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 #merged file for previous jobs
+ IN2=$4 # current job
+ RESULT=$6 #output merged file
-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 ${line2} | cut -f3 -d' ')
- edep3=$(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}
+ if [ $nblines -ne $nb2 ] || [ $nblines -ne $nb3 ]; then
+ echo "Files does not have the same size"
+ exit 1
+ fi
+
+ # Find the number of primaries for this job (the same for all line and different of 0)
+ # Get the number of primaries from edep and square_edep to determine the std.
+ nbPrimary=0
+ for i in $(seq 2 $nblines); do
+ #Get the line
+ file2=`sed -n "${i}p" < ${IN2}`
+
+ edep2=$(echo ${file2} | cut -f3 -d' ')
+ stdEdep2=$(echo ${file2} | cut -f4 -d' ')
+ sqEdep2=$(echo ${file2} | cut -f5 -d' ')
+ nbPrimary=$(python <<EOP
+if ($edep2 == 0 or $sqEdep2 == 0):
+ print(0)
+else:
+ temp=pow($edep2,2)*(pow($stdEdep2,2)-1)/(pow($stdEdep2*$edep2,2)-$sqEdep2)
+ print(int(round(temp)))
+EOP
+ )
+ if [ $nbPrimary -ne 0 ]; then
+ break
+ fi
+
+ dose2=$(echo ${file2} | cut -f6 -d' ')
+ stdDose2=$(echo ${file2} | cut -f7 -d' ')
+ sqDose2=$(echo ${file2} | cut -f8 -d' ')
+ nbPrimary=$(python <<EOP
+if ($dose2 == 0 or $sqDose2 == 0):
+ print(0)
+else:
+ temp=pow($dose2,2)*(pow($stdDose2,2)-1)/(pow($stdDose2*$dose2,2)-$sqDose2)
+ print(int(round(temp)))
+EOP
+ )
+ if [ $nbPrimary -ne 0 ]; then
+ break
+ fi
+ done
+
+ #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} '{$3=r}1')
+
+ # sum square_edep: get the 2 values, sum them and replace it in the file3
+ sqEdep1=$(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} '{$5=r}1')
+
+ # Get the number of primaries from edep and square_edep to determine the std.
+ # Sum the number of primaries with the latter ones
+ nbPrimaryEdep1=$(echo ${file1} | cut -f4 -d' ')
+ nbPrimaryEdep3=$(python <<EOP
+print($nbPrimary+$nbPrimaryEdep1)
+EOP
+ )
+ nbPrimaryEdep3=${nbPrimaryEdep3/#./0.}
+ file3=$(echo $file3 |awk -v r=${nbPrimaryEdep3} '{$4=r}1')
+
+ # sum dose: get the 2 values, sum them and replace it in the file3
+ dose1=$(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} '{$6=r}1')
+
+ # sum square_dose: get the 2 values, sum them and replace it in the file3
+ sqDose1=$(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} '{$8=r}1')
+
+ # Get the number of primaries from dose and square_dose to determine the std.
+ # Sum the number of primaries with the latter ones
+ nbPrimaryDose1=$(echo ${file1} | cut -f7 -d' ')
+ stdDose2=$(echo ${file2} | cut -f7 -d' ')
+ nbPrimaryDose3=$(python <<EOP
+print($nbPrimary+$nbPrimaryDose1)
+EOP
+ )
+ nbPrimaryDose3=${nbPrimaryDose3/#./0.}
+ file3=$(echo $file3 |awk -v r=${nbPrimaryDose3} '{$7=r}1')
+
+ # sum n_hits: get the 2 values, sum them and replace it in the file3
+ hit1=$(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 copyFirstPartialResult {
+ IN1=$2
+ RESULT=$4
+
+ TMP="$(mktemp)"
+
+ # check if all 2 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
+ # Find the number of primaries for this job (the same for all line and different of 0)
+ # Get the number of primaries from edep and square_edep to determine the std.
+ nbPrimary=0
+ for i in $(seq 2 $nblines); do
+ #Get the line
+ file2=`sed -n "${i}p" < ${IN1}`
+
+ edep2=$(echo ${file2} | cut -f3 -d' ')
+ stdEdep2=$(echo ${file2} | cut -f4 -d' ')
+ sqEdep2=$(echo ${file2} | cut -f5 -d' ')
+ nbPrimary=$(python <<EOP
+if ($edep2 == 0 or $sqEdep2 == 0):
+ print(0)
+else:
+ temp=pow($edep2,2)*(pow($stdEdep2,2)-1)/(pow($stdEdep2*$edep2,2)-$sqEdep2)
+ print(int(round(temp)))
+EOP
+ )
+ if [ $nbPrimary -ne 0 ]; then
+ break
+ fi
+
+ dose2=$(echo ${file2} | cut -f6 -d' ')
+ stdDose2=$(echo ${file2} | cut -f7 -d' ')
+ sqDose2=$(echo ${file2} | cut -f8 -d' ')
+ nbPrimary=$(python <<EOP
+if ($dose2 == 0 or $sqDose2 == 0):
+ print(0)
+else:
+ temp=pow($dose2,2)*(pow($stdDose2,2)-1)/(pow($stdDose2*$dose2,2)-$sqDose2)
+ print(int(round(temp)))
+EOP
+ )
+ if [ $nbPrimary -ne 0 ]; then
+ break
+ fi
+ done
+
+ #Copy the 1st line in output
+ line1=`sed -n "1p" < ${RESULT}`
+ echo "${line1}" >> ${TMP}
+ # for all lines (except the 1st), split according tab
+ # write the number of primaries
+ for i in $(seq 2 $nblines); do
+ #Get the lines
+ file3=`sed -n "${i}p" < ${RESULT}`
+
+ file3=$(echo $file3 |awk -v r=${nbPrimary} '{$4=r}1')
+ file3=$(echo $file3 |awk -v r=${nbPrimary} '{$7=r}1')
+
+ #Write the output
+ echo "${file3}" >> ${TMP}
+ done
+ mv -f ${TMP} ${RESULT}
+}
+
+function divideUncertaintyResult {
+ IN1=$2
+ RESULT=$4
+
+ TMP="$(mktemp)"
+
+ # check if all 2 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 ${file1} | cut -f3 -d' ')
+ nbPrimaryEdep1=$(echo ${file1} | cut -f4 -d' ')
+ sqEdep1=$(echo ${file1} | cut -f5 -d' ')
+ stdEdep3=$(python <<EOP
+import math
+if ($edep1 == 0 or $sqEdep1 == 0):
+ print(1.0)
+else:
+ temp=math.sqrt(($sqEdep1/$nbPrimaryEdep1-pow($edep1/$nbPrimaryEdep1, 2))/($nbPrimaryEdep1-1))/($edep1/$nbPrimaryEdep1)
+ 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 ${file1} | cut -f6 -d' ')
+ nbPrimaryDose1=$(echo ${file1} | cut -f7 -d' ')
+ sqDose1=$(echo ${file1} | cut -f8 -d' ')
+ stdDose3=$(python <<EOP
+import math
+if ($edep1 == 0 or $sqEdep1 == 0):
+ print(1.0)
+else:
+ temp=math.sqrt(($sqDose1/$nbPrimaryDose1-pow($dose1/$nbPrimaryDose1, 2))/($nbPrimaryDose1-1))/($dose1/$nbPrimaryDose1)
+ 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}
+}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff