setenv_extra.sh

# script to set extra env variables
# taking some stuff from alien

# process flags passed to the script

# check if this is a production on skimmed data
if grep -q /skimmed/ wn.xml ; then
  export ON_SKIMMED_DATA=1;
fi

if [[ $RUNNUMBER -lt 544772 ]]; then
  # these runs were using external dictionaries
  : ${RANS_OPT:="--ans-version compat"}
  export RANS_OPT
fi
echo "RSRUNNUMBER = $RUNNUMBER RANS_OPT = $RANS_OPT"

# IR, duration, B field, detector list
if [[ -z $RUN_IR ]] || [[ -z $RUN_DURATION ]] || [[ -z $RUN_BFIELD ]]; then
  echo "In setenv_extra: time used so far = $timeUsed"
  timeStart=`date +%s`
  time o2-calibration-get-run-parameters -r $RUNNUMBER
  timeEnd=`date +%s`
  timeUsed=$(( $timeUsed+$timeEnd-$timeStart ))
  delta=$(( $timeEnd-$timeStart ))
  echo "Time spent in getting run parameters = $delta s"
  export RUN_IR=`cat IR.txt`
  export RUN_DURATION=`cat Duration.txt`
  export RUN_BFIELD=`cat BField.txt`
  export RUN_DETECTOR_LIST=`cat DetList.txt`
fi
echo -e "\n"
echo "Printing run features"
echo "DETECTOR LIST for current run ($RUNNUMBER) = $RUN_DETECTOR_LIST"
echo "DURATION for current run ($RUNNUMBER) = $RUN_DURATION"
echo "B FIELD for current run ($RUNNUMBER) = $RUN_BFIELD"
echo "IR for current run ($RUNNUMBER) = $RUN_IR"
if (( $(echo "$RUN_IR <= 0" | bc -l) )); then
  echo "Changing run IR to 1 Hz, because $RUN_IR makes no sense"
  RUN_IR=1
fi
echo "BeamType = $BEAMTYPE"
echo "PERIOD = $PERIOD"


if [[ $BEAMTYPE == "pO" ]] || [[ $BEAMTYPE == "Op" ]] || [[ $BEAMTYPE == "Op" ]] || [[ $BEAMTYPE == "OO" ]] || [[ $BEAMTYPE == "NeNe" ]] ; then
  export LIGHTNUCLEI=1
else
  export LIGHTNUCLEI=0
fi


# detector list
echo -e "\n"
echo "Printing detector list for reconstruction"
if [[ -n $ALIEN_JDL_WORKFLOWDETECTORS ]]; then
  echo "WORKFLOW_DETECTORS taken from JDL, ALIEN_JDL_WORKFLOWDETECTORS = $ALIEN_JDL_WORKFLOWDETECTORS"
  export WORKFLOW_DETECTORS=$ALIEN_JDL_WORKFLOWDETECTORS
else
  export WORKFLOW_DETECTORS=`echo $RUN_DETECTOR_LIST | sed 's/ /,/g'`
  if [[ $RUNNUMBER == 528529 ]] || [[ $RUNNUMBER == 528530 ]]; then
    # removing MID for these runs: it was noisy and therefore declared bad, and makes the reco crash
    echo "Excluding MID since RUNNUMBER = $RUNNUMBER"
    export WORKFLOW_DETECTORS_EXCLUDE="MID"
  fi
  # list of detectors to possibly exclude
  if [[ -n $ALIEN_JDL_DETECTORSEXCLUDE ]]; then
    echo "DETECTORS_EXCLUDE taken from JDL, ALIEN_JDL_DETECTORSEXCLUDE = $ALIEN_JDL_DETECTORSEXCLUDE"
    export DETECTORS_EXCLUDE=$ALIEN_JDL_DETECTORSEXCLUDE  # will be used in the async_pass.sh if we run in split mode
    if [[ -z ${WORKFLOW_DETECTORS_EXCLUDE:+x} ]]; then # there is no WORKFLOW_DETECTORS_EXCLUDE, or it is NULL
      export WORKFLOW_DETECTORS_EXCLUDE=$DETECTORS_EXCLUDE
    else
      export WORKFLOW_DETECTORS_EXCLUDE+=",$DETECTORS_EXCLUDE"
    fi
  fi
fi

echo "Final settings for detectors to be processed:"
echo "WORKFLOW_DETECTORS = $WORKFLOW_DETECTORS"
echo "WORKFLOW_DETECTORS_EXCLUDE = $WORKFLOW_DETECTORS_EXCLUDE"

# ad-hoc settings for CTF reader: we are on the grid, we read the files remotely
echo -e "\nProcessing mode = ${MODE}"
#unset ARGS_EXTRA_PROCESS_o2_ctf_reader_workflow

if [[ $MODE == "remote" ]]; then
  if [[ $ALIEN_JDL_REMOTEREADING != 1 ]]; then
    echo "Files will be copied locally: we expect that the JDL has the \"nodownload\" option"
    export INPUT_FILE_COPY_CMD="\"alien_cp ?src file://?dst\""
    export ARGS_EXTRA_PROCESS_o2_ctf_reader_workflow+=" --remote-regex \"^alien:///alice/data/.+\""
  else
    echo "Files will NOT be copied locally: we expect that the job agent takes care"
    export INPUT_FILE_COPY_CMD="no-copy"
  fi
fi

echo -e "\nSetting up workflow options"

# adjusting for trigger LM_L0 correction, which was not there before July 2022
if [[ $PERIOD == "LHC22c" ]] || [[ $PERIOD == "LHC22d" ]] || [[ $PERIOD == "LHC22e" ]] || [[ $PERIOD == "JUN" ]] || [[ $PERIOD == "LHC22f" ]] ; then
  if [[ $ALIEN_JDL_LPMPRODUCTIONTYPE != "MC" ]]; then
    export ARGS_EXTRA_PROCESS_o2_ctf_reader_workflow+=" --correct-trd-trigger-offset"
  fi
fi

# checking for remapping
if [[ $remappingITS == 1 ]] || [[ $remappingMFT == 1 ]]; then
  REMAPPING="--condition-remap \"http://alice-ccdb.cern.ch/RecITSMFT="
  if [[ $remappingITS == 1 ]]; then
    REMAPPING=$REMAPPING"ITS/Calib/ClusterDictionary"
    if [[ $remappingMFT == 1 ]]; then
      REMAPPING=$REMAPPING","
    fi
  fi
  if [[ $remappingMFT == 1 ]]; then
    REMAPPING=$REMAPPING"MFT/Calib/ClusterDictionary"
  fi
  REMAPPING=$REMAPPING\"
fi

# generic remapping string
if [[ -n "$ALIEN_JDL_REMAPPINGS" ]]; then
  if [[ -n "$REMAPPING" ]]; then
    REMAPPING="${REMAPPING::-1};$ALIEN_JDL_REMAPPINGS\""
  else
    REMAPPING="--condition-remap \"$ALIEN_JDL_REMAPPINGS\""
  fi
fi

echo "Remapping = $REMAPPING"

# needed if we need more wf
export ADD_EXTRA_WORKFLOW=

# other ad-hoc settings for CTF reader
export ARGS_EXTRA_PROCESS_o2_ctf_reader_workflow+=" --allow-missing-detectors $REMAPPING"

# possibility to only process some TFs
if [[ ! -z ${ALIEN_JDL_RUN_TIME_SPAN_FILE} ]]; then
  export ARGS_EXTRA_PROCESS_o2_ctf_reader_workflow+=" --run-time-span-file $ALIEN_JDL_RUN_TIME_SPAN_FILE "
  # the following option makes sense only if we have the previous
  if [[ ${ALIEN_JDL_INVERT_IRFRAME_SELECTION} == 1 ]]; then
    export ARGS_EXTRA_PROCESS_o2_ctf_reader_workflow+=" --invert-irframe-selection "
  fi
fi

# other settings
echo RUN = $RUNNUMBER
if [[ $RUNNUMBER -ge 521889 ]]; then
  export ARGS_EXTRA_PROCESS_o2_ctf_reader_workflow+=" --its-digits --mft-digits"
  export DISABLE_DIGIT_CLUSTER_INPUT="--digits-from-upstream"
  MAXBCDIFFTOMASKBIAS_ITS="ITSClustererParam.maxBCDiffToMaskBias=-10"    # this explicitly disables ITS masking
  MAXBCDIFFTOSQUASHBIAS_ITS="ITSClustererParam.maxBCDiffToSquashBias=10" # this explicitly enables ITS squashing
  MAXBCDIFFTOMASKBIAS_MFT="MFTClustererParam.maxBCDiffToMaskBias=-10"    # this explicitly disables MFT masking
  MAXBCDIFFTOSQUASHBIAS_MFT="MFTClustererParam.maxBCDiffToSquashBias=10" # this explicitly enables MFT squashing
fi
# shift by +1 BC TRD(2), PHS(4), CPV(5), EMC(6), HMP(7) and by (orbitShift-1)*3564+1 BCs the ZDC since it internally resets the orbit to 1 at SOR and BC is shifted by -1 like for triggered detectors.
# run 520403: orbitShift = 59839744 --> final shift = 213268844053
# run 520418: orbitShift = 28756480 --> final shift = 102488091157
# The "wrong" +1 offset request for ITS (0) must produce alarm since shifts are not supported there
CTP_BC_SHIFT=0
if [[ $ALIEN_JDL_LPMANCHORYEAR == "2022" ]]; then
  CTP_BC_SHIFT=-294
fi
if [[ $RUNNUMBER -ge 538923 ]] && [[ $RUNNUMBER -le 539700 ]]; then
  # 3 BC offset (future direction) in CTP data observed for LHC23zd - LHC23zs
  CTP_BC_SHIFT=-3
fi
if [[ $PERIOD == "LHC22s" ]]; then
  # CTP asked to extract their digits
  add_comma_separated ADD_EXTRA_WORKFLOW "o2-ctp-digit-writer"
  # set all TPC shifts to 86 BCs (= -10.75 TB) as the jitter is due to the bad VDrift calibration
  TPCITSTIMEERR="0.3"
  TPCITSTIMEBIAS="0"
  if [[ $RUNNUMBER -eq 529397 ]]; then
    ZDC_BC_SHIFT=0
    TPCCLUSTERTIMESHIFT="-10.75"
  elif [[ $RUNNUMBER -eq 529399 ]]; then
    ZDC_BC_SHIFT=0
    TPCCLUSTERTIMESHIFT="-10.75"
  elif [[ $RUNNUMBER -eq 529403 ]]; then
    ZDC_BC_SHIFT=213268844053
    TPCCLUSTERTIMESHIFT="-10.75"
  elif [[ $RUNNUMBER -eq 529414 ]]; then
    ZDC_BC_SHIFT=0
    TPCCLUSTERTIMESHIFT="-10.75"
  elif [[ $RUNNUMBER -eq 529418 ]]; then
    ZDC_BC_SHIFT=102488091157
    TPCCLUSTERTIMESHIFT="-10.75"
  else
    ZDC_BC_SHIFT=0
  fi
  CTP_BC_SHIFT=-293
  if [[ $ALIEN_JDL_LPMPRODUCTIONTYPE != "MC" ]]; then
    export CONFIG_EXTRA_PROCESS_o2_ctf_reader_workflow+=";TriggerOffsetsParam.customOffset[2]=1;TriggerOffsetsParam.customOffset[4]=1;TriggerOffsetsParam.customOffset[5]=1;TriggerOffsetsParam.customOffset[6]=1;TriggerOffsetsParam.customOffset[7]=1;TriggerOffsetsParam.customOffset[11]=$ZDC_BC_SHIFT"
  fi
  export PVERTEXER+=";pvertexer.dbscanDeltaT=1;pvertexer.maxMultRatDebris=1.;"
fi

# fix also ZDC in the pp run 529038
if [[ $PERIOD == "LHC22q" ]]; then
  if [[ $RUNNUMBER -eq 529003 ]]; then
    ZDC_BC_SHIFT=427744319508;
  elif [[ $RUNNUMBER -eq 529005 ]]; then
    ZDC_BC_SHIFT=585290682900
  elif [[ $RUNNUMBER -eq 529006 ]]; then
    ZDC_BC_SHIFT=1007373207060
  elif [[ $RUNNUMBER -eq 529008 ]]; then
    ZDC_BC_SHIFT=1379963461140
  elif [[ $RUNNUMBER -eq 529009 ]]; then
    ZDC_BC_SHIFT=1454804952084
  elif [[ $RUNNUMBER -eq 529015 ]]; then
    ZDC_BC_SHIFT=2244823203348
  elif [[ $RUNNUMBER -eq 529037 ]]; then
    ZDC_BC_SHIFT=256033194516
  elif [[ $RUNNUMBER -eq 529038 ]]; then
    ZDC_BC_SHIFT=486590350356
  elif [[ $RUNNUMBER -eq 529039 ]]; then
    ZDC_BC_SHIFT=1399525886484
  elif [[ $RUNNUMBER -eq 529043 ]]; then
    ZDC_BC_SHIFT=3079675091988
  fi
  if [[ $ALIEN_JDL_LPMPRODUCTIONTYPE != "MC" ]]; then
    [[ ! -z $ZDC_BC_SHIFT ]] && export CONFIG_EXTRA_PROCESS_o2_ctf_reader_workflow+=";TriggerOffsetsParam.customOffset[11]=$ZDC_BC_SHIFT;"
  fi
fi

# Apply BC shift of CTP IRs (whenever it is defined)
if [[ $CTP_BC_SHIFT -ne 0 ]]; then
  if [[ $ALIEN_JDL_LPMPRODUCTIONTYPE != "MC" ]]; then
    export CONFIG_EXTRA_PROCESS_o2_ctf_reader_workflow+=";TriggerOffsetsParam.customOffset[16]=$CTP_BC_SHIFT"
  fi
fi

# ITSTPC vs FT0 time shift
if [[ -z $TPCCLUSTERTIMESHIFT ]]; then
  SHIFTSCRIPT="$O2DPG_ROOT/DATA/production/configurations/asyncReco/ShiftMap.sh"
  if [[ -f "ShiftMap.sh" ]]; then
    SHIFTSCRIPT="ShiftMap.sh"
  fi
  source $SHIFTSCRIPT $RUNNUMBER
fi
if [[ -z $TPCCLUSTERTIMESHIFT ]]; then
  echo "TPC cluster time shift not defined for current run"
  TPCCLUSTERTIMESHIFT=0
fi
echo "TPC cluster time will be shifted by $TPCCLUSTERTIMESHIFT"

# run-dependent options
if [[ -f "setenv_run.sh" ]]; then
    source setenv_run.sh
else
    echo "************************************************************"
    echo No ad-hoc run-dependent settings for current async processing
    echo "************************************************************"
fi

echo -e "\nTPC vdrift:"
# TPC vdrift
PERIODLETTER=${PERIOD: -1}
VDRIFTPARAMOPTION=
if [[ $ALIEN_JDL_LPMANCHORYEAR == "2022" ]] && [[ $PERIODLETTER < m ]]; then
  echo "In setenv_extra: time used so far = $timeUsed s"
  timeStart=`date +%s`
  time root -b -q "$O2DPG_ROOT/DATA/production/common/getTPCvdrift.C+($RUNNUMBER)"
  timeEnd=`date +%s`
  timeUsed=$(( $timeUsed+$timeEnd-$timeStart ))
  delta=$(( $timeEnd-$timeStart ))
  echo "Time spent to get VDrift for TPC = $delta s"
  export VDRIFT=`cat vdrift.txt`
  VDRIFTPARAMOPTION="TPCGasParam.DriftV=$VDRIFT"
  echo "Setting TPC vdrift to $VDRIFT"
else
  echo "TPC vdrift will be taken from CCDB"
fi

echo -e "\nTPC calib configuration:"
# Let's check if ZDC is in the detector list; this is needed for TPC dist correction scaling in PbPb 2023
SCALE_WITH_ZDC=1
SCALE_WITH_FT0=1
isZDCinDataTaking=`echo $RUN_DETECTOR_LIST | grep ZDC`
isFT0inDataTaking=`echo $RUN_DETECTOR_LIST | grep FT0`
[[ -z $isZDCinDataTaking ]] && SCALE_WITH_ZDC=0
[[ -z $isFT0inDataTaking ]] && SCALE_WITH_FT0=0

# For runs shorter than 10 minutes we have only a single slot.
# In that case we have to adopt the slot length in order to
# set the maximum number of processed tracks per TF correctly
if (( RUN_DURATION < 600 )); then
  export CALIB_TPC_SCDCALIB_SLOTLENGTH=$RUN_DURATION
fi

if [[ $ALIEN_JDL_ENABLEMONITORING != "0" ]]; then
  # add the performance metrics
  export ENABLE_METRICS=1
  export ARGS_ALL_EXTRA+=" --resources-monitoring 50 --resources-monitoring-dump-interval 50"
else
  # remove monitoring-backend
  export ENABLE_METRICS=0
fi

if [ -z ${ALIEN_JDL_LPMANCHOREDPASSNUMBER+x} ]; then
  export ANCHORED_PASS_NUMBER=$(echo $ALIEN_JDL_LPMPASSNAME | sed 's/^apass//' | cut -c1-1)
  echo "using ANCHORED_PASS_NUMBER from pass name $ALIEN_JDL_LPMPASSNAME, ANCHORED_PASS_NUMBER=$ANCHORED_PASS_NUMBER"
else
  # variable exported, takes precedence over anything else
  export ANCHORED_PASS_NUMBER=$ALIEN_JDL_LPMANCHOREDPASSNUMBER
  echo "using ANCHORED_PASS_NUMBER from $ALIEN_JDL_LPMANCHOREDPASSNUMBER defined by JDL, ANCHORED_PASS_NUMBER=$ANCHORED_PASS_NUMBER"
fi

echo "Checking ANCHORED_PASS_NUMBER"
if [ -n "$ANCHORED_PASS_NUMBER" ] && [ "$ANCHORED_PASS_NUMBER" -eq "$ANCHORED_PASS_NUMBER" ] 2>/dev/null; then
  echo "ANCHORED_PASS_NUMBER set to $ANCHORED_PASS_NUMBER"
else
  echo "[Warning] undetermined ANCHORED_PASS_NUMBER"
fi


#ALIGNLEVEL=0: before December 2022 alignment, 1: after December 2022 alignment
ALIGNLEVEL=1
if [[ "0$OLDVERSION" == "01" ]] && [[ $BEAMTYPE == "PbPb" || $PERIOD == "MAY" || $PERIOD == "JUN" || $PERIOD == "LHC22c" || $PERIOD == "LHC22d" || $PERIOD == "LHC22e" || $PERIOD == "LHC22f" ]]; then
  ALIGNLEVEL=0
  if [[ $ALIEN_JDL_LPMPRODUCTIONTYPE == "MC" ]]; then
    # extract pass number
    ANCHORED_PASS=$ALIEN_JDL_LPMANCHOREDPASSNAME
    ANCHORED_PASS_NUMBER=`echo $ANCHORED_PASS | sed 's/^apass//'`
    echo "ANCHORED_PASS_NUMER = $ANCHORED_PASS_NUMBER"
    if [[ $PERIOD == "MAY" || $PERIOD == "JUN" ]] && [[ $ANCHORED_PASS_NUMBER -gt 1 ]]; then
      ALIGNLEVEL=1
    elif [[ $PERIOD == "LHC22c" || $PERIOD == "LHC22d" || $PERIOD == "LHC22e" || $PERIOD == "LHC22f" ]] && [[ $ANCHORED_PASS_NUMBER -gt 2 ]]; then
      ALIGNLEVEL=1
    fi
  fi
fi

# some settings in common between workflows and affecting ITS-TPC matching
: ${CUT_MATCH_CHI2:=250}
if [[ $ALIGNLEVEL == 0 ]]; then
  ERRIB="9e-4"
  ERROB="1e-2"
  CUT_MATCH_CHI2=160
  export ITS_CONFIG=" --tracking-mode sync_misaligned"
  export ITSTPCMATCH="tpcitsMatch.safeMarginTimeCorrErr=10.;tpcitsMatch.cutMatchingChi2=$CUT_MATCH_CHI2;tpcitsMatch.crudeAbsDiffCut[0]=5;tpcitsMatch.crudeAbsDiffCut[1]=5;tpcitsMatch.crudeAbsDiffCut[2]=0.3;tpcitsMatch.crudeAbsDiffCut[3]=0.3;tpcitsMatch.crudeAbsDiffCut[4]=10;tpcitsMatch.crudeNSigma2Cut[0]=200;tpcitsMatch.crudeNSigma2Cut[1]=200;tpcitsMatch.crudeNSigma2Cut[2]=200;tpcitsMatch.crudeNSigma2Cut[3]=200;tpcitsMatch.crudeNSigma2Cut[4]=900;"
elif [[ $ALIGNLEVEL == 1 ]]; then
  ERRIB="100e-8"
  ERROB="100e-8"
  [[ -z $TPCITSTIMEERR ]] && TPCITSTIMEERR="0.2"
  if [[ $ALIEN_JDL_LPMANCHORYEAR == "2023" && $BEAMTYPE == "PbPb" && $ANCHORED_PASS_NUMBER -lt 5 ]] || [[ $PERIOD == "LHC24al" ]] ; then
    [[ $ALIEN_JDL_LPMANCHORYEAR == "2023" ]] && [[ $BEAMTYPE == "PbPb" ]] && CUT_MATCH_CHI2=80 || CUT_MATCH_CHI2=100
    export ITSTPCMATCH="tpcitsMatch.safeMarginTimeCorrErr=2.;tpcitsMatch.XMatchingRef=60.;tpcitsMatch.cutMatchingChi2=$CUT_MATCH_CHI2;;tpcitsMatch.crudeAbsDiffCut[0]=6;tpcitsMatch.crudeAbsDiffCut[1]=6;tpcitsMatch.crudeAbsDiffCut[2]=0.3;tpcitsMatch.crudeAbsDiffCut[3]=0.3;tpcitsMatch.crudeAbsDiffCut[4]=2.5;tpcitsMatch.crudeNSigma2Cut[0]=64;tpcitsMatch.crudeNSigma2Cut[1]=64;tpcitsMatch.crudeNSigma2Cut[2]=64;tpcitsMatch.crudeNSigma2Cut[3]=64;tpcitsMatch.crudeNSigma2Cut[4]=64;"
    export ITSTPCMATCH="${ITSTPCMATCH};tpcitsMatch.askMinTPCRow[0]=20;tpcitsMatch.askMinTPCRow[1]=20;tpcitsMatch.askMinTPCRow[2]=20;tpcitsMatch.askMinTPCRow[3]=20;tpcitsMatch.askMinTPCRow[4]=20;tpcitsMatch.askMinTPCRow[5]=20;tpcitsMatch.askMinTPCRow[6]=20;tpcitsMatch.askMinTPCRow[7]=20;tpcitsMatch.askMinTPCRow[8]=20;tpcitsMatch.askMinTPCRow[9]=20;tpcitsMatch.askMinTPCRow[10]=20;tpcitsMatch.askMinTPCRow[12]=20;tpcitsMatch.askMinTPCRow[13]=20;tpcitsMatch.askMinTPCRow[14]=20;"
    export ITSTPCMATCH="${ITSTPCMATCH};tpcitsMatch.askMinTPCRow[15]=20;tpcitsMatch.askMinTPCRow[16]=20;tpcitsMatch.askMinTPCRow[17]=20;tpcitsMatch.askMinTPCRow[18]=20;tpcitsMatch.askMinTPCRow[19]=20;tpcitsMatch.askMinTPCRow[20]=20;tpcitsMatch.askMinTPCRow[21]=20;tpcitsMatch.askMinTPCRow[22]=20;tpcitsMatch.askMinTPCRow[23]=20;tpcitsMatch.askMinTPCRow[24]=20;tpcitsMatch.askMinTPCRow[25]=20;tpcitsMatch.askMinTPCRow[26]=20;tpcitsMatch.askMinTPCRow[27]=20;tpcitsMatch.askMinTPCRow[28]=20;tpcitsMatch.askMinTPCRow[29]=20;"
    export ITSTPCMATCH="${ITSTPCMATCH};tpcitsMatch.askMinTPCRow[30]=20;tpcitsMatch.askMinTPCRow[31]=20;tpcitsMatch.askMinTPCRow[32]=20;tpcitsMatch.askMinTPCRow[33]=20;tpcitsMatch.askMinTPCRow[34]=20;tpcitsMatch.askMinTPCRow[35]=20;"
    if [[ $RUNNUMBER -ge 544512 ]] ; then
      # runs below as well as LHC24al suffer from TPC IROC11 missing but should not reprocessed with tpcitsMatch.askMinTPCRow[11]=78
      RUNSI11BAD=(544947 545289 545004 545060 544931 545184 545345 544963 544991 544911 545103 545086)
      [[ $PERIOD != "LHC24al" ]] && APPLYS11=1 || APPLYS11=0
      for irs11 in "${RUNSI11BAD[@]}" ; do
        if [[ $RUNNUMBER == $irs11 ]] ; then
          APPLYS11=0;
          break;
        fi
      done
    fi
    [[ $APPLYS11 == 1 ]] && export ITSTPCMATCH="${ITSTPCMATCH};tpcitsMatch.askMinTPCRow[11]=78;" || export ITSTPCMATCH="${ITSTPCMATCH};tpcitsMatch.askMinTPCRow[11]=20;"
  elif [[ $BEAMTYPE == "PbPb" && ( ( $ALIEN_JDL_LPMANCHORYEAR == "2023" && $ANCHORED_PASS_NUMBER -gt 4 ) || ( $ALIEN_JDL_LPMANCHORYEAR == "2024" && $ANCHORED_PASS_NUMBER -gt 1 )  ) ]] ; then
    export ITSTPCMATCH="${ITSTPCMATCH};tpcitsMatch.askMinTPCRow[0]=78;tpcitsMatch.askMinTPCRow[1]=78;tpcitsMatch.askMinTPCRow[2]=78;tpcitsMatch.askMinTPCRow[3]=78;tpcitsMatch.askMinTPCRow[4]=78;tpcitsMatch.askMinTPCRow[5]=78;tpcitsMatch.askMinTPCRow[6]=78;tpcitsMatch.askMinTPCRow[7]=78;tpcitsMatch.askMinTPCRow[8]=78;tpcitsMatch.askMinTPCRow[9]=78;tpcitsMatch.askMinTPCRow[10]=78;tpcitsMatch.askMinTPCRow[11]=78;tpcitsMatch.askMinTPCRow[12]=78;tpcitsMatch.askMinTPCRow[13]=78;tpcitsMatch.askMinTPCRow[14]=78;tpcitsMatch.askMinTPCRow[15]=78;tpcitsMatch.askMinTPCRow[16]=78;tpcitsMatch.askMinTPCRow[17]=78;tpcitsMatch.askMinTPCRow[18]=78;tpcitsMatch.askMinTPCRow[19]=78;tpcitsMatch.askMinTPCRow[20]=78;tpcitsMatch.askMinTPCRow[21]=78;tpcitsMatch.askMinTPCRow[22]=78;tpcitsMatch.askMinTPCRow[23]=78;tpcitsMatch.askMinTPCRow[24]=78;tpcitsMatch.askMinTPCRow[25]=78;tpcitsMatch.askMinTPCRow[26]=78;tpcitsMatch.askMinTPCRow[27]=78;tpcitsMatch.askMinTPCRow[28]=78;tpcitsMatch.askMinTPCRow[29]=78;tpcitsMatch.askMinTPCRow[30]=78;tpcitsMatch.askMinTPCRow[31]=78;tpcitsMatch.askMinTPCRow[32]=78;tpcitsMatch.askMinTPCRow[33]=78;tpcitsMatch.askMinTPCRow[34]=78;tpcitsMatch.askMinTPCRow[35]=78;"
  elif [[ $BEAMTYPE == "pp" || $LIGHTNUCLEI == "1" ]] ; then
    export ITSTPCMATCH="${ITSTPCMATCH};tpcitsMatch.askMinTPCRow[0]=78;tpcitsMatch.askMinTPCRow[1]=78;tpcitsMatch.askMinTPCRow[2]=78;tpcitsMatch.askMinTPCRow[3]=78;tpcitsMatch.askMinTPCRow[4]=78;tpcitsMatch.askMinTPCRow[5]=78;tpcitsMatch.askMinTPCRow[6]=78;tpcitsMatch.askMinTPCRow[7]=78;tpcitsMatch.askMinTPCRow[8]=78;tpcitsMatch.askMinTPCRow[9]=78;tpcitsMatch.askMinTPCRow[10]=78;tpcitsMatch.askMinTPCRow[11]=78;tpcitsMatch.askMinTPCRow[12]=78;tpcitsMatch.askMinTPCRow[13]=78;tpcitsMatch.askMinTPCRow[14]=78;tpcitsMatch.askMinTPCRow[15]=78;tpcitsMatch.askMinTPCRow[16]=78;tpcitsMatch.askMinTPCRow[17]=78;tpcitsMatch.askMinTPCRow[18]=78;tpcitsMatch.askMinTPCRow[19]=78;tpcitsMatch.askMinTPCRow[20]=78;tpcitsMatch.askMinTPCRow[21]=78;tpcitsMatch.askMinTPCRow[22]=78;tpcitsMatch.askMinTPCRow[23]=78;tpcitsMatch.askMinTPCRow[24]=78;tpcitsMatch.askMinTPCRow[25]=78;tpcitsMatch.askMinTPCRow[26]=78;tpcitsMatch.askMinTPCRow[27]=78;tpcitsMatch.askMinTPCRow[28]=78;tpcitsMatch.askMinTPCRow[29]=78;tpcitsMatch.askMinTPCRow[30]=78;tpcitsMatch.askMinTPCRow[31]=78;tpcitsMatch.askMinTPCRow[32]=78;tpcitsMatch.askMinTPCRow[33]=78;tpcitsMatch.askMinTPCRow[34]=78;tpcitsMatch.askMinTPCRow[35]=78;"
  fi


  # settings to improve inner pad-rows contribution
  export CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+=";GPU_rec_tpc.trackletMinSharedNormFactor=1.;GPU_rec_tpc.trackletMaxSharedFraction=0.3;GPU_rec_tpc.rejectIFCLowRadiusCluster=1;"
  if grep extrapolationTrackingRowRange $O2_ROOT/include/GPU/GPUSettingsList.h &> /dev/null ; then
    export CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+="GPU_rec_tpc.extrapolationTrackingRowRange=100;"
  else
    export CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+="GPU_rec_tpc.globalTrackingRowRange=100;"
  fi

  if [[ -n "$ALIEN_JDL_TPCDEDXCLMASK" ]]; then
    CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+="GPU_rec_tpc.dEdxClusterRejectionFlagMask=$ALIEN_JDL_TPCDEDXCLMASK;"
  fi

  if [[ -n "$ALIEN_JDL_TPCDEDXCLMASKALT" ]]; then
    CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+="GPU_rec_tpc.dEdxClusterRejectionFlagMaskAlt=$ALIEN_JDL_TPCDEDXCLMASKALT;"
  fi

  if [[ -n "$ALIEN_JDL_TPCEDGETWOPADS" ]]; then
    CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+="GPU_rec_tpc.cfEdgeTwoPads=$ALIEN_JDL_TPCEDGETWOPADS;"
  fi

  if [[ -n "$ALIEN_JDL_TPCCLUSTERFILTER" ]]; then
    CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+="GPU_proc.tpcUseOldCPUDecoding=1;GPU_proc.tpcApplyClusterFilterOnCPU=$ALIEN_JDL_TPCCLUSTERFILTER;"
  fi

  if [[ -n "$ALIEN_JDL_TPCCHICUTOPT" ]]; then # 0 or 1 to disable or enable (default) the chi2 cut both on one-side and smoothed Kalman chi2
    CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+="GPU_rec_tpc.mergerInterpolateRejectAlsoOnCurrentPosition=$ALIEN_JDL_TPCCHICUTOPT;"
  fi

  if [[ -n "$ALIEN_JDL_TPCCLUSEDGEREDEF" ]]; then # if >0 (float) undo the edge cluster bit for TPC clusters with distance to the edge exceeding this value
    CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+="GPU_rec_tpc.clustersEdgeFixDistance=$ALIEN_JDL_TPCCLUSEDGEREDEF;"
  fi

  #-------------------------------------- TPC corrections -----------------------------------------------
  # we need to provide to TPC
  # 1) interaction rate info (lumi) used for scaling or errors and possible of the corrections : INST_IR_FOR_TPC
  # 2) what to use for corrections scaling (lumi or IDC scalers or no scaling at all) : TPC_SCALING_SOURCE
  # the default is to use CTP, unless specified differently in the JDL...
  INST_IR_FOR_TPC=${ALIEN_JDL_INSTIRFORTPC-CTP}
  TPC_SCALING_SOURCE=${ALIEN_JDL_TPCSCALINGSOURCE-IDCCCDB}
  # MEAN_IR_FOR_TPC allows (1) to alter the map mean IR if >0 or (2) disable  all corrections if <0
  MEAN_IR_FOR_TPC=${ALIEN_JDL_MEANIRFORTPC-}
  # optional mean IR to impose for the ref. map
  MEAN_IR_REF_FOR_TPC=${ALIEN_JDL_MEANIRREFFORTPC-}

  if [[ $ALIEN_JDL_LPMANCHORYEAR == "2022" ]]; then
    INST_IR_FOR_TPC=${ALIEN_JDL_INSTIRFORTPC-CTPCCDB} # by default override inst.IR by the mean IR from CCDB and use it for scaling
  fi
  if [[ $PERIOD == "LHC22s" ]]; then
    TPC_SCALING_SOURCE=${ALIEN_JDL_TPCSCALINGSOURCE-NO_SCALING}  # in this way, only TPC/Calib/CorrectionMaps is applied, and we know that for 22s it is the same as TPC/Calib/CorrectionMapsRef;
  elif [[ $PERIOD == @(LHC22c|LHC22d|LHC22e|JUN|LHC22f) ]]; then
    INST_IR_FOR_TPC=${ALIEN_JDL_INSTIRFORTPC-1} # scaling with very small value for low IR
  fi
  # in MC, we disable completely the corrections
  # note that if ALIEN_JDL_INSTIRFORTPC is set, it has precedence
  if [[ $ALIEN_JDL_LPMPRODUCTIONTYPE == "MC" ]] && [[ $O2DPG_ENABLE_TPC_DISTORTIONS != "ON" ]]; then
    MEAN_IR_FOR_TPC=${ALIEN_JDL_MEANIRFORTPC--1}
  fi

  DISABLE_CORRECTIONS=
  [[ -n "$ALIEN_JDL_MSHAPECORRECTION" && $ALIEN_JDL_MSHAPECORRECTION == "0" ]] && ENABLE_MSHAPE=0 || ENABLE_MSHAPE=1

  if [[ -n $MEAN_IR_FOR_TPC ]] ; then  # firs check if corrections were not disabled via MEAN_IR_FOR_TPC
    if (( $(echo "$MEAN_IR_FOR_TPC > 0" | bc -l) )) ; then # positive value overrides map mean lumi
      echo "Applying externally provided map mean IR for scaling, $MEAN_IR_FOR_TPC"
      export TPC_CORR_SCALING+=";TPCCorrMap.lumiMean=$MEAN_IR_FOR_TPC;" # take mean lumy at face value
    elif (( $(echo "$MEAN_IR_FOR_TPC < 0" | bc -l) )) ; then # negative mean lumi disables all corrections
      echo "Negative MEAN_IR_FOR_TPC -> all TPC corrections will be ignored"
      export TPC_CORR_SCALING+=" --lumi-type 0 "
      export TPC_CORR_SCALING+=";TPCCorrMap.lumiMean=$MEAN_IR_FOR_TPC;"
      ENABLE_MSHAPE=0
      DISABLE_CORRECTIONS=1
    else
      echo "Did not recognize MEAN_IR_FOR_TPC = $MEAN_IR_FOR_TPC"
      return 1
    fi
  fi # MEAN_IR_FOR_TPC overridden

  if [[ -n $MEAN_IR_REF_FOR_TPC ]] ; then
    echo "Applying externally provided map mean reference map IR, $MEAN_IR_REF_FOR_TPC"
    export TPC_CORR_SCALING+=";TPCCorrMap.lumiMeanRef=$MEAN_IR_REF_FOR_TPC"
  fi


  # set IR for TPC, even if it is not used for corrections scaling
  if [[ "$INST_IR_FOR_TPC" =~ ^-?[0-9]*\.?[0-9]+$ ]] && (( $(echo "$INST_IR_FOR_TPC > 0" | bc -l) )) ; then # externally imposed CTP IR
    echo "Applying externally provided istantaneous IR $INST_IR_FOR_TPC Hz"
    export TPC_CORR_SCALING+=";TPCCorrMap.lumiInst=$INST_IR_FOR_TPC"
  elif [[ $INST_IR_FOR_TPC == "CTP" ]]; then
    if ! has_detector CTP ; then
      echo "CTP Lumi is for TPC corrections but CTP is not in the WORKFLOW_DETECTORS=$WORKFLOW_DETECTORS"
      return 1
    fi
    echo "Using CTP inst lumi stored in data"
  elif [[ $INST_IR_FOR_TPC == "CTPCCDB" ]]; then # using what we have in the CCDB CTP counters, extracted at the beginning of the script
    echo "Using CTP CCDB which gave the mean IR of the run at the beginning of the script ($RUN_IR Hz)"
    export TPC_CORR_SCALING+=";TPCCorrMap.lumiInst=$RUN_IR"
  else echo "Unknown setting for INST_IR_FOR_TPC = $INST_IR_FOR_TPC (with ALIEN_JDL_INSTIRFORTPC = $ALIEN_JDL_INSTIRFORTPC)"
    return 1
  fi

  # now set the source of the corrections
  if [[ $DISABLE_CORRECTIONS != 1 ]] ; then
    if [[ $TPC_SCALING_SOURCE == "NO_SCALING" ]]; then
      echo "NO SCALING is requested: only TPC/Calib/CorrectionMapsV2... will be applied"
      export TPC_CORR_SCALING+=" --lumi-type 0 "
    elif [[ $TPC_SCALING_SOURCE == "CTP" ]]; then
      echo "CTP Lumi from data will be used for TPC scaling"
      export TPC_CORR_SCALING+=" --lumi-type 1 "
      if [[ $ALIEN_JDL_USEDERIVATIVESFORSCALING == "1" ]]; then
        export TPC_CORR_SCALING+=" --corrmap-lumi-mode 1 "
      fi
    elif [[ $TPC_SCALING_SOURCE == "IDCCCDB" ]]; then
      echo "TPC correction with IDC from CCDB will be used"
      export TPC_CORR_SCALING+=" --lumi-type 2 "
      if [[ $ALIEN_JDL_USEDERIVATIVESFORSCALING == "1" ]]; then
        export TPC_CORR_SCALING+=" --corrmap-lumi-mode 1 "
      fi
    else
      echo "Unknown setting for TPC_SCALING_SOURCE = $TPC_SCALING_SOURCE (with ALIEN_JDL_TPCSCALINGSOURCE = $ALIEN_JDL_TPCSCALINGSOURCE)"
    fi
  fi

  if ! has_detector CTP ; then
    echo "CTP is not in the list of detectors, disabling CTP Lumi input request"
    export TPC_CORR_SCALING+=" --disable-ctp-lumi-request "
  fi

  if [[ $ENABLE_MSHAPE == "1" ]]; then
    export TPC_CORR_SCALING+=" --enable-M-shape-correction "
  fi

  if [[ $ALIEN_JDL_LPMANCHORYEAR -ge 2023 ]] && [[ $BEAMTYPE == "PbPb" ]] ; then
    # adding additional cluster errors
    # the values below should be squared, but the validation of those values (0.01 and 0.0225) is ongoing
    TPCEXTRAERR=";GPU_rec_tpc.clusterError2AdditionalYSeeding=0.1;GPU_rec_tpc.clusterError2AdditionalZSeeding=0.15;"
    if [[ $SCALE_WITH_ZDC == 1 ]]; then
      echo "For 2023 PbPb ZDC inst. lumi applying factor 2.414"
      export TPC_CORR_SCALING+=";TPCCorrMap.lumiInstFactor=2.414;"
    elif [[ $SCALE_WITH_FT0 == 1 ]]; then
      echo "For 2023 PbPb FT0 inst. lumi applying factor 135."
      export TPC_CORR_SCALING+="TPCCorrMap.lumiInstFactor=135.;"
    else
      echo "Neither ZDC nor FT0 are in the run, and this is from 2023 PbPb: we cannot scale TPC ditortion corrections, aborting..."
      return 1
    fi
  fi

  echo "Final setting for TPC scaling is:"
  echo $TPC_CORR_SCALING
  #-------------------------------------- TPC corrections (end)--------------------------------------------

  if [[ $PERIOD != @(LHC22c|LHC22d|LHC22e|JUN|LHC22f) ]] ; then
    echo "Setting TPCCLUSTERTIMESHIFT to 0"
    TPCCLUSTERTIMESHIFT=0
  else
    echo "We are in period $PERIOD, we need to keep the correction for the TPC cluster time, since no new vdrift was extracted"
  fi

  TRACKTUNETPCINNER="trackTuneParams.tpcCovInnerType=2;trackTuneParams.tpcCovInner[0]=0.05;trackTuneParams.tpcCovInner[1]=0.2;trackTuneParams.tpcCovInner[2]=0.0003;trackTuneParams.tpcCovInner[3]=0.0013;trackTuneParams.tpcCovInner[4]=0.0059300284;trackTuneParams.tpcCovInnerSlope[0]=1.4794650254467986e-08;trackTuneParams.tpcCovInnerSlope[1]=5.9178601017871944e-08;trackTuneParams.tpcCovInnerSlope[2]=8.87679015268079e-11;trackTuneParams.tpcCovInnerSlope[3]=3.846609066161676e-10;trackTuneParams.tpcCovInnerSlope[4]=1.7546539235412473e-09;"
  TRACKTUNETPCOUTER="trackTuneParams.tpcCovOuterType=2;trackTuneParams.tpcCovOuter[0]=0.05;trackTuneParams.tpcCovOuter[1]=0.2;trackTuneParams.tpcCovOuter[2]=0.0003;trackTuneParams.tpcCovOuter[3]=0.0013;trackTuneParams.tpcCovOuter[4]=0.0059300284;trackTuneParams.tpcCovOuterSlope[0]=1.4794650254467986e-08;trackTuneParams.tpcCovOuterSlope[1]=5.9178601017871944e-08;trackTuneParams.tpcCovOuterSlope[2]=8.87679015268079e-11;trackTuneParams.tpcCovOuterSlope[3]=3.846609066161676e-10;trackTuneParams.tpcCovOuterSlope[4]=1.7546539235412473e-09;"


fi

TRACKTUNETPC=${TPCEXTRAERR-}

# combining parameters
[[ ! -z ${TRACKTUNETPCINNER:-} || ! -z ${TRACKTUNETPCOUTER:-} ]] && TRACKTUNETPC="$TRACKTUNETPC;trackTuneParams.sourceLevelTPC=true;$TRACKTUNETPCINNER;$TRACKTUNETPCOUTER"

export ITSEXTRAERR="ITSCATrackerParam.sysErrY2[0]=$ERRIB;ITSCATrackerParam.sysErrZ2[0]=$ERRIB;ITSCATrackerParam.sysErrY2[1]=$ERRIB;ITSCATrackerParam.sysErrZ2[1]=$ERRIB;ITSCATrackerParam.sysErrY2[2]=$ERRIB;ITSCATrackerParam.sysErrZ2[2]=$ERRIB;ITSCATrackerParam.sysErrY2[3]=$ERROB;ITSCATrackerParam.sysErrZ2[3]=$ERROB;ITSCATrackerParam.sysErrY2[4]=$ERROB;ITSCATrackerParam.sysErrZ2[4]=$ERROB;ITSCATrackerParam.sysErrY2[5]=$ERROB;ITSCATrackerParam.sysErrZ2[5]=$ERROB;ITSCATrackerParam.sysErrY2[6]=$ERROB;ITSCATrackerParam.sysErrZ2[6]=$ERROB;"

# ad-hoc options for ITS reco workflow
EXTRA_ITSRECO_CONFIG=
if [[ $BEAMTYPE == "PbPb" ]]; then
  EXTRA_ITSRECO_CONFIG="ITSCATrackerParam.deltaRof=0;ITSVertexerParam.clusterContributorsCut=16;ITSVertexerParam.lowMultBeamDistCut=0;ITSCATrackerParam.nROFsPerIterations=12;ITSCATrackerParam.perPrimaryVertexProcessing=false;ITSCATrackerParam.fataliseUponFailure=false;ITSCATrackerParam.dropTFUponFailure=true"
  if [[ -z "$ALIEN_JDL_DISABLE_UPC" || $ALIEN_JDL_DISABLE_UPC != 1 ]]; then
    EXTRA_ITSRECO_CONFIG+=";ITSVertexerParam.nIterations=2;ITSCATrackerParam.doUPCIteration=true;"
  fi
elif [[ $BEAMTYPE == "pp" || $LIGHTNUCLEI == "1" ]]; then
  EXTRA_ITSRECO_CONFIG="ITSVertexerParam.phiCut=0.5;ITSVertexerParam.clusterContributorsCut=3;ITSVertexerParam.tanLambdaCut=0.2;"
  EXTRA_ITSRECO_CONFIG+=";ITSCATrackerParam.startLayerMask[0]=127;ITSCATrackerParam.startLayerMask[1]=127;ITSCATrackerParam.startLayerMask[2]=127;"
  EXTRA_ITSRECO_CONFIG+=";ITSCATrackerParam.minPtIterLgt[0]=0.05;ITSCATrackerParam.minPtIterLgt[1]=0.05;ITSCATrackerParam.minPtIterLgt[2]=0.05;ITSCATrackerParam.minPtIterLgt[3]=0.05;ITSCATrackerParam.minPtIterLgt[4]=0.05;ITSCATrackerParam.minPtIterLgt[5]=0.05;ITSCATrackerParam.minPtIterLgt[6]=0.05;ITSCATrackerParam.minPtIterLgt[7]=0.05;ITSCATrackerParam.minPtIterLgt[8]=0.05;ITSCATrackerParam.minPtIterLgt[9]=0.09;ITSCATrackerParam.minPtIterLgt[10]=0.167;ITSCATrackerParam.minPtIterLgt[11]=0.125;"
#  this is to impose old pp pT cuts (overriding hardcoded pbpb24 apass1 settings)
#  EXTRA_ITSRECO_CONFIG+=";ITSCATrackerParam.minPtIterLgt[0]=0.05;ITSCATrackerParam.minPtIterLgt[1]=0.05;ITSCATrackerParam.minPtIterLgt[2]=0.05;ITSCATrackerParam.minPtIterLgt[3]=0.05;ITSCATrackerParam.minPtIterLgt[4]=0.05;ITSCATrackerParam.minPtIterLgt[5]=0.05;ITSCATrackerParam.minPtIterLgt[6]=0.05;ITSCATrackerParam.minPtIterLgt[7]=0.05;ITSCATrackerParam.minPtIterLgt[8]=0.05;ITSCATrackerParam.minPtIterLgt[9]=0.05;ITSCATrackerParam.minPtIterLgt[10]=0.05;ITSCATrackerParam.minPtIterLgt[11]=0.05;"
fi
export CONFIG_EXTRA_PROCESS_o2_its_reco_workflow+=";$MAXBCDIFFTOMASKBIAS_ITS;$MAXBCDIFFTOSQUASHBIAS_ITS;$EXTRA_ITSRECO_CONFIG;"

# in the ALIGNLEVEL there was inconsistency between the internal errors of sync_misaligned and ITSEXTRAERR
if [[ $ALIGNLEVEL != 0 ]]; then
 export CONFIG_EXTRA_PROCESS_o2_its_reco_workflow+=";$ITSEXTRAERR;"
fi

# ad-hoc options for GPU reco workflow
export CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+=";GPU_global.dEdxDisableResidualGainMap=1;$TRACKTUNETPC;$VDRIFTPARAMOPTION;"

[[ ! -z $TPCCLUSTERTIMESHIFT ]] && [[ $ALIEN_JDL_LPMPRODUCTIONTYPE != "MC" ]] && export CONFIG_EXTRA_PROCESS_o2_gpu_reco_workflow+=";GPU_rec_tpc.clustersShiftTimebins=$TPCCLUSTERTIMESHIFT;"

# ad-hoc settings for TOF reco
# export ARGS_EXTRA_PROCESS_o2_tof_reco_workflow+="--use-ccdb --ccdb-url-tof \"http://alice-ccdb.cern.ch\""
# since commit on Dec, 4
export ARGS_EXTRA_PROCESS_o2_tof_reco_workflow+=" --use-ccdb"

# ad-hoc options for primary vtx workflow
#export PVERTEXER="pvertexer.acceptableScale2=9;pvertexer.minScale2=2.;pvertexer.nSigmaTimeTrack=4.;pvertexer.timeMarginTrackTime=0.5;pvertexer.timeMarginVertexTime=7.;pvertexer.nSigmaTimeCut=10;pvertexer.dbscanMaxDist2=30;pvertexer.dcaTolerance=3.;pvertexer.pullIniCut=100;pvertexer.addZSigma2=0.1;pvertexer.tukey=20.;pvertexer.addZSigma2Debris=0.01;pvertexer.addTimeSigma2Debris=1.;pvertexer.maxChi2Mean=30;pvertexer.timeMarginReattach=3.;pvertexer.addTimeSigma2Debris=1.;"
# following comment https://alice.its.cern.ch/jira/browse/O2-2691?focusedCommentId=278262&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-278262
#export PVERTEXER="pvertexer.acceptableScale2=9;pvertexer.minScale2=2.;pvertexer.nSigmaTimeTrack=4.;pvertexer.timeMarginTrackTime=0.5;pvertexer.timeMarginVertexTime=7.;pvertexer.nSigmaTimeCut=10;pvertexer.dbscanMaxDist2=36;pvertexer.dcaTolerance=3.;pvertexer.pullIniCut=100;pvertexer.addZSigma2=0.1;pvertexer.tukey=20.;pvertexer.addZSigma2Debris=0.01;pvertexer.addTimeSigma2Debris=1.;pvertexer.maxChi2Mean=30;pvertexer.timeMarginReattach=3.;pvertexer.addTimeSigma2Debris=1.;pvertexer.dbscanDeltaT=24;pvertexer.maxChi2TZDebris=100;pvertexer.maxMultRatDebris=1.;pvertexer.dbscanAdaptCoef=20.;pvertexer.timeMarginVertexTime=1.3"
# updated on 7 Sept 2022
EXTRA_PRIMVTX_TimeMargin=""
if [[ $BEAMTYPE == "PbPb" || $PERIOD == "MAY" || $PERIOD == "JUN" || $PERIOD == LHC22* || $PERIOD == LHC23* ]]; then
  EXTRA_PRIMVTX_TimeMargin="pvertexer.timeMarginVertexTime=1.3"
fi

export PVERTEXER+=";pvertexer.acceptableScale2=9;pvertexer.minScale2=2;$EXTRA_PRIMVTX_TimeMargin;"
if [[ $ALIGNLEVEL == 1 ]]; then
  if [[ $BEAMTYPE == "PbPb" ]]; then
    export PVERTEXER+=";pvertexer.addTimeSigma2Debris=1e-2;pvertexer.meanVertexExtraErrSelection=0.03;pvertexer.maxITSOnlyFraction=0.85;pvertexer.maxTDiffDebris=1.5;pvertexer.maxZDiffDebris=0.3;pvertexer.addZSigma2Debris=0.09;pvertexer.addTimeSigma2Debris=2.25;pvertexer.maxChi2TZDebris=100;pvertexer.maxMultRatDebris=1.;pvertexer.maxTDiffDebrisExtra=-1.;pvertexer.dbscanDeltaT=-0.55;pvertexer.maxTMAD=1.;pvertexer.maxZMAD=0.04;"
    has_detector_reco FT0 && PVERTEX_CONFIG+=" --validate-with-ft0 "
  elif [[ $BEAMTYPE == "pp" ]]; then
    export PVERTEXER+=";pvertexer.maxChi2TZDebris=40;pvertexer.maxChi2Mean=12;pvertexer.maxMultRatDebris=1.;pvertexer.addTimeSigma2Debris=1e-2;pvertexer.meanVertexExtraErrSelection=0.03;"
  elif [[ $LIGHTNUCLEI == "1" ]]; then
    export PVERTEXER+="pvertexer.maxChi2TZDebris=3000;pvertexer.maxTDiffDebris=0.7;pvertexer.maxZDiffDebris=0.5;pvertexer.maxMultRatDebris=0.25;pvertexer.addTimeSigma2Debris=0.2;pvertexer.addZSigma2Debris=0.2;pvertexer.maxChi2TZDebrisExtra=50;pvertexer.maxTDiffDebrisExtra=-1;pvertexer.maxZDiffDebrisExtra=0.03;pvertexer.maxMultRatDebrisExtra=0.25;pvertexer.meanVertexExtraErrSelection=0.03;pvertexer.maxITSOnlyFraction=0.8;pvertexer.meanVertexExtraErrSelection=0.03;"
  fi
fi


# secondary vertexing
if [[ $ALIEN_JDL_DISABLESTRTRACKING == 1 ]]; then
  export STRTRACKING=" --disable-strangeness-tracker "
fi
if [[ $ALIEN_JDL_DISABLECASCADES == 1 ]]; then
  export ARGS_EXTRA_PROCESS_o2_secondary_vertexing_workflow+=" --disable-cascade-finder  "
fi
# allow usage of TPC-only in svertexer (default: do use them, as in default in O2 and CCDB)
if [[ $ALIEN_JDL_DISABLETPCONLYFORV0S == 1 ]]; then
  export CONFIG_EXTRA_PROCESS_o2_secondary_vertexing_workflow+=";svertexer.mExcludeTPCtracks=true"
fi

export CONFIG_EXTRA_PROCESS_o2_primary_vertexing_workflow+=";$PVERTEXER;$VDRIFTPARAMOPTION;"

export CONFIG_EXTRA_PROCESS_o2_tpcits_match_workflow+=";$ITSEXTRAERR;$ITSTPCMATCH;$TRACKTUNETPC;$VDRIFTPARAMOPTION;"
[[ ! -z "${TPCITSTIMEBIAS}" ]] && export CONFIG_EXTRA_PROCESS_o2_tpcits_match_workflow+=";tpcitsMatch.globalTimeBiasMUS=$TPCITSTIMEBIAS;"
[[ ! -z "${TPCITSTIMEERR}" ]] && export CONFIG_EXTRA_PROCESS_o2_tpcits_match_workflow+=";tpcitsMatch.globalTimeExtraErrorMUS=$TPCITSTIMEERR;"

# enabling AfterBurner
has_detector FT0 && export ARGS_EXTRA_PROCESS_o2_tpcits_match_workflow+=" --use-ft0"

# ad-hoc settings for TOF matching
export ARGS_EXTRA_PROCESS_o2_tof_matcher_workflow+=" --output-type matching-info,calib-info --enable-dia"
export CONFIG_EXTRA_PROCESS_o2_tof_matcher_workflow+=";$ITSEXTRAERR;$TRACKTUNETPC;$VDRIFTPARAMOPTION;"

if [[ $ALIEN_JDL_LPMPASSNAME == "cpass0" ]]; then
   CONFIG_EXTRA_PROCESS_o2_tof_matcher_workflow+=";MatchTOF.nsigmaTimeCut=6;"
   ARGS_EXTRA_PROCESS_o2_tof_reco_workflow+=" --for-calib"
fi

# ad-hoc settings for TRD matching
export CONFIG_EXTRA_PROCESS_o2_trd_global_tracking+=";$ITSEXTRAERR;$TRACKTUNETPC;$VDRIFTPARAMOPTION;GPU_rec_trd.minTrackPt=0.3;"

# ad-hoc settings for FT0
export ARGS_EXTRA_PROCESS_o2_ft0_reco_workflow+=" --ft0-reconstructor"
if [[ $BEAMTYPE == "PbPb" ]]; then
  export CONFIG_EXTRA_PROCESS_o2_ft0_reco_workflow+=";FT0TimeFilterParam.mAmpLower=10;"
fi

# ad-hoc settings for FV0
export ARGS_EXTRA_PROCESS_o2_fv0_reco_workflow+=" --fv0-reconstructor"

# ad-hoc settings for FDD
#...

# ad-hoc settings for MFT
if [[ $BEAMTYPE == "pp" || $LIGHTNUCLEI == "1" || $PERIOD == "LHC22s" ]]; then
  export CONFIG_EXTRA_PROCESS_o2_mft_reco_workflow+=";MFTTracking.RBins=30;MFTTracking.PhiBins=120;MFTTracking.ZVtxMin=-13;MFTTracking.ZVtxMax=13;MFTTracking.MFTRadLength=0.084;$MAXBCDIFFTOMASKBIAS_MFT;$MAXBCDIFFTOSQUASHBIAS_MFT"
else
  export CONFIG_EXTRA_PROCESS_o2_mft_reco_workflow+=";MFTTracking.MFTRadLength=0.084;$MAXBCDIFFTOMASKBIAS_MFT;$MAXBCDIFFTOSQUASHBIAS_MFT"
fi

# ad-hoc settings for MCH
if [[ $BEAMTYPE == "pp" || $LIGHTNUCLEI == "1" ]]; then
  export CONFIG_EXTRA_PROCESS_o2_mch_reco_workflow+=";MCHTracking.chamberResolutionX=0.4;MCHTracking.chamberResolutionY=0.4;MCHTracking.sigmaCutForTracking=7;MCHTracking.sigmaCutForImprovement=6"
fi

# ad-hoc settings for MFT-MCH matching
# Number of MFT-MCH matching candidates to be stored in AO2Ds
# Setting MUON_MATCHING_NCANDIDATES=0 disables the storage of multiple candidates
if [[ -z "${MUON_MATCHING_NCANDIDATES:-}" ]]; then
  MUON_MATCHING_NCANDIDATES=0 # disable the saving of nCandidated by default
  if [[ $BEAMTYPE == "pp" || $LIGHTNUCLEI == "1" ]]; then MUON_MATCHING_NCANDIDATES=5; fi
  if [[ $BEAMTYPE == "PbPb" ]]; then MUON_MATCHING_NCANDIDATES=20; fi
fi
if [[ "x${MUON_MATCHING_NCANDIDATES}" != "x0" ]]; then
    export CONFIG_EXTRA_PROCESS_o2_globalfwd_matcher_workflow+=";FwdMatching.saveMode=3;FwdMatching.nCandidates=${MUON_MATCHING_NCANDIDATES};"
fi


# possibly adding calib steps as done online
# could be done better, so that more could be enabled in one go
if [[ $ADD_CALIB == "1" ]]; then
  export WORKFLOW_PARAMETERS="CALIB,CALIB_LOCAL_INTEGRATED_AGGREGATOR,${WORKFLOW_PARAMETERS}"
  export CALIB_DIR="./"
  export CALIB_TPC_SCDCALIB_SENDTRKDATA=0
  export CALIB_PRIMVTX_MEANVTX=0
  export CALIB_TOF_LHCPHASE=0
  export CALIB_TOF_CHANNELOFFSETS=0
  export CALIB_TOF_DIAGNOSTICS=0
  export CALIB_EMC_BADCHANNELCALIB=0
  export CALIB_EMC_TIMECALIB=0
  export CALIB_PHS_ENERGYCALIB=0
  export CALIB_PHS_BADMAPCALIB=0
  export CALIB_PHS_TURNONCALIB=0
  export CALIB_PHS_RUNBYRUNCALIB=0
  export CALIB_PHS_L1PHASE=0
  export CALIB_TRD_VDRIFTEXB=0
  export CALIB_TRD_T0=0
  export CALIB_TRD_GAIN=0
  export CALIB_TPC_TIMEGAIN=0
  export CALIB_TPC_RESPADGAIN=0
  export CALIB_TPC_VDRIFTTGL=0
  export CALIB_CPV_GAIN=0
  export CALIB_ZDC_TDC=0
  export CALIB_FT0_TIMEOFFSET=0
  export CALIB_TPC_SCDCALIB=0
  export CALIB_FT0_INTEGRATEDCURR=0
  export CALIB_FV0_INTEGRATEDCURR=0
  export CALIB_FDD_INTEGRATEDCURR=0
  export CALIB_TOF_INTEGRATEDCURR=0
  export CALIB_ITS_DEADMAP_TIME=0
  export CALIB_MFT_DEADMAP_TIME=0
  if [[ $DO_TPC_RESIDUAL_EXTRACTION == "1" ]]; then
    export CALIB_TPC_SCDCALIB=1
    export CALIB_TPC_SCDCALIB_SENDTRKDATA=1
    export CONFIG_EXTRA_PROCESS_o2_tpc_scdcalib_interpolation_workflow+=";scdcalib.additionalTracksMap=35000000;scdcalib.minPtNoOuterPoint=0.2;scdcalib.maxQ2Pt=5;scdcalib.minITSNClsNoOuterPoint=6;scdcalib.minITSNCls=4;scdcalib.minTPCNClsNoOuterPoint=90;scdcalib.minTOFTRDPVContributors=2"
    : ${TPC_RESIDUAL_TRK_SOURCES_MAP_EXTRACTION:="ITS-TPC"}
    export ARGS_EXTRA_PROCESS_o2_tpc_scdcalib_interpolation_workflow+=" --tracking-sources-map-extraction $TPC_RESIDUAL_TRK_SOURCES_MAP_EXTRACTION"
    # ad-hoc settings for TPC residual extraction
    export ARGS_EXTRA_PROCESS_o2_calibration_residual_aggregator+=" --output-type trackParams,unbinnedResid"
    if [[ $ALIEN_JDL_DEBUGRESIDUALEXTRACTION == "1" ]]; then
      export CONFIG_EXTRA_PROCESS_o2_tpc_scdcalib_interpolation_workflow+=";scdcalib.maxTracksPerCalibSlot=-1;scdcalib.minPtNoOuterPoint=0.8;scdcalib.minTPCNClsNoOuterPoint=120"
      export ARGS_EXTRA_PROCESS_o2_trd_global_tracking+=" --enable-qc"
    fi
  fi
  export CALIB_EMC_ASYNC_RECALIB="$ALIEN_JDL_DOEMCCALIB"
  if [[ $ALIEN_JDL_DOTRDVDRIFTEXBCALIB == "1" ]]; then
    export CALIB_TRD_VDRIFTEXB="$ALIEN_JDL_DOTRDVDRIFTEXBCALIB"
    export ARGS_EXTRA_PROCESS_o2_calibration_trd_workflow+=" --enable-root-output"
    export ARGS_EXTRA_PROCESS_o2_trd_global_tracking+=" --enable-qc"
  fi
  if [[ $ALIEN_JDL_DOMEANVTXCALIB == 1 ]]; then
    export CALIB_PRIMVTX_MEANVTX="$ALIEN_JDL_DOMEANVTXCALIB"
    export TFPERSLOTS_MEANVTX=550000 # 1 hour
    export DELAYINTFS_MEANVTX=55000  # 10 minutes
    export SVERTEXING_SOURCES=none # disable secondary vertexing
  fi
  if [[ $ALIEN_JDL_DOTRDGAINCALIB == 1 ]]; then
    export CONFIG_EXTRA_PROCESS_o2_calibration_trd_workflow+=";TRDCalibParams.minEntriesChamberGainCalib=999999999;TRDCalibParams.minEntriesTotalGainCalib=10000;TRDCalibParams.nTrackletsMinGainCalib=4"
    export ARGS_EXTRA_PROCESS_o2_calibration_trd_workflow+=" --enable-root-output"
    export CALIB_TRD_GAIN=1
  fi
  # extra workflows in case we want to process the currents for FT0, FV0, TOF, TPC
  if [[ -n $ALIEN_JDL_EXTRACTCURRENTS ]] ; then
    export CALIB_FT0_INTEGRATEDCURR=$ALIEN_JDL_EXTRACTCURRENTS
    export CALIB_FV0_INTEGRATEDCURR=$ALIEN_JDL_EXTRACTCURRENTS
    export CALIB_FDD_INTEGRATEDCURR=$ALIEN_JDL_EXTRACTCURRENTS
    export CALIB_TOF_INTEGRATEDCURR=$ALIEN_JDL_EXTRACTCURRENTS
    export CALIB_ASYNC_EXTRACTTPCCURRENTS=$ALIEN_JDL_EXTRACTCURRENTS
  fi
  if [[ -n $ALIEN_JDL_DISABLE3DCURRENTS ]]; then
    export CALIB_ASYNC_DISABLE3DCURRENTS=$ALIEN_JDL_DISABLE3DCURRENTS
  fi

  # extra workflows in case we want to process the currents for time series
  if [[ -n $ALIEN_JDL_EXTRACTTIMESERIES ]] ; then
    echo "Adding timeseries in setenv_extra.sh"
    export CALIB_ASYNC_EXTRACTTIMESERIES=$ALIEN_JDL_EXTRACTTIMESERIES
    if [[ -n $ALIEN_JDL_ENABLEUNBINNEDTIMESERIES ]]; then
      export CALIB_ASYNC_ENABLEUNBINNEDTIMESERIES=$ALIEN_JDL_ENABLEUNBINNEDTIMESERIES
    fi
    if [[ -n $ALIEN_JDL_SAMPLINGFACTORTIMESERIES ]]; then
      export CALIB_ASYNC_SAMPLINGFACTORTIMESERIES=$ALIEN_JDL_SAMPLINGFACTORTIMESERIES
    fi
  fi
  if [[ $ALIEN_JDL_DOUPLOADSLOCALLY == 1 ]]; then
    export CCDB_POPULATOR_UPLOAD_PATH="file://$PWD"
  fi
fi

# Enabling AOD
if [[ $ALIEN_JDL_AODOFF != "1" ]]; then
  export WORKFLOW_PARAMETERS="AOD,${WORKFLOW_PARAMETERS}"
fi

# ad-hoc settings for AOD
echo -e "\nNeeded for AODs:"
echo ALIEN_JDL_LPMPRODUCTIONTAG = $ALIEN_JDL_LPMPRODUCTIONTAG
echo ALIEN_JDL_LPMPASSNAME = $ALIEN_JDL_LPMPASSNAME
# Track QC table sampling
if [[ -n $ALIEN_JDL_TRACKQCFRACTION ]]; then
  TRACKQC_FRACTION=$ALIEN_JDL_TRACKQCFRACTION
else
  if [[ $ALIEN_JDL_ENABLEPERMILFULLTRACKQC == "1" ]]; then
    PERMIL_FULLTRACKQC=${ALIEN_JDL_PERMILFULLTRACKQC:-100}
    INVERSE_PERMIL_FULLTRACKQC=$((1000/PERMIL_FULLTRACKQC))
    if [[ -f wn.xml ]]; then
      HASHCODE=`grep alien:// wn.xml | tr ' ' '\n' | grep ^lfn | cut -d\" -f2 | head -1 | cksum | cut -d ' ' -f 1`
    else
      HASHCODE=`echo "${inputarg}" | cksum | cut -d ' ' -f 1`
    fi
    if [[ "$((HASHCODE%INVERSE_PERMIL_FULLTRACKQC))" -eq "0" ]]; then
      TRACKQC_FRACTION=1
    else
      TRACKQC_FRACTION=0.1
    fi
  else
    TRACKQC_FRACTION=0.1
  fi
fi
echo TRACKQC_FRACTION = $TRACKQC_FRACTION
export ARGS_EXTRA_PROCESS_o2_aod_producer_workflow+=" --aod-writer-maxfilesize $AOD_FILE_SIZE --lpmp-prod-tag $ALIEN_JDL_LPMPRODUCTIONTAG --reco-pass $ALIEN_JDL_LPMPASSNAME --trackqc-fraction $TRACKQC_FRACTION"
if [[ $PERIOD == "LHC22c" ]] || [[ $PERIOD == "LHC22d" ]] || [[ $PERIOD == "LHC22e" ]] || [[ $PERIOD == "JUN" ]] || [[ $PERIOD == "LHC22f" ]] || [[ $PERIOD == "LHC22m" ]] || [[ "$RUNNUMBER" == @(526463|526465|526466|526467|526468|526486|526505|526508|526510|526512|526525|526526|526528|526534|526559|526596|526606|526612|526638|526639|526641|526643|526647|526649|526689|526712|526713|526714|526715|526716|526719|526720|526776|526886|526926|526927|526928|526929|526934|526935|526937|526938|526963|526964|526966|526967|526968|527015|527016|527028|527031|527033|527034|527038|527039|527041|527057|527076|527108|527109|527228|527237|527259|527260|527261|527262|527345|527347|527349|527446|527518|527523|527734) ]] ; then
  export ARGS_EXTRA_PROCESS_o2_aod_producer_workflow+=" --ctpreadout-create 1"
fi

if [[ $ALIEN_JDL_THINAODS == "1" ]] ; then
  export ARGS_EXTRA_PROCESS_o2_aod_producer_workflow+=" --thin-tracks"
fi

if [[ $ALIEN_JDL_PREPROPAGATE == "1" ]] ; then
  export ARGS_EXTRA_PROCESS_o2_aod_producer_workflow+=" --propagate-tracks --propagate-tracks-max-xiu 5"
fi

# Enabling QC
if [[ $ALIEN_JDL_QCOFF != "1" ]]; then
  export WORKFLOW_PARAMETERS="QC,${WORKFLOW_PARAMETERS}"
fi

export QC_CONFIG_OVERRIDE+=";qc.config.Activity.number=$RUNNUMBER;qc.config.Activity.type=PHYSICS;qc.config.Activity.passName=$PASS;qc.config.Activity.periodName=$PERIOD;qc.config.Activity.beamType=$BEAMTYPE;"

export QC_CONFIG_PARAM+=" --local-batch=QC.root "
export GEN_TOPO_WORKDIR="./"
#export QC_JSON_FROM_OUTSIDE="QC-20211214.json"

if [[ -n $ALIEN_JDL_QCJSONFROMOUTSIDE ]]; then
  export QC_JSON_FROM_OUTSIDE=$ALIEN_JDL_QCJSONFROMOUTSIDE
fi
if [[ ! -z $QC_JSON_FROM_OUTSIDE ]]; then
    sed -i 's/REPLACE_ME_RUNNUMBER/'"${RUNNUMBER}"'/g' $QC_JSON_FROM_OUTSIDE
    sed -i 's/REPLACE_ME_PASS/'"${PASS}"'/g' $QC_JSON_FROM_OUTSIDE
    sed -i 's/REPLACE_ME_PERIOD/'"${PERIOD}"'/g' $QC_JSON_FROM_OUTSIDE
fi