From d27b2f45396b69a0d3e61a2179b3d0c784ff9652 Mon Sep 17 00:00:00 2001
From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Wed, 14 Nov 2018 13:28:25 +0100
Subject: [PATCH] Merge dose by region uncertainties using Gate uncertainty
calculation
Instead of using partial uncertainty, I use the total dose or edep and the square of the dose and edep like
I removed a bash function because it's useless
---
cluster_tools/gate_power_merge.sh | 3 +-
cluster_tools/mergeDoseByRegions.sh | 132 ++--------------------------
2 files changed, 8 insertions(+), 127 deletions(-)
diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index bc3b3e0..b2ced88 100755
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -217,14 +217,13 @@ function merge_doseByRegions {
if test ! -f "${merged}"
then
update_bar ${count} "copying first partial result ${partial}"
- addWithoutPartialResult -i "${partial}" -o "${merged}"
+ cp "${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 ${doseMerger}"
done
- divideUncertaintyResult -i "${merged}" -j "${count}" -o "${merged}"
end_bar
echo " ${indent}merged ${count} files"
}
diff --git a/cluster_tools/mergeDoseByRegions.sh b/cluster_tools/mergeDoseByRegions.sh
index 0548db6..598df69 100755
--- a/cluster_tools/mergeDoseByRegions.sh
+++ b/cluster_tools/mergeDoseByRegions.sh
@@ -44,18 +44,6 @@ function addToPartialResult {
edep3=${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 ${file2} | cut -f5 -d' ')
@@ -70,18 +58,6 @@ EOP
dose3=${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' ')
@@ -107,94 +83,6 @@ EOP
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=$4
@@ -202,7 +90,7 @@ function divideUncertaintyResult {
TMP="$(mktemp)"
- # check if all 3 text files have the same number of lines
+ # check if all 2 text files have the same number of lines
nblines=`cat ${IN1} | wc -l`
nb3=`cat ${RESULT} | wc -l`
@@ -223,13 +111,10 @@ function divideUncertaintyResult {
# Divide uncertainty and replace it in the file3
edep1=$(echo ${file1} | cut -f3 -d' ')
- stdEdep1=$(echo ${file1} | cut -f4 -d' ')
+ sqEdep1=$(echo ${file1} | cut -f5 -d' ')
stdEdep3=$(python <<EOP
-temp=$stdEdep1/$value
-if $edep1!=0:
- temp/=$edep1
-if temp==0:
- temp=1
+import math
+temp=math.sqrt(($sqEdep1/$value-pow($edep1/$value, 2))/($value-1))/$edep1/$value
print(temp)
EOP
)
@@ -238,13 +123,10 @@ EOP
# Divide uncertainty and replace it in the file3
dose1=$(echo ${file1} | cut -f6 -d' ')
- stdDose1=$(echo ${file1} | cut -f7 -d' ')
+ sqDose1=$(echo ${file1} | cut -f8 -d' ')
stdDose3=$(python <<EOP
-temp=$stdDose1/$value
-if $dose1!=0:
- temp/=$dose1
-if temp==0:
- temp=1
+import math
+temp=math.sqrt(($sqDose1/$value-pow($dose1/$value, 2))/($value-1))/$dose1/$value
print(temp)
EOP
)
--
2.49.0