X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=cluster_tools%2Fgate_power_merge.sh;h=bc3b3e033450749631b4fe60401c04a86b6d6a2f;hb=88759fd450cc61a1b6818f80548c8632b2a3ffea;hp=aaf063b18d4f8cc85be856ef0f19df1087c1570d;hpb=8eccf1e25d2ab7273145d2475ae015aea5f6ff94;p=clitk.git

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index aaf063b..bc3b3e0 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 +196,39 @@ 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 ${partial}"
+            addWithoutPartialResult -i "${partial}" -o "${merged}"
+            continue
+        fi
+
+        update_bar ${count} "adding ${partial}"
+        addToPartialResult -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+    done
+    divideUncertaintyResult -i "${merged}" -j "${count}" -o "${merged}"
+    end_bar
+    echo "  ${indent}merged ${count} files"
+}
+
 txtImageMerger="clitkMergeAsciiDoseActor"
 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 
@@ -329,9 +362,9 @@ function merge_dispatcher {
     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)"
@@ -347,7 +380,7 @@ 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
@@ -409,6 +442,15 @@ 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"
@@ -450,7 +492,7 @@ function merge_dispatcher_uncertainty {
 
     if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
     then
-    	if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
+    	  if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
         then
             echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
             ## search for sum
@@ -472,7 +514,14 @@ function merge_dispatcher_uncertainty {
             echo "${indent}${squared_merged_file} found"
             ## search for NumberOfEvent
             totalEvents=0;
-            for outputfile in $(find -L "${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
+            for outputfile in ${files}
             do
                 #echo $outputfile
                 if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
@@ -491,7 +540,7 @@ function merge_dispatcher_uncertainty {
                 warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
                 return;
             fi
-	else
+	      else
             error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
         fi
     fi
@@ -520,18 +569,39 @@ echo "output dir is ${outputdir}"
 
 test -d "${outputdir}" && rm -r "${outputdir}"
 mkdir "${outputdir}"
-for outputfile in $(find -L "${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}" "${force}"
 done
 
 echo ""
 echo "Merging done. Special case for statistical uncertainty"
-for outputfile in $(find -L "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|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}" "${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"