ZDCPulseAnalyzer.cxx

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/*
  Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
*/
 
#include "ZdcAnalysis/ZDCPulseAnalyzer.h"
 
#include "TFitResult.h"
#include "TFitResultPtr.h"
#include "TVirtualFitter.h"
#include "TList.h"
#include "TMinuit.h"
 
#include <algorithm>
#include <sstream>
#include <cmath>
#include <numeric>
#include <iomanip>
#include <stdexcept>
 
ATLAS_NO_CHECK_FILE_THREAD_SAFETY;
 
extern int gErrorIgnoreLevel;
 
bool ZDCPulseAnalyzer::s_quietFits         = true;
bool ZDCPulseAnalyzer::s_saveFitFunc       = false;
TH1* ZDCPulseAnalyzer::s_undelayedFitHist  = nullptr;
TH1* ZDCPulseAnalyzer::s_delayedFitHist    = nullptr;
TF1* ZDCPulseAnalyzer::s_combinedFitFunc   = nullptr;
float ZDCPulseAnalyzer::s_combinedFitTMax  = 1000;
float ZDCPulseAnalyzer::s_combinedFitTMin  = -0.5;   // add to allow switch to high gain by skipping early samples
std::vector<float> ZDCPulseAnalyzer::s_pullValues;
 
void ZDCPulseAnalyzer::CombinedPulsesFCN(int& /*numParam*/, double*, double& f, double* par, int flag)
{
  //  The first parameter is a correction factor to account for decrease in beam intensity between x
  //    and y scan. It is applied here and not passed to the actual fit function
  //
  int nSamples = s_undelayedFitHist->GetNbinsX();
 
  if (flag == 3) {
    s_pullValues.assign(nSamples * 2, 0);
  }
 
  double chiSquare = 0;
 
  float delayBaselineAdjust = par[0];
 
  // undelayed
  //
  for (int isample = 0; isample < nSamples; isample++) {
    double histValue = s_undelayedFitHist->GetBinContent(isample + 1);
    double histError = std::max(s_undelayedFitHist->GetBinError(isample + 1), 1.0);
    double t = s_undelayedFitHist->GetBinCenter(isample + 1);
 
    if (t > s_combinedFitTMax) break;
    if (t < s_combinedFitTMin) continue;
 
    double funcVal = s_combinedFitFunc->EvalPar(&t, &par[1]);
 
    double pull = (histValue - funcVal) / histError;
 
    if (flag == 3) s_pullValues[2 * isample] = pull;
    chiSquare += pull * pull;
  }
 
  // delayed
  //
  for (int isample = 0; isample < nSamples; isample++) {
    double histValue = s_delayedFitHist->GetBinContent(isample + 1);
    double histError = std::max(s_delayedFitHist->GetBinError(isample + 1), 1.0);
    double t = s_delayedFitHist->GetBinCenter(isample + 1);
 
    if (t > s_combinedFitTMax) break;
    if (t < s_combinedFitTMin) continue;
 
    double funcVal = s_combinedFitFunc->EvalPar(&t, &par[1]) + delayBaselineAdjust;
    double pull = (histValue - funcVal) / histError;
 
    if (flag == 3) s_pullValues[2 * isample + 1] = pull;
    chiSquare += pull * pull;
  }
 
  f = chiSquare;
}
 
 
ZDCPulseAnalyzer::ZDCPulseAnalyzer(ZDCMsg::MessageFunctionPtr msgFunc_p, const std::string& tag, int Nsample, float deltaTSample, size_t preSampleIdx, int pedestal,
                                   float gainHG, const std::string& fitFunction, int peak2ndDerivMinSample,
                                   float peak2ndDerivMinThreshHG, float peak2ndDerivMinThreshLG) :
  m_msgFunc_p(std::move(msgFunc_p)),
  m_tag(tag), m_Nsample(Nsample),
  m_preSampleIdx(preSampleIdx),
  m_deltaTSample(deltaTSample),
  m_pedestal(pedestal), m_gainHG(gainHG), m_fitFunction(fitFunction),
  m_peak2ndDerivMinSample(peak2ndDerivMinSample),
    m_peak2ndDerivMinThreshLG(peak2ndDerivMinThreshLG),
  m_peak2ndDerivMinThreshHG(peak2ndDerivMinThreshHG),
  m_ADCSamplesHGSub(Nsample, 0), m_ADCSamplesLGSub(Nsample, 0),
  m_ADCSSampSigHG(Nsample, 0), m_ADCSSampSigLG(Nsample, 0), 
  m_samplesSub(Nsample, 0)
{
  // Create the histogram used for fitting
  //
  m_tmin = -deltaTSample / 2;
  m_tmax = m_tmin + ((float) Nsample) * deltaTSample;
 
  std::string histName = "ZDCFitHist" + tag;
  std::string histNameLGRefit = "ZDCFitHist" + tag + "_LGRefit";
 
  m_fitHist = std::make_unique<TH1F>(histName.c_str(), "", m_Nsample, m_tmin, m_tmax);
  m_fitHistLGRefit = std::make_unique<TH1F>(histNameLGRefit.c_str(), "", m_Nsample, m_tmin, m_tmax);
 
  m_fitHist->SetDirectory(0);
  m_fitHistLGRefit->SetDirectory(0);
 
  SetDefaults();
  Reset();
}
 
 
void ZDCPulseAnalyzer::enableDelayed(float deltaT, float pedestalShift, bool fixedBaseline)
{
  m_useDelayed = true;
  m_useFixedBaseline = fixedBaseline;
 
  m_delayedDeltaT = deltaT;
  m_delayedPedestalDiff = pedestalShift;
 
  m_deltaTSample /= 2.;
 
  std::string delayedHGName = std::string(m_fitHist->GetName()) + "delayed";
  std::string delayedLGName = std::string(m_fitHistLGRefit->GetName()) + "delayed";
 
  m_delayedHist = std::make_unique<TH1F>(delayedHGName.c_str(), "", m_Nsample, m_tmin + m_delayedDeltaT, m_tmax + m_delayedDeltaT);
  m_delayedHist->SetDirectory(0);
 
  m_delayedHistLGRefit = std::make_unique<TH1F>(delayedLGName.c_str(), "", m_Nsample, m_tmin + m_delayedDeltaT, m_tmax + m_delayedDeltaT);
  m_delayedHistLGRefit->SetDirectory(0);
 
  m_ADCSamplesHGSub.assign(2 * m_Nsample, 0);
  m_ADCSamplesLGSub.assign(2 * m_Nsample, 0);
}
 
void ZDCPulseAnalyzer::enableRepass(float peak2ndDerivMinRepassHG, float peak2ndDerivMinRepassLG)
{
  m_enableRepass = true;
  m_peak2ndDerivMinRepassHG = peak2ndDerivMinRepassHG;
  m_peak2ndDerivMinRepassLG = peak2ndDerivMinRepassLG;
}
 
void ZDCPulseAnalyzer::SetDefaults()
{
  m_LGMode = LGModeNormal;
  
  m_nominalTau1 = 4;
  m_nominalTau2 = 21;
 
  m_fixTau1 = false;
  m_fixTau2 = false;
 
  m_HGOverflowADC  = 900;
  m_HGUnderflowADC = 20;
  m_LGOverflowADC  = 1000;
 
  // Default values for the gain factors uswed to match low and high gain
  //
  m_gainFactorLG = m_gainHG;
  m_gainFactorHG = 1;
 
  m_2ndDerivStep = 1;
 
  m_noiseSigHG = 1;
  m_noiseSigLG = 1;
 
  m_timeCutMode = 0;
  m_chisqDivAmpCutLG = 100;
  m_chisqDivAmpCutHG = 100;
 
  m_T0CutLowLG = m_tmin;
  m_T0CutLowHG = m_tmin;
 
  m_T0CutHighLG = m_tmax;
  m_T0CutHighHG = m_tmax;
 
  m_LGT0CorrParams.assign(4, 0);
  m_HGT0CorrParams.assign(4, 0);
 
  m_defaultFitTMax = m_tmax;
  m_defaultFitTMin = m_tmin;
  
  m_fitAmpMinHG = 1;
  m_fitAmpMinLG = 1;
 
  m_fitAmpMaxHG = 1500;
  m_fitAmpMaxLG = 1500;
 
  m_postPulse = false;
  m_prePulse = false;
 
  m_initialPrePulseT0  = -10;
  m_initialPrePulseAmp = 5;
 
  m_initialPostPulseT0  = 100;
 
  m_initialExpAmp = 0;
  m_fitPostT0lo   = 0;
 
  m_useDelayed = false;
  m_enablePreExcl = false;
  m_enablePostExcl = false;
  
  m_timingCorrMode = NoTimingCorr;
  m_haveNonlinCorr = false;
  
  m_fitOptions = "s";
}
 
void ZDCPulseAnalyzer::Reset(bool repass)
{
  if (!repass) {
    m_haveData  = false;
 
    m_useLowGain = false;
    m_fail       = false;
    m_HGOverflow = false;
 
    m_HGUnderflow       = false;
    m_PSHGOverUnderflow = false;
    m_LGOverflow        = false;
    m_LGUnderflow       = false;
 
    m_ExcludeEarly = false;
    m_ExcludeLate  = false;
 
    m_adjTimeRangeEvent = false;
    m_backToHG_pre      = false;
    m_fixPrePulse       = false;
 
    int sampleVecSize = m_Nsample;
    if (m_useDelayed) sampleVecSize *= 2;
 
    m_ADCSamplesHG.clear();
    m_ADCSamplesLG.clear();
    
    m_ADCSamplesHGSub.clear();
    m_ADCSamplesLGSub.clear();
 
    m_ADCSSampSigHG.assign(sampleVecSize, m_noiseSigHG);
    m_ADCSSampSigLG.assign(sampleVecSize, m_noiseSigLG); 
 
    m_minSampleEvt = 0;
    m_maxSampleEvt = (m_useDelayed ? 2 * m_Nsample - 1 : m_Nsample - 1);
 
    m_usedPresampIdx = 0;
 
    m_fitTMax = m_defaultFitTMax;
    m_fitTMin = m_defaultFitTMin;
 
    m_lastHGOverFlowSample  = -999;
    m_firstHGOverFlowSample = 999;
  }
 
  
  m_defaultT0Max = m_deltaTSample * (m_peak2ndDerivMinSample + m_peak2ndDerivMinTolerance + 0.5);
  m_defaultT0Min = m_deltaTSample * (m_peak2ndDerivMinSample - m_peak2ndDerivMinTolerance - 0.5);
 
  if (m_initializedFits) {
    m_defaultFitWrapper ->SetT0Range(m_defaultT0Min, m_defaultT0Max);
    m_prePulseFitWrapper->SetT0Range(m_defaultT0Min, m_defaultT0Max);
    m_preExpFitWrapper->SetT0Range(m_defaultT0Min, m_defaultT0Max);
  }
  
  // -----------------------
  // Statuses
  //
  m_havePulse  = false;
  
  m_prePulse  = false;
  m_postPulse = false;
  m_fitFailed = false;
  m_badChisq  = false;
 
  m_badT0        = false;
  m_preExpTail   = false;
  m_repassPulse = false;
 
  m_fitMinAmp = false;
  m_evtLGRefit = false;
  
 
  // -----------------------
 
  m_delayedBaselineShift = 0;
 
  m_fitAmplitude = 0;
  m_ampNoNonLin = 0;
  m_fitTime      = -100;
  m_fitTimeSub   = -100;
  m_fitTimeCorr  = -100;
  m_fitTCorr2nd  = -100;
 
  m_fitPreT0   = -100;
  m_fitPreAmp  = -100;
  m_fitPostT0  = -100;
  m_fitPostAmp = -100;
  m_fitExpAmp  = -100;
 
  m_minDeriv2ndSig = -10;
  m_preExpSig = -10;
  m_prePulseSig = -10;
 
  m_fitChisq = 0;
 
  m_amplitude       = 0;
  m_ampError        = 0;
  m_preSampleAmp    = 0;
  m_preAmplitude    = 0;
  m_postAmplitude   = 0;
  m_expAmplitude    = 0;
  m_bkgdMaxFraction = 0;
 
  m_refitLGAmpl = 0;
  m_refitLGAmpError = 0;
  m_refitLGChisq = 0;
  m_refitLGTime = -100;
  m_refitLGTimeSub = -100;
    
  m_initialPrePulseT0  = -10;
  m_initialPrePulseAmp = 5;
 
  m_initialPostPulseT0  = 100;
 
  m_initialExpAmp = 0;
  m_fitPostT0lo   = 0;
 
  m_fitPulls.clear();
  
  m_samplesSub.clear();
  m_samplesDeriv2nd.clear();
}
 
void ZDCPulseAnalyzer::SetGainFactorsHGLG(float gainFactorHG, float gainFactorLG)
{
  m_gainFactorHG = gainFactorHG;
  m_gainFactorLG = gainFactorLG;
}
 
void ZDCPulseAnalyzer::SetFitMinMaxAmp(float minAmpHG, float minAmpLG, float maxAmpHG, float maxAmpLG)
{
  m_fitAmpMinHG = minAmpHG;
  m_fitAmpMinLG = minAmpLG;
 
  m_fitAmpMaxHG = maxAmpHG;
  m_fitAmpMaxLG = maxAmpLG;
}
 
void ZDCPulseAnalyzer::SetTauT0Values(bool fixTau1, bool fixTau2, float tau1, float tau2, float t0HG, float t0LG)
{
  m_fixTau1     = fixTau1;
  m_fixTau2     = fixTau2;
  m_nominalTau1 = tau1;
  m_nominalTau2 = tau2;
 
  m_nominalT0HG = t0HG;
  m_nominalT0LG = t0LG;
 
  std::ostringstream ostrm;
  ostrm << "ZDCPulseAnalyzer::SetTauT0Values:: m_fixTau1=" << m_fixTau1 << "  m_fixTau2=" << m_fixTau2 << "  m_nominalTau1=" << m_nominalTau1 << "  m_nominalTau2=" << m_nominalTau2 << "  m_nominalT0HG=" << m_nominalT0HG << "  m_nominalT0LG=" << m_nominalT0LG;
 
  (*m_msgFunc_p)(ZDCMsg::Info, ostrm.str());
 
  m_initializedFits = false;
}
 
void ZDCPulseAnalyzer::SetFitTimeMax(float tmax)
{
  if (tmax < m_tmin) {
    (*m_msgFunc_p)(ZDCMsg::Error, ("ZDCPulseAnalyzer::SetFitTimeMax:: invalid FitTimeMax: " + std::to_string(tmax)));
    return;
  }
 
  m_defaultFitTMax = std::min(tmax, m_defaultFitTMax);
 
  (*m_msgFunc_p)(ZDCMsg::Verbose, ("Setting FitTMax to " + std::to_string(m_defaultFitTMax)));
 
  if (m_initializedFits) SetupFitFunctions();
}
 
void ZDCPulseAnalyzer::SetADCOverUnderflowValues(int HGOverflowADC, int HGUnderflowADC, int LGOverflowADC)
{
  m_HGOverflowADC  = HGOverflowADC;
  m_LGOverflowADC  = LGOverflowADC;
  m_HGUnderflowADC = HGUnderflowADC;
}
 
void ZDCPulseAnalyzer::SetCutValues(float chisqDivAmpCutHG, float chisqDivAmpCutLG,
                                    float deltaT0MinHG, float deltaT0MaxHG,
                                    float deltaT0MinLG, float deltaT0MaxLG)
{
  m_chisqDivAmpCutHG = chisqDivAmpCutHG;
  m_chisqDivAmpCutLG = chisqDivAmpCutLG;
 
  m_T0CutLowHG = deltaT0MinHG;
  m_T0CutLowLG = deltaT0MinLG;
 
  m_T0CutHighHG = deltaT0MaxHG;
  m_T0CutHighLG = deltaT0MaxLG;
}
 
void ZDCPulseAnalyzer::enableTimeSigCut(bool AND, float sigCut, const std::string& TF1String,
                    const std::vector<double>& parsHG, 
                    const std::vector<double>& parsLG)
{
  m_timeCutMode = AND ? 2 : 1;
  m_t0CutSig = sigCut;
 
  // Make the TF1's that provide the resolution
  //
  std::string timeResHGName = "TimeResFuncHG_" + m_tag;
  std::string timeResLGName = "TimeResFuncLG_" + m_tag;
 
  TF1* funcHG_p = new TF1(timeResHGName.c_str(), TF1String.c_str(), 0, m_HGOverflowADC);
  TF1* funcLG_p = new TF1(timeResLGName.c_str(), TF1String.c_str(), 0, m_LGOverflowADC);
 
  if (parsHG.size() != static_cast<unsigned int>(funcHG_p->GetNpar()) ||
      parsLG.size() != static_cast<unsigned int>(funcLG_p->GetNpar())) {
    //
    // generate an error message
  }
 
  funcHG_p->SetParameters(&parsHG[0]);
  funcLG_p->SetParameters(&parsLG[0]);
  
  m_timeResFuncHG_p.reset(funcHG_p);
  m_timeResFuncLG_p.reset(funcLG_p);
 
}
 
 
std::vector<float>  ZDCPulseAnalyzer::GetFitPulls(bool refitLG) const
{
  //
  // If there was no pulse for this event, return an empty vector (see reset() method)
  //
  if (!m_havePulse) {
    return m_fitPulls;
  }
 
  //
  // The combined (delayed+undelayed) pulse fitting fills out m_fitPulls directly
  //
  if (m_useDelayed) {
    return m_fitPulls;
  }
  else {
    //
    // When not using combined fitting, We don't have the pre-calculated pulls. Calculate them on the fly. 
    //
    std::vector<float> pulls(m_Nsample, -100);
    
    const TH1* dataHist_p = refitLG ? m_fitHistLGRefit.get() : m_fitHist.get();
    const TF1* fit_p = static_cast<const TF1*>(dataHist_p->GetListOfFunctions()->Last());
    
    for (size_t ibin = 0; ibin < m_Nsample ; ibin++) {
      float t = dataHist_p->GetBinCenter(ibin + 1);
      float fitVal = fit_p->Eval(t);
      float histVal = dataHist_p->GetBinContent(ibin + 1);
      float histErr = dataHist_p->GetBinError(ibin + 1);
      float pull = (histVal - fitVal)/histErr;
      pulls[ibin] = pull;
    }
 
    return pulls;
  }
}
 
void ZDCPulseAnalyzer::SetupFitFunctions()
{
  float prePulseTMin = 0;
  float prePulseTMax = prePulseTMin + m_deltaTSample * (m_peak2ndDerivMinSample - m_peak2ndDerivMinTolerance);
 
  if (m_fitFunction == "FermiExp") {
    if (!m_fixTau1 || !m_fixTau2) {
      //
      // Use the variable tau version of the expFermiFit
      //
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiVariableTaus(m_tag, m_tmin, m_tmax, m_fixTau1, m_fixTau2, m_nominalTau1, m_nominalTau2));
    }
    else {
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiFixedTaus(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
    }
 
    m_preExpFitWrapper = std::unique_ptr<ZDCFitExpFermiPreExp>(new ZDCFitExpFermiPreExp(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2, m_nominalTau2, false));
    m_prePulseFitWrapper = std::unique_ptr<ZDCPrePulseFitWrapper>(new ZDCFitExpFermiPrePulse(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
  }
  else if (m_fitFunction == "FermiExpRun3") {
    if (!m_fixTau1 || !m_fixTau2) {
      //
      // Use the variable tau version of the expFermiFit
      //
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiVariableTausRun3(m_tag, m_tmin, m_tmax, m_fixTau1, m_fixTau2, m_nominalTau1, m_nominalTau2));
    }
    else {
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiFixedTaus(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
    }
 
    m_preExpFitWrapper = std::unique_ptr<ZDCFitExpFermiPreExp>(new ZDCFitExpFermiPreExp(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2, 6, false));
    m_prePulseFitWrapper = std::unique_ptr<ZDCPrePulseFitWrapper>(new ZDCFitExpFermiPrePulse(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
  }
  else if (m_fitFunction == "FermiExpLHCf") {
    //
    // Use the variable tau version of the expFermiFit
    //
    m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiVariableTausLHCf(m_tag, m_tmin, m_tmax, m_fixTau1, m_fixTau2,
                                                  m_nominalTau1, m_nominalTau2));
 
    m_preExpFitWrapper = std::unique_ptr<ZDCFitExpFermiLHCfPreExp>(new ZDCFitExpFermiLHCfPreExp(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2, 6, false));
    
    m_prePulseFitWrapper = std::unique_ptr<ZDCPrePulseFitWrapper>(new ZDCFitExpFermiPrePulse(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
  }
  else if (m_fitFunction == "FermiExpLinear") {
    if (!m_fixTau1 || !m_fixTau2) {
      //
      // Use the variable tau version of the expFermiFit
      //
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiVariableTaus(m_tag, m_tmin, m_tmax, m_fixTau1, m_fixTau2, m_nominalTau1, m_nominalTau2));
    }
    else {
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiLinearFixedTaus(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
    }
 
    m_preExpFitWrapper = std::unique_ptr<ZDCFitExpFermiPreExp>(new ZDCFitExpFermiPreExp(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2, 6, false));
    m_prePulseFitWrapper = std::unique_ptr<ZDCPrePulseFitWrapper>(new ZDCFitExpFermiLinearPrePulse(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
  }
  else if (m_fitFunction == "ComplexPrePulse") {
    if (!m_fixTau1 || !m_fixTau2) {
      //
      // Use the variable tau version of the expFermiFit
      //
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiVariableTaus(m_tag, m_tmin, m_tmax, m_fixTau1, m_fixTau2, m_nominalTau1, m_nominalTau2));
    }
    else {
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiLinearFixedTaus(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
    }
 
    m_prePulseFitWrapper  = std::unique_ptr<ZDCPrePulseFitWrapper>(new ZDCFitComplexPrePulse(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
  }
  else if (m_fitFunction == "GeneralPulse") {
    if (!m_fixTau1 || !m_fixTau2) {
      //
      // Use the variable tau version of the expFermiFit
      //
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiVariableTaus(m_tag, m_tmin, m_tmax, m_fixTau1, m_fixTau2, m_nominalTau1, m_nominalTau2));
    }
    else {
      m_defaultFitWrapper = std::unique_ptr<ZDCFitWrapper>(new ZDCFitExpFermiLinearFixedTaus(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
    }
 
    m_prePulseFitWrapper  = std::unique_ptr<ZDCPrePulseFitWrapper>(new ZDCFitGeneralPulse(m_tag, m_tmin, m_tmax, m_nominalTau1, m_nominalTau2));
  }
  else {
    (*m_msgFunc_p)(ZDCMsg::Fatal, "Wrong fit function type: " + m_fitFunction);
  }
 
  m_prePulseFitWrapper->SetPrePulseT0Range(prePulseTMin, prePulseTMax);
  
  m_initializedFits = true;
}
 
bool ZDCPulseAnalyzer::LoadAndAnalyzeData(const std::vector<float>& ADCSamplesHG, const std::vector<float>&  ADCSamplesLG)
{
  if (m_useDelayed) {
    (*m_msgFunc_p)(ZDCMsg::Fatal, "ZDCPulseAnalyzer::LoadAndAnalyzeData:: Wrong LoadAndAnalyzeData called -- expecting both delayed and undelayed samples");
  }
 
  if (!m_initializedFits) SetupFitFunctions();
 
  // Clear any transient data
  //
  Reset(false);
 
  // Make sure we have the right number of samples. Should never fail. necessry?
  //
  if (ADCSamplesHG.size() != m_Nsample || ADCSamplesLG.size() != m_Nsample) {
    m_fail = true;
    return false;
  }
 
  m_ADCSamplesHG = ADCSamplesHG;
  m_ADCSamplesLG = ADCSamplesLG;
  
  return DoAnalysis(false);
}
 
bool ZDCPulseAnalyzer::LoadAndAnalyzeData(const std::vector<float>& ADCSamplesHG, const std::vector<float>&  ADCSamplesLG,
                      const std::vector<float>& ADCSamplesHGDelayed, const std::vector<float>& ADCSamplesLGDelayed)
{
  if (!m_useDelayed) {
    (*m_msgFunc_p)(ZDCMsg::Fatal, "ZDCPulseAnalyzer::LoadAndAnalyzeData:: Wrong LoadAndAnalyzeData called -- expecting only undelayed samples");
  }
 
  if (!m_initializedFits) SetupFitFunctions();
 
  // Clear any transient data
  //
  Reset();
 
  // Make sure we have the right number of samples. Should never fail. necessry?
  //
  if (ADCSamplesHG.size() != m_Nsample || ADCSamplesLG.size() != m_Nsample ||
      ADCSamplesHGDelayed.size() != m_Nsample || ADCSamplesLGDelayed.size() != m_Nsample) {
    m_fail = true;
    return false;
  }
 
  m_ADCSamplesHG.reserve(m_Nsample*2);
  m_ADCSamplesLG.reserve(m_Nsample*2);
  
  // Now do pedestal subtraction and check for overflows
  //
  for (size_t isample = 0; isample < m_Nsample; isample++) {
    float ADCHG = ADCSamplesHG[isample];
    float ADCLG = ADCSamplesLG[isample];
 
    float ADCHGDelay = ADCSamplesHGDelayed[isample] - m_delayedPedestalDiff;
    float ADCLGDelay = ADCSamplesLGDelayed[isample] - m_delayedPedestalDiff;
 
    if (m_delayedDeltaT > 0) {
      m_ADCSamplesHG.push_back(ADCHG);
      m_ADCSamplesHG.push_back(ADCHGDelay);
      
      m_ADCSamplesLG.push_back(ADCLG);
      m_ADCSamplesLG.push_back(ADCLGDelay);
    }
    else {
      m_ADCSamplesHG.push_back(ADCHGDelay);
      m_ADCSamplesHG.push_back(ADCHG);
      
      m_ADCSamplesLG.push_back(ADCLGDelay);
      m_ADCSamplesLG.push_back(ADCLG);
    }
  }
    
  return DoAnalysis(false);
}
 
bool ZDCPulseAnalyzer::ReanalyzeData()
{
  Reset(true);
 
  bool result = DoAnalysis(true);
  if (result && HavePulse()) {
    m_repassPulse = true;
  }
 
  return result;
}
 
bool ZDCPulseAnalyzer::ScanAndSubtractSamples()
{
  //
  // Dump samples to verbose output
  //
  bool doDump = (*m_msgFunc_p)(ZDCMsg::Verbose, "Dumping all samples before subtraction: ");
  if (doDump) {
    std::ostringstream dumpStringHG;
    dumpStringHG << "HG: ";
    for (auto val : m_ADCSamplesHG) {
      dumpStringHG << std::setw(4) << val << " ";
    }
    
    (*m_msgFunc_p)(ZDCMsg::Verbose, dumpStringHG.str().c_str());
    
    
    // Now low gain
    //
    std::ostringstream dumpStringLG;
    dumpStringLG << "LG: " << std::setw(4) << std::setfill(' ');
    for (auto val : m_ADCSamplesLG) {
      dumpStringLG <<  std::setw(4) << val << " ";
    }
 
    (*m_msgFunc_p)(ZDCMsg::Verbose, dumpStringLG.str().c_str());
  }
  
  m_NSamplesAna = m_ADCSamplesHG.size();
 
  m_ADCSamplesHGSub.assign(m_NSamplesAna, 0);
  m_ADCSamplesLGSub.assign(m_NSamplesAna, 0);
 
  m_useSampleHG.assign(m_NSamplesAna, true);
  m_useSampleLG.assign(m_NSamplesAna, true);
 
  // Now do pedestal subtraction and check for overflows
  //
  for (size_t isample = 0; isample < m_NSamplesAna; isample++) {
    float ADCHG = m_ADCSamplesHG[isample];
    float ADCLG = m_ADCSamplesLG[isample];
 
    //
    // We always pedestal subtract even if the sample isn't going to be used in analysis
    //  basically for diagnostics
    //
    m_ADCSamplesHGSub[isample] = ADCHG - m_pedestal;
    m_ADCSamplesLGSub[isample] = ADCLG - m_pedestal;
 
    if (m_useSampleHG[isample]) {
      if (m_enablePreExcl) {
    if (ADCHG > m_preExclHGADCThresh && isample < m_maxSamplesPreExcl) {
      m_useSampleHG[isample] = false;
      continue;
    }
      }
 
      if (m_enablePostExcl) {
    if (ADCHG > m_postExclHGADCThresh && isample >= m_NSamplesAna - m_maxSamplesPostExcl) {
      m_useSampleHG[isample] = false;
      continue;
    }
      }
 
      // If we get here, we've passed the above filters on the sample
      //
      if (ADCHG > m_HGOverflowADC) {
    m_HGOverflow = true;
    
    if (isample == m_preSampleIdx) m_PSHGOverUnderflow = true;
 
    // Note: the implementation of the explicit pre- and post- sample exclusion should make this
    //   code obselete but before removing it we first need to validate the pre- and post-exclusion
    //
    if ((int) isample > m_lastHGOverFlowSample)  m_lastHGOverFlowSample  = isample;
    if ((int) isample < m_firstHGOverFlowSample) m_firstHGOverFlowSample = isample;
      }
      else if (ADCHG < m_HGUnderflowADC) {
    m_HGUnderflow = true;
    
    if (isample == m_preSampleIdx) m_PSHGOverUnderflow  = true;
      }
    }
 
    // Now the low gain sample
    //
    if (m_useSampleLG[isample]) {
      if (m_enablePreExcl) {
    if (ADCLG > m_preExclLGADCThresh && isample <= m_maxSamplesPreExcl) {
      m_useSampleLG[isample] = false;
      continue;
    }
      }
      
      if (m_enablePostExcl) {
    if (ADCLG > m_postExclLGADCThresh && isample >= m_NSamplesAna - m_maxSamplesPostExcl) {
      m_useSampleLG[isample] = false;
      m_ExcludeLate = true;
      continue;
    }
      }
 
      if (ADCLG > m_LGOverflowADC) {
    m_LGOverflow = true;
    m_fail = true;
    m_amplitude = m_LGOverflowADC * m_gainFactorLG; // Give a vale here even though we know it's wrong because
    //   the user may not check the return value and we know that
    //   amplitude is bigger than this
      }
      
      if (ADCLG == 0) {
    m_LGUnderflow = true;
    m_fail = true;
      }
    }
  }
 
  if (doDump) {
    (*m_msgFunc_p)(ZDCMsg::Verbose, "Dump of useSamples: ");
    
    std::ostringstream dumpStringUseHG;
    dumpStringUseHG << "HG: ";
    for (auto val : m_useSampleHG) {
      dumpStringUseHG  << val << " ";
    }
    (*m_msgFunc_p)(ZDCMsg::Verbose, dumpStringUseHG.str().c_str());
    
    std::ostringstream dumpStringUseLG;
    dumpStringUseLG << "LG: ";
    for (auto val : m_useSampleLG) {
      dumpStringUseLG  << val << " ";
    }
    (*m_msgFunc_p)(ZDCMsg::Verbose, dumpStringUseLG.str().c_str());
  }
 
  // This ugly code should be obseleted by the introduction of the better, pre- and post-sample exclusion but
  //   that code still has to be fully validated.
  //
  // See if we can still use high gain even in the case of HG overflow if the overflow results from
  //   the first few samples or the last few samples
  //
  if (m_HGOverflow && !m_HGUnderflow) {
    if (m_lastHGOverFlowSample < 2 && m_lastHGOverFlowSample > -1) {
      m_HGOverflow = false;
      m_minSampleEvt = m_lastHGOverFlowSample + 1;
      m_adjTimeRangeEvent = true;
      m_backToHG_pre = true;
      m_ExcludeEarly = true;
    }
    else if (m_firstHGOverFlowSample < static_cast<int>(m_NSamplesAna) && m_firstHGOverFlowSample >= static_cast<int>(m_NSamplesAna - 2) ) {
      m_maxSampleEvt = m_firstHGOverFlowSample - 1;
      m_HGOverflow = false;
      m_adjTimeRangeEvent = true;
      m_ExcludeLate = true;
    }
  }
 
  (*m_msgFunc_p)(ZDCMsg::Verbose, "ZDCPulseAnalyzer:: " + m_tag + ": ScanAndSubtractSamples done");
 
  return true;
}
 
bool ZDCPulseAnalyzer::DoAnalysis(bool repass)
{
  float deriv2ndThreshHG = 0;
  float deriv2ndThreshLG = 0;
 
  if (!repass) {
    ScanAndSubtractSamples();
    
    deriv2ndThreshHG = m_peak2ndDerivMinThreshHG;
    deriv2ndThreshLG = m_peak2ndDerivMinThreshLG;
  }
  else {
    deriv2ndThreshHG = m_peak2ndDerivMinRepassHG;
    deriv2ndThreshLG = m_peak2ndDerivMinRepassLG;
  }
 
  m_useLowGain = m_HGUnderflow || m_HGOverflow || (m_LGMode == LGModeForceLG);
  if (m_useLowGain) {
    (*m_msgFunc_p)(ZDCMsg::Verbose, "ZDCPulseAnalyzer:: " + m_tag + " using low gain data ");
 
    bool result = AnalyzeData(m_NSamplesAna, m_preSampleIdx, m_ADCSamplesLGSub, m_useSampleLG,
                  deriv2ndThreshLG, m_noiseSigLG, m_LGT0CorrParams, 
                              m_chisqDivAmpCutLG, m_T0CutLowLG, m_T0CutHighLG);
    if (result) {
      //
      // +++BAC
      //
      // I have removed some code that attempted a refit in case of failure of the chi-square cut
      // Instead, we should implement an analysis of the failure with possible re-fit afterwards
      //  with possible change of the pre- or post-pulse condition
      //
      // --BAC
      //
      
       // If we have a non-linear correction, apply it here   
       //   We apply it as an inverse correction - i.e. we divide by a correction
       //     term tha is a sum of coefficients times the ADC minus a reference
       //     to a power. The lowest power is 1, the highest is deteremined by
       //     the number of provided coefficients 
 
      double invNLCorr = 1.0;
      if (m_haveNonlinCorr) {
        float ampCorrFact = (m_fitAmplitude - m_nonLinCorrRefADC) / m_nonLinCorrRefScale;
    
    for (size_t power = 1; power <= m_nonLinCorrParamsLG.size(); power++) {
      invNLCorr += m_nonLinCorrParamsLG[power - 1]*pow(ampCorrFact, power);
    }
      }
      
      //
      // Multiply amplitude by gain factor
      //
      m_ampNoNonLin   = m_fitAmplitude * m_gainFactorLG;
      m_amplitude     = m_fitAmplitude / invNLCorr * m_gainFactorLG;
      m_ampError      = m_fitAmpError / invNLCorr * m_gainFactorLG;
      m_preSampleAmp  = m_preSample    * m_gainFactorLG;
      m_preAmplitude  = m_fitPreAmp    * m_gainFactorLG;
      m_postAmplitude = m_fitPostAmp   * m_gainFactorLG;
      m_expAmplitude  = m_fitExpAmp    * m_gainFactorLG;
 
      // BAC: also scale up the 2nd derivative so low and high gain can be treated on the same footing
      //
      m_minDeriv2nd *= m_gainFactorLG;
    }
 
    return result;
  }
  else {
    (*m_msgFunc_p)(ZDCMsg::Verbose, "ZDCPulseAnalyzer:: " + m_tag + " using high gain data ");
 
    bool result = AnalyzeData(m_NSamplesAna, m_preSampleIdx, m_ADCSamplesHGSub, m_useSampleHG,
                  deriv2ndThreshHG, m_noiseSigHG, m_HGT0CorrParams, 
                              m_chisqDivAmpCutHG, m_T0CutLowHG, m_T0CutHighHG);
    if (result) {
      // +++BAC
      //
      // I have removed some code that attempted a refit in case of failure of the chi-square cut
      // Instead, we should implement an analysis of the failure with possible re-fit afterwards
      //  with possible change of the pre- or post-pulse condition
      //
      // --BAC
 
      m_preSampleAmp = m_preSample  * m_gainFactorHG;
      m_amplitude = m_fitAmplitude  * m_gainFactorHG;
      m_ampNoNonLin   = m_amplitude;
      m_ampError = m_fitAmpError    * m_gainFactorHG;
      m_preAmplitude  = m_fitPreAmp * m_gainFactorHG;
      m_postAmplitude = m_fitPostAmp* m_gainFactorHG;
      m_expAmplitude  = m_fitExpAmp * m_gainFactorHG;
 
      m_minDeriv2nd *= m_gainFactorHG;
 
      //  If we have a non-linear correction, apply it here
      //
      //    We apply it as an inverse correction - i.e. we divide by a correction
      //      term tha is a sum of coefficients times the ADC minus a reference
      //      to a power. The lowest power is 1, the highest is deteremined by
      //      the number of provided coefficients 
      //
      if (m_haveNonlinCorr) {
        float ampCorrFact = (m_fitAmplitude - m_nonLinCorrRefADC) / m_nonLinCorrRefScale;
    
    float invNLCorr = 1.0;
    for (size_t power = 1; power <= m_nonLinCorrParamsHG.size(); power++) {
      invNLCorr += m_nonLinCorrParamsHG[power - 1]*pow(ampCorrFact, power);
    }
 
        m_amplitude /= invNLCorr;
        m_ampError /= invNLCorr;
      }
    }
 
    // If LG refit has been requested, do it now
    //
    if (m_LGMode == LGModeRefitLG && m_havePulse) {
      prepareLGRefit(m_ADCSamplesLGSub, m_ADCSSampSigLG, m_useSampleLG);
      DoFit(true);
 
      if (m_haveNonlinCorr) {
        float ampCorrFact = (m_refitLGAmpl - m_nonLinCorrRefADC) / m_nonLinCorrRefScale;
    
    float invNLCorr = 1.0;
    for (size_t power = 1; power <= m_nonLinCorrParamsHG.size(); power++) {
      invNLCorr += m_nonLinCorrParamsHG[power - 1]*pow(ampCorrFact, power);
    }
 
    m_refitLGAmplCorr = m_refitLGAmpl/invNLCorr;
      }
    }
    
    return result;
  }
}
 
bool ZDCPulseAnalyzer::AnalyzeData(size_t nSamples, size_t preSampleIdx,
                                   const std::vector<float>& samples,        // The samples used for this event
                                   const std::vector<bool>& useSample,       // The samples used for this event
                                   float peak2ndDerivMinThresh,
                   float noiseSig,
                                   const std::vector<float>& t0CorrParams,   // The parameters used to correct the t0
                                   float maxChisqDivAmp,                     // The maximum chisq / amplitude ratio
                                   float minT0Corr, float maxT0Corr          // The minimum and maximum corrected T0 values
                                  )
{
 
  // We keep track of which sample we used to do the subtraction sepaate from m_minSampleEvt
  //  because the corresponding time is the reference time we provide to the fit function when
  //  we have pre-pulses and in case we change the m_minSampleEvt after doing the subtraction
  //
  //    e.g. our refit when the chisquare cuts fails
  //
 
  // Find the first used sample in the event
  //
  bool haveFirst = false;
  unsigned int lastUsed = 0;
  
  for (unsigned int sample = preSampleIdx; sample < nSamples; sample++) {
    if (useSample[sample]) {
      //
      // We're going to use this sample in the analysis, update bookeeping
      //
      if (!haveFirst) {
    if (sample > m_minSampleEvt) m_minSampleEvt = sample;
    haveFirst = true;
      }
      else {
    lastUsed = sample;
      }
    }
  }
 
  if (lastUsed < m_maxSampleEvt) m_maxSampleEvt = lastUsed;
 
  // Check to see whether we've changed the range of samples used in the analysis
  //
  // Should be obseleted with reworking of the fitting using Root::Fit package
  //
  if (m_minSampleEvt > preSampleIdx) {
     m_ExcludeEarly = true;
     m_adjTimeRangeEvent = true;
  }
 
  if (m_maxSampleEvt < nSamples - 1) {
    m_adjTimeRangeEvent = true;
    m_ExcludeLate = true;
  }
 
  // Prepare for subtraction
  //
  m_usedPresampIdx = m_minSampleEvt;
  m_preSample = samples[m_usedPresampIdx];
 
  std::ostringstream pedMessage;
  pedMessage << "Pedestal index = " << m_usedPresampIdx << ", value = " << m_preSample;
  (*m_msgFunc_p)(ZDCMsg::Verbose, pedMessage.str().c_str());
 
  m_samplesSub = samples;
  m_samplesSig.assign(m_NSamplesAna, noiseSig);
      
  
  //
  // When we are combinig delayed and undelayed samples we have to deal with the fact that
  //   the two readouts can have different noise and thus different baselines. Which is a huge
  //   headache.
  //
  if (m_useDelayed) {
    if (m_useFixedBaseline) {
      m_baselineCorr = m_delayedPedestalDiff;
    }
    else {
      //
      //  Use much-improved method to match delayed and undelayed baselines
      //
      m_baselineCorr = obtainDelayedBaselineCorr(m_samplesSub);
      std::ostringstream baselineMsg;
      baselineMsg << "Delayed samples baseline correction = " << m_baselineCorr << std::endl;
      (*m_msgFunc_p)(ZDCMsg::Debug, baselineMsg.str().c_str());
    }
 
    // Now apply the baseline correction to align ADC values for delayed and undelayed samples
    //
    for (size_t isample = 0; isample < nSamples; isample++) {
      if (isample % 2) m_samplesSub[isample] -= m_baselineCorr;
    }
 
    // If we use one of the delayed samples for presample, we have to adjust the presample value as well
    //
    if (m_usedPresampIdx % 2) m_preSample -= m_baselineCorr;
  }
 
  // Do the presample subtraction
  //
  std::for_each(m_samplesSub.begin(), m_samplesSub.end(), [ = ] (float & adcUnsub) {return adcUnsub -= m_preSample;} );
 
  // Find maximum and minimum values, not necessarily those of the actual pulse
  //
  std::pair<SampleCIter, SampleCIter> minMaxIters = std::minmax_element(m_samplesSub.cbegin() + m_minSampleEvt, m_samplesSub.cbegin() + m_maxSampleEvt);
  SampleCIter minIter = minMaxIters.first;
  SampleCIter maxIter = minMaxIters.second;
 
  m_maxADCValue = *maxIter;
  m_minADCValue = *minIter;
 
  m_maxSampl = std::distance(m_samplesSub.cbegin(), maxIter);
  m_minSampl = std::distance(m_samplesSub.cbegin(), minIter);
 
  // Calculate the second derivatives using step size m_2ndDerivStep
  //
  m_samplesDeriv2nd = Calculate2ndDerivative(m_samplesSub, m_2ndDerivStep);
 
  // Find the sample which has the lowest 2nd derivative. We loop over the range defined by the
  //  tolerance on the position of the minimum second derivative. Note: the +1 in the upper iterator is because
  //  that's where the loop terminates, not the last element.
  //
  SampleCIter minDeriv2ndIter;
 
  int upperDelta = std::min(m_peak2ndDerivMinSample + m_peak2ndDerivMinTolerance + 1, nSamples);
 
  minDeriv2ndIter = std::min_element(m_samplesDeriv2nd.begin() + m_peak2ndDerivMinSample - m_peak2ndDerivMinTolerance, m_samplesDeriv2nd.begin() + upperDelta);
 
  m_minDeriv2nd = *minDeriv2ndIter;
  m_minDeriv2ndSig = -m_minDeriv2nd/(std::sqrt(6.0)*noiseSig);
 
  m_minDeriv2ndIndex = std::distance(m_samplesDeriv2nd.cbegin(), minDeriv2ndIter);
 
  // BAC 02-04-23 This check turned out to be problematic. Todo: figure out how to replace
  //
  // // Also check the ADC value for the "peak" sample to make sure it is significant (at least 3 sigma)
  // // The factor of sqrt(2) on the noise is because we have done a pre-sample subtraction
  // //
  if (m_minDeriv2nd <= peak2ndDerivMinThresh) {
    m_havePulse = true;
    (*m_msgFunc_p)(ZDCMsg::Verbose, "ZDCPulseAnalyzer:: " + m_tag + " has pulse ");
  }
  else {
    (*m_msgFunc_p)(ZDCMsg::Verbose, "ZDCPulseAnalyzer:: " + m_tag + " does not have pulse ");
    m_havePulse = false;
  }
 
 
  
  // Now decide whether we have a preceeding pulse or not. There are two possible kinds of preceeding pulses:
  //   1) exponential tail from a preceeding pulse
  //   2) peaked pulse before the main pulse
  //
  //   we can, of course, have both
  //
 
  // To check for exponential tail, test the slope determined by the minimum ADC value (and pre-sample)
  // **beware** this can cause trouble in 2015 data where the pulses had overshoot due to the transformers
  //
 
  // Implement a much simpler test for presence of an exponential tail from an OOT pulse
  //   namely if the slope evaluated at the presample is significantly negative, then 
  //   we have a preceeding pulse.
  //
  // Note that we don't have to subtract the FADC value corresponding to the presample because 
  //   that subtraction has already been done.
  //
  if (m_havePulse) {
    // If we've alreday excluded early samples, we have almost by construction have negative exponential tail
    //
    if (m_ExcludeEarly) m_preExpTail = true;
 
    //
    //  The subtracted ADC value at m_usedPresampIdx is, by construction, zero
    //    The next sample has had the pre-sample subtracted, so it represents the initial derivative
    //
    float derivPresampleSig = m_samplesSub[m_usedPresampIdx+1]/(std::sqrt(2.0)*noiseSig);
    if (derivPresampleSig < -5) {
      m_preExpTail = true;
      m_preExpSig = derivPresampleSig;
    }
    
    for (unsigned int isample = m_usedPresampIdx; isample < m_samplesSub.size(); isample++) {
      if (!useSample[isample]) continue;
 
      float sampleSig = -m_samplesSub[isample]/(std::sqrt(2.0)*noiseSig);
      float sigRatio = sampleSig/m_minDeriv2ndSig;
          
      if ((sampleSig > 5 && sigRatio > 0.02) || sigRatio > 0.5) {
    m_preExpTail = true;
    if (sampleSig > m_preExpSig) m_preExpSig = sampleSig;
      }
    }
    
    int loopLimit = (m_havePulse ? m_minDeriv2ndIndex - 2 : m_peak2ndDerivMinSample - 2);
    int loopStart = m_minSampleEvt == 0 ? 1 : m_minSampleEvt;
    
    for (int isample = loopStart; isample <= loopLimit; isample++) {
      if (!useSample[isample]) continue;
      
      //
      // If any of the second derivatives prior to the peak are significantly negative, we have a an extra pulse
      //   prior to the main one -- as opposed to just an expnential tail
      //
      m_prePulseSig = -m_samplesDeriv2nd[isample]/(std::sqrt(6.0)*noiseSig);
      
      if ((m_prePulseSig > 6 && m_samplesDeriv2nd[isample] < 0.05 * m_minDeriv2nd) ||
      m_samplesDeriv2nd[isample]  < 0.5*m_minDeriv2nd)
      {
    if (m_preExpTail) {
      //
      // We have a prepulse. If we already indicated an negative exponential,
      //   if the prepulse has greater significance, we override the negative exponential
      //
      if (m_prePulseSig >  m_preExpSig) {
        m_prePulse = true;
        m_preExpTail = false;
      }
    }
    else {
      m_prePulse = true;
    }
    
    if (m_prePulse && m_samplesSub[isample] > m_initialPrePulseAmp) {
      m_initialPrePulseAmp = m_samplesSub[isample];
      m_initialPrePulseT0 = m_deltaTSample * (isample);
    }
      }
    }
 
    //    if (m_preExpTail) m_prePulse = true;    
 
    // -----------------------------------------------------
    // Post pulse detection
    //
    unsigned int postStartIdx = std::max(static_cast<unsigned int>(m_minDeriv2ndIndex + 2),
                     static_cast<unsigned int>(m_peak2ndDerivMinSample + m_peak2ndDerivMinTolerance + 1));
 
    
    for (int isample = postStartIdx; isample < (int) m_samplesDeriv2nd.size() - 1; isample++) {
      if (!useSample[isample]) continue;
      
      // +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
      // BAC 12-01-2024
      //
      // The following code is commented out as a temporary measure to deal with apparent reflections
      //   associated with large out-of-time pulses that introduce a "kink" that triggers the derivative
      //   test. A work-around that doesn't introduce specific code for the 2023 Pb+Pb run but allows
      //   adaption for this specific issue is going to take some work. For now we leave the 2nd derivative
      //   test, but will also need to introduce some configurability of the cut -- which we need anyway
      //
      // Calculate the forward derivative. the pulse should never increase on the tail. If it
      //   does, we almost certainly have a post-pulse
      //
      // float deriv = m_samplesSub[isample + 1] - m_samplesSub[isample];
      // if (deriv/(std::sqrt(2)*noiseSig) > 6) {
      //   m_postPulse = true;
      //   m_maxSampleEvt = isample;
      //   m_adjTimeRangeEvent = true;
      //   break;
      // }
      // else {
      //----------------------------------------------------------------------------------------------
      //
      // Now we check the second derivative which might also indicate a post pulse
      //   even if the derivative is not sufficiently large
      //
      // add small 1e-3 in division to avoid floating overflow
      //
 
      float deriv = m_samplesSub[isample + 1] - m_samplesSub[isample];
      float derivSig = deriv/(std::sqrt(2)*noiseSig);
      float deriv2ndSig = -m_samplesDeriv2nd[isample] / (std::sqrt(6)*noiseSig);
 
      float deriv2ndTest = m_samplesDeriv2nd[isample] / (-m_minDeriv2nd + 1.0e-3);
 
      if (derivSig > 5) {
    //
    // Check the 2nd derivative -- we should be at a minimum(?)
    //  
    if (std::abs(deriv2ndTest) > 0.15) {
      m_postPulse = true;
      m_maxSampleEvt = std::min<int>(isample - (m_2ndDerivStep - 1), m_maxSampleEvt);
 
      m_adjTimeRangeEvent = true;
      break;
    }
      }
          
      // The place to apply the cut on samples depends on whether we have found a "minimum" or a "maximum"
      //   The -m_2ndDerivStep for the minimum accounts for the shift between 2nd derivative and the samples
      //   if we find a maximum we cut one sample lower
      //
      if (deriv2ndSig > 5 && deriv2ndTest < -0.1) {
    m_postPulse = true;
    m_maxSampleEvt = std::min<int>(isample - m_2ndDerivStep, m_maxSampleEvt);
 
    m_adjTimeRangeEvent = true;
    break;
      }
    }
  }
 
  if (m_postPulse) {
    std::ostringstream ostrm;
    ostrm << "Post pulse found, m_maxSampleEvt = " << m_maxSampleEvt;
    (*m_msgFunc_p)(ZDCMsg::Debug, ostrm.str());
  }
 
  
  // -----------------------------------------------------
 
  //  Stop now if we have no pulse or we've detected a failure
  //
  if (m_fail || !m_havePulse) return false;
 
  if (!m_useDelayed) DoFit();
  else DoFitCombined();
  
  if (FitFailed()) {
    m_fail = true;
  }
  else {
    std::ostringstream ostrm;
    ostrm << "Pulse fit successful with chisquare = " << m_fitChisq;
    (*m_msgFunc_p)(ZDCMsg::Debug, ostrm.str());
 
    m_fitTimeCorr = m_fitTimeSub;
 
    if (m_timingCorrMode != NoTimingCorr) {
      //
      // We correct relative to the m_timingCorrRefADC using m_timingCorrScale to scale
      //
      double t0CorrFact = (m_fitAmplitude - m_timingCorrRefADC) / m_timingCorrScale;
      if (m_timingCorrMode == TimingCorrLog) t0CorrFact = std::log(t0CorrFact);
 
      // Calculate the correction using a polynomial of power determined by the size of the vector.
      //   For historical reasons we include here a constant term, though it is degenerate with
      //   the nominal t0 and/or timing calibrations.
      //
      float correction = 0;
 
      for (unsigned int ipow = 0; ipow < t0CorrParams.size(); ipow++) {
    correction += t0CorrParams[ipow]*std::pow(t0CorrFact, double(ipow));
      }
 
      // The correction represents the offset of the timing value from zero so we subtract the result
      //
      m_fitTimeCorr -= correction; 
    }
 
    bool failFixedCut = m_fitTimeCorr < minT0Corr || m_fitTimeCorr > maxT0Corr;
 
    // Calculate the timing significance. Note this implementation breaks the model for
    //  how DoAnalysis is currently used by explicitly testing m_useLowGain, but that model
    //  needs adjustment anyway ... (one step at a time)
    //
    // Note that to avoid coupling non-linear corrections to the amplitude and the 
    //   timing significance we evaluate the time resolution using the fit amplitude
    //
    if (m_timeCutMode != 0) {
      double timeResolution = 0;
      if (m_useLowGain) timeResolution = m_timeResFuncLG_p->Eval(m_fitAmplitude);
      else timeResolution = m_timeResFuncHG_p->Eval(m_fitAmplitude);
 
      m_timeSig = m_fitTimeCorr/timeResolution;
      if (std::abs(m_timeSig) > m_t0CutSig) {
    //
    // We've failed the significance cut. In OR mode (1) we mark the time
    //  as bad if we've lso failed the fixed cut. In AND mode, we mark it
    //  as bad regardless of the fixed cut.
    //
    if (m_timeCutMode == 1) {
      if (failFixedCut) m_badT0 = true;
    }
    else m_badT0 = true;
      }
      else if (m_timeCutMode == 2 && failFixedCut) m_badT0 = failFixedCut;
    }
    else {
      m_timeSig = -1;
      m_badT0 = failFixedCut;
    }
    
    // Now check for valid chisq and valid time
    //
    if (m_fitChisq/m_fitNDoF > 2 && m_fitChisq / (m_fitAmplitude + 1.0e-6) > maxChisqDivAmp) m_badChisq = true;
  }
 
  return !m_fitFailed;
}
 
void ZDCPulseAnalyzer::prepareLGRefit(const std::vector<float>& samplesLG, const std::vector<float>& samplesSig,
                      const std::vector<bool>& useSamples)
{
  m_samplesLGRefit.clear();
  m_samplesSigLGRefit.clear();
 
  float presampleLG = m_ADCSamplesLGSub[m_usedPresampIdx];
    
  // Do the presample subtraction
  //
  for (unsigned int idx = 0; idx < samplesLG.size(); idx++) {
    m_samplesLGRefit.push_back(samplesLG[idx] - presampleLG);
 
    if (useSamples[idx]) {
      m_samplesSigLGRefit.push_back(samplesSig[idx]);
    }
    else {
      m_samplesSigLGRefit.push_back(0);
    }
  }
}
 
 
void ZDCPulseAnalyzer::DoFit(bool refitLG)
{
  bool fitLG = m_useLowGain || refitLG;
  
  TH1* hist_p = nullptr;
  FillHistogram(refitLG);
    
  // Set the initial values
  //
  float ampInitial, fitAmpMin, fitAmpMax, t0Initial;
 
  if (fitLG) {
    fitAmpMin = m_fitAmpMinLG;
    fitAmpMax = m_fitAmpMaxLG;
    t0Initial = m_nominalT0LG;
  }
  else {
    fitAmpMin = m_fitAmpMinHG;
    fitAmpMax = m_fitAmpMaxHG;
    t0Initial = m_nominalT0HG;
 }
 
  if (refitLG) {
    hist_p = m_fitHistLGRefit.get();
    ampInitial = (m_maxADCValue - m_minADCValue)*m_gainFactorHG/m_gainFactorLG;
  }
  else {
    hist_p = m_fitHist.get();
    ampInitial = m_maxADCValue - m_minADCValue;
  }
  if (ampInitial < fitAmpMin) ampInitial = fitAmpMin * 1.5;
 
 
  ZDCFitWrapper* fitWrapper = m_defaultFitWrapper.get();
  if (preExpTail()) {
    fitWrapper = m_preExpFitWrapper.get();
    (static_cast<ZDCPreExpFitWrapper*>(m_preExpFitWrapper.get()))->SetInitialExpPulse(m_initialExpAmp);
  }
  else if (PrePulse()) {
    fitWrapper = m_prePulseFitWrapper.get();
    (static_cast<ZDCPrePulseFitWrapper*>(fitWrapper))->SetInitialPrePulse(m_initialPrePulseAmp, m_initialPrePulseT0,0,25);
  }
  
  if (m_adjTimeRangeEvent) {
    m_fitTMin = std::max(m_fitTMin, m_deltaTSample * m_minSampleEvt - m_deltaTSample / 2);
    m_fitTMax = std::min(m_fitTMax, m_deltaTSample * m_maxSampleEvt + m_deltaTSample / 2);
 
    float fitTReference = m_deltaTSample * m_usedPresampIdx;
 
    fitWrapper->Initialize(ampInitial, t0Initial, fitAmpMin, fitAmpMax, m_fitTMin, m_fitTMax, fitTReference);
  }
  else {
    fitWrapper->Initialize(ampInitial, t0Initial, fitAmpMin, fitAmpMax);
  }
 
  // Now perform the fit
  //
  std::string options = m_fitOptions + "Ns";
  if (QuietFits()) {
    options += "Q";
  }
 
  bool fitFailed = false;
 
  dumpTF1(fitWrapper->GetWrapperTF1RawPtr());
  
  //
  //  Fit the data with the function provided by the fit wrapper
  //
  TFitResultPtr result_ptr = hist_p->Fit(fitWrapper->GetWrapperTF1RawPtr(), options.c_str(), "", m_fitTMin, m_fitTMax);
  int fitStatus = result_ptr;
  
  //
  // If the first fit failed, also check the EDM. If sufficiently small, the failure is almost surely due
  //   to parameter limits and we just accept the result
  //
  if (fitStatus != 0 && result_ptr->Edm() > 0.001) 
    {
    //
    // We contstrain the fit and try again
    //
    fitWrapper->ConstrainFit();
 
    TFitResultPtr constrFitResult_ptr = hist_p->Fit(fitWrapper->GetWrapperTF1RawPtr(), options.c_str(), "", m_fitTMin, m_fitTMax);
    fitWrapper->UnconstrainFit();
 
    if ((int) constrFitResult_ptr != 0) {
      //
      // Even the constrained fit failed, so we quit.
      //
      fitFailed = true;
    }
    else {
      // Now we try the fit again with the constraint removed
      //
      TFitResultPtr unconstrFitResult_ptr = hist_p->Fit(fitWrapper->GetWrapperTF1RawPtr(), options.c_str(), "", m_fitTMin, m_fitTMax);
      if ((int) unconstrFitResult_ptr != 0) {
    //
    // The unconstrained fit failed again, so we redo the constrained fit
    //
    fitWrapper->ConstrainFit();
      
    TFitResultPtr constrFit2Result_ptr = hist_p->Fit(fitWrapper->GetWrapperTF1RawPtr(), options.c_str(), "", m_fitTMin, m_fitTMax);
    if ((int) constrFit2Result_ptr != 0) {
      //
      // Even the constrained fit failed the second time, so we quit.
      //
      fitFailed = true;
    }
 
    result_ptr = constrFit2Result_ptr;
    fitWrapper->UnconstrainFit();
      }
      else {
    result_ptr = unconstrFitResult_ptr;
      }
    }
  }
 
  if (!m_fitFailed && s_saveFitFunc) {
    hist_p->GetListOfFunctions()->Clear();
 
    TF1* func = fitWrapper->GetWrapperTF1RawPtr();
    std::string name = func->GetName();
 
    TF1* copyFunc = static_cast<TF1*>(func->Clone((name + "_copy").c_str()));
    hist_p->GetListOfFunctions()->Add(copyFunc);
  }
 
  if (!refitLG) {
    m_fitFailed = fitFailed;
    m_bkgdMaxFraction = fitWrapper->GetBkgdMaxFraction();
    m_fitAmplitude = fitWrapper->GetAmplitude();
    m_fitAmpError = fitWrapper->GetAmpError();
 
    if (preExpTail()) {
      m_fitExpAmp  = (static_cast<ZDCPreExpFitWrapper*>(m_preExpFitWrapper.get()))->GetExpAmp();
    }
    else {
      m_fitExpAmp = 0;
    }
    
    m_fitTime      = fitWrapper->GetTime();
    m_fitTimeSub = m_fitTime - t0Initial;
 
    m_fitChisq = result_ptr->Chi2();
    m_fitNDoF = result_ptr->Ndf();
    
    m_fitTau1 = fitWrapper->GetTau1();
    m_fitTau2 = fitWrapper->GetTau2();
    
    // Here we need to check if the fit amplitude is small (close) enough to fitAmpMin.
    // with "< 1+epsilon" where epsilon ~ 1%
    if (m_fitAmplitude < fitAmpMin * 1.01) {
      m_fitMinAmp = true;
    }
  }
  else {
    m_evtLGRefit = true;
    m_refitLGAmpl = fitWrapper->GetAmplitude();
    m_refitLGAmpError = fitWrapper->GetAmpError();
    m_refitLGChisq = result_ptr->Chi2();
    m_refitLGTime = fitWrapper->GetTime();
    m_refitLGTimeSub = m_refitLGTime - t0Initial;
  }
}
 
void ZDCPulseAnalyzer::DoFitCombined(bool refitLG)
{
  bool fitLG = refitLG || m_useLowGain;
  TH1* hist_p = nullptr, *delayedHist_p = nullptr;
 
  FillHistogram(refitLG);
  if (refitLG) {
    hist_p = m_fitHistLGRefit.get();
    delayedHist_p = m_delayedHistLGRefit.get();
  }
  else {
    hist_p = m_fitHist.get();
    delayedHist_p = m_delayedHist.get();
  }
  
  float fitAmpMin, fitAmpMax, t0Initial;
  if (fitLG) {
    fitAmpMin = m_fitAmpMinLG;
    fitAmpMax = m_fitAmpMaxLG;
    t0Initial = m_nominalT0LG;
  }
  else {
    fitAmpMin = m_fitAmpMinHG;
    fitAmpMax = m_fitAmpMaxHG;
    t0Initial = m_nominalT0HG;
  }
 
  // Set the initial values
  //
  float ampInitial = m_maxADCValue - m_minADCValue;
  if (ampInitial < fitAmpMin) ampInitial = fitAmpMin * 1.5;
 
  ZDCFitWrapper* fitWrapper = m_defaultFitWrapper.get();
  //if (PrePulse()) fitWrapper = fitWrapper = m_preExpFitWrapper.get();
 
  if (preExpTail()) {
    fitWrapper = m_preExpFitWrapper.get();
    (static_cast<ZDCPreExpFitWrapper*>(m_preExpFitWrapper.get()))->SetInitialExpPulse(m_initialExpAmp);
  }
  else if (PrePulse()) {
    fitWrapper = m_prePulseFitWrapper.get();
    (static_cast<ZDCPrePulseFitWrapper*>(fitWrapper))->SetInitialPrePulse(m_initialPrePulseAmp, m_initialPrePulseT0,0,25);
  }
 
  // Initialize the fit wrapper for this event, specifying a
  //   per-event fit range if necessary
  //
  if (m_adjTimeRangeEvent) {
    m_fitTMin = std::max(m_fitTMin, m_deltaTSample * m_minSampleEvt - m_deltaTSample / 2);
    m_fitTMax = std::min(m_fitTMax, m_deltaTSample * m_maxSampleEvt + m_deltaTSample / 2);
 
    float fitTReference = m_deltaTSample * m_usedPresampIdx;
 
    fitWrapper->Initialize(ampInitial, t0Initial, fitAmpMin, fitAmpMax, m_fitTMin, m_fitTMax, fitTReference);
  }
  else {
    fitWrapper->Initialize(ampInitial, t0Initial, fitAmpMin, fitAmpMax);
  }
 
  // Set up the virtual fitter
  //
  TFitter* theFitter = nullptr;
 
  if (PrePulse()) {
    m_prePulseCombinedFitter = MakeCombinedFitter(fitWrapper->GetWrapperTF1RawPtr());
 
    theFitter = m_prePulseCombinedFitter.get();
  }
  else {
    m_defaultCombinedFitter = MakeCombinedFitter(fitWrapper->GetWrapperTF1RawPtr());
 
    theFitter = m_defaultCombinedFitter.get();
  }
 
  dumpTF1(fitWrapper->GetWrapperTF1RawPtr());
 
  // Set the static pointers to histograms and function for use in FCN
  //
  s_undelayedFitHist = hist_p;
  s_delayedFitHist = delayedHist_p;
  s_combinedFitFunc = fitWrapper->GetWrapperTF1RawPtr();
  s_combinedFitTMax = m_fitTMax;
  s_combinedFitTMin = m_fitTMin;
 
  
  size_t numFitPar = theFitter->GetNumberTotalParameters();
 
  theFitter->GetMinuit()->fISW[4] = -1;
 
  // Now perform the fit
  //
  if (s_quietFits) {
    theFitter->GetMinuit()->fISW[4] = -1;
 
    int  ierr= 0; 
    theFitter->GetMinuit()->mnexcm("SET NOWarnings",nullptr,0,ierr);
  }
  else theFitter->GetMinuit()->fISW[4] = 0;
 
  // Only include baseline shift in fit for pre-pulses. Otherwise baseline matching should work
  //
  if (PrePulse()) {
    theFitter->SetParameter(0, "delayBaselineAdjust", 0, 0.01, -100, 100);
    theFitter->ReleaseParameter(0);
  }
  else {
    theFitter->SetParameter(0, "delayBaselineAdjust", 0, 0.01, -100, 100);
    theFitter->FixParameter(0);
  }
 
  
  double arglist[100];
  arglist[0] = 5000; // number of function calls
  arglist[1] = 0.01; // tolerance
  int status = theFitter->ExecuteCommand("MIGRAD", arglist, 2);
 
  double fitAmp = theFitter->GetParameter(1);
  
  // Capture the chi-square etc.
  //
  double chi2, edm, errdef;
  int nvpar, nparx;
  
  theFitter->GetStats(chi2, edm, errdef, nvpar, nparx);
 
  // Here we need to check if fitAmp is small (close) enough to fitAmpMin.
  // with "< 1+epsilon" where epsilon ~ 1%
  //
  if (status || fitAmp < fitAmpMin * 1.01 || edm > 0.01){
 
    //
    // We first retry the fit with no baseline adjust
    //
    theFitter->SetParameter(0, "delayBaselineAdjust", 0, 0.01, -100, 100);
    theFitter->FixParameter(0);
 
    // Here we need to check if fitAmp is small (close) enough to fitAmpMin.
    // with "< 1+epsilon" where epsilon ~ 1%
    if (fitAmp < fitAmpMin * 1.01) {
      if (m_adjTimeRangeEvent) {
        float fitTReference = m_deltaTSample * m_usedPresampIdx;
        fitWrapper->Initialize(ampInitial, t0Initial, fitAmpMin, fitAmpMax, m_fitTMin, m_fitTMax, fitTReference);
      }
      else {
        fitWrapper->Initialize(ampInitial, t0Initial, fitAmpMin, fitAmpMax);
      }
    }
 
    status = theFitter->ExecuteCommand("MIGRAD", arglist, 2);
    if (status != 0) {
      //
      // Fit failed event with no baseline adust, so be it
      //
      theFitter->ReleaseParameter(0);
      m_fitFailed = true;
    }
    else {
      //
      // The fit succeeded with no baseline adjust, re-fit allowing for baseline adjust using
      //  the parameters from previous fit as the starting point
      //
      theFitter->ReleaseParameter(0);
      status = theFitter->ExecuteCommand("MIGRAD", arglist, 2);
 
      if (status) {
        // Since we know the fit can succeed without the baseline adjust, go back to it
        //
        theFitter->SetParameter(0, "delayBaselineAdjust", 0, 0.01, -100, 100);
        theFitter->FixParameter(0);
        status = theFitter->ExecuteCommand("MIGRAD", arglist, 2);
      }
    }
  }
  else m_fitFailed = false;
 
  // Check to see if the fit forced the amplitude to the minimum, if so set the corresponding status bit
  //
  fitAmp = theFitter->GetParameter(1);
 
  // Here we need to check if fitAmp is small (close) enough to fitAmpMin.
  // with "< 1+epsilon" where epsilon ~ 1%
  if (fitAmp < fitAmpMin * 1.01) {
    m_fitMinAmp = true;
  }
 
  if (!s_quietFits) theFitter->GetMinuit()->fISW[4] = -1;
 
  std::vector<double> funcParams(numFitPar - 1);
  std::vector<double> funcParamErrs(numFitPar - 1);
 
  // Save the baseline shift between delayed and undelayed samples
  //
  m_delayedBaselineShift = theFitter->GetParameter(0);
 
  // Capture and store the fit function parameteds and errors
  //
  for (size_t ipar = 1; ipar < numFitPar; ipar++) {
    funcParams[ipar - 1] = theFitter->GetParameter(ipar);
    funcParamErrs[ipar - 1] = theFitter->GetParError(ipar);
  }
 
  s_combinedFitFunc->SetParameters(&funcParams[0]);
  s_combinedFitFunc->SetParErrors(&funcParamErrs[0]);
 
  // Capture the chi-square etc.
  //
  theFitter->GetStats(chi2, edm, errdef, nvpar, nparx);
 
  int ndf = 2 * m_Nsample - nvpar;
 
  s_combinedFitFunc->SetChisquare(chi2);
  s_combinedFitFunc->SetNDF(ndf);
 
  // add to list of functions
  if (s_saveFitFunc) {
    s_undelayedFitHist->GetListOfFunctions()->Clear();
    s_undelayedFitHist->GetListOfFunctions()->Add(s_combinedFitFunc);
 
    s_delayedFitHist->GetListOfFunctions()->Clear();
    s_delayedFitHist->GetListOfFunctions()->Add(s_combinedFitFunc);
  }
 
  if (!refitLG) {
    // Save the pull values from the last call to FCN
    //
    arglist[0] = 3; // number of function calls
    theFitter->ExecuteCommand("Cal1fcn", arglist, 1);
    m_fitPulls = s_pullValues;
    
    m_fitAmplitude = fitWrapper->GetAmplitude();
    m_fitTime      = fitWrapper->GetTime();
    if (PrePulse()) {
      m_fitPreT0   = (static_cast<ZDCPrePulseFitWrapper*>(m_prePulseFitWrapper.get()))->GetPreT0();
      m_fitPreAmp  = (static_cast<ZDCPrePulseFitWrapper*>(m_prePulseFitWrapper.get()))->GetPreAmp();
      m_fitPostT0  = (static_cast<ZDCPrePulseFitWrapper*>(m_prePulseFitWrapper.get()))->GetPostT0();
      m_fitPostAmp = (static_cast<ZDCPrePulseFitWrapper*>(m_prePulseFitWrapper.get()))->GetPostAmp();
    }
    
    if (preExpTail()) {
      m_fitExpAmp  = (static_cast<ZDCPreExpFitWrapper*>(m_preExpFitWrapper.get()))->GetExpAmp();
    }
    else {
      m_fitExpAmp = 0;
    }
    
    m_fitTimeSub = m_fitTime - t0Initial;
    m_fitChisq = chi2;
    m_fitNDoF = ndf;
    
    m_fitTau1 = fitWrapper->GetTau1();
    m_fitTau2 = fitWrapper->GetTau2();
    
    m_fitAmpError = fitWrapper->GetAmpError();
    m_bkgdMaxFraction = fitWrapper->GetBkgdMaxFraction();
  }
  else {
    m_evtLGRefit = true;
    m_refitLGAmpl = fitWrapper->GetAmplitude();
    m_refitLGAmpError = fitWrapper->GetAmpError();
    m_refitLGChisq = chi2;
    m_refitLGTime = fitWrapper->GetTime();
    m_refitLGTimeSub = m_refitLGTime - t0Initial;
  }
}
 
 
std::unique_ptr<TFitter> ZDCPulseAnalyzer::MakeCombinedFitter(TF1* func)
{
  TVirtualFitter::SetDefaultFitter("Minuit");
 
  size_t nFitParams = func->GetNpar() + 1;
  std::unique_ptr<TFitter> fitter = std::make_unique<TFitter>(nFitParams);
 
  fitter->GetMinuit()->fISW[4] = -1;
  fitter->SetParameter(0, "delayBaselineAdjust", 0, 0.01, -100, 100);
 
  for (size_t ipar = 0; ipar < nFitParams - 1; ipar++) {
    double parLimitLow, parLimitHigh;
 
    func->GetParLimits(ipar, parLimitLow, parLimitHigh);
    if (std::abs(parLimitHigh / parLimitLow - 1) < 1e-6) {
      double value   = func->GetParameter(ipar);
      double lowLim  = std::min(value * 0.99, value * 1.01);
      double highLim = std::max(value * 0.99, value * 1.01);
 
      fitter->SetParameter(ipar + 1, func->GetParName(ipar), func->GetParameter(ipar), 0.01, lowLim, highLim);
      fitter->FixParameter(ipar + 1);
    }
    else {
      double value = func->GetParameter(ipar);
      if (value >= parLimitHigh)     value = parLimitHigh * 0.99;
      else if (value <= parLimitLow) value = parLimitLow * 1.01;
 
      double step = std::min((parLimitHigh - parLimitLow)/100., (value - parLimitLow)/100.);
      
      fitter->SetParameter(ipar + 1, func->GetParName(ipar), value, step, parLimitLow, parLimitHigh);
    }
  }
 
  fitter->SetFCN(ZDCPulseAnalyzer::CombinedPulsesFCN);
 
  return fitter;
}
 
void ZDCPulseAnalyzer::UpdateFitterTimeLimits(TFitter* fitter, ZDCFitWrapper* wrapper, bool prePulse)
{
  double parLimitLow, parLimitHigh;
 
  auto func_p = wrapper->GetWrapperTF1();
  func_p->GetParLimits(1, parLimitLow, parLimitHigh);
 
  fitter->SetParameter(2, func_p->GetParName(1), func_p->GetParameter(1), 0.01, parLimitLow, parLimitHigh);
 
  if (prePulse) {
    unsigned int parIndex = static_cast<ZDCPrePulseFitWrapper*>(wrapper)->GetPreT0ParIndex();
 
    func_p->GetParLimits(parIndex, parLimitLow, parLimitHigh);
    fitter->SetParameter(parIndex + 1, func_p->GetParName(parIndex), func_p->GetParameter(parIndex), 0.01, parLimitLow, parLimitHigh);
  }
}
 
void ZDCPulseAnalyzer::dump() const
{
  (*m_msgFunc_p)(ZDCMsg::Info, ("ZDCPulseAnalyzer dump for tag = " + m_tag));
 
  (*m_msgFunc_p)(ZDCMsg::Info, ("Presample index, value = " + std::to_string(m_preSampleIdx) +  ", " + std::to_string(m_preSample)));
 
  if (m_useDelayed) {
    (*m_msgFunc_p)(ZDCMsg::Info, ("using delayed samples with delta T = " + std::to_string(m_delayedDeltaT) + ", and pedestalDiff == " +
                                  std::to_string(m_delayedPedestalDiff)));
  }
 
  std::ostringstream message1;
  message1 << "samplesSub ";
  for (size_t sample = 0; sample < m_samplesSub.size(); sample++) {
    message1 << ", [" << sample << "] = " << m_samplesSub[sample];
  }
  (*m_msgFunc_p)(ZDCMsg::Info, message1.str());
 
  std::ostringstream message3;
  message3 << "samplesDeriv2nd ";
  for (size_t sample = 0; sample < m_samplesDeriv2nd.size(); sample++) {
    message3 << ", [" << sample << "] = " << m_samplesDeriv2nd[sample];
  }
  (*m_msgFunc_p)(ZDCMsg::Info, message3.str());
 
  (*m_msgFunc_p)(ZDCMsg::Info, ("minimum 2nd deriv sample, value = " + std::to_string(m_minDeriv2ndIndex) + ", " + std::to_string(m_minDeriv2nd)));
}
 
void ZDCPulseAnalyzer::dumpTF1(const TF1* func) const
{
  std::string message = "Dump of TF1: " + std::string(func->GetName());
  bool continueDump = (*m_msgFunc_p)(ZDCMsg::Verbose, std::move(message));
  if (!continueDump) return;
  
  unsigned int npar = func->GetNpar();
  for (unsigned int ipar = 0; ipar < npar; ipar++) {
    std::ostringstream msgstr;
 
    double parMin = 0, parMax = 0;
    func->GetParLimits(ipar, parMin, parMax);
               
    msgstr << "Parameter " << ipar << ", value = " << func->GetParameter(ipar) << ", error = "
       << func->GetParError(ipar) << ", min = " << parMin << ", max = " << parMax;
    (*m_msgFunc_p)(ZDCMsg::Verbose, msgstr.str());
  }
}
 
void ZDCPulseAnalyzer::dumpSetting() const    // setting
{
  if (m_useDelayed) {
    (*m_msgFunc_p)(ZDCMsg::Info, ("using delayed samples with delta T = " + std::to_string(m_delayedDeltaT) + ", and pedestalDiff == " + std::to_string(m_delayedPedestalDiff)));
  }
 
  (*m_msgFunc_p)(ZDCMsg::Info, ("m_fixTau1 = " + std::to_string(m_fixTau1) + "  m_fixTau2=" + std::to_string(m_fixTau2) + "  m_nominalTau1=" + std::to_string(m_nominalTau1) + "  m_nominalTau2=" + std::to_string(m_nominalTau2) + "  m_nominalT0HG=" + std::to_string(m_nominalT0HG) + "  m_nominalT0LG=" + std::to_string(m_nominalT0LG)));
 
  (*m_msgFunc_p)(ZDCMsg::Info, ("m_defaultFitTMax = " + std::to_string(m_defaultFitTMax)));
 
  (*m_msgFunc_p)(ZDCMsg::Info, ("m_HGOverflowADC = " + std::to_string(m_HGOverflowADC) + "  m_HGUnderflowADC=" + std::to_string(m_HGUnderflowADC) + "  m_LGOverflowADC=" + std::to_string(m_LGOverflowADC)));
 
  (*m_msgFunc_p)(ZDCMsg::Info, ("m_chisqDivAmpCutLG = " + std::to_string(m_chisqDivAmpCutLG) + "  m_chisqDivAmpCutHG=" + std::to_string(m_chisqDivAmpCutHG)));
 
  (*m_msgFunc_p)(ZDCMsg::Info, ("m_T0CutLowLG = " + std::to_string(m_T0CutLowLG) + "  m_T0CutHighLG=" + std::to_string(m_T0CutHighLG) + "  m_T0CutLowHG=" + std::to_string(m_T0CutLowHG) + "  m_T0CutHighHG=" + std::to_string(m_T0CutHighHG)));
}
 
unsigned int ZDCPulseAnalyzer::GetStatusMask() const
{
  unsigned int statusMask = 0;
 
  if (HavePulse())  statusMask |= 1 << PulseBit;
  if (UseLowGain()) statusMask |= 1 << LowGainBit;
  if (Failed())     statusMask |= 1 << FailBit;
  if (HGOverflow()) statusMask |= 1 << HGOverflowBit;
 
  if (HGUnderflow())       statusMask |= 1 << HGUnderflowBit;
  if (PSHGOverUnderflow()) statusMask |= 1 << PSHGOverUnderflowBit;
  if (LGOverflow())        statusMask |= 1 << LGOverflowBit;
  if (LGUnderflow())       statusMask |= 1 << LGUnderflowBit;
 
  if (PrePulse())  statusMask |= 1 << PrePulseBit;
  if (PostPulse()) statusMask |= 1 << PostPulseBit;
  if (FitFailed()) statusMask |= 1 << FitFailedBit;
  if (BadChisq())  statusMask |= 1 << BadChisqBit;
 
  if (BadT0())          statusMask |= 1 << BadT0Bit;
  if (ExcludeEarlyLG()) statusMask |= 1 << ExcludeEarlyLGBit;
  if (ExcludeLateLG())  statusMask |= 1 << ExcludeLateLGBit;
  if (preExpTail())     statusMask |= 1 << preExpTailBit;
  if (fitMinimumAmplitude()) statusMask |= 1 << FitMinAmpBit;
  if (repassPulse()) statusMask |= 1 << RepassPulseBit;
 
  return statusMask;
}
 
std::shared_ptr<TGraphErrors> ZDCPulseAnalyzer::GetCombinedGraph(bool LGRefit) const
{
  //
  // We defer filling the histogram if we don't have a pulse until the histogram is requested
  //
  GetHistogramPtr(LGRefit);
 
  TH1* hist_p = nullptr, *delayedHist_p = nullptr;
  if (LGRefit) {
    hist_p = m_fitHistLGRefit.get();
    delayedHist_p = m_delayedHistLGRefit.get();
  }
  else {
    hist_p = m_fitHist.get();
    delayedHist_p = m_delayedHist.get();
  }
  
  std::shared_ptr<TGraphErrors> theGraph = std::make_shared<TGraphErrors>(TGraphErrors(2 * m_Nsample));
  size_t npts = 0;
 
  for (int ipt = 0; ipt < hist_p->GetNbinsX(); ipt++) {
    theGraph->SetPoint(npts, hist_p->GetBinCenter(ipt + 1), hist_p->GetBinContent(ipt + 1));
    theGraph->SetPointError(npts++, 0, hist_p->GetBinError(ipt + 1));
  }
 
  for (int iDelayPt = 0; iDelayPt < delayedHist_p->GetNbinsX(); iDelayPt++) {
    theGraph->SetPoint(npts, delayedHist_p->GetBinCenter(iDelayPt + 1), delayedHist_p->GetBinContent(iDelayPt + 1) - m_delayedBaselineShift);
    theGraph->SetPointError(npts++, 0, delayedHist_p->GetBinError(iDelayPt + 1));
  }
  if (m_havePulse) {
    TF1* func_p = static_cast<TF1*>(hist_p->GetListOfFunctions()->Last());
    if (func_p) {
      theGraph->GetListOfFunctions()->Add(new TF1(*func_p));
      hist_p->GetListOfFunctions()->SetOwner (false);
    }
  }
  theGraph->SetName(( std::string(hist_p->GetName()) + "combinaed").c_str());
 
  theGraph->SetMarkerStyle(20);
  theGraph->SetMarkerColor(1);
 
  return theGraph;
}
 
 
std::shared_ptr<TGraphErrors> ZDCPulseAnalyzer::GetGraph(bool forceLG) const
{
  //
  // We defer filling the histogram if we don't have a pulse until the histogram is requested
  //
  const TH1* hist_p = GetHistogramPtr(forceLG);
 
  std::shared_ptr<TGraphErrors> theGraph = std::make_shared<TGraphErrors>(TGraphErrors(m_Nsample));
  size_t npts = 0;
 
  for (int ipt = 0; ipt < hist_p->GetNbinsX(); ipt++) {
    theGraph->SetPoint(npts, hist_p->GetBinCenter(ipt + 1), hist_p->GetBinContent(ipt + 1));
    theGraph->SetPointError(npts++, 0, hist_p->GetBinError(ipt + 1));
  }
 
  TF1* func_p = static_cast<TF1*>(hist_p->GetListOfFunctions()->Last());
  theGraph->GetListOfFunctions()->Add(func_p);
  theGraph->SetName(( std::string(hist_p->GetName()) + "not_combinaed").c_str());
 
  theGraph->SetMarkerStyle(20);
  theGraph->SetMarkerColor(1);
 
  return theGraph;
}
 
 
std::vector<float> ZDCPulseAnalyzer::CalculateDerivative(const std::vector <float>& inputData, unsigned int step)
{
  unsigned int nSamples = inputData.size();
 
  // So we pad at the beginning and end based on step (i.e. with step - 1 zeros). Fill out the fill vector with zeros initially
  //
  unsigned int vecSize = 2*(step - 1) + nSamples - step - 1;
  std::vector<float> results(vecSize, 0);
 
  // Now fill out the values
  //
  unsigned int fillIdx = step - 1;
  
  for (unsigned int sample = 0; sample < nSamples - step; sample++) {
    int deriv = inputData[sample + step] - inputData[sample];
    results.at(fillIdx++) = deriv;
  }
 
  return results;
}
 
std::vector<float> ZDCPulseAnalyzer::Calculate2ndDerivative(const std::vector <float>& inputData, unsigned int step)
{
  unsigned int nSamples = inputData.size();
 
  // We start with two zero entries for which we can't calculate the double-step derivative
  //   and woud pad with two zero entries at the end. Start by initializing 
  //
  unsigned int vecSize = 2*step + nSamples - step - 1;
  std::vector<float> results(vecSize, 0);
 
  unsigned int fillIndex = step;
  for (unsigned int sample = step; sample < nSamples - step; sample++) {
    int deriv2nd = inputData[sample + step] + inputData[sample - step] - 2*inputData[sample];
    results.at(fillIndex++) = deriv2nd;
  }
 
  return results;
}
 
// Implement a more general method for the nasty problem (Runs 1 & 2 only) of matching
//   the baselines on the delayed and undelayed data. Instead of specifically looking
//   for early samples or late samples, find the region of the waveform with the smallest
//   combination of slope and second derivative in both sets of samples and match there.
//
// Depending on the second derivative 
//   we match using linear or (negative) exponential interpolation
//
// Note: the samples have already been combined so we distinguish by even or odd index
//  we use step = 2 for the derivative and 2nd derivative calculation to handle
//  the delayed and undelayed separately.
//
//
float ZDCPulseAnalyzer::obtainDelayedBaselineCorr(const std::vector<float>& samples)
{
  const unsigned int nsamples = samples.size();
  
  std::vector<float> derivVec = CalculateDerivative(samples, 2);
  std::vector<float> deriv2ndVec = Calculate2ndDerivative(samples, 2);
 
  // Now step through and check even and odd samples values for 2nd derivative and derivative 
  //  we start with index 2 since the 2nd derivative calculation has 2 initial zeros with nstep = 2
  //
  float minScore = 1.0e9;
  unsigned int minIndex = 0;
  
  for (unsigned int idx = 2; idx < nsamples - 1; idx++) {
    float deriv = derivVec[idx];
    float prevDeriv = derivVec[idx - 1];
 
    float derivDiff = deriv - prevDeriv;
    
    float deriv2nd = deriv2ndVec[idx];
    if (idx > nsamples - 2) deriv2nd = deriv2ndVec[idx - 1];
    
    // Calculate a score based on the actual derivatives (squared) and 2nd derivatives (squared)
    //   and the slope differences (squared). The relative weights are not adjustable for now
    //
    float score = (deriv*deriv + 2*derivDiff*derivDiff +
           0.5*deriv2nd*deriv2nd);
 
    if (score < minScore) {
      minScore = score;
      minIndex = idx;
    }
  }
 
  // We use four samples, two each of "even" and "odd".
  // Because of the way the above analysis is done, we can always
  // Go back one even and one odd sample and forward one odd sample.
  //
  //if minIndex is < 2 or >samples.size() the result is undefined; prevent this:
  if (minIndex<2 or (minIndex+1) >=nsamples){
    throw std::out_of_range("minIndex out of range in ZDCPulseAnalyzer::obtainDelayedBaselineCorr");
  }
  float sample0 = samples[minIndex - 2];
  float sample1 = samples[minIndex - 1];
  float sample2 = samples[minIndex];
  float sample3 = samples[minIndex + 1];
 
  // Possibility -- implement logarithmic interpolation for large 2nd derivative?
  //
  float baselineCorr = (0.5 * (sample1 - sample0 + sample3 - sample2) -
            0.25 * (sample3 - sample1 + sample2 - sample0));
 
  if (minIndex % 2 != 0) baselineCorr =-baselineCorr;
 
  return baselineCorr;
}