Add merger for DoseByRegions

diff --git a/cluster_tools/CMakeLists.txt b/cluster_tools/CMakeLists.txt
index f0167f6ee934cec9d524515cbdd6d87a4379a36d..e208df41b3bb500fd69aeb9bf8adfac3d2dac8c8 100644 (file)
--- a/cluster_tools/CMakeLists.txt
+++ b/cluster_tools/CMakeLists.txt
@@ -10,6 +10,7 @@ if(CLITK_BUILD_TOOLS)
     gate_run_submit_cluster.sh
     gate_upload_release.sh
     mergeDosePerEnergyFile.sh
+    mergeDoseByRegions.sh
     mergeStatFile.py
     mergeStatFile.sh
     gate_run_submit_cluster_nomove.sh

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index a0c3e183318d0fbdd17c338dc6e2ecdaa315c303..7717c578fe355975af3d6aeeea5d2969ab5feeae 100755 (executable)
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -196,6 +196,37 @@ 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 $#
+    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"
+}
+
 txtImageMerger="clitkMergeAsciiDoseActor"
 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 
@@ -409,6 +440,15 @@ 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"

diff --git a/cluster_tools/mergeDoseByRegions.sh b/cluster_tools/mergeDoseByRegions.sh
new file mode 100755 (executable)
index 0000000..d7a390a
--- /dev/null
+++ b/cluster_tools/mergeDoseByRegions.sh
@@ -0,0 +1,103 @@
+#!/bin/bash
+set -u
+
+function usage {
+  echo "$0 -i <file1> -j <file2> -o <result>"
+  exit 1
+}
+
+if [ $# != 6 ]
+then
+  usage
+fi
+
+IN1=$2
+IN2=$4
+RESULT=$6
+
+test -f ${IN1} && test -f ${IN2} || usage
+
+TMP="$(mktemp)"
+echo "merging dose by regions file"
+# check if all 3 text files have the same number of lines
+nblines=`cat ${IN1} | wc -l`
+nb2=`cat ${IN2} | wc -l`
+nb3=`cat ${RESULT} | wc -l`
+
+if [ $nblines -ne $nb2 ] || [ $nblines -ne $nb3 ]; then
+  echo "Files does not have the same size"
+  exit 1
+fi
+
+#Copy the 1st line in output
+line1=`sed -n "1p" < ${RESULT}`
+echo "${line1}" >> ${TMP}
+
+# for all lines (except the 1st), split according tab
+# sum the some elements (dose, edep) ...
+for i in $(seq 2 $nblines); do
+  #Get the 3 lines
+  line1=`sed -n "${i}p" < ${IN1}`
+  line2=`sed -n "${i}p" < ${IN2}`
+  line3=`sed -n "${i}p" < ${RESULT}`
+
+  # sum edep: get the 2 values, sum them and replace it in the line3
+  # The /#./0. is important to add 0 for decimal value between 0 and 1
+  edep1=$(echo ${line1} | cut -f3 -d' ')
+  edep2=$(echo ${line2} | cut -f3 -d' ')
+  edep3=$(echo "scale=30;$edep1+$edep2" | bc)
+  edep3=${edep3/#./0.}
+  line3=$(echo $line3 |awk -v r=${edep3} '{$3=r}1')
+
+  # sqrt sum square std_edep: get the 2 values, sum the square, take the sqrt and replace it in the line3
+  edep1=$(echo ${line1} | cut -f4 -d' ')
+  edep2=$(echo ${line2} | cut -f4 -d' ')
+  edep3=$(echo "scale=30;sqrt($edep1*$edep1+$edep2*$edep2)" | bc)
+  edep3=${edep3/#./0.}
+  line3=$(echo $line3 |awk -v r=${edep3} '{$4=r}1')
+
+  # sum square_edep: get the 2 values, sum them and replace it in the line3
+  edep1=$(echo ${line1} | cut -f5 -d' ')
+  edep2=$(echo ${line2} | cut -f5 -d' ')
+  edep3=$(echo "scale=30;$edep1+$edep2" | bc)
+  edep3=${edep3/#./0.}
+  line3=$(echo $line3 |awk -v r=${edep3} '{$5=r}1')
+
+  # sum dose: get the 2 values, sum them and replace it in the line3
+  edep1=$(echo ${line1} | cut -f6 -d' ')
+  edep2=$(echo ${line2} | cut -f6 -d' ')
+  edep3=$(echo "scale=30;$edep1+$edep2" | bc)
+  edep3=${edep3/#./0.}
+  line3=$(echo $line3 |awk -v r=${edep3} '{$6=r}1')
+
+  # sqrt sum square std_dose: get the 2 values, sum the square, take the sqrt and replace it in the line3
+  edep1=$(echo ${line1} | cut -f7 -d' ')
+  edep2=$(echo ${line2} | cut -f7 -d' ')
+  edep3=$(echo "scale=30;sqrt($edep1*$edep1+$edep2*$edep2)" | bc)
+  edep3=${edep3/#./0.}
+  line3=$(echo $line3 |awk -v r=${edep3} '{$7=r}1')
+
+  # sum square_dose: get the 2 values, sum them and replace it in the line3
+  edep1=$(echo ${line1} | cut -f8 -d' ')
+  edep2=$(echo ${line2} | cut -f8 -d' ')
+  edep3=$(echo "scale=30;$edep1+$edep2" | bc)
+  edep3=${edep3/#./0.}
+  line3=$(echo $line3 |awk -v r=${edep3} '{$8=r}1')
+
+  # sum n_hits: get the 2 values, sum them and replace it in the line3
+  edep1=$(echo ${line1} | cut -f9 -d' ')
+  edep2=$(echo ${line2} | cut -f9 -d' ')
+  edep3=$(echo "scale=30;$edep1+$edep2" | bc)
+  line3=$(echo $line3 |awk -v r=${edep3} '{$9=r}1')
+
+  # sum n_event_hits: get the 2 values, sum them and replace it in the line3
+  edep1=$(echo ${line1} | cut -f10 -d' ')
+  edep2=$(echo ${line2} | cut -f10 -d' ')
+  edep3=$(echo "scale=30;$edep1+$edep2" | bc)
+  line3=$(echo $line3 |awk -v r=${edep3} '{$10=r}1')
+
+  #Write the output
+  echo "${line3}" >> ${TMP}
+done
+mv -f ${TMP} ${RESULT}
+