SN_timecalib.sh

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#!/bin/zsh
script=${0##*/}

if [ -z $JPP_DIR ]; then
    echo "Variable JPP_DIR undefined."
    exit
fi

source $JPP_DIR/setenv.sh $JPP_DIR >& /dev/null

if do_usage $*; then
    usage "$script <input detector file> <output detector file> <first run> <last run> <name suffix> <output directory> <data directory>"
fi

DETECTOR_IN=$1
DETECTOR_OUT=$2
RUNFIRST=$3
RUNSECOND=$4
EXT=$5
OUTDIR=$6
DATADIR=$7

eval `JPrintDetector -a $DETECTOR_IN -O IDENTIFIER`

#--- copy detector

JConvertDetectorFormat -a $DETECTOR_IN -o $DETECTOR_OUT

#--- remove the base modules

eval `JPrintDetector -a $DETECTOR_OUT -O SUMMARY`


for STRING in $STRINGS; do

 JEditDetector -a $DETECTOR_OUT -o $DETECTOR_OUT -D "$STRING 0"
 
done

#--- sort modules 1-18
JEditDetector -a $DETECTOR_OUT -o $DETECTOR_OUT -O 2

#--- remove here malfunctioning strings if present in the detector file

#JEditDetector -a $DETECTOR_OUT -o $DETECTOR_OUT -r 18
#JEditDetector -a $DETECTOR_OUT -o $DETECTOR_OUT -r 19

#--- loop over data files

rm $OUTDIR/${EXT}.root

for RUN_IN in `seq $RUNFIRST $RUNSECOND`; do

RUN=$(printf %08d $RUN_IN)
INFILE=$DATADIR/KM3NeT_000000${DETECTOR_ID}_${RUN}.root

#---- process JMonitorL1dt

$JPP_DIR/examples/JCalibrate/JMonitorL1dt -a $DETECTOR_OUT -C JDAQTimesliceSN -f $INFILE  -o $OUTDIR/temp_$RUN_IN.root

if [ -f "$OUTDIR/${EXT}.root" ]
then
echo "JMonitorL1dt output added to previous results"
 hadd $OUTDIR/sum.root $OUTDIR/temp_$RUN_IN.root $OUTDIR/${EXT}.root
 mv $OUTDIR/sum.root $OUTDIR/${EXT}.root
else
   echo "No previous output from JMonitorL1dt found, new output file created"
 cp $OUTDIR/temp_$RUN_IN.root $OUTDIR/${EXT}.root
fi


done

#--- determine time offsets between DU pairs (for 1-8 neighboured levels)

rm -i $OUTDIR/${EXT}_*.txt
for nei in 2 3 4 5 6 7 8; do
$JPP_DIR/examples/JCalibrate/JOffset_extract -a $DETECTOR_OUT -f $OUTDIR/${EXT}.root -m 0 -n $nei > $OUTDIR/${EXT}_$nei.txt
done
cat $OUTDIR/${EXT}_*.txt > $OUTDIR/${EXT}.txt
#--- evaluate best inter-DU offsets
#
#   The argument "-m 5.5" needs to be tuned to the amount of data used, for 30 hours of ARCA a value of 5.5 was found reasonable,
#     for 6 hours of ORCA a value of 20 is suggested 
#   Some tuning will be required, it should be a high enough value to remove 'noise' correlations and a low enough to keep enough correlations
#   Possibly some further cuts on the quality of the correlations need to be applied
file=$OUTDIR/offsets_${EXT}.txt
$JPP_DIR/examples/JCalibrate/JMatrix_sol -a $DETECTOR_OUT -f $OUTDIR/${EXT}.txt -m 5.5 -r 0  > $file

#--- adapt detector file

while read line; do
 read -r a b <<< $line
 if [ $a -gt 0 ] 
 then
  JEditDetector -a $DETECTOR_OUT -S "$a add $b" -o $DETECTOR_OUT --!
 fi
done < $file