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%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
  23 }
  24
  25 function end_bar {
  26 unset count_max
  27 echo -ne '\n'
  28 }
  29
  30 rootMerger="clitkMergeRootFiles"
  31 test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
  32
  33 function merge_root {
  34 local merged="$1"
  35 shift
  36 echo "  ${indent}entering root merger"
  37 echo "  ${indent}merger is ${rootMerger}"
  38 echo "  ${indent}creating ${merged}"
  39 local count=0
  40 local arguments=" -o ${merged}"
  41 while test $# -gt 0
  42 do
  43     local partial="$1"
  44     shift
  45     let count++
  46     local arguments=" -i ${partial} ${arguments}"
  47 done
  48 ${rootMerger} ${arguments} > /dev/null || warning "error while calling ${rootMerger}"
  49 echo "  ${indent}merged ${count} files"
  50 }
  51
  52 statMerger="mergeStatFile.py"
  53 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
  54
  55 function merge_stat {
  56 local merged="$1"
  57 shift
  58 echo "  ${indent}entering stat merger"
  59 echo "  ${indent}merger is ${statMerger}"
  60 echo "  ${indent}creating ${merged}"
  61 local count=0
  62 start_bar $#
  63 while test $# -gt 0
  64 do
  65     local partial="$1"
  66     shift
  67     let count++
  68
  69     if test ! -f "${merged}"
  70     then
  71         update_bar ${count} "copying first partial result ${partial}"
  72         cp "${partial}" "${merged}"
  73         continue
  74     fi
  75
  76     update_bar ${count} "adding ${partial}"
  77     ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
  78 done
  79 end_bar
  80 echo "  ${indent}merged ${count} files"
  81 }
  82
  83 txtImageMerger="clitkMergeAsciiDoseActor"
  84 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
  85
  86 function merge_txt_image {
  87 local merged="$1"
  88 shift
  89 echo "  ${indent}entering text image merger"
  90 echo "  ${indent}merger is ${txtImageMerger}"
  91 echo "  ${indent}creating ${merged}"
  92 local count=0
  93 start_bar $#
  94 while test $# -gt 0
  95 do
  96     local partial="$1"
  97     shift
  98     let count++
  99
 100     if test ! -f "${merged}"
 101     then
 102         update_bar ${count} "copying first partial result ${partial}"
 103         cp "${partial}" "${merged}"
 104         continue
 105     fi
 106
 107     update_bar ${count} "adding ${partial}"
 108     local header="$(cat "${merged}" | head -n 6)"
 109     local tmp="$(mktemp)"
 110     ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
 111     echo "${header}" > "${merged}"
 112     grep -v '## Merge' "${tmp}" >> "${merged}"
 113     rm "${tmp}"
 114 done
 115 end_bar
 116 echo "  ${indent}merged ${count} files"
 117 }
 118
 119 hdrImageMerger="clitkImageArithm"
 120 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
 121
 122 function merge_hdr_image {
 123 local merged="$1"
 124 local merged_bin="${merged%.*}.img"
 125 shift
 126 echo "  ${indent}entering hdr image merger"
 127 echo "  ${indent}merger is ${hdrImageMerger}"
 128 echo "  ${indent}creating ${merged}"
 129 local count=0
 130 start_bar $#
 131 while test $# -gt 0
 132 do
 133     local partial="$1"
 134     local partial_bin="${partial%.*}.img"
 135     shift
 136     let count++
 137
 138     if test ! -f "${merged}"
 139     then
 140         update_bar ${count} "copying first partial result ${partial}"
 141         cp "${partial}" "${merged}"
 142         cp "${partial_bin}" "${merged_bin}"
 143         continue
 144     fi
 145
 146     update_bar ${count} "adding ${partial}"
 147     ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
 148 done
 149 end_bar
 150 echo "  ${indent}merged ${count} files"
 151 }
 152
 153 function merge_dispatcher {
 154     local indent="  ** "
 155     local outputfile="${1:?"provide output filename"}"
 156     echo "merging ${outputfile}"
 157
 158     local partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
 159     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 160     if test ${nboutputdirs} -ne ${nboutputfiles}
 161     then
 162         warning "missing files"
 163         return
 164     fi
 165
 166     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 167     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 168     echo "${indent}testing file type on ${firstpartialoutputfile}"
 169
 170     if test "${firstpartialoutputextension}" == "hdr"
 171     then
 172         echo "${indent}this is a analyse image"
 173         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 174         merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 175         return
 176     fi
 177
 178     if test "${firstpartialoutputextension}" == "root"
 179     then
 180         echo "${indent}this is a root file"
 181         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 182         merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 183         return
 184     fi
 185
 186     if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
 187     then
 188         echo "${indent}this is a stat file"
 189         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 190         merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 191         return
 192     fi
 193
 194     if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
 195     then
 196         local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
 197         local resolx="$(echo "${resol}" | cut -d',' -f1)"
 198         local resoly="$(echo "${resol}" | cut -d',' -f2)"
 199         local resolz="$(echo "${resol}" | cut -d',' -f3)"
 200         if test "${resol}" == "1,1,1"
 201         then
 202             echo "${indent}this is a txt integral value"
 203             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 204             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 205             return
 206         fi
 207         if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
 208         then
 209             echo "${indent}this is a txt profile"
 210             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 211             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 212             return
 213         fi
 214     fi
 215
 216     warning "unknown file type"
 217 }
 218
 219 rundir="${1?"provide run dir"}"
 220 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
 221
 222 test ${nboutputdirs} -gt 0 || error "no output dir found"
 223 echo "found ${nboutputdirs} partial output dirs"
 224
 225 outputdir="results"
 226 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
 227 then
 228     outputdir="results.${rundir##*.}"
 229 fi
 230 outputdir="$(basename "${outputdir}")"
 231 echo "output dir is ${outputdir}"
 232 test -d "${outputdir}" && rm -r "${outputdir}"
 233 mkdir "${outputdir}"
 234
 235 for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(hdr|root|txt)' | awk -F '/' '{ print $NF }' | sort | uniq)
 236 do
 237         merge_dispatcher "${outputfile}"
 238 done
 239