X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=cluster_tools%2Fgate_power_merge.sh;h=b2ced88862b9f61b4f6cd20ab4c45006502b68ac;hb=d27b2f45396b69a0d3e61a2179b3d0c784ff9652;hp=e35a683fb2bcf3694eed7f10519995efe4333d58;hpb=97a3a9ed3f33ab0316bd4613c8aae404de40dad1;p=clitk.git

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index e35a683..b2ced88 100755
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -165,7 +165,7 @@ function merge_stat {
     echo "  ${indent}merged ${count} files"
 }
 
-doseMerger="mergeDosePerEnegryFile.sh"
+doseMerger="mergeDosePerEnergyFile.sh"
 test -x "./mergeDosePerEnergyFile.sh" && doseMerger="./mergeDosePerEnergyFile.sh"
 
 function merge_dose {
@@ -196,6 +196,38 @@ function merge_dose {
     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}"
+            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
+    end_bar
+    echo "  ${indent}merged ${count} files"
+}
+
 txtImageMerger="clitkMergeAsciiDoseActor"
 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 
@@ -272,6 +304,7 @@ 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}"
@@ -289,14 +322,20 @@ function merge_mhd_image {
         then
             update_bar ${count} "copying first partial result ${partial}"
             cp "${partial}" "${merged}"
-            cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+            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 ${mhdImageMerger}"
-        mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
-        sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
+        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 ${count} files"
@@ -307,21 +346,24 @@ function merge_dispatcher {
     local outputfile="${1:?"provide output filename"}"
     echo "merging ${outputfile}"
 
-    local partialoutputfiles="$(find "${rundir}" -mindepth 2 -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 "${firstpartialoutputextension}" == "hdr" && grep -qs 'INTERFILE' "${firstpartialoutputfile}"
+    if test "${firstpartialoutputextension}" == "hdr" && test grep -qs 'INTERFILE' "${firstpartialoutputfile}"
     then
-        echo "${indent}this is a interfile image"
+        echo "${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)"
@@ -337,7 +379,7 @@ function merge_dispatcher {
 
     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
@@ -399,6 +441,15 @@ 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 "${indent}this is a non specific txt output"
@@ -424,12 +475,15 @@ function merge_dispatcher_uncertainty {
     local indent="  ** "
     local outputfile="${1:?"provide output filename"}"
 
-    local partialoutputfiles="$(find "${rundir}" -mindepth 2 -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)"
@@ -437,7 +491,7 @@ function merge_dispatcher_uncertainty {
 
     if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
     then
-        if test "${firstpartialoutputextension}" == "mhd"
+    	  if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
         then
             echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
             ## search for sum
@@ -459,7 +513,14 @@ function merge_dispatcher_uncertainty {
             echo "${indent}${squared_merged_file} found"
             ## search for NumberOfEvent
             totalEvents=0;
-            for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|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
+            for outputfile in ${files}
             do
                 #echo $outputfile
                 if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
@@ -478,16 +539,21 @@ function merge_dispatcher_uncertainty {
                 warning "${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
 
 }
 
 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"
@@ -503,22 +569,48 @@ 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|mhd|mha|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"
-for outputfile in $(find "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+
+unamestr=`uname`
+if [[ "$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}"
+    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"
 fi
 
+if [ -d "${rundir}/mac" ]
+then
+    echo "copying mac folder"
+    cp -r "${rundir}/mac" "${outputdir}/mac"
+fi
+
 echo "these was ${warning_count} warning(s)"