From: Pierre Gueth (kingkong) <pierre.gueth@creatis.insa-lyon.fr>
Date: Fri, 10 Jun 2011 09:19:00 +0000 (+0200)
Subject: renamed
X-Git-Tag: v1.4.0~177^2~26
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=bf5a80ba7b50d2f4edd1ca9a0eb0c0750cdeb9f2;p=clitk.git

renamed
---

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
new file mode 100755
index 0000000..b9842dd
--- /dev/null
+++ b/cluster_tools/gate_power_merge.sh
@@ -0,0 +1,215 @@
+#!/usr/bin/env bash
+
+set -u 
+
+function error {
+echo "ERROR: $1"
+exit 1
+}
+
+function warning {
+echo "WARNING: $1"
+}
+
+function start_bar {
+count_max="${1:?"provide count max"}"
+}
+
+function update_bar {
+local count="${1:?"provide count"}"
+local message="${2:?"provide message"}"
+local percent=$(echo "100*${count}/${count_max}" | bc)
+printf "[%03d/%03d] %3d%% %-80s\r" ${count} ${count_max} ${percent} "${message}"
+}
+
+function end_bar {
+unset count_max
+echo -ne '\n'
+}
+
+function merge_root {
+local merged="$1"
+shift
+echo "  ${indent}entering root merger"
+echo "  ${indent}creating ${merged}"
+local count=0
+local arguments=" -o ${merged}"
+while test $# -gt 0
+do
+    local partial="$1"
+    shift
+    let count++
+    local arguments=" -i ${partial} ${arguments}"
+done
+clitkMergeRootFiles ${arguments} 2> /dev/null > /dev/null || error "error while calling clitkMergeRootFiles"
+echo "  ${indent}merged ${count} files"
+}
+
+function merge_stat {
+local merged="$1"
+shift
+echo "  ${indent}entering stat merger"
+echo "  ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+    local partial="$1"
+    shift
+    let count++
+
+    if test ! -f "${merged}"
+    then
+        update_bar ${count} "copying first partial result ${partial}"
+        cp "${partial}" "${merged}"
+        continue
+    fi
+
+    update_bar ${count} "adding ${partial}"
+    mergeStatFile.py -i "${merged}" -j "${partial}" -o "${merged}" > /dev/null || error "error while calling mergeStatFile"
+done
+end_bar
+echo "  ${indent}merged ${count} files"
+}
+
+function merge_txt_image {
+local merged="$1"
+shift
+echo "  ${indent}entering text image merger"
+echo "  ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+    local partial="$1"
+    shift
+    let count++
+
+    if test ! -f "${merged}"
+    then
+        update_bar ${count} "copying first partial result ${partial}"
+        cp "${partial}" "${merged}"
+        continue
+    fi
+
+    update_bar ${count} "adding ${partial}"
+    local header="$(cat "${merged}" | head -n 6)"
+    local tmp="$(mktemp)"
+    clitkMergeAsciiDoseActor -i "${partial}" -j "${merged}" -o "${tmp}" > /dev/null || error "error while calling clitkMergeAsciiDoseActor"
+    echo "${header}" > "${merged}"
+    grep -v '## Merge' "${tmp}" >> "${merged}"
+    rm "${tmp}"
+done
+end_bar
+echo "  ${indent}merged ${count} files"
+}
+
+function merge_hdr_image {
+local merged="$1"
+local merged_bin="${merged%.*}.img"
+shift
+echo "  ${indent}entering hdr image merger"
+echo "  ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+    local partial="$1"
+    local partial_bin="${partial%.*}.img"
+    shift
+    let count++
+
+    if test ! -f "${merged}"
+    then
+        update_bar ${count} "copying first partial result ${partial}"
+        cp "${partial}" "${merged}"
+        cp "${partial_bin}" "${merged_bin}"
+        continue
+    fi
+
+    update_bar ${count} "adding ${partial}"
+    clitkImageArithm -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || error "error while calling clitkImageArithm"
+done
+end_bar
+echo "  ${indent}merged ${count} files"
+}
+
+rundir="${1?"provide run dir"}"
+nboutputdirs="$(find "${rundir}" -mindepth 1 -type d | wc -l)"
+
+test ${nboutputdirs} -gt 0 || error "no output dir found"
+echo "found ${nboutputdirs} partial output dirs"
+
+outputdir="merged.${rundir##*.}"
+outputdir="$(basename "${outputdir}")"
+echo "output dir is ${outputdir}"
+test -d "${outputdir}" && rm -r "${outputdir}"
+mkdir "${outputdir}"
+
+for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(hdr|root|txt)' | awk -F '/' '{ print $NF }' | sort | uniq)
+do
+    indent="  ** "
+    echo "merging ${outputfile}"
+
+    partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
+    nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
+    if test ${nboutputdirs} -ne ${nboutputfiles}
+    then
+        warning "missing files"
+        continue
+    fi
+
+    firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
+    firstpartialoutputextension="${firstpartialoutputfile##*.}"
+    echo "${indent}testing file type on ${firstpartialoutputfile}"
+
+    if test "${firstpartialoutputextension}" == "hdr"
+    then
+        echo "${indent}this is a analyse image"
+        mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+        merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+        continue
+    fi
+
+    if test "${firstpartialoutputextension}" == "root"
+    then
+        echo "${indent}this is a root file"
+        mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+        merge_root "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+        continue
+    fi
+
+    if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
+    then
+        echo "${indent}this is a stat file"
+        mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+        merge_stat "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+        continue
+    fi
+
+    if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
+    then
+        resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
+        resolx="$(echo "${resol}" | cut -d',' -f1)"
+        resoly="$(echo "${resol}" | cut -d',' -f2)"
+        resolz="$(echo "${resol}" | cut -d',' -f3)"
+        if test "${resol}" == "1,1,1"
+        then
+            echo "${indent}this is a txt integral value"
+            mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+            merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+            continue
+        fi
+        if test \( "${resolx}" == "1" -a "${resoly}" == "1" \) -o \( "${resoly}" == "1" -a "${resolz}" == "1" \) -o \( "${resolz}" == "1" -a "${resolx}" == "1" \)
+        then
+            echo "${indent}this is a txt profile"
+            mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+            merge_txt_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+            continue
+        fi
+    fi
+
+
+    warning "unknown file type"
+done
+