cluster_tools/gate_power_merge.sh

   1 #!/usr/bin/env bash
   2
   3 set -u
   4
   5 function error {
   6     echo "ERROR: $1"
   7     exit 1
   8 }
   9
  10 warning_count=0
  11 function warning {
  12     let "warning_count++"
  13     echo "MERGE_WARNING: $1"
  14 }
  15
  16 function start_bar {
  17     count_max="${1:?"provide count max"}"
  18 }
  19
  20 function update_bar {
  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}"
  26 }
  27
  28 function end_bar {
  29     unset count_max
  30     #echo -ne '\n'
  31 }
  32
  33 function check_interfile {
  34     local input_interfile="${1:?"provide input interfile"}"
  35
  36     grep -qs '!INTERFILE :=' "${input_interfile}" || return 1
  37
  38     local header_byte_size=$(awk -F' ' '
  39 BEGIN { zsize = 0; }
  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}")
  45
  46     local raw_interfile="$(dirname "${input_interfile}")/$(awk -F' := ' '/name of data file/ { print $2; }' "${input_interfile}")"
  47
  48     test -f "${raw_interfile}" || return 1
  49     test $(stat -c%s "${raw_interfile}") -eq ${header_byte_size} || return 1
  50 }
  51
  52 function write_mhd_header {
  53     local input_interfile="${1:?"provide input interfile"}"
  54     local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
  55
  56     check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
  57
  58     local header_start='ObjectType = Image
  59 NDims = 3
  60 AcquisitionDate = none
  61 BinaryData = True
  62 BinaryDataByteOrderMSB = False
  63 CompressedData = False
  64 TransformMatrix = 1 0 0 0 1 0 0 0 1
  65 Offset = 0 0 0
  66 CenterOfRotation = 0 0 0
  67 DistanceUnits = mm
  68 AnatomicalOrientation = RIP'
  69
  70     echo "${header_start}" > "${output_mhd}"
  71
  72     awk -F' ' '
  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}"
  76
  77     awk -F' ' '
  78 BEGIN { zsize = 0; }
  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}"
  83
  84     awk -F' := ' '
  85 /number format/ { format = $2; }
  86 /number of bytes per pixel/ { byte_per_pixel = $2 }
  87 END {
  88 if (format == "unsigned integer" && byte_per_pixel == 8) { print "ElementType = MET_ULONG"; exit };
  89 if (format == "unsigned integer" && byte_per_pixel == 4) { print "ElementType = MET_UINT"; exit };
  90 if (format == "unsigned integer" && byte_per_pixel == 2) { print "ElementType = MET_USHORT"; exit };
  91 if (format == "unsigned integer" && byte_per_pixel == 1) { print "ElementType = MET_UCHAR"; exit };
  92 if (format == "integer" && byte_per_pixel == 8) { print "ElementType = MET_LONG"; exit };
  93 if (format == "integer" && byte_per_pixel == 4) { print "ElementType = MET_INT"; exit };
  94 if (format == "integer" && byte_per_pixel == 2) { print "ElementType = MET_SHORT"; exit };
  95 if (format == "integer" && byte_per_pixel == 1) { print "ElementType = MET_CHAR"; exit };
  96 if (format == "float" && byte_per_pixel == 8) { print "ElementType = MET_FLOAT"; exit };
  97 if (format == "float" && byte_per_pixel == 4) { print "ElementType = MET_DOUBLE"; exit };
  98 print "ElementType = MET_INT";
  99 }' "${input_interfile}" >> "${output_mhd}"
 100
 101     awk -F' := ' '
 102 /name of data file/ { print "ElementDataFile = " $2; }' "${input_interfile}" >> "${output_mhd}"
 103 }
 104
 105 rootMerger="clitkMergeRootFiles"
 106 test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
 107
 108 function merge_root {
 109     local merged="$1"
 110     shift
 111     echo "  ${indent}entering root merger"
 112     echo "  ${indent}merger is ${rootMerger}"
 113     echo "  ${indent}creating ${merged}"
 114     #echo "######## $#"
 115     #echo "######## $*"
 116
 117     if test $# -eq 1
 118     then
 119         echo "  ${indent}just one partial file => just copy it"
 120         cp "$1" "${merged}"
 121         return
 122     fi
 123
 124     local count=0
 125     local arguments=" -o ${merged}"
 126     while test $# -gt 0
 127     do
 128         local partial="$1"
 129         shift
 130         let count++
 131         local arguments=" -i ${partial} ${arguments}"
 132     done
 133     ${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
 134     echo "  ${indent}merged ${count} files"
 135 }
 136
 137 statMerger="mergeStatFile.py"
 138 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
 139
 140 function merge_stat {
 141     local merged="$1"
 142     shift
 143     echo "  ${indent}entering stat merger"
 144     echo "  ${indent}merger is ${statMerger}"
 145     echo "  ${indent}creating ${merged}"
 146     local count=0
 147     start_bar $#
 148     while test $# -gt 0
 149     do
 150         local partial="$1"
 151         shift
 152         let count++
 153
 154         if test ! -f "${merged}"
 155         then
 156             update_bar ${count} "copying first partial result ${partial}"
 157             cp "${partial}" "${merged}"
 158             continue
 159         fi
 160
 161         update_bar ${count} "adding ${partial}"
 162         ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
 163     done
 164     end_bar
 165     echo "  ${indent}merged ${count} files"
 166 }
 167
 168 doseMerger="mergeDosePerEnergyFile.sh"
 169 test -x "./mergeDosePerEnergyFile.sh" && doseMerger="./mergeDosePerEnergyFile.sh"
 170
 171 function merge_dose {
 172     local merged="$1"
 173     shift
 174     echo "  ${indent}entering dose merger"
 175     echo "  ${indent}merger is ${doseMerger}"
 176     echo "  ${indent}creating ${merged}"
 177     local count=0
 178     start_bar $#
 179     while test $# -gt 0
 180     do
 181         local partial="$1"
 182         shift
 183         let count++
 184
 185         if test ! -f "${merged}"
 186         then
 187             update_bar ${count} "copying first partial result ${partial}"
 188             cp "${partial}" "${merged}"
 189             continue
 190         fi
 191
 192         update_bar ${count} "adding ${partial}"
 193         ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
 194     done
 195     end_bar
 196     echo "  ${indent}merged ${count} files"
 197 }
 198
 199 doseMerger="mergeDoseByRegions.sh"
 200 test -x "./mergeDoseByRegions.sh" && doseMerger="./mergeDoseByRegions.sh"
 201
 202 function merge_doseByRegions {
 203     local merged="$1"
 204     shift
 205     echo "  ${indent}entering dose merger"
 206     echo "  ${indent}merger is ${doseMerger}"
 207     echo "  ${indent}creating ${merged}"
 208     local count=0
 209     start_bar $#
 210     source ${doseMerger}
 211     while test $# -gt 0
 212     do
 213         local partial="$1"
 214         shift
 215         let count++
 216
 217         if test ! -f "${merged}"
 218         then
 219             update_bar ${count} "copying first partial result ${partial}"
 220             addWithoutPartialResult -i "${partial}" -o "${merged}"
 221             continue
 222         fi
 223
 224         update_bar ${count} "adding ${partial}"
 225         addToPartialResult -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
 226     done
 227     divideUncertaintyResult -i "${merged}" -j "${count}" -o "${merged}"
 228     end_bar
 229     echo "  ${indent}merged ${count} files"
 230 }
 231
 232 txtImageMerger="clitkMergeAsciiDoseActor"
 233 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 234
 235 function merge_txt_image {
 236     local merged="$1"
 237     shift
 238     echo "  ${indent}entering text image merger"
 239     echo "  ${indent}merger is ${txtImageMerger}"
 240     echo "  ${indent}creating ${merged}"
 241     local count=0
 242     start_bar $#
 243     while test $# -gt 0
 244     do
 245         local partial="$1"
 246         shift
 247         let count++
 248
 249         if test ! -f "${merged}"
 250         then
 251             update_bar ${count} "copying first partial result ${partial}"
 252             cp "${partial}" "${merged}"
 253             continue
 254         fi
 255
 256         update_bar ${count} "adding ${partial}"
 257         local header="$(cat "${merged}" | head -n 6)"
 258         local tmp="$(mktemp)"
 259         ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
 260         echo "${header}" > "${merged}"
 261         grep -v '## Merge' "${tmp}" >> "${merged}"
 262         rm "${tmp}"
 263     done
 264     end_bar
 265     echo "  ${indent}merged ${count} files"
 266 }
 267
 268 hdrImageMerger="clitkImageArithm"
 269 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
 270
 271 function merge_hdr_image {
 272     local merged="$1"
 273     local merged_bin="${merged%.*}.img"
 274     shift
 275     echo "  ${indent}entering hdr image merger"
 276     echo "  ${indent}merger is ${hdrImageMerger}"
 277     echo "  ${indent}creating ${merged}"
 278     local count=0
 279     start_bar $#
 280     while test $# -gt 0
 281     do
 282         local partial="$1"
 283         local partial_bin="${partial%.*}.img"
 284         shift
 285         let count++
 286
 287         if test ! -f "${merged}"
 288         then
 289             update_bar ${count} "copying first partial result ${partial}"
 290             cp "${partial}" "${merged}"
 291             cp "${partial_bin}" "${merged_bin}"
 292             continue
 293         fi
 294
 295         update_bar ${count} "adding ${partial}"
 296         ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
 297     done
 298     end_bar
 299     echo "  ${indent}merged ${count} files"
 300 }
 301
 302 mhdImageMerger="clitkImageArithm"
 303 test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
 304
 305 function merge_mhd_image {
 306     local merged="$1"
 307     local merged_bin="${merged%.*}.raw"
 308     local last_character=${merged#${merged%?}}
 309     shift
 310     echo "  ${indent}entering mhd image merger"
 311     echo "  ${indent}merger is ${mhdImageMerger}"
 312     echo "  ${indent}creating ${merged}"
 313     local count=0
 314     start_bar $#
 315     while test $# -gt 0
 316     do
 317         local partial="$1"
 318         local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
 319         shift
 320         let count++
 321
 322         if test ! -f "${merged}"
 323         then
 324             update_bar ${count} "copying first partial result ${partial}"
 325             cp "${partial}" "${merged}"
 326             if test "$last_character" = "d"
 327             then
 328                 cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
 329             fi
 330             continue
 331         fi
 332
 333         update_bar ${count} "adding ${partial}"
 334         ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
 335         if test "$last_character" = "d" && test "${merged_bin}" != "${merged_bin%.*}.${partial_bin##*.}"
 336         then
 337             mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
 338             sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
 339         fi
 340     done
 341     end_bar
 342     echo "  ${indent}merged ${count} files"
 343 }
 344
 345 function merge_dispatcher {
 346     local indent="  ** "
 347     local outputfile="${1:?"provide output filename"}"
 348     echo "merging ${outputfile}"
 349
 350     local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
 351     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 352     if test ${nboutputdirs} -ne ${nboutputfiles}
 353     then
 354         warning "missing files"
 355         if ! test "${2}" == "--force"
 356         then
 357             return
 358         fi
 359     fi
 360
 361     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 362     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 363     echo "${indent}testing file type on ${firstpartialoutputfile}"
 364
 365     if test "${firstpartialoutputextension}" == "hdr" && test grep -qs 'INTERFILE' "${firstpartialoutputfile}"
 366     then
 367         echo "${indent}this is an interfile image"
 368         echo "${indent}creating mhd headers"
 369         for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
 370         local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
 371         local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
 372         merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
 373         echo "${indent}cleaning mhd headers"
 374         for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done
 375         rm "${mhd_mergedfile}"
 376         echo "${indent}copy interfile header"
 377         cp "${firstpartialoutputfile}" "${outputdir}"
 378         return
 379     fi
 380
 381     if test "${firstpartialoutputextension}" == "hdr"
 382     then
 383         echo "${indent}this is an analyse image"
 384         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 385         merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 386         return
 387     fi
 388
 389     if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
 390     then
 391         echo "${indent}this is a mhd image"
 392         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 393         merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 394         return
 395     fi
 396
 397     if test "${firstpartialoutputextension}" == "root"
 398     then
 399         echo "${indent}this is a root file"
 400         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 401         merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 402         return
 403     fi
 404
 405     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
 406     then
 407         echo "${indent}this is a stat file"
 408         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 409         merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 410         return
 411     fi
 412
 413     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'energydose' "${firstpartialoutputfile}"
 414     then
 415         echo "${indent}this is a dose file"
 416         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 417         merge_dose "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 418         return
 419     fi
 420
 421
 422
 423     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'Resol' "${firstpartialoutputfile}"
 424     then
 425         local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
 426         local resolx="$(echo "${resol}" | cut -d',' -f1)"
 427         local resoly="$(echo "${resol}" | cut -d',' -f2)"
 428         local resolz="$(echo "${resol}" | cut -d',' -f3)"
 429         if test "${resol}" == "1,1,1"
 430         then
 431             echo "${indent}this is a txt integral value"
 432             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 433             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 434             return
 435         fi
 436         if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
 437         then
 438             echo "${indent}this is a txt profile"
 439             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 440             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 441             return
 442         fi
 443     fi
 444
 445     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'vol(mm3)' "${firstpartialoutputfile}"
 446     then
 447         echo "${indent}this is a DoseByRegions file"
 448         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 449         merge_doseByRegions "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 450         return
 451     fi
 452
 453
 454     if test "${firstpartialoutputextension}" == "txt"
 455     then
 456         echo "${indent}this is a non specific txt output"
 457         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 458         local nbdifferent="$(md5sum ${partialoutputfiles} | awk '{ print $1; }' | sort | uniq | wc -l)"
 459         echo "  ${indent}${nbdifferent} different files"
 460         if test ${nbdifferent} -gt 1
 461         then
 462             echo "  ${indent}catting to ${mergedfile}"
 463             cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
 464             return
 465         else
 466             echo "  ${indent}moving to ${mergedfile}"
 467             cp "${firstpartialoutputfile}" "${mergedfile}" || error "error while merging"
 468             return
 469         fi
 470     fi
 471
 472     error "unknown file type"
 473 }
 474
 475 function merge_dispatcher_uncertainty {
 476     local indent="  ** "
 477     local outputfile="${1:?"provide output filename"}"
 478
 479     local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
 480     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 481     if test ${nboutputdirs} -ne ${nboutputfiles}
 482     then
 483         warning "missing files"
 484         if ! test "${2}" == "--force"
 485         then
 486             return
 487         fi
 488     fi
 489
 490     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 491     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 492
 493     if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
 494     then
 495           if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
 496         then
 497             echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
 498             ## search for sum
 499             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 500             summed_merged_file=${mergedfile//-Uncertainty/}
 501             if [ ! -f ${summed_merged_file} ];
 502             then
 503                 warning "${summed_merged_file} does not exist. Error, no uncertainty computed"
 504                 return;
 505             fi
 506             echo "${indent}${summed_merged_file} found"
 507             ## search for Squared
 508             squared_merged_file=${mergedfile//-Uncertainty/-Squared}
 509             if [ ! -f ${squared_merged_file} ];
 510             then
 511                 warning "${squared_merged_file} does not exist. Error, no uncertainty computed"
 512                 return;
 513             fi
 514             echo "${indent}${squared_merged_file} found"
 515             ## search for NumberOfEvent
 516             totalEvents=0;
 517             unamestr=`uname`
 518             if [[ "$unamestr" == 'Darwin' ]]; then
 519                 files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 520             else
 521                 files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 522             fi
 523             echo $files
 524             for outputfile in ${files}
 525             do
 526                 #echo $outputfile
 527                 if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
 528                 then
 529                     totalEvents="$(grep "NumberOfEvents" "${outputdir}/${outputfile}" | cut -d' ' -f4)"
 530                     echo "${indent}Find the NumberOfEvent in $outputfile: ${totalEvents}"
 531                 fi
 532             done
 533
 534             if test ${totalEvents} -gt 0
 535             then
 536                 uncerImageMerger="clitkImageUncertainty"
 537                 test -x "./clitkImageUncertainty" && uncerImageMerger="./clitkImageUncertainty"
 538                 ${uncerImageMerger} -i ${summed_merged_file} -s ${squared_merged_file} -o ${mergedfile} -n ${totalEvents}
 539             else
 540                 warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
 541                 return;
 542             fi
 543               else
 544             error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
 545         fi
 546     fi
 547
 548 }
 549
 550 echo "!!!! this is $0 v0.3k !!!!"
 551 echo "Usage: gate_power_merge.sh run.dir [--force]"
 552 echo "   where --force allows to merge files even if the file is missing in some output directories"
 553
 554 rundir="${1?"provide run dir"}"
 555 force=${2:-""}
 556 rundir="$(echo "${rundir}" | sed 's|/*$||')"
 557 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' -o -type l -name 'output*' | wc -l)"
 558
 559 test ${nboutputdirs} -gt 0 || error "no output dir found"
 560 echo "found ${nboutputdirs} partial output dirs"
 561
 562 outputdir="results"
 563 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
 564 then
 565     outputdir="results.${rundir##*.}"
 566 fi
 567 outputdir="$(basename "${outputdir}")"
 568 echo "output dir is ${outputdir}"
 569
 570 test -d "${outputdir}" && rm -r "${outputdir}"
 571 mkdir "${outputdir}"
 572
 573 unamestr=`uname`
 574 if [[ "$unamestr" == 'Darwin' ]]; then
 575     files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 576 else
 577     files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 578 fi
 579 echo files $files
 580 for outputfile in ${files}
 581 do
 582     merge_dispatcher "${outputfile}" "${force}"
 583 done
 584
 585 echo ""
 586 echo "Merging done. Special case for statistical uncertainty"
 587
 588 unamestr=`uname`
 589 if [[ "$unamestr" == 'Darwin' ]]; then
 590     files=$(find -L "${outputdir}" -type f -regex ".*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 591 else
 592     files=$(find -L "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 593 fi
 594 echo files = $files
 595 for outputfile in ${files}
 596 do
 597     merge_dispatcher_uncertainty "${outputfile}" "${force}"
 598 done
 599
 600 echo "compute job statistics"
 601 python computeEnlapsedTime.py ${rundir} gate
 602 mv "statJobs.txt" "${outputdir}/statJobs.txt"
 603
 604
 605 if [ -f "${rundir}/params.txt" ]
 606 then
 607     echo "copying params file"
 608     cp "${rundir}/params.txt" "${outputdir}/params.txt"
 609 fi
 610
 611 if [ -d "${rundir}/mac" ]
 612 then
 613     echo "copying mac folder"
 614     cp -r "${rundir}/mac" "${outputdir}/mac"
 615 fi
 616
 617 echo "these was ${warning_count} warning(s)"