#!/bin/bash


if [ -z "$MacroDir" ]; then
  if [ -z "$1" ]; then
    echo 'no macro directory specified'
    exit 1
  else
    MacroDir=$1
  fi
fi

if [ -z "$UnpackDir" ]; then
  if [ -z "$2" ]; then
    echo 'no unpack directory specified'
    exit 1
  else
    UnpackDir=$2
  fi
fi

if [ -z "$CluDir" ]; then
  if [ -z "$3" ]; then
    echo 'no clu directory specified'
    exit 1
  else
    CluDir=$3
  fi
fi

if [ -z "$AnaDir" ]; then
  if [ -z "$4" ]; then
    echo 'no ana directory specified'
    exit 1
  else
    AnaDir=$4
  fi
fi

if [ -z "$SimulationDir" ]; then
  if [ -z "$5" ]; then
    echo 'no simulation directory specified'
    exit 1
  else
    SimulationDir=$5
  fi
fi

if [ -z "$iNDigiFiles" ]; then
  if [ -z "$6" ]; then
    echo 'no number of digi files specified'
    exit 1
  else
    iNDigiFiles=$6
  fi
fi

if [ -z "$MCFileName" ]; then
  if [ -z "$7" ]; then
    echo 'no MC file name specified'
    exit 1
  else
    MCFileName=$7
  fi
fi

if [ -z "$iNMCFiles" ]; then
  if [ -z "$8" ]; then
    echo 'no number of MC files specified'
    exit 1
  else
    iNMCFiles=$8
  fi
fi

if [ -z "$cGeometry" ]; then
  if [ -z "$9" ]; then
    echo 'no geometry tag specified'
    exit 1
  else
    cGeometry=$9
  fi
fi

if [ -z "$iDut" -o "${#iDut}" != "3" ]; then
  if [ -z "${10}" -o "${#10}" != "3" ]; then
    echo 'no valid Dut specified'
    exit 1
  else
    iDut=${10}
  fi
fi

if [ -z "$iMRef" -o "${#iMRef}" != "3" ]; then
  if [ -z "${11}" -o "${#11}" != "3" ]; then
    echo 'no valid MRef specified'
    exit 1
  else
    iMRef=${11}
  fi
fi

if [ -z "$iBRef" -o "${#iBRef}" != "3" ]; then
  if [ -z "${12}" -o "${#12}" != "3" ]; then
    echo 'no valid BRef specified'
    exit 1
  else
    iBRef=${12}
  fi
fi

if [ -z "$iSel2" -o "${#iSel2}" != "3" ]; then
  if [ -z "${13}" -o "${#13}" != "3" ]; then
    echo 'no valid Sel2 specified'
    exit 1
  else
    iSel2=${13}
  fi
fi

if [ -z "$dScaleFactor" ]; then
  if [ -z "${14}" ]; then
    echo 'no scale factor specified'
    exit 1
  else
    dScaleFactor=${14}
  fi
fi

if [ -z "$bIdealCalibration" ]; then
  if [ -z "${15}" ]; then
    echo 'no calibration flag specified'
    exit 1
  else
    bIdealCalibration=${15}
  fi
fi

if [ -z "$bHeavyIonCollisions" ]; then
  if [ -z "${16}" ]; then
    echo 'no collision flag specified'
    exit 1
  else
    bHeavyIonCollisions=${16}
  fi
fi

if [ -z "$bSeparateHitFile" ]; then
  if [ -z "${17}" ]; then
    echo 'no hit file flag specified'
    exit 1
  else
    bSeparateHitFile=${17}
  fi
fi

if [ -z "$bIdealClustering" ]; then
  if [ -z "${18}" ]; then
    echo 'no clustering flag specified'
    exit 1
  else
    bIdealClustering=${18}
  fi
fi

if [ -z "$bAnalysisMCQA" ]; then
  if [ -z "${19}" ]; then
    echo 'no analysis MC QA flag specified'
    exit 1
  else
    bAnalysisMCQA=${19}
  fi
fi

if [ -z "$cSetupName" ]; then
  if [ -z "${20}" ]; then
    echo 'no setup specified'
    exit 1
  else
    cSetupName=${20}
  fi
fi

if [ -z "$bSimData" ]; then
  if [ -z "${21}" ]; then
    echo 'no data type specified'
    exit 1
  else
    bSimData=${21}
  fi
fi

if [ -z "$iCalibrationMode" ]; then
  if [ -z "${22}" ]; then
    echo 'no calibration mode specified'
    exit 1
  else
    iCalibrationMode=${22}
  fi
fi

if [ -z "$iAnalysisMode" ]; then
  if [ -z "${23}" ]; then
    echo 'no analysis mode specified'
    exit 1
  else
    iAnalysisMode=${23}
  fi
fi

if [ -z "$bDifferentialTISAnalysis" ]; then
  if [ -z "${24}" ]; then
    echo 'no TIS mode specified'
    exit 1
  else
    bDifferentialTISAnalysis=${24}
  fi
fi

if [ -z "$dTimeInSpill" ]; then
  if [ -z "${25}" ]; then
    echo 'no time in spill specified'
    exit 1
  else
    dTimeInSpill=${25}
  fi
fi

if [ -z "$iNTISBins" ]; then
  if [ -z "${26}" ]; then
    echo 'no N TIS bins specified'
    exit 1
  else
    iNTISBins=${26}
  fi
fi

if [ -z "$dChi2SHT" ]; then
  if [ -z "${27}" ]; then
    echo 'no SHT chi2 specified'
    exit 1
  else
    dChi2SHT=${27}
  fi
fi

if [ -z "$dChi2SHTNN" ]; then
  if [ -z "${28}" ]; then
    echo 'no SHT NN chi2 specified'
    exit 1
  else
    dChi2SHTNN=${28}
  fi
fi

if [ -z "$iTISBin" ]; then
  if [ -z "${29}" ]; then
    echo 'no TIS bin specified'
    exit 1
  else
    iTISBin=${29}
  fi
fi


if [ -z "$VMCWORKDIR" ]; then
  echo 'no ROOT environment available'
  exit 1
fi


if [ ! -d "${MacroDir}" ]; then
  echo 'macro directory does not exist'
  exit 1
fi


if [ ! -d "${UnpackDir}" -o ! -d "${CluDir}" -o ! -d "${AnaDir}" ]; then
  echo 'unpack/clu/ana directory does not exist'
  exit 1
fi



if [ "${iAnalysisMode}" == "1" ]; then
  WorkDir=${AnaDir}/FindBRefPeak
  iCorMode=10

  mkdir ${WorkDir}

  cp -v ${MacroDir}/.rootrc ${WorkDir}/
  cp -v ${MacroDir}/rootlogon.C ${WorkDir}/
  cp -v ${MacroDir}/ana_hits.C ${WorkDir}/

  cd ${WorkDir}

  root -b -q './ana_hits.C(1000000000,'${iCorMode}',"'${UnpackDir}'","'${CluDir}'",\
                           "'${SimulationDir}'",'${iNDigiFiles}',"'${MCFileName}'",'${iNMCFiles}',\
                           "'${cGeometry}'","'${cSetupName}'",'${bIdealCalibration}','${bHeavyIonCollisions}',\
                           '${bIdealClustering}','${bSeparateHitFile}','${bAnalysisMCQA}',\
                           '${iDut}','${iMRef}','${iBRef}','${iSel2}','${dScaleFactor}','${bSimData}',\
                           '${iCalibrationMode}',kTRUE,'${dTimeInSpill}','${iNTISBins}')'

  rm ${WorkDir}/all_*
  rm ${WorkDir}/hits.out.root


  WorkDir=${AnaDir}/FindSHTPeaks
  iCorMode=20

  mkdir ${WorkDir}

  cp -v ${MacroDir}/.rootrc ${WorkDir}/
  cp -v ${MacroDir}/rootlogon.C ${WorkDir}/
  cp -v ${MacroDir}/ana_hits.C ${WorkDir}/

  InputCalibFile=${AnaDir}/FindBRefPeak/calib_ana.cor_out.root

  if [ ! -f "${InputCalibFile}" ]; then
    echo "input calib file ${InputCalibFile} does not exist"
    exit 1
  fi

  cp -v ${InputCalibFile} ${WorkDir}/calib_ana.cor_in.root

  cd ${WorkDir}

  root -b -q './ana_hits.C(1000000000,'${iCorMode}',"'${UnpackDir}'","'${CluDir}'",\
                           "'${SimulationDir}'",'${iNDigiFiles}',"'${MCFileName}'",'${iNMCFiles}',\
                           "'${cGeometry}'","'${cSetupName}'",'${bIdealCalibration}','${bHeavyIonCollisions}',\
                           '${bIdealClustering}','${bSeparateHitFile}','${bAnalysisMCQA}',\
                           '${iDut}','${iMRef}','${iBRef}','${iSel2}','${dScaleFactor}','${bSimData}',\
                           '${iCalibrationMode}',kTRUE,'${dTimeInSpill}','${iNTISBins}')'

  rm ${WorkDir}/all_*
  rm ${WorkDir}/hits.out.root

elif [ "${iAnalysisMode}" == "2" ]; then
  WorkDir=${AnaDir}/FindChi2Sigmas
  iCorMode=0
  iExtSigMode=2

  mkdir ${WorkDir}

  cp -v ${MacroDir}/.rootrc ${WorkDir}/
  cp -v ${MacroDir}/rootlogon.C ${WorkDir}/
  cp -v ${MacroDir}/ana_hits.C ${WorkDir}/
  cp -v ${MacroDir}/find_chi2_weights.C ${WorkDir}/

  InputCalibFile=${AnaDir}/../FindSHTPeaks/calib_ana.cor_out.root

  if [ ! -f "${InputCalibFile}" ]; then
    echo "input calib file ${InputCalibFile} does not exist"
    exit 1
  fi

  cp -v ${InputCalibFile} ${WorkDir}/calib_ana.cor_in.root

  cd ${WorkDir}

  root -b -q './find_chi2_weights.C+(1000000000,'${iCorMode}',"'${UnpackDir}'","'${CluDir}'",\
                                     "'${SimulationDir}'",'${iNDigiFiles}',"'${MCFileName}'",'${iNMCFiles}',\
                                     "'${cGeometry}'","'${cSetupName}'",'${bIdealCalibration}','${bHeavyIonCollisions}',\
                                     '${bIdealClustering}','${bSeparateHitFile}','${bAnalysisMCQA}',\
                                     '${iDut}','${iMRef}','${iBRef}','${iSel2}','${dScaleFactor}','${bSimData}',\
                                     '${iCalibrationMode}',kTRUE,'${dTimeInSpill}','${iNTISBins}',\
                                     1000000.,'${dChi2SHT}','${iExtSigMode}',".")'

  rm ${WorkDir}/all_*
  rm ${WorkDir}/hits.out.root


  WorkDir=${AnaDir}/FindSHTNNPeaks

  if [ "${bSimData}" == "1" ]; then
    SHTNNCalList=(30 9 30)
  else
    SHTNNCalList=(30 52 52 5 6 9 30)
  fi

  iStep=0
  iStepLast=0

  for iCorMode in ${SHTNNCalList[@]}
  do
    ((iStepLast = ${iStep}))
    ((iStep += 1))

    mkdir -p ${WorkDir}/Iter${iStep}

    cp -v ${MacroDir}/.rootrc ${WorkDir}/Iter${iStep}
    cp -v ${MacroDir}/rootlogon.C ${WorkDir}/Iter${iStep}
    cp -v ${MacroDir}/ana_hits.C ${WorkDir}/Iter${iStep}

    if [ "${iStep}" == "1" ]; then
      InputCalibFile=${AnaDir}/FindChi2Sigmas/calib_ana.cor_out.root
    else
      InputCalibFile=${WorkDir}/Iter${iStepLast}/calib_ana.cor_out.root
    fi

    if [ ! -f "${InputCalibFile}" ]; then
      echo "input calib file ${InputCalibFile} does not exist"
      exit 1
    fi

    cp -v ${InputCalibFile} ${WorkDir}/Iter${iStep}/calib_ana.cor_in.root

    cd ${WorkDir}/Iter${iStep}

    root -b -q './ana_hits.C(1000000000,'${iCorMode}',"'${UnpackDir}'","'${CluDir}'",\
                             "'${SimulationDir}'",'${iNDigiFiles}',"'${MCFileName}'",'${iNMCFiles}',\
                             "'${cGeometry}'","'${cSetupName}'",'${bIdealCalibration}','${bHeavyIonCollisions}',\
                             '${bIdealClustering}','${bSeparateHitFile}','${bAnalysisMCQA}',\
                             '${iDut}','${iMRef}','${iBRef}','${iSel2}','${dScaleFactor}','${bSimData}',\
                             '${iCalibrationMode}',kTRUE,'${dTimeInSpill}','${iNTISBins}',\
                             1000000.,'${dChi2SHT}')'

    rm ${WorkDir}/Iter${iStep}/all_*
    rm ${WorkDir}/Iter${iStep}/hits.out.root

  done


  WorkDir=${AnaDir}/FindSHTNNPeaksTIS
  iCorMode=40

  mkdir ${WorkDir}

  cp -v ${MacroDir}/.rootrc ${WorkDir}/
  cp -v ${MacroDir}/rootlogon.C ${WorkDir}/
  cp -v ${MacroDir}/ana_hits.C ${WorkDir}/

  InputCalibFile=${AnaDir}/FindSHTNNPeaks/Iter${iStep}/calib_ana.cor_out.root

  if [ ! -f "${InputCalibFile}" ]; then
    echo "input calib file ${InputCalibFile} does not exist"
    exit 1
  fi

  cp -v ${InputCalibFile} ${WorkDir}/calib_ana.cor_in.root

  cd ${WorkDir}

  root -b -q './ana_hits.C(1000000000,'${iCorMode}',"'${UnpackDir}'","'${CluDir}'",\
                           "'${SimulationDir}'",'${iNDigiFiles}',"'${MCFileName}'",'${iNMCFiles}',\
                           "'${cGeometry}'","'${cSetupName}'",'${bIdealCalibration}','${bHeavyIonCollisions}',\
                           '${bIdealClustering}','${bSeparateHitFile}','${bAnalysisMCQA}',\
                           '${iDut}','${iMRef}','${iBRef}','${iSel2}','${dScaleFactor}','${bSimData}',\
                           '${iCalibrationMode}',kTRUE,'${dTimeInSpill}','${iNTISBins}',\
                           1000000.,'${dChi2SHT}')'

  rm ${WorkDir}/all_*
  rm ${WorkDir}/hits.out.root

elif [ "${iAnalysisMode}" == "3" ]; then
  WorkDir=${AnaDir}/FindChi2Sigmas
  iCorMode=0
  iExtSigMode=1

  mkdir ${WorkDir}

  cp -v ${MacroDir}/.rootrc ${WorkDir}/
  cp -v ${MacroDir}/rootlogon.C ${WorkDir}/
  cp -v ${MacroDir}/ana_hits.C ${WorkDir}/
  cp -v ${MacroDir}/find_chi2_weights.C ${WorkDir}/

  if [ "${iTISBin}" != "0" ]; then
    InputCalibFile=${AnaDir}/../../FindSHTNNPeaksTIS/calib_ana.cor_out.root
  else
    InputCalibFile=${AnaDir}/../FindSHTNNPeaksTIS/calib_ana.cor_out.root
  fi

  if [ ! -f "${InputCalibFile}" ]; then
    echo "input calib file ${InputCalibFile} does not exist"
    exit 1
  fi

  cp -v ${InputCalibFile} ${WorkDir}/calib_ana.cor_in.root

  cd ${WorkDir}

  root -b -q './find_chi2_weights.C+(1000000000,'${iCorMode}',"'${UnpackDir}'","'${CluDir}'",\
                                     "'${SimulationDir}'",'${iNDigiFiles}',"'${MCFileName}'",'${iNMCFiles}',\
                                     "'${cGeometry}'","'${cSetupName}'",'${bIdealCalibration}','${bHeavyIonCollisions}',\
                                     '${bIdealClustering}','${bSeparateHitFile}','${bAnalysisMCQA}',\
                                     '${iDut}','${iMRef}','${iBRef}','${iSel2}','${dScaleFactor}','${bSimData}',\
                                     '${iCalibrationMode}',kTRUE,'${dTimeInSpill}','${iNTISBins}',\
                                     '${dChi2SHTNN}','${dChi2SHT}','${iExtSigMode}',".",'${iTISBin}')'

  rm ${WorkDir}/all_*
  rm ${WorkDir}/hits.out.root

elif [ "${iAnalysisMode}" == "4" ]; then
  WorkDir=${AnaDir}/TISIntegral
  iCorMode=0
  iExtSigMode=0

  mkdir ${WorkDir}

  cp -v ${MacroDir}/.rootrc ${WorkDir}/
  cp -v ${MacroDir}/rootlogon.C ${WorkDir}/
  cp -v ${MacroDir}/ana_hits.C ${WorkDir}/
  cp -v ${MacroDir}/merge_TIS_calib.C ${WorkDir}/

  cd ${WorkDir}

  if [ "${bDifferentialTISAnalysis}" == "0" ]; then
    InputCalibFile=${AnaDir}/../FindChi2Sigmas/calib_ana.cor_out.root

    if [ ! -f "${InputCalibFile}" ]; then
      echo "input calib file ${InputCalibFile} does not exist"
      exit 1
    fi

    cp -v ${InputCalibFile} ${WorkDir}/calib_ana.cor_in.root

  else
    root -b -q './merge_TIS_calib.C('${iNTISBins}')'

  fi

  root -b -q './ana_hits.C(1000000000,'${iCorMode}',"'${UnpackDir}'","'${CluDir}'",\
                           "'${SimulationDir}'",'${iNDigiFiles}',"'${MCFileName}'",'${iNMCFiles}',\
                           "'${cGeometry}'","'${cSetupName}'",'${bIdealCalibration}','${bHeavyIonCollisions}',\
                           '${bIdealClustering}','${bSeparateHitFile}','${bAnalysisMCQA}',\
                           '${iDut}','${iMRef}','${iBRef}','${iSel2}','${dScaleFactor}','${bSimData}',\
                           '${iCalibrationMode}',kTRUE,'${dTimeInSpill}','${iNTISBins}',\
                           '${dChi2SHTNN}','${dChi2SHT}','${iExtSigMode}',0.,0.,0.,kFALSE)'

  rm ${WorkDir}/all_*
  rm ${WorkDir}/hits.out.root


  if [ "${bDifferentialTISAnalysis}" == "1" ]; then
    WorkDir=${AnaDir}/TISDifferential

    mkdir ${WorkDir}

    cp -v ${MacroDir}/.rootrc ${WorkDir}/
    cp -v ${MacroDir}/rootlogon.C ${WorkDir}/
    cp -v ${MacroDir}/ana_hits.C ${WorkDir}/

    InputCalibFile=${AnaDir}/TISIntegral/calib_ana.cor_in.root

    if [ ! -f "${InputCalibFile}" ]; then
      echo "input calib file ${InputCalibFile} does not exist"
      exit 1
    fi

    cp -v ${InputCalibFile} ${WorkDir}/

    cd ${WorkDir}

    root -b -q './ana_hits.C(1000000000,'${iCorMode}',"'${UnpackDir}'","'${CluDir}'",\
                             "'${SimulationDir}'",'${iNDigiFiles}',"'${MCFileName}'",'${iNMCFiles}',\
                             "'${cGeometry}'","'${cSetupName}'",'${bIdealCalibration}','${bHeavyIonCollisions}',\
                             '${bIdealClustering}','${bSeparateHitFile}','${bAnalysisMCQA}',\
                             '${iDut}','${iMRef}','${iBRef}','${iSel2}','${dScaleFactor}','${bSimData}',\
                             '${iCalibrationMode}',kTRUE,'${dTimeInSpill}','${iNTISBins}',\
                             '${dChi2SHTNN}','${dChi2SHT}','${iExtSigMode}',0.,0.,0.,kTRUE)'

    rm ${WorkDir}/all_*
    rm ${WorkDir}/hits.out.root

  fi

fi