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 function warning {
  11 echo "WARNING: $1"
  12 }
  13
  14 function start_bar {
  15 count_max="${1:?"provide count max"}"
  16 }
  17
  18 function update_bar {
  19 local count="${1:?"provide count"}"
  20 local message="${2:?"provide message"}"
  21 local percent=$(echo "100*${count}/${count_max}" | bc)
  22 printf "[%03d/%03d] %3d%% %-80s\r" ${count} ${count_max} ${percent} "${message}"
  23 }
  24
  25 function end_bar {
  26 unset count_max
  27 echo -ne '\n'
  28 }
  29
  30 function merge_root {
  31 local merged="$1"
  32 shift
  33 echo "  ${indent}entering root merger"
  34 echo "  ${indent}creating ${merged}"
  35 local count=0
  36 local arguments=" -o ${merged}"
  37 while test $# -gt 0
  38 do
  39     local partial="$1"
  40     shift
  41     let count++
  42     local arguments=" -i ${partial} ${arguments}"
  43 done
  44 clitkMergeRootFiles ${arguments} 2> /dev/null > /dev/null || error "error while calling clitkMergeRootFiles"
  45 echo "  ${indent}merged ${count} files"
  46 }
  47
  48 function merge_stat {
  49 local merged="$1"
  50 shift
  51 echo "  ${indent}entering stat merger"
  52 echo "  ${indent}creating ${merged}"
  53 local count=0
  54 start_bar $#
  55 while test $# -gt 0
  56 do
  57     local partial="$1"
  58     shift
  59     let count++
  60
  61     if test ! -f "${merged}"
  62     then
  63         update_bar ${count} "copying first partial result ${partial}"
  64         cp "${partial}" "${merged}"
  65         continue
  66     fi
  67
  68     update_bar ${count} "adding ${partial}"
  69     mergeStatFile.py -i "${merged}" -j "${partial}" -o "${merged}" > /dev/null || error "error while calling mergeStatFile"
  70 done
  71 end_bar
  72 echo "  ${indent}merged ${count} files"
  73 }
  74
  75 function merge_txt_image {
  76 local merged="$1"
  77 shift
  78 echo "  ${indent}entering text image merger"
  79 echo "  ${indent}creating ${merged}"
  80 local count=0
  81 start_bar $#
  82 while test $# -gt 0
  83 do
  84     local partial="$1"
  85     shift
  86     let count++
  87
  88     if test ! -f "${merged}"
  89     then
  90         update_bar ${count} "copying first partial result ${partial}"
  91         cp "${partial}" "${merged}"
  92         continue
  93     fi
  94
  95     update_bar ${count} "adding ${partial}"
  96     local header="$(cat "${merged}" | head -n 6)"
  97     local tmp="$(mktemp)"
  98     clitkMergeAsciiDoseActor -i "${partial}" -j "${merged}" -o "${tmp}" > /dev/null || error "error while calling clitkMergeAsciiDoseActor"
  99     echo "${header}" > "${merged}"
 100     grep -v '## Merge' "${tmp}" >> "${merged}"
 101     rm "${tmp}"
 102 done
 103 end_bar
 104 echo "  ${indent}merged ${count} files"
 105 }
 106
 107 function merge_hdr_image {
 108 local merged="$1"
 109 local merged_bin="${merged%.*}.img"
 110 shift
 111 echo "  ${indent}entering hdr image merger"
 112 echo "  ${indent}creating ${merged}"
 113 local count=0
 114 start_bar $#
 115 while test $# -gt 0
 116 do
 117     local partial="$1"
 118     local partial_bin="${partial%.*}.img"
 119     shift
 120     let count++
 121
 122     if test ! -f "${merged}"
 123     then
 124         update_bar ${count} "copying first partial result ${partial}"
 125         cp "${partial}" "${merged}"
 126         cp "${partial_bin}" "${merged_bin}"
 127         continue
 128     fi
 129
 130     update_bar ${count} "adding ${partial}"
 131     clitkImageArithm -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || error "error while calling clitkImageArithm"
 132 done
 133 end_bar
 134 echo "  ${indent}merged ${count} files"
 135 }
 136
 137 rundir="${1?"provide run dir"}"
 138 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d | wc -l)"
 139
 140 test ${nboutputdirs} -gt 0 || error "no output dir found"
 141 echo "found ${nboutputdirs} partial output dirs"
 142
 143 outputdir="merged.${rundir##*.}"
 144 outputdir="$(basename "${outputdir}")"
 145 echo "output dir is ${outputdir}"
 146 test -d "${outputdir}" && rm -r "${outputdir}"
 147 mkdir "${outputdir}"
 148
 149 for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(hdr|root|txt)' | awk -F '/' '{ print $NF }' | sort | uniq)
 150 do
 151     indent="  ** "
 152     echo "merging ${outputfile}"
 153
 154     partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
 155     nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 156     if test ${nboutputdirs} -ne ${nboutputfiles}
 157     then
 158         warning "missing files"
 159         continue
 160     fi
 161
 162     firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 163     firstpartialoutputextension="${firstpartialoutputfile##*.}"
 164     echo "${indent}testing file type on ${firstpartialoutputfile}"
 165
 166     if test "${firstpartialoutputextension}" == "hdr"
 167     then
 168         echo "${indent}this is a analyse image"
 169         mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 170         merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 171         continue
 172     fi
 173
 174     if test "${firstpartialoutputextension}" == "root"
 175     then
 176         echo "${indent}this is a root file"
 177         mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 178         merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 179         continue
 180     fi
 181
 182     if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
 183     then
 184         echo "${indent}this is a stat file"
 185         mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 186         merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 187         continue
 188     fi
 189
 190     if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
 191     then
 192         resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
 193         resolx="$(echo "${resol}" | cut -d',' -f1)"
 194         resoly="$(echo "${resol}" | cut -d',' -f2)"
 195         resolz="$(echo "${resol}" | cut -d',' -f3)"
 196         if test "${resol}" == "1,1,1"
 197         then
 198             echo "${indent}this is a txt integral value"
 199             mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 200             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 201             continue
 202         fi
 203         if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
 204         then
 205             echo "${indent}this is a txt profile"
 206             mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 207             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 208             continue
 209         fi
 210     fi
 211
 212
 213     warning "unknown file type"
 214 done
 215