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}" "${merged}"
 221             copyFirstPartialResult -i "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
 222             continue
 223         fi
 224
 225         update_bar ${count} "adding ${partial}"
 226         addToPartialResult -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
 227     done
 228     divideUncertaintyResult -i "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
 229     end_bar
 230     echo "  ${indent}merged ${count} files"
 231 }
 232
 233 txtImageMerger="clitkMergeAsciiDoseActor"
 234 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 235
 236 function merge_txt_image {
 237     local merged="$1"
 238     shift
 239     echo "  ${indent}entering text image merger"
 240     echo "  ${indent}merger is ${txtImageMerger}"
 241     echo "  ${indent}creating ${merged}"
 242     local count=0
 243     start_bar $#
 244     while test $# -gt 0
 245     do
 246         local partial="$1"
 247         shift
 248         let count++
 249
 250         if test ! -f "${merged}"
 251         then
 252             update_bar ${count} "copying first partial result ${partial}"
 253             cp "${partial}" "${merged}"
 254             continue
 255         fi
 256
 257         update_bar ${count} "adding ${partial}"
 258         local header="$(cat "${merged}" | head -n 6)"
 259         local tmp="$(mktemp)"
 260         ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
 261         echo "${header}" > "${merged}"
 262         grep -v '## Merge' "${tmp}" >> "${merged}"
 263         rm "${tmp}"
 264     done
 265     end_bar
 266     echo "  ${indent}merged ${count} files"
 267 }
 268
 269 hdrImageMerger="clitkImageArithm"
 270 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
 271
 272 function merge_hdr_image {
 273     local merged="$1"
 274     local merged_bin="${merged%.*}.img"
 275     shift
 276     echo "  ${indent}entering hdr image merger"
 277     echo "  ${indent}merger is ${hdrImageMerger}"
 278     echo "  ${indent}creating ${merged}"
 279     local count=0
 280     start_bar $#
 281     while test $# -gt 0
 282     do
 283         local partial="$1"
 284         local partial_bin="${partial%.*}.img"
 285         shift
 286         let count++
 287
 288         if test ! -f "${merged}"
 289         then
 290             update_bar ${count} "copying first partial result ${partial}"
 291             cp "${partial}" "${merged}"
 292             cp "${partial_bin}" "${merged_bin}"
 293             continue
 294         fi
 295
 296         update_bar ${count} "adding ${partial}"
 297         ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
 298     done
 299     end_bar
 300     echo "  ${indent}merged ${count} files"
 301 }
 302
 303 mhdImageMerger="clitkImageArithm"
 304 test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
 305
 306 function merge_mhd_image {
 307     local merged="$1"
 308     local merged_bin="${merged%.*}.raw"
 309     local last_character=${merged#${merged%?}}
 310     shift
 311     echo "  ${indent}entering mhd image merger"
 312     echo "  ${indent}merger is ${mhdImageMerger}"
 313     echo "  ${indent}creating ${merged}"
 314     local count=0
 315     start_bar $#
 316     while test $# -gt 0
 317     do
 318         local partial="$1"
 319         local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
 320         shift
 321         let count++
 322
 323         if test ! -f "${merged}"
 324         then
 325             update_bar ${count} "copying first partial result ${partial}"
 326             cp "${partial}" "${merged}"
 327             if test "$last_character" = "d"
 328             then
 329                 cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
 330             fi
 331             continue
 332         fi
 333
 334         update_bar ${count} "adding ${partial}"
 335         ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
 336         if test "$last_character" = "d" && test "${merged_bin}" != "${merged_bin%.*}.${partial_bin##*.}"
 337         then
 338             mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
 339             sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
 340         fi
 341     done
 342     end_bar
 343     echo "  ${indent}merged ${count} files"
 344 }
 345
 346 function merge_dispatcher {
 347     local indent="  ** "
 348     local outputfile="${1:?"provide output filename"}"
 349     echo "merging ${outputfile}"
 350
 351     local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
 352     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 353     if test ${nboutputdirs} -ne ${nboutputfiles}
 354     then
 355         warning "missing files"
 356         if ! test "${2}" == "--force"
 357         then
 358             return
 359         fi
 360     fi
 361
 362     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 363     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 364     echo "${indent}testing file type on ${firstpartialoutputfile}"
 365
 366     if test "${firstpartialoutputextension}" == "hdr" && test grep -qs 'INTERFILE' "${firstpartialoutputfile}"
 367     then
 368         echo "${indent}this is an interfile image"
 369         echo "${indent}creating mhd headers"
 370         for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
 371         local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
 372         local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
 373         merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
 374         echo "${indent}cleaning mhd headers"
 375         for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done
 376         rm "${mhd_mergedfile}"
 377         echo "${indent}copy interfile header"
 378         cp "${firstpartialoutputfile}" "${outputdir}"
 379         return
 380     fi
 381
 382     if test "${firstpartialoutputextension}" == "hdr"
 383     then
 384         echo "${indent}this is an analyse image"
 385         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 386         merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 387         return
 388     fi
 389
 390     if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
 391     then
 392         echo "${indent}this is a mhd image"
 393         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 394         merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 395         return
 396     fi
 397
 398     if test "${firstpartialoutputextension}" == "root"
 399     then
 400         echo "${indent}this is a root file"
 401         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 402         merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 403         return
 404     fi
 405
 406     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
 407     then
 408         echo "${indent}this is a stat file"
 409         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 410         merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 411         return
 412     fi
 413
 414     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'energydose' "${firstpartialoutputfile}"
 415     then
 416         echo "${indent}this is a dose file"
 417         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 418         merge_dose "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 419         return
 420     fi
 421
 422
 423
 424     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'Resol' "${firstpartialoutputfile}"
 425     then
 426         local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
 427         local resolx="$(echo "${resol}" | cut -d',' -f1)"
 428         local resoly="$(echo "${resol}" | cut -d',' -f2)"
 429         local resolz="$(echo "${resol}" | cut -d',' -f3)"
 430         if test "${resol}" == "1,1,1"
 431         then
 432             echo "${indent}this is a txt integral value"
 433             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 434             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 435             return
 436         fi
 437         if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
 438         then
 439             echo "${indent}this is a txt profile"
 440             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 441             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 442             return
 443         fi
 444     fi
 445
 446     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'vol(mm3)' "${firstpartialoutputfile}"
 447     then
 448         echo "${indent}this is a DoseByRegions file"
 449         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 450         merge_doseByRegions "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 451         return
 452     fi
 453
 454
 455     if test "${firstpartialoutputextension}" == "txt"
 456     then
 457         echo "${indent}this is a non specific txt output"
 458         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 459         local nbdifferent="$(md5sum ${partialoutputfiles} | awk '{ print $1; }' | sort | uniq | wc -l)"
 460         echo "  ${indent}${nbdifferent} different files"
 461         if test ${nbdifferent} -gt 1
 462         then
 463             echo "  ${indent}catting to ${mergedfile}"
 464             cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
 465             return
 466         else
 467             echo "  ${indent}moving to ${mergedfile}"
 468             cp "${firstpartialoutputfile}" "${mergedfile}" || error "error while merging"
 469             return
 470         fi
 471     fi
 472
 473     error "unknown file type"
 474 }
 475
 476 function merge_dispatcher_uncertainty {
 477     local indent="  ** "
 478     local outputfile="${1:?"provide output filename"}"
 479
 480     local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
 481     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 482     if test ${nboutputdirs} -ne ${nboutputfiles}
 483     then
 484         warning "missing files"
 485         if ! test "${2}" == "--force"
 486         then
 487             return
 488         fi
 489     fi
 490
 491     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 492     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 493
 494     if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
 495     then
 496           if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
 497         then
 498             echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
 499             ## search for sum
 500             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 501             summed_merged_file=${mergedfile//-Uncertainty/}
 502             if [ ! -f ${summed_merged_file} ];
 503             then
 504                 warning "${summed_merged_file} does not exist. Error, no uncertainty computed"
 505                 return;
 506             fi
 507             echo "${indent}${summed_merged_file} found"
 508             ## search for Squared
 509             squared_merged_file=${mergedfile//-Uncertainty/-Squared}
 510             if [ ! -f ${squared_merged_file} ];
 511             then
 512                 warning "${squared_merged_file} does not exist. Error, no uncertainty computed"
 513                 return;
 514             fi
 515             echo "${indent}${squared_merged_file} found"
 516             ## search for NumberOfEvent
 517             totalEvents=0;
 518             unamestr=`uname`
 519             if [[ "$unamestr" == 'Darwin' ]]; then
 520                 files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 521             else
 522                 files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 523             fi
 524             echo $files
 525             for outputfile in ${files}
 526             do
 527                 #echo $outputfile
 528                 if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
 529                 then
 530                     totalEvents="$(grep "NumberOfEvents" "${outputdir}/${outputfile}" | cut -d' ' -f4)"
 531                     echo "${indent}Find the NumberOfEvent in $outputfile: ${totalEvents}"
 532                 fi
 533             done
 534
 535             if test ${totalEvents} -gt 0
 536             then
 537                 uncerImageMerger="clitkImageUncertainty"
 538                 test -x "./clitkImageUncertainty" && uncerImageMerger="./clitkImageUncertainty"
 539                 ${uncerImageMerger} -i ${summed_merged_file} -s ${squared_merged_file} -o ${mergedfile} -n ${totalEvents}
 540             else
 541                 warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
 542                 return;
 543             fi
 544               else
 545             error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
 546         fi
 547     fi
 548
 549 }
 550
 551 echo "!!!! this is $0 v0.3k !!!!"
 552 echo "Usage: gate_power_merge.sh run.dir [--force]"
 553 echo "   where --force allows to merge files even if the file is missing in some output directories"
 554
 555 rundir="${1?"provide run dir"}"
 556 force=${2:-""}
 557 rundir="$(echo "${rundir}" | sed 's|/*$||')"
 558 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' -o -type l -name 'output*' | wc -l)"
 559
 560 test ${nboutputdirs} -gt 0 || error "no output dir found"
 561 echo "found ${nboutputdirs} partial output dirs"
 562
 563 outputdir="results"
 564 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
 565 then
 566     outputdir="results.${rundir##*.}"
 567 fi
 568 outputdir="$(basename "${outputdir}")"
 569 echo "output dir is ${outputdir}"
 570
 571 test -d "${outputdir}" && rm -r "${outputdir}"
 572 mkdir "${outputdir}"
 573
 574 unamestr=`uname`
 575 if [[ "$unamestr" == 'Darwin' ]]; then
 576     files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 577 else
 578     files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 579 fi
 580 echo files $files
 581 for outputfile in ${files}
 582 do
 583     merge_dispatcher "${outputfile}" "${force}"
 584 done
 585
 586 echo ""
 587 echo "Merging done. Special case for statistical uncertainty"
 588
 589 unamestr=`uname`
 590 if [[ "$unamestr" == 'Darwin' ]]; then
 591     files=$(find -L "${outputdir}" -type f -regex ".*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
 592 else
 593     files=$(find -L "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 594 fi
 595 echo files = $files
 596 for outputfile in ${files}
 597 do
 598     merge_dispatcher_uncertainty "${outputfile}" "${force}"
 599 done
 600
 601 echo "compute job statistics"
 602 python computeEnlapsedTime.py ${rundir} gate
 603 mv "statJobs.txt" "${outputdir}/statJobs.txt"
 604
 605
 606 if [ -f "${rundir}/params.txt" ]
 607 then
 608     echo "copying params file"
 609     cp "${rundir}/params.txt" "${outputdir}/params.txt"
 610 fi
 611
 612 if [ -d "${rundir}/mac" ]
 613 then
 614     echo "copying mac folder"
 615     cp -r "${rundir}/mac" "${outputdir}/mac"
 616 fi
 617
 618 echo "these was ${warning_count} warning(s)"