X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=cluster_tools%2Fgate_power_merge.sh;h=43d90d02c496d6dba5c3f696a88b195c4b535f0c;hb=HEAD;hp=caec94a252cd829af0fc575a04c4bcc5fe9041cc;hpb=6d806c6fa5c860e1d469f5e947b9473c569bd75e;p=clitk.git

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index caec94a..43d90d0 100755
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -1,166 +1,346 @@
 #!/usr/bin/env bash
 
-set -u 
+set -u
 
 function error {
-echo "ERROR: $1"
-exit 1
+    echo "ERROR: $1"
+    exit 1
 }
 
 warning_count=0
 function warning {
-let "warning_count++"
-echo "MERGE_WARNING: $1"
+    let "warning_count++"
+    echo "MERGE_WARNING: $1"
 }
 
 function start_bar {
-count_max="${1:?"provide count max"}"
+    count_max="${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%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
-printf "[%03d/%03d] %3d%% %-80.80s\n" ${count} ${count_max} ${percent} "${message}"
+    local count="${1:?"provide count"}"
+    local message="${2:?"provide message"}"
+    local percent=$(echo "100*${count}/${count_max}" | bc)
+    #printf "[%03d/%03d] %3d%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
+    printf "[%03d/%03d] %3d%% %-80.80s\n" ${count} ${count_max} ${percent} "${message}"
 }
 
 function end_bar {
-unset count_max
-#echo -ne '\n'
+    unset count_max
+    #echo -ne '\n'
+}
+
+function check_interfile {
+    local input_interfile="${1:?"provide input interfile"}"
+
+    grep -qs '!INTERFILE :=' "${input_interfile}" || return 1
+
+    local header_byte_size=$(awk -F' ' '
+BEGIN { zsize = 0; }
+/matrix size/ && $3 == "[1]" { xsize = $5; }
+/matrix size/ && $3 == "[2]" { ysize = $5; }
+/number of projections/ { zsize += $5; }
+/number of bytes per pixel/ { byte_per_pixel = $7; }
+END { print xsize * ysize * zsize * byte_per_pixel; }' "${input_interfile}")
+
+    local raw_interfile="$(dirname "${input_interfile}")/$(awk -F' := ' '/name of data file/ { print $2; }' "${input_interfile}")"
+
+    test -f "${raw_interfile}" || return 1
+    test $(stat -c%s "${raw_interfile}") -eq ${header_byte_size} || return 1
+}
+
+function write_mhd_header {
+    local input_interfile="${1:?"provide input interfile"}"
+    local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
+
+    check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
+
+    local header_start='ObjectType = Image
+NDims = 3
+AcquisitionDate = none
+BinaryData = True
+BinaryDataByteOrderMSB = False
+CompressedData = False
+TransformMatrix = 1 0 0 0 1 0 0 0 1
+Offset = 0 0 0
+CenterOfRotation = 0 0 0
+DistanceUnits = mm
+AnatomicalOrientation = RIP'
+
+    echo "${header_start}" > "${output_mhd}"
+
+    awk -F' ' '
+/scaling factor/ && $4 == "[1]" { xspacing = $6; }
+/scaling factor/ && $4 == "[2]" { yspacing = $6; }
+END { print "ElementSpacing = " xspacing " " yspacing " 1"; }' "${input_interfile}" >> "${output_mhd}"
+
+    awk -F' ' '
+BEGIN { zsize = 0; }
+/matrix size/ && $3 == "[1]" { xsize = $5; }
+/matrix size/ && $3 == "[2]" { ysize = $5; }
+/number of projections/ { zsize += $5; }
+END { print "DimSize = " xsize " " ysize " " zsize; }' "${input_interfile}" >> "${output_mhd}"
+
+    awk -F' := ' '
+/number format/ { format = $2; }
+/number of bytes per pixel/ { byte_per_pixel = $2 }
+END {
+if (format == "unsigned integer" && byte_per_pixel == 8) { print "ElementType = MET_ULONG"; exit };
+if (format == "unsigned integer" && byte_per_pixel == 4) { print "ElementType = MET_UINT"; exit };
+if (format == "unsigned integer" && byte_per_pixel == 2) { print "ElementType = MET_USHORT"; exit };
+if (format == "unsigned integer" && byte_per_pixel == 1) { print "ElementType = MET_UCHAR"; exit };
+if (format == "integer" && byte_per_pixel == 8) { print "ElementType = MET_LONG"; exit };
+if (format == "integer" && byte_per_pixel == 4) { print "ElementType = MET_INT"; exit };
+if (format == "integer" && byte_per_pixel == 2) { print "ElementType = MET_SHORT"; exit };
+if (format == "integer" && byte_per_pixel == 1) { print "ElementType = MET_CHAR"; exit };
+if (format == "float" && byte_per_pixel == 8) { print "ElementType = MET_FLOAT"; exit };
+if (format == "float" && byte_per_pixel == 4) { print "ElementType = MET_DOUBLE"; exit };
+print "ElementType = MET_INT";
+}' "${input_interfile}" >> "${output_mhd}"
+
+    awk -F' := ' '
+/name of data file/ { print "ElementDataFile = " $2; }' "${input_interfile}" >> "${output_mhd}"
 }
 
 rootMerger="clitkMergeRootFiles"
 test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
 
 function merge_root {
-local merged="$1"
-shift
-echo "  ${indent}entering root merger"
-echo "  ${indent}merger is ${rootMerger}"
-echo "  ${indent}creating ${merged}"
-#echo "######## $#"
-#echo "######## $*"
-
-if test $# -eq 1
-then
-    echo "  ${indent}just one partial file => just copy it"
-    cp "$1" "${merged}"
-    return
-fi
-
-local count=0
-local arguments=" -o ${merged}"
-while test $# -gt 0
-do
-    local partial="$1"
+    local merged="$1"
     shift
-    let count++
-    local arguments=" -i ${partial} ${arguments}"
-done
-${rootMerger} ${arguments} > /dev/null || warning "error while calling ${rootMerger}"
-echo "  ${indent}merged ${count} files"
+    echo "  ${indent}entering root merger"
+    echo "  ${indent}merger is ${rootMerger}"
+    echo "  ${indent}creating ${merged}"
+    #echo "######## $#"
+    #echo "######## $*"
+
+    if test $# -eq 1
+    then
+        echo "  ${indent}just one partial file => just copy it"
+        cp "$1" "${merged}"
+        return
+    fi
+
+    local count=0
+    local arguments=" -o ${merged}"
+    while test $# -gt 0
+    do
+        local partial="$1"
+        shift
+        let count++
+        local arguments=" -i ${partial} ${arguments}"
+    done
+    ${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
+    echo "  ${indent}merged ${count} files"
 }
 
 statMerger="mergeStatFile.py"
 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
 
 function merge_stat {
-local merged="$1"
-shift
-echo "  ${indent}entering stat merger"
-echo "  ${indent}merger is ${statMerger}"
-echo "  ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
-    local partial="$1"
+    local merged="$1"
     shift
-    let count++
+    echo "  ${indent}entering stat merger"
+    echo "  ${indent}merger is ${statMerger}"
+    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
 
-    if test ! -f "${merged}"
-    then
-        update_bar ${count} "copying first partial result ${partial}"
-        cp "${partial}" "${merged}"
-        continue
-    fi
+        update_bar ${count} "adding ${partial}"
+        ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
+}
 
-    update_bar ${count} "adding ${partial}"
-    ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
-done
-end_bar
-echo "  ${indent}merged ${count} files"
+doseMerger="mergeDosePerEnergyFile.sh"
+test -x "./mergeDosePerEnergyFile.sh" && doseMerger="./mergeDosePerEnergyFile.sh"
+
+function merge_dose {
+    local merged="$1"
+    shift
+    echo "  ${indent}entering dose merger"
+    echo "  ${indent}merger is ${doseMerger}"
+    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}"
+        ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
+}
+
+doseMerger="mergeDoseByRegions.sh"
+test -x "./mergeDoseByRegions.sh" && doseMerger="./mergeDoseByRegions.sh"
+
+function merge_doseByRegions {
+    local merged="$1"
+    shift
+    echo "  ${indent}entering dose merger"
+    echo "  ${indent}merger is ${doseMerger}"
+    echo "  ${indent}creating ${merged}"
+    local count=0
+    start_bar $#
+    source ${doseMerger}
+    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}" "${merged}"
+            copyFirstPartialResult -i "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+            continue
+        fi
+
+        update_bar ${count} "adding ${partial}"
+        addToPartialResult -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+    done
+    divideUncertaintyResult -i "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+    end_bar
+    echo "  ${indent}merged ${count} files"
 }
 
 txtImageMerger="clitkMergeAsciiDoseActor"
 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 
 function merge_txt_image {
-local merged="$1"
-shift
-echo "  ${indent}entering text image merger"
-echo "  ${indent}merger is ${txtImageMerger}"
-echo "  ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
-    local partial="$1"
+    local merged="$1"
     shift
-    let count++
-
-    if test ! -f "${merged}"
-    then
-        update_bar ${count} "copying first partial result ${partial}"
-        cp "${partial}" "${merged}"
-        continue
-    fi
+    echo "  ${indent}entering text image merger"
+    echo "  ${indent}merger is ${txtImageMerger}"
+    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)"
-    ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
-    echo "${header}" > "${merged}"
-    grep -v '## Merge' "${tmp}" >> "${merged}"
-    rm "${tmp}"
-done
-end_bar
-echo "  ${indent}merged ${count} files"
+        update_bar ${count} "adding ${partial}"
+        local header="$(cat "${merged}" | head -n 6)"
+        local tmp="$(mktemp)"
+        ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
+        echo "${header}" > "${merged}"
+        grep -v '## Merge' "${tmp}" >> "${merged}"
+        rm "${tmp}"
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
 }
 
 hdrImageMerger="clitkImageArithm"
 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
 
 function merge_hdr_image {
-local merged="$1"
-local merged_bin="${merged%.*}.img"
-shift
-echo "  ${indent}entering hdr image merger"
-echo "  ${indent}merger is ${hdrImageMerger}"
-echo "  ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
-    local partial="$1"
-    local partial_bin="${partial%.*}.img"
+    local merged="$1"
+    local merged_bin="${merged%.*}.img"
     shift
-    let count++
+    echo "  ${indent}entering hdr image merger"
+    echo "  ${indent}merger is ${hdrImageMerger}"
+    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
 
-    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}"
+        ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
+}
 
-    update_bar ${count} "adding ${partial}"
-    ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
-done
-end_bar
-echo "  ${indent}merged ${count} files"
+mhdImageMerger="clitkImageArithm"
+test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
+
+function merge_mhd_image {
+    local merged="$1"
+    local merged_bin="${merged%.*}.raw"
+    local last_character=${merged#${merged%?}}
+    shift
+    echo "  ${indent}entering mhd image merger"
+    echo "  ${indent}merger is ${mhdImageMerger}"
+    echo "  ${indent}creating ${merged}"
+    local count=0
+    start_bar $#
+    while test $# -gt 0
+    do
+        local partial="$1"
+        local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
+        shift
+        let count++
+
+        if test ! -f "${merged}"
+        then
+            update_bar ${count} "copying first partial result ${partial}"
+            cp "${partial}" "${merged}"
+            if test "$last_character" = "d"
+            then
+                cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+            fi
+            continue
+        fi
+
+        update_bar ${count} "adding ${partial}"
+        ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
+        if test "$last_character" = "d" && test "${merged_bin}" != "${merged_bin%.*}.${partial_bin##*.}"
+        then
+            mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+            sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
+        fi
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
 }
 
 function merge_dispatcher {
@@ -168,26 +348,53 @@ function merge_dispatcher {
     local outputfile="${1:?"provide output filename"}"
     echo "merging ${outputfile}"
 
-    local partialoutputfiles="$(find "${rundir}" -type f -name "${outputfile}")"
+    local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
     local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
     if test ${nboutputdirs} -ne ${nboutputfiles}
     then
         warning "missing files"
-        return
+        if ! test "${2}" == "--force"
+        then
+            return
+        fi
     fi
 
     local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
     local firstpartialoutputextension="${firstpartialoutputfile##*.}"
     echo "${indent}testing file type on ${firstpartialoutputfile}"
 
+    if test "${firstpartialoutputextension}" == "hdr" && test grep -qs 'INTERFILE' "${firstpartialoutputfile}"
+    then
+        echo "${indent}this is an interfile image"
+        echo "${indent}creating mhd headers"
+        for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
+        local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
+        local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
+        merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
+        echo "${indent}cleaning mhd headers"
+        for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done
+        rm "${mhd_mergedfile}"
+        echo "${indent}copy interfile header"
+        cp "${firstpartialoutputfile}" "${outputdir}"
+        return
+    fi
+
     if test "${firstpartialoutputextension}" == "hdr"
     then
-        echo "${indent}this is a analyse image"
+        echo "${indent}this is an analyse image"
         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
         merge_hdr_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
         return
     fi
 
+    if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
+    then
+        echo "${indent}this is a mhd image"
+        local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+        merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+        return
+    fi
+
     if test "${firstpartialoutputextension}" == "root"
     then
         echo "${indent}this is a root file"
@@ -196,7 +403,7 @@ function merge_dispatcher {
         return
     fi
 
-    if test "${firstpartialoutputextension}" == "txt" && grep 'NumberOfEvent' "${firstpartialoutputfile}" > /dev/null
+    if test "${firstpartialoutputextension}" == "txt" && grep -qs 'NumberOfEvent' "${firstpartialoutputfile}"
     then
         echo "${indent}this is a stat file"
         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
@@ -204,7 +411,17 @@ function merge_dispatcher {
         return
     fi
 
-    if test "${firstpartialoutputextension}" == "txt" && grep 'Resol' "${firstpartialoutputfile}" > /dev/null
+    if test "${firstpartialoutputextension}" == "txt" && grep -qs 'energydose' "${firstpartialoutputfile}"
+    then
+        echo "${indent}this is a dose file"
+        local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+        merge_dose "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+        return
+    fi
+
+
+
+    if test "${firstpartialoutputextension}" == "txt" && grep -qs 'Resol' "${firstpartialoutputfile}"
     then
         local resol="$(sed -nr '/Resol/s/^.*=\s+\((.+)\)\s*$/\1/p' "${firstpartialoutputfile}")"
         local resolx="$(echo "${resol}" | cut -d',' -f1)"
@@ -226,23 +443,119 @@ function merge_dispatcher {
         fi
     fi
 
+    if test "${firstpartialoutputextension}" == "txt" && grep -qs 'vol(mm3)' "${firstpartialoutputfile}"
+    then
+        echo "${indent}this is a DoseByRegions file"
+        local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+        merge_doseByRegions "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+        return
+    fi
+
+
     if test "${firstpartialoutputextension}" == "txt"
     then
         echo "${indent}this is a non specific txt output"
         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
-        echo "  ${indent}catting ${mergedfile}"
-        cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
-        return
+        local nbdifferent="$(md5sum ${partialoutputfiles} | awk '{ print $1; }' | sort | uniq | wc -l)"
+        echo "  ${indent}${nbdifferent} different files"
+        if test ${nbdifferent} -gt 1
+        then
+            echo "  ${indent}catting to ${mergedfile}"
+            cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
+            return
+        else
+            echo "  ${indent}moving to ${mergedfile}"
+            cp "${firstpartialoutputfile}" "${mergedfile}" || error "error while merging"
+            return
+        fi
+    fi
+
+    error "unknown file type"
+}
+
+function merge_dispatcher_uncertainty {
+    local indent="  ** "
+    local outputfile="${1:?"provide output filename"}"
+
+    local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
+    local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
+    if test ${nboutputdirs} -ne ${nboutputfiles}
+    then
+        warning "missing files"
+        if ! test "${2}" == "--force"
+        then
+            return
+        fi
+    fi
+
+    local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
+    local firstpartialoutputextension="${firstpartialoutputfile##*.}"
+
+    if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
+    then
+    	  if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
+        then
+            echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
+            ## search for sum
+            local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+            summed_merged_file=${mergedfile//-Uncertainty/}
+            if [ ! -f ${summed_merged_file} ];
+            then
+                warning "${summed_merged_file} does not exist. Error, no uncertainty computed"
+                return;
+            fi
+            echo "${indent}${summed_merged_file} found"
+            ## search for Squared
+            squared_merged_file=${mergedfile//-Uncertainty/-Squared}
+            if [ ! -f ${squared_merged_file} ];
+            then
+                warning "${squared_merged_file} does not exist. Error, no uncertainty computed"
+                return;
+            fi
+            echo "${indent}${squared_merged_file} found"
+            ## search for NumberOfEvent
+            totalEvents=0;
+            unamestr=`uname`
+            if [[ "$unamestr" == 'Darwin' ]]; then
+                files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
+            else
+                files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+            fi
+            echo $files
+            for outputfile in ${files}
+            do
+                #echo $outputfile
+                if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
+                then
+                    totalEvents="$(grep "NumberOfEvents" "${outputdir}/${outputfile}" | cut -d' ' -f4)"
+                    echo "${indent}Find the NumberOfEvent in $outputfile: ${totalEvents}"
+                fi
+            done
+
+            if test ${totalEvents} -gt 0
+            then
+                uncerImageMerger="clitkImageUncertainty"
+                test -x "./clitkImageUncertainty" && uncerImageMerger="./clitkImageUncertainty"
+                ${uncerImageMerger} -i ${summed_merged_file} -s ${squared_merged_file} -o ${mergedfile} -n ${totalEvents}
+            else
+                warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
+                return;
+            fi
+	      else
+            error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
+        fi
     fi
 
-    warning "unknown file type"
 }
 
-echo "!!!! this is $0 v0.3g !!!!"
+echo "!!!! this is $0 v0.3k !!!!"
+echo "Usage: gate_power_merge.sh run.dir [--force]"
+echo "   where --force allows to merge files even if the file is missing in some output directories"
 
 rundir="${1?"provide run dir"}"
+force=${2:-""}
 rundir="$(echo "${rundir}" | sed 's|/*$||')"
-nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
+nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' -o -type l -name 'output*' | wc -l)"
 
 test ${nboutputdirs} -gt 0 || error "no output dir found"
 echo "found ${nboutputdirs} partial output dirs"
@@ -254,18 +567,52 @@ then
 fi
 outputdir="$(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 "${rundir}/output.*\.(hdr|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+unamestr=`uname`
+if [[ "$unamestr" == 'Darwin' ]]; then
+    files=$(find -L "${rundir}" -type f -regex ".*output.*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
+else
+    files=$(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+fi
+echo files $files
+for outputfile in ${files}
 do
-    merge_dispatcher "${outputfile}"
+    merge_dispatcher "${outputfile}" "${force}"
 done
 
+echo ""
+echo "Merging done. Special case for statistical uncertainty"
+
+unamestr=`uname`
+if [[ "$unamestr" == 'Darwin' ]]; then
+    files=$(find -L "${outputdir}" -type f -regex ".*[hdr|mhd|mha|root|txt]" | awk -F '/' '{ print $NF; }' | sort | uniq)
+else
+    files=$(find -L "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+fi
+echo files = $files
+for outputfile in ${files}
+do
+    merge_dispatcher_uncertainty "${outputfile}" "${force}"
+done
+
+echo "compute job statistics"
+python computeEnlapsedTime.py ${rundir} gate
+mv "statJobs.txt" "${outputdir}/statJobs.txt"
+
+
 if [ -f "${rundir}/params.txt" ]
 then
-	echo "copying params file"
-	cp "${rundir}/params.txt" "${outputdir}/params.txt"
+    echo "copying params file"
+    cp "${rundir}/params.txt" "${outputdir}/params.txt"
+fi
+
+if [ -d "${rundir}/mac" ]
+then
+    echo "copying mac folder"
+    cp -r "${rundir}/mac" "${outputdir}/mac"
 fi
 
 echo "these was ${warning_count} warning(s)"