Optimize_Voltage_local.sh

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#!/bin/zsh

#
#         _   _   _                           ____                                              
#        | | | \ | |                         |  _ \                                             
#        | | |  \| |   __ _   _ __     ___   | |_) |   ___    __ _    ___    ___    _ __    ___ 
#    _   | | | . ` |  / _` | | '_ \   / _ \  |  _ <   / _ \  / _` |  / __|  / _ \  | '_ \  / __|
#   | |__| | | |\  | | (_| | | | | | | (_) | | |_) | |  __/ | (_| | | (__  | (_) | | | | | \__ \
#    \____/  |_| \_|  \__,_| |_| |_|  \___/  |____/   \___|  \__,_|  \___|  \___/  |_| |_| |___/
#                                                                                               
#         


#This script should be launched everytime a new DU is deployed in the sea, and a set of runs with the nanobeacons tuned at different voltages has been taken. It runs several programs. 


#First, it copies the run files from irods to a temporary directory and launches JPulseFinder to analyze each of them. JPulseFinder searches for the NB pulses detected by the different PMTs in the neighbor DOMs. Once JPulseFinder has finished, its output is stored and the run files removed from the temporary directory.

# 

script=${0##*/}

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

if ( do_usage $* ); then
    usage "$script [edit the different options within]"
fi


# ------------------------------------------------------------------------------------------
#
#          Script to find the optimal voltage of the nanobeacons in a DU
#
# ------------------------------------------------------------------------------------------

echo $*

WORKDIR=$PWD

JNANODIR="/data/stu18q3km3/src/Jpp/trunk/examples/JNanobeacon"

function usage()

{

    print -u2 "$script"

    exit 1

}

#------------------------------------
# Input-Output definitions
#------------------------------------

#    ____    ___   _____   ___ 
#   / __ \  / _ \ / ___/  / _ |
#  / /_/ / / , _// /__   / __ |
#  \____/ /_/|_| \___/  /_/ |_|
#                              

detector="ORCA"

string=2

path_to_run_files="/data/stu18q3km3/data/KM3NeT_00000029/"

filename="KM3NeT_00000029_0000"

#runs=(2660 2661 2662 2663 2664 2665 2666 2667 2668) 

runs=(2745 2746 2747 2748 2749 2750 2751 2752 2753)

#runs=(2813 2814 2815 2816 2817 2818 2819 2820 2821)

#runs=(2906 2907 2908 2909 2910 2911 2912 2913 2914)

#runs=(2986 2987 2988 2989 2990 2991 2992 2993 2994)

voltages=(5.5 6 6.5 7 7.5 8 8.5 10 15)

in_detx="/data/stu18q3km3/detectors/KM3NeT_00000029_20170920.detx"

analysis_level=0

top_pmts=1

bottom_pmts=4

max_neighbors=2

max_tot=26.4

pulse_period=6250 #in units of 16 ns

stagger_period=220 #in units of 16 ns


#####################################################################################################################


##################################
#     ___    ___   _____   ___   #
#    / _ |  / _ \ / ___/  / _ |  #
#   / __ | / , _// /__   / __ |  #
#  /_/ |_|/_/|_| \___/  /_/ |_|  #                              
#                                #   
##################################

#detector="ARCA"

#string=1

#path_to_run_files="/in2p3/km3net/data/raw/darkroom/KM3NeT_00000038/0/"

#filename="KM3NeT_00000..."

#runs=()

#voltages=()

#in_detx="path_to_the_following_detector_file/KM3NeT_00000014_20170327.detx"

#####################################################################################################################

cd "${JNANODIR}"

################################################################################################################
#LAUNCH JPULSEFINDER FOR EACH OF THE RUN FILES GRABBED FROM IRODS. STORE THE OUTPUT, AND REMOVE THE RUN FILES.
################################################################################################################

outdir_pulse="${WORKDIR}/out/$detector/JPulseFinder"

if [ ! -d ${outdir_pulse} ] 

then     

    mkdir -p ${outdir_pulse} 

fi

outfiles_pulse=""

for i in {1..$((${#runs[@]}))}

do

  infile=$path_to_run_files/${filename}${runs[i]}.root  

  outfile=$outdir_pulse/JPF_${runs[i]}.root

  outfiles_pulse="${outfiles_pulse} ${outfile}"

  if [ ! -f $outfile ]; then

      JPulseFinder                          \
     -f $infile                        \
     -a $in_detx                       \
     -s $string                        \
     -p $pulse_period                  \
     -stagger $stagger_period          \
     -o $outfile                       \
     -V ${voltages[i]}                 \
          -n $max_neighbors                 \
     -t $top_pmts                      \
     -b $bottom_pmts

  else
      
      echo "\nThe pulses for run $runs[i] already exist in file\n$outfile\nContinue..."

  fi

done


###############################################################################
#LAUNCH JVOLTAGEOPTIMIZER USING THE OUTPUT FROM JPULSEFINDER. STORE THE OUTPUT.
###############################################################################

outdir_optimizer="${WORKDIR}/out/$detector/JVoltageOptimizer"

if [ ! -d ${outdir_optimizer} ] 

then     

    mkdir -p ${outdir_optimizer} 

fi

outfile_opt="$outdir_optimizer/JVO_OPT_${runs[1]}_${runs[${#runs[@]}]}.root"

outfile_cal="$outdir_optimizer/JVO_CAL_${runs[1]}_${runs[${#runs[@]}]}.root"

outfile_txt="$outdir_optimizer/JVO_OPT_${runs[1]}_${runs[${#runs[@]}]}.txt"

if [[ ! -f $outfile_opt || ! -f $outfile_cal || ! -f $outfile_txt ]]; then

    JVoltageOptimizer \
   -f "${outfiles_pulse}" \
   -a $in_detx \
   -s $string \
   -o $outfile_opt \
   -t $outfile_txt \
   -c $outfile_cal \
   -u $top_pmts \
   -d $bottom_pmts \
   -n $max_neighbors \
   -S $max_tot

else

    echo "\n\nThe voltage has been optimized. Continue...\n"

fi

outdir_calibrator="${WORKDIR}/out/$detector/JInterDomCal"

if [ ! -d ${outdir_calibrator} ] 

then     

    mkdir -p ${outdir_calibrator} 

fi

outfile_txt="$outdir_calibrator/JNBCal_${runs[1]}_${runs[${#runs[@]}]}.txt"

outfile_checks="$outdir_calibrator/JNBCal_${runs[1]}_${runs[${#runs[@]}]}.root"

outfile_detx="$outdir_calibrator/JNBCal_${runs[1]}_${runs[${#runs[@]}]}.detx"


#####################################################################
#LAUNCH JINTERDOMCAL USING THE OUTPUT PRODUCED BY JVOLTAGEOPTIMIZER.#
#####################################################################


JInterDomCal \
    -a $in_detx \
    -f $outfile_cal \
    -s $string \
    -t $outfile_txt \
    -x $outfile_detx \
    -c $outfile_checks \
    -u $top_pmts \
    -d $bottom_pmts \
    -l $analysis_level



##########################################################################
#PRODUCE REPORTS FROM THE OUTPUT FILES FROM CALIBRATION AND OPTIMIZATION.#
##########################################################################



calibration_report_name="$outdir_calibrator/calibration_report_${runs[1]}_${runs[${#runs[@]}]}.pdf"

optimization_report_name="$outdir_optimizer/optimization_report_${runs[1]}_${runs[${#runs[@]}]}.pdf"


echo "Writing calibration report in file:" 
echo $calibration_report_name
echo "------------------------------------\n"

python plot_report_calibration.py -ir $outfile_checks -it $outfile_txt -o $calibration_report_name

echo "\nDone!"

echo "Writing optimization report in file:" 
echo $optimization_report_name
echo "------------------------------------\n"

python plot_report_optimization.py -i $outfile_opt -o $optimization_report_name

echo "Done... Hasta pronto!"