seaTimeCalibration.sh

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#!/bin/zsh
#
#
# \author acreusot 
#
version=1.0
script=${0##*/}
 
# ------------------------------------------------------------------------------------------
#
#                         Utility script to test sea time calibration.
#
# ------------------------------------------------------------------------------------------
# all data related to intradom time calibration have to be set in the same directory
#
# When performing a time calibration between DOMs, some PMT time offsets must be kept fixed.
# for standard sea time calibration, the time offsets kept fixed are those of the 
# reference PMTs. The identity of the reference PMT can be given in argument as an integer 
# (since all DOMs are supposed to have the same reference PMT, 7 or 15 most of the time).
#
# In case of a time calibration after a threshold tuning, or in case of different 
# reference PMT identity for each DOM, a file can be given as an argument. The file 
# contains a list of DOM and PMT identities that must have a fix time offset. 
 
if [ -z $JPP_DIR ]; then
    echo "Variable JPP_DIR undefined."
    exit
fi
 
source $JPP_DIR/setenv.sh $JPP_DIR
 
set_variable    DEBUG           1    
 
if do_usage $*; then
    usage "$script <working directory> <detector file> <intra data directory> <reference PMTs>"
fi
 
case $# in
    4)  set_variable    PMT             $4;
        set_variable    INTRADIR        $3;
        set_variable    DETX            $2;
        set_variable    WORKDIR         $1;;
    *) fatal "wrong number of arguments!";;
esac
 
if [[ ${PMT} =~ ^[+-]?[0-9]+$ ]]; then
    set_variable        pmtList "-1 ${PMT}"
    set_variable        pmtName ${PMT}
else
    set_variable    pmtList "`cat ${WORKDIR}/${PMT}`"
    set_variable    pmtName "Mixed"
fi
 
FILELISTINTRA1=()
for FILEPATH in $(ls ${WORKDIR}/${INTRADIR}/); do
    FILELISTINTRA1+=("${WORKDIR}/${INTRADIR}/${FILEPATH}")
done
set_variable    FILELISTINTRA2  ${FILELISTINTRA1}
set_variable    BASENAME        ${DETX%.detx}
 
JCalibrateK40 \
    -d $DEBUG \
    -f ${FILELISTINTRA2} \
    -a ${WORKDIR}/${DETX} \
    -o calibrateK40_sea.root \
    -b rates \
    -C JDAQTimesliceL1 \
    -V0+1e5 \
    -M2+31
 
JMergeCalibrateK40 \
    -d $DEBUG \
    -f calibrateK40_sea.root \
    -o mergecalibrateK40_sea.root
 
JConvertDetectorFormat -a ${WORKDIR}/${DETX} -o ${WORKDIR}/${BASENAME}_seaCalibration_pmt${pmtName}.detx 
 
JFitK40 \
    -d $DEBUG \
    -f mergecalibrateK40_sea.root \
    -a ${WORKDIR}/${BASENAME}_seaCalibration_pmt${pmtName}.detx \
    -o fitK40_pmt${pmtName}_sea.root \
    -! ${pmtList} \
    -A \
    -w