From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Fri, 9 Nov 2018 08:49:28 +0000 (+0100)
Subject: Modify mergeDoseByRegion
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=88759fd450cc61a1b6818f80548c8632b2a3ffea;p=clitk.git

Modify mergeDoseByRegion

Before, it summed 2 files to write the result.
But I had to modify it to be able to sum partial std. So I created 3 functions:
 -addToPartialResult with the previous code
 - addWithoutPartialResult for the first file
 - divideUncertaintyResult for the last step
---

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index 8fa4cfc..bc3b3e0 100755
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -207,6 +207,7 @@ function merge_doseByRegions {
     echo "  ${indent}creating ${merged}"
     local count=0
     start_bar $#
+    source ${doseMerger}
     while test $# -gt 0
     do
         local partial="$1"
@@ -216,13 +217,14 @@ function merge_doseByRegions {
         if test ! -f "${merged}"
         then
             update_bar ${count} "copying first partial result ${partial}"
-            cp "${partial}" "${merged}"
+            addWithoutPartialResult -i "${partial}" -o "${merged}"
             continue
         fi
 
         update_bar ${count} "adding ${partial}"
-        ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+        addToPartialResult -i "${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"
 }
diff --git a/cluster_tools/mergeDoseByRegions.sh b/cluster_tools/mergeDoseByRegions.sh
index f6a438c..0548db6 100755
--- a/cluster_tools/mergeDoseByRegions.sh
+++ b/cluster_tools/mergeDoseByRegions.sh
@@ -2,102 +2,258 @@
 set -u
 
 function usage {
-  echo "$0 -i <file1> -j <file2> -o <result>"
+  echo "$0 -i <result> -j <file2> -o <result>"
   exit 1
 }
 
-if [ $# != 6 ]
-then
-  usage
-fi
+function addToPartialResult {
+  IN1=$2
+  IN2=$4
+  RESULT=$6
 
-IN1=$2
-IN2=$4
-RESULT=$6
+  test -f ${IN1} && test -f ${IN2} || usage
 
-test -f ${IN1} && test -f ${IN2} || usage
+  TMP="$(mktemp)"
 
-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`
+  # 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 ${line2} | cut -f3 -d' ')
-  edep3=$(python -c "print($edep1+$edep2)")
-  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 ${line2} | cut -f4 -d' ')
-  edep3=$(python -c "import math; print(math.sqrt($edep1*$edep1+$edep2*$edep2))")
-  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 ${line2} | cut -f5 -d' ')
-  edep3=$(python -c "print($edep1+$edep2)")
-  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 ${line2} | cut -f6 -d' ')
-  edep3=$(python -c "print($edep1+$edep2)")
-  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 ${line2} | cut -f7 -d' ')
-  edep3=$(python -c "import math; print(math.sqrt($edep1*$edep1+$edep2*$edep2))")
-  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 ${line2} | cut -f8 -d' ')
-  edep3=$(python -c "print($edep1+$edep2)")
-  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 ${line2} | cut -f9 -d' ')
-  edep3=$(python -c "print($edep1+$edep2)")
-  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 ${line2} | cut -f10 -d' ')
-  edep3=$(python -c "print($edep1+$edep2)")
-  line3=$(echo $line3 |awk -v r=${edep3} '{$10=r}1')
-
-  #Write the output
-  echo "${line3}" >> ${TMP}
-done
-mv -f ${TMP} ${RESULT}
+  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 $nblines); do
+    #Get the 3 lines
+    file1=`sed -n "${i}p" < ${IN1}`
+    file2=`sed -n "${i}p" < ${IN2}`
+    file3=`sed -n "${i}p" < ${RESULT}`
+
+    # sum edep: get the 2 values, sum them and replace it in the file3
+    # The /#./0. is important to add 0 for decimal value between 0 and 1
+    edep1=$(echo ${file1} | cut -f3 -d' ')
+    edep2=$(echo ${file2} | cut -f3 -d' ')
+    edep3=$(python -c "print($edep1+$edep2)")
+    edep3=${edep3/#./0.}
+    file3=$(echo $file3 |awk -v r=${edep3} '{$3=r}1')
+
+    # sqrt sum square std_edep*edep: get the 2 values, sum the square, take the sqrt and replace it in the file3
+    stdEdep1=$(echo ${file1} | cut -f4 -d' ')
+    stdEdep2=$(echo ${file2} | cut -f4 -d' ')
+    stdEdep3=$(python <<EOP
+import math;
+temp=$edep2*$stdEdep2;
+print(math.sqrt($stdEdep1*$stdEdep1+temp*temp))
+EOP
+    )
+    stdEdep3=${stdEdep3/#./0.}
+    file3=$(echo $file3 |awk -v r=${stdEdep3} '{$4=r}1')
+
+    # sum square_edep: get the 2 values, sum them and replace it in the file3
+    sqEdep1=$(echo ${file1} | cut -f5 -d' ')
+    sqEdep2=$(echo ${file2} | cut -f5 -d' ')
+    sqEdep3=$(python -c "print($sqEdep1+$sqEdep2)")
+    sqEdep3=${sqEdep3/#./0.}
+    file3=$(echo $file3 |awk -v r=${sqEdep3} '{$5=r}1')
+
+    # sum dose: get the 2 values, sum them and replace it in the file3
+    dose1=$(echo ${file1} | cut -f6 -d' ')
+    dose2=$(echo ${file2} | cut -f6 -d' ')
+    dose3=$(python -c "print($dose1+$dose2)")
+    dose3=${dose3/#./0.}
+    file3=$(echo $file3 |awk -v r=${dose3} '{$6=r}1')
+
+    # sqrt sum square std_dose*dose: get the 2 values, sum the square, take the sqrt and replace it in the file3
+    stdDose1=$(echo ${file1} | cut -f7 -d' ')
+    stdDose2=$(echo ${file2} | cut -f7 -d' ')
+    stdDose3=$(python <<EOP
+import math;
+temp=$dose2*$stdDose2;
+print(math.sqrt($stdDose1*$stdDose1+temp*temp))
+EOP
+    )
+    stdDose3=${stdDose3/#./0.}
+    file3=$(echo $file3 |awk -v r=${stdDose3} '{$7=r}1')
+
+    # sum square_dose: get the 2 values, sum them and replace it in the file3
+    sqDose1=$(echo ${file1} | cut -f8 -d' ')
+    sqDose2=$(echo ${file2} | cut -f8 -d' ')
+    sqDose3=$(python -c "print($sqDose1+$sqDose2)")
+    sqDose3=${sqDose3/#./0.}
+    file3=$(echo $file3 |awk -v r=${sqDose3} '{$8=r}1')
+
+    # sum n_hits: get the 2 values, sum them and replace it in the file3
+    hit1=$(echo ${file1} | cut -f9 -d' ')
+    hit2=$(echo ${file2} | cut -f9 -d' ')
+    hit3=$(python -c "print($hit1+$hit2)")
+    file3=$(echo $file3 |awk -v r=${hit3} '{$9=r}1')
+
+    # sum n_event_hits: get the 2 values, sum them and replace it in the file3
+    event1=$(echo ${file1} | cut -f10 -d' ')
+    event2=$(echo ${file2} | cut -f10 -d' ')
+    event3=$(python -c "print($event1+$event2)")
+    file3=$(echo $file3 |awk -v r=${event3} '{$10=r}1')
+
+    #Write the output
+    echo "${file3}" >> ${TMP}
+  done
+  mv -f ${TMP} ${RESULT}
+}
+
+function addWithoutPartialResult {
+  IN1=$2
+  RESULT=$4
+
+  test -f ${IN1} || usage
+
+  TMP="$(mktemp)"
+
+  nblines=`cat ${IN1} | wc -l`
+
+  #Copy the 1st line in output
+  line1=`sed -n "1p" < ${IN1}`
+  echo "${line1}" >> ${TMP}
+  # for all lines (except the 1st), split according tab
+  # sum the some elements (dose, edep) ...
+  for i in $(seq 2 $nblines); do
+    #Get the lines
+    file1=`sed -n "${i}p" < ${IN1}`
+
+    # copy id
+    id1=$(echo ${file1} | cut -f1 -d' ')
+    id1=${id1/#./0.}
+    file3=$(echo $id1)
+
+    # copy volume
+    vol1=$(echo ${file1} | cut -f2 -d' ')
+    vol1=${vol1/#./0.}
+    file3=$(echo "$file3 $vol1")
+
+    # copy edep
+    edep1=$(echo ${file1} | cut -f3 -d' ')
+    edep1=${edep1/#./0.}
+    file3=$(echo "$file3 $edep1")
+
+    # sqrt sum square std_edep*edep
+    stdEdep1=$(echo ${file1} | cut -f4 -d' ')
+    stdEdep3=$(python <<EOP
+import math;
+temp=$edep1*$stdEdep1;
+print(math.sqrt(temp*temp))
+EOP
+    )
+    stdEdep3=${stdEdep3/#./0.}
+    file3=$(echo "$file3 $stdEdep3")
+
+    # copy square_edep
+    sqEdep1=$(echo ${file1} | cut -f5 -d' ')
+    sqEdep1=${sqEdep1/#./0.}
+    file3=$(echo "$file3 $sqEdep1")
+
+    # copy dose
+    dose1=$(echo ${file1} | cut -f6 -d' ')
+    dose1=${dose1/#./0.}
+    file3=$(echo "$file3 $dose1")
+
+    # sqrt sum square std_dose*dose
+    stdDose1=$(echo ${file1} | cut -f7 -d' ')
+    stdDose3=$(python <<EOP
+import math;
+temp=$dose1*$stdDose1;
+print(math.sqrt(temp*temp))
+EOP
+    )
+    stdDose3=${stdDose3/#./0.}
+    file3=$(echo "$file3 $stdDose3")
+
+    # copy square_dose
+    sqDose1=$(echo ${file1} | cut -f8 -d' ')
+    sqDose1=${sqDose1/#./0.}
+    file3=$(echo "$file3 $sqDose1")
+
+    # copy n_hits
+    hit1=$(echo ${file1} | cut -f9 -d' ')
+    hit1=${hit1/#./0.}
+    file3=$(echo "$file3 $hit1")
+
+    # copy n_event_hits
+    event1=$(echo ${file1} | cut -f10 -d' ')
+    event1=${event1/#./0.}
+    file3=$(echo "$file3 $event1")
+
+    #Write the output
+    echo "${file3}" >> ${TMP}
+  done
+  mv -f ${TMP} ${RESULT}
+}
+
+
+function divideUncertaintyResult {
+  IN1=$2
+  value=$4
+  RESULT=$6
+
+  TMP="$(mktemp)"
+
+  # check if all 3 text files have the same number of lines
+  nblines=`cat ${IN1} | wc -l`
+  nb3=`cat ${RESULT} | wc -l`
+
+  if [ $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 $nblines); do
+    #Get the lines
+    file1=`sed -n "${i}p" < ${IN1}`
+    file3=`sed -n "${i}p" < ${RESULT}`
+
+    # Divide uncertainty and replace it in the file3
+    edep1=$(echo ${file1} | cut -f3 -d' ')
+    stdEdep1=$(echo ${file1} | cut -f4 -d' ')
+    stdEdep3=$(python <<EOP
+temp=$stdEdep1/$value
+if $edep1!=0:
+  temp/=$edep1
+if temp==0:
+  temp=1
+print(temp)
+EOP
+    )
+    stdEdep3=${stdEdep3/#./0.}
+    file3=$(echo $file3 |awk -v r=${stdEdep3} '{$4=r}1')
+
+    # Divide uncertainty and replace it in the file3
+    dose1=$(echo ${file1} | cut -f6 -d' ')
+    stdDose1=$(echo ${file1} | cut -f7 -d' ')
+    stdDose3=$(python <<EOP
+temp=$stdDose1/$value
+if $dose1!=0:
+  temp/=$dose1
+if temp==0:
+  temp=1
+print(temp)
+EOP
+    )
+    stdDose3=${stdDose3/#./0.}
+    file3=$(echo $file3 |awk -v r=${stdDose3} '{$7=r}1')
+
+    #Write the output
+    echo "${file3}" >> ${TMP}
+  done
+  mv -f ${TMP} ${RESULT}
+}