysize = $5; }
42 /number of projections/ { zsize += $5; }
43 /number of bytes per pixel/ { byte_per_pixel = $7; }
44 END { print xsize * ysize * zsize * byte_per_pixel; }' "${input_interfile}")
46 local raw_interfile="$(dirname "${input_interfile}")/$(awk -F' := ' '/name of data file/ { print $2; }' "${input_interfile}")"
48 test -f "${raw_interfile}" || return 1
49 test $(stat -c%s "${raw_interfile}") -eq ${header_byte_size} || return 1
52 function write_mhd_header {
53 local input_interfile="${1:?"provide input interfile"}"
54 local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
56 check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
58 local header_start='ObjectType = Image
60 AcquisitionDate = none
62 BinaryDataByteOrderMSB = False
63 CompressedData = False
64 TransformMatrix = 1 0 0 0 1 0 0 0 1
66 CenterOfRotation = 0 0 0
68 AnatomicalOrientation = RIP'
70 echo "${header_start}" > "${output_mhd}"
73 /scaling factor/ && $4 == "[1]" { xspacing = $6; }
74 /scaling factor/ && $4 == "[2]" { yspacing = $6; }
75 END { print "ElementSpacing = " xspacing " " yspacing " 1"; }' "${input_interfile}" >> "${output_mhd}"
79 /matrix size/ && $3 == "[1]" { xsize = $5; }
80 /matrix size/ && $3 == "[2]" { ysize = $5; }
81 /number of projections/ { zsize += $5; }
82 END { print "DimSize = " xsize " " ysize " " zsize; }' "${input_interfile}" >> "${output_mhd}"
85 /number format/ { format = $2; }
86 /number of bytes per pixel/ { byte_per_pixel = $2 }
88 if (format == "unsigned integer" && byte_per_pixel == 8) { print "ElementType = MET_ULONG"; exit };
89 if (format == "unsigned integer" && byte_per_pixel == 4) { print "ElementType = MET_UINT"; exit };
90 if (format == "unsigned integer" && byte_per_pixel == 2) { print "ElementType = MET_USHORT"; exit };
91 if (format == "unsigned integer" && byte_per_pixel == 1) { print "ElementType = MET_UCHAR"; exit };
92 if (format == "integer" && byte_per_pixel == 8) { print "ElementType = MET_LONG"; exit };
93 if (format == "integer" && byte_per_pixel == 4) { print "ElementType = MET_INT"; exit };
94 if (format == "integer" && byte_per_pixel == 2) { print "ElementType = MET_SHORT"; exit };
95 if (format == "integer" && byte_per_pixel == 1) { print "ElementType = MET_CHAR"; exit };
96 if (format == "float" && byte_per_pixel == 8) { print "ElementType = MET_FLOAT"; exit };
97 if (format == "float" && byte_per_pixel == 4) { print "ElementType = MET_DOUBLE"; exit };
98 print "ElementType = MET_INT";
99 }' "${input_interfile}" >> "${output_mhd}"
102 /name of data file/ { print "ElementDataFile = " $2; }' "${input_interfile}" >> "${output_mhd}"
105 rootMerger="clitkMergeRootFiles"
106 test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
108 function merge_root {
111 echo " ${indent}entering root merger"
112 echo " ${indent}merger is ${rootMerger}"
113 echo " ${indent}creating ${merged}"
119 echo " ${indent}just one partial file => just copy it"
125 local arguments=" -o ${merged}"
131 local arguments=" -i ${partial} ${arguments}"
133 ${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
134 echo " ${indent}merged ${count} files"
137 statMerger="mergeStatFile.py"
138 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
140 function merge_stat {
143 echo " ${indent}entering stat merger"
144 echo " ${indent}merger is ${statMerger}"
145 echo " ${indent}creating ${merged}"
154 if test ! -f "${merged}"
156 update_bar ${count} "copying first partial result ${partial}"
157 cp "${partial}" "${merged}"
161 update_bar ${count} "adding ${partial}"
162 ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
165 echo " ${indent}merged ${count} files"
168 doseMerger="mergeDosePerEnegryFile.sh"
169 test -x "./mergeDosePerEnergyFile.sh" && doseMerger="./mergeDosePerEnergyFile.sh"
171 function merge_dose {
174 echo " ${indent}entering dose merger"
175 echo " ${indent}merger is ${doseMerger}"
176 echo " ${indent}creating ${merged}"
185 if test ! -f "${merged}"
187 update_bar ${count} "copying first partial result ${partial}"
188 cp "${partial}" "${merged}"
192 update_bar ${count} "adding ${partial}"
193 ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
196 echo " ${indent}merged ${count} files"
199 txtImageMerger="clitkMergeAsciiDoseActor"
200 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
202 function merge_txt_image {
205 echo " ${indent}entering text image merger"
206 echo " ${indent}merger is ${txtImageMerger}"
207 echo " ${indent}creating ${merged}"
216 if test ! -f "${merged}"
218 update_bar ${count} "copying first partial result ${partial}"
219 cp "${partial}" "${merged}"
223 update_bar ${count} "adding ${partial}"
224 local header="$(cat "${merged}" | head -n 6)"
225 local tmp="$(mktemp)"
226 ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
227 echo "${header}" > "${merged}"
228 grep -v '## Merge' "${tmp}" >> "${merged}"
232 echo " ${indent}merged ${count} files"
235 hdrImageMerger="clitkImageArithm"
236 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
238 function merge_hdr_image {
240 local merged_bin="${merged%.*}.img"
242 echo " ${indent}entering hdr image merger"
243 echo " ${indent}merger is ${hdrImageMerger}"
244 echo " ${indent}creating ${merged}"
250 local partial_bin="${partial%.*}.img"
254 if test ! -f "${merged}"
256 update_bar ${count} "copying first partial result ${partial}"
257 cp "${partial}" "${merged}"
258 cp "${partial_bin}" "${merged_bin}"
262 update_bar ${count} "adding ${partial}"
263 ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
266 echo " ${indent}merged ${count} files"
269 mhdImageMerger="clitkImageArithm"
270 test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
272 function merge_mhd_image {
274 local merged_bin="${merged%.*}.raw"
275 local last_character=${merged#${merged%?}}
277 echo " ${indent}entering mhd image merger"
278 echo " ${indent}merger is ${mhdImageMerger}"
279 echo " ${indent}creating ${merged}"
285 local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
289 if test ! -f "${merged}"
291 update_bar ${count} "copying first partial result ${partial}"
292 cp "${partial}" "${merged}"
293 if test "$last_character" = "d"
295 cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
300 update_bar ${count} "adding ${partial}"
301 ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
302 if test "$last_character" = "d" && test "${merged_bin}" != "${merged_bin%.*}.${partial_bin##*.}"
304 mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
305 sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
309 echo " ${indent}merged ${count} files"
312 function merge_dispatcher {
314 local outputfile="${1:?"provide output filename"}"
315 echo "merging ${outputfile}"
317 local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
318 local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
319 if test ${nboutputdirs} -ne ${nboutputfiles}
321 warning "missing files"
325 local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
326 local firstpartialoutputextension="${firstpartialoutputfile##*.}"
327 echo "${indent}testing file type on ${firstpartialoutputfile}"
329 if test "${firstpartialoutputextension}" == "hdr" && grep -qs 'INTERFILE' "${firstpartialoutputfile}"
331 echo "${indent}this is a interfile image"
332 echo "${indent}creating mhd headers"
333 for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
334 local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
335 local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
336 merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
337 echo "${indent}cleaning mhd headers"
338 for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done
339 rm "${mhd_mergedfile}"
340 echo "${indent}copy interfile header"
341 cp "${firstpartialoutputfile}" "${outputdir}"
345 if test "${firstpartialoutputextension}" == "hdr"
347 echo "${indent}this is a analyse image"
348 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
349 merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
353 if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
355 echo "${indent}this is a mhd image"
356 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
357 merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
361 if test "${firstpartialoutputextension}" == "root"
363 echo "${indent}this is a root file"
364 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
365 merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
369 if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
371 echo "${indent}this is a stat file"
372 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
373 merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
377 if test "${firstpartialoutputextension}" == "txt" && grep -qs 'energydose' "${firstpartialoutputfile}"
379 echo "${indent}this is a dose file"
380 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
381 merge_dose "${mergedfile}" ${partialoutputfiles} || error "error while merging"
387 if test "${firstpartialoutputextension}" == "txt" && grep -qs 'Resol' "${firstpartialoutputfile}"
389 local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
390 local resolx="$(echo "${resol}" | cut -d',' -f1)"
391 local resoly="$(echo "${resol}" | cut -d',' -f2)"
392 local resolz="$(echo "${resol}" | cut -d',' -f3)"
393 if test "${resol}" == "1,1,1"
395 echo "${indent}this is a txt integral value"
396 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
397 merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
400 if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
402 echo "${indent}this is a txt profile"
403 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
404 merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
409 if test "${firstpartialoutputextension}" == "txt"
411 echo "${indent}this is a non specific txt output"
412 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
413 local nbdifferent="$(md5sum ${partialoutputfiles} | awk '{ print $1; }' | sort | uniq | wc -l)"
414 echo " ${indent}${nbdifferent} different files"
415 if test ${nbdifferent} -gt 1
417 echo " ${indent}catting to ${mergedfile}"
418 cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
421 echo " ${indent}moving to ${mergedfile}"
422 cp "${firstpartialoutputfile}" "${mergedfile}" || error "error while merging"
427 error "unknown file type"
430 function merge_dispatcher_uncertainty {
432 local outputfile="${1:?"provide output filename"}"
434 local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
435 local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
436 if test ${nboutputdirs} -ne ${nboutputfiles}
438 warning "missing files"
442 local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
443 local firstpartialoutputextension="${firstpartialoutputfile##*.}"
445 if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
447 if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
449 echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
451 local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
452 summed_merged_file=${mergedfile//-Uncertainty/}
453 if [ ! -f ${summed_merged_file} ];
455 warning "${summed_merged_file} does not exist. Error, no uncertainty computed"
458 echo "${indent}${summed_merged_file} found"
459 ## search for Squared
460 squared_merged_file=${mergedfile//-Uncertainty/-Squared}
461 if [ ! -f ${squared_merged_file} ];
463 warning "${squared_merged_file} does not exist. Error, no uncertainty computed"
466 echo "${indent}${squared_merged_file} found"
467 ## search for NumberOfEvent
469 for outputfile in $(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
472 if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
474 totalEvents="$(grep "NumberOfEvents" "${outputdir}/${outputfile}" | cut -d' ' -f4)"
475 echo "${indent}Find the NumberOfEvent in $outputfile: ${totalEvents}"
479 if test ${totalEvents} -gt 0
481 uncerImageMerger="clitkImageUncertainty"
482 test -x "./clitkImageUncertainty" && uncerImageMerger="./clitkImageUncertainty"
483 ${uncerImageMerger} -i ${summed_merged_file} -s ${squared_merged_file} -o ${mergedfile} -n ${totalEvents}
485 warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
489 error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
495 echo "!!!! this is $0 v0.3k !!!!"
497 rundir="${1?"provide run dir"}"
498 rundir="$(echo "${rundir}" | sed 's|/*$||')"
499 nboutputdirs="$(find "${rundir}" -mindepth 1 -name 'output*' -type d -o -type l | wc -l)"
501 test ${nboutputdirs} -gt 0 || error "no output dir found"
502 echo "found ${nboutputdirs} partial output dirs"
505 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
507 outputdir="results.${rundir##*.}"
509 outputdir="$(basename "${outputdir}")"
510 echo "output dir is ${outputdir}"
512 test -d "${outputdir}" && rm -r "${outputdir}"
515 for outputfile in $(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
517 merge_dispatcher "${outputfile}"
521 echo "Merging done. Special case for statistical uncertainty"
522 for outputfile in $(find -L "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
524 merge_dispatcher_uncertainty "${outputfile}"
527 if [ -f "${rundir}/params.txt" ]
529 echo "copying params file"
530 cp "${rundir}/params.txt" "${outputdir}/params.txt"
533 echo "these was ${warning_count} warning(s)"