eclTimeShiftsAlgorithm.cc

/**************************************************************************
 * basf2 (Belle II Analysis Software Framework)                           *
 * Author: The Belle II Collaboration                                     *
 *                                                                        *
 * See git log for contributors and copyright holders.                    *
 * This file is licensed under LGPL-3.0, see LICENSE.md.                  *
 **************************************************************************/
 
/* Own header. */
#include <ecl/calibration/eclTimeShiftsAlgorithm.h>
 
/* ECL headers. */
#include <ecl/dbobjects/ECLCrystalCalib.h>
#include <ecl/dbobjects/ECLReferenceCrystalPerCrateCalib.h>
#include <ecl/digitization/EclConfiguration.h>
#include <ecl/mapper/ECLChannelMapper.h>
 
/* Basf2 headers. */
#include <framework/dbobjects/HardwareClockSettings.h>
 
/* ROOT headers. */
#include <TCanvas.h>
#include <TDirectory.h>
#include <TFile.h>
#include <TGraphErrors.h>
#include <TH1F.h>
#include <TLatex.h>
#include <TString.h>
 
/* C++ headers. */
#include <iomanip>
#include <sstream>
 
using namespace std;
using namespace Belle2;
using namespace ECL;
using namespace Calibration;
 
//eclTimeShiftsAlgorithm::eclTimeShiftsAlgorithm(): CalibrationAlgorithm("DummyCollector"),
eclTimeShiftsAlgorithm::eclTimeShiftsAlgorithm():
  CalibrationAlgorithm("eclTimeShiftsPlottingCollector"),
  debugFilenameBase("ECL_time_offsets"),
  timeShiftForPlotStyle{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
  crysCrateShift_min(-20),
  crysCrateShift_max(20),
  algorithmReadPayloads(false),
  m_ECLCrystalTimeOffset("ECLCrystalTimeOffset"),
  m_ECLCrateTimeOffset("ECLCrateTimeOffset"),
  m_refCrysIDzeroingCrate("ECLReferenceCrystalPerCrateCalib")//,
{
  setDescription(
    "Plots the ecl crystal and crate time calibations."
  );
}
 
CalibrationAlgorithm::EResult eclTimeShiftsAlgorithm::calibrate()
{
  gROOT->SetBatch();
 
  B2INFO("eclTimeShiftsAlgorithm parameters:");
  B2INFO("debugFilenameBase = " << debugFilenameBase);
  B2INFO("algorithmReadPayloads = " << algorithmReadPayloads);
  B2INFO("timeShiftForPlotStyle = {");
  for (int crateTest = 0; crateTest < 51; crateTest++) {
    B2INFO(timeShiftForPlotStyle[crateTest] << ",");
  }
  B2INFO(timeShiftForPlotStyle[51] << "}");
 
 
  //------------------------------------------------------------------------
  /* Conversion coefficient from ADC ticks to nanoseconds
     1/(4fRF) = 0.4913 ns/clock tick, where fRF is the accelerator RF frequency.
     Same for all crystals.  */
 
  //..First need to set event, run, exp number
  const auto expRunList =  getRunList();
  const int iEvt = 1;
  const int iRun = expRunList[0].second;
  const int iExp = expRunList[0].first;
  DBObjPtr<Belle2::HardwareClockSettings> clock_info("HardwareClockSettings");
  updateDBObjPtrs(iEvt, iRun, iExp);
  const double TICKS_TO_NS = 1.0 / (4.0 * EclConfiguration::getRF()) * 1e3;
 
 
  //------------------------------------------------------------------------
  /* Set up variables for storing timing information and cutting on
     timing quality */
 
  vector< vector<double> > allCrates_crate_times ;
  vector< vector<double> > allCrates_run_nums ;  // not an integer for plotting purposes
  vector< vector<double> > allCrates_time_unc ;
  vector< vector<double> > allCrates_crystalCrate_times ;
  vector< vector<double> > allCrates_crystalCrate_times_unc ;
 
  vector<int> allRunNums;
 
  vector<double> mean_crystalCrate_time_ns(m_numCrates, 0);
 
  vector< double > blank_vector = {} ;
  vector< int > blank_vector_int = {} ;
  for (int temp_crate_id = 0; temp_crate_id < m_numCrates; temp_crate_id++) {
    allCrates_crate_times.push_back(blank_vector) ;
    allCrates_run_nums.push_back(blank_vector) ;
    allCrates_time_unc.push_back(blank_vector) ;
    allCrates_crystalCrate_times.push_back(blank_vector) ;
    allCrates_crystalCrate_times_unc.push_back(blank_vector) ;
  }
  // This results in : allCrates_crate_time[index for crate number][index for run number]
 
 
 
  //------------------------------------------------------------------------
  /* Extract the crystal and crate calibration constant information from the
     tree as extracted by the collector. */
 
  // Pulling in data from collector output. It now returns shared_ptr<T> so the underlying pointer
  // will delete itself automatically at the end of this scope unless you do something
  auto tree_perCrys = getObjectPtr<TTree>("tree_perCrystal");
  if (!tree_perCrys) {
    B2ERROR("Tree of calibration constants does not exist.");
    return c_Failure;
  }
  B2INFO("Number of Entries in tree_perCrystal was " << tree_perCrys->GetEntries());
  B2INFO("Number of Entries in tree_perCrystal / 8736 = " << float(tree_perCrys->GetEntries()) / ECLElementNumbers::c_NCrystals);
 
 
  // Define the variables to be read in from the tree
  tree_perCrys->SetBranchAddress("run", &m_run_perCrystal);
  tree_perCrys->SetBranchAddress("exp", &m_exp_perCrystal);
  tree_perCrys->SetBranchAddress("crystalID", &m_crystalID);
  tree_perCrys->SetBranchAddress("crateID", &m_crateID);
  tree_perCrys->SetBranchAddress("crateTimeConst", &m_crateTimeConst);
  tree_perCrys->SetBranchAddress("crateTimeUnc", &m_crateTimeUnc);
  tree_perCrys->SetBranchAddress("crystalTimeConst", &m_crystalTimeConst);
  tree_perCrys->SetBranchAddress("crystalTimeUnc", &m_crystalTimeUnc);
  tree_perCrys->SetBranchAddress("refCrystalID", &m_refCrystalID);
 
 
  int referenceRunNum = -1;
  int referenceExpNum = -1;
  //int numAnalysedRuns = 0 ;
  int previousRunNumTree = -1 ;
  vector<double> Crate_time_ns_tree(m_numCrates) ;
  vector<double> Crate_time_tick_tree(m_numCrates) ;
  vector<double> Crate_time_unc_ns_tree(m_numCrates) ;
  vector<double> crystalCrate_time_ns_tree(m_numCrates);
  vector<double> crystalCrate_time_unc_ns_tree(m_numCrates);
 
 
  Int_t numEntriesCrysTree = (Int_t)tree_perCrys->GetEntries();
 
  // Loop through the entire tree
  for (Int_t tree_crys_i = 0; tree_crys_i < numEntriesCrysTree; tree_crys_i++) {
    for (Int_t tree_crys_j = 0; tree_crys_j < m_numCrystals; tree_crys_j++) {
      tree_perCrys->GetEntry(tree_crys_i);
      //B2INFO("tree_crys_i, tree_crys_j = " << tree_crys_i << ", " << tree_crys_j);
      if (tree_crys_j != m_numCrystals - 1) {
        tree_crys_i++;
      }
 
      // Make sure that all the information read in for 8736 crystals are all from one (exp,run).
      if (tree_crys_j == 0) {
        referenceExpNum = m_exp_perCrystal;
        referenceRunNum = m_run_perCrystal;
        B2INFO("Looking at exp,run " << m_exp_perCrystal << ", " << m_run_perCrystal);
      }
      if ((m_exp_perCrystal != referenceExpNum)      or
          (m_run_perCrystal != referenceRunNum)      or
          (m_run_perCrystal == previousRunNumTree)) {
 
        B2ERROR("m_exp_perCrystal, referenceExpNum" << m_exp_perCrystal << ", " << referenceExpNum);
        B2ERROR("m_run_perCrystal, referenceRunNum" << m_run_perCrystal << ", " << referenceRunNum);
        B2ERROR("m_run_perCrystal, previousRunNumTree" << m_run_perCrystal << ", " << previousRunNumTree);
        B2ERROR("Exp/run number problem");
        return c_Failure;
      }
 
 
      int crateID_temp = m_crateID;
      Crate_time_ns_tree[crateID_temp - 1] = m_crateTimeConst * TICKS_TO_NS ;
      Crate_time_tick_tree[crateID_temp - 1] = m_crateTimeConst ;
      Crate_time_unc_ns_tree[crateID_temp - 1] = m_crateTimeUnc * TICKS_TO_NS ;
 
      if (m_crystalID == m_refCrystalID) {
        B2INFO("m_exp_perCrystal, m_run_perCrystal, cell ID (0..8735), m_crateID, m_crateTimeConst = " << m_exp_perCrystal << ", " <<
               m_run_perCrystal << ", " << tree_crys_j << ", " << m_crateID << ", " << m_crateTimeConst << " ticks") ;
        crystalCrate_time_ns_tree[crateID_temp - 1] = (m_crystalTimeConst + m_crateTimeConst) * TICKS_TO_NS;
 
        crystalCrate_time_unc_ns_tree[crateID_temp - 1] = TICKS_TO_NS * sqrt(
                                                            (m_crateTimeUnc * m_crateTimeUnc) +
                                                            (m_crystalTimeUnc * m_crystalTimeUnc)) ;
      } else if (tree_crys_j == 0 || tree_crys_j == 8735) {
        B2INFO("m_exp_perCrystal, m_run_perCrystal, cell ID (0..8735), m_crateID, m_crateTimeConst = " << m_exp_perCrystal << ", " <<
               m_run_perCrystal << ", " << tree_crys_j << ", " << m_crateID << ", " << m_crateTimeConst << " ns") ;
      } else {
        B2DEBUG(22, "m_exp_perCrystal, m_run_perCrystal, cell ID (0..8735), m_crateID, m_crateTimeConst = " << m_exp_perCrystal << ", " <<
                m_run_perCrystal << ", " << tree_crys_j << ", " << m_crateID << ", " << m_crateTimeConst << " ns") ;
      }
 
    }
 
    //------------------------------------------------------------------------
    bool savedThisRunNum = false;
    for (int iCrate = 0; iCrate < m_numCrates; iCrate++) {
      double tcrate = Crate_time_ns_tree[iCrate] ;
      double tcrate_unc = Crate_time_unc_ns_tree[iCrate];
      double tcrystalCrate = crystalCrate_time_ns_tree[iCrate];
      double tcrystalCrate_unc = crystalCrate_time_unc_ns_tree[iCrate];
 
      if ((tcrate < m_tcrate_max_cut) &&
          (tcrate > m_tcrate_min_cut) &&
          (fabs(tcrate_unc) > m_tcrate_unc_min_cut) &&
          (fabs(tcrate_unc) < m_tcrate_unc_max_cut)) {
        allCrates_crate_times[iCrate].push_back(tcrate) ;
        allCrates_run_nums[iCrate].push_back(m_run_perCrystal) ;
        allCrates_time_unc[iCrate].push_back(tcrate_unc) ;
        allCrates_crystalCrate_times[iCrate].push_back(tcrystalCrate) ;
        allCrates_crystalCrate_times_unc[iCrate].push_back(tcrystalCrate_unc) ;
 
        mean_crystalCrate_time_ns[iCrate] += tcrystalCrate ;
 
        if (!savedThisRunNum) {
          allRunNums.push_back(m_run_perCrystal);
          savedThisRunNum = true;
        }
      }
    }
 
    //------------------------------------------------------------------------
    for (int ic = 0; ic < m_numCrates; ic++) {
      B2INFO("Crate " << ic + 1 << ", t_crate = " << Crate_time_tick_tree[ic] << " ticks = "
             << Crate_time_ns_tree[ic] << " +- " << Crate_time_unc_ns_tree[ic]
             << " ns;    t crys+crate (no shifts) = " << crystalCrate_time_ns_tree[ic] << " +- "
             << crystalCrate_time_unc_ns_tree[ic] << " ns") ;
    }
 
    previousRunNumTree = m_run_perCrystal;
 
  }
 
 
  B2INFO("Finished reading tree calibration constants.  Now extracting here by stepping through runs.");
 
 
 
 
 
  //------------------------------------------------------------------------
  bool minRunNumBool = false;
  bool maxRunNumBool = false;
  int minRunNum = -1;
  int maxRunNum = -1;
  int minExpNum = -1;
  int maxExpNum = -1;
  for (auto expRun : getRunList()) {
    int expNumber = expRun.first;
    int runNumber = expRun.second;
    if (!minRunNumBool) {
      minExpNum = expNumber;
      minRunNum = runNumber;
      minRunNumBool = true;
    }
    if (!maxRunNumBool) {
      maxExpNum = expNumber;
      maxRunNum = runNumber;
      maxRunNumBool = true;
    }
    if (((minRunNum > runNumber)   && (minExpNum >= expNumber))  ||
        (minExpNum > expNumber)) {
      minExpNum = expNumber;
      minRunNum = runNumber;
    }
    if (((maxRunNum < runNumber)   && (maxExpNum <= expNumber))  ||
        (maxExpNum < expNumber)) {
      maxExpNum = expNumber;
      maxRunNum = runNumber;
    }
  }
 
  B2INFO("minExpNum = " << minExpNum) ;
  B2INFO("minRunNum = " << minRunNum) ;
  B2INFO("maxExpNum = " << maxExpNum) ;
  B2INFO("maxRunNum = " << maxRunNum) ;
 
 
  if (minExpNum != maxExpNum) {
    B2ERROR("The runs must all come from the same experiment");
    return c_Failure;
  }
 
  int experiment = minExpNum;
 
 
  //------------------------------------------------------------------------
  //------------------------------------------------------------------------
  //------------------------------------------------------------------------
  //------------------------------------------------------------------------
  /* Extract out the time offset information from the database directly.
     This method loops over all run numbers so it can more easily pick up
     old payloads.  It is not the preferred method to use if the payloads
     have iov gaps.*/
 
  if (algorithmReadPayloads) {
    //------------------------------------------------------------------------
    // Get the input run list (should be only 1) for us to use to update the DBObjectPtrs
    auto runs = getRunList();
    /* Take the first run.  For the crystal cosmic calibrations, because of the crate
       calibrations, there is not a known correct run to use within the range. */
    ExpRun chosenRun = runs.front();
    B2INFO("merging using the ExpRun (" << chosenRun.second << "," << chosenRun.first << ")");
    // After here your DBObjPtrs are correct
    updateDBObjPtrs(1, chosenRun.second, chosenRun.first);
 
    //------------------------------------------------------------------------
    // Test the DBObjects we want to exist and fail if not all of them do.
    bool allObjectsFound = true;
 
    // Check that the payloads we want to merge are sufficiently loaded
    if (!m_ECLCrystalTimeOffset) {
      allObjectsFound = false;
      B2ERROR("No valid DBObject found for 'ECLCrystalTimeOffset'");
    }
 
    // Check that the crate payload is loaded (used for transforming cosmic payload)
    if (!m_ECLCrateTimeOffset) {
      allObjectsFound = false;
      B2ERROR("No valid DBObject found for 'ECLCrateTimeOffset'");
    }
 
    if (!m_refCrysIDzeroingCrate) {
      allObjectsFound = false;
      B2ERROR("No valid DBObject found for 'refCrysIDzeroingCrate'");
    }
 
 
    if (allObjectsFound) {
      B2INFO("Valid objects found for 'ECLCrystalTimeOffset'");
      B2INFO("Valid object found for 'ECLCrateTimeOffset'");
      B2INFO("Valid object found for 'refCrysIDzeroingCrate'");
    } else {
      B2INFO("eclTimeShiftsAlgorithm: Exiting with failure.  Some missing valid objects.");
      return c_Failure;
    }
 
 
    //------------------------------------------------------------------------
    vector<float> crystalCalib = m_ECLCrystalTimeOffset->getCalibVector();
    vector<float> crystalCalibUnc = m_ECLCrystalTimeOffset->getCalibUncVector();
    B2INFO("Loaded 'ECLCrystalTimeOffset' calibrations");
 
    vector<float> crateCalib = m_ECLCrateTimeOffset->getCalibVector();
    vector<float> crateCalibUnc = m_ECLCrateTimeOffset->getCalibUncVector();
 
    B2INFO("Loaded 'ECLCrateTimeOffset' calibration with default exp/run");
 
    B2INFO("eclTimeShiftsAlgorithm:: loaded ECLCrateTimeOffset from the database"
           << LogVar("IoV", m_ECLCrateTimeOffset.getIoV())
           << LogVar("Checksum", m_ECLCrateTimeOffset.getChecksum()));
 
    for (int cellID = 1; cellID <= m_numCrystals; cellID += 511) {
      B2INFO("crystalCalib = " << crystalCalib[cellID - 1]);
      B2INFO("crateCalib = " << crateCalib[cellID - 1]);
    }
 
    vector<short> refCrystals = m_refCrysIDzeroingCrate->getReferenceCrystals();
    for (int icrate = 0; icrate < m_numCrates; icrate++) {
      B2INFO("reference crystal for crate " << icrate + 1 << " = " << refCrystals[icrate]);
    }
 
 
 
    //------------------------------------------------------------------------
    for (int run = minRunNum; run <= maxRunNum; run++) {
      B2INFO("---------") ;
      B2INFO("Looking at run " << run) ;
 
      vector<int>::iterator it = find(allRunNums.begin(), allRunNums.end(), run);
      if (it != allRunNums.end()) {
        int pos = it - allRunNums.begin() ;
        B2INFO("allRunNums[" << pos << "] = " << allRunNums[pos]);
        B2INFO("Run " << run << " already processed so skipping it.");
        continue;
      } else {
        B2INFO("New run.  Starting to extract information");
      }
 
      // Forloading database for a specific run
      int eventNumberForCrates = 1;
 
      StoreObjPtr<EventMetaData> evtPtr;
      // simulate the initialize() phase where we can register objects in the DataStore
      DataStore::Instance().setInitializeActive(true);
      evtPtr.registerInDataStore();
      DataStore::Instance().setInitializeActive(false);
      // now construct the event metadata
      evtPtr.construct(eventNumberForCrates, run, experiment);
      // and update the database contents
      DBStore& dbstore = DBStore::Instance();
      dbstore.update();
      // this is only needed it the payload might be intra-run dependent,
      // that is if it might change during one run as well
      dbstore.updateEvent();
      updateDBObjPtrs(eventNumberForCrates, run, experiment);
 
 
      //------------------------------------------------------------------------
      shared_ptr< ECL::ECLChannelMapper > crystalMapper(new ECL::ECLChannelMapper()) ;
      crystalMapper->initFromDB();
 
      B2INFO("eclTimeShiftsAlgorithm:: loaded ECLCrystalTimeOffset from the database"
             << LogVar("IoV", m_ECLCrystalTimeOffset.getIoV())
             << LogVar("Checksum", m_ECLCrystalTimeOffset.getChecksum()));
      B2INFO("eclTimeShiftsAlgorithm:: loaded ECLCrateTimeOffset from the database"
             << LogVar("IoV", m_ECLCrateTimeOffset.getIoV())
             << LogVar("Checksum", m_ECLCrateTimeOffset.getChecksum()));
 
 
      //------------------------------------------------------------------------
      vector<float> crystalTimeOffsetsCalib;
      vector<float> crystalTimeOffsetsCalibUnc;
      crystalTimeOffsetsCalib = m_ECLCrystalTimeOffset->getCalibVector();
      crystalTimeOffsetsCalibUnc = m_ECLCrystalTimeOffset->getCalibUncVector();
 
      vector<float> crateTimeOffsetsCalib;
      vector<float> crateTimeOffsetsCalibUnc;
      crateTimeOffsetsCalib = m_ECLCrateTimeOffset->getCalibVector();
      crateTimeOffsetsCalibUnc = m_ECLCrateTimeOffset->getCalibUncVector();
 
      //------------------------------------------------------------------------
      vector<double> Crate_time_ns(m_numCrates) ;
      vector<double> Crate_time_tick(m_numCrates) ;
      vector<double> Crate_time_unc_ns(m_numCrates) ;
      vector<double> crystalCrate_time_ns(m_numCrates);
      vector<double> crystalCrate_time_unc_ns(m_numCrates);
 
      for (int crysID = 1; crysID <= m_numCrystals; crysID++) {
        int crateID_temp = crystalMapper->getCrateID(crysID) ;
        Crate_time_ns[crateID_temp - 1] = crateTimeOffsetsCalib[crysID - 1] * TICKS_TO_NS ;
        Crate_time_tick[crateID_temp - 1] = crateTimeOffsetsCalib[crysID - 1] ;
        Crate_time_unc_ns[crateID_temp - 1] = crateTimeOffsetsCalibUnc[crysID - 1] * TICKS_TO_NS ;
 
        if (crysID == refCrystals[crateID_temp - 1]) {
          crystalCrate_time_ns[crateID_temp - 1] = (crystalTimeOffsetsCalib[crysID - 1] +
                                                    crateTimeOffsetsCalib[crysID - 1]) * TICKS_TO_NS;
 
          crystalCrate_time_unc_ns[crateID_temp - 1] = TICKS_TO_NS * sqrt(
                                                         (crateTimeOffsetsCalibUnc[crysID - 1] * crateTimeOffsetsCalibUnc[crysID - 1]) +
                                                         (crystalTimeOffsetsCalibUnc[crysID - 1] * crystalTimeOffsetsCalibUnc[crysID - 1])) ;
        }
      }
 
 
      for (int iCrate = 0; iCrate < m_numCrates; iCrate++) {
        double tcrate = Crate_time_ns[iCrate] ;
        double tcrate_unc = Crate_time_unc_ns[iCrate];
        double tcrystalCrate = crystalCrate_time_ns[iCrate];
        double tcrystalCrate_unc = crystalCrate_time_unc_ns[iCrate];
 
        if ((tcrate < m_tcrate_max_cut) &&
            (tcrate > m_tcrate_min_cut) &&
            (fabs(tcrate_unc) > m_tcrate_unc_min_cut) &&
            (fabs(tcrate_unc) < m_tcrate_unc_max_cut)) {
          allCrates_crate_times[iCrate].push_back(tcrate) ;
          allCrates_run_nums[iCrate].push_back(run) ;
          allCrates_time_unc[iCrate].push_back(tcrate_unc) ;
          allCrates_crystalCrate_times[iCrate].push_back(tcrystalCrate) ;
          allCrates_crystalCrate_times_unc[iCrate].push_back(tcrystalCrate_unc) ;
 
          mean_crystalCrate_time_ns[iCrate] += tcrystalCrate ;
        }
      }
 
 
      //------------------------------------------------------------------------
      for (int ic = 0; ic < m_numCrates; ic++) {
        B2INFO("Crate " << ic + 1 << ", t_crate = " << Crate_time_tick[ic] << " ticks = "
               << Crate_time_ns[ic] << " +- " << Crate_time_unc_ns[ic]
               << " ns;    t crys+crate (no shift) = " << crystalCrate_time_ns[ic] << " +- "
               << crystalCrate_time_unc_ns[ic] << " ns") ;
      }
 
      /* Shift the run number to the end of the iov so that we can skip runs
         that have the payload with the same revision number */
      int IOV_exp_high = m_ECLCrateTimeOffset.getIoV().getExperimentHigh() ;
      int IOV_run_high = m_ECLCrateTimeOffset.getIoV().getRunHigh() ;
      B2INFO(LogVar("IOV_exp_high", IOV_exp_high));
      B2INFO(LogVar("IOV_run_high", IOV_run_high));
      if (IOV_run_high == -1) {
        B2INFO("IOV_run_high is -1 so stop looping over all runs");
        break;
      } else {
        B2INFO("Set run number to higher iov run number");
        run = IOV_run_high;
      }
      B2INFO("now set run = " << run);
    }
  }
 
 
 
 
  //------------------------------------------------------------------------
  //------------------------------------------------------------------------
  //------------------------------------------------------------------------
  //------------------------------------------------------------------------
  B2INFO("Shift all run crys+crate+off times.  Show the results for a subset of crates/runs:");
  for (int iCrate = 0; iCrate < m_numCrates; iCrate++) {
    double mean_time = mean_crystalCrate_time_ns[iCrate] / allCrates_crate_times[iCrate].size() ;
    B2INFO("Mean crys+crate times for all runs used as offset (crate " << iCrate + 1 << ") = " << mean_time);
 
    for (long unsigned int jRun = 0; jRun < allCrates_crate_times[iCrate].size(); jRun++) {
      allCrates_crystalCrate_times[iCrate][jRun] += -mean_time + timeShiftForPlotStyle[iCrate] ;
      if (jRun < 50 || iCrate == 1 || iCrate == 40 || iCrate == 51) {
        B2INFO("allCrates_crystalCrate_times(crate " << iCrate + 1 << ", run counter " << jRun + 1 << ", runNum " <<
               allCrates_run_nums[iCrate][jRun] << " | after shifting mean) = " <<
               allCrates_crystalCrate_times[iCrate][jRun]);
      }
    }
  }
 
 
 
  //------------------------------------------------------------------------
  //------------------------------------------------------------------------
  TFile* tcratefile = 0;
 
  B2INFO("Debug output rootfile: " << debugFilenameBase);
  string runNumsString = string("_") + to_string(minExpNum) + "_" + to_string(minRunNum) + string("-") +
                         to_string(maxExpNum) + "_" + to_string(maxRunNum);
  string debugFilename = debugFilenameBase + runNumsString + string(".root");
  TString fname = debugFilename;
 
  tcratefile = new TFile(fname, "recreate");
  tcratefile->cd();
  B2INFO("Debugging histograms written to " << fname);
 
  for (int i = 0; i < m_numCrates; i++) {
    B2INFO("Starting to make crate time jump plots for crate " << i + 1);
    shared_ptr< TCanvas > cSmart(new TCanvas);
 
    Double_t* single_crate_crate_times = &allCrates_crate_times[i][0] ;
    Double_t* single_crate_run_nums = &allCrates_run_nums[i][0] ;
    Double_t* single_crate_time_unc = &allCrates_time_unc[i][0] ;
    Double_t* single_crate_crystalCrate_times = &allCrates_crystalCrate_times[i][0] ;
    Double_t* single_crate_crystalCrate_times_unc = &allCrates_crystalCrate_times_unc[i][0] ;
    B2INFO("Done setting up the arrays for the crate " << i + 1);
 
    ostringstream ss;
    ss << setw(2) << setfill('0') << i + 1 ;
    string paddedCrateID(ss.str());
 
    // ----- crate time constants vs run number ------
    shared_ptr< TGraphErrors > g_tcrate_vs_runNum(new TGraphErrors(allCrates_crate_times[i].size(), single_crate_run_nums,
                                                  single_crate_crate_times, NULL, single_crate_time_unc)) ;
    // NULL for run number errors = 0 for all
 
    string tgraph_title = string("e") + to_string(minExpNum) + string("r") + to_string(minRunNum) +
                          string("-e") + to_string(maxExpNum) + string("r") + to_string(maxRunNum) ;
 
    string tgraph_name_short = "crateTimeVSrunNum_" ;
    tgraph_name_short = tgraph_name_short + runNumsString + "_crate";
 
    tgraph_title = tgraph_title + string("_crate") + paddedCrateID ;
    tgraph_name_short = tgraph_name_short + paddedCrateID ;
    tgraph_title = tgraph_title + string(" (") + to_string(m_tcrate_min_cut) + string(" < tcrate < ") +
                   to_string(m_tcrate_max_cut) + string(" ns, ") + to_string(m_tcrate_unc_min_cut) +
                   string(" < tcrate unc. < ") + to_string(m_tcrate_unc_max_cut) + string(" ns cuts)")  ;
 
    g_tcrate_vs_runNum->SetName(tgraph_name_short.c_str()) ;
    g_tcrate_vs_runNum->SetTitle(tgraph_title.c_str()) ;
    g_tcrate_vs_runNum->GetXaxis()->SetTitle("Run number") ;
    g_tcrate_vs_runNum->GetYaxis()->SetTitle("Crate time [ns]") ;
 
    g_tcrate_vs_runNum->GetYaxis()->SetRangeUser(m_tcrate_min_cut, m_tcrate_max_cut) ;
 
    g_tcrate_vs_runNum->Draw("AP") ;
    g_tcrate_vs_runNum->SetMarkerSize(0.8) ;
    g_tcrate_vs_runNum->Draw("AP") ;
 
    shared_ptr< TLatex > Leg1(new TLatex);
    Leg1->SetNDC();
    Leg1->SetTextAlign(11);
    Leg1->SetTextFont(42);
    Leg1->SetTextSize(0.035);
    Leg1->SetTextColor(1);
    Leg1->AppendPad();
 
    g_tcrate_vs_runNum->Write() ;
    cSmart->SaveAs((tgraph_name_short + string(".pdf")).c_str()) ;
 
    B2INFO("Saved pdf: " << tgraph_name_short << ".pdf");
 
 
    // ----- crystal + crate time constants + offset vs run number ------
    shared_ptr< TGraphErrors > g_crateCrystalTime_vs_runNum(new TGraphErrors(allCrates_crystalCrate_times[i].size(),
                                                            single_crate_run_nums,
                                                            single_crate_crystalCrate_times, NULL, single_crate_crystalCrate_times_unc)) ;
 
    tgraph_title = string("e") + to_string(minExpNum) + string("r") + to_string(minRunNum) +
                   string("-e") + to_string(maxExpNum) + string("r") + to_string(maxRunNum) ;
 
    tgraph_name_short = "crystalCrateTimeVSrunNum_" ;
    tgraph_name_short = tgraph_name_short + runNumsString + "_crate";
 
    tgraph_title = tgraph_title + string("_crate") + paddedCrateID ;
    tgraph_name_short = tgraph_name_short + paddedCrateID ;
    tgraph_title = tgraph_title + string(" (") + to_string(m_tcrate_min_cut) + string(" < tcrate < ") +
                   to_string(m_tcrate_max_cut) + string(" ns, ") + to_string(m_tcrate_unc_min_cut) +
                   string(" < tcrate unc. < ") + to_string(m_tcrate_unc_max_cut) + string(" ns cuts)")  ;
 
 
    g_crateCrystalTime_vs_runNum->SetName(tgraph_name_short.c_str()) ;
    g_crateCrystalTime_vs_runNum->SetTitle(tgraph_title.c_str()) ;
    g_crateCrystalTime_vs_runNum->GetXaxis()->SetTitle("Run number") ;
    g_crateCrystalTime_vs_runNum->GetYaxis()->SetTitle("Crate time + Crystal time + centring overall offset [ns]") ;
 
    g_crateCrystalTime_vs_runNum->GetYaxis()->SetRangeUser(crysCrateShift_min, crysCrateShift_max) ;
 
    g_crateCrystalTime_vs_runNum->Draw("AP") ;
    g_crateCrystalTime_vs_runNum->SetMarkerSize(0.8) ;
    g_crateCrystalTime_vs_runNum->Draw("AP") ;
 
    g_crateCrystalTime_vs_runNum->Write() ;
    cSmart->SaveAs((tgraph_name_short + string(".pdf")).c_str()) ;
 
    B2INFO("Saved pdf: " << tgraph_name_short << ".pdf");
 
    // ----- crystal + crate time constants + offset vs run counter------
    // This will remove gaps and ignore the actual run number
 
    /* Define a vector to store a renumbering of the run numbers, incrementing
       by +1 so that there are no gaps.  The runs are not in order so the
       run numbers&indices first have to be sorted before the "run counter"
       numbers can used.*/
    int numRunsWithCrateTimes = allCrates_crystalCrate_times[i].size();
    vector<Double_t> counterVec(numRunsWithCrateTimes);
 
 
    // Vector to store element
    // with respective present index
    vector<pair<int, double> > runNum_index_pairs;
 
    // Inserting element in pair vector
    // to keep track of previous indexes
    for (int pairIndex = 0; pairIndex < numRunsWithCrateTimes; pairIndex++) {
      runNum_index_pairs.push_back(make_pair(allCrates_run_nums[i][pairIndex], pairIndex));
    }
 
    B2INFO("Crate id = " << i + 1);
    B2INFO("Unsorted run numbers");
    for (int runCounter = 0; runCounter < numRunsWithCrateTimes; runCounter++) {
      B2INFO("Run number, run number vector index = " << runNum_index_pairs[runCounter].first << ", " <<
             runNum_index_pairs[runCounter].second);
    }
 
    // Sorting pair vector
    sort(runNum_index_pairs.begin(), runNum_index_pairs.end());
 
    // Fill the run counter vector
    for (int runCounter = 0; runCounter < numRunsWithCrateTimes; runCounter++) {
      counterVec[runNum_index_pairs[runCounter].second] = runCounter + 1;
    }
 
    B2INFO("Run numbers with index and times");
    for (int runCounter = 0; runCounter < numRunsWithCrateTimes; runCounter++) {
      int idx = (int) round(counterVec[runCounter]);
      B2INFO("Vector index, Run number, run number sorting order index, tcrystal+tcrate+shifts = " << runCounter << ", " <<
             allCrates_run_nums[i][runCounter] << ", " << idx << ", " << single_crate_crystalCrate_times[idx - 1] << " ns");
    }
 
 
    if (numRunsWithCrateTimes > 0) {
      shared_ptr< TGraphErrors > g_crateCrystalTime_vs_runCounter(new TGraphErrors(numRunsWithCrateTimes, &counterVec[0],
                                                                  single_crate_crystalCrate_times, NULL, single_crate_crystalCrate_times_unc)) ;
 
      tgraph_title = string("e") + to_string(minExpNum) + string("r") + to_string(minRunNum) +
                     string("-e") + to_string(maxExpNum) + string("r") + to_string(maxRunNum) ;
 
 
      tgraph_name_short = "crystalCrateTimeVSrunCounter_" ;
      tgraph_name_short = tgraph_name_short + runNumsString + "_crate";
 
 
      tgraph_title = tgraph_title + string("_crate") + paddedCrateID ;
      tgraph_name_short = tgraph_name_short + paddedCrateID ;
      tgraph_title = tgraph_title + string(" (") + to_string(m_tcrate_min_cut) + string(" < tcrate < ") +
                     to_string(m_tcrate_max_cut) + string(" ns, ") + to_string(m_tcrate_unc_min_cut) +
                     string(" < tcrate unc. < ") + to_string(m_tcrate_unc_max_cut) + string(" ns cuts)")  ;
 
 
      g_crateCrystalTime_vs_runCounter->SetName(tgraph_name_short.c_str()) ;
      g_crateCrystalTime_vs_runCounter->SetTitle(tgraph_title.c_str()) ;
      g_crateCrystalTime_vs_runCounter->GetXaxis()->SetTitle("Run counter (remove gaps from run numbers)") ;
      g_crateCrystalTime_vs_runCounter->GetYaxis()->SetTitle("Crate time + Crystal time + centring overall offset [ns]") ;
 
      g_crateCrystalTime_vs_runCounter->GetYaxis()->SetRangeUser(crysCrateShift_min, crysCrateShift_max) ;
      g_crateCrystalTime_vs_runCounter->GetXaxis()->SetRangeUser(0, numRunsWithCrateTimes + 1) ;
 
      g_crateCrystalTime_vs_runCounter->Draw("AP") ;
      g_crateCrystalTime_vs_runCounter->SetMarkerSize(0.8) ;
      g_crateCrystalTime_vs_runCounter->Draw("AP") ;
 
      g_crateCrystalTime_vs_runCounter->Write() ;
      cSmart->SaveAs((tgraph_name_short + string(".pdf")).c_str()) ;
      B2INFO("Saved pdf: " << tgraph_name_short << ".pdf");
 
      B2INFO("Finished making crate time jump plots for crate " << i + 1);
    } else {
      B2INFO("Crate " << i + 1 << " has no entries that pass all the cuts so no crystalCrateTimeVSrunCounter_crate plot will be made.");
    }
  }
 
 
 
 
  /* Loop over all the runs and crates and let the user know when a crate time jump
     has occurred.  Jumps can be of various sizes so have different thresholds. */
  double smallThreshold = 1 ;    //ns
  double largeThreshold = 6.5 ;  //ns
 
  B2INFO("======================= Crate time jumps =========================");
  B2INFO("======================= Small threshold jumps ====================");
  B2INFO("Crate ID = 1..52");
  B2INFO("==================================================================");
 
  for (int i = 0; i < m_numCrates; i++) {
    int numRunsWithCrateTimes = allCrates_crystalCrate_times[i].size();
    for (int runCounter = 0; runCounter < numRunsWithCrateTimes - 1; runCounter++) {
      int run_i = allCrates_run_nums[i][runCounter] ;
      int run_f = allCrates_run_nums[i][runCounter + 1] ;
      double time_i = allCrates_crystalCrate_times[i][runCounter] ;
      double time_f = allCrates_crystalCrate_times[i][runCounter + 1] ;
 
      if (fabs(time_f - time_i) > smallThreshold) {
        B2INFO("Crate " << i + 1 << " has crate time jump > " << smallThreshold << " ns: t(run " << run_f << ") = " << time_f <<
               " ns - t(run " << run_i << ") = " << time_i << " ns = " << time_f - time_i);
      }
    }
  }
 
 
  B2INFO("~~~~~~~~~~~~~~~~~~~~~~~ Large threshold jumps ~~~~~~~~~~~~~~~~~~~~");
  B2INFO("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
 
  for (int i = 0; i < m_numCrates; i++) {
    int numRunsWithCrateTimes = allCrates_crystalCrate_times[i].size();
    for (int runCounter = 0; runCounter < numRunsWithCrateTimes - 1; runCounter++) {
      int run_i = allCrates_run_nums[i][runCounter] ;
      int run_f = allCrates_run_nums[i][runCounter + 1] ;
      double time_i = allCrates_crystalCrate_times[i][runCounter] ;
      double time_f = allCrates_crystalCrate_times[i][runCounter + 1] ;
 
      if (fabs(time_f - time_i) > largeThreshold) {
        B2INFO("WARNING: Crate " << i + 1 << " has crate time jump > " << largeThreshold << " ns: t(run " << run_f << ") = " << time_f <<
               " ns - t(run " << run_i << ") = " << time_i << " ns = " << time_f - time_i);
      }
    }
  }
 
 
 
 
  // Just in case, we remember the current TDirectory so we can return to it
  TDirectory* executeDir = gDirectory;
 
  tcratefile->Write();
  tcratefile->Close();
  // Go back to original TDirectory
  executeDir->cd();
 
  return c_OK;
}