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     while test $# -gt 0
 211     do
 212         local partial="$1"
 213         shift
 214         let count++
 215
 216         if test ! -f "${merged}"
 217         then
 218             update_bar ${count} "copying first partial result ${partial}"
 219             cp "${partial}" "${merged}"
 220             continue
 221         fi
 222
 223         update_bar ${count} "adding ${partial}"
 224         ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
 225     done
 226     end_bar
 227     echo "  ${indent}merged ${count} files"
 228 }
 229
 230 txtImageMerger="clitkMergeAsciiDoseActor"
 231 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 232
 233 function merge_txt_image {
 234     local merged="$1"
 235     shift
 236     echo "  ${indent}entering text image merger"
 237     echo "  ${indent}merger is ${txtImageMerger}"
 238     echo "  ${indent}creating ${merged}"
 239     local count=0
 240     start_bar $#
 241     while test $# -gt 0
 242     do
 243         local partial="$1"
 244         shift
 245         let count++
 246
 247         if test ! -f "${merged}"
 248         then
 249             update_bar ${count} "copying first partial result ${partial}"
 250             cp "${partial}" "${merged}"
 251             continue
 252         fi
 253
 254         update_bar ${count} "adding ${partial}"
 255         local header="$(cat "${merged}" | head -n 6)"
 256         local tmp="$(mktemp)"
 257         ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
 258         echo "${header}" > "${merged}"
 259         grep -v '## Merge' "${tmp}" >> "${merged}"
 260         rm "${tmp}"
 261     done
 262     end_bar
 263     echo "  ${indent}merged ${count} files"
 264 }
 265
 266 hdrImageMerger="clitkImageArithm"
 267 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
 268
 269 function merge_hdr_image {
 270     local merged="$1"
 271     local merged_bin="${merged%.*}.img"
 272     shift
 273     echo "  ${indent}entering hdr image merger"
 274     echo "  ${indent}merger is ${hdrImageMerger}"
 275     echo "  ${indent}creating ${merged}"
 276     local count=0
 277     start_bar $#
 278     while test $# -gt 0
 279     do
 280         local partial="$1"
 281         local partial_bin="${partial%.*}.img"
 282         shift
 283         let count++
 284
 285         if test ! -f "${merged}"
 286         then
 287             update_bar ${count} "copying first partial result ${partial}"
 288             cp "${partial}" "${merged}"
 289             cp "${partial_bin}" "${merged_bin}"
 290             continue
 291         fi
 292
 293         update_bar ${count} "adding ${partial}"
 294         ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
 295     done
 296     end_bar
 297     echo "  ${indent}merged ${count} files"
 298 }
 299
 300 mhdImageMerger="clitkImageArithm"
 301 test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
 302
 303 function merge_mhd_image {
 304     local merged="$1"
 305     local merged_bin="${merged%.*}.raw"
 306     local last_character=${merged#${merged%?}}
 307     shift
 308     echo "  ${indent}entering mhd image merger"
 309     echo "  ${indent}merger is ${mhdImageMerger}"
 310     echo "  ${indent}creating ${merged}"
 311     local count=0
 312     start_bar $#
 313     while test $# -gt 0
 314     do
 315         local partial="$1"
 316         local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
 317         shift
 318         let count++
 319
 320         if test ! -f "${merged}"
 321         then
 322             update_bar ${count} "copying first partial result ${partial}"
 323             cp "${partial}" "${merged}"
 324             if test "$last_character" = "d"
 325             then
 326                 cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
 327             fi
 328             continue
 329         fi
 330
 331         update_bar ${count} "adding ${partial}"
 332         ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
 333         if test "$last_character" = "d" && test "${merged_bin}" != "${merged_bin%.*}.${partial_bin##*.}"
 334         then
 335             mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
 336             sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
 337         fi
 338     done
 339     end_bar
 340     echo "  ${indent}merged ${count} files"
 341 }
 342
 343 function merge_dispatcher {
 344     local indent="  ** "
 345     local outputfile="${1:?"provide output filename"}"
 346     echo "merging ${outputfile}"
 347
 348     local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
 349     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 350     if test ${nboutputdirs} -ne ${nboutputfiles}
 351     then
 352         warning "missing files"
 353         if ! test "${2}" == "--force"
 354         then
 355             return
 356         fi
 357     fi
 358
 359     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 360     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 361     echo "${indent}testing file type on ${firstpartialoutputfile}"
 362
 363     if test "${firstpartialoutputextension}" == "hdr" && test grep -qs 'INTERFILE' "${firstpartialoutputfile}"
 364     then
 365         echo "${indent}this is an interfile image"
 366         echo "${indent}creating mhd headers"
 367         for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
 368         local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
 369         local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
 370         merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
 371         echo "${indent}cleaning mhd headers"
 372         for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done
 373         rm "${mhd_mergedfile}"
 374         echo "${indent}copy interfile header"
 375         cp "${firstpartialoutputfile}" "${outputdir}"
 376         return
 377     fi
 378
 379     if test "${firstpartialoutputextension}" == "hdr"
 380     then
 381         echo "${indent}this is an analyse image"
 382         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 383         merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 384         return
 385     fi
 386
 387     if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
 388     then
 389         echo "${indent}this is a mhd image"
 390         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 391         merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 392         return
 393     fi
 394
 395     if test "${firstpartialoutputextension}" == "root"
 396     then
 397         echo "${indent}this is a root file"
 398         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 399         merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 400         return
 401     fi
 402
 403     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
 404     then
 405         echo "${indent}this is a stat file"
 406         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 407         merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 408         return
 409     fi
 410
 411     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'energydose' "${firstpartialoutputfile}"
 412     then
 413         echo "${indent}this is a dose file"
 414         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 415         merge_dose "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 416         return
 417     fi
 418
 419
 420
 421     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'Resol' "${firstpartialoutputfile}"
 422     then
 423         local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
 424         local resolx="$(echo "${resol}" | cut -d',' -f1)"
 425         local resoly="$(echo "${resol}" | cut -d',' -f2)"
 426         local resolz="$(echo "${resol}" | cut -d',' -f3)"
 427         if test "${resol}" == "1,1,1"
 428         then
 429             echo "${indent}this is a txt integral value"
 430             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 431             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 432             return
 433         fi
 434         if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
 435         then
 436             echo "${indent}this is a txt profile"
 437             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 438             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 439             return
 440         fi
 441     fi
 442
 443     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'vol(mm3)' "${firstpartialoutputfile}"
 444     then
 445         echo "${indent}this is a DoseByRegions file"
 446         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 447         merge_doseByRegions "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 448         return
 449     fi
 450
 451
 452     if test "${firstpartialoutputextension}" == "txt"
 453     then
 454         echo "${indent}this is a non specific txt output"
 455         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 456         local nbdifferent="$(md5sum ${partialoutputfiles} | awk '{ print $1; }' | sort | uniq | wc -l)"
 457         echo "  ${indent}${nbdifferent} different files"
 458         if test ${nbdifferent} -gt 1
 459         then
 460             echo "  ${indent}catting to ${mergedfile}"
 461             cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
 462             return
 463         else
 464             echo "  ${indent}moving to ${mergedfile}"
 465             cp "${firstpartialoutputfile}" "${mergedfile}" || error "error while merging"
 466             return
 467         fi
 468     fi
 469
 470     error "unknown file type"
 471 }
 472
 473 function merge_dispatcher_uncertainty {
 474     local indent="  ** "
 475     local outputfile="${1:?"provide output filename"}"
 476
 477     local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
 478     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 479     if test ${nboutputdirs} -ne ${nboutputfiles}
 480     then
 481         warning "missing files"
 482         if ! test "${2}" == "--force"
 483         then
 484             return
 485         fi
 486     fi
 487
 488     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 489     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 490
 491     if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
 492     then
 493           if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
 494         then
 495             echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
 496             ## search for sum
 497             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 498             summed_merged_file=${mergedfile//-Uncertainty/}
 499             if [ ! -f ${summed_merged_file} ];
 500             then
 501                 warning "${summed_merged_file} does not exist. Error, no uncertainty computed"
 502                 return;
 503             fi
 504             echo "${indent}${summed_merged_file} found"
 505             ## search for Squared
 506             squared_merged_file=${mergedfile//-Uncertainty/-Squared}
 507             if [ ! -f ${squared_merged_file} ];
 508             then
 509                 warning "${squared_merged_file} does not exist. Error, no uncertainty computed"
 510                 return;
 511             fi
 512             echo "${indent}${squared_merged_file} found"
 513             ## search for NumberOfEvent
 514             totalEvents=0;
 515             unamestr=`uname`
 516             if [[ "$unamestr" == 'Darwin' ]]; then
 517                 files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 518             else
 519                 files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 520             fi
 521             echo $files
 522             for outputfile in ${files}
 523             do
 524                 #echo $outputfile
 525                 if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
 526                 then
 527                     totalEvents="$(grep "NumberOfEvents" "${outputdir}/${outputfile}" | cut -d' ' -f4)"
 528                     echo "${indent}Find the NumberOfEvent in $outputfile: ${totalEvents}"
 529                 fi
 530             done
 531
 532             if test ${totalEvents} -gt 0
 533             then
 534                 uncerImageMerger="clitkImageUncertainty"
 535                 test -x "./clitkImageUncertainty" && uncerImageMerger="./clitkImageUncertainty"
 536                 ${uncerImageMerger} -i ${summed_merged_file} -s ${squared_merged_file} -o ${mergedfile} -n ${totalEvents}
 537             else
 538                 warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
 539                 return;
 540             fi
 541               else
 542             error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
 543         fi
 544     fi
 545
 546 }
 547
 548 echo "!!!! this is $0 v0.3k !!!!"
 549 echo "Usage: gate_power_merge.sh run.dir [--force]"
 550 echo "   where --force allows to merge files even if the file is missing in some output directories"
 551
 552 rundir="${1?"provide run dir"}"
 553 force=${2:-""}
 554 rundir="$(echo "${rundir}" | sed 's|/*$||')"
 555 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' -o -type l -name 'output*' | wc -l)"
 556
 557 test ${nboutputdirs} -gt 0 || error "no output dir found"
 558 echo "found ${nboutputdirs} partial output dirs"
 559
 560 outputdir="results"
 561 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
 562 then
 563     outputdir="results.${rundir##*.}"
 564 fi
 565 outputdir="$(basename "${outputdir}")"
 566 echo "output dir is ${outputdir}"
 567
 568 test -d "${outputdir}" && rm -r "${outputdir}"
 569 mkdir "${outputdir}"
 570
 571 unamestr=`uname`
 572 if [[ "$unamestr" == 'Darwin' ]]; then
 573     files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 574 else
 575     files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 576 fi
 577 echo files $files
 578 for outputfile in ${files}
 579 do
 580     merge_dispatcher "${outputfile}" "${force}"
 581 done
 582
 583 echo ""
 584 echo "Merging done. Special case for statistical uncertainty"
 585
 586 unamestr=`uname`
 587 if [[ "$unamestr" == 'Darwin' ]]; then
 588     files=$(find -L "${outputdir}" -type f -regex ".*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 589 else
 590     files=$(find -L "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 591 fi
 592 echo files = $files
 593 for outputfile in ${files}
 594 do
 595     merge_dispatcher_uncertainty "${outputfile}" "${force}"
 596 done
 597
 598 echo "compute job statistics"
 599 python computeEnlapsedTime.py ${rundir} gate
 600 mv "statJobs.txt" "${outputdir}/statJobs.txt"
 601
 602
 603 if [ -f "${rundir}/params.txt" ]
 604 then
 605     echo "copying params file"
 606     cp "${rundir}/params.txt" "${outputdir}/params.txt"
 607 fi
 608
 609 if [ -d "${rundir}/mac" ]
 610 then
 611     echo "copying mac folder"
 612     cp -r "${rundir}/mac" "${outputdir}/mac"
 613 fi
 614
 615 echo "these was ${warning_count} warning(s)"