Calibrate.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 launches 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.

# 

version=1.0
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

function usage()

{

    print -u2 "$script \n\t Choose the adequate options and run it!"

    exit 1

}

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

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

# detector="ORCA"

# string=2

# irods_path="/in2p3/km3net/data/raw/sea/KM3NeT_00000029/${string}/"

# filename="KM3NeT_00000029_0000"

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

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

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

# in_detx="/afs/in2p3.fr/home/r/rgracia/sps/KM3NeT/ORCA/Calibration/data/det/ORCA/KM3NeT_00000029_20170920.detx"

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



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

detector="ARCA"

#DU3

#string=1

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

#filename="KM3NeT_00000038_00000"

#runs=(207 208 209 211)

#voltages=(15 15 8 8)

#in_detx="/afs/in2p3.fr/home/r/rgracia/sps/Soft/src/Jpp_trunk/examples/JMonitor/JNanoBeacon/JPulseFinder/temp/KM3NeT_00000038_intrainterDOM_final_pmt7_v1.detx"

#DU1

string=1

irods_path="/in2p3/km3net/data/raw/sea/KM3NeT_00000014/5/"

filename="KM3NeT_00000014_0000"

runs=(5077)

in_detx="/afs/in2p3.fr/home/r/rgracia/sps/KM3NeT/ORCA/Calibration/data/det/ARCA/KM3NeT_00000014_20170327.detx"

top_pmts=1

bottom_pmts=4

max_neighbors=2

analysis_level=1

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




###################################################################################################################
#GET RUN FILES FROM IRODS AND STORE THEM IN A TEMPORARY DIRECTORY
###################################################################################################################


tmpdir="${WORKDIR}/tmp"

if [ ! -d ${tmpdir} ] 

then     

    mkdir -p ${tmpdir} 

fi

source /usr/local/shared/bin/irods_env.sh >& /dev/null

iinit


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

#cd ./../JPulseFinder

pulse_period=6250 #in units of 16 ns

stagger_period=220 #in units of 16 ns

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

do

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

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

  if [ ! -f $outfile_pulse ]; then

      if [ ! -f $infile ]; then

     echo "\nGetting file ${filename}${runs[i]}.root from ${irods_path}. Please wait..."

     iget -f ${irods_path}${filename}${${runs[i]}}.root $tmpdir/

      else

     echo "\n\nThe file \n${filename}${${runs[i]}}.root \nalready exists in \n$tmpdir.\nContinue..."

      fi

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

      #rm -f ${infile}

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

  outdir_calibrator="${WORKDIR}/out/$detector/JInterDomCal"
  
  if [ ! -d ${outdir_calibrator} ] 

  then     

      mkdir -p ${outdir_calibrator} 

  fi

  outfile_txt="$outdir_calibrator/JNBCal_${runs[i]}.txt"

  outfile_checks="$outdir_calibrator/JNBCal_${runs[i]}.root"

  outfile_detx="$outdir_calibrator/JNBCal_${runs[i]}.detx"
  
  JInterDomCal \
      -a $in_detx \
      -f $outfile_pulse \
      -s $string \
      -t $outfile_txt \
      -x $outfile_detx \
      -c $outfile_checks \
      -u $top_pmts \
      -d $bottom_pmts \
      -n $max_neighbors \
      -l $analysis_level

  report_name="$outdir_calibrator/calibration_report_${runs[i]}.pdf"


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

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

  echo "Done... Hasta pronto!"

done