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