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="mergeDosePerEnegryFile.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 txtImageMerger="clitkMergeAsciiDoseActor"
 200 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 201
 202 function merge_txt_image {
 203     local merged="$1"
 204     shift
 205     echo "  ${indent}entering text image merger"
 206     echo "  ${indent}merger is ${txtImageMerger}"
 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 ${partial}"
 224         local header="$(cat "${merged}" | head -n 6)"
 225         local tmp="$(mktemp)"
 226         ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
 227         echo "${header}" > "${merged}"
 228         grep -v '## Merge' "${tmp}" >> "${merged}"
 229         rm "${tmp}"
 230     done
 231     end_bar
 232     echo "  ${indent}merged ${count} files"
 233 }
 234
 235 hdrImageMerger="clitkImageArithm"
 236 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
 237
 238 function merge_hdr_image {
 239     local merged="$1"
 240     local merged_bin="${merged%.*}.img"
 241     shift
 242     echo "  ${indent}entering hdr image merger"
 243     echo "  ${indent}merger is ${hdrImageMerger}"
 244     echo "  ${indent}creating ${merged}"
 245     local count=0
 246     start_bar $#
 247     while test $# -gt 0
 248     do
 249         local partial="$1"
 250         local partial_bin="${partial%.*}.img"
 251         shift
 252         let count++
 253
 254         if test ! -f "${merged}"
 255         then
 256             update_bar ${count} "copying first partial result ${partial}"
 257             cp "${partial}" "${merged}"
 258             cp "${partial_bin}" "${merged_bin}"
 259             continue
 260         fi
 261
 262         update_bar ${count} "adding ${partial}"
 263         ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
 264     done
 265     end_bar
 266     echo "  ${indent}merged ${count} files"
 267 }
 268
 269 mhdImageMerger="clitkImageArithm"
 270 test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
 271
 272 function merge_mhd_image {
 273     local merged="$1"
 274     local merged_bin="${merged%.*}.raw"
 275     local last_character=${merged#${merged%?}}
 276     shift
 277     echo "  ${indent}entering mhd image merger"
 278     echo "  ${indent}merger is ${mhdImageMerger}"
 279     echo "  ${indent}creating ${merged}"
 280     local count=0
 281     start_bar $#
 282     while test $# -gt 0
 283     do
 284         local partial="$1"
 285         local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
 286         shift
 287         let count++
 288
 289         if test ! -f "${merged}"
 290         then
 291             update_bar ${count} "copying first partial result ${partial}"
 292             cp "${partial}" "${merged}"
 293             if test "$last_character" = "d"
 294             then
 295                 cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
 296             fi
 297             continue
 298         fi
 299
 300         update_bar ${count} "adding ${partial}"
 301         ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
 302         if test "$last_character" = "d"
 303         then
 304             mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
 305             sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
 306         fi
 307     done
 308     end_bar
 309     echo "  ${indent}merged ${count} files"
 310 }
 311
 312 function merge_dispatcher {
 313     local indent="  ** "
 314     local outputfile="${1:?"provide output filename"}"
 315     echo "merging ${outputfile}"
 316
 317     local partialoutputfiles="$(find "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
 318     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 319     if test ${nboutputdirs} -ne ${nboutputfiles}
 320     then
 321         warning "missing files"
 322         return
 323     fi
 324
 325     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 326     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 327     echo "${indent}testing file type on ${firstpartialoutputfile}"
 328
 329     if test "${firstpartialoutputextension}" == "hdr" && grep -qs 'INTERFILE' "${firstpartialoutputfile}"
 330     then
 331         echo "${indent}this is a interfile image"
 332         echo "${indent}creating mhd headers"
 333         for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
 334         local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
 335         local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
 336         merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
 337         echo "${indent}cleaning mhd headers"
 338         for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done
 339         rm "${mhd_mergedfile}"
 340         echo "${indent}copy interfile header"
 341         cp "${firstpartialoutputfile}" "${outputdir}"
 342         return
 343     fi
 344
 345     if test "${firstpartialoutputextension}" == "hdr"
 346     then
 347         echo "${indent}this is a analyse image"
 348         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 349         merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 350         return
 351     fi
 352
 353     if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
 354     then
 355         echo "${indent}this is a mhd image"
 356         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 357         merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 358         return
 359     fi
 360
 361     if test "${firstpartialoutputextension}" == "root"
 362     then
 363         echo "${indent}this is a root file"
 364         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 365         merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 366         return
 367     fi
 368
 369     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
 370     then
 371         echo "${indent}this is a stat file"
 372         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 373         merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 374         return
 375     fi
 376
 377     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'energydose' "${firstpartialoutputfile}"
 378     then
 379         echo "${indent}this is a dose file"
 380         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 381         merge_dose "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 382         return
 383     fi
 384
 385
 386
 387     if test "${firstpartialoutputextension}" == "txt" && grep -qs 'Resol' "${firstpartialoutputfile}"
 388     then
 389         local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
 390         local resolx="$(echo "${resol}" | cut -d',' -f1)"
 391         local resoly="$(echo "${resol}" | cut -d',' -f2)"
 392         local resolz="$(echo "${resol}" | cut -d',' -f3)"
 393         if test "${resol}" == "1,1,1"
 394         then
 395             echo "${indent}this is a txt integral value"
 396             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 397             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 398             return
 399         fi
 400         if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
 401         then
 402             echo "${indent}this is a txt profile"
 403             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 404             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 405             return
 406         fi
 407     fi
 408
 409     if test "${firstpartialoutputextension}" == "txt"
 410     then
 411         echo "${indent}this is a non specific txt output"
 412         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 413         local nbdifferent="$(md5sum ${partialoutputfiles} | awk '{ print $1; }' | sort | uniq | wc -l)"
 414         echo "  ${indent}${nbdifferent} different files"
 415         if test ${nbdifferent} -gt 1
 416         then
 417             echo "  ${indent}catting to ${mergedfile}"
 418             cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
 419             return
 420         else
 421             echo "  ${indent}moving to ${mergedfile}"
 422             cp "${firstpartialoutputfile}" "${mergedfile}" || error "error while merging"
 423             return
 424         fi
 425     fi
 426
 427     error "unknown file type"
 428 }
 429
 430 function merge_dispatcher_uncertainty {
 431     local indent="  ** "
 432     local outputfile="${1:?"provide output filename"}"
 433
 434     local partialoutputfiles="$(find "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
 435     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 436     if test ${nboutputdirs} -ne ${nboutputfiles}
 437     then
 438         warning "missing files"
 439         return
 440     fi
 441
 442     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 443     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 444
 445     if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
 446     then
 447         if test "${firstpartialoutputextension}" == "mhd"
 448         then
 449             echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
 450             ## search for sum
 451             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 452             summed_merged_file=${mergedfile//-Uncertainty/}
 453             if [ ! -f ${summed_merged_file} ];
 454             then
 455                 warning "${summed_merged_file} does not exist. Error, no uncertainty computed"
 456                 return;
 457             fi
 458             echo "${indent}${summed_merged_file} found"
 459             ## search for Squared
 460             squared_merged_file=${mergedfile//-Uncertainty/-Squared}
 461             if [ ! -f ${squared_merged_file} ];
 462             then
 463                 warning "${squared_merged_file} does not exist. Error, no uncertainty computed"
 464                 return;
 465             fi
 466             echo "${indent}${squared_merged_file} found"
 467             ## search for NumberOfEvent
 468             totalEvents=0;
 469             for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 470             do
 471                 #echo $outputfile
 472                 if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
 473                 then
 474                     totalEvents="$(grep "NumberOfEvents" "${outputdir}/${outputfile}" | cut -d' ' -f4)"
 475                     echo "${indent}Find the NumberOfEvent in $outputfile: ${totalEvents}"
 476                 fi
 477             done
 478
 479             if test ${totalEvents} -gt 0
 480             then
 481                 uncerImageMerger="clitkImageUncertainty"
 482                 test -x "./clitkImageUncertainty" && uncerImageMerger="./clitkImageUncertainty"
 483                 ${uncerImageMerger} -i ${summed_merged_file} -s ${squared_merged_file} -o ${mergedfile} -n ${totalEvents}
 484             else
 485                 warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
 486                 return;
 487             fi
 488         fi
 489     fi
 490
 491 }
 492
 493 echo "!!!! this is $0 v0.3k !!!!"
 494
 495 rundir="${1?"provide run dir"}"
 496 rundir="$(echo "${rundir}" | sed 's|/*$||')"
 497 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
 498
 499 test ${nboutputdirs} -gt 0 || error "no output dir found"
 500 echo "found ${nboutputdirs} partial output dirs"
 501
 502 outputdir="results"
 503 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
 504 then
 505     outputdir="results.${rundir##*.}"
 506 fi
 507 outputdir="$(basename "${outputdir}")"
 508 echo "output dir is ${outputdir}"
 509
 510 test -d "${outputdir}" && rm -r "${outputdir}"
 511 mkdir "${outputdir}"
 512
 513 for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 514 do
 515     merge_dispatcher "${outputfile}"
 516 done
 517
 518 echo ""
 519 echo "Merging done. Special case for statistical uncertainty"
 520 for outputfile in $(find "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 521 do
 522     merge_dispatcher_uncertainty "${outputfile}"
 523 done
 524
 525 if [ -f "${rundir}/params.txt" ]
 526 then
 527     echo "copying params file"
 528     cp "${rundir}/params.txt" "${outputdir}/params.txt"
 529 fi
 530
 531 echo "these was ${warning_count} warning(s)"