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