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 "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 rootMerger="clitkMergeRootFiles"
  34 test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
  35
  36 function merge_root {
  37 local merged="$1"
  38 shift
  39 echo "  ${indent}entering root merger"
  40 echo "  ${indent}merger is ${rootMerger}"
  41 echo "  ${indent}creating ${merged}"
  42 local count=0
  43 local arguments=" -o ${merged}"
  44 while test $# -gt 0
  45 do
  46     local partial="$1"
  47     shift
  48     let count++
  49     local arguments=" -i ${partial} ${arguments}"
  50 done
  51 ${rootMerger} ${arguments} > /dev/null || { warning "error while calling ${rootMerger}" && return; }
  52 echo "  ${indent}merged ${count} files"
  53 }
  54
  55 statMerger="mergeStatFile.py"
  56 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
  57 test -x "./mergeStatFile.py" && statMerger="./mergeStatFile.py"
  58
  59 function merge_stat {
  60 local merged="$1"
  61 shift
  62 echo "  ${indent}entering stat merger"
  63 echo "  ${indent}merger is ${statMerger}"
  64 echo "  ${indent}creating ${merged}"
  65 local count=0
  66 start_bar $#
  67 while test $# -gt 0
  68 do
  69     local partial="$1"
  70     shift
  71     let count++
  72
  73     if test ! -f "${merged}"
  74     then
  75         update_bar ${count} "copying first partial result ${partial}"
  76         cp "${partial}" "${merged}"
  77         continue
  78     fi
  79
  80     update_bar ${count} "adding ${partial}"
  81     ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || { warning "error while calling ${statMerger}" && return; }
  82 done
  83 end_bar
  84 echo "  ${indent}merged ${count} files"
  85 }
  86
  87 txtImageMerger="clitkMergeAsciiDoseActor"
  88 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
  89
  90 function merge_txt_image {
  91 local merged="$1"
  92 shift
  93 echo "  ${indent}entering text image merger"
  94 echo "  ${indent}merger is ${txtImageMerger}"
  95 echo "  ${indent}creating ${merged}"
  96 local count=0
  97 start_bar $#
  98 while test $# -gt 0
  99 do
 100     local partial="$1"
 101     shift
 102     let count++
 103
 104     if test ! -f "${merged}"
 105     then
 106         update_bar ${count} "copying first partial result ${partial}"
 107         cp "${partial}" "${merged}"
 108         continue
 109     fi
 110
 111     update_bar ${count} "adding ${partial}"
 112     local header="$(cat "${merged}" | head -n 6)"
 113     local tmp="$(mktemp)"
 114     ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || { warning "error while calling ${txtImageMerger}" && return; }
 115     echo "${header}" > "${merged}"
 116     grep -v '## Merge' "${tmp}" >> "${merged}"
 117     rm "${tmp}"
 118 done
 119 end_bar
 120 echo "  ${indent}merged ${count} files"
 121 }
 122
 123 hdrImageMerger="clitkImageArithm"
 124 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
 125
 126 function merge_hdr_image {
 127 local merged="$1"
 128 local merged_bin="${merged%.*}.img"
 129 shift
 130 echo "  ${indent}entering hdr image merger"
 131 echo "  ${indent}merger is ${hdrImageMerger}"
 132 echo "  ${indent}creating ${merged}"
 133 local count=0
 134 start_bar $#
 135 while test $# -gt 0
 136 do
 137     local partial="$1"
 138     local partial_bin="${partial%.*}.img"
 139     shift
 140     let count++
 141
 142     if test ! -f "${merged}"
 143     then
 144         update_bar ${count} "copying first partial result ${partial}"
 145         cp "${partial}" "${merged}"
 146         cp "${partial_bin}" "${merged_bin}"
 147         continue
 148     fi
 149
 150     update_bar ${count} "adding ${partial}"
 151     ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || { warning "error while calling ${hdrImageMerger}" && return; }
 152 done
 153 end_bar
 154 echo "  ${indent}merged ${count} files"
 155 }
 156
 157 function merge_dispatcher {
 158     local indent="  ** "
 159     local outputfile="${1:?"provide output filename"}"
 160     echo "merging ${outputfile}"
 161
 162     local partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
 163     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
 164     if test ${nboutputdirs} -ne ${nboutputfiles}
 165     then
 166         warning "missing files"
 167         return
 168     fi
 169
 170     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
 171     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
 172     echo "${indent}testing file type on ${firstpartialoutputfile}"
 173
 174     if test "${firstpartialoutputextension}" == "hdr"
 175     then
 176         echo "${indent}this is a analyse image"
 177         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 178         merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 179         return
 180     fi
 181
 182     if test "${firstpartialoutputextension}" == "root"
 183     then
 184         echo "${indent}this is a root file"
 185         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 186         merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 187         return
 188     fi
 189
 190     if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
 191     then
 192         echo "${indent}this is a stat file"
 193         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 194         merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 195         return
 196     fi
 197
 198     if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
 199     then
 200         local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
 201         local resolx="$(echo "${resol}" | cut -d',' -f1)"
 202         local resoly="$(echo "${resol}" | cut -d',' -f2)"
 203         local resolz="$(echo "${resol}" | cut -d',' -f3)"
 204         if test "${resol}" == "1,1,1"
 205         then
 206             echo "${indent}this is a txt integral value"
 207             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 208             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 209             return
 210         fi
 211         if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
 212         then
 213             echo "${indent}this is a txt profile"
 214             local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
 215             merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
 216             return
 217         fi
 218     fi
 219
 220     warning "unknown file type"
 221 }
 222
 223 rundir="${1?"provide run dir"}"
 224 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
 225
 226 test ${nboutputdirs} -gt 0 || error "no output dir found"
 227 echo "found ${nboutputdirs} partial output dirs"
 228
 229 outputdir="results"
 230 if [ "${rundir}" != "." -a "${rundir##*.}" != "${rundir}" ]
 231 then
 232     outputdir="results.${rundir##*.}"
 233 fi
 234 outputdir="$(basename "${outputdir}")"
 235 echo "output dir is ${outputdir}"
 236 test -d "${outputdir}" && rm -r "${outputdir}"
 237 mkdir "${outputdir}"
 238
 239 for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(hdr|root|txt)' | awk -F '/' '{ print $NF }' | sort | uniq)
 240 do
 241         merge_dispatcher "${outputfile}"
 242 done
 243
 244 echo "these was ${warning_count} warning(s)"