pre-calibration_D0ORCA042.sh

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#!/bin/zsh
script=${0##*/}
 
# --------------------------------------------------------------------------------------------
#
# Steering script for the global-fit-of-global-fits procedure of the D0ORCA042 (???) detector.
#
# --------------------------------------------------------------------------------------------
 
if [ -z $JPP_DIR ]; then
    echo "Variable JPP_DIR undefined."
    exit
fi
 
source $JPP_DIR/setenv.sh $JPP_DIR >& /dev/null
 
set_variable  DETECTOR_ID                         300
set_array     RUNS                                30086-30094
set_variable  ARCHIVE_INPUT_BRANCH                D0ORCA033_fixed
set_variable  INPUT_DETECTOR_ID                   291
set_variable: THREADS                             ACOUSTICS_THREADS       32
set_variable  SINGULARITY                         -
set_variable: WORKDIR                             ACOUSTICS_WORKDIR     ./
set_variable  HOMEDIR                             $WORKDIR
 
 
if do_usage $*; then
    usage "$script"\
          "\nRequires variable CALIBRATION_ARCHIVE to be set for the user."
fi
 
source JAcousticsToolkit.sh
 
set_variable  DETECTOR               $WORKDIR/detector.datx
set_variable  TRIPOD                 $WORKDIR/tripod.txt
set_variable  DETECTOR_INITIAL       detector_initial.datx
set_variable  TRIPOD_INITIAL         tripod_initial.txt
set_variable  TRANSMITTER_INITIAL    transmitter_initial.txt
set_variable  HYDROPHONE_INITIAL     hydrophone_initial.txt
expand_array  RUNS
 
 
# Run in HOMEDIR
mkdir -p $HOMEDIR
cd       $HOMEDIR
 
# -------------------------------------------------------------------------------------------------------------
#
# 1. Clone the git calibration archive to workdir to retrieve the required detector, tripod and transmitter inputs
#
# -------------------------------------------------------------------------------------------------------------
 
git clone \
    --recursive \
    --branch $ARCHIVE_INPUT_BRANCH \
    git@git.km3net.de:auxiliary_data/calibration \
    $WORKDIR/auxiliary_data/calibration
 
# Retrieve D0ORCA038 detector, tripod, transmitter and hydrophone from the calibration archive
getFile.sh "$WORKDIR/auxiliary_data/calibration" $INPUT_DETECTOR_ID 1 detector G_1.3.1 "$WORKDIR/D0ORCA038"
getFile.sh "$WORKDIR/auxiliary_data/calibration" $INPUT_DETECTOR_ID 1 tripod A_1.3.0 "$WORKDIR/tripod_D0ORCA038"
getFile.sh "$WORKDIR/auxiliary_data/calibration" $INPUT_DETECTOR_ID 1 transmitter A_1.3.0 "$WORKDIR/transmitter_D0ORCA038"
getFile.sh "$WORKDIR/auxiliary_data/calibration" $INPUT_DETECTOR_ID 1 hydrophone A_1.3.0 "$WORKDIR/hydrophone_D0ORCA038"
 
# retrieve D0ORCA038 mechanics, fit parameters, sound velocity from JPP inputs
getFile.sh "$JPP_DIR/inputs/" $INPUT_DETECTOR_ID 1 mechanics "$WORKDIR/mechanics"
getFile.sh "$JPP_DIR/inputs/" $INPUT_DETECTOR_ID 1 acoustics_fit_parameters "$WORKDIR/acoustics_fit_parameters"
getFile.sh "$JPP_DIR/inputs/" $INPUT_DETECTOR_ID 1 sound_velocity "$WORKDIR/sound_velocity"
 
# -------------------------------------------------------------------------------------------------------------
#
# 2. Retrieve online ORCA42 inputs to merge with ORCA38 calibration outputs
#
# -------------------------------------------------------------------------------------------------------------
 
# Get a initial detector for D0ORCA042 from the JDetectorDB, to be optimised in the global-fit-of-global-fits procedure.
JDetectorDB \
    -D $DETECTOR_ID       \
    -@ "tcal=A07004647; pcal=A07004636; rcal=A07004637; acal=A07004638; ccal=A07004639; scal=A07004640" \
    -WW                   \
    -o $DETECTOR_INITIAL
 
# From input_tables of D0ORCA042
cat>$TRIPOD_INITIAL<<EOF
# Data from D0ORCA038 input_tables
11 257208.80 4743611.20 -2440.19
12 257000.30 4743616.80 -2441.30
15 257222.80 4743333.20 -2438.49
EOF
 
# From input_tables of D0ORCA042
cat>$TRANSMITTER_INITIAL<<EOF
# Data from D0ORCA042 input_tables
 9   27  0  -0.74  -0.64   0.71
10   41  0  -0.40  -0.89   0.71
14   50  0  -0.27  -0.94   0.71
17   75  0   0.50  -0.84   0.71
18   82  0   0.15  -0.96   0.71
EOF
 
# From input_tables of D0ORCA042
cat>$HYDROPHONE_INITIAL<<EOF
# Data from D0ORCA042 input_tables
   2  0   0.02   1.04   0.55
   3  0   0.46   0.93   0.55
   9  0  -0.75  -0.72   0.55
  10 -1   0.11   1.04   0.55
  12  0   0.46   0.93   0.55
   4  0   0.20   1.02   0.55
  18  0   0.61   0.84   0.55
  28  0   0.69   0.78   0.55
  11  0  -0.07   1.04   0.55
  19  0   0.46   0.93   0.55
  20  0   0.61   0.84   0.55
  29  0   0.46   0.93   0.55
  30  0   0.46   0.93   0.55
  21  0   0.11   1.04   0.55
  17  0   0.46   0.93   0.55
  27  0   1.04   0.07   0.55
  31  0   0.75   0.72   0.55
  39  0   0.46   0.93   0.55
  40  0   0.46   0.93   0.55
  41  0   0.91   0.50   0.55
  42  0   0.29   1.00   0.55
  38  0   0.89  -0.54   0.55
   1  0  -0.25   1.01   0.55
  49  0   0.32  -0.99   0.55
  50  0   0.83   0.62   0.55
  51  0   0.54   0.89   0.55
  52  0   0.82   0.64   0.55
  53  0   0.43   0.95   0.55
  60  0  -0.16   1.03   0.55
  61  0  -0.42   0.95   0.55
  62  0   1.01   0.25   0.55
  63  0   0.20   1.02   0.55
  64 -1  -0.07   1.04   0.55
  72  0  -0.25   1.01   0.55
  73  0   0.46   0.93   0.55
  74  0   0.38   0.97   0.55
  48  0  -1.03  -0.16   0.55
  37  0  -1.01  -0.25   0.55
  26  0  -0.84   0.61   0.55
  75  0   0.11   1.04   0.55
  82  0   0.49   0.92   0.55
  83  0   0.17   1.03   0.55
EOF
 
eval `JPrintDetector -a $DETECTOR_INITIAL -O SUMMARY`;  FINAL_STRINGS=($STRINGS[*])
eval `JPrintDetector -a D0ORCA038.datx -O SUMMARY`;  FIXED_STRINGS=($STRINGS[*])
 
# Apply merging.
 
# Detector
JEditDetector \
    -a $DETECTOR_INITIAL \
    -o detector.datx --!
 
eval `JPrintDetector -a detector.datx -O SUMMARY`
 
JEditDetector   -a detector.datx  -r "$FIXED_STRINGS[*]"  -o detector.datx --!
JMergeDetector  -a detector.datx  -a D0ORCA038.datx       -o detector.datx --!
JEditDetector   -a detector.datx  -k "$FINAL_STRINGS[*]"  -o detector.datx --!
 
# Tripod
typeset -A TRIPODS
 
get_tripods  $TRIPOD_INITIAL              TRIPODS;  FINAL_TRIPODS=(${(k)TRIPODS[*]})
echo "Final tripods: ${FINAL_TRIPODS[*]}"
get_tripods  $WORKDIR/tripod_D0ORCA038.txt   TRIPODS;  FIXED_TRIPODS=(${(k)TRIPODS[*]})
echo "Fixed tripods: ${FIXED_TRIPODS[*]}"
cp -p  $TRIPOD_INITIAL  tripod.txt
 
JEditTripod   -f tripod.txt  -r "${FIXED_TRIPODS}" -o tripod.txt
JMergeTripod  -f tripod.txt  -f $WORKDIR/tripod_D0ORCA038.txt    -o tripod.txt
JEditTripod   -f tripod.txt  -k "${FINAL_TRIPODS}" -o tripod.txt
JEditTripod   -f tripod.txt  -r "16" -o tripod.txt # remove tripod 16, which was recovered during D0ORCA042 sea campaign
 
# Transmitter
cp -p  $TRANSMITTER_INITIAL  transmitter.txt
 
JEditTransmitter   -f transmitter.txt  -r "${FIXED_STRINGS[*]}" -o transmitter.txt
JMergeTransmitter  -f transmitter.txt  -f $WORKDIR/transmitter_D0ORCA038.txt    -o transmitter.txt
JEditTransmitter   -f transmitter.txt  -k "${FINAL_STRINGS[*]}" -o transmitter.txt
 
# Hydrophone
# temporary use hydrophone_ititial.txt for hydrophone.txt, as the hydrophone_D0ORCA038.txt is not calibrated
cp -p  $WORKDIR/$HYDROPHONE_INITIAL  hydrophone.txt
 
# -------------------------------------------------------------------------------------------------------------
#
# 3. Acoustic event building
#
# -------------------------------------------------------------------------------------------------------------
 
cat>waveform.txt<<EOF
# Data from D2ORCA024_waveforms.csv
 35   9
-36   9
 34  10
-35  10
 28  11
-29  11
 48  12
-49  12
 49  14
-50  14
 16  15
-17  15
 51  17
-52  17
 52  18
-53  18
EOF
 
# Changed to 550 based on investigation average number of hits per event in D0ORCA042
cat>acoustics_trigger_parameters.txt<<EOF
# Trigger parameters D0ORCA042
Q             = 0.0;
TMax_s        = 0.020;
numberOfHits  = 550;
EOF
 
# Updated disable file for D0ORCA042
cat>disable.txt<<EOF
# b39669d0-1781-4395-8490-b27e826c4bdb$
# GIT 20.0.0
# ROOT 6.32.02
# application JEditDisable
# command /pbs/throng/km3net/software/RHEL9/jpp/v20.0.0/out/Linux/bin/JEditDisable -f ../disable.txt -o new_disable.txt -a ../detector.datx -q
# namespace KM3NET
# system Linux cca018 5.14.0-687.29.1.el9_8.x86_64 #1 SMP PREEMPT_DYNAMIC Tue Jul 21 03:19:43 EDT 2026 x86_64
9 813524210
10 808972598
10 813524210
11 808489117
11 809161495
11 809175478
11 809187005
11 813524210
11 816928387
11 817317552
11 817331139
11 817338029
11 819737869
11 819740066
12 808972598
12 809161495
12 809521500
12 813524210
12 813709200
12 817320256
12 817355794
14 808961480
14 813524210
15 808981510
15 809076040
15 809161495
15 813524210
15 817295057
15 817301191
17 813524210
18 813524210
EOF
 
expand_array  RUNS
 
set_variable:  QUALITY_FACTOR  ACOUSTICS_QUALITYFACTOR  2.0e3
 
BUFFER=(`JRuns -D $DETECTOR_ID -F RUN`)
let "NUMBER_OF_ERRORS = 0"
for RUN in ${RUNS:*BUFFER}; do
    
    set_variable  INPUT_FILE   $WORKDIR/KM3NeT_${(l:8::0::0:)DETECTOR_ID}_${(l:8::0::0:)RUN}_toa.root
    set_variable  OUTPUT_FILE  $WORKDIR/KM3NeT_${(l:8::0::0:)DETECTOR_ID}_${(l:8::0::0:)RUN}_event.root
 
    if [[ ! -f $INPUT_FILE ]]; then
 
            JToA \
                -@ "detid  = `getDetector -D $DETECTOR_ID`"  \
                -@ "minrun = $RUN"                           \
                -@ "maxrun = $RUN"                           \
                -@ "QUALITYFACTOR >= $QUALITY_FACTOR"        \
                -o $INPUT_FILE                               \
                -d $DEBUG --!
 
        if (( $? != 0 )); then
            let "NUMBER_OF_ERRORS = $NUMBER_OF_ERRORS + 1"
        fi
    fi
 
    if [[ -f $INPUT_FILE ]] && [[ ! -f $OUTPUT_FILE ]]; then
 
            timer_start
 
            JAcousticsEventBuilder \
                -a $DETECTOR                                 \
                -f $INPUT_FILE                               \
                -T $WORKDIR/tripod.txt                       \
                -Y $WORKDIR/transmitter.txt                  \
            -V $WORKDIR/sound_velocity.txt               \
                -W $WORKDIR/waveform.txt                     \
                -@ $WORKDIR/acoustics_trigger_parameters.txt \
                -H $WORKDIR/hydrophone.txt                   \
                -o $OUTPUT_FILE                              \
                -d $DEBUG --!
 
        if (( $? != 0 )); then
            let "NUMBER_OF_ERRORS = $NUMBER_OF_ERRORS + 1"
        fi
 
            timer_stop
            timer_print
    fi
done
 
 
if (( $NUMBER_OF_ERRORS != 0 )); then
    error "Number of errors $NUMBER_OF_ERRORS"
fi
 
# -------------------------------------------------------------------------------------------------------------
#
# 4. Run the global-fit-of-global-fits procedure to optimise the detector and tripod and transmitter positions
#
# -------------------------------------------------------------------------------------------------------------
 
INPUT_FILES=(`ls KM3NeT_${(l:8::0::0:)DETECTOR_ID}_0*${^RUNS}_event.root`)
 
# Run in WORKDIR
 
cd  $WORKDIR
 
if [ ! $HOMEDIR -ef $WORKDIR ]; then
    cp -p $HOMEDIR/$ACOUSTICS_DETECTOR     $WORKDIR
    cp -p $HOMEDIR/${^ACOUSTICS_KEYS}.txt  $WORKDIR
    cp -p $HOMEDIR/${^ACOUSTICS_AUXS}.txt  $WORKDIR
    cp -p $HOMEDIR/${^INPUT_FILES}         $WORKDIR
fi
 
cat>script.txt<<EOF
 
fix  string  $FIXED_STRINGS[*]
fix  tripod  $FIXED_TRIPODS[*]
 
stage   0  ${SINGULARITY}1  0  100.0e-6  10.0  10  0.5       
stage  1B  ${SINGULARITY}1  0  100.0e-6  10.0   0  0.001  0.1
stage  2A  ${SINGULARITY}1  0  100.0e-6  10.0  20  0.2    0.5
stage  2C  ${SINGULARITY}1  0  100.0e-6  10.0  20  0.2     
stage  3A  ${SINGULARITY}1  0   50.0e-6  10.0  20  0.2    0.5
stage  3C  ${SINGULARITY}1  0   50.0e-6  10.0  20  0.2        
 
initialise
 
stage  3a  ${SINGULARITY}1  0   50.0e-6  10.0  20  0.2    0.5
stage  3c  ${SINGULARITY}1  0   50.0e-6  10.0  20  0.2
EOF
 
JSydney \
    -a $DETECTOR                               \
    -f "$INPUT_FILES[*]"                       \
    -T tripod.txt                              \
    -Y transmitter.txt                         \
    -V sound_velocity.txt                      \
    -M mechanics.txt                           \
    -@ acoustics_fit_parameters.txt            \
    -! disable.txt                             \
    -N $THREADS                                \
    -s script.txt                              \
    -d $DEBUG --!
 
if [ ! $HOMEDIR -ef $WORKDIR ]; then
    cp -vru * $HOMEDIR
fi
 
# Require Katoomba for Creep correction
JKatoomba \
    -a $DETECTOR                              \
    -f "$INPUT_FILES[*]"                      \
    -o $WORKDIR/katoomba.root                 \
    -T $WORKDIR/tripod.txt                    \
    -Y $WORKDIR/transmitter.txt               \
    -V $WORKDIR/sound_velocity.txt            \
    -M $WORKDIR/mechanics.txt                 \
    -@ $WORKDIR/acoustics_fit_parameters.txt  \
    -! $WORKDIR/disable.txt                   \
    ${HYDROPHONE}                             \
    $STRIP                                    \
    $SQUASH                                   \
    -d $DEBUG --!
 
 
# copy detector to apply creep correction and z-adjustment
cp -p $WORKDIR/$DETECTOR $WORKDIR/detector_creep.datx
 
JCreep \
    -a $WORKDIR/detector_creep.datx \
    -f $WORKDIR/katoomba.root \
    -A
 
JAdjustZpos \
    -a $WORKDIR/detector_creep.datx \
    -f $WORKDIR/KM3NeT_00000300_*event.root \
    -o $WORKDIR/detector_z_adjusted.datx \
    -m 1
 
#copy detector and tripod to align with ROV measurements
cp -p $WORKDIR/detector_z_adjusted.datx $WORKDIR/aligned_detector.datx
cp -p $TRIPOD $WORKDIR/aligned_tripod.txt    
 
#Align with ROV measurements (xyz only)
JAlignDetector \
    -a $WORKDIR/aligned_detector.datx \
    -b $WORKDIR/$DETECTOR_INITIAL \
    -P "x y z" \
    -O \
    -T $WORKDIR/aligned_tripod.txt \
    -A \