CandHitMorphological_tool.cc

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////////////////////////////////////////////////////////////////////////
/// \file   CandHitMorphological.cc
/// \author T. Usher
// MT note: This implementation is not thread-safe.
////////////////////////////////////////////////////////////////////////

#include "larreco/HitFinder/HitFinderTools/ICandidateHitFinder.h"
#include "larreco/HitFinder/HitFinderTools/IWaveformTool.h"

#include "art/Utilities/ToolMacros.h"
#include "art/Utilities/make_tool.h"
#include "art/Utilities/Globals.h"
#include "art_root_io/TFileService.h"
#include "cetlib_except/exception.h"
#include "larcore/Geometry/Geometry.h"

#include "TProfile.h"

#include <cmath>

namespace reco_tool {

  class CandHitMorphological : ICandidateHitFinder {
  public:
    explicit CandHitMorphological(const fhicl::ParameterSet& pset);

    void findHitCandidates(const recob::Wire::RegionsOfInterest_t::datarange_t&,
                           const size_t,
                           const size_t,
                           const size_t,
                           HitCandidateVec&) const override;

    void MergeHitCandidates(const recob::Wire::RegionsOfInterest_t::datarange_t&,
                            const HitCandidateVec&,
                            MergeHitCandidateVec&) const override;

  private:
    // Internal functions
    //< Top level hit finding using erosion/dilation vectors
    void findHitCandidates(Waveform::const_iterator,
                           Waveform::const_iterator, //< derivative
                           Waveform::const_iterator,
                           Waveform::const_iterator, //< erosion
                           Waveform::const_iterator,
                           Waveform::const_iterator, //< dilation
                           const size_t,
                           float,
                           HitCandidateVec&) const;

    //< Fine grain hit finding within candidate peak regions using derivative method
    void findHitCandidates(Waveform::const_iterator,
                           Waveform::const_iterator,
                           const size_t,
                           int,
                           float,
                           HitCandidateVec&) const;

    //< For a given range, return the list of max/min pairs
    using MaxMinPair = std::pair<Waveform::const_iterator, Waveform::const_iterator>;
    using CandHitParams = std::tuple<Waveform::const_iterator,
                                     Waveform::const_iterator,
                                     Waveform::const_iterator,
                                     Waveform::const_iterator>;
    using CandHitParamsVec = std::vector<CandHitParams>;

    bool getListOfHitCandidates(Waveform::const_iterator,
                                Waveform::const_iterator,
                                int,
                                float,
                                CandHitParamsVec&) const;

    // Finding the nearest maximum/minimum from current point
    Waveform::const_iterator findNearestMax(Waveform::const_iterator,
                                            Waveform::const_iterator) const;
    Waveform::const_iterator findNearestMin(Waveform::const_iterator,
                                            Waveform::const_iterator) const;

    // handle finding the "start" and "stop" of a candidate hit
    Waveform::const_iterator findStartTick(Waveform::const_iterator,
                                           Waveform::const_iterator) const;
    Waveform::const_iterator findStopTick(Waveform::const_iterator, Waveform::const_iterator) const;

    // some fhicl control variables
    const size_t fPlane;               //< Identifies the plane this tool is meant to operate on
    const float fDilationThreshold;    //< Dilation threshold
    const float fDilationFraction;     //< Fraction of max dilation to set for min dilation
    const float fErosionFraction;      //< Fraction of max dilation value to set min erosion
    const int fMinDeltaTicks;          //< minimum ticks from max to min to consider
    const float fMinDeltaPeaks;        //< minimum maximum to minimum peak distance
    const float fMinHitHeight;         //< Drop candidate hits with height less than this
    const size_t fNumInterveningTicks; //< Number ticks between candidate hits to merge
    const int fStructuringElement;     //< Window size for morphologcial filter
    const bool fOutputHistograms;      //< If true will generate summary style histograms
    const bool
      fOutputWaveforms; //< If true will output waveform related info <<< very big output file!
    const float
      fFitNSigmaFromCenter; //< Limit ticks to fit to NSigma from hit center; not applied if zero or negative

    art::TFileDirectory* fHistDirectory;

    // Global histograms
    TH1F* fDStopStartHist;        //< Basically keeps track of the length of hit regions
    TH1F* fDMaxTickMinTickHist;   //< This will be a measure of the width of candidate hits
    TH1F* fDMaxDerivMinDerivHist; //< This is the difference peak to peak of derivative for cand hit
    TH1F* fMaxErosionHist;        //< Keep track of the maximum erosion
    TH1F* fMaxDilationHist;       //< Keep track of the maximum dilation
    TH1F* fMaxDilEroRatHist;      //< Ratio of the maxima of the two

    //MT note: The mutable data members are only used in the histogram filling functions
    //and histogram filling can only be done in single-threaded mode.
    //Will need to consider design changes if this behavior changes.
    mutable size_t
      fLastChannel; //< Kludge to keep track of last channel when histogramming in effect
    mutable size_t fChannelCnt; //< Counts the number of times a channel is used (assumed in order)

    //< All of the real work is done in the waveform tool
    std::unique_ptr<reco_tool::IWaveformTool> fWaveformTool;

    const geo::GeometryCore* fGeometry = lar::providerFrom<geo::Geometry>();
  };

  //----------------------------------------------------------------------
  // Constructor.
  CandHitMorphological::CandHitMorphological(const fhicl::ParameterSet& pset)
    : fPlane(pset.get<size_t>("Plane", 0))
    , fDilationThreshold(pset.get<float>("DilationThreshold", 4.))
    , fDilationFraction(pset.get<float>("DilationFraction", 0.75))
    , fErosionFraction(pset.get<float>("ErosionFraction", 0.2))
    , fMinDeltaTicks(pset.get<int>("MinDeltaTicks", 0))
    , fMinDeltaPeaks(pset.get<float>("MinDeltaPeaks", 0.025))
    , fMinHitHeight(pset.get<float>("MinHitHeight", 1.0))
    , fNumInterveningTicks(pset.get<size_t>("NumInterveningTicks", 6))
    , fStructuringElement(pset.get<int>("StructuringElement", 20))
    , fOutputHistograms(pset.get<bool>("OutputHistograms", false))
    , fOutputWaveforms(pset.get<bool>("OutputWaveforms", false))
    , fFitNSigmaFromCenter(pset.get<float>("FitNSigmaFromCenter", 5.))
  {

    if (art::Globals::instance()->nthreads() > 1u) {
      if (fOutputHistograms) {
        throw art::Exception(art::errors::Configuration)
          << "Cannot fill histograms when multiple threads configured, please set "
             "fOutputHistograms to false or change number of threads to 1\n";
      }

      if (fOutputWaveforms) {
        throw art::Exception(art::errors::Configuration)
          << "Cannot write output waveforms when multiple threads configured, please set "
             "fOutputHistograms to false or change number of threads to 1\n";
      }
    }
    // Recover the baseline tool
    fWaveformTool =
      art::make_tool<reco_tool::IWaveformTool>(pset.get<fhicl::ParameterSet>("WaveformAlgs"));

    // Set the last channel to some nonsensical value
    fLastChannel = std::numeric_limits<size_t>::max();
    fChannelCnt = 0;

    // If asked, define the global histograms
    if (fOutputHistograms) {
      // Access ART's TFileService, which will handle creating and writing
      // histograms and n-tuples for us.
      art::ServiceHandle<art::TFileService> tfs;

      fHistDirectory = tfs.get();

      // Make a directory for these histograms
      art::TFileDirectory dir = fHistDirectory->mkdir(Form("HitPlane_%1zu", fPlane));

      fDStopStartHist =
        dir.make<TH1F>(Form("DStopStart_%1zu", fPlane), ";Delta Stop/Start;", 100, 0., 100.);
      fDMaxTickMinTickHist =
        dir.make<TH1F>(Form("DMaxTMinT_%1zu", fPlane), ";Delta Max/Min Tick;", 100, 0., 100.);
      fDMaxDerivMinDerivHist =
        dir.make<TH1F>(Form("DMaxDMinD_%1zu", fPlane), ";Delta Max/Min Deriv;", 200, 0., 100.);
      fMaxErosionHist =
        dir.make<TH1F>(Form("MaxErosion_%1zu", fPlane), ";Max Erosion;", 200, -50., 150.);
      fMaxDilationHist =
        dir.make<TH1F>(Form("MaxDilation_%1zu", fPlane), ";Max Dilation;", 200, -50., 150.);
      fMaxDilEroRatHist =
        dir.make<TH1F>(Form("MaxDilEroRat_%1zu", fPlane), ";Max Dil/Ero;", 200, -1., 1.);
    }

    return;
  }

  void
  CandHitMorphological::findHitCandidates(
    const recob::Wire::RegionsOfInterest_t::datarange_t& dataRange,
    const size_t roiStartTick,
    const size_t channel,
    const size_t eventCount,
    HitCandidateVec& hitCandidateVec) const
  {
    // In this case we want to find hit candidates based on the derivative of of the input waveform
    // We get this from our waveform algs too...
    Waveform rawDerivativeVec;
    Waveform derivativeVec;

    // Recover the actual waveform
    const Waveform& waveform = dataRange.data();

    fWaveformTool->firstDerivative(waveform, rawDerivativeVec);
    fWaveformTool->triangleSmooth(rawDerivativeVec, derivativeVec);

    // Now we get the erosion/dilation vectors
    Waveform erosionVec;
    Waveform dilationVec;
    Waveform averageVec;
    Waveform differenceVec;

    reco_tool::HistogramMap histogramMap;

    // Compute the morphological filter vectors
    fWaveformTool->getErosionDilationAverageDifference(waveform,
                                                       fStructuringElement,
                                                       histogramMap,
                                                       erosionVec,
                                                       dilationVec,
                                                       averageVec,
                                                       differenceVec);

    // Now find the hits
    findHitCandidates(derivativeVec.begin(),
                      derivativeVec.end(),
                      erosionVec.begin(),
                      erosionVec.end(),
                      dilationVec.begin(),
                      dilationVec.end(),
                      roiStartTick,
                      fDilationThreshold,
                      hitCandidateVec);

    // Limit start and stop tick to the neighborhood of the peak
    if (fFitNSigmaFromCenter > 0) {
      for (auto& hc : hitCandidateVec) {
        auto startCand = hc.hitCenter - fFitNSigmaFromCenter * hc.hitSigma;
        if (startCand >= 0) hc.startTick = std::max(hc.startTick, size_t(startCand));
        hc.stopTick =
          std::min(hc.stopTick, size_t(hc.hitCenter + fFitNSigmaFromCenter * hc.hitSigma));
      }
    }

    // Reset the hit height from the input waveform
    for (auto& hitCandidate : hitCandidateVec) {
      size_t centerIdx = hitCandidate.hitCenter;

      hitCandidate.hitHeight = waveform.at(centerIdx);
    }

    // Keep track of histograms if requested
    if (fOutputWaveforms) {
      // Recover the details...
      std::vector<geo::WireID> wids = fGeometry->ChannelToWire(channel);
      size_t plane = wids[0].Plane;
      size_t cryo = wids[0].Cryostat;
      size_t tpc = wids[0].TPC;
      size_t wire = wids[0].Wire;

      if (channel != fLastChannel) fChannelCnt = 0;

      // Make a directory for these histograms
      art::TFileDirectory dir = fHistDirectory->mkdir(
        Form("Event%04zu/c%1zuT%1zuP%1zu/Wire_%05zu", eventCount, cryo, tpc, plane, wire));

      size_t waveformSize = waveform.size();
      size_t waveStart = dataRange.begin_index();

      TProfile* waveHist =
        dir.make<TProfile>(Form("HWfm_%03zu_roiStart-%05zu", fChannelCnt, waveStart),
                           "Waveform",
                           waveformSize,
                           0,
                           waveformSize,
                           -500.,
                           500.);
      TProfile* derivHist =
        dir.make<TProfile>(Form("HDer_%03zu_roiStart-%05zu", fChannelCnt, waveStart),
                           "Derivative",
                           waveformSize,
                           0,
                           waveformSize,
                           -500.,
                           500.);
      TProfile* erosionHist =
        dir.make<TProfile>(Form("HEro_%03zu_roiStart-%05zu", fChannelCnt, waveStart),
                           "Erosion",
                           waveformSize,
                           0,
                           waveformSize,
                           -500.,
                           500.);
      TProfile* dilationHist =
        dir.make<TProfile>(Form("HDil_%03zu_roiStart-%05zu", fChannelCnt, waveStart),
                           "Dilation",
                           waveformSize,
                           0,
                           waveformSize,
                           -500.,
                           500.);
      TProfile* candHitHist =
        dir.make<TProfile>(Form("HCan_%03zu_roiStart-%05zu", fChannelCnt, waveStart),
                           "Cand Hits",
                           waveformSize,
                           0,
                           waveformSize,
                           -500.,
                           500.);
      TProfile* maxDerivHist =
        dir.make<TProfile>(Form("HMax_%03zu_roiStart-%05zu", fChannelCnt, waveStart),
                           "Maxima",
                           waveformSize,
                           0,
                           waveformSize,
                           -500.,
                           500.);
      TProfile* strtStopHist =
        dir.make<TProfile>(Form("HSSS_%03zu_roiStart-%05zu", fChannelCnt, waveStart),
                           "Start/Stop",
                           waveformSize,
                           0,
                           waveformSize,
                           -500.,
                           500.);

      // Fill wave/derivative
      for (size_t idx = 0; idx < waveform.size(); idx++) {
        waveHist->Fill(roiStartTick + idx, waveform.at(idx));
        derivHist->Fill(roiStartTick + idx, derivativeVec.at(idx));
        erosionHist->Fill(roiStartTick + idx, erosionVec.at(idx));
        dilationHist->Fill(roiStartTick + idx, dilationVec.at(idx));
      }

      // Fill hits
      for (const auto& hitCandidate : hitCandidateVec) {
        candHitHist->Fill(hitCandidate.hitCenter, hitCandidate.hitHeight);
        maxDerivHist->Fill(hitCandidate.maxTick, hitCandidate.maxDerivative);
        maxDerivHist->Fill(hitCandidate.minTick, hitCandidate.minDerivative);
        strtStopHist->Fill(hitCandidate.startTick, waveform.at(hitCandidate.startTick));
        strtStopHist->Fill(hitCandidate.stopTick, waveform.at(hitCandidate.stopTick));
      }

      fLastChannel = channel;
      fChannelCnt++;
    }

    if (fOutputHistograms) {
      // Fill hits
      for (const auto& hitCandidate : hitCandidateVec) {
        fDStopStartHist->Fill(hitCandidate.stopTick - hitCandidate.startTick, 1.);
        fDMaxTickMinTickHist->Fill(hitCandidate.minTick - hitCandidate.maxTick, 1.);
        fDMaxDerivMinDerivHist->Fill(hitCandidate.maxDerivative - hitCandidate.minDerivative, 1.);
      }

      // Get the max dilation/erosion
      Waveform::const_iterator maxDilationItr =
        std::max_element(dilationVec.begin(), dilationVec.end());
      Waveform::const_iterator maxErosionItr =
        std::max_element(erosionVec.begin(), erosionVec.end());

      float dilEroRat(1.);

      if (std::abs(*maxDilationItr) > 0.) dilEroRat = *maxErosionItr / *maxDilationItr;

      fMaxErosionHist->Fill(*maxErosionItr, 1.);
      fMaxDilationHist->Fill(*maxDilationItr, 1.);
      fMaxDilEroRatHist->Fill(dilEroRat, 1.);
    }

    return;
  }

  void
  CandHitMorphological::findHitCandidates(Waveform::const_iterator derivStartItr,
                                          Waveform::const_iterator derivStopItr,
                                          Waveform::const_iterator erosionStartItr,
                                          Waveform::const_iterator erosionStopItr,
                                          Waveform::const_iterator dilationStartItr,
                                          Waveform::const_iterator dilationStopItr,
                                          const size_t roiStartTick,
                                          float dilationThreshold,
                                          HitCandidateVec& hitCandidateVec) const
  {
    // This function aims to use the erosion/dilation vectors to find candidate hit regions
    // Once armed with a region then the "standard" differential approach is used to return the candidate peaks

    // Don't do anything if not enough ticks
    int ticksInInputWaveform = std::distance(derivStartItr, derivStopItr);

    if (ticksInInputWaveform < fMinDeltaTicks) return;

    // This function is recursive, we start by finding the largest element of the dilation vector
    Waveform::const_iterator maxItr = std::max_element(dilationStartItr, dilationStopItr);
    float maxVal = *maxItr;

    // Check that the peak is of reasonable height...
    if (maxVal < dilationThreshold) return;

    int maxBin = std::distance(dilationStartItr, maxItr);

    // The candidate hit region we want lies between the two nearest minima to the maximum we just found
    // subject to the condition that the erosion vector has return to less than zero
    Waveform::const_iterator firstDerItr = derivStartItr + maxBin;
    Waveform::const_iterator erosionItr = erosionStartItr + maxBin;

    float firstDerivValue = -1.;
    float erosionCutValue = fErosionFraction * maxVal;

    // Search for starting point
    while (firstDerItr != derivStartItr) {
      // Look for the turnover point
      if (*erosionItr-- < erosionCutValue) {
        // We are looking for the zero crossing signifying a minimum value in the waveform
        // (so the previous derivative < 0 while current is > 0)
        // We are moving "backwards" so the current value <= 0, the previous value > 0
        if (*firstDerItr * firstDerivValue <= 0. && firstDerivValue > 0.) break;
      }

      firstDerivValue = *firstDerItr--;
    }

    // Set the start bin
    int hitRegionStart = std::distance(derivStartItr, firstDerItr);

    // Now go the other way
    Waveform::const_iterator lastDerItr = derivStartItr + maxBin;

    // Reset the local variables
    float lastDerivValue = 1.;

    erosionItr = erosionStartItr + maxBin;

    // Search for starting point
    while (lastDerItr != derivStopItr) {
      if (*erosionItr++ <= erosionCutValue) {
        // We are again looking for the zero crossing signifying a minimum value in the waveform
        // This time we are moving forward, so test is that previous value < 0, new value >= 0
        if (*lastDerItr * lastDerivValue <= 0. && lastDerivValue < 0.) break;
      }

      lastDerivValue = *lastDerItr++;
    }

    // Set the stop bin
    int hitRegionStop = std::distance(derivStartItr, lastDerItr);

    // Recursive call to find any hits in front of where we are now
    if (hitRegionStart > fMinDeltaTicks)
      findHitCandidates(derivStartItr,
                        derivStartItr + hitRegionStart,
                        erosionStartItr,
                        erosionStartItr + hitRegionStart,
                        dilationStartItr,
                        dilationStartItr + hitRegionStart,
                        roiStartTick,
                        fDilationThreshold,
                        hitCandidateVec);

    // Call the differential hit finding to get the actual hits within the region
    findHitCandidates(derivStartItr + hitRegionStart,
                      derivStartItr + hitRegionStop,
                      roiStartTick + hitRegionStart,
                      fMinDeltaTicks,
                      fMinDeltaPeaks,
                      hitCandidateVec);

    // Now call ourselves again to find any hits trailing the region we just identified
    if (std::distance(lastDerItr, derivStopItr) > fMinDeltaTicks)
      findHitCandidates(derivStartItr + hitRegionStop,
                        derivStopItr,
                        erosionStartItr + hitRegionStop,
                        erosionStopItr,
                        dilationStartItr + hitRegionStop,
                        dilationStopItr,
                        roiStartTick + hitRegionStop,
                        fDilationThreshold,
                        hitCandidateVec);

    return;
  }

  void
  CandHitMorphological::findHitCandidates(Waveform::const_iterator startItr,
                                          Waveform::const_iterator stopItr,
                                          const size_t roiStartTick,
                                          int dTicksThreshold,
                                          float dPeakThreshold,
                                          HitCandidateVec& hitCandidateVec) const
  {
    // Search for candidate hits...
    // Strategy is to get the list of all possible max/min pairs of the input derivative vector and then
    // look for candidate hits in that list
    CandHitParamsVec candHitParamsVec;

    if (getListOfHitCandidates(
          startItr, stopItr, dTicksThreshold, dPeakThreshold, candHitParamsVec)) {
      // We've been given a list of candidate hits so now convert to hits
      // Version one... simply convert all the candidates
      for (const auto& tuple : candHitParamsVec) {
        // Create a new hit candidate and store away
        HitCandidate hitCandidate;

        Waveform::const_iterator candStartItr = std::get<0>(tuple);
        Waveform::const_iterator maxItr = std::get<1>(tuple);
        Waveform::const_iterator minItr = std::get<2>(tuple);
        Waveform::const_iterator candStopItr = std::get<3>(tuple);

        Waveform::const_iterator peakItr =
          std::min_element(maxItr, minItr, [](const auto& left, const auto& right) {
            return std::fabs(left) < std::fabs(right);
          });

        // Check balance
        if (2 * std::distance(peakItr, minItr) < std::distance(maxItr, peakItr))
          peakItr--;
        else if (2 * std::distance(maxItr, peakItr) < std::distance(peakItr, minItr))
          peakItr++;

        // Special handling of the start tick for multiple hits
        size_t hitCandidateStartTick = roiStartTick + std::distance(startItr, candStartItr);

        if (!hitCandidateVec.empty()) {
          int deltaTicks = hitCandidateStartTick - hitCandidateVec.back().stopTick;

          if (deltaTicks > 0) {
            hitCandidateStartTick -= deltaTicks / 2;
            hitCandidateVec.back().stopTick += deltaTicks / 2;
          }
        }

        hitCandidate.startTick = hitCandidateStartTick;
        hitCandidate.stopTick = roiStartTick + std::distance(startItr, candStopItr);
        hitCandidate.maxTick = roiStartTick + std::distance(startItr, maxItr);
        hitCandidate.minTick = roiStartTick + std::distance(startItr, minItr);
        hitCandidate.maxDerivative = maxItr != stopItr ? *maxItr : 0.;
        hitCandidate.minDerivative = minItr != stopItr ? *minItr : 0.;
        hitCandidate.hitCenter = roiStartTick + std::distance(startItr, peakItr) + 0.5;
        hitCandidate.hitSigma = 0.5 * float(hitCandidate.minTick - hitCandidate.maxTick);
        hitCandidate.hitHeight = hitCandidate.hitSigma *
                                 (hitCandidate.maxDerivative - hitCandidate.minDerivative) / 1.2130;

        hitCandidateVec.push_back(hitCandidate);
      }
    }

    //    // The idea will be to find the largest deviation in the input derivative waveform as the starting point. Depending
    //    // on if a maximum or minimum, we search forward or backward to find the minimum or maximum that our extremum
    //    // corresponds to.
    //    std::pair<Waveform::const_iterator, Waveform::const_iterator> minMaxPair = std::minmax_element(startItr, stopItr);
    //
    //    Waveform::const_iterator maxItr = minMaxPair.second;
    //    Waveform::const_iterator minItr = minMaxPair.first;
    //
    //    // Use the larger of the two as the starting point and recover the nearest max or min
    //    if (std::fabs(*maxItr) > std::fabs(*minItr)) minItr = findNearestMin(maxItr, stopItr);
    //    else                                         maxItr = findNearestMax(minItr,startItr);
    //
    //    int   deltaTicks = std::distance(maxItr,minItr);
    //    float range      = *maxItr - *minItr;
    //
    //    // At some point small rolling oscillations on the waveform need to be ignored...
    //    if (deltaTicks >= dTicksThreshold && range > dPeakThreshold)
    //    {
    //        // Need to back up to find zero crossing, this will be the starting point of our
    //        // candidate hit but also the endpoint of the pre sub-waveform we'll search next
    //        Waveform::const_iterator newEndItr = findStartTick(maxItr, startItr);
    //
    //        int startTick = std::distance(startItr,newEndItr);
    //
    //        // Now need to go forward to again get close to zero, this will then be the end point
    //        // of our candidate hit and the starting point for the post sub-waveform to search
    //        Waveform::const_iterator newStartItr = findStopTick(minItr, stopItr);
    //
    //        int stopTick = std::distance(startItr,newStartItr);
    //
    //        // Find hits in the section of the waveform leading up to this candidate hit
    //        if (startTick > 2)
    //        {
    //            // Special handling for merged hits
    //            if (*(newEndItr-1) > 0.) {dTicksThreshold = 2;              dPeakThreshold = 0.;            }
    //            else                     {dTicksThreshold = fMinDeltaTicks; dPeakThreshold = fMinDeltaPeaks;}
    //
    //            findHitCandidates(startItr,newEndItr+1,roiStartTick,dTicksThreshold,dPeakThreshold,hitCandidateVec);
    //        }
    //
    //        // Create a new hit candidate and store away
    //        HitCandidate_t hitCandidate;
    //
    //        Waveform::const_iterator peakItr = std::min_element(maxItr,minItr,[](const auto& left, const auto& right){return std::fabs(left) < std::fabs(right);});
    //
    //        // Check balance
    //        if      (2 * std::distance(peakItr,minItr) < std::distance(maxItr,peakItr)) peakItr--;
    //        else if (2 * std::distance(maxItr,peakItr) < std::distance(peakItr,minItr)) peakItr++;
    //
    //        // Special handling of the start tick for multiple hits
    //        size_t hitCandidateStartTick = roiStartTick + startTick;
    //
    //        if (!hitCandidateVec.empty())
    //        {
    //            int deltaTicks = hitCandidateStartTick - hitCandidateVec.back().stopTick;
    //
    //            if (deltaTicks > 0)
    //            {
    //                hitCandidateStartTick           -= deltaTicks / 2;
    //                hitCandidateVec.back().stopTick += deltaTicks / 2;
    //            }
    //        }
    //
    //        hitCandidate.startTick     = hitCandidateStartTick;
    //        hitCandidate.stopTick      = roiStartTick + stopTick;
    //        hitCandidate.maxTick       = roiStartTick + std::distance(startItr,maxItr);
    //        hitCandidate.minTick       = roiStartTick + std::distance(startItr,minItr);
    //        hitCandidate.maxDerivative = maxItr != stopItr ? *maxItr : 0.;
    //        hitCandidate.minDerivative = minItr != stopItr ? *minItr : 0.;
    //        hitCandidate.hitCenter     = roiStartTick + std::distance(startItr,peakItr) + 0.5;
    //        hitCandidate.hitSigma      = 0.5 * float(hitCandidate.minTick - hitCandidate.maxTick);
    //        hitCandidate.hitHeight     = hitCandidate.hitSigma * (hitCandidate.maxDerivative - hitCandidate.minDerivative) / 1.2130;
    //
    //        hitCandidateVec.push_back(hitCandidate);
    //
    //        // Finally, search the section of the waveform following this candidate for more hits
    //        if (std::distance(newStartItr,stopItr) > 2)
    //        {
    //            // Special handling for merged hits
    //            if (*(newStartItr+1) < 0.) {dTicksThreshold = 2;              dPeakThreshold = 0.;            }
    //            else                       {dTicksThreshold = fMinDeltaTicks; dPeakThreshold = fMinDeltaPeaks;}
    //
    //            findHitCandidates(newStartItr,stopItr,roiStartTick + stopTick,dTicksThreshold,dPeakThreshold,hitCandidateVec);
    //        }
    //    }

    return;
  }

  bool
  CandHitMorphological::getListOfHitCandidates(Waveform::const_iterator startItr,
                                               Waveform::const_iterator stopItr,
                                               int dTicksThreshold,
                                               float dPeakThreshold,
                                               CandHitParamsVec& candHitParamsVec) const
  {
    // We'll check if any of our candidates meet the requirements so declare the result here
    bool foundCandidate(false);

    int dTicks = std::distance(startItr, stopItr);

    // Search for candidate hits...
    // But only if enough ticks
    if (dTicks < fMinDeltaTicks) return foundCandidate;

    // Generally, the mission is simple... the goal is to find all possible combinations of maximum/minimum pairs in
    // the input (presumed) derivative waveform. We can do this with a divice and conquer approach where we start by
    // finding the largerst max or min and start from there
    MaxMinPair minMaxPair = std::minmax_element(startItr, stopItr);

    Waveform::const_iterator maxItr = minMaxPair.second;
    Waveform::const_iterator minItr = minMaxPair.first;

    // Use the larger of the two as the starting point and recover the nearest max or min
    if (std::fabs(*maxItr) > std::fabs(*minItr))
      minItr = findNearestMin(maxItr, stopItr);
    else
      maxItr = findNearestMax(minItr, startItr);

    int deltaTicks = std::distance(maxItr, minItr);
    float range = *maxItr - *minItr;

    if (deltaTicks < 2) return foundCandidate;

    // Check if this particular max/min pair would meet the requirements...
    if (deltaTicks >= dTicksThreshold && range > dPeakThreshold) foundCandidate = true;

    // Need to back up to find zero crossing, this will be the starting point of our
    // candidate hit but also the endpoint of the pre sub-waveform we'll search next
    Waveform::const_iterator candStartItr = findStartTick(maxItr, startItr);

    // Now need to go forward to again get close to zero, this will then be the end point
    // of our candidate hit and the starting point for the post sub-waveform to search
    Waveform::const_iterator candStopItr = findStopTick(minItr, stopItr);

    // Call ourself to find hit candidates preceding this one
    bool prevTicks = getListOfHitCandidates(
      startItr, candStartItr, dTicksThreshold, dPeakThreshold, candHitParamsVec);

    // The above call will have populated the list of candidate max/min pairs preceding this one, so now add our contribution
    candHitParamsVec.emplace_back(candStartItr, maxItr, minItr, candStopItr);

    // Now catch any that might follow this one
    bool postTicks = getListOfHitCandidates(
      candStopItr, stopItr, dTicksThreshold, dPeakThreshold, candHitParamsVec);

    return foundCandidate || prevTicks || postTicks;
  }

  void
  CandHitMorphological::MergeHitCandidates(
    const recob::Wire::RegionsOfInterest_t::datarange_t& rangeData,
    const HitCandidateVec& hitCandidateVec,
    MergeHitCandidateVec& mergedHitsVec) const
  {
    // If nothing on the input end then nothing to do
    if (hitCandidateVec.empty()) return;

    // The idea is to group hits that "touch" so they can be part of common fit, those that
    // don't "touch" are fit independently. So here we build the output vector to achieve that
    // Get a container for the hits...
    HitCandidateVec groupedHitVec;

    // Initialize the end of the last hit which we'll set to the first input hit's stop
    size_t lastStopTick = hitCandidateVec.front().stopTick;

    // Step through the input hit candidates and group them by proximity
    for (const auto& hitCandidate : hitCandidateVec) {
      // Small pulse height hits should not be considered?
      if (hitCandidate.hitHeight > fMinHitHeight) {
        // Check condition that we have a new grouping
        if (hitCandidate.startTick > lastStopTick + fNumInterveningTicks &&
            !groupedHitVec.empty()) {
          mergedHitsVec.emplace_back(groupedHitVec);

          groupedHitVec.clear();
        }

        // Add the current hit to the current group
        groupedHitVec.emplace_back(hitCandidate);

        lastStopTick = hitCandidate.stopTick;
      }
    }

    // Check end condition
    if (!groupedHitVec.empty()) mergedHitsVec.emplace_back(groupedHitVec);

    return;
  }

  ICandidateHitFinder::Waveform::const_iterator
  CandHitMorphological::findNearestMin(Waveform::const_iterator maxItr,
                                       Waveform::const_iterator stopItr) const
  {
    // reset the min iterator and search forward to find the nearest minimum
    Waveform::const_iterator lastItr = maxItr;

    // The strategy is simple...
    // We are at a maximum so we search forward until we find the lowest negative point
    while ((lastItr + 1) != stopItr) {
      if (*(lastItr + 1) > *lastItr) break;

      lastItr++;
    }

    // The minimum will be the last iterator value...
    return lastItr;
  }

  ICandidateHitFinder::Waveform::const_iterator
  CandHitMorphological::findNearestMax(Waveform::const_iterator minItr,
                                       Waveform::const_iterator startItr) const
  {
    // Set the internal loop variable...
    Waveform::const_iterator lastItr = minItr;

    // One extra condition to watch for here, make sure we can actually back up!
    if (std::distance(startItr, minItr) > 0) {
      // Similar to searching for a maximum, we loop backward over ticks looking for the waveform to start decreasing
      while ((lastItr - 1) != startItr) {
        if (*(lastItr - 1) < *lastItr) break;

        lastItr--;
      }
    }

    return lastItr;
  }

  ICandidateHitFinder::Waveform::const_iterator
  CandHitMorphological::findStartTick(Waveform::const_iterator maxItr,
                                      Waveform::const_iterator startItr) const
  {
    Waveform::const_iterator lastItr = maxItr;

    // If we can't back up then there is nothing to do
    if (std::distance(startItr, lastItr) > 0) {
      // In theory, we are starting at a maximum and want to find the "start" of the candidate peak
      // Ideally we would look to search backward to the point where the (derivative) waveform crosses zero again.
      // However, the complication is that we need to watch for the case where two peaks are merged together and
      // we might run through another peak before crossing zero...
      // So... loop until we hit the startItr...
      Waveform::const_iterator loopItr = lastItr - 1;

      while (loopItr != startItr) {
        // Ideal world case, we cross zero... but we might encounter a minimum... or an inflection point
        if (*loopItr < 0. || !(*loopItr < *lastItr)) break;

        lastItr = loopItr--;
      }
    }
    else
      lastItr = startItr;

    return lastItr;
  }

  ICandidateHitFinder::Waveform::const_iterator
  CandHitMorphological::findStopTick(Waveform::const_iterator minItr,
                                     Waveform::const_iterator stopItr) const
  {
    Waveform::const_iterator lastItr = minItr;

    // If we can't go forward then there is really nothing to do
    if (std::distance(minItr, stopItr) > 1) {
      // Pretty much the same strategy as for finding the start tick...
      Waveform::const_iterator loopItr = lastItr + 1;

      while (loopItr != stopItr) {
        // Ideal case that we have crossed zero coming from a minimum... but watch for a maximum as well
        if (*loopItr > 0. || !(*loopItr > *lastItr)) break;

        lastItr = loopItr++;
      }
    }

    return lastItr;
  }

  DEFINE_ART_CLASS_TOOL(CandHitMorphological)
}