SeedFinderAlgorithm.cxx

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//
// Name: SeedFinderAlgorithm.cxx
//
// Purpose: Implementation file for module SeedFinderAlgorithm.
//
// Ben Jones, MIT
//

#include <stdint.h>

#include "art/Framework/Principal/Event.h"
#include "art/Framework/Services/Registry/ServiceHandle.h"
#include "canvas/Utilities/Exception.h"
#include "messagefacility/MessageLogger/MessageLogger.h"

#include "larcore/Geometry/Geometry.h"
#include "larcore/Geometry/WireReadout.h"
#include "larcorealg/Geometry/PlaneGeo.h"
#include "lardata/DetectorInfoServices/DetectorPropertiesService.h"
#include "lardataobj/RecoBase/Hit.h"
#include "lardataobj/RecoBase/Seed.h"
#include "lardataobj/RecoBase/SpacePoint.h"
#include "larreco/RecoAlg/SeedFinderAlgorithm.h"
#include "larreco/RecoAlg/SpacePointAlg.h"

namespace trkf {

  //----------------------------------------------------------------------------
  SeedFinderAlgorithm::SeedFinderAlgorithm(const fhicl::ParameterSet& pset)
  {
    fSptalg = new trkf::SpacePointAlg(pset.get<fhicl::ParameterSet>("SpacePointAlg"));

    fInitSeedLength = pset.get<double>("InitSeedLength");
    fMinPointsInSeed = pset.get<int>("MinPointsInSeed");

    fRefits = pset.get<double>("Refits");

    fHitResolution = pset.get<double>("HitResolution");

    fOccupancyCut = pset.get<double>("OccupancyCut");
    fLengthCut = pset.get<double>("LengthCut");
    fExtendSeeds = pset.get<bool>("ExtendSeeds");

    fAllow2DSeeds = pset.get<bool>("Allow2DSeeds", false);

    fMaxViewRMS.resize(3);
    fMaxViewRMS = pset.get<std::vector<double>>("MaxViewRMS");

    CalculateGeometricalElements();
  }

  //------------------------------------------------------------
  // Given a set of spacepoints, find seeds, and catalogue
  //  spacepoints by the seeds they formed
  //
  std::vector<recob::Seed> SeedFinderAlgorithm::FindSeeds(
    detinfo::DetectorClocksData const& clockData,
    detinfo::DetectorPropertiesData const& detProp,
    art::PtrVector<recob::Hit> const& HitsFlat,
    std::vector<art::PtrVector<recob::Hit>>& CataloguedHits,
    unsigned int StopAfter) const
  {
    // Vector of seeds found to return
    std::vector<recob::Seed> ReturnVector;

    // First check if there is any overlap
    std::vector<recob::SpacePoint> spts;

    fSptalg->clearHitMap();
    fSptalg->makeSpacePoints(clockData, detProp, HitsFlat, spts);

    if (int(spts.size()) < fMinPointsInSeed) { return std::vector<recob::Seed>(); }

    // If we got here, we have enough spacepoints to potentially make seeds from these hits.

    // This is table will let us quickly look up which hits are in a given view / channel.
    //  structure is OrgHits[View][Channel] = {index1,index2...}
    // where the indices are of HitsFlat[index].

    std::vector<std::vector<std::vector<int>>> OrgHits(3);
    for (size_t n = 0; n != 3; ++n)
      OrgHits[n].resize(fNChannels);

    // These two tables contain the hit to spacepoint mappings

    std::vector<std::vector<int>> SpacePointsPerHit(HitsFlat.size(), std::vector<int>());
    std::vector<std::vector<int>> HitsPerSpacePoint(spts.size(), std::vector<int>());

    // This vector records the status of each hit.
    // The possible values are:
    //  0. hit unused
    //  1. hit used in a seed
    // Initially none are used.

    std::vector<char> HitStatus(HitsFlat.size(), 0);

    // Fill the organizing map

    for (size_t i = 0; i != HitsFlat.size(); ++i) {
      OrgHits[HitsFlat.at(i)->View()][HitsFlat.at(i)->Channel()].push_back(i);
    }

    // Fill the spacepoint / hit lookups

    for (size_t iSP = 0; iSP != spts.size(); ++iSP) {
      art::PtrVector<recob::Hit> HitsThisSP = fSptalg->getAssociatedHits(spts.at(iSP));

      for (size_t iH = 0; iH != HitsThisSP.size(); ++iH) {
        geo::View_t ThisView = HitsThisSP.at(iH)->View();
        uint32_t ThisChannel = HitsThisSP.at(iH)->Channel();
        float ThisTime = HitsThisSP.at(iH)->PeakTime();
        float eta = 0.001;

        for (size_t iOrg = 0; iOrg != OrgHits[ThisView][ThisChannel].size(); ++iOrg) {
          if (fabs(ThisTime - HitsFlat.at(OrgHits[ThisView][ThisChannel][iOrg])->PeakTime()) <
              eta) {
            SpacePointsPerHit.at(OrgHits[ThisView][ThisChannel][iOrg]).push_back(iSP);
            HitsPerSpacePoint.at(iSP).push_back(OrgHits[ThisView][ThisChannel][iOrg]);
          }
        }
      }
    }

    // The general idea will be:
    //  A. Make spacepoints from remaining hits
    //  B. Look for 1 seed in that vector
    //  C. Discard used hits
    //  D. Repeat

    // This vector keeps track of the status of each space point.
    // The key is the position in the AllSpacePoints vector.
    // The value is
    //    0: point unused
    //    1: point used in seed
    //    2: point thrown but unused
    //    3: flag to terminate seed finding

    std::vector<char> PointStatus(spts.size(), 0);

    std::vector<std::map<geo::View_t, std::vector<int>>> WhichHitsPerSeed;

    bool KeepChopping = true;

    while (KeepChopping) {
      // This vector keeps a list of the points used in this seed
      std::vector<int> PointsUsed;

      // Find exactly one seed, starting at high Z
      recob::Seed TheSeed =
        FindSeedAtEnd(detProp, spts, PointStatus, PointsUsed, HitsFlat, OrgHits);

      // If it was a good seed, collect up the relevant spacepoints
      // and add the seed to the return vector

      if (TheSeed.IsValid()) {

        for (size_t iP = 0; iP != PointsUsed.size(); ++iP) {
          for (size_t iH = 0; iH != HitsPerSpacePoint.at(PointsUsed.at(iP)).size(); ++iH) {
            int UsedHitID = HitsPerSpacePoint.at(PointsUsed.at(iP)).at(iH);
            HitStatus[UsedHitID] = 2;
          }
        }
        PointStatus[PointsUsed.at(0)] = 1;
        ConsolidateSeed(detProp, TheSeed, HitsFlat, HitStatus, OrgHits, false);
      }

      if (TheSeed.IsValid()) {
        if (fRefits > 0) {
          std::vector<char> HitStatusGood;
          recob::Seed SeedGood;
          for (size_t r = 0; r != (unsigned int)fRefits; ++r) {
            double PrevLength = TheSeed.GetLength();

            SeedGood = TheSeed;
            HitStatusGood = HitStatus;

            std::vector<int> PresentHitList;
            for (size_t iH = 0; iH != HitStatus.size(); ++iH) {
              if (HitStatus[iH] == 2) { PresentHitList.push_back(iH); }
            }
            double pt[3], dir[3], err[3];

            TheSeed.GetPoint(pt, err);
            TheSeed.GetDirection(dir, err);

            TVector3 Center, Direction;
            std::vector<double> ViewRMS;
            std::vector<int> HitsPerView;
            GetCenterAndDirection(
              detProp, HitsFlat, PresentHitList, Center, Direction, ViewRMS, HitsPerView);

            Direction = Direction.Unit() * TheSeed.GetLength();

            int nViewsWithHits(0);
            for (size_t n = 0; n != 3; ++n) {
              pt[n] = Center[n];
              dir[n] = Direction[n];

              TheSeed.SetPoint(pt, err);
              TheSeed.SetDirection(dir, err);

              if (HitsPerView[n] > 0) nViewsWithHits++;
            }

            if (nViewsWithHits < 2) TheSeed.SetValidity(false);

            if (TheSeed.IsValid())
              ConsolidateSeed(detProp, TheSeed, HitsFlat, HitStatus, OrgHits, fExtendSeeds);

            // if we accidentally invalidated the seed, go back to the old one and escape
            else {
              // If we invalidated the seed, go back one interaction
              //  and kill the loop
              HitStatus = HitStatusGood;
              TheSeed = SeedGood;
              break;
            }
            if ((r > 0) && (fabs(PrevLength - TheSeed.GetLength()) < fPitches.at(0))) {
              // If we didn't change much, kill the loop
              break;
            }
          }
        }
      }

      if (TheSeed.IsValid()) {
        WhichHitsPerSeed.push_back(std::map<geo::View_t, std::vector<int>>());

        art::PtrVector<recob::Hit> HitsWithThisSeed;
        for (size_t iH = 0; iH != HitStatus.size(); ++iH) {
          if (HitStatus.at(iH) == 2) {
            WhichHitsPerSeed.at(WhichHitsPerSeed.size() - 1)[HitsFlat[iH]->View()].push_back(iH);
            HitsWithThisSeed.push_back(HitsFlat.at(iH));
            HitStatus.at(iH) = 1;

            for (size_t iSP = 0; iSP != SpacePointsPerHit.at(iH).size(); ++iSP) {
              PointStatus[SpacePointsPerHit.at(iH).at(iSP)] = 1;
            }
          }
        }

        // Record that we used this set of hits with this seed in the return catalogue
        ReturnVector.push_back(TheSeed);
        CataloguedHits.push_back(HitsWithThisSeed);

        // Tidy up
        HitsWithThisSeed.clear();
      }
      else {
        // If it was not a good seed, throw out the top SP and try again
        PointStatus.at(PointsUsed.at(0)) = 2;
      }

      int TotalSPsUsed = 0;
      for (size_t i = 0; i != PointStatus.size(); ++i) {
        if (PointStatus[i] != 0) TotalSPsUsed++;
      }

      if ((int(spts.size()) - TotalSPsUsed) < fMinPointsInSeed) KeepChopping = false;

      if ((PointStatus[0] == 3) || (PointStatus.size() == 0)) KeepChopping = false;

      PointsUsed.clear();

      if ((ReturnVector.size() >= StopAfter) && (StopAfter > 0)) break;

    } // end spt-level loop

    // If we didn't find any seeds, we can make one last ditch attempt. See
    //  if the whole collection is colinear enough to make one megaseed
    //  (good for patching up high angle tracks)

    if (ReturnVector.size() == 0) {
      std::vector<int> ListAllHits;
      for (size_t i = 0; i != HitsFlat.size(); ++i) {
        ListAllHits.push_back(i);
        HitStatus[i] = 2;
      }
      TVector3 SeedCenter(0, 0, 0);
      TVector3 SeedDirection(0, 0, 0);

      std::vector<double> ViewRMS;
      std::vector<int> HitsPerView;

      std::vector<art::PtrVector<recob::Hit>> HitsInThisCollection(3);

      GetCenterAndDirection(
        detProp, HitsFlat, ListAllHits, SeedCenter, SeedDirection, ViewRMS, HitsPerView);

      bool ThrowOutSeed = false;

      double PtArray[3], DirArray[3];
      int nViewsWithHits(0);
      for (size_t n = 0; n != 3; ++n) {
        PtArray[n] = SeedCenter[n];
        DirArray[n] = SeedDirection[n];
        if (HitsPerView[n] > 0) nViewsWithHits++;
      }
      recob::Seed TheSeed(PtArray, DirArray);

      if (nViewsWithHits < 2 || (nViewsWithHits < 3 && !fAllow2DSeeds)) ThrowOutSeed = true;

      if (!ThrowOutSeed) {
        ConsolidateSeed(detProp, TheSeed, HitsFlat, HitStatus, OrgHits, false);

        // Now we have consolidated, grab the right
        //  hits to find the RMS and refitted direction
        ListAllHits.clear();
        for (size_t i = 0; i != HitStatus.size(); ++i) {
          if (HitStatus.at(i) == 2) ListAllHits.push_back(i);
        }
        std::vector<int> HitsPerView;
        GetCenterAndDirection(
          detProp, HitsFlat, ListAllHits, SeedCenter, SeedDirection, ViewRMS, HitsPerView);

        int nViewsWithHits(0);
        for (size_t n = 0; n != 3; ++n) {
          PtArray[n] = SeedCenter[n];
          DirArray[n] = SeedDirection[n];
          //                ThrowOutSeed = true;
          if (HitsPerView[n] > 0) nViewsWithHits++;
        }

        if (nViewsWithHits < 2 || (nViewsWithHits < 3 && !fAllow2DSeeds)) ThrowOutSeed = true;

        TheSeed = recob::Seed(PtArray, DirArray);

        if (fMaxViewRMS.at(0) > 0) {
          for (size_t j = 0; j != fMaxViewRMS.size(); j++) {
            if (fMaxViewRMS.at(j) < ViewRMS.at(j)) { ThrowOutSeed = true; }
          }
        }
      }

      if ((!ThrowOutSeed) && (TheSeed.IsValid())) {
        ReturnVector.push_back(TheSeed);
        art::PtrVector<recob::Hit> HitsThisSeed;
        for (size_t i = 0; i != ListAllHits.size(); ++i) {
          HitsThisSeed.push_back(HitsFlat.at(ListAllHits.at(i)));
        }
        CataloguedHits.push_back(HitsThisSeed);
      }
    }

    // Tidy up
    SpacePointsPerHit.clear();
    HitsPerSpacePoint.clear();
    PointStatus.clear();
    OrgHits.clear();
    HitStatus.clear();

    for (size_t i = 0; i != ReturnVector.size(); ++i) {
      double CrazyValue = 1000000;
      double Length = ReturnVector.at(i).GetLength();
      if (!((Length > fLengthCut) && (Length < CrazyValue))) {
        ReturnVector.erase(ReturnVector.begin() + i);
        CataloguedHits.erase(CataloguedHits.begin() + i);
        --i;
      }
    }

    return ReturnVector;
  }

  //------------------------------------------------------------
  // Latest extendseed method
  //

  void SeedFinderAlgorithm::ConsolidateSeed(detinfo::DetectorPropertiesData const& detProp,
                                            recob::Seed& TheSeed,
                                            art::PtrVector<recob::Hit> const& HitsFlat,
                                            std::vector<char>& HitStatus,
                                            std::vector<std::vector<std::vector<int>>>& OrgHits,
                                            bool Extend) const
  {

    bool ThrowOutSeed = false;

    // This will keep track of what hits are in this seed
    std::map<geo::View_t, std::map<uint32_t, std::vector<int>>> HitsInThisSeed;

    int NHitsThisSeed = 0;

    double MinS = 1000, MaxS = -1000;
    for (size_t i = 0; i != HitStatus.size(); ++i) {
      if (HitStatus.at(i) == 2) {
        double disp, s;
        GetHitDistAndProj(detProp, TheSeed, HitsFlat.at(i), disp, s);
        if (fabs(s) > 1.2) {
          // This hit is not rightfully part of this seed, toss it.
          HitStatus[i] = 0;
        }
        else {
          NHitsThisSeed++;

          if (s < MinS) MinS = s;
          if (s > MaxS) MaxS = s;
          HitsInThisSeed[HitsFlat.at(i)->View()][HitsFlat.at(i)->Channel()].push_back(i);
        }
      }
    }

    double LengthRescale = (MaxS - MinS) / 2.;
    double PositionShift = (MaxS + MinS) / 2.;

    double pt[3], dir[3], err[3];
    TheSeed.GetPoint(pt, err);
    TheSeed.GetDirection(dir, err);

    for (size_t n = 0; n != 3; ++n) {
      pt[n] += dir[n] * PositionShift;
      dir[n] *= LengthRescale;
    }

    TheSeed.SetPoint(pt, err);
    TheSeed.SetDirection(dir, err);

    // Run through checking if we missed any hits
    for (auto itP = HitsInThisSeed.begin(); itP != HitsInThisSeed.end(); ++itP) {
      double dist, s;
      geo::View_t View = itP->first;
      uint32_t LowestChan = itP->second.begin()->first;
      uint32_t HighestChan = itP->second.rbegin()->first;
      for (uint32_t c = LowestChan; c != HighestChan; ++c) {
        for (size_t h = 0; h != OrgHits[View][c].size(); ++h) {
          if (HitStatus[OrgHits[View][c].at(h)] == 0) {
            GetHitDistAndProj(detProp, TheSeed, HitsFlat[OrgHits[View][c].at(h)], dist, s);
            if (dist < fHitResolution) {
              NHitsThisSeed++;

              HitStatus[OrgHits[View][c].at(h)] = 2;

              HitsInThisSeed[View][c].push_back(OrgHits[View][c].at(h));
            }
            else
              HitStatus[OrgHits[View][c].at(h)] = 0;
          }
        }
      }
    }

    if (NHitsThisSeed == 0) ThrowOutSeed = true;

    // Check seed occupancy

    uint32_t LowestChanInSeed[3], HighestChanInSeed[3];
    double Occupancy[] = {0., 0., 0.};
    int nHitsPerView[] = {0, 0, 0};

    for (auto itP = HitsInThisSeed.begin(); itP != HitsInThisSeed.end(); ++itP) {

      geo::View_t View = itP->first;

      LowestChanInSeed[View] = itP->second.begin()->first;
      HighestChanInSeed[View] = itP->second.rbegin()->first;

      nHitsPerView[View]++;

      int FilledChanCount = 0;

      for (size_t c = LowestChanInSeed[View]; c != HighestChanInSeed[View]; ++c) {
        if (itP->second[c].size() > 0) ++FilledChanCount;
      }

      Occupancy[View] =
        float(FilledChanCount) / float(HighestChanInSeed[View] - LowestChanInSeed[View]);
    }

    int nBelowCut(0);
    int nViewsWithHits(0);
    for (size_t n = 0; n != 3; ++n) {
      if (Occupancy[n] < fOccupancyCut) nBelowCut++;
      if (nHitsPerView[n] > 0) nViewsWithHits++;
    }

    int belowCut(0);

    if (fAllow2DSeeds && nViewsWithHits < 3) belowCut = 1;

    if (nBelowCut > belowCut) ThrowOutSeed = true;

    if ((Extend) && (!ThrowOutSeed)) {
      std::vector<std::vector<double>> ToAddNegativeS(3, std::vector<double>());
      std::vector<std::vector<double>> ToAddPositiveS(3, std::vector<double>());
      std::vector<std::vector<int>> ToAddNegativeH(3, std::vector<int>());
      std::vector<std::vector<int>> ToAddPositiveH(3, std::vector<int>());

      for (auto itP = HitsInThisSeed.begin(); itP != HitsInThisSeed.end(); ++itP) {
        double dist, s;

        geo::View_t View = itP->first;

        if (LowestChanInSeed[View] > 0) {
          for (uint32_t c = LowestChanInSeed[View] - 1; c != 0; --c) {
            bool GotOneThisChannel = false;
            for (size_t h = 0; h != OrgHits[View][c].size(); ++h) {
              if (HitStatus[OrgHits[View][c][h]] == 0) {
                GetHitDistAndProj(detProp, TheSeed, HitsFlat[OrgHits[View][c].at(h)], dist, s);
                if (dist < fHitResolution) {
                  GotOneThisChannel = true;
                  if (s < 0) {
                    ToAddNegativeS[View].push_back(s);
                    ToAddNegativeH[View].push_back(OrgHits[View][c].at(h));
                  }
                  else {
                    ToAddPositiveS[View].push_back(s);
                    ToAddPositiveH[View].push_back(OrgHits[View][c].at(h));
                  }
                }
              }
            }
            if (GotOneThisChannel == false) break;
          }
        }
        if (HighestChanInSeed[View] < fNChannels)

          for (uint32_t c = HighestChanInSeed[View] + 1; c != fNChannels; ++c) {
            bool GotOneThisChannel = false;
            for (size_t h = 0; h != OrgHits[View][c].size(); ++h) {
              if (HitStatus[OrgHits[View][c][h]] == 0) {
                GetHitDistAndProj(detProp, TheSeed, HitsFlat[OrgHits[View][c].at(h)], dist, s);
                if (dist < fHitResolution) {
                  GotOneThisChannel = true;
                  if (s < 0) {

                    ToAddNegativeS[View].push_back(s);
                    ToAddNegativeH[View].push_back(OrgHits[View][c].at(h));
                  }
                  else {
                    ToAddPositiveS[View].push_back(s);
                    ToAddPositiveH[View].push_back(OrgHits[View][c].at(h));
                  }
                }
              }
            }
            if (GotOneThisChannel == false) break;
          }
      }

      double ExtendPositiveS = 0, ExtendNegativeS = 0;

      if ((ToAddPositiveS[0].size() > 0) && (ToAddPositiveS[1].size() > 0) &&
          (ToAddPositiveS[2].size() > 0)) {
        for (size_t n = 0; n != 3; ++n) {
          int n1 = (n + 1) % 3;
          int n2 = (n + 2) % 3;

          if ((ToAddPositiveS[n].back() <= ToAddPositiveS[n1].back()) &&
              (ToAddPositiveS[n].back() <= ToAddPositiveS[n2].back())) {
            ExtendPositiveS = ToAddPositiveS[n].back();
          }
        }
      }

      if ((ToAddNegativeS[0].size() > 0) && (ToAddNegativeS[1].size() > 0) &&
          (ToAddNegativeS[2].size() > 0)) {
        for (size_t n = 0; n != 3; ++n) {
          int n1 = (n + 1) % 3;
          int n2 = (n + 2) % 3;
          if ((ToAddNegativeS[n].back() >= ToAddNegativeS[n1].back()) &&
              (ToAddNegativeS[n].back() >= ToAddNegativeS[n2].back())) {
            ExtendNegativeS = ToAddNegativeS[n].back();
          }
        }
      }

      if (fabs(ExtendNegativeS) < 1.) ExtendNegativeS = -1.;
      if (fabs(ExtendPositiveS) < 1.) ExtendPositiveS = 1.;

      LengthRescale = (ExtendPositiveS - ExtendNegativeS) / 2.;
      PositionShift = (ExtendPositiveS + ExtendNegativeS) / 2.;

      for (size_t n = 0; n != 3; ++n) {
        pt[n] += dir[n] * PositionShift;
        dir[n] *= LengthRescale;

        for (size_t i = 0; i != ToAddPositiveS[n].size(); ++i) {
          if (ToAddPositiveS[n].at(i) < ExtendPositiveS)
            HitStatus[ToAddPositiveH[n].at(i)] = 2;
          else
            HitStatus[ToAddPositiveH[n].at(i)] = 0;
        }

        for (size_t i = 0; i != ToAddNegativeS[n].size(); ++i) {
          if (ToAddNegativeS[n].at(i) > ExtendNegativeS)
            HitStatus[ToAddNegativeH[n].at(i)] = 2;
          else
            HitStatus[ToAddNegativeH[n].at(i)] = 0;
        }
      }

      TheSeed.SetPoint(pt, err);
      TheSeed.SetDirection(dir, err);
    }

    if (ThrowOutSeed) TheSeed.SetValidity(false);
  }

  //------------------------------------------------------------

  void SeedFinderAlgorithm::GetHitDistAndProj(detinfo::DetectorPropertiesData const& detProp,
                                              recob::Seed const& ASeed,
                                              art::Ptr<recob::Hit> const& AHit,
                                              double& disp,
                                              double& s) const
  {
    auto const& wireReadoutGeom = art::ServiceHandle<geo::WireReadout>()->Get();

    constexpr geo::TPCID tpcid{0, 0};
    geo::PlaneID const planeID{tpcid, AHit->WireID().Plane};

    auto const [start, end] = wireReadoutGeom.WireEndPoints(geo::WireID{planeID, 0});

    double HitX = detProp.ConvertTicksToX(AHit->PeakTime(), planeID);
    double HitXHigh = detProp.ConvertTicksToX(AHit->PeakTimePlusRMS(), planeID);
    double HitXLow = detProp.ConvertTicksToX(AHit->PeakTimeMinusRMS(), planeID);

    double HitWidth = HitXHigh - HitXLow;

    double pt[3], dir[3], err[3];

    ASeed.GetDirection(dir, err);
    ASeed.GetPoint(pt, err);

    TVector3 sPt(pt[0], pt[1], pt[2]);
    TVector3 sDir(dir[0], dir[1], dir[2]);
    TVector3 hPt(HitX, start.Y(), start.Z());
    TVector3 hDir(0, start.Y() - end.Y(), start.Z() - end.Z());

    s = (sPt - hPt).Dot(hDir * (hDir.Dot(sDir)) - sDir * (hDir.Dot(hDir))) /
        (hDir.Dot(hDir) * sDir.Dot(sDir) - pow(hDir.Dot(sDir), 2));

    disp = fabs((sPt - hPt).Dot(sDir.Cross(hDir)) / (sDir.Cross(hDir)).Mag()) / HitWidth;
  }

  //------------------------------------------------------------
  // Try to find one seed at the high Z end of a set of spacepoints
  //

  recob::Seed SeedFinderAlgorithm::FindSeedAtEnd(
    detinfo::DetectorPropertiesData const& detProp,
    std::vector<recob::SpacePoint> const& Points,
    std::vector<char>& PointStatus,
    std::vector<int>& PointsInRange,
    art::PtrVector<recob::Hit> const& HitsFlat,
    std::vector<std::vector<std::vector<int>>>& OrgHits) const
  {
    // This pointer will be returned later
    recob::Seed ReturnSeed;

    // Keep track of spacepoints we used, not just their IDs
    std::vector<recob::SpacePoint> PointsUsed;

    // Clear output vector
    PointsInRange.clear();

    // Loop through hits looking for highest Z seedable point
    TVector3 HighestZPoint;
    bool NoPointFound = true;
    int counter = Points.size() - 1;
    while ((NoPointFound == true) && (counter >= 0)) {
      if (PointStatus[counter] == 0) {
        HighestZPoint = TVector3(
          Points.at(counter).XYZ()[0], Points.at(counter).XYZ()[1], Points.at(counter).XYZ()[2]);
        NoPointFound = false;
      }
      else
        counter--;
    }
    if (NoPointFound) {
      // We didn't find a high point at all
      //  - let the algorithm know to give up.
      PointStatus[0] = 3;
    }

    // Now we have the high Z point, loop through collecting
    // near enough hits.  We look 2 seed lengths away, since
    // the seed is bidirectional from the central point

    double TwiceLength = 2.0 * fInitSeedLength;

    for (int index = Points.size() - 1; index != -1; --index) {
      if (PointStatus[index] == 0) {
        // first check z, then check total distance
        //  (much faster, since most will be out of range in z anyway)
        if ((HighestZPoint[2] - Points.at(index).XYZ()[2]) < TwiceLength) {
          double DistanceToHighZ = pow(pow(HighestZPoint[1] - Points.at(index).XYZ()[1], 2) +
                                         pow(HighestZPoint[2] - Points.at(index).XYZ()[2], 2),
                                       0.5);
          if (DistanceToHighZ < TwiceLength) {
            PointsInRange.push_back(index);
            PointsUsed.push_back(Points.at(index));
          }
        }
        else
          break;
      }
    }

    TVector3 SeedCenter(0, 0, 0);
    TVector3 SeedDirection(0, 0, 0);

    // Check we have enough points in here to form a seed,
    // otherwise return a dud
    int NPoints = PointsInRange.size();

    if (NPoints < fMinPointsInSeed) return recob::Seed();

    std::map<int, bool> HitMap;
    std::vector<int> HitList;

    for (unsigned int i = 0; i != PointsInRange.size(); i++) {
      std::vector<art::PtrVector<recob::Hit>> HitsInThisCollection(3);

      art::PtrVector<recob::Hit> HitsThisSP =
        fSptalg->getAssociatedHits((Points.at(PointsInRange.at(i))));
      for (art::PtrVector<recob::Hit>::const_iterator itHit = HitsThisSP.begin();
           itHit != HitsThisSP.end();
           ++itHit) {
        uint32_t Channel = (*itHit)->Channel();
        geo::View_t View = (*itHit)->View();

        double eta = 0.01;
        for (size_t iH = 0; iH != OrgHits[View][Channel].size(); ++iH) {
          if (fabs(HitsFlat[OrgHits[View][Channel][iH]]->PeakTime() - (*itHit)->PeakTime()) < eta) {
            HitMap[OrgHits[View][Channel][iH]] = true;
          }
        }
      }
    }

    for (auto itH = HitMap.begin(); itH != HitMap.end(); ++itH) {
      HitList.push_back(itH->first);
    }

    std::vector<double> ViewRMS;
    std::vector<int> HitsPerView;

    GetCenterAndDirection(
      detProp, HitsFlat, HitList, SeedCenter, SeedDirection, ViewRMS, HitsPerView);

    HitMap.clear();
    HitList.clear();

    // See if seed points have some linearity

    bool ThrowOutSeed = false;

    double PtArray[3], DirArray[3];
    double AngleFactor =
      pow(pow(SeedDirection.Y(), 2) + pow(SeedDirection.Z(), 2), 0.5) / SeedDirection.Mag();

    int nViewsWithHits(0);

    for (size_t n = 0; n != 3; ++n) {
      DirArray[n] = SeedDirection[n] * fInitSeedLength / AngleFactor;
      PtArray[n] = SeedCenter[n];
      if (HitsPerView[n] > 0) nViewsWithHits++;
    }

    if (nViewsWithHits < 2 || (nViewsWithHits < 3 && !fAllow2DSeeds)) ThrowOutSeed = true;

    ReturnSeed = recob::Seed(PtArray, DirArray);

    if (fMaxViewRMS.at(0) > 0) {

      for (size_t j = 0; j != fMaxViewRMS.size(); j++) {
        if (fMaxViewRMS.at(j) < ViewRMS.at(j)) { ThrowOutSeed = true; }
        //   mf::LogVerbatim("SeedFinderAlgorithm") << RMS.at(j);
      }
    }

    // If the seed is marked as bad, return a dud, otherwise
    //  return the ReturnSeed pointer
    if (!ThrowOutSeed)
      return ReturnSeed;
    else
      return recob::Seed();
  }

  //-----------------------------------------------------------

  void SeedFinderAlgorithm::GetCenterAndDirection(detinfo::DetectorPropertiesData const& detProp,
                                                  art::PtrVector<recob::Hit> const& HitsFlat,
                                                  std::vector<int>& HitsToUse,
                                                  TVector3& Center,
                                                  TVector3& Direction,
                                                  std::vector<double>& ViewRMS,
                                                  std::vector<int>& N) const
  {
    N.resize(3);

    std::map<uint32_t, bool> HitsClaimed;

    // We'll store hit coordinates in each view into this vector

    std::vector<std::vector<double>> HitTimes(3);
    std::vector<std::vector<double>> HitWires(3);
    std::vector<std::vector<double>> HitWidths(3);
    std::vector<double> MeanWireCoord(3, 0);
    std::vector<double> MeanTimeCoord(3, 0);

    // Run through the collection getting hit info for these spacepoints

    std::vector<double> x(3, 0), y(3, 0), xx(3, 0), xy(3, 0), yy(3, 0), sig(3, 0);

    for (size_t i = 0; i != HitsToUse.size(); ++i) {
      auto itHit = HitsFlat.begin() + HitsToUse[i];

      size_t ViewIndex;

      auto const hitView = (*itHit)->View();
      if (hitView == geo::kU)
        ViewIndex = 0;
      else if (hitView == geo::kV)
        ViewIndex = 1;
      else if (hitView == geo::kW)
        ViewIndex = 2;
      else {
        throw art::Exception(art::errors::LogicError)
          << "SpacePointAlg does not support view " << geo::PlaneGeo::ViewName(hitView) << " (#"
          << hitView << ")\n";
      }
      double WireCoord = (*itHit)->WireID().Wire * fPitches.at(ViewIndex);
      double TimeCoord = detProp.ConvertTicksToX((*itHit)->PeakTime(), ViewIndex, 0, 0);
      double TimeUpper = detProp.ConvertTicksToX((*itHit)->PeakTimePlusRMS(), ViewIndex, 0, 0);
      double TimeLower = detProp.ConvertTicksToX((*itHit)->PeakTimeMinusRMS(), ViewIndex, 0, 0);
      double Width = fabs(0.5 * (TimeUpper - TimeLower));
      double Width2 = pow(Width, 2);

      HitWires.at(ViewIndex).push_back(WireCoord);
      HitTimes.at(ViewIndex).push_back(TimeCoord);
      HitWidths.at(ViewIndex).push_back(fabs(0.5 * (TimeUpper - TimeLower)));

      MeanWireCoord.at(ViewIndex) += WireCoord;
      MeanTimeCoord.at(ViewIndex) += TimeCoord;

      // Elements for LS
      x.at(ViewIndex) += WireCoord / Width2;
      y.at(ViewIndex) += TimeCoord / Width2;
      xy.at(ViewIndex) += (TimeCoord * WireCoord) / Width2;
      xx.at(ViewIndex) += (WireCoord * WireCoord) / Width2;
      yy.at(ViewIndex) += (TimeCoord * TimeCoord) / Width2;
      sig.at(ViewIndex) += 1. / Width2;
      N.at(ViewIndex)++;
    }

    ViewRMS.clear();
    ViewRMS.resize(3);
    std::vector<double> ViewGrad(3);
    std::vector<double> ViewOffset(3);

    for (size_t n = 0; n != 3; ++n) {
      MeanWireCoord[n] /= N[n];
      MeanTimeCoord[n] /= N[n];

      double BigN = 1000000;
      double SmallN = 1. / BigN;

      if (N[n] > 2) {
        double Numerator = (y[n] / sig[n] - xy[n] / x[n]);
        double Denominator = (x[n] / sig[n] - xx[n] / x[n]);
        if (fabs(Denominator) > SmallN)
          ViewGrad.at(n) = Numerator / Denominator;
        else
          ViewGrad[n] = BigN;
      }
      else if (N[n] == 2)
        ViewGrad[n] = xy[n] / xx[n];
      else
        ViewGrad[n] = BigN;

      ViewOffset.at(n) = (y[n] - ViewGrad[n] * x[n]) / sig[n];
      ViewRMS.at(n) = pow((yy[n] + pow(ViewGrad[n], 2) * xx[n] + pow(ViewOffset[n], 2) * sig[n] -
                           2 * ViewGrad[n] * xy[n] - 2 * ViewOffset[n] * y[n] +
                           2 * ViewGrad[n] * ViewOffset[n] * x[n]) /
                            N[n],
                          0.5);
      // Make RMS rotation perp to track
      if (ViewGrad.at(n) != 0) ViewRMS[n] *= sin(atan(1. / ViewGrad.at(n)));
    }

    for (size_t n = 0; n != 3; ++n) {
      size_t n1 = (n + 1) % 3;
      size_t n2 = (n + 2) % 3;
      if ((N[n] <= N[n1]) && (N[n] <= N[n2])) {

        if (N[n1] < N[n2]) { std::swap(n1, n2); }
        if ((N[n1] == 0) || (N[n2] == 0)) continue;

        Direction =
          (fXDir + fPitchDir[n1] * (1. / ViewGrad[n1]) +
           fWireDir[n1] *
             (((1. / ViewGrad[n2]) - fPitchDir[n1].Dot(fPitchDir[n2]) * (1. / ViewGrad[n1])) /
              fWireDir[n1].Dot(fPitchDir[n2])))
            .Unit();

        /*
                 Center2D[n] =
                 fXDir * 0.5 * (MeanTimeCoord[n1]+MeanTimeCoord[n2])
                 + fPitchDir[n1] * (MeanWireCoord[n1] + fWireZeroOffset[n1])
                 + fWireDir[n1] *  ( ((MeanWireCoord[n2] + fWireZeroOffset[n2]) - ( MeanWireCoord[n1] + fWireZeroOffset[n1] )*fPitchDir[n1].Dot(fPitchDir[n2]))/(fPitchDir[n2].Dot(fWireDir[n1])) );
                 */

        double TimeCoord = 0.5 * (MeanTimeCoord[n1] + MeanTimeCoord[n2]);
        double WireCoordIn1 = (TimeCoord - ViewOffset[n1]) / ViewGrad[n1] + fWireZeroOffset[n1];
        double WireCoordIn2 = (TimeCoord - ViewOffset[n2]) / ViewGrad[n2] + fWireZeroOffset[n2];

        Center = fXDir * TimeCoord + fPitchDir[n1] * WireCoordIn1 +
                 fWireDir[n1] * ((WireCoordIn2 - WireCoordIn1 * fPitchDir[n1].Dot(fPitchDir[n2])) /
                                 (fPitchDir[n2].Dot(fWireDir[n1])));

        ViewRMS[n] = -fabs(ViewRMS[n]);
        ViewRMS[n1] = fabs(ViewRMS[n1]);
        ViewRMS[n2] = fabs(ViewRMS[n2]);

        break;
      }
    }
  }

  //-----------------------------------------------
  void SeedFinderAlgorithm::CalculateGeometricalElements()
  {
    art::ServiceHandle<geo::Geometry const> geom;
    auto const& wireReadoutGeom = art::ServiceHandle<geo::WireReadout const>()->Get();

    // Total number of channels in the detector
    fNChannels = wireReadoutGeom.Nchannels();

    // Find pitch of each wireplane
    fPitches.resize(3);
    fPitches.at(0) = fabs(wireReadoutGeom.Plane({0, 0, geo::kU}).WirePitch());
    fPitches.at(1) = fabs(wireReadoutGeom.Plane({0, 0, geo::kV}).WirePitch());
    fPitches.at(2) = fabs(wireReadoutGeom.Plane({0, 0, geo::kW}).WirePitch());

    // Setup basis vectors
    fXDir = TVector3(1, 0, 0);
    fYDir = TVector3(0, 1, 0);
    fZDir = TVector3(0, 0, 1);

    fWireDir.resize(3);
    fPitchDir.resize(3);
    fWireZeroOffset.resize(3);

    double xyzStart1[3], xyzStart2[3];
    double xyzEnd1[3], xyzEnd2[3];

    // Calculate wire coordinate systems
    for (unsigned int n = 0; n != 3u; ++n) {
      wireReadoutGeom.WireEndPoints(geo::WireID{0, 0, n, 0}, xyzStart1, xyzEnd1);
      wireReadoutGeom.WireEndPoints(geo::WireID{0, 0, n, 1}, xyzStart2, xyzEnd2);
      fWireDir[n] =
        TVector3(xyzEnd1[0] - xyzStart1[0], xyzEnd1[1] - xyzStart1[1], xyzEnd1[2] - xyzStart1[2])
          .Unit();
      fPitchDir[n] = fWireDir[n].Cross(fXDir).Unit();
      if (fPitchDir[n].Dot(TVector3(
            xyzEnd2[0] - xyzEnd1[0], xyzEnd2[1] - xyzEnd1[1], xyzEnd2[2] - xyzEnd1[2])) < 0)
        fPitchDir[n] = -fPitchDir[n];

      fWireZeroOffset[n] =
        xyzEnd1[0] * fPitchDir[n][0] + xyzEnd1[1] * fPitchDir[n][1] + xyzEnd1[2] * fPitchDir[n][2];
    }
  }

  //-----------------------------------------------

  std::vector<recob::Seed> SeedFinderAlgorithm::GetSeedsFromUnSortedHits(
    detinfo::DetectorClocksData const& clockData,
    detinfo::DetectorPropertiesData const& detProp,
    art::PtrVector<recob::Hit> const& Hits,
    std::vector<art::PtrVector<recob::Hit>>& HitCatalogue,
    unsigned int StopAfter) const
  {
    return FindSeeds(clockData, detProp, Hits, HitCatalogue, StopAfter);
  }

  //---------------------------------------------

  std::vector<std::vector<recob::Seed>> SeedFinderAlgorithm::GetSeedsFromSortedHits(
    detinfo::DetectorClocksData const& clockData,
    detinfo::DetectorPropertiesData const& detProp,
    std::vector<std::vector<art::PtrVector<recob::Hit>>> const& SortedHits,
    std::vector<std::vector<art::PtrVector<recob::Hit>>>& HitsPerSeed,
    unsigned int StopAfter) const
  {

    std::vector<std::vector<recob::Seed>> ReturnVec;

    // This piece of code looks detector specific, but its not -
    //   it also works for 2 planes, but one vector is empty.

    if (!(fSptalg->enableU() && fSptalg->enableV() && fSptalg->enableW()))
      mf::LogWarning("BezierTrackerModule")
        << "Warning: SpacePointAlg is does not have three views enabled. This may cause unexpected "
           "behaviour in the bezier tracker.";

    try {
      for (std::vector<art::PtrVector<recob::Hit>>::const_iterator itU =
             SortedHits.at(geo::kU).begin();
           itU != SortedHits.at(geo::kU).end();
           ++itU)
        for (std::vector<art::PtrVector<recob::Hit>>::const_iterator itV =
               SortedHits.at(geo::kV).begin();
             itV != SortedHits.at(geo::kV).end();
             ++itV)
          for (std::vector<art::PtrVector<recob::Hit>>::const_iterator itW =
                 SortedHits.at(geo::kW).begin();
               itW != SortedHits.at(geo::kW).end();
               ++itW) {
            art::PtrVector<recob::Hit> HitsThisComboFlat;

            if (fSptalg->enableU())
              for (size_t i = 0; i != itU->size(); ++i)
                HitsThisComboFlat.push_back(itU->at(i));

            if (fSptalg->enableV())
              for (size_t i = 0; i != itV->size(); ++i)
                HitsThisComboFlat.push_back(itV->at(i));

            if (fSptalg->enableW())
              for (size_t i = 0; i != itW->size(); ++i)
                HitsThisComboFlat.push_back(itW->at(i));

            std::vector<art::PtrVector<recob::Hit>> CataloguedHits;

            std::vector<recob::Seed> Seeds =
              FindSeeds(clockData, detProp, HitsThisComboFlat, CataloguedHits, StopAfter);

            // Add this harvest to return vectors
            HitsPerSeed.push_back(CataloguedHits);
            ReturnVec.push_back(Seeds);

            // Tidy up
            CataloguedHits.clear();
            Seeds.clear();
          }
    }
    catch (...) {
      mf::LogWarning("SeedFinderTrackerModule")
        << " bailed during hit map lookup - have you enabled all 3 planes?";
      ReturnVec.push_back(std::vector<recob::Seed>());
    }

    return ReturnVec;
  }

}