cluster::ClusterCrawlerAlg Class Reference

#include "ClusterCrawlerAlg.h"

Classes
struct	ClusterStore
	struct of temporary clusters More...
struct	Vtx3Store
	struct of temporary 3D vertices More...
struct	VtxStore
	struct of temporary 2D vertices (end points) More...

Public Types
typedef unsigned int	CTP_t

Public Member Functions
Data structures for the reconstruction results
	ClusterCrawlerAlg (fhicl::ParameterSet const &pset)
virtual void	reconfigure (fhicl::ParameterSet const &pset)
void	RunCrawler (std::vector< recob::Hit > const &srchits)
Result retrieval
std::vector< short > const &	GetinClus () const
	Returns (and loses) the collection of reconstructed hits. More...
std::vector< recob::Hit > &&	YieldHits ()
	Returns (and loses) the collection of reconstructed hits. More...
std::vector< ClusterStore > const &	GetClusters () const
	Returns a constant reference to the clusters found. More...
std::vector< VtxStore > const &	GetEndPoints () const
	Returns a constant reference to the 2D end points found. More...
std::vector< Vtx3Store > const &	GetVertices () const
	Returns a constant reference to the 3D vertices found. More...
void	ClearResults ()

Static Public Member Functions
static CTP_t	EncodeCTP (unsigned int cryo, unsigned int tpc, unsigned int plane)
static CTP_t	EncodeCTP (const geo::PlaneID &planeID)
static geo::PlaneID	DecodeCTP (CTP_t CTP)
static bool	SortByMultiplet (recob::Hit const &a, recob::Hit const &b)
	Comparison for sorting hits by wire and hit multiplet. More...

Static Public Attributes
static constexpr unsigned int	CTPpad = 1000

Private Member Functions
void	ClusterLoop ()
bool	ClusterHitsOK (short nHitChk)
void	AddHit (unsigned int kwire, bool &HitOK, bool &SigOK)
void	AddLAHit (unsigned int kwire, bool &ChkCharge, bool &HitOK, bool &SigOK)
void	FitCluster ()
void	FitClusterChg ()
void	FitClusterMid (unsigned short it1, unsigned int iht, short nhit)
void	FitClusterMid (std::vector< unsigned int > &hitVec, unsigned int iht, short nhit)
void	CrawlUS ()
void	LACrawlUS ()
void	KillGarbageClusters ()
void	ChkMerge ()
void	ChkMerge12 (unsigned short it1, unsigned short it2, bool &didit)
void	DoMerge (unsigned short it1, unsigned short it2, short ProcCode)
void	ChkClusterNearbyHits (bool prt)
void	MergeHits (const unsigned int theHit, bool &didMerge)
void	FixMultipletLocalIndices (size_t begin, size_t end, short int multiplicity=-1)
	Resets the local index and multiplicity of all the hits in [begin;end[. More...
void	CheckClusterHitFrac (bool prt)
void	ChkClusterDS ()
void	MergeOverlap ()
void	MakeClusterObsolete (unsigned short icl)
	Marks the cluster as obsolete and frees hits still associated with it. More...
void	RestoreObsoleteCluster (unsigned short icl)
	Restores an obsolete cluster. More...
void	RemoveObsoleteHits ()
	Removes obsolete hits from hits, updating the indices. More...
void	FindVertices ()
void	FindStarVertices ()
void	ChkVertex (float fvw, float fvt, unsigned short it1, unsigned short it2, short topo)
void	ClusterVertex (unsigned short it2)
void	VertexCluster (unsigned short ivx)
void	RefineVertexClusters (unsigned short ivx)
bool	VtxClusterSplit ()
bool	CrawlVtxChk (unsigned int kwire)
bool	CrawlVtxChk2 ()
void	VtxConstraint (unsigned int iwire, unsigned int ihit, unsigned int jwire, unsigned int &useHit, bool &doConstrain)
void	FitVtx (unsigned short iv)
void	FitAllVtx (CTP_t inCTP)
void	VtxMatch (geo::TPCID const &tpcid)
void	Vtx3ClusterMatch (geo::TPCID const &tpcid)
void	Vtx3ClusterSplit (geo::TPCID const &tpcid)
void	FindHammerClusters ()
void	CrawlInit ()
void	ClusterInit ()
void	GetHitRange (CTP_t CTP)
bool	TmpStore ()
void	TmpGet (unsigned short it1)
void	CalculateAveHitWidth ()
void	FclTrimUS (unsigned short nTrim)
bool	SplitCluster (unsigned short icl, unsigned short pos, unsigned short ivx)
unsigned int	DeadWireCount ()
unsigned int	DeadWireCount (unsigned int inWire1, unsigned int inWire2)
bool	ChkMergedClusterHitFrac (unsigned short it1, unsigned short it2)
void	PrintClusters ()
void	PrintVertices ()
bool	ChkSignal (unsigned int iht, unsigned int jht)
bool	ChkSignal (unsigned int wire1, float time1, unsigned int wire2, float time2)
float	AngleFactor (float slope)
float	EndKinkAngle ()
bool	CheckHitDuplicates (std::string location, std::string marker="") const
	Returns true if there are no duplicates in the hit list for next cluster. More...
float	DoCA (short icl, unsigned short end, float vwire, float vtick)
float	ClusterVertexChi (short icl, unsigned short end, unsigned short ivx)
float	PointVertexChi (float wire, float tick, unsigned short ivx)
std::string	PrintHit (unsigned int iht)
std::pair< size_t, size_t >	FindHitMultiplet (size_t iHit) const
void	CheckHitClusterAssociations ()

Static Private Member Functions
static bool	areInSameMultiplet (recob::Hit const &first_hit, recob::Hit const &second_hit)
	Returns whether the two hits belong to the same multiplet. More...

Private Attributes
unsigned short	fNumPass
	number of passes over the hit collection More...
std::vector< unsigned short >	fMaxHitsFit
	Max number of hits fitted. More...
std::vector< unsigned short >	fMinHits
	Min number of hits to make a cluster. More...
std::vector< unsigned short >	fNHitsAve
	set to > 2 to do a charge fit using fNHitsAve hits More...
std::vector< float >	fChiCut
	stop adding hits to clusters if chisq too high More...
std::vector< float >	fKinkChiRat
std::vector< float >	fKinkAngCut
	kink angle cut made after fKinkChiRat More...
std::vector< float >	fChgCut
	charge difference cut for adding a hit to a cluster More...
std::vector< unsigned short >	fMaxWirSkip
	max number of wires that can be skipped while crawling More...
std::vector< unsigned short >	fMinWirAfterSkip
	after skipping More...
std::vector< bool >	fDoMerge
	try to merge clusters? More...
std::vector< float >	fTimeDelta
	max time difference for matching More...
std::vector< float >	fMergeChgCut
	max charge ratio for matching More...
std::vector< bool >	fFindVertices
	run vertexing code after clustering? More...
std::vector< bool >	fLACrawl
	Crawl Large Angle clusters on pass? More...
bool	fFindHammerClusters
	look for hammer type clusters More...
bool	fRefineVertexClusters
std::vector< float >	fMinAmp
	expected minimum signal in each wire plane More...
float	fKillGarbageClusters
bool	fChkClusterDS
bool	fVtxClusterSplit
bool	fFindStarVertices
float	fHitErrFac
	hit time error = fHitErrFac * hit RMS used for cluster fit More...
float	fHitMinAmp
	< ignore hits with Amp < this value More...
float	fClProjErrFac
	cluster projection error factor More...
float	fMinHitFrac
float	fLAClusAngleCut
	call Large Angle Clustering code if > 0 More...
unsigned short	fLAClusMaxHitsFit
	max hits fitted on a Large Angle cluster More...
float	fLAClusSlopeCut
bool	fMergeAllHits
float	fHitMergeChiCut
	is < cut. Set < 0 for no merging More...
float	fMergeOverlapAngCut
	angle cut for merging overlapping clusters More...
unsigned short	fAllowNoHitWire
float	fVertex2DCut
	2D vtx -> cluster matching cut (chisq/dof) More...
float	fVertex2DWireErrCut
float	fVertex3DCut
	2D vtx -> 3D vtx matching cut (chisq/dof) More...
int	fDebugPlane
int	fDebugWire
	set to the Begin Wire and Hit of a cluster to print More...
int	fDebugHit
	out detailed information while crawling More...
std::vector< geo::WireID >	fFilteredWires
float	clpar [3]
float	clparerr [2]
	cluster parameter errors More...
float	clChisq
	chisq of the current fit More...
float	fAveChg
	average charge at leading edge of cluster More...
float	fChgSlp
	slope of the charge vs wire More...
float	fAveHitWidth
	average width (EndTick - StartTick) of hits More...
bool	prt
bool	vtxprt
unsigned short	NClusters
art::ServiceHandle< geo::Geometry >	geom
std::vector< recob::Hit >	fHits
	our version of the hits More...
std::vector< short >	inClus
	Hit used in cluster (-1 = obsolete, 0 = free) More...
std::vector< bool >	mergeAvailable
	set true if hit is with HitMergeChiCut of a neighbor hit More...
std::vector< ClusterStore >	tcl
	the clusters we are creating More...
std::vector< VtxStore >	vtx
	the endpoints we are reconstructing More...
std::vector< Vtx3Store >	vtx3
	the 3D vertices we are reconstructing More...
trkf::LinFitAlg	fLinFitAlg
float	clBeginSlp
	begin slope (= DS end = high wire number) More...
float	clBeginAng
float	clBeginSlpErr
unsigned int	clBeginWir
	begin wire More...
float	clBeginTim
	begin time More...
float	clBeginChg
	begin average charge More...
float	clBeginChgNear
	nearby charge More...
float	clEndSlp
	slope at the end (= US end = low wire number) More...
float	clEndAng
float	clEndSlpErr
unsigned int	clEndWir
	begin wire More...
float	clEndTim
	begin time More...
float	clEndChg
	end average charge More...
float	clEndChgNear
	nearby charge More...
short	clStopCode
	8 = SPECIAL CODE FOR STEP CRAWLING More...
short	clProcCode
CTP_t	clCTP
	Cryostat/TPC/Plane code. More...
bool	clLA
	using Large Angle crawling code More...
unsigned int	fFirstWire
	the first wire with a hit More...
unsigned int	fFirstHit
	first hit used More...
unsigned int	fLastWire
	the last wire with a hit More...
unsigned int	cstat
unsigned int	tpc
unsigned int	plane
unsigned int	fNumWires
unsigned int	fMaxTime
float	fScaleF
	scale factor from Tick/Wire to dx/du More...
unsigned short	pass
std::vector< std::pair< int, int > >	WireHitRange
std::vector< unsigned int >	fcl2hits
	vector of hits used in the cluster More...
std::vector< float >	chifits
	fit chisq for monitoring kinks, etc More...
std::vector< short >	hitNear
std::vector< float >	chgNear
	charge near a cluster on each wire More...
float	fChgNearWindow
	window (ticks) for finding nearby charge More...
float	fChgNearCut
	to define a shower-like cluster More...
std::string	fhitsModuleLabel

Detailed Description

Definition at line 36 of file ClusterCrawlerAlg.h.

Member Typedef Documentation

typedef unsigned int cluster::ClusterCrawlerAlg::CTP_t

Definition at line 40 of file ClusterCrawlerAlg.h.

Constructor & Destructor Documentation

cluster::ClusterCrawlerAlg::ClusterCrawlerAlg

(

fhicl::ParameterSet const &

pset

)

Definition at line 45 of file ClusterCrawlerAlg.cxx.

  {
    reconfigure(pset);
  }

Member Function Documentation

void cluster::ClusterCrawlerAlg::AddHit ( unsigned int  kwire, bool &  HitOK, bool &  SigOK  )

private

Definition at line 4907 of file ClusterCrawlerAlg.cxx.

References util::absDiff(), recob::Hit::Integral(), recob::Hit::LocalIndex(), recob::Hit::Multiplicity(), recob::Hit::PeakTime(), tca::PrintHit(), recob::Hit::RMS(), and cluster::SortByLowHit().

  {
    // Add a hit to the cluster if it meets several criteria:
    // similar pulse height to the cluster (if fAveChg is defined)
    // closest hit to the project cluster position.
    // Return SigOK if there is a nearby hit that was missed due to the cuts
    
    SigOK = false;
    HitOK = false;
    
    // not in the range of wires with hits
    if(kwire < fFirstWire || kwire > fLastWire) return;
    
    unsigned int lastClHit = UINT_MAX;
    if(fcl2hits.size() > 0) lastClHit = fcl2hits[fcl2hits.size()-1];

    // the last hit added to the cluster
    unsigned int wire0 = clpar[2];
    
    // return if no signal and no hit
    if(fAllowNoHitWire == 0) {
      if(WireHitRange[kwire].first == -2) return;
    } else {
      // allow a number of wires with no hits
      if(WireHitRange[kwire].first == -2 &&
        (wire0 - kwire) > fAllowNoHitWire) {
        SigOK = true;
        return;
      }
    }
    // skip bad wire, but assume the track was there
    if(WireHitRange[kwire].first == -1) {
      SigOK = true;
      return;
    }

    unsigned int firsthit = WireHitRange[kwire].first;
    unsigned int lasthit = WireHitRange[kwire].second;
    
    // the projected time of the cluster on this wire
    float dw = (float)kwire - (float)wire0;
    float prtime = clpar[0] + dw * clpar[1];
    if(prtime < 0 || (unsigned int)prtime > fMaxTime) return;
    // Find the projected time error including the projection error and the
    // error from the last hit added
    float prtimerr2 = std::abs(dw)*clparerr[1]*clparerr[1];
   
    // apply an angle dependent scale factor to the hit error. Default is very large error
    float hiterr = 10;
    if(lastClHit != UINT_MAX) hiterr = 3 * fHitErrFac * fHits[lastClHit].RMS();
    float err = std::sqrt(prtimerr2 + hiterr * hiterr);
    // Time window for accepting a hit.
    float hitWin = fClProjErrFac * err;
    
    float prtimeLo = prtime - hitWin;
    float prtimeHi = prtime + hitWin;
    float chgWinLo = prtime - fChgNearWindow;
    float chgWinHi = prtime + fChgNearWindow;
    if(prt) {
      mf::LogVerbatim("CC")<<"AddHit: wire "<<kwire<<" prtime Lo "<<(int)prtimeLo<<" prtime "<<(int)prtime<<" Hi "<<(int)prtimeHi<<" prtimerr "<<sqrt(prtimerr2)<<" hiterr "<<hiterr<<" fAveChg "<<(int)fAveChg<<" fAveHitWidth "<<std::setprecision(3)<<fAveHitWidth;
    }
    // loop through the hits
    unsigned int imbest = INT_MAX;
    float best = 9999., dtime;
    float cnear = 0;
    float hitTime, hitChg, hitStartTick, hitEndTick;
    for(unsigned int khit = firsthit; khit < lasthit; ++khit) {
      // obsolete hit?
      if(inClus[khit] < 0) continue;
      hitTime = fHits[khit].PeakTime();
      dtime = std::abs(hitTime - prtime);
      if(dtime > 1000) continue;
      hitStartTick = fHits[khit].StartTick();
      hitEndTick = fHits[khit].EndTick();
      // weight by the charge difference
      if(fAveChg > 0) dtime *= std::abs(fHits[khit].Integral() - fAveChg) / fAveChg;
      if(prt && std::abs(dtime) < 100) {
        mf::LogVerbatim("CC")
          <<" Chk W:T "<<PrintHit(khit)
          <<" dT "<<std::fixed<<std::setprecision(1)<<(hitTime - prtime)
          <<" InClus "<<inClus[khit]
          <<" mult "<<fHits[khit].Multiplicity()
          <<" RMS "<<std::fixed<<std::setprecision(1)<<fHits[khit].RMS()
          <<" Chi2 "<<std::fixed<<std::setprecision(1)<<fHits[khit].GoodnessOfFit()
          <<" Charge "<<(int)fHits[khit].Integral()
          <<" Peak "<<std::fixed<<std::setprecision(1)<<fHits[khit].PeakAmplitude()
          <<" LoT "<<(int)hitStartTick
          <<" HiT "<<(int)hitEndTick
          <<" index " << khit;
      }
      // count charge in the window
      if(fHits[khit].StartTick() > chgWinLo && fHits[khit].EndTick() < chgWinHi) cnear += fHits[khit].Integral();
      // check for signal
      if(prtimeHi < hitStartTick) continue;
      if(prtimeLo > hitEndTick) continue;
      SigOK = true;
      // check for good hit
      if(hitTime < prtimeLo) continue;
      if(hitTime > prtimeHi) continue;
      // hit used?
      if(inClus[khit] > 0) continue;
      if(dtime < best) {
        best = dtime;
        imbest = khit;
      }
    } // khit
    
    if(!SigOK) {
      if(fAllowNoHitWire == 0) return;
      if(prt) mf::LogVerbatim("CC")<<" wire0 "<<wire0<<" kwire "<<kwire<<" max "<<fAllowNoHitWire<<" imbest "<<imbest;
      if((wire0 - kwire) > fAllowNoHitWire) return;
      SigOK = true;
    }

    if(imbest == INT_MAX) return;
    
    recob::Hit const& hit = fHits[imbest];
    hitChg = hit.Integral();
    
    if(prt) mf::LogVerbatim("CC")<<" Best hit time "<<(int)hit.PeakTime();
    
    short hnear = 0;
    // merge hits in a doublet?
    bool didMerge = false;
    if(lastClHit != UINT_MAX && fAveHitWidth > 0 && fHitMergeChiCut > 0 && hit.Multiplicity() == 2) {
      bool doMerge = true;
      for(unsigned short ivx = 0; ivx < vtx.size(); ++ivx) {
        if(std::abs(kwire - vtx[ivx].Wire) < 10 &&
           std::abs(int(hit.PeakTime() - vtx[ivx].Time)) < 20 )
        {
          doMerge = false;
          break;
        }
      } // ivx
      // quit if localindex does not make sense. 
      if (hit.LocalIndex() != 0 && imbest == 0) doMerge = false;
      if (doMerge) {
        // find the neighbor hit
        unsigned int oht;
        if(hit.LocalIndex() == 0) {
          oht = imbest + 1;
        } else {
          oht = imbest - 1;
        } // hit.LocalIndex() == 0
        // check the hit time separation
        recob::Hit const& other_hit = fHits[oht];
        float hitSep = std::abs(hit.PeakTime() - other_hit.PeakTime());
        hitSep /= hit.RMS();
        // check the the charge similarity
        float totChg = hitChg + other_hit.Integral();
        float lastHitChg = fAveChg;
        if(lastHitChg < 0) lastHitChg = fHits[lastClHit].Integral();
        hnear = 1;
        if(prt) mf::LogVerbatim("CC")<<" Chk hit merge hitsep "<<hitSep<<" dChg "<<std::abs(totChg - lastHitChg)<<" Cut "<<std::abs(hit.Integral() - lastHitChg);
//        if(inClus[oht] == 0 && hitSep < fHitMergeChiCut && std::abs(totChg - lastHitChg) < std::abs(hit.Integral() - lastHitChg)) {
        if(inClus[oht] == 0 && hitSep < fHitMergeChiCut) {
          if(prt) mf::LogVerbatim("CC")<<"  Merging hit doublet "<<imbest;
          MergeHits(imbest, didMerge);
          if(prt && !didMerge) mf::LogVerbatim("CC")<<"  Hit merge failed ";
        } // not in a cluster, hitSep OK, total charge OK
      } // doMerge
    } // fHitMergeChiCut > 0 && hit.Multiplicity() == 2
    
    // Make a charge similarity cut if the average charge is defined
    bool fitChg = true;
    if(fAveChg > 0.) {
      
      float chgrat = (hitChg - fAveChg) / fAveChg;
      if(prt) mf::LogVerbatim("CC")<<" Chgrat "<<std::setprecision(2)<<chgrat;
      
      // charge is way too high?
      if(chgrat > 3 * fChgCut[pass]) {
        if(prt) mf::LogVerbatim("CC")<<" fails 3 x high charge cut "<<fChgCut[pass]<<" on pass "<<pass;
        return;
      }

      // Determine if the last hit added was a large (low) charge hit
      // This will be used to prevent adding large (low) charge hits on two
      // consecutive fits. This cut is only applied to hits on adjacent wires
      float bigchgcut = 1.5 * fChgCut[pass];
      bool lasthitbig = false;
      bool lasthitlow = false;
      if(lastClHit != UINT_MAX && util::absDiff(wire0, kwire) == 1) {
        float lastchgrat = (fHits[lastClHit].Integral() - fAveChg) / fAveChg;
        lasthitbig = ( lastchgrat > bigchgcut);
        lasthitlow = ( lastchgrat < -fChgCut[pass]);
      }
      
      // the last hit added was low charge and this one is as well
      if(lasthitlow && chgrat < -fChgCut[pass]) {
        if(prt) mf::LogVerbatim("CC")<<" fails low charge cut. Stop crawling.";
        SigOK = false;
        return;
      } // lasthitlow
    
      // the last hit was high charge and this one is also
      if(lasthitbig && chgrat > fChgCut[pass]) {
        if(prt) mf::LogVerbatim("CC")<<" fails 2nd hit high charge cut. Last hit was high also. ";
        return;
      } // lasthitbig

    
      // require that large charge hits have a very good projection error
      if(chgrat > fChgCut[pass]) {
        if(best > 2 * err) {
          if(prt) mf::LogVerbatim("CC")<<" high charge && bad dT= "<<best<<" err= "<<err;
          return;
        }
      } // chgrat > fChgCut[pass]

      // decide whether to fit the charge
      fitChg = (chgrat < std::abs(fChgCut[pass]) );
    } // fAveChg > 0
    
    // we now have a hit that meets all the criteria. Fit it
    fcl2hits.push_back(imbest);
    // This is strictly only necessary when calling AddHit for seed clusters
    if(fcl2hits.size() == 3) std::sort(fcl2hits.begin(), fcl2hits.end(), SortByLowHit);
    FitCluster();
    chifits.push_back(clChisq);
    hitNear.push_back(hnear);
    // remove the charge of the just added hit
    cnear -= fHits[imbest].Integral();
    if(cnear < 0) cnear = 0;
    // divide by the just added hit charge
    cnear /= fHits[imbest].Integral();
    chgNear.push_back(cnear);
    // nearby hit check
//    ChkClusterNearbyHits(prt);
    HitOK = true;
    
    if(chgNear.size() != fcl2hits.size()) {
      mf::LogError("CC")<<"AddHit: Bad length";
      return;
    }

    if(prt) mf::LogVerbatim("CC")<<" >>ADD"<<pass
      <<" W:T "<<PrintHit(imbest)
      <<" dT "<<best<<" clChisq "<<clChisq
      <<" Chg "<<(int)fHits[imbest].Integral()
      <<" AveChg "<<(int)fAveChg
 //     <<" width "<<(int)hitWidth<<" fAveHitWidth "<<(int)fAveHitWidth
      <<" fcl2hits size "<<fcl2hits.size();

    if(!fitChg) return;
  if(prt) mf::LogVerbatim("CC")<<" Fit charge ";
    FitClusterChg();
  } // AddHit()

void cluster::ClusterCrawlerAlg::AddLAHit ( unsigned int  kwire, bool &  ChkCharge, bool &  HitOK, bool &  SigOK  )

private

Definition at line 4643 of file ClusterCrawlerAlg.cxx.

References tca::PrintHit().

  {
    // A variant of AddHit for large angle clusters
    
    SigOK = false;
    HitOK = false;
    
    // not in the range of wires with hits
    if(kwire < fFirstWire || kwire > fLastWire) return;
    
    if(fcl2hits.size() == 0) return;

    // skip bad wire and assume the track was there
    if(WireHitRange[kwire].first == -1) {
      SigOK = true;
      return;
    }
    // return SigOK false if no hit on a good wire
    if(WireHitRange[kwire].first == -2) return;
    
    unsigned int firsthit = WireHitRange[kwire].first;
    unsigned int lasthit = WireHitRange[kwire].second;

    // max allowable time difference between projected cluster and a hit
    float timeDiff = 40 * AngleFactor(clpar[1]);
    float dtime;
    
    // the last hit added to the cluster
    unsigned int lastClHit = UINT_MAX;
    if(fcl2hits.size() > 0) {
      lastClHit = fcl2hits[fcl2hits.size()-1];
      if(lastClHit == 0) {
        fAveChg = fHits[lastClHit].Integral();
        fAveHitWidth = fHits[lastClHit].EndTick() - fHits[lastClHit].StartTick();
      }
    } // fcl2hits.size() > 0

    // the projected time of the cluster on this wire
    float prtime = clpar[0] + ((float)kwire - clpar[2]) * clpar[1];
    float chgWinLo = prtime - fChgNearWindow;
    float chgWinHi = prtime + fChgNearWindow;
    float chgrat, hitWidth;
    float hitWidthCut = 0.5 * fAveHitWidth;
    float cnear = 0;
//    float fom;
    if(prt) mf::LogVerbatim("CC")<<"AddLAHit: wire "<<kwire<<" prtime "<<prtime<<" max timeDiff "<<timeDiff<<" fAveChg "<<fAveChg;
    unsigned int imbest = 0;
    unsigned int khit;
    for(khit = firsthit; khit < lasthit; ++khit) {
      // obsolete hit?
      if(inClus[khit] < 0) continue;
      dtime = std::abs(fHits[khit].PeakTime() - prtime);
//      fom = dtime;
      hitWidth = fHits[khit].EndTick() - fHits[khit].StartTick();
      chgrat = 1;
      if(ChkCharge && fAveChg > 0) {
        chgrat = fHits[khit].Integral() / fAveChg;
//        fom *= std::abs(chgrat - 1);
//        fom *= fAveHitWidth / hitWidth;
      }
      if(prt) mf::LogVerbatim("CC")
        <<" Chk W:T "<<kwire<<":"<<(short)fHits[khit].PeakTime()
        <<" dT "<<std::fixed<<std::setprecision(1)<<dtime
        <<" InClus "<<inClus[khit]
        <<" mult "<<fHits[khit].Multiplicity()
        <<" width "<<(int)hitWidth
        <<" MergeAvail "<<mergeAvailable[khit]
        <<" Chi2 "<<std::fixed<<std::setprecision(2)<<fHits[khit].GoodnessOfFit()
        <<" Charge "<<(int)fHits[khit].Integral()
        <<" chgrat "<<std::fixed<<std::setprecision(1)<<chgrat
//        <<" fom "<<std::fixed<<std::setprecision(1)<<fom
//        <<" LoT "<<(int)fHits[khit].StartTick()
//        <<" HiT "<<(int)fHits[khit].EndTick()
        <<" index "<<khit;
      // count charge in the window
      if(fHits[khit].PeakTime() > chgWinLo && fHits[khit].PeakTime() < chgWinHi) cnear += fHits[khit].Integral();
      // projected time outside the Signal time window?
      if(prtime < fHits[khit].StartTick() - timeDiff) continue;
      if(prtime > fHits[khit].EndTick() + timeDiff) continue;
      SigOK = true;
      // hit used?
      if(inClus[khit] > 0) continue;
      // ignore narrow width hits
      if(hitWidth < hitWidthCut) continue;
      // ignore very low charge hits
      if(chgrat < 0.1) continue;
//      dtime = std::abs(prtime - fHits[khit].PeakTime());
      if(dtime < timeDiff) {
        HitOK = true;
        imbest = khit;
        timeDiff = dtime;
      }
    } // khit
    
    if(prt && !HitOK) mf::LogVerbatim("CC")<<" no hit found ";

    if(!HitOK) return;

    if(prt) mf::LogVerbatim("CC")<<" Pick hit time "<<(int)fHits[imbest].PeakTime()<<" hit index "<<imbest;
    
    // merge hits in a multiplet?
    short hnear = 0;
    if(lastClHit != UINT_MAX && fHits[imbest].Multiplicity() > 1) {
      bool doMerge = true;
      // Standard code
      // don't merge if we are close to a vertex
      for(unsigned short ivx = 0; ivx < vtx.size(); ++ivx) {
        if(vtx[ivx].CTP != clCTP) continue;
        if(prt) mf::LogVerbatim("CC")<<" close vtx chk W:T "<<vtx[ivx].Wire<<":"<<(int)vtx[ivx].Time;
        if(std::abs(kwire - vtx[ivx].Wire) < 5 && std::abs(int(fHits[imbest].PeakTime() - vtx[ivx].Time)) < 20 ) {
          if(prt) mf::LogVerbatim("CC")<<" Close to a vertex. Don't merge hits";
          doMerge = false;
        }
      } // ivx
      // Decide which hits in the multiplet to merge. Hits that are well
      // separated from each other should not be merged
      if(doMerge) {
        unsigned short nused = 0;
        // the total charge of the hit multiplet
        float multipletChg = 0.;
        float chicut = AngleFactor(clpar[1]) * fHitMergeChiCut * fHits[lastClHit].RMS();
        // look for a big separation between adjacent hits
        std::pair<size_t, size_t> MultipletRange = FindHitMultiplet(imbest);
        for(size_t jht = MultipletRange.first; jht < MultipletRange.second; ++jht) {
          if(inClus[jht] < 0) continue;
          if(inClus[jht] == 0) multipletChg += fHits[jht].Integral();
          else ++nused;
          // check the neighbor hit separation
          if(jht > MultipletRange.first) {
            // pick the larger RMS of the two hits
            float hitRMS = fHits[jht].RMS();
            if(fHits[jht - 1].RMS() > hitRMS) hitRMS = fHits[jht-1].RMS();
            const float tdiff = std::abs(fHits[jht].PeakTime() - fHits[jht-1].PeakTime()) / hitRMS;
            if(prt) mf::LogVerbatim("CC")<<" Hit RMS chisq "<<tdiff<<" chicut "<<chicut;
            if(tdiff > chicut) doMerge = false;
          } // jht > 0
        } // jht
        if(prt) {
          if(!doMerge) mf::LogVerbatim("CC")
            <<" Hits are well separated. Don't merge them ";
        }
        if(doMerge && nused == 0) {
          // compare the charge with the last hit added?
          if(ChkCharge) {
            // there is a nearby hit
            hnear = 1;
            float chgrat = multipletChg / fHits[lastClHit].Integral();
            if(prt) mf::LogVerbatim("CC")<<" merge hits charge check "
              <<(int)multipletChg<<" Previous hit charge "<<(int)fHits[lastClHit].Integral();
            if(chgrat > 2) doMerge = false;
          }
        } // doMerge && nused == 0
      } // doMerge true
      if(doMerge) {
        // there is a nearby hit and it will be merged
        hnear = -1;
        bool didMerge;
        MergeHits(imbest, didMerge);
      } // doMerge
    } // Hits[imbest].Multiplicity() > 1
    
    // attach to the cluster and fit
    fcl2hits.push_back(imbest);
    FitCluster();
    FitClusterChg();
    chifits.push_back(clChisq);
    hitNear.push_back(hnear);
    // remove the charge of the just added hit
    cnear -= fHits[imbest].Integral();
    if(cnear < 0) cnear = 0;
    // divide by the just added hit charge
    cnear /= fHits[imbest].Integral();
    chgNear.push_back(cnear);
    if(prt) {
      hitWidth = fHits[imbest].EndTick() - fHits[imbest].StartTick();
      mf::LogVerbatim("CC")
      <<" >>LADD"<<pass<<" W:T "<<PrintHit(imbest)
      <<" dT "<<timeDiff
      <<" clChisq "<<clChisq
      <<" Chg "<<(int)fHits[imbest].Integral()
      <<" AveChg "<<(int)fAveChg
      <<" width "<<(int)hitWidth
      <<" AveWidth "<<(int)fAveHitWidth
      <<" fcl2hits size "<<fcl2hits.size();
    } // prt
    // decide what to do with a bad fit
    if(clChisq > fChiCut[pass]) {
      FclTrimUS(1);
      FitCluster();
      HitOK = false;
//      if(prt) mf::LogVerbatim("CC")<<"   LADD- Removed hit. New clChisq "<<std::setprecision(3)<<clChisq<<" nhits "<<fcl2hits.size();
      SigOK = false;
      if(prt) mf::LogVerbatim("CC")<<"   LADD- Removed bad hit. Stopped tracking";
    }
/*
    // stop tracking if previous chisq values were close to the cut.
      // this is an indicator that the track is wandering too much for this pass
    if(chifits.size() > 2 &&
       chifits[chifits.size()-2] > 0.8 * fChiCut[pass]) SigOK = false;
    if(prt) mf::LogVerbatim("CC")<<"  Set SigOK = "<<SigOK;
*/
  } // AddLAHit()

float cluster::ClusterCrawlerAlg::AngleFactor ( float  slope )

private

Definition at line 4506 of file ClusterCrawlerAlg.cxx.

  {
    // returns an angle dependent cluster projection error factor for fitting
    // and hit finding
    
    float slp = std::abs(slope);
    if(slp > 15) slp = 15;
    // return a value between 1 and 4
    float angfac = 1 + 0.03 * slp * slp;
    return angfac;
  }

bool cluster::ClusterCrawlerAlg::areInSameMultiplet ( recob::Hit const &  first_hit, recob::Hit const &  second_hit  )

staticprivate

Returns whether the two hits belong to the same multiplet.

Definition at line 6219 of file ClusterCrawlerAlg.cxx.

References recob::Hit::StartTick(), and recob::Hit::WireID().

    {
      return (first_hit.StartTick() == second_hit.StartTick())
        && (first_hit.WireID() == second_hit.WireID());
    } // ClusterCrawlerAlg::areInSameMultiplet()

void cluster::ClusterCrawlerAlg::CalculateAveHitWidth ( )

private

Definition at line 4519 of file ClusterCrawlerAlg.cxx.

  {
    fAveHitWidth = 0;
    for(unsigned short ii = 0; ii < fcl2hits.size(); ++ii)
      fAveHitWidth += fHits[fcl2hits[ii]].EndTick() - fHits[fcl2hits[ii]].StartTick();
    fAveHitWidth /= (float)fcl2hits.size();
  } // CalculateAveHitWidth

void cluster::ClusterCrawlerAlg::CheckClusterHitFrac ( bool  prt )

private

Definition at line 4238 of file ClusterCrawlerAlg.cxx.

References tca::DeadWireCount().

  {


    // Find the fraction of the wires on the cluster that have
    // hits.
    unsigned int iht = fcl2hits[fcl2hits.size() - 1];
    clEndWir = fHits[iht].WireID().Wire;
    clBeginWir = fHits[fcl2hits[0]].WireID().Wire;
    float hitFrac = (float)(fcl2hits.size() + DeadWireCount()) / (float)(clBeginWir - clEndWir + 1);

    if(hitFrac < fMinHitFrac) {
//      RestoreUnMergedClusterHits(-1);
      if(prt) mf::LogVerbatim("CC")<<"CheckClusterHitFrac: Poor hit fraction "<<hitFrac<<" clBeginWir "<<clBeginWir
        <<" clEndWir "<<clEndWir<<" size "<<fcl2hits.size()<<" DeadWireCount "<<DeadWireCount();
      fcl2hits.clear();
      return;
    } // hitFrac
    
/* TODO: Does this make sense?
    // lop off the last hit if it is part of a hit multiplet
    if(fHits[iht].Multiplicity() > 1) {
      fcl2hits.resize(fcl2hits.size() - 1);
    }
*/
    // check for short track ghosts
    if(fcl2hits.size() < 5) {
      unsigned short nsing = 0;
      for(unsigned short iht = 0; iht < fcl2hits.size(); ++iht) if(fHits[fcl2hits[iht]].Multiplicity() == 1) ++nsing;
      hitFrac = (float)nsing / (float)fcl2hits.size();
      if(hitFrac < fMinHitFrac) {
//        RestoreUnMergedClusterHits(-1);
        fcl2hits.clear();
        if(prt) mf::LogVerbatim("CC")<<"CheckClusterHitFrac: Poor short track hit fraction "<<hitFrac;
        return;
      } // hitFrac
    } // short ghost track check

    // analyze the pattern of nearby charge
    // will need the cluster charge so calculate it here if it isn't defined yet
    if(clBeginChg <= 0) {
      unsigned int iht, nht = 0;
      for(unsigned short ii = 0; ii < fcl2hits.size(); ++ii) {
        iht = fcl2hits[ii];
        clBeginChg += fHits[iht].Integral();
        ++nht;
        if(nht == 8) break;
      }
      clBeginChg /= (float)nht;
    } // clBeginChg == 0
    // handle short vs long clusters
    unsigned short cnt = chgNear.size()/2;
    // get the average charge from <= 30 hits at each end
    if(chgNear.size() > 60) cnt = 30;
    clBeginChgNear = 0;
    clEndChgNear = 0;
    for(unsigned short ids = 0; ids < cnt; ++ids) {
      clBeginChgNear += chgNear[ids];
      clEndChgNear += chgNear[chgNear.size() - 1 - ids];
    }
    clBeginChgNear /= (float)cnt;
    clEndChgNear /= (float)cnt;
    
  } // CheckClusterHitFrac()

void cluster::ClusterCrawlerAlg::CheckHitClusterAssociations ( )

private

Definition at line 1006 of file ClusterCrawlerAlg.cxx.

  {
    // check hit - cluster associations
    
    if(fHits.size() != inClus.size()) {
      mf::LogError("CC")<<"CHCA: Sizes wrong "<<fHits.size()<<" "<<inClus.size();
      return;
    }
    
    unsigned int iht, nErr = 0;
    short clID;
    
    // check cluster -> hit association
    for(unsigned short icl = 0; icl < tcl.size(); ++icl) {
      if(tcl[icl].ID < 0) continue;
      clID = tcl[icl].ID;
      for(unsigned short ii = 0; ii < tcl[icl].tclhits.size(); ++ii) {
        iht = tcl[icl].tclhits[ii];
        if(iht > fHits.size() - 1) {
          mf::LogError("CC")<<"CHCA: Bad tclhits index "<<iht<<" fHits size "<<fHits.size();
          return;
        } // iht > fHits.size() - 1
        if(inClus[iht] != clID) {
          mf::LogError("CC")<<"CHCA: Bad cluster -> hit association. clID "<<clID<<" hit inClus "<<inClus[iht]<<" ProcCode "<<tcl[icl].ProcCode<<" CTP "<<tcl[icl].CTP;
          ++nErr;
          if(nErr > 10) return;
        }
      } // ii
    } // icl
    
    // check hit -> cluster association
    unsigned short icl;
    for(iht = 0; iht < fHits.size(); ++iht) {
      if(inClus[iht] <= 0) continue;
      icl = inClus[iht] - 1;
      // see if the cluster is obsolete
      if(tcl[icl].ID < 0) {
        mf::LogError("CC")<<"CHCA: Hit associated with an obsolete cluster. hit W:T "<<fHits[iht].WireID().Wire<<":"<<(int)fHits[iht].PeakTime()
        <<" tcl[icl].ID "<<tcl[icl].ID;
        ++nErr;
        if(nErr > 10) return;
      }
      if (std::find(tcl[icl].tclhits.begin(), tcl[icl].tclhits.end(), iht) == tcl[icl].tclhits.end()) {
        mf::LogError("CC")<<"CHCA: Bad hit -> cluster association. hit index "<<iht
          <<" W:T "<<fHits[iht].WireID().Wire<<":"<<(int)fHits[iht].PeakTime()<<" inClus "<<inClus[iht];
        ++nErr;
        if(nErr > 10) return;
      }
    } // iht
    
  } // CheckHitClusterAssociations()

bool cluster::ClusterCrawlerAlg::CheckHitDuplicates ( std::string  location, std::string  marker = ""  ) const

private

Returns true if there are no duplicates in the hit list for next cluster.

Definition at line 6257 of file ClusterCrawlerAlg.cxx.

References hits().

    {
      // currently unused, only for debug
      unsigned int nDuplicates = 0;
      std::set<unsigned int> hits;
      for (unsigned int hit: fcl2hits) {
        if (hits.count(hit)) {
          ++nDuplicates;
          mf::LogProblem log("CC");
          log << "Hit #" << hit
            << " being included twice in the future cluster (ID="
            << (tcl.size() + 1) << "?) at location: " << location;
         if (!marker.empty()) log << " (marker: '" << marker << "')";
        }
        hits.insert(hit);
      } // for
      return nDuplicates > 0;
    } // ClusterCrawlerAlg::CheckHitDuplicates()

void cluster::ClusterCrawlerAlg::ChkClusterDS ( )

private

Definition at line 1095 of file ClusterCrawlerAlg.cxx.

References cluster::SortByLowHit().

                                         {
      // Try to extend clusters DS by a few wires. 
      // DS hits may not have been  included in a cluster if they have high 
      // multiplicity or high charge. 
      // Ref ClusterLoop cuts for starting a seed cluster.

      prt = (fDebugPlane == 3);
      
      // use the most generous kink angle cut
      float dThCut = fKinkAngCut[fNumPass - 1];

      if(prt) mf::LogVerbatim("CC")<<"ChkClusterDS clCTP "<<clCTP<<" kink angle cut "<<dThCut;

      const unsigned short tclsize = tcl.size();
      bool didMerge, skipit;
      unsigned short icl, ii, nhm, iv;
      unsigned int iht;
      
      // first merge any hits on the DS end of clusters
      for(icl = 0; icl < tclsize; ++icl) {
        if(tcl[icl].ID < 0) continue;
        if(tcl[icl].CTP != clCTP) continue;
        // ignore clusters that have a Begin vertex
        if(tcl[icl].BeginVtx >= 0) continue;
        // and clusters near a vertex
        skipit = false;
        for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
          if(vtx[iv].CTP != clCTP) continue;
          if(std::abs(vtx[iv].Wire - tcl[icl].BeginWir) > 4) continue;
          if(std::abs(vtx[iv].Time - tcl[icl].BeginTim) > 20) continue;
          skipit = true;
          break;
        }
        if(skipit) continue;
        // check the first few hits
        nhm = 0;
        for(ii = 0; ii < 3; ++ii) {
          iht = fcl2hits[ii];
          if(fHits[iht].Multiplicity() > 1) {
            MergeHits(iht, didMerge);
            if(didMerge) ++nhm;
          }
        } // ii
        if(nhm > 0) {
          // update the Begin parameters in-place
          FitClusterMid(icl, 0, 3);
          tcl[icl].BeginTim = clpar[0];
          tcl[icl].BeginSlp = clpar[1];
          tcl[icl].BeginAng = atan(fScaleF * clpar[1]);
          tcl[icl].BeginSlpErr = clparerr[1];
          tcl[icl].BeginChg = fAveChg;
          tcl[icl].ProcCode += 5000;
          if(prt) mf::LogVerbatim("CC")<<"ChkClusterDS: Merge hits on cluster "<<tcl[icl].ID;
        } // nhm > 0
      } // icl

      float thhits, prevth, hitrms, rmsrat;
      bool ratOK;
      std::vector<unsigned int> dshits;
      for(icl = 0; icl < tclsize; ++icl) {
        if(tcl[icl].ID < 0) continue;
        if(tcl[icl].CTP != clCTP) continue;
        // ignore clusters that have a Begin vertex
        if(tcl[icl].BeginVtx >= 0) continue;
        // and clusters near a vertex
        skipit = false;
        for(iv = 0; iv < vtx.size(); ++iv) {
          if(vtx[iv].CTP != clCTP) continue;
          if(std::abs(vtx[iv].Wire - tcl[icl].BeginWir) > 4) continue;
          if(std::abs(vtx[iv].Time - tcl[icl].BeginTim) > 20) continue;
          skipit = true;
          break;
        }
        if(skipit) continue;
        // ignore clusters with lots of nearby charge
//        if(tcl[icl].BeginChgNear > fChgNearCut) continue;
        // find the angle using the first 2 hits
        unsigned int ih0 = tcl[icl].tclhits[1];
        unsigned int ih1 = tcl[icl].tclhits[0];
        const float slp = (fHits[ih1].PeakTime()    - fHits[ih0].PeakTime()) / 
                          (fHits[ih1].WireID().Wire - fHits[ih0].WireID().Wire);
        prevth = std::atan(fScaleF * slp);
        // move the "origin" to the first hit
        ih0 = ih1;
        unsigned int wire = fHits[ih0].WireID().Wire;
        hitrms = fHits[ih0].RMS();
        float time0 = fHits[ih0].PeakTime();
        float prtime;
        dshits.clear();
        // follow DS a few wires. Stop if any encountered
        // hit is associated with a cluster
        for(ii = 0; ii < 4; ++ii) {
          ++wire;
          if(wire > fLastWire) break;
          prtime = time0 + slp;
          if(prt) mf::LogVerbatim("CC")<<"ChkClusterDS: Try to extend "
            <<tcl[icl].ID<<" to W:T "<<wire<<" hitrms "<<hitrms<<" prevth "<<prevth<<" prtime "<<(int)prtime;
          // stop if no hits on this wire
          if(WireHitRange[wire].first == -2) break;
          unsigned int firsthit = WireHitRange[wire].first;
          unsigned int lasthit = WireHitRange[wire].second;
          bool hitAdded = false;
          for(ih1 = firsthit; ih1 < lasthit; ++ih1) {
            if(inClus[ih1] != 0) continue;
            if(prtime < fHits[ih1].PeakTimeMinusRMS(5)) continue;
            if(prtime > fHits[ih1].PeakTimePlusRMS(5)) continue;
            const float slp = (fHits[ih1].PeakTime() - fHits[ih0].PeakTime()) /
                              (fHits[ih1].WireID().Wire - fHits[ih0].WireID().Wire);
            thhits = std::atan(fScaleF * slp);
            if(prt) mf::LogVerbatim("CC")<<" theta "<<thhits<<" prevth "<<prevth<<" cut "<<dThCut;
            if(std::abs(thhits - prevth) > dThCut) continue;
            // make a hit rms cut for small angle clusters
            ratOK = true;
            if(std::abs(slp) < fLAClusSlopeCut) {
              rmsrat = fHits[ih1].RMS() / hitrms;
              ratOK = rmsrat > 0.3 && rmsrat < 3;
            } else {
              // merge the hits
              bool didMerge;
              MergeHits(ih1, didMerge);
            }
            if(prt) mf::LogVerbatim("CC")<<" rmsrat "<<rmsrat<<" OK? "<<ratOK;
            // require small angle and not wildly different width compared
            // to the first hit in the cluster
            // TODO handle hit multiplets here
            if(ratOK) {
              dshits.push_back(ih1);
              hitAdded = true;
              prevth = thhits;
              ih0 = ih1;
              if(prt) mf::LogVerbatim("CC")<<" Add hit "<<fHits[ih1].WireID().Wire
                <<":"<<(int)fHits[ih1].PeakTime()<<" rmsrat "<<rmsrat;
              break;
            }
          } // ih1
          // stop looking if no hit was added on this wire
          if(!hitAdded) break;
        } // ii
        // Found hits not associated with a different cluster
        if(dshits.size() > 0) {
          // put the tcl cluster into the working vectors
          TmpGet(icl);
          // clobber the hits
          fcl2hits.clear();
          // sort the DS hits
          if(dshits.size() > 1) std::sort(dshits.begin(), dshits.end(), SortByLowHit);
          // stuff them into fcl2hits
          fcl2hits = dshits;
          // Append the existing hits
          for(ii = 0; ii < tcl[icl].tclhits.size(); ++ii) {
            // un-assign the hits so that TmpStore will re-assign them
            iht = tcl[icl].tclhits[ii];
            inClus[iht] = 0;
            fcl2hits.push_back(iht);
          }
          clProcCode += 5000;
          pass = fNumPass - 1;
          FitClusterChg();
          clBeginChg = fAveChg;
          // declare the old one obsolete
          MakeClusterObsolete(icl);
          // add the new one
          if(!TmpStore()) {
            mf::LogError("CC")<<"ChkClusterDS TmpStore failed while extending cluster ID "<<tcl[icl].ID;
            continue;
          }
          const size_t newcl = tcl.size() -1;
          if(prt) {  mf::LogVerbatim("CC")<<" Store "<<newcl; }
          tcl[newcl].BeginVtx = tcl[icl].BeginVtx;
          tcl[newcl].EndVtx = tcl[icl].EndVtx;
        } // dshits.size() > 0
      } // icl
    } // ChkClusterDS

void cluster::ClusterCrawlerAlg::ChkClusterNearbyHits ( bool  prt )

private

Definition at line 5158 of file ClusterCrawlerAlg.cxx.

References recob::Hit::LocalIndex(), recob::Hit::Multiplicity(), recob::Hit::PeakTime(), and recob::Hit::RMS().

    {
      // analyze the hitnear vector
      //  0 = no nearby hit exists
      //  1 = a nearby hit exists but was not merged
      // -1 = a nearby hit was merged
      
      if(fHitMergeChiCut <= 0) return;
      
      if(hitNear.size() != fcl2hits.size()) {
        mf::LogWarning("CC")<<"Coding error: hitNear size != fcl2hits";
        return;
      }
      
      // Analyze the last 6 hits added but don't consider the first few hits
      if(hitNear.size() < 12) return;
      
      // TODO move into loops
      unsigned short ii, indx;
      unsigned short merged = 0;
      unsigned short notmerged = 0;
      for(ii = 0; ii < 6; ++ii) {
        indx = hitNear.size() - 1 - ii;
        if(hitNear[indx] > 0) ++notmerged;
        if(hitNear[indx] < 0) ++merged;
      }
      
      if(prt) mf::LogVerbatim("CC")<<"ChkClusterNearbyHits: nearby hits merged "<<merged<<" not merged "<<notmerged;

      if(notmerged < 2) return;
      
      // a number of nearby hits were not merged while crawling, so the 
      // average charge is probably wrong. Look at the last 6 hits added
      // and merge them if they are close
      bool didMerge;
      for(ii = 0; ii < 6; ++ii) {
        indx = fcl2hits.size() - 1 - ii;
        const unsigned int iht = fcl2hits[indx];
        recob::Hit const& hit = fHits[iht];
        if(hit.Multiplicity() == 2) {
          // quit if localindex does not make sense.
          if (hit.LocalIndex() != 0 && iht == 0) continue;
          // hit doublet. Get the index of the other hit
          unsigned int oht;
          if(hit.LocalIndex() == 0) {
            oht = iht + 1;
          } else {
            oht = iht - 1;
          } // hit.LocalIndex() == 0
          recob::Hit const& other_hit = fHits[oht];
          // TODO use Hit::TimeDistanceAsRMS()
          float hitSep = std::abs(hit.PeakTime() - other_hit.PeakTime());
          hitSep /= hit.RMS();
          if(hitSep < fHitMergeChiCut && inClus[oht] == 0) {
            if(prt) mf::LogVerbatim("CC")<<"Merging hit doublet "
              <<iht<<" W:T "<<fHits[iht].WireID().Wire<<":"<<fHits[iht].PeakTime();
            MergeHits(iht, didMerge);
            if(didMerge) hitNear[indx] = -1;
          } // hitSep OK and not in a cluster
        } // hit doublet
      } // ii
      
      // now re-fit
      FitCluster();
      FitClusterChg();

      if(prt) mf::LogVerbatim("CC")<<"ChkClusterNearbyHits refit cluster. fAveChg= "<<fAveChg;
      
    } // ChkClusterHitNear()

void cluster::ClusterCrawlerAlg::ChkMerge ( )

private

Definition at line 2954 of file ClusterCrawlerAlg.cxx.

References tca::DeadWireCount().

    {
      // Try to merge clusters. Clusters that have been subsumed in other
      // clusters, i.e. no longer valid, have ID < 0
      
      if(tcl.size() < 2) return;
      // The size of the ClusterStore vector will increase while merging
      // is on-going so the upper limit on it1 is fixed tcl.size() - 1 
      // before merging starts

      prt = (fDebugPlane == (short)plane && fDebugWire < 0);
      if(prt) mf::LogVerbatim("CC")<<"ChkMerge on pass "<<pass;
      
      unsigned short it1, it2, nh1, pass1, pass2;
      float bs1, bth1, bt1, bc1, es1, eth1, et1, ec1;
      float bs2, bth2, bt2, bc2, es2, eth2, et2, ec2;
      int bw1, ew1, bw2, ew2, ndead;
      float dth, dw, angcut, chgrat, chgcut, dtim, timecut, bigslp;
      bool bothLong, NoVtx;
      
      int skipcut, tclsize = tcl.size();
      int maxOverlap = 3;
      
      for(it1 = 0; it1 < tclsize - 1; ++it1) {
        // ignore already merged clusters
        if(tcl[it1].ID < 0) continue;
        if(tcl[it1].CTP != clCTP) continue;
        bs1 = tcl[it1].BeginSlp;
        // convert slope to angle
        bth1 = std::atan(fScaleF * bs1);
        // more compact notation for begin/end, wire/time/chg/slp/theta, 1/2
        bw1 = tcl[it1].BeginWir;
        bt1 = tcl[it1].BeginTim;
        bc1 = tcl[it1].BeginChg;
        es1 = tcl[it1].EndSlp;
        eth1 = tcl[it1].EndAng;
        ew1 = tcl[it1].EndWir;
        et1 = tcl[it1].EndTim;
        ec1 = tcl[it1].EndChg;
        nh1 = tcl[it1].tclhits.size();
        pass1 = tcl[it1].ProcCode - 10 * (tcl[it1].ProcCode / 10);
        if(pass1 > fNumPass) pass1 = fNumPass;
        for(it2 = it1 + 1; it2 < tclsize; ++it2) {
          // ignore already merged clusters
          if(tcl[it1].ID < 0) continue;
          if(tcl[it2].ID < 0) continue;
          // only merge if they are in the right cryostat/TPC/plane
          if(tcl[it2].CTP != clCTP) continue;
          // Don't bother if these clusters, if merged, would fail the
          // cluster hit fraction cut
          if(!ChkMergedClusterHitFrac(it1, it2)) {
//            if(prt) mf::LogVerbatim("CC")<<"ID1-2 "<<tcl[it1].ID<<"-"<<tcl[it2].ID<<" fails ChkMergedClusterHitFrac";
            continue;
          }
          bs2 = tcl[it2].BeginSlp;
          bth2 = std::atan(fScaleF * bs2);
          bw2 = tcl[it2].BeginWir;
          bt2 = tcl[it2].BeginTim;
          bc2 = tcl[it2].BeginChg;
          es2 = tcl[it2].EndSlp;
          eth2 = tcl[it2].EndAng;
          ew2 = tcl[it2].EndWir;
          et2 = tcl[it2].EndTim;
          ec2 = tcl[it2].EndChg;
          pass2 = tcl[it2].ProcCode - 10 * (tcl[it2].ProcCode / 10);
          if(pass2 > fNumPass) pass2 = fNumPass;
          // use the more promiscuous pass for cuts
          angcut = fKinkAngCut[pass1];
          if(fKinkAngCut[pass2] > angcut) angcut = fKinkAngCut[pass2];
          skipcut = fMaxWirSkip[pass1];
          if(fMaxWirSkip[pass2] > skipcut) skipcut = fMaxWirSkip[pass2];
          chgcut = fMergeChgCut[pass1];
          if(fMergeChgCut[pass2] > chgcut) chgcut = fMergeChgCut[pass2];
/*
          timecut = fTimeDelta[pass];
          if(fTimeDelta[pass2] > timecut) timecut = fTimeDelta[pass2];
          // increase the time cut for large angle clusters
          timecut *= AngleFactor(clpar[1]);
*/
          // tweak the cuts for long straight tracks
          bothLong = (nh1 > 100 && tcl[it2].tclhits.size() > 100);
          
          // look for US and DS broken clusters w similar angle.
          // US cluster 2 merge with DS cluster 1?
          // This is the most likely occurrence given the order in which
          // clusters are created so put it first.
          dth = std::abs(bth2 - eth1);
          ndead = DeadWireCount(bw2, ew1);
          dw = ew1 - bw2 - ndead;
          // require no vertex between
          NoVtx = (tcl[it1].EndVtx < 0) && (tcl[it2].BeginVtx < 0);
          if(prt && bw2 < (ew1 + maxOverlap) ) mf::LogVerbatim("CC")<<"Chk1 ID1-2 "<<tcl[it1].ID<<"-"<<tcl[it2].ID<<" "<<ew1<<":"<<(int)et1<<" "<<bw2<<":"<<(int)bt2<<" dw "<<dw<<" ndead "<<ndead<<" skipcut "<<skipcut<<" dth "<<dth<<" angcut "<<angcut;
          if(NoVtx && bw2 < (ew1 + maxOverlap) && dw  < skipcut && dth < angcut) {
            chgrat = 2 * fabs(bc2 - ec1) / (bc2 + ec1);
            // ignore the charge cut for long tracks with small dth
            if(bothLong && dth < 0.05) chgrat = 0.;
            // project bw2,bt2 to ew1
            dtim = fabs(bt2 + (ew1-bw2)*bs2 - et1);
            bigslp = std::abs(bs2);
            if(std::abs(es1) > bigslp) bigslp = std::abs(es1);
            timecut = fTimeDelta[pass2] * AngleFactor(bigslp);
            if(prt) mf::LogVerbatim("CC")<<" dtim "<<dtim<<" timecut "<<(int)timecut<<" ec1 "<<ec1<<" bc2 "<<bc2<<" chgrat "<<chgrat<<" chgcut "<<chgcut<<" es1 "<<es1<<" ChkSignal "<<ChkSignal(ew1, et1, bw2, bt2);
            if(chgrat < chgcut && dtim < timecut) {
              // ensure there is a signal between cluster ends
              if(ChkSignal(ew1, et1, bw2, bt2)) {
                DoMerge(it2, it1, 10);
                tclsize = tcl.size();
                break;
              }
            } // chgrat < chgcut ...
          } // US cluster 2 merge with DS cluster 1?
          
          // look for US and DS broken clusters w similar angle
          // US cluster 1 merge with DS cluster 2?
          dth = fabs(bth1 - eth2);
          ndead = DeadWireCount(bw1, ew2);
          dw = ew2 - bw1 - ndead;
          if(prt && bw1 < (ew2 + maxOverlap) && dw  < skipcut) mf::LogVerbatim("CC")<<"Chk2 ID1-2 "<<tcl[it1].ID<<"-"<<tcl[it2].ID<<" "<<bw1<<":"<<(int)bt1<<" "<<bw2<<":"<<(int)et2<<" dw "<<dw<<" ndead "<<ndead<<" skipcut "<<skipcut<<" dth "<<dth<<" angcut "<<angcut;
          // require no vertex between
          NoVtx = (tcl[it2].EndVtx < 0) && (tcl[it1].BeginVtx < 0);
          if(NoVtx && bw1 < (ew2 + maxOverlap) && dw  < skipcut && dth < angcut ) {
            chgrat = 2 * fabs((bc1 - ec2) / (bc1 + ec2));
            // ignore the charge cut for long tracks with small dth
            if(bothLong && dth < 0.05) chgrat = 0.;
            // project sw1,st1 to ew2
            dtim = std::abs(bt1 + (ew2-bw1)*bs1 - et2);
            bigslp = std::abs(bs1);
            if(std::abs(bs2) > bigslp) bigslp = std::abs(bs2);
            timecut = fTimeDelta[pass2] * AngleFactor(bigslp);
            if(prt) mf::LogVerbatim("CC")<<" dtim "<<dtim<<" err "<<dtim<<" timecut "<<(int)timecut<<" chgrat "<<chgrat<<" chgcut "<<chgcut<<" ChkSignal "<<ChkSignal(bw1, bt1, ew2, et2);
            // TODO: we should be checking for a signal here like we did above
            if(chgrat < chgcut && dtim < timecut) {
              if(ChkSignal(bw1, bt1, ew2, et2)) {
                DoMerge(it1, it2, 10);
                tclsize = tcl.size();
                break;
              }
            } // chgrat < chgcut ...
          } // US cluster 1 merge with DS cluster 2
          
          if(bw2 < bw1 && ew2 > ew1) {
            // look for small cl2 within the wire boundary of cl1
            // with similar times and slopes for both clusters
            dth = fabs(eth2 - eth1);
            dtim = fabs(et1 +(ew2 - ew1 - 1)*es1 - et2);
            bigslp = std::abs(es1);
            if(std::abs(es1) > bigslp) bigslp = std::abs(es1);
            timecut = fTimeDelta[pass2] * AngleFactor(bigslp);
            // count the number of wires with no hits on cluster 1
            short nmiss1 = bw1 - ew1 + 1 - tcl[it1].tclhits.size();
            // compare with the number of hits in cluster 2
            short nin2 = tcl[it2].tclhits.size();
            if(prt) mf::LogVerbatim("CC")<<"cl2: "<<ew2<<":"<<(int)et2<<" - "<<bw2<<":"<<(int)bt2
              <<" within cl1 "<<ew1<<":"<<(int)et1<<" - "<<bw1<<":"<<(int)bt1
              <<" ? dth "<<dth<<" dtim "<<dtim<<" nmissed "<<nmiss1<<" timecut "<<timecut<<" FIX THIS CODE";
            // make rough cuts before calling ChkMerge12
            // this may not work well for long wandering clusters
            // TODO fix this code
            bool didit = false;
            if(dth < 1 && dtim < timecut && nmiss1 >= nin2) 
                ChkMerge12(it1, it2, didit);
            if(didit) {
              tclsize = tcl.size();
              break;
            } //didit
          } // small cl2 within the wire boundary of cl1
          
          if(bw1 < bw2 && ew1 > ew2) {
            // look for small cl1 within the wire boundary of cl2
            // with similar times and slopes for both clusters
            dth = std::abs(eth2 - eth1);
            dtim = std::abs(et2 +(ew1 - ew2 - 1)*es2 - et1);
            bigslp = std::abs(es1);
            if(std::abs(es1) > bigslp) bigslp = std::abs(es1);
            timecut = fTimeDelta[pass2] * AngleFactor(bigslp);
            // count the number of wires with no hits on cluster 2
            short nmiss2 = bw2 - ew2 + 1 - tcl[it2].tclhits.size();
            // compare with the number of hits in cluster 1
            short nin1 = tcl[it1].tclhits.size();
            if(prt) mf::LogVerbatim("CC")<<"cl1: "<<ew1<<":"<<(int)et1<<" - "<<bw1<<":"<<(int)bt1
              <<" within cl2 "<<ew2<<":"<<(int)et2<<" - "<<bw2<<":"<<(int)bt2
              <<" ? dth "<<dth<<" dtim "<<dtim<<" nmissed "<<nmiss2<<" timecut "<<timecut<<" FIX THIS CODE";
            // make rough cuts before calling ChkMerge12
            // this may not work well for long wandering clusters
            bool didit = false;
            if(dth < 1 && dtim < timecut && nmiss2 >= nin1) ChkMerge12(it2, it1, didit);
            if(didit) {
              tclsize = tcl.size();
              break;
            } // didit
          } // small cl1 within the wire boundary of cl2
          
          if(tcl[it1].ID < 0) break;
        } // cluster 2
        if(tcl[it1].ID < 0) continue;
      } // cluster 1
    }

void cluster::ClusterCrawlerAlg::ChkMerge12 ( unsigned short  it1, unsigned short  it2, bool &  didit  )

private

Definition at line 3153 of file ClusterCrawlerAlg.cxx.

References cluster::ClusterCrawlerAlg::ClusterStore::EndWir, and cluster::ClusterCrawlerAlg::ClusterStore::tclhits.

  {
    // Calling routine has done a rough check that cluster it2 is a candidate
    // for merging with cluster it1. The wire range spanned by it2 lies
    // within the wire range of it1 and the clusters are reasonably close
    // together in time.
    
    // assume that no merging was done
    didit = false;
    
  if(prt) mf::LogVerbatim("CC")<<"ChkMerge12 "<<tcl[it1].ID<<" "<<tcl[it2].ID;
    
    ClusterStore& cl1 = tcl[it1];
    // fill a vector spanning the length of cluster 1 and filled with the hit time
    int ew1 = tcl[it1].EndWir;
    int bw1 = tcl[it1].BeginWir;
    unsigned int iht, hit;
    int wire;
    std::vector<unsigned int> cl1hits(bw1+1-ew1);
/*
    // fill the vector with 0s
    for(unsigned int wire = ew1; wire <= bw1; ++wire) {
      cl1hits.push_back(0);
    }
*/
    // put in the hit IDs
    for(iht = 0; iht < cl1.tclhits.size(); ++iht) {
      hit = cl1.tclhits[iht];
      wire = fHits[hit].WireID().Wire;
      if(wire - ew1 < 0 || wire - ew1 > (int)cl1hits.size()) {
//        mf::LogError("CC")<<"ChkMerge12 bad wire "<<(wire-ew1);
        return;
      }
      cl1hits[wire - ew1] = hit;
    }
    unsigned int ew2 = tcl[it2].EndWir;
    float et2 = tcl[it2].EndTim;
    // look for the closest wire with a hit on cluster 1
    unsigned int wiron1 = 0;
    // count the number of missing hits
    short nmiss = 0;
    for(wire = ew2 - 1; wire > ew1; --wire) {
      if(cl1hits[wire - ew1] > 0) {
        wiron1 = wire;
        break;
      }
      ++nmiss;
    } // wire
  if(prt) mf::LogVerbatim("CC")<<"chk next US wire "<<wiron1<<" missed "<<nmiss;
    if(wiron1 == 0) return;
    if(nmiss > fMaxWirSkip[pass]) return;
    
    // compare the wires with hits on cluster 2 with the gap in cluster 1
    // the number of hit wires that fit in the gap
    unsigned int hiton2;
    int wiron2;
    unsigned short nfit = 0;
    for(iht = 0; iht < tcl[it2].tclhits.size(); ++iht) {
      hiton2 = tcl[it2].tclhits[iht];
      wiron2 = fHits[hiton2].WireID().Wire;
      if(wiron2 < ew1 || wiron2 > bw1) return;
      if(cl1hits[wiron2 - ew1] == 0) ++nfit;
    }
    // require complete filling of the gap
    if(nfit < tcl[it2].tclhits.size()) return;
    
    // decode the pass for both clusters and select the matching cuts
    unsigned short pass1 = tcl[it1].ProcCode - 10 * (tcl[it1].ProcCode / 10);
    unsigned short pass2 = tcl[it2].ProcCode - 10 * (tcl[it2].ProcCode / 10);
    unsigned short cpass = pass1;
    // use the tighter cuts
    if(pass2 < pass1) cpass = pass2;
    
    // ***** Check End of Cluster 2 matching with middle of cluster 1
    if((int) wiron1 - ew1 < 0) return;
    unsigned int hiton1 = cl1hits[wiron1 - ew1];
    if(hiton1 > fHits.size() - 1) {
//      mf::LogError("CC")<<"ChkMerge12 bad hiton1 "<<hiton1;
      return;
    }
    // check the time difference
    float timon1 = fHits[hiton1].PeakTime();
    float dtim = std::abs(et2 + (wiron1 - ew2) * tcl[it2].EndSlp - timon1);
    if(dtim > fTimeDelta[cpass]) return;
    // check the slope difference. First do a local fit on cluster 1 near
    // the matching point
    FitClusterMid(it1, hiton1, 3);
    if(clChisq > 20.) return;
    // fit parameters are now in clpar.
    // check for angle consistency
    float dth = std::abs(std::atan(fScaleF * clpar[1]) - std::atan(fScaleF * tcl[it2].EndSlp));
  if(prt) mf::LogVerbatim("CC")<<"US dtheta "<<dth<<" cut "<<fKinkAngCut[cpass];
    if(dth > fKinkAngCut[cpass]) return;
    // make a charge ratio cut. fAveChg was calculated in FitClusterMid
    float chgrat = 2 * std::abs(fAveChg - tcl[it2].EndChg) / (fAveChg + tcl[it2].EndChg);
  if(prt) mf::LogVerbatim("CC")<<"US chgrat "<<chgrat<<" cut "<<fMergeChgCut[pass];
    // ensure that there is a signal on any missing wires at the US end of 1
    bool SigOK;
    SigOK = ChkSignal(wiron1, timon1, ew2, et2);
    if(prt) mf::LogVerbatim("CC")<<"US SigOK? "<<SigOK;
    if( !SigOK ) return;


    // ***** Check Begin of Cluster 2 matching with middle of cluster 1
    unsigned int bw2 = tcl[it2].BeginWir;
    float bt2 = tcl[it2].BeginTim;
    nmiss = 0;
    wiron1 = 0;
    for(wire = bw2 + 1; wire < bw1; ++wire) {
      if(cl1hits[wire - ew1] > 0) {
        wiron1 = wire;
        break;
      }
      ++nmiss;
    }
    if(wiron1 == 0) return;
    if(nmiss > fMaxWirSkip[pass]) return;
    // fit this section of cluster 1 with 4 hits starting at the hit on the
    // closest wire and moving DS
    hiton1 = cl1hits[wiron1 - ew1];
    if(hiton1 > fHits.size() - 1) {
//      mf::LogError("CC")<<"ChkMerge12 bad hiton1 "<<hiton1;
      return;
    }
    timon1 = fHits[hiton1].PeakTime();
    dtim = std::abs(bt2 - (wiron1 - bw2) *tcl[it2].BeginSlp - timon1);
    if(dtim > fTimeDelta[cpass]) return;
    FitClusterMid(it1, hiton1, -3);
    if(clChisq > 20.) return;
    // check for angle consistency
    dth = std::abs(std::atan(fScaleF * clpar[1]) - std::atan(fScaleF * tcl[it2].BeginSlp));
  if(prt) mf::LogVerbatim("CC")
      <<"DS dtheta "<<dth<<" cut "<<fKinkAngCut[cpass];
    if(dth > fKinkAngCut[cpass]) return;
    // make a charge ratio cut
    chgrat = 2 * std::abs(fAveChg - tcl[it2].BeginChg) / (fAveChg + tcl[it2].BeginChg);
  if(prt) mf::LogVerbatim("CC")
      <<"DS chgrat "<<chgrat<<" cut "<<fMergeChgCut[pass];
    // ensure that there is a signal on any missing wires at the US end of 1
    SigOK = ChkSignal(wiron1, timon1, bw2, bt2);
 if(prt) mf::LogVerbatim("CC")<<"DS SigOK? "<<SigOK;
    if( !SigOK ) return;

  if(prt) mf::LogVerbatim("CC")<<"Merge em";
    // success. Merge them
    DoMerge(it1, it2, 100);
    didit = true;
  } // ChkMerge12()

bool cluster::ClusterCrawlerAlg::ChkMergedClusterHitFrac ( unsigned short  it1, unsigned short  it2  )

private

Definition at line 4191 of file ClusterCrawlerAlg.cxx.

  {
    // This routine is called before two tcl clusters, it1 and it2, are slated to be
    // merged to see if they will satisfy the minimum hit fraction criterion
    if(it1 > tcl.size()-1) return false;
    if(it2 > tcl.size()-1) return false;
    unsigned int eWire = 99999;
    unsigned int bWire = 0, wire;
    if(tcl[it1].BeginWir > bWire) bWire = tcl[it1].BeginWir;
    if(tcl[it2].BeginWir > bWire) bWire = tcl[it2].BeginWir;
    if(tcl[it1].EndWir < eWire) eWire = tcl[it1].EndWir;
    if(tcl[it2].EndWir < eWire) eWire = tcl[it2].EndWir;
    unsigned int mergedClusterLength = bWire - eWire + 1;
    // define a vector of size = length of the wire range
    std::vector<bool> cHits(mergedClusterLength, false);
    // set the elements true if there is a hit
    unsigned int ii, iht, indx;
    for(ii = 0; ii < tcl[it1].tclhits.size(); ++ii) {
      iht = tcl[it1].tclhits[ii];
      if(iht > fHits.size()-1) {
        mf::LogError("CC")<<"ChkMergedClusterHitFrac bad iht ";
        return false;
      }
      indx = fHits[iht].WireID().Wire - eWire;
      cHits[indx] = true;
    } // ii
    for(ii = 0; ii < tcl[it2].tclhits.size(); ++ii) {
      iht = tcl[it2].tclhits[ii];
      if(iht > fHits.size()-1) {
        mf::LogError("CC")<<"ChkMergedClusterHitFrac bad iht ";
        return false;
      }
      indx = fHits[iht].WireID().Wire - eWire;
      cHits[indx] = true;
    } // ii
    // set cHits true if the wire is dead
    for(ii = 0; ii < cHits.size(); ++ii) {
      wire = eWire + ii;
      if(WireHitRange[wire].first == -1) cHits[ii] = true;
    }
    // count the number of wires with hits
    float nhits = std::count(cHits.begin(), cHits.end(), true);
    float hitFrac = nhits / (float)cHits.size();
    return (hitFrac > fMinHitFrac);
  } // ChkMergedClusterHitFrac

bool cluster::ClusterCrawlerAlg::ChkSignal ( unsigned int  iht, unsigned int  jht  )

private

Definition at line 2735 of file ClusterCrawlerAlg.cxx.

  {
    if(iht > fHits.size() - 1) return false;
    if(jht > fHits.size() - 1) return false;
    unsigned int wire1 = fHits[iht].WireID().Wire;
    float time1 = fHits[iht].PeakTime();
    unsigned int wire2 = fHits[jht].WireID().Wire;
    float time2 = fHits[jht].PeakTime();
    return ChkSignal(wire1, time1, wire2, time2);
  } // ChkSignal

bool cluster::ClusterCrawlerAlg::ChkSignal ( unsigned int  wire1, float  time1, unsigned int  wire2, float  time2  )

private

Definition at line 2747 of file ClusterCrawlerAlg.cxx.

References bin.

  {
    // returns  true if there is a signal on the line between
    // (wire1, time1) and (wire2, time2).
    // Be sure to set time1 < time2 if you are checking for signals on a single wire
    
    // Gaussian amplitude in bins of size 0.15
    const float gausAmp[20] = {1, 0.99, 0.96, 0.90, 0.84, 0.75, 0.67, 0.58, 0.49, 0.40, 0.32, 0.26, 0.20, 0.15, 0.11, 0.08, 0.06, 0.04, 0.03, 0.02};
    
    // return true if fMinAmp is set ignore wire signal checking in this plane
    if(fMinAmp[plane] <= 0) return true;
    
    // get the begin and end right
    unsigned int wireb = wire1;
    float timeb = time1;
    unsigned int wiree = wire2;
    float timee = time2;
    // swap them?
    if(wiree > wireb) {
      wireb = wire2;
      timeb = time2;
      wiree = wire1;
      timee = time1;
    }
    if(wiree < fFirstWire || wiree > fLastWire) return false;
    if(wireb < fFirstWire || wireb > fLastWire) return false;
    
    int wire0 = wiree;
    // checking a single wire?
    float slope = 0;
    bool oneWire = false;
    float prTime, prTimeLo = 0, prTimeHi = 0;
    if(wireb == wiree) {
      oneWire = true;
      if(time1 < time2) {
        prTimeLo = time1;
        prTimeHi = time2;
      } else {
        prTimeLo = time2;
        prTimeHi = time1;
      }
    } else {
      slope = (timeb - timee) / (wireb - wiree);
    }
    
    int bin;
    unsigned short nmissed = 0;
    for(unsigned int wire = wiree; wire < wireb + 1; ++wire) {
      if(oneWire) {
        prTime = (prTimeLo + prTimeHi) / 2;
      } else {
        prTime = timee + (wire - wire0) * slope;
      }
      // skip dead wires
      if(WireHitRange[wire].first == -1) continue;
      // no hits on this wire
      if(WireHitRange[wire].first == -2) ++nmissed;
      unsigned int firsthit = WireHitRange[wire].first;
      unsigned int lasthit = WireHitRange[wire].second;
      //        if(vtxprt) mf::LogVerbatim("CC")<<" wire "<<wire<<" Hit range "<<firsthit<<" "<<lasthit<<" prTime "<<prTime;
      float amp = 0;
      for(unsigned int khit = firsthit; khit < lasthit; ++khit) {
        //          if(vtxprt) mf::LogVerbatim("CC")<<"  hit time "<<fHits[khit].PeakTime()<<" rms "<<fHits[khit].RMS()<<" amp "<<fHits[khit].PeakAmplitude()<<" StartTick "<<fHits[khit].StartTick()<<" EndTick "<<fHits[khit].EndTick();
        if(oneWire) {
          // TODO: This sometimes doesn't work with overlapping hits
          //            if(prTimeHi > fHits[khit].EndTick()) continue;
          //            if(prTimeLo < fHits[khit].StartTick()) continue;
          // A not totally satisfactory solution
          if(prTime < fHits[khit].StartTick()) continue;
          if(prTime > fHits[khit].EndTick()) continue;
          return true;
        } else {
          // skip checking if we are far away from prTime on the positive side
          if(fHits[khit].PeakTime() - prTime > 500) continue;
          bin = std::abs(fHits[khit].PeakTime() - prTime) / fHits[khit].RMS();
          bin /= 0.15;
          if(bin > 19) continue;
          if(bin < 0) continue;
          //            if(vtxprt) mf::LogVerbatim("CC")<<"  bin "<<bin<<" add "<<fHits[khit].PeakAmplitude() * gausAmp[bin]<<" to amp "<<amp;
          // add amplitude from all hits
          amp += fHits[khit].PeakAmplitude() * gausAmp[bin];
        }
      } // khit
      if(amp < fMinAmp[plane]) ++nmissed;
    } // wire
    if(nmissed > fAllowNoHitWire) return false;
    return true;
    
  } // ChkSignal()

void cluster::ClusterCrawlerAlg::ChkVertex ( float  fvw, float  fvt, unsigned short  it1, unsigned short  it2, short  topo  )

private

Definition at line 2539 of file ClusterCrawlerAlg.cxx.

References cluster::ClusterCrawlerAlg::VtxStore::CTP, cluster::ClusterCrawlerAlg::VtxStore::Fixed, cluster::ClusterCrawlerAlg::VtxStore::Time, cluster::ClusterCrawlerAlg::VtxStore::Topo, and cluster::ClusterCrawlerAlg::VtxStore::Wire.

      {
        // Checks the vertex (vw, fvt) against the existing set of vertices.
        // If there a match, clusters it1 and/or it2 are associated with it
        // if there is signal between the existing vertex and the start of
        // the cluster. The topo flag indicates the type of vertex that was
        // found: 1 = US of it1 && US of it2, 2 = US of it1 && DS of it2,
        // 3 = DS of it1 && US of it2, 4 = DS of it1 and DS of it2.
        // didit is set true if a cluster is attached to a (new or old) vertex
        
        if(vtxprt) mf::LogVerbatim("CC")<<" ChkVertex "
          <<tcl[it1].EndWir<<":"<<(int)tcl[it1].EndTim<<" - "<<tcl[it1].BeginWir<<":"<<(int)tcl[it1].BeginTim<<" and "
          <<tcl[it2].EndWir<<":"<<(int)tcl[it2].EndTim<<" - "<<tcl[it2].BeginWir<<":"<<(int)tcl[it2].BeginTim
          <<" topo "<<topo<<" fvw "<<fvw<<" fvt "<<fvt;

        unsigned int vw = (unsigned int)(0.5 + fvw);
        unsigned int iht;

        // don't make vertices using short tracks that are close to
        // long straight clusters. These are most likely due to numerous
        // short delta ray clusters
        if(tcl[it1].tclhits.size() < 10 && tcl[it2].tclhits.size() < 10) {
          for(unsigned short it = 0; it < tcl.size(); ++it) {
            if(it == it1 || it == it2) continue;
            if(tcl[it].ID < 0) continue;
            if(tcl[it].CTP != clCTP) continue;
            if(tcl[it].tclhits.size() < 100) continue;
            if(std::abs(tcl[it].BeginAng - tcl[it].EndAng) > 0.1) continue;
            // don't reject because it is near the end of a long cluster
            if(vw <  tcl[it].EndWir + 5) continue;
            if(vw >  tcl[it].BeginWir - 5) continue;
            for(unsigned short ii = 0; ii < tcl[it].tclhits.size(); ++ii) {
              iht = tcl[it].tclhits[ii];
              if(fHits[iht].WireID().Wire <= vw) {
                if(std::abs(fHits[iht].PeakTime() - fvt) < 60) return;
              } // fHits[iht].WireID().Wire <= vWire
            } // ii
          } // it
        }
        
//        if(vtxprt) mf::LogVerbatim("CC")<<" passed cut1";

        // check vertex and clusters for proximity to existing vertices
        unsigned short nFitOK = 0;
        for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
          if(vtx[iv].CTP != clCTP) continue;
          // make this a really loose cut since the errors on the prospective vertex aren't known yet
          if(PointVertexChi(fvw, fvt, iv) > 300) continue;
          if(vtxprt) mf::LogVerbatim("CC")<<" vtx "<<iv<<" PointVertexChi "<<PointVertexChi(fvw, fvt, iv);
          // got a match. Check the appropriate cluster end and attach
          if( (topo == 1 || topo == 2) && tcl[it1].EndVtx < 0) {
            if(ChkSignal(vw, fvt, tcl[it1].EndWir, tcl[it1].EndTim)) {
              // try to fit
              tcl[it1].EndVtx = iv;
              FitVtx(iv);
              if(vtxprt) mf::LogVerbatim("CC")<<" FitVtx "<<iv<<" WireErr "<<vtx[iv].WireErr<<" ChiDOF "<<vtx[iv].ChiDOF;
              if(vtx[iv].WireErr < fVertex2DWireErrCut && vtx[iv].ChiDOF < 5) {
                ++nFitOK;
              } else {
                // bad fit
                tcl[it1].EndVtx = -99;
                FitVtx(iv);
              } // check fit
            } // ChkSignal
//            if(vtxprt)  mf::LogVerbatim("CC")<<" 12 Attach cl "<<tcl[it1].ID<<" to vtx? "<<iv;
          } else if( (topo == 3 || topo == 4) && tcl[it1].BeginVtx < 0) {
            if(ChkSignal(vw, fvt, tcl[it1].BeginWir, tcl[it1].BeginTim)) {
              tcl[it1].BeginVtx = iv;
              FitVtx(iv);
              if(vtxprt) mf::LogVerbatim("CC")<<" FitVtx "<<iv<<" WireErr "<<vtx[iv].WireErr<<" ChiDOF "<<vtx[iv].ChiDOF;
              if(vtx[iv].WireErr < fVertex2DWireErrCut && vtx[iv].ChiDOF < 5) {
                ++nFitOK;
              } else {
                // bad fit
                tcl[it1].BeginVtx = -99;
                FitVtx(iv);
              } // bad fit
            } // ChkSignal
//            if(vtxprt)  mf::LogVerbatim("CC")<<" 34 Attach cl "<<tcl[it1].ID<<" to vtx? "<<iv;
          } // cluster it2
          if( (topo == 1 || topo == 3) && tcl[it2].EndVtx < 0) {
            if(ChkSignal(vw, fvt, tcl[it2].EndWir, tcl[it2].EndTim)) {
              tcl[it2].EndVtx = iv;
              FitVtx(iv);
              if(vtxprt) mf::LogVerbatim("CC")<<" FitVtx "<<iv<<" WireErr "<<vtx[iv].WireErr<<" ChiDOF "<<vtx[iv].ChiDOF;
              if(vtx[iv].WireErr < fVertex2DWireErrCut && vtx[iv].ChiDOF < 5) {
                ++nFitOK;
              } else {
                // bad fit
                tcl[it2].EndVtx = -99;
                FitVtx(iv);
              } // bad fit
            } // ChkSignal
          } else if( (topo == 2 || topo == 4) && tcl[it2].BeginVtx < 0) {
            if(ChkSignal(vw, fvt, tcl[it2].BeginWir, tcl[it2].BeginTim)) {
              tcl[it2].BeginVtx = iv;
              FitVtx(iv);
              if(vtxprt) mf::LogVerbatim("CC")<<" FitVtx "<<iv<<" WireErr "<<vtx[iv].WireErr<<" ChiDOF "<<vtx[iv].ChiDOF;
              if(vtx[iv].WireErr < fVertex2DWireErrCut && vtx[iv].ChiDOF < 5) {
                ++nFitOK;
              } else {
                // bad fit
                tcl[it2].BeginVtx = -99;
                FitVtx(iv);
              } // bad fit
            } // ChkSignal
          } // cluster it2
          if(nFitOK > 0) {
            if(vtxprt) mf::LogVerbatim("CC")<<" Attached "<<nFitOK<<" clusters to vertex "<<iv;
            return;
          }
        } // iv
        
//        if(vtxprt) mf::LogVerbatim("CC")<<" passed cut2";

        // no match to existing vertices. Ensure that there is a wire signal between
        // the vertex and the appropriate ends of the clusters
        bool SigOK = false;
        if(topo == 1 || topo == 2) {
          SigOK = ChkSignal(vw, fvt, tcl[it1].EndWir, tcl[it1].EndTim);
//          if(vtxprt) mf::LogVerbatim("CC")<<" chk1 vtx W:T "<<vw<<":"<<(int)fvt<<" "<<tcl[it1].EndWir<<":"<<(int)tcl[it1].EndTim<<" SigOK "<<SigOK;
        } else {
          SigOK = ChkSignal(vw, fvt, tcl[it1].BeginWir, tcl[it1].BeginTim);
//          if(vtxprt) mf::LogVerbatim("CC")<<" chk1 vtx W:T "<<vw<<":"<<(int)fvt<<" "<<tcl[it1].BeginWir<<":"<<(int)tcl[it1].BeginTim<<" SigOK "<<SigOK;
        }
//        if(vtxprt) mf::LogVerbatim("CC")<<" SigOK it1 "<<SigOK;
        if(!SigOK) return;
        
        if(topo == 1 || topo == 3) {
          SigOK = ChkSignal(vw, fvt, tcl[it2].EndWir, tcl[it2].EndTim);
//          if(vtxprt) mf::LogVerbatim("CC")<<" chk2 vtx W:T "<<vw<<":"<<(int)fvt<<" "<<tcl[it2].EndWir<<":"<<(int)tcl[it2].EndTim<<" SigOK "<<SigOK;
        } else {
          SigOK = ChkSignal(vw, fvt, tcl[it2].BeginWir, tcl[it2].BeginTim);
//          if(vtxprt) mf::LogVerbatim("CC")<<" chk2 vtx W:T "<<vw<<":"<<(int)fvt<<" "<<tcl[it2].BeginWir<<":"<<(int)tcl[it2].BeginTim<<" SigOK "<<SigOK;
        }
//        if(vtxprt) mf::LogVerbatim("CC")<<" SigOK it2 "<<SigOK;
        if(!SigOK) return;

        VtxStore newvx;
        newvx.Wire = vw;
        newvx.Time = fvt;
        newvx.Topo = topo;
        newvx.CTP = clCTP;
        newvx.Fixed = false;
        vtx.push_back(newvx);
        unsigned short iv = vtx.size() - 1;
        if(topo == 1 || topo == 2) {
          if(tcl[it1].EndVtx >= 0) {
//            mf::LogError("CC")<<"ChkVertex: Coding error trying to make new vtx "<<iv<<"\n";
            vtx.pop_back();
            return;
          }
          tcl[it1].EndVtx = iv;
        } else {
          if(tcl[it1].BeginVtx >= 0) {
//            mf::LogError("CC")<<"ChkVertex: Coding error trying to make new vtx "<<iv<<"\n";
            vtx.pop_back();
            return;
          }
          tcl[it1].BeginVtx = iv;
        }
        if(topo == 1 || topo == 3) {
          if(tcl[it2].EndVtx >= 0) {
//            mf::LogError("CC")<<"ChkVertex: Coding error trying to make new vtx "<<iv<<"\n";
            vtx.pop_back();
            return;
          }
          tcl[it2].EndVtx = iv;
        } else {
          if(tcl[it2].BeginVtx >= 0) {
//            mf::LogError("CC")<<"ChkVertex: Coding error trying to make new vtx "<<iv<<"\n";
            vtx.pop_back();
            return;
          }
          tcl[it2].BeginVtx = iv;
        }
        // fit it
        FitVtx(iv);
        // reject it if the fit is bad
        if(vtx[iv].ChiDOF < 5 && vtx[iv].WireErr < fVertex2DWireErrCut && vtx[iv].TimeErr < 20) {
          if(vtxprt) mf::LogVerbatim("CC")<<" New vtx "<<iv<<" in plane "<<plane<<" topo "<<topo<<" cls "<<tcl[it1].ID<<" "<<tcl[it2].ID<<" W:T "<<(int)vw<<":"<<(int)fvt<<" NClusters "<<vtx[iv].NClusters;
          // Try to refine the cluster hits and vertex position
          if(fRefineVertexClusters) RefineVertexClusters(iv);
        } else {
          if(vtxprt) mf::LogVerbatim("CC")<<" Bad vtx fit "<<vtx[iv].ChiDOF<<" wire err "<<vtx[iv].WireErr<<" TimeErr "<<vtx[iv].TimeErr;
          // clobber the vertex and references to it
          vtx.pop_back();
          if(tcl[it1].BeginVtx == iv) tcl[it1].BeginVtx = -99;
          if(tcl[it1].EndVtx == iv) tcl[it1].EndVtx = -99;
          if(tcl[it2].BeginVtx == iv) tcl[it2].BeginVtx = -99;
          if(tcl[it2].EndVtx == iv) tcl[it2].EndVtx = -99;
        } // bad fit

      } // ChkVertex()

void cluster::ClusterCrawlerAlg::ClearResults

(

)

Deletes all the results (might saves memory)

Note

The current implementation typically does NOT save memory.

Definition at line 142 of file ClusterCrawlerAlg.cxx.

Referenced by GetVertices(), and cluster::ClusterCrawler::produce().

                                       {
    fHits.clear();
    tcl.clear();
    vtx.clear();
    vtx3.clear();
    inClus.clear();
  } // ClusterCrawlerAlg::ClearResults()

bool cluster::ClusterCrawlerAlg::ClusterHitsOK ( short  nHitChk )

private

Definition at line 4847 of file ClusterCrawlerAlg.cxx.

References util::absDiff(), max, and min.

  {
    // Check StartTick and EndTick of hits on adjacent wires overlap as illustrated below.
    // >>>>>> This is OK
    // Wire StartTick    EndTick
    // n    |--------------|
    // n+1              |--------------|
    // n+2                        |--------------|
    // >>>>>> This is NOT OK
    // n    |------|
    // n+1              |-----|
    // n+2                        |------|
    
    if(fcl2hits.size() == 0) return true;
//    if(fAveHitWidth == 0) return true;
   
    unsigned short nHitToChk = fcl2hits.size();
    if(nHitChk > 0) nHitToChk = nHitChk + 1;
    unsigned short ii, indx;

    // require that they overlap
    // add a tolerance to the StartTick - EndTick overlap
    raw::TDCtick_t tol = 30;
    // expand the tolerance for induction planes
    if(plane < geom->Cryostat(cstat).TPC(tpc).Nplanes()-1) tol = 40;
    
    bool posSlope = (fHits[fcl2hits[0]].PeakTime() > fHits[fcl2hits[fcl2hits.size() - 1]].PeakTime());

    if(prt) {
      for(ii = 0; ii < nHitToChk; ++ii) {
        indx = fcl2hits.size() - 1 - ii;
        mf::LogVerbatim("CC")<<"ClusterHitsOK chk "<<fHits[fcl2hits[indx]].WireID().Wire<<" start "<<fHits[fcl2hits[indx]].StartTick()<<" peak "<<fHits[fcl2hits[indx]].PeakTime()<<" end "<<fHits[fcl2hits[indx]].EndTick()<<" posSlope "<<posSlope;
      }
    }

    raw::TDCtick_t hiStartTick, loEndTick;
    for(ii = 0; ii < nHitToChk - 1; ++ii) {
      indx = fcl2hits.size() - 1 - ii;
      // ignore if not on adjacent wires
      if(util::absDiff(fHits[fcl2hits[indx]].WireID().Wire, fHits[fcl2hits[indx-1]].WireID().Wire) > 1) continue;
      hiStartTick = std::max(fHits[fcl2hits[indx]].StartTick(), fHits[fcl2hits[indx-1]].StartTick());
      loEndTick = std::min(fHits[fcl2hits[indx]].EndTick(), fHits[fcl2hits[indx-1]].EndTick());
      if(posSlope) {
        if(loEndTick + tol < hiStartTick) {
//          if(prt) mf::LogVerbatim("CC")<<" bad overlap pos Slope "<<loEndTick<<" > "<<hiStartTick;
          return false;
        }
      } else {
        if(loEndTick + tol < hiStartTick) {
//          if(prt) mf::LogVerbatim("CC")<<" bad overlap neg Slope "<<loEndTick<<" < "<<hiStartTick;
          return false;
        }
      }
    } // ii
//    if(prt) mf::LogVerbatim("CC")<<" Cluster hits are OK";
    return true;
  } // ClusterHitsOK

void cluster::ClusterCrawlerAlg::ClusterInit ( )

private

Definition at line 166 of file ClusterCrawlerAlg.cxx.

  {
    fcl2hits.clear();
    chifits.clear();
    hitNear.clear();
    chgNear.clear();
    fAveChg = -1.;
    fAveHitWidth = -1;
//    unMergedHits.clear();
    clEndChg = -1.;
    clStopCode = 0;
    clProcCode = pass;
  }

void cluster::ClusterCrawlerAlg::ClusterLoop ( )

private

Definition at line 329 of file ClusterCrawlerAlg.cxx.

References art::errors::LogicError, tca::MergeOverlap(), recob::Hit::PeakTime(), tca::PrintClusters(), and tca::PrintHit().

    {
      // looks for seed clusters in a plane and crawls along a trail of hits

      unsigned int nHitsUsed = 0, iwire, jwire, kwire;
      bool AllDone = false, SigOK = false, HitOK = false;
      unsigned int ihit, jhit;
      for(unsigned short thispass = 0; thispass < fNumPass; ++thispass) {
        pass = thispass;
        // look for a starting cluster that spans a block of wires
        unsigned int span = 3;
        if(fMinHits[pass] < span) span = fMinHits[pass];
        for(iwire = fLastWire; iwire > fFirstWire + span; --iwire) {
          // skip bad wires or no hits on the wire
          if(WireHitRange[iwire].first < 0) continue;
          auto ifirsthit = (unsigned int)WireHitRange[iwire].first;
          auto ilasthit = (unsigned int)WireHitRange[iwire].second;
          for(ihit = ifirsthit; ihit < ilasthit; ++ihit) {
            bool ClusterAdded = false;
            recob::Hit const& hit = fHits[ihit];
            // skip used hits
            if(ihit > fHits.size()-1) {
              mf::LogError("CC")<<"ClusterLoop bad ihit "<<ihit<<" fHits size "<<fHits.size();
              return;
            }
            // skip used and obsolete hits
            if(inClus[ihit] != 0) continue;
            // skip narrow hits
            if(fHits[ihit].PeakAmplitude() < fHitMinAmp) continue;
//            prt = (fDebugPlane == (int)plane && (int)iwire == fDebugWire && std::abs((int)hit.PeakTime() - fDebugHit) < 20);
            if((iwire + 1) < span) continue;
            jwire = iwire - span + 1;
            if(prt) mf::LogVerbatim("CC")<<"Found debug hit "<<PrintHit(ihit)<<" on pass"<<pass;
            // skip if good wire and no hit
            if(WireHitRange[jwire].first == -2) continue;
            if(WireHitRange[jwire].first == -1) {
              // Found a dead jwire. Keep looking upstream until we find a good wire
              unsigned int nmissed = 0;
              while(WireHitRange[jwire].first == -1 && jwire > 1 && nmissed < fMaxWirSkip[pass]) {
                --jwire;
                ++nmissed;
              }
              if(prt) mf::LogVerbatim("CC")<<" new jwire "<<jwire<<" dead? "<<WireHitRange[jwire].first;
              if(WireHitRange[jwire].first < 0) continue;
            } // dead jwire
            // Find the hit on wire jwire that best matches a line between
            // a nearby vertex and hit ihit. No constraint if useHit < 0
            unsigned int useHit = 0;
            bool doConstrain = false;
            VtxConstraint(iwire, ihit, jwire, useHit, doConstrain);
            unsigned int jfirsthit = (unsigned int)WireHitRange[jwire].first;
            unsigned int jlasthit = (unsigned int)WireHitRange[jwire].second;
            if(jfirsthit > fHits.size()-1 || jfirsthit > fHits.size()-1) throw art::Exception(art::errors::LogicError)
              <<"ClusterLoop jwire "<<jwire<<" bad firsthit "<<jfirsthit<<" lasthit "<<jlasthit<<" fhits size "<<fHits.size();
            //            if(prt) mf::LogVerbatim("CC")<<" jhit range "<<jfirsthit<<" "<<jlasthit;
            for(jhit = jfirsthit; jhit < jlasthit; ++jhit) {
              if(jhit > fHits.size()-1) throw art::Exception(art::errors::LogicError)
                <<"ClusterLoop bad jhit "<<jhit<<" firsthit "<<jfirsthit<<" lasthit "<<jlasthit<<" fhits size"<<fHits.size();
              // Constraint?
              if(doConstrain && jhit != useHit) continue;
              recob::Hit const& other_hit = fHits[jhit];
              // skip used and obsolete hits
              if(inClus[jhit] != 0) continue;
              // skip narrow hits
              if(fHits[jhit].PeakAmplitude() < fHitMinAmp) continue;
              // start a cluster with these two hits
              ClusterInit();
              fcl2hits.push_back(ihit);
              chifits.push_back(0.);
              hitNear.push_back(0);
              chgNear.push_back(0); // These will be defined if the cluster survives the cuts
              // enter the jhit
              fcl2hits.push_back(jhit);
              chifits.push_back(0.);
              hitNear.push_back(0);
              chgNear.push_back(0);
              clLA = false;
              clpar[0] = other_hit.PeakTime();
              clpar[1] = (hit.PeakTime() - other_hit.PeakTime()) / (iwire - jwire);
              // increase slope errors for large angle clusters
              clparerr[1] = 0.2 * std::abs(clpar[1]);
              clpar[2] = fHits[jhit].WireID().Wire;
              clChisq = 0;
              // now look for hits to add on the intervening wires
              bool clok = false;
              for(kwire = jwire+1; kwire < iwire; ++kwire) {
                // ensure this cluster doesn't cross a vertex
                if(CrawlVtxChk(kwire)) {
                  clok = false;
                  break;
                }
                AddHit(kwire, HitOK, SigOK);
                if(prt) mf::LogVerbatim("CC")<<" HitOK "<<HitOK<<" clChisq "<<clChisq<<" cut "<<fChiCut[pass]<<" ClusterHitsOK "<<ClusterHitsOK(-1);
                // No hit found
                if(!HitOK) break;
                // This should be a really good chisq
                if(clChisq > 2) break;
                // hit widths & overlap not consistent
                if(!ClusterHitsOK(-1)) continue;
                clok = true;
              }
              // drop it?
              if(!clok) continue;
              prt = (fDebugPlane == (int)plane && (int)iwire == fDebugWire && std::abs((int)hit.PeakTime() - fDebugHit) < 20);
              if(prt) mf::LogVerbatim("CC")<<"ADD >>>>> Starting cluster with hits "<<PrintHit(fcl2hits[0])<<" "<<PrintHit(fcl2hits[1])<<" "<<PrintHit(fcl2hits[2])<<" on pass "<<pass;
              // save the cluster begin info
              clBeginWir = iwire;
              clBeginTim = hit.PeakTime();
              clBeginSlp = clpar[1];
              // don't do a small angle crawl if the cluster slope is too large
              // and Large Angle crawling is NOT requested on this pass
              if(!fLACrawl[pass] && std::abs(clBeginSlp) > fLAClusSlopeCut) continue;
              // See if we are trying to start a cluster between a vertex
              // and a cluster that is associated to that vertex. If so, skip it
              if(CrawlVtxChk2()) continue;
              clBeginSlpErr = clparerr[1];
              clBeginChg = 0;
              // Calculate the average width
              fAveHitWidth = 0;
              float chg = 0;
              for(unsigned short kk = 0; kk < fcl2hits.size(); ++kk) {
                fAveHitWidth += fHits[fcl2hits[kk]].EndTick() - fHits[fcl2hits[kk]].StartTick();
                chg += fHits[fcl2hits[kk]].Integral();
              }
              fAveHitWidth /= (float)fcl2hits.size();
              // decide whether to crawl a large angle cluster. Requirements are:
              // 1) the user has set the LACluster angle cut > 0, AND
              // 2) the cluster slope exceeds the cut
              // Note that if condition 1 is met, normal cluster crawling is done
              // only if the slope is less than the cut
              if(fLACrawl[pass] && fLAClusSlopeCut > 0) {
                // LA cluster crawling requested
                if(std::abs(clBeginSlp) > fLAClusSlopeCut) {
                  LACrawlUS();
                } else {
                  CrawlUS();
                } // std::abs(clBeginSlp) > fLAClusAngleCut
              } else {
                // allow clusters of any angle
                CrawlUS();
              } // fLAClusSlopeCut > 0
              if(fcl2hits.size() >= fMinHits[pass]) {
                // it's long enough so save it
                clEndSlp = clpar[1]; // save the slope at the end
                clEndSlpErr = clparerr[1];
                // store the cluster
                if(!TmpStore()) {
                  mf::LogError("CC")<<"Failed to store cluster in plane "<<plane;
                  continue;
                }
                ClusterAdded = true;
                nHitsUsed += fcl2hits.size();
                AllDone = (nHitsUsed == fHits.size());
                break;
              } else {
                // abandon it
                if(prt) mf::LogVerbatim("CC")<<"ClusterLoop: dropped the cluster";
              }
              if(ClusterAdded || AllDone) break;
            } // jhit
            if(AllDone) break;
          } // ihit
          if(AllDone) break;
        } // iwire

        // try to merge clusters 
        if(fDoMerge[pass]) ChkMerge();
        // form 2D vertices
        if(fFindVertices[pass]) FindVertices();

        if(AllDone) break;
        
      } // pass

      // Kill Garbage clusters
      if(fKillGarbageClusters > 0 && !tcl.empty()) KillGarbageClusters();
      // Merge overlapping clusters
      if(fMergeOverlapAngCut > 0) MergeOverlap();
      // Check the DS end of clusters
      if(fChkClusterDS) ChkClusterDS();
      // split clusters using vertices
      if(fVtxClusterSplit) {
        bool didSomething = VtxClusterSplit();
        // iterate once to handle the case where a cluster crosses two vertices
        if(didSomething) VtxClusterSplit();
      }
      // Look for 2D vertices with star topology - short, back-to-back clusters
      if(fFindStarVertices) FindStarVertices();

      if(fDebugPlane == (int)plane) {
        mf::LogVerbatim("CC")<<"Clustering done in plane "<<plane;
        PrintClusters();
      }
      
//      if(unMergedHits.size() > 0) mf::LogError("CC")<<"Found unMergedHits > 0 after post-pass processing";
      
      CheckHitClusterAssociations();
    
  } // ClusterLoop()

void cluster::ClusterCrawlerAlg::ClusterVertex ( unsigned short  it2 )

private

Definition at line 2456 of file ClusterCrawlerAlg.cxx.

    {
      // try to attach cluster it to an existing vertex
      
      if(vtx.size() == 0) return;
      
      unsigned short iv, jv;
      short dwib, dwjb, dwie, dwje;
      bool matchEnd, matchBegin;
      
//      if(vtxprt) mf::LogVerbatim("CC")<<"ClusterVertex: Try to attach cluster "<<tcl[it].ID<<" to existing vertices";
      
      for(iv = 0; iv < vtx.size(); ++iv) {
        // ignore vertices in the wrong cryostat/TPC/Plane
        if(vtx[iv].CTP != clCTP) continue;
        // ignore deleted vertices
        if(vtx[iv].NClusters == 0) continue;
        // determine which end to match - begin or end. Handle short tracks
        matchEnd = false; matchBegin = false;
        if(tcl[it].tclhits.size() < 6) {
          // See which end is closer to this vertex vs other vertices
          dwib = std::abs(vtx[iv].Wire - tcl[it].BeginWir);
          if(dwib > 2) dwib = 2;
          dwie = std::abs(vtx[iv].Wire - tcl[it].EndWir);
          if(dwie > 2) dwie = 2;
          dwjb = 999; dwje = 999;
          for(jv = 0; jv < vtx.size(); ++jv) {
            if(iv == jv) continue;
            if(std::abs(vtx[jv].Time - tcl[it].BeginTim) < 50) {
              if(std::abs(vtx[jv].Wire - tcl[it].BeginWir) < dwjb) 
                dwjb = std::abs(vtx[jv].Wire - tcl[it].BeginWir);
            } // std::abs(vtx[jv].Time - tcl[it].BeginTim) < 50
            if(std::abs(vtx[jv].Time - tcl[it].EndTim) < 50) {
              if(std::abs(vtx[jv].Wire - tcl[it].EndWir) < dwje) 
                dwje = std::abs(vtx[jv].Wire - tcl[it].EndWir);
            } // std::abs(vtx[jv].Time - tcl[it].EndTim) < 50
          } // jv
          matchEnd = tcl[it].EndVtx != iv &&
                    dwie < 3 && dwie < dwje && dwie < dwib;
          matchBegin = tcl[it].BeginVtx != iv && 
                    dwib < 3 && dwib < dwjb && dwib < dwie;
//          if(vtxprt) mf::LogVerbatim("CC")<<" dwib "<<dwib<<" dwie " <<dwie<<" dwjb "<<dwjb<<" dwje "<<dwje;
        } else {
          matchEnd = tcl[it].EndVtx < 0   && vtx[iv].Wire <= tcl[it].EndWir + 2;
          matchBegin = tcl[it].BeginVtx < 0 && vtx[iv].Wire >= tcl[it].BeginWir - 2;
        }
        if(matchEnd) {
          if(vtxprt) mf::LogVerbatim("CC")<<" Match End chi "<<ClusterVertexChi(it, 1, iv)<<" to vtx "<<iv
            <<" signalOK "<<ChkSignal(vtx[iv].Wire, vtx[iv].Time, tcl[it].EndWir, tcl[it].EndTim);
          if(ClusterVertexChi(it, 1, iv) < fVertex2DCut && ChkSignal(vtx[iv].Wire, vtx[iv].Time, tcl[it].EndWir, tcl[it].EndTim)) {
            // good match
            tcl[it].EndVtx = iv;
            // re-fit it
            FitVtx(iv);
            if(vtxprt) mf::LogVerbatim("CC")<<" Add End "<<tcl[it].ID<<" to vtx "<<iv<<" NClusters "<<vtx[iv].NClusters;
            if(vtx[iv].ChiDOF < fVertex2DCut && vtx[iv].WireErr < fVertex2DWireErrCut) return;
            if(vtxprt) mf::LogVerbatim("CC")<<" Bad fit. ChiDOF "<<vtx[iv].ChiDOF<<" WireErr "<<vtx[iv].WireErr<<" Undo it";
            tcl[it].EndVtx = -99;
            FitVtx(iv);
          } // tChi < 3
        } // matchEnd
        
        if(matchBegin) {
          if(vtxprt) mf::LogVerbatim("CC")<<" Match Begin chi "<<ClusterVertexChi(it, 0, iv)<<" to vtx "<<iv
            <<" signalOK "<<ChkSignal(vtx[iv].Wire, vtx[iv].Time, tcl[it].BeginWir, tcl[it].BeginTim);
          if(ClusterVertexChi(it, 0, iv) < fVertex2DCut && ChkSignal(vtx[iv].Wire, vtx[iv].Time, tcl[it].BeginWir, tcl[it].BeginTim)) {
            // good match
            tcl[it].BeginVtx = iv;
            // re-fit it
            FitVtx(iv);
            if(vtxprt) mf::LogVerbatim("CC")<<" Add Begin "<<tcl[it].ID<<" to vtx "<<iv<<" NClusters "<<vtx[iv].NClusters;
            if(vtx[iv].ChiDOF < fVertex2DCut && vtx[iv].WireErr < fVertex2DWireErrCut) return;
            if(vtxprt) mf::LogVerbatim("CC")<<" Bad fit. ChiDOF "<<vtx[iv].ChiDOF<<" WireErr "<<vtx[iv].WireErr<<" Undo it";
            tcl[it].BeginVtx = -99;
            FitVtx(iv);
          } // tChi < 3
        } // matchBegin
      } // iv
    } // ClusterVertex()

float cluster::ClusterCrawlerAlg::ClusterVertexChi ( short  icl, unsigned short  end, unsigned short  ivx  )

private

Definition at line 6320 of file ClusterCrawlerAlg.cxx.

References E.

  {
    // Returns the chisq/DOF between a cluster and a vertex
    
    if(icl > (short)tcl.size()) return 9999;
    if(ivx > vtx.size()) return 9999;
    
    float cwire, cslp, cslpErr, ctick;
    // figure out which cluster to use
    if(icl < 0) {
      if(fcl2hits.size() == 0) return 9999;
      // cluster under construction
      if(end == 0) {
        cwire = clBeginWir;
        cslp = clBeginSlp;
        cslpErr = clBeginSlpErr;
        ctick = clBeginTim;
      } else {
        cwire = clpar[2];
        cslp = clpar[1];
        cslpErr = clparerr[1];
        ctick = clpar[0];
      } // end
    } else {
      // tcl cluster
      if(end == 0) {
        cwire = tcl[icl].BeginWir;
        cslp = tcl[icl].BeginSlp;
        cslpErr = tcl[icl].BeginSlpErr;
        ctick = tcl[icl].BeginTim;
      } else {
        cwire = tcl[icl].EndWir;
        cslp = tcl[icl].EndSlp;
        cslpErr = tcl[icl].EndSlpErr;
        ctick = tcl[icl].EndTim;
      } // end
    }
    
    // Closest approach wire
    float docaW = (vtx[ivx].Wire + cslp * (vtx[ivx].Time - ctick) + cwire * cslp * cslp) / (1 + cslp * cslp);
    float dW = docaW - vtx[ivx].Wire;
    float chi = dW / vtx[ivx].WireErr;
    float totChi = chi * chi;
    dW = vtx[ivx].Wire - cwire;
    float dT = ctick + dW * cslp - vtx[ivx].Time;
    if(cslpErr < 1E-3) cslpErr = 1E-3;
    // increase slope error for large angle clusters
    cslpErr *= AngleFactor(cslp);
    // cluster slope projection error
    float dTErr = dW * cslpErr;
    // squared
    dTErr *= dTErr;
    // add the vertex time error^2 to the cluster projection error^2
    dTErr += vtx[ivx].TimeErr * vtx[ivx].TimeErr;
    if(dTErr < 1E-3) dTErr = 1E-3;
    totChi += dT * dT / dTErr;
    totChi /= 2;
    
    return totChi;
    
  } // ClusterVertexChi

void cluster::ClusterCrawlerAlg::CrawlInit ( )

private

Definition at line 152 of file ClusterCrawlerAlg.cxx.

                                    {
    prt = false; vtxprt = false;
    NClusters = 0;  clBeginSlp = 0; clBeginSlpErr = 0; clBeginTim = 0;
    clBeginWir = 0; clBeginChg = 0; clBeginChgNear = 0; clEndSlp = 0;      clEndSlpErr = 0;
    clEndTim = 0;   clEndWir = 0;   clEndChg = 0; clEndChgNear = 0; clChisq = 0;
    clStopCode = 0; clProcCode = 0; fFirstWire = 0;
    fLastWire = 0; fAveChg = 0.; fChgSlp = 0.; pass = 0;
    fScaleF = 0; WireHitRange.clear();
    // unMergedHits.clear();
    
    ClearResults();
  }

void cluster::ClusterCrawlerAlg::CrawlUS ( )

private

Definition at line 3876 of file ClusterCrawlerAlg.cxx.

  {
    // Crawl along a trail of hits moving upstream

    if(fcl2hits.size() < 2) return;

    unsigned int dhit = fcl2hits[0];
    int dwir = fHits[dhit].WireID().Wire;
    clLA = false;
    
    prt = false;
  if(fDebugPlane == (short)plane && dwir == fDebugWire && fDebugHit > 0)
    prt = std::abs(fHits[dhit].PeakTime() - fDebugHit) < 20;

  if(prt) {
    mf::LogVerbatim myprt("CC");
    myprt<<"******************* Start CrawlUS on pass "<<pass<<" Hits: ";
    for(unsigned short ii = 0; ii < fcl2hits.size(); ++ii) {
      unsigned int iht = fcl2hits[fcl2hits.size() - 1 - ii];
      myprt<<fHits[iht].WireID().Wire<<":"<<(int)fHits[iht].PeakTime()<<" ";
    }
    myprt<<"\n";
  }

    // SigOK = true if there is a ADC signal near the projected cluster position
    bool SigOK = true;
    bool HitOK = true;
    // count the number of missed hits on adjacent wires
    short nmissed = 0;
    // count the number of added hits after skipping
    short nHitAfterSkip = 0;
    bool DidaSkip = false;
    bool PostSkip = false;
    unsigned int it = fcl2hits.size() - 1;
    unsigned int lasthit = fcl2hits[it];
    if(lasthit > fHits.size() - 1) {
      mf::LogError("CC")<<"CrawlUS bad lasthit "<<lasthit;
      return;
    }
    unsigned int lastwire = fHits[lasthit].WireID().Wire;
    if(prt) mf::LogVerbatim("CC")<<"CrawlUS: last wire "<<lastwire<<" hit "<<lasthit;
    
    unsigned int lastWireWithSignal = lastwire;
    unsigned short nDroppedHit = 0;

    for(unsigned int nextwire = lastwire-1; nextwire > fFirstWire; --nextwire) {
      if(prt) mf::LogVerbatim("CC")<<"CrawlUS: next wire "<<nextwire<<" HitRange "<<WireHitRange[nextwire].first;
      // stop crawling if there is a nearby vertex
      if(CrawlVtxChk(nextwire)) {
        if(prt) mf::LogVerbatim("CC")<<"CrawlUS: stop at vertex";
        clStopCode = 6;
        break;
      }
      // Switch to large angle crawling?
      if(std::abs(clpar[1]) > fLAClusSlopeCut) {
        if(prt) mf::LogVerbatim("CC")<<">>>>> CrawlUS: Switching to LACrawlUS";
        LACrawlUS();
        return;
      }
      // add hits and check for PH and width consistency
      AddHit(nextwire, HitOK, SigOK);
      if(prt) mf::LogVerbatim("CC")<<"CrawlUS: HitOK "<<HitOK<<" SigOK "<<SigOK<<" nmissed "<<nmissed;
      if(SigOK) lastWireWithSignal = nextwire;
      if(!HitOK) {
        // no hit on this wire. Was there a signal or dead wire?
        if(SigOK) {
        // no hit on the wire but there is a signal
          ++nmissed;
/*
          // stop if too many missed wires
          if(prt) mf::LogVerbatim("CC")<<" nmissed "<<nmissed<<" cut "<<fMaxWirSkip[pass];
          if(nmissed > fMaxWirSkip[pass]) {
            clStopCode = 1;
            break;
          }
*/
          // see if we are in the PostSkip phase and missed more than 1 wire
          if(PostSkip && nmissed > fMinWirAfterSkip[pass]) {
            // cluster is really short
            if((int)(fcl2hits.size() - nHitAfterSkip) < 4) {
//              RestoreUnMergedClusterHits(-1);
              fcl2hits.clear();
              return;
            }
            if(prt) mf::LogVerbatim("CC")<<" PostSkip && nmissed = "<<nmissed;
            clStopCode = 2;
            FclTrimUS(nHitAfterSkip);
            FitCluster();
            if(clChisq > 90.) {
//              RestoreUnMergedClusterHits(-1);
              fcl2hits.clear();
              return;
            }
            FitCluster();
            return;
          } // PostSkip && nmissed > 
          if(nmissed > 1) {
            DidaSkip = true;
            PostSkip = false;
          }
        } // SigOK
        else {
          // SigOK is false
          clStopCode = 0;
          lasthit = fcl2hits[fcl2hits.size() - 1];
          if((lastWireWithSignal - nextwire) > fAllowNoHitWire) {
            if(prt) mf::LogVerbatim("CC")<<"No hit or signal on wire "<<nextwire<<" last wire with signal "<<lastWireWithSignal<<" exceeding fAllowNoHitWire "<<fAllowNoHitWire<<" Break!";
            break;
          }
        } // else SigOK false
      } // !HitOK
      else {
        if(prt) mf::LogVerbatim("CC")<<" CrawlUS check clChisq "<<clChisq<<" cut "<<fChiCut[pass];
        if(clChisq > fChiCut[pass]) {
          if(fcl2hits.size() < 3) {
            fcl2hits.clear();
            return;
          }
          // a fit error occurred. Lop off the leading hit and refit
          if(prt) mf::LogVerbatim("CC")<<"ADD- Bad clChisq "<<clChisq<<" dropping hit";
          FclTrimUS(1);
          FitCluster();
          ++nDroppedHit;
          if(nDroppedHit > 4) {
            if(prt) mf::LogVerbatim("CC")<<" Too many dropped hits: "<<nDroppedHit<<" Stop crawling";
            break;
          } // too many dropped hits
          if(clChisq > fChiCut[pass]) {
            if(prt) mf::LogVerbatim("CC")<<" Bad clChisq "<<clChisq<<" after dropping hit. Stop crawling";
            break;
          }
          FitClusterChg();
/*
          // bail out if we have had repeated failures
          lasthit = fcl2hits[fcl2hits.size() - 1];
          if((fHits[lasthit].WireID().Wire - nextwire) > fMinWirAfterSkip[pass]) {
            if(prt) mf::LogVerbatim("CC")<<" Too many missed wires "<<(fHits[lasthit].WireID().Wire - nextwire)<<" cut "<<fMinWirAfterSkip[pass];
            break;
          }
*/
          continue;
        } // clChisq > fChiCut[0]
        // monitor the onset of a kink. Look for a progressive increase
        // in chisq for the previous 0 - 2 hits.
        if(chifits.size() > 5 && fKinkChiRat[pass] > 0) {
          if(chifits.size() != fcl2hits.size()) {
            mf::LogError("CC")<<"CrawlUS: chifits size error "<<chifits.size()<<" "<<fcl2hits.size();
            return;
          }
          unsigned short chsiz = chifits.size()-1;
          if(prt) mf::LogVerbatim("CC")<<"Kink chk "<<chifits[chsiz]<<" "<<chifits[chsiz-1]<<" "<<chifits[chsiz-2]<<" "<<chifits[chsiz-3];
          if( chifits[chsiz-1] > fKinkChiRat[pass] * chifits[chsiz-2] &&
              chifits[chsiz]   > fKinkChiRat[pass] * chifits[chsiz-1]) {
            if(fcl2hits.size() != chifits.size()) {
              mf::LogError("CC")<<"bad kink check size "<<chifits.size()<<" "<<fcl2hits.size()<<" plane "<<plane<<" cluster "<<dwir<<":"<<dhit;
              continue;
            }
            if(EndKinkAngle() > fKinkAngCut[pass]) {
              if(prt) mf::LogVerbatim("CC")<<"******************* Stopped tracking - kink angle "<<EndKinkAngle()
                <<" > "<<fKinkAngCut[pass]<<" Removing 3 hits";
              // kill the last 3 hits and refit
              FclTrimUS(3);
              FitCluster();
              FitClusterChg();
              // set the kink stop code and quit
//              clStopCode = 3;
//              break;
            } // kinkang check
          } // chifits check
        } // chifits.size() > 5
        // done with kink check
        // update the cluster Begin information?
        if(fcl2hits.size() == fMaxHitsFit[pass] ||
           fcl2hits.size() == fMinHits[pass]) {
          clBeginSlp = clpar[1];
          clBeginSlpErr = clparerr[1];
        }
        // define the begin cluster charge if it's not defined yet
        if(clBeginChg <= 0 && fAveChg > 0) {
          clBeginChg = fAveChg;
          if(prt) mf::LogVerbatim("CC")<<" Set clBeginChg "<<clBeginChg;
        }
        // reset nmissed
        nmissed = 0;
        // start counting hits added after skipping
        if(DidaSkip) {
          // start PostSkip phase
          PostSkip = true;
          DidaSkip = false;
          nHitAfterSkip = 0;
        } // DidaSkip
        // check for PostSkip phase
        if(PostSkip) {
          // end the PostSkip phase if there are enough hits
          ++nHitAfterSkip;
          if(nHitAfterSkip == fMinWirAfterSkip[pass]) PostSkip = false;
        } 
        // check for bad chisq
        if(clChisq > fChiCut[pass]) {
          if(prt) mf::LogVerbatim("CC")<<"<<ADD- Bad chisq "<<clChisq;
          // remove the last few hits if there is a systematic increase in chisq and re-fit
          float chirat;
          unsigned short lopped = 0;
          for(unsigned short nlop = 0; nlop < 4; ++nlop) {
            unsigned short cfsize = chifits.size() - 1;
            chirat = chifits[cfsize] / chifits[cfsize - 1];
            if(prt) mf::LogVerbatim("CC")<<"chirat "<<chirat<<" last hit "<<fcl2hits[fcl2hits.size()-1];
            if(chirat < 1.2) break;
            if(prt) mf::LogVerbatim("CC")<<"<<ADD- Bad chisq. Bad chirat "<<chirat;
            FclTrimUS(1);
            ++lopped;
            if(fcl2hits.size() < 6) break;
            if(chifits.size() < 6) break;
          } // nlop
          if(fcl2hits.size() < 6) {
            clStopCode = 4;
            if(prt) mf::LogVerbatim("CC")<<"Bad fit chisq - short cluster. Break";
            break;
          }
          if(lopped == 0 && fcl2hits.size() > 5) {
            if(prt) mf::LogVerbatim("CC")<<"<<ADD- Bad chisq. remove 1 hit";
            FclTrimUS(1);
            ++lopped;
          }
          FitCluster();
          FitClusterChg();
          if(prt) mf::LogVerbatim("CC")<<"Bad fit chisq - removed "<<lopped<<" hits. Continue";
        } // clChisq > fChiCut[pass]
      } // !HitOK check
    } // nextwire
    if(prt) mf::LogVerbatim("CC")<<"******************* CrawlUS normal stop. size "<<fcl2hits.size();

    bool reFit = false;
    // end kink angle check
    if(fcl2hits.size() > 5) {
      // check for a kink at the US end
      if(prt) mf::LogVerbatim("CC")<<"EndKinkAngle check "<<EndKinkAngle()<<" cut "<<fKinkAngCut[pass];
      if(EndKinkAngle() > fKinkAngCut[pass]) {
        if(prt) mf::LogVerbatim("CC")<<"EndKinkAngle removes 3 hits ";
        FclTrimUS(3);
        reFit = true;
      }
    } // fcl2hits.size() > 5
    
    // count the number of hits on adjacent wires at the leading edge and
    // ensure that the count is consistent with fMinWirAfterSkip
    if((unsigned short)fcl2hits.size() > fMinWirAfterSkip[pass] + 3) {
      unsigned int ih0 = fcl2hits.size() - 1;
      unsigned int hit0 = fcl2hits[ih0];
      unsigned int uswir = fHits[hit0].WireID().Wire;
      unsigned int nxtwir;
      unsigned short nAdjHit = 0;
      for(unsigned short ii = ih0 - 1; ii > 0; --ii) {
        nxtwir = fHits[ fcl2hits[ii] ].WireID().Wire;
        ++nAdjHit;
        if(nxtwir != uswir + 1) break;
        // break if there are enough hits
        if( nAdjHit == fMinWirAfterSkip[pass] ) break;
        uswir = nxtwir;
      } // ii
      // lop off hits?
      if(nAdjHit < fMinWirAfterSkip[pass]) {
        if(prt) mf::LogVerbatim("CC")<<"fMinWirAfterSkip removes "<<nAdjHit<<" hits ";
        FclTrimUS(nAdjHit);
        reFit = true;
      }
    } // fcl2hits.size() > fMinWirAfterSkip[pass] + 3
    
    // check for a bad hit on the end
    if(!reFit && fcl2hits.size() > 3) {
      float chirat = chifits[chifits.size()-1] / chifits[chifits.size()-2];
      if(prt) mf::LogVerbatim("CC")<<"Last hit chirat "<<chirat<<" cut "<<fKinkChiRat[pass];
      if(prt) mf::LogVerbatim("CC")<<"Check "<<clChisq<<" "<<chifits[chifits.size()-1]<<" "<<chifits[chifits.size()-2];
      if(chirat > fKinkChiRat[pass]) {
        if(prt) mf::LogVerbatim("CC")<<"<<ADD- at end";
        FclTrimUS(1);
        reFit = true;
      }
    } // !reFit
    
    if(reFit) {
      FitCluster();
      FitClusterChg();
    }
    CheckClusterHitFrac(prt);
    if(prt) mf::LogVerbatim("CC")<<"******************* CrawlUS done. Size "
      <<fcl2hits.size()<<" min length for this pass "<<fMinHits[pass];

    prt = false;
  } // CrawlUS()

bool cluster::ClusterCrawlerAlg::CrawlVtxChk ( unsigned int  kwire )

private

Definition at line 1306 of file ClusterCrawlerAlg.cxx.

  {
    
    // returns true if the cluster is near a vertex on wire kwire
    if(vtx.size() == 0) return false;
    unsigned int iht = fcl2hits.size() - 1;
    float wire0 = (0.5 + fHits[fcl2hits[iht]].WireID().Wire);
    float prtime = clpar[0] + (kwire - wire0) * clpar[1];
    for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
      if(vtx[iv].CTP != clCTP) continue;
      if((unsigned int)(0.5 + vtx[iv].Wire) != kwire) continue;
      if(std::abs(prtime - vtx[iv].Time) < 10) return true;
    }
    return false;
  } // CrawlVtxChk()

bool cluster::ClusterCrawlerAlg::CrawlVtxChk2 ( )

private

Definition at line 1271 of file ClusterCrawlerAlg.cxx.

  {
    // returns true if the (presumably short) cluster under construction
    // resides between a vertex and another cluster that is associated with
    // that vertex
    
    if(vtx.size() == 0) return false;
    if(fcl2hits.size() == 0) return false;
    
    unsigned int iht = fcl2hits.size() - 1;
    unsigned short icl;
    float wire0 = (0.5 + fHits[fcl2hits[iht]].WireID().Wire);
    float dt;
    float thclus = std::atan(fScaleF * clpar[1]);

    for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
      if(vtx[iv].CTP != clCTP) continue;
      if(wire0 < vtx[iv].Wire) continue;
      if(wire0 > vtx[iv].Wire + 10) continue;
      dt = clpar[0] + (vtx[iv].Wire - wire0) * clpar[1] - vtx[iv].Time;
      if(std::abs(dt) > 10) continue;
      // cluster points to an US vertex. See if the angle is similar to
      // cluster associated with this vertex
      for(icl = 0; icl < tcl.size(); ++icl) {
        if(tcl[icl].CTP != clCTP) continue;
        if(tcl[icl].EndVtx != iv) continue;
        if(std::abs(tcl[icl].EndAng - thclus) < fKinkAngCut[pass]) return true;
      }
    }
    
    return false;
    
  } // CrawlVtxChk2()

unsigned int cluster::ClusterCrawlerAlg::DeadWireCount ( )

private

Definition at line 6204 of file ClusterCrawlerAlg.cxx.

  {
    // Counts the number of dead wires in the range spanned by fcl2hits
    if(fcl2hits.size() < 2) return 0;
    unsigned int wire, ndead = 0;
    unsigned int iht = fcl2hits[fcl2hits.size()-1];
    unsigned int eWire = fHits[iht].WireID().Wire;
    iht = fcl2hits[0];
    unsigned int bWire = fHits[iht].WireID().Wire + 1;
    for(wire = eWire; wire < bWire; ++wire) if(WireHitRange[wire].first == -1) ++ndead;
    return ndead;
  } // DeadWireCount

unsigned int cluster::ClusterCrawlerAlg::DeadWireCount ( unsigned int  inWire1, unsigned int  inWire2  )

private

Definition at line 6189 of file ClusterCrawlerAlg.cxx.

References tmp.

  {
    if(inWire1 > inWire2) {
      // put in increasing order
      unsigned int tmp = inWire1;
      inWire1 = inWire2;
      inWire2 = tmp;
    } // inWire1 > inWire2
    ++inWire2;
    unsigned int wire, ndead = 0;
    for(wire = inWire1; wire < inWire2; ++wire) if(WireHitRange[wire].first == -1) ++ndead;
    return ndead;
  } // DeadWireCount

static geo::PlaneID cluster::ClusterCrawlerAlg::DecodeCTP ( CTP_t  CTP )

inlinestatic

Definition at line 48 of file ClusterCrawlerAlg.h.

References CTPpad.

Referenced by cluster::LineCluster::produce(), and cluster::ClusterCrawler::produce().

      { return { CTP / (CTPpad*CTPpad), CTP / CTPpad % CTPpad, CTP % CTPpad }; }

float cluster::ClusterCrawlerAlg::DoCA ( short  icl, unsigned short  end, float  vwire, float  vtick  )

private

Definition at line 6277 of file ClusterCrawlerAlg.cxx.

  {
    // Find the Distance of Closest Approach betweeen a cluster and a point (vwire, vtick). The
    // DoCA is returned in Tick units.
    
    if(icl > (short)tcl.size()) return 9999;
    
    float cwire, cslp, ctick;
    // figure out which cluster to use
    if(icl < 0) {
      if(fcl2hits.size() == 0) return 9999;
      // cluster under construction
      if(end == 0) {
        cwire = clBeginWir;
        cslp = clBeginSlp;
        ctick = clBeginTim;
      } else {
        cwire = clpar[2];
        cslp = clpar[1];
        ctick = clpar[0];
      } // end
    } else {
      // tcl cluster
      if(end == 0) {
        cwire = tcl[icl].BeginWir;
        cslp = tcl[icl].BeginSlp;
        ctick = tcl[icl].BeginTim;
      } else {
        cwire = tcl[icl].EndWir;
        cslp = tcl[icl].EndSlp;
        ctick = tcl[icl].EndTim;
      } // end
    }
    
    // Closest approach wire
    float docaW = (vwire + cslp * (vtick - ctick) + cwire * cslp * cslp) / (1 + cslp * cslp);
    float dW = docaW - vwire;
    float dT = ctick + (vwire - cwire) * cslp - vtick;
    return sqrt(dW * dW + dT * dT);
    
  } // DoCA

void cluster::ClusterCrawlerAlg::DoMerge ( unsigned short  it1, unsigned short  it2, short  ProcCode  )

private

Definition at line 3303 of file ClusterCrawlerAlg.cxx.

References cluster::ClusterCrawlerAlg::ClusterStore::BeginAng, cluster::ClusterCrawlerAlg::ClusterStore::BeginChg, cluster::ClusterCrawlerAlg::ClusterStore::BeginChgNear, cluster::ClusterCrawlerAlg::ClusterStore::BeginSlp, cluster::ClusterCrawlerAlg::ClusterStore::BeginSlpErr, cluster::ClusterCrawlerAlg::ClusterStore::BeginTim, cluster::ClusterCrawlerAlg::ClusterStore::BeginVtx, cluster::ClusterCrawlerAlg::ClusterStore::BeginWir, cluster::ClusterCrawlerAlg::ClusterStore::CTP, cluster::ClusterCrawlerAlg::ClusterStore::EndAng, cluster::ClusterCrawlerAlg::ClusterStore::EndChg, cluster::ClusterCrawlerAlg::ClusterStore::EndChgNear, cluster::ClusterCrawlerAlg::ClusterStore::EndSlp, cluster::ClusterCrawlerAlg::ClusterStore::EndSlpErr, cluster::ClusterCrawlerAlg::ClusterStore::EndTim, cluster::ClusterCrawlerAlg::ClusterStore::EndVtx, cluster::ClusterCrawlerAlg::ClusterStore::EndWir, cluster::ClusterCrawlerAlg::ClusterStore::ID, cluster::ClusterCrawlerAlg::ClusterStore::StopCode, and cluster::ClusterCrawlerAlg::ClusterStore::tclhits.

  {
    // Merge clusters.
    
    ClusterStore& cl1 = tcl[it1];
    ClusterStore& cl2 = tcl[it2];
    
    if(cl1.tclhits.size() < 3) return;
    if(cl2.tclhits.size() < 3) return;
/*
    bool myprt = false;
    if(plane == 1 && cl1.ID == 84 && cl2.ID == 63) myprt = true;
*/
    
    unsigned int lowire, hiwire, whsize, ii, iht, indx;
    // do a fit across the boundary between cl1 and cl2 to
    // ensure that they truly should be merged
    unsigned int fithit;
    // Find the low and high wire for both clusters.
    // Assume that cluster 1 is DS
    bool cl1DS = true;
    hiwire = cl1.BeginWir;
    fithit = cl1.tclhits[cl1.tclhits.size() - 2];
    if(cl2.BeginWir > hiwire) {
      hiwire = cl2.BeginWir;
      fithit = cl2.tclhits[cl2.tclhits.size() - 2];
      cl1DS = false;
    }
    lowire = cl1.EndWir;
    if(cl2.EndWir < lowire) lowire = cl2.EndWir;
 
    // make a vector of wire hits
    whsize = hiwire + 2 - lowire;
    std::vector<int> wirehit(whsize, -1);
    // put in the hit IDs for cluster 2
    for(ii = 0; ii < cl2.tclhits.size(); ++ii) {
      iht = cl2.tclhits[ii];
      indx = fHits[iht].WireID().Wire - lowire;
      wirehit[indx] = iht;
     } // iht
    // now cluster 1
    for(ii = 0; ii < cl1.tclhits.size(); ++ii) {
      iht = cl1.tclhits[ii];
      indx = fHits[iht].WireID().Wire - lowire;
      wirehit[indx] = iht;
/*
  if(myprt) mf::LogVerbatim("CC")
    <<"Cl1 hit "<<wire<<":"<<(int)fHits[hit].PeakTime()
    <<" wire index "<<index<<" hit index "<<hit;
*/
    } // iht
    // make the new cluster
    fcl2hits.clear();
    for(std::vector<int>::reverse_iterator rit = wirehit.rbegin(); rit != wirehit.rend(); ++rit) {
      if(*rit < 0) continue;
      fcl2hits.push_back(*rit);
    } // rit
    
    // fit the 6 hits that are near the merging point
    short nhitfit = 6;
    FitClusterMid(fcl2hits, fithit, nhitfit);
//    std::cout<<"Merge "<<cl1.ID<<" "<<cl2.ID<<" clChisq "<<clChisq<<"\n";
    if(clChisq > 5) return;
    
    // mark cl1 and cl2 obsolete
    MakeClusterObsolete(it1);
    MakeClusterObsolete(it2);
 
    short endVtx = 0;
    short begVtx = 0;
    short del1Vtx = -99;
    short del2Vtx = -99;
    if(cl1DS) {
      // use cluster 1 Begin info
      clBeginSlp = cl1.BeginSlp;
      clBeginSlpErr = cl1.BeginSlpErr;
      clBeginAng = cl1.BeginAng;
      clBeginWir = cl1.BeginWir;
      clBeginTim = cl1.BeginTim;
      clBeginChg = cl1.BeginChg;
      clBeginChgNear = cl1.BeginChgNear;
      begVtx = cl1.BeginVtx;
      del1Vtx = cl1.EndVtx;
      // and cluster 2 End info
      clEndSlp = cl2.EndSlp;
      clEndSlpErr = cl2.EndSlpErr;
      clEndAng = cl2.EndAng;
      clEndWir = cl2.EndWir;
      clEndTim = cl2.EndTim;
      clEndChg = cl2.EndChg;
      clEndChgNear = cl2.EndChgNear;
      endVtx = cl2.EndVtx;
      del2Vtx = cl2.BeginVtx;
      clStopCode = cl2.StopCode;
    } else {
      // use cluster 2 Begin info
      clBeginSlp = cl2.BeginSlp;
      clBeginSlpErr = cl2.BeginSlpErr;
      clBeginAng = cl2.BeginAng;
      clBeginWir = cl2.BeginWir;
      clBeginTim = cl2.BeginTim;
      clBeginChg = cl2.BeginChg;
      clBeginChgNear = cl2.BeginChgNear;
      begVtx = cl2.BeginVtx;
      del2Vtx = cl2.EndVtx;
      // and cluster 1 End info
      clEndSlp = cl1.EndSlp;
      clEndSlpErr = cl1.EndSlpErr;
      clEndWir = cl1.EndWir;
      clEndTim = cl1.EndTim;
      clEndChg = cl1.EndChg;
      clEndChgNear = cl1.EndChgNear;
      endVtx = cl1.EndVtx;
      del1Vtx = cl1.BeginVtx;
      clStopCode = cl1.StopCode;
    }

    // append it to the tcl vector
    clCTP = cl1.CTP;
    if(!TmpStore()) return;
    unsigned short itnew = tcl.size()-1;
  if(prt) mf::LogVerbatim("CC")<<"DoMerge "<<cl1.ID<<" "<<cl2.ID<<" -> "<<tcl[itnew].ID;
    // stuff the processor code with the current pass
    tcl[itnew].ProcCode = inProcCode + pass;
    // transfer the vertex info
    // delete a vertex between these two?
    if(del1Vtx >= 0 && del1Vtx == del2Vtx) vtx[del1Vtx].NClusters = 0;
    // preserve the vertex assignments
    tcl[itnew].BeginVtx = begVtx;
    tcl[itnew].EndVtx = endVtx;
  } // DoMerge

static CTP_t cluster::ClusterCrawlerAlg::EncodeCTP ( unsigned int  cryo, unsigned int  tpc, unsigned int  plane  )

inlinestatic

Definition at line 44 of file ClusterCrawlerAlg.h.

References plane.

Referenced by EncodeCTP().

      { return cryo * CTPpad*CTPpad + tpc * CTPpad + plane; }

static CTP_t cluster::ClusterCrawlerAlg::EncodeCTP ( const geo::PlaneID &  planeID )

inlinestatic

Definition at line 46 of file ClusterCrawlerAlg.h.

References geo::CryostatID::Cryostat, EncodeCTP(), geo::PlaneID::Plane, and geo::TPCID::TPC.

      { return EncodeCTP(planeID.Cryostat, planeID.TPC, planeID.Plane); }

float cluster::ClusterCrawlerAlg::EndKinkAngle ( )

private

Definition at line 4168 of file ClusterCrawlerAlg.cxx.

  {
    // find the kink angle (crudely) from the 0th and 2nd hit on the cluster under construction
    
    unsigned int ih0 = fcl2hits.size() - 1;
    unsigned int hit0 = fcl2hits[ih0];
    unsigned int ih2 = ih0 - 2;
    unsigned int hit2 = fcl2hits[ih2];
    float dt02 = fHits[hit2].PeakTime() - fHits[hit0].PeakTime();
    float dw02 = fHits[hit2].WireID().Wire - fHits[hit0].WireID().Wire;
    float th02 = std::atan( fScaleF * dt02 / dw02);
    // and the 3rd and 5th hit
    unsigned int ih3 = ih2 - 1;
    unsigned int hit3 = fcl2hits[ih3];
    unsigned int ih5 = ih3 - 2;
    unsigned int hit5 = fcl2hits[ih5];
    float dt35 = fHits[hit5].PeakTime() - fHits[hit3].PeakTime();
    float dw35 = fHits[hit5].WireID().Wire - fHits[hit3].WireID().Wire;
    float th35 = std::atan(fScaleF * dt35 / dw35);
    return std::abs(th02 - th35);
  }

void cluster::ClusterCrawlerAlg::FclTrimUS ( unsigned short  nTrim )

private

Definition at line 882 of file ClusterCrawlerAlg.cxx.

  {
    
    // Trims nTrim hits off the UpStream end of the fcl2hits, etc vectors.
    if(nTrim == 0) return;
    
    if(nTrim >= fcl2hits.size()) nTrim = fcl2hits.size();
    
//    RestoreUnMergedClusterHits((short)nTrim);
    for(unsigned short ii = 0; ii < nTrim; ++ii) {
      fcl2hits.pop_back();
      chifits.pop_back();
      hitNear.pop_back();
      chgNear.pop_back();
    } // ii
    
  } // FclTrim

void cluster::ClusterCrawlerAlg::FindHammerClusters ( )

private

Definition at line 5638 of file ClusterCrawlerAlg.cxx.

References detinfo::DetectorProperties::ConvertTicksToX(), cluster::ClusterCrawlerAlg::Vtx3Store::CStat, cluster::ClusterCrawlerAlg::VtxStore::CTP, e, tca::EncodeCTP(), cluster::ClusterCrawlerAlg::VtxStore::Fixed, geo::TPCGeo::LocalToWorld(), cluster::ClusterCrawlerAlg::Vtx3Store::ProcCode, cluster::ClusterCrawlerAlg::Vtx3Store::Ptr2D, geo::InvalidWireError::suggestedWireID(), cluster::ClusterCrawlerAlg::VtxStore::Time, cluster::ClusterCrawlerAlg::VtxStore::TimeErr, cluster::ClusterCrawlerAlg::VtxStore::Topo, cluster::ClusterCrawlerAlg::Vtx3Store::TPC, cluster::ClusterCrawlerAlg::VtxStore::Wire, cluster::ClusterCrawlerAlg::Vtx3Store::Wire, geo::WireID::Wire, cluster::ClusterCrawlerAlg::VtxStore::WireErr, X, cluster::ClusterCrawlerAlg::Vtx3Store::X, cluster::ClusterCrawlerAlg::Vtx3Store::XErr, y, cluster::ClusterCrawlerAlg::Vtx3Store::Y, cluster::ClusterCrawlerAlg::Vtx3Store::YErr, cluster::ClusterCrawlerAlg::Vtx3Store::Z, z, and cluster::ClusterCrawlerAlg::Vtx3Store::ZErr.

  {
    // look for a long cluster that stops at a short cluster in two views. This can occur in a CCmu
    // interaction where two protons are emitted back-to-back and are therefore reconstructed as one cluster
    // This routine looks for this signature, and if found, splits the short clusters and creates a new 3D vertex.
    // This routine only considers the case where the long cluster intersects the short cluster at the US (End) end.
    
    unsigned int nPln = geom->Cryostat(cstat).TPC(tpc).Nplanes();
    if(nPln != 3) return;
    
    float ew1, ew2, bw2, fvw;
    
    struct Hammer {
      bool Used;
      unsigned int Wire;  // intersection point of the long cluster and the short cluster
      float Tick;  // intersection point of the long cluster and the short cluster
      float X;
      unsigned short longClIndex;
      unsigned short shortClIndex;
      unsigned short splitPos;
    };
    std::array< std::vector<Hammer>, 3> hamrVec;
    
    const detinfo::DetectorProperties* detprop = lar::providerFrom<detinfo::DetectorPropertiesService>();

    unsigned int ipl;
    bool useit = false;
    for(ipl = 0; ipl < 3; ++ipl) {
      clCTP = EncodeCTP(cstat, tpc, ipl);
      for(unsigned short ic1 = 0; ic1 < tcl.size(); ++ic1) {
        if(tcl[ic1].ID < 0) continue;
        // require a long cluster
        if(tcl[ic1].tclhits.size() < 20) continue;
        if(tcl[ic1].CTP != clCTP) continue;
        // ignore long clusters with an End vertex assignment
        if(tcl[ic1].EndVtx >= 0) continue;
        ew1 = tcl[ic1].EndWir;
        for(unsigned short ic2 = 0; ic2 < tcl.size(); ++ic2) {
          if(tcl[ic2].ID < 0) continue;
          // require a short cluster
          if(tcl[ic2].tclhits.size() > 20) continue;
          // but not too short cluster
          if(tcl[ic2].tclhits.size() < 6) continue;
          if(tcl[ic2].CTP != clCTP) continue;
          ew2 = tcl[ic2].EndWir;
          bw2 = tcl[ic2].BeginWir;
          // check the US end. The End of the long cluster must lie between the Begin and End wire of the
          // short cluster
          if(ew1 < ew2 || ew1 > bw2 ) continue;
          // look for intersection of the two clusters
          float best = 10;
          short ibst = -1;
          unsigned short spos = 0;
          for(unsigned short ii = 0; ii < tcl[ic2].tclhits.size(); ++ii) {
            unsigned int iht = tcl[ic2].tclhits[ii];
            float dw = fHits[iht].WireID().Wire - tcl[ic1].EndWir;
            float dt = fabs(fHits[iht].PeakTime() - tcl[ic1].EndTim - tcl[ic1].EndSlp * dw);
            if(dt < best) {
              best = dt;
              ibst = iht;
              spos = ii;
            }
          } // ii
          if(ibst < 0) continue;
          fvw = 0.5 + fHits[ibst].WireID().Wire;
          Hammer aHam;
          aHam.Used = false;
          aHam.Wire = (0.5 + fvw);
          aHam.Tick = fHits[ibst].PeakTime();
          aHam.X = detprop->ConvertTicksToX((double)aHam.Tick, (int)ipl, (int)tpc, (int)cstat);
//          std::cout<<"aHam "<<" fvw "<<fvw<<" X "<<aHam.X<<" ic1 ID "<<tcl[ic1].ID<<" ic2 ID "<<tcl[ic2].ID<<"\n";
          aHam.longClIndex = ic1;
          aHam.shortClIndex = ic2;
          aHam.splitPos = spos;
          unsigned short indx = hamrVec[ipl].size();
          hamrVec[ipl].resize(indx + 1);
          hamrVec[ipl][indx] = aHam;
//          hamrVec[ipl].push_back(aHam);
          useit = true;
        } // ic2
        if(useit) break;
      } // ic1
    } // ipl
    
    unsigned short noham = 0;
    for(ipl = 0; ipl < 3; ++ipl) if(hamrVec[ipl].size() == 0) ++noham;
    if(noham > 1) return;
    
    // Y,Z limits of the detector
    double local[3] = {0.,0.,0.};
    double world[3] = {0.,0.,0.};
    
    const geo::TPCGeo &thetpc = geom->TPC(tpc, cstat);
    thetpc.LocalToWorld(local,world);
    float YLo = world[1]-geom->DetHalfHeight(tpc,cstat) + 1;
    float YHi = world[1]+geom->DetHalfHeight(tpc,cstat) - 1;
    float ZLo = world[2]-geom->DetLength(tpc,cstat)/2 + 1;
    float ZHi = world[2]+geom->DetLength(tpc,cstat)/2 - 1;

    // Match in 3D
    float dX;
    double y, z;
    unsigned short icl, jpl, jcl, kpl, splitPos;
    for(ipl = 0; ipl < 3; ++ipl) {
      if(hamrVec[ipl].size() == 0) continue;
      jpl = (ipl + 1) % nPln;
      kpl = (jpl + 1) % nPln;
      for(unsigned short ii = 0; ii < hamrVec[ipl].size(); ++ii) {
        if(hamrVec[ipl][ii].Used) continue;
        for(unsigned short jj = 0; jj < hamrVec[jpl].size(); ++jj) {
          if(hamrVec[jpl][jj].Used) continue;
          dX = hamrVec[ipl][ii].X - hamrVec[jpl][jj].X;
          if(fabs(dX) > fVertex3DCut) continue;
          geom->IntersectionPoint(hamrVec[ipl][ii].Wire, hamrVec[jpl][jj].Wire, ipl, jpl, cstat, tpc, y, z);
          if(y < YLo || y > YHi || z < ZLo || z > ZHi) continue;
          // mark them used
          hamrVec[ipl][ii].Used = true;
          hamrVec[jpl][jj].Used = true;
          // make a new 3D vertex
          Vtx3Store newVtx3;
          newVtx3.ProcCode = 7;
          newVtx3.X = 0.5 * (hamrVec[ipl][ii].X + hamrVec[jpl][jj].X);
          // TODO: do this correctly;
          newVtx3.XErr = fabs(hamrVec[ipl][ii].X - hamrVec[jpl][jj].X);
          newVtx3.Y = y;
          newVtx3.YErr = 1; // TODO
          newVtx3.Z = z;
          newVtx3.ZErr = 1;  // TODO
          newVtx3.CStat = cstat;
          newVtx3.TPC = tpc;
          
          // make 2D vertex in ipl
          VtxStore newVtx2;
          newVtx2.Wire = hamrVec[ipl][ii].Wire;
          newVtx2.WireErr = 2;
          newVtx2.Time = hamrVec[ipl][ii].Tick;
          newVtx2.TimeErr = 5;
          newVtx2.Topo = 6;
          newVtx2.Fixed = false;
          icl = hamrVec[ipl][ii].longClIndex;
          newVtx2.CTP = tcl[icl].CTP;
          vtx.push_back(newVtx2);
          unsigned short ivnew = vtx.size() - 1;
          // associate the new vertex with the long cluster
          tcl[icl].EndVtx = ivnew;
          FitVtx(ivnew);
          // stash the index in newVtx3
          newVtx3.Ptr2D[ipl] = (short)ivnew;
          // split the short cluster and associate the new clusters with the new vtx
          icl = hamrVec[ipl][ii].shortClIndex;
          splitPos = hamrVec[ipl][ii].splitPos;
          if(!SplitCluster(icl, splitPos, ivnew)) return;
          
          // make 2D vertex in jpl
          newVtx2.Wire = hamrVec[jpl][jj].Wire;
          newVtx2.Time = hamrVec[jpl][jj].Tick;
          newVtx2.Topo = 6;
          jcl = hamrVec[jpl][jj].longClIndex;
          newVtx2.CTP = tcl[jcl].CTP;
          vtx.push_back(newVtx2);
          ivnew = vtx.size() - 1;
//          std::cout<<"newVtx2 jpl index "<<vtx.size()-1<<" CTP "<<newVtx2.CTP<<"\n";
          // associate the new vertex with the long cluster
          tcl[jcl].EndVtx = ivnew;
          // stash the index in newVtx3
          newVtx3.Ptr2D[jpl] = (short)(vtx.size() - 1);
          // split the short cluster and associate the new clusters with the new vtx
          jcl = hamrVec[jpl][jj].shortClIndex;
          splitPos = hamrVec[jpl][jj].splitPos;
          if(!SplitCluster(jcl, splitPos, vtx.size() - 1)) return;
          FitVtx(ivnew);
//          std::cout<<"Split jpl "<<jpl<<" cl ID "<<tcl[jcl].ID<<" pos "<<splitPos<<" vtx "<<vtx.size()-1<<"\n";
          
          // set the kpl 2D vertex index < 0. Let follow-on code find the 3rd plane vertex
          newVtx3.Ptr2D[kpl] = -1;
          double WPos[3] = {0, y, z};
          try{
            newVtx3.Wire = geom->NearestWire(WPos, kpl, tpc, cstat);
          }
          catch(geo::InvalidWireError const& e) {
            newVtx3.Wire = e.suggestedWireID().Wire; // pick the closest valid wire
          }
//          std::cout<<"3D Vtx "<<ipl<<":"<<ii<<" "<<jpl<<":"<<jj<<" kpl "<<kpl<<" wire "<<newVtx3.Wire<<"\n";
          vtx3.push_back(newVtx3);
        } // jj
      } // ii
    }
    
  } // FindHammerClusters

std::pair< size_t, size_t > cluster::ClusterCrawlerAlg::FindHitMultiplet ( size_t  iHit ) const

private

Returns a pair of first and past-the-last index of all the contiguous hits belonging to the same multiplet

Definition at line 6227 of file ClusterCrawlerAlg.cxx.

    {
      std::pair<size_t, size_t> range{ iHit, iHit };

      range.first = iHit - fHits[iHit].LocalIndex();
      range.second = range.first + fHits[iHit].Multiplicity();
      
      return range;
/*
      const raw::TDCtick_t MultipletStartTime = fHits[iHit].StartTick();
      geo::WireID const& wid = fHits[iHit].WireID();
    
      // detect the first hit with the same start time as the reference hit
      while (range.first > 0) {
        if (fHits[range.first - 1].StartTick() != MultipletStartTime) break;
        if (fHits[range.first - 1].WireID() != wid) break;
        --range.first;
      } // while
      
      // detect the last hit with the same start time as the reference hit
      while (++range.second < fHits.size()) {
        if (fHits[range.second].StartTick() != MultipletStartTime) break;
        if (fHits[range.second].WireID() != wid) break;
      } // while
      return range;
 */
    } // ClusterCrawlerAlg::FindHitMultiplet()

void cluster::ClusterCrawlerAlg::FindStarVertices ( )

private

Definition at line 1916 of file ClusterCrawlerAlg.cxx.

References cluster::ClusterCrawlerAlg::VtxStore::CTP, cluster::ClusterCrawlerAlg::VtxStore::Fixed, tca::PrintClusters(), cluster::ClusterCrawlerAlg::VtxStore::Time, cluster::ClusterCrawlerAlg::VtxStore::TimeErr, cluster::ClusterCrawlerAlg::VtxStore::Topo, cluster::ClusterCrawlerAlg::VtxStore::Wire, and cluster::ClusterCrawlerAlg::VtxStore::WireErr.

    {
      // Make 2D vertices with a star topology with short back-to-back
      // clusters. Vertices must reside on the US end of the longest
      // cluster, so vertex finding uses the End information only.
      // This routine is called after all passes are completed
      // in the current CTP
      if(tcl.size() < 2) return;
      
      // This code has some issues...
      return;

      vtxprt = (fDebugPlane == (int)plane && fDebugHit < 0);
      if(vtxprt) {
        mf::LogVerbatim("CC")<<"FindStarVertices";
        PrintClusters();
      }

      unsigned short vtxSizeIn = vtx.size();

      float fvw = 0.;
      float fvt = 0.;
      float dsl = 0, dth = 0;
      float es1 = 0, es2 = 0;
      float eth1 = 0, eth2 = 0;
      float bt1 = 0, bt2 = 0;
      float et1 = 0, et2 = 0;
      float bw1 = 0, bw2 = 0;
      float ew1 = 0, ew2 = 0;
      float lotime = 0, hitime = 0, nwirecut = 0;
      unsigned short tclsize = tcl.size();
      for(unsigned short it1 = 0; it1 < tclsize - 1; ++it1) {
        // ignore obsolete clusters
        if(tcl[it1].ID < 0) continue;
        if(tcl[it1].CTP != clCTP) continue;
        // long dead-straight cluster?
        if(tcl[it1].tclhits.size() > 100) { 
          dth = tcl[it1].BeginAng - tcl[it1].EndAng;
          if(std::abs(dth) < 0.1) continue;
        }
        es1 = tcl[it1].EndSlp;
        eth1 = tcl[it1].EndAng;
        ew1 = tcl[it1].EndWir;
        et1 = tcl[it1].EndTim;
        bw1 = tcl[it1].BeginWir;
        bt1 = tcl[it1].BeginTim;
        for(unsigned short it2 = it1 + 1; it2 < tclsize; ++it2) {
          if(tcl[it2].ID < 0) continue;
          if(tcl[it2].CTP != clCTP) continue;
          // long dead-straight cluster?
          if(tcl[it2].tclhits.size() > 100) { 
            dth = tcl[it2].BeginAng - tcl[it2].EndAng;
            if(std::abs(dth) < 0.05) continue;
          }
          es2 = tcl[it2].EndSlp;
          eth2 = tcl[it2].EndAng;
          ew2 = tcl[it2].EndWir;
          et2 = tcl[it2].EndTim;
          bw2 = tcl[it2].BeginWir;
          bt2 = tcl[it2].BeginTim;
          // require angle difference
          dth = std::abs(eth1 - eth2);
          if(dth < 0.3) continue;
          dsl = es2 - es1;
          fvw = (et1 - ew1 * es1 - et2 + ew2 * es2) / dsl;
          // intersection within the wire boundaries
          if(fvw < ew1 || fvw > bw1) continue;
          if(fvw < ew2 || fvw > bw2) continue;
          if(vtxprt) mf::LogVerbatim("CC")<<"Chk clusters "<<tcl[it1].ID<<" "<<tcl[it2].ID<<" topo5 vtx wire "<<fvw;
          // ensure that the intersection is close to the US end of the longer
          // cluster if it is more than 20 hits long
          if(tcl[it1].tclhits.size() > tcl[it2].tclhits.size()) {
            if(tcl[it1].tclhits.size() > 20) {
              nwirecut = 0.5 * tcl[it1].tclhits.size();
              if((fvw - ew1) > nwirecut) continue;
            }
          } else {
            if(tcl[it2].tclhits.size() > 20) {
              nwirecut = 0.5 * tcl[it2].tclhits.size();
              if((fvw - ew2) > nwirecut) continue;
            }
          }
          fvt = et1 + (fvw - ew1) * es1;
          // and time boundaries
          lotime = 9999;
          if(et1 < lotime) lotime = et1;
          if(bt1 < lotime) lotime = bt1;
          if(et2 < lotime) lotime = et2;
          if(bt2 < lotime) lotime = bt2;
          hitime = 0;
          if(et1 > hitime) hitime = et1;
          if(bt1 > hitime) hitime = bt1;
          if(et2 > hitime) hitime = et2;
          if(bt2 > hitime) hitime = bt2;
          if(fvt < lotime || fvt > hitime) continue;
          if(vtxprt) mf::LogVerbatim("CC")<<" vertex time "<<fvt<<" lotime "<<lotime<<" hitime "<<hitime;
          unsigned int vw = (0.5 + fvw);
          // ensure that the vertex is near a hit on both clusters
          unsigned int pos1 = 0;
          for(unsigned short ii = 0; ii < tcl[it1].tclhits.size(); ++ii) {
            if(fHits[tcl[it1].tclhits[ii]].WireID().Wire <= vw) {
              if(std::abs(int(fHits[tcl[it1].tclhits[ii]].PeakTime() - fvt)) < 10) pos1 = ii;
              break;
            }
          } // ii
          // vertex is not near a hit on cluster 1
          if(pos1 == 0) continue;
          unsigned short pos2 = 0;
          for(unsigned short ii = 0; ii < tcl[it2].tclhits.size(); ++ii) {
            if(fHits[tcl[it2].tclhits[ii]].WireID().Wire <= vw) {
              if(std::abs(int(fHits[tcl[it2].tclhits[ii]].PeakTime() - fvt)) < 10) pos2 = ii;
              break;
            }
          } // ii
          // vertex is not near a hit on cluster 2
          if(pos2 == 0) continue;
          // ensure we aren't near an existing vertex
          for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
            if(std::abs(fvw - vtx[iv].Wire) < 2 &&
               std::abs(fvt - vtx[iv].Time) < 10) continue;
          }
          // make a new vertex
          VtxStore newvx;
          newvx.Wire = fvw;
          newvx.WireErr = 1;
          newvx.Time = fvt;
          newvx.TimeErr = 1;
          newvx.Topo = 5;
          newvx.CTP = clCTP;
          newvx.Fixed = false;
          vtx.push_back(newvx);
          unsigned short ivx = vtx.size() - 1;
          if(vtxprt) mf::LogVerbatim("CC")<<" new vertex "<<ivx<<" cluster "<<tcl[it1].ID<<" split pos "<<pos1;
          if(!SplitCluster(it1, pos1, ivx)) continue;
          tcl[tcl.size()-1].ProcCode += 1000;
          tcl[tcl.size()-2].ProcCode += 1000;
          if(vtxprt) mf::LogVerbatim("CC")<<" new vertex "<<ivx<<" cluster "<<tcl[it2].ID<<" split pos "<<pos2;
          if(!SplitCluster(it2, pos2, ivx)) continue;
          tcl[tcl.size()-1].ProcCode += 1000;
          tcl[tcl.size()-2].ProcCode += 1000;
          FitVtx(ivx);
          break;
        } // it2
      } // it1
            
      if(vtx.size() > vtxSizeIn) {
        // try to split other clusters
        VtxClusterSplit();
        // try to attach other clusters to it
        VertexCluster(vtx.size() - 1);
        FitAllVtx(clCTP);
      } // new vertex

  if(vtxprt) {
    mf::LogVerbatim("CC")<<"Vertices "<<vtx.size();
    for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
      if(vtx[iv].CTP != clCTP) continue;
      mf::LogVerbatim("CC")
        <<"vtx "<<iv<<" wire "<<vtx[iv].Wire<<" time "<<(int)vtx[iv].Time
        <<" NClusters "<<vtx[iv].NClusters<<" topo "<<vtx[iv].Topo;
    }
    PrintClusters();
  }
      
    } // FindStarVertices()

void cluster::ClusterCrawlerAlg::FindVertices ( )

private

Definition at line 2217 of file ClusterCrawlerAlg.cxx.

References greaterThan(), CluLen::index, CluLen::length, and tca::PrintClusters().

    {
      // try to make 2D vertices
      
      if(tcl.size() < 2) return;

      // sort clusters starting with the longest
      std::vector<CluLen> clulens;
      CluLen clulen;
      for(unsigned short icl = 0; icl < tcl.size(); ++icl) {
        if(tcl[icl].ID < 0) continue;
        if(tcl[icl].CTP != clCTP) continue;
        if(tcl[icl].BeginVtx >= 0 && tcl[icl].EndVtx >= 0) continue;
        clulen.index = icl;
        clulen.length = tcl[icl].tclhits.size();
        clulens.push_back(clulen);
      }
      if(clulens.size() == 0) return;
      std::sort (clulens.begin(),clulens.end(), greaterThan);
      
      float nwires = fNumWires;
      float maxtime = fMaxTime;
      
      unsigned short vtxSizeIn = vtx.size();

      vtxprt = (fDebugPlane == (short)plane && fDebugHit < 0);
      if(vtxprt) {
        mf::LogVerbatim("CC")<<"FindVertices plane "<<plane<<" pass "<<pass;
        PrintClusters();
      }

      float es1 = 0, eth1 = 0, ew1 = 0, et1 = 0;
      float bs1 = 0, bth1 = 0, bw1 = 0, bt1 = 0;
      float es2 = 0, eth2 = 0, ew2 = 0, et2 = 0;
      float bs2 = 0, bth2 = 0, bw2 = 0, bt2 = 0;
      float dth = 0,  dsl = 0, fvw = 0, fvt = 0;
      float angcut = 0;
      unsigned int vw = 0, pass1, pass2, ii1, it1, ii2, it2;
      bool SigOK = false;
      for(ii1 = 0; ii1 < clulens.size() - 1; ++ii1) {
        it1 = clulens[ii1].index;
        es1 = tcl[it1].EndSlp;
        eth1 = tcl[it1].EndAng;
        ew1 = tcl[it1].EndWir;
        et1 = tcl[it1].EndTim;
        bs1 = tcl[it1].BeginSlp;
        bth1 = tcl[it1].BeginAng;
        bw1 = tcl[it1].BeginWir;
        bt1 = tcl[it1].BeginTim;
        pass1 = tcl[it1].ProcCode - 10 *(tcl[it1].ProcCode / 10);
        for(ii2 = ii1 + 1; ii2 < clulens.size(); ++ii2) {
          it2 = clulens[ii2].index;
          // try to attach cluster to existing vertices at either end
          ClusterVertex(it2);
          // ignore if both clusters are short
          if(tcl[it1].tclhits.size() < 5 &&
             tcl[it2].tclhits.size() < 5) continue;
          es2 = tcl[it2].EndSlp;
          eth2 = tcl[it2].EndAng;
          ew2 = tcl[it2].EndWir;
          et2 = tcl[it2].EndTim;
          bs2 = tcl[it2].BeginSlp;
          bth2 = tcl[it2].BeginAng;
          bw2 = tcl[it2].BeginWir;
          bt2 = tcl[it2].BeginTim;
          pass2 = tcl[it2].ProcCode - 10 *(tcl[it2].ProcCode / 10);
          if(pass1 < pass2) {
            angcut = fKinkAngCut[pass2];
          } else {
            angcut = fKinkAngCut[pass1];
          }
  // topo 1: check for vtx US of the ends of both clusters
          dth = fabs(eth1 - eth2);
          if(tcl[it1].EndVtx < 0 && tcl[it2].EndVtx < 0 && dth > 0.1) {
            dsl = es2 - es1;
            // find vertex wire and vertex time in float precision (fvw, fvt)
            fvw = (et1 - ew1 * es1 - et2 + ew2 * es2) / dsl;
            // vertex wire in the detector?
            if(fvw > 0. && fvw < nwires) {
              // require vtx in the range of wires with hits AND
              vw = (0.5 + fvw);
              // vtx US of both clusters AND
              // vtx not too far US of both clusters
              if(vw >= fFirstWire - 1 &&
                 fvw <= ew1 + 3    && fvw <= ew2 + 3 &&
                 fvw > (ew1 - 10)  && fvw > (ew2 - 10) ) {
                fvt = et1 + (fvw - ew1) * es1;
                if(vtxprt) mf::LogVerbatim("CC")<<"Chk clusters topo1 "<<tcl[it1].ID<<" "<<tcl[it2].ID<<"  vtx wire "<<vw<<" time "<<(int)fvt<<" dth "<<dth;
                if(fvt > 0 && fvt < maxtime) {
                  // Vertex wire US of cluster ends and time in the detector.
                  // Check for signal at the vertex position and adjust the vertex by 1 wire
                  // if necessary
                  SigOK = ChkSignal(vw, fvt, vw, fvt);
                  if(!SigOK) {
                    fvw += 1.;
                    vw = (0.5 + fvw);
                    SigOK = ChkSignal(vw, fvt, vw, fvt);
                  }
                  // Check this against existing vertices and update
                  if(SigOK) ChkVertex(fvw, fvt, it1, it2, 1);
                } // fvt in detector
              } // vw topo 1 check
            } // fvw in detector
          } // topo 1
  // topo 2: check for vtx US of it1 and DS of it2
          dth = std::abs(eth1 - bth2);
          if(tcl[it1].EndVtx < 0 && tcl[it2].BeginVtx < 0 && dth > angcut) {
            dsl = bs2 - es1;
            if(fabs(ew1 - bw2) < 3 && fabs(et1 - bt2) < 500) {
              fvw = 0.5 * (ew1 + bw2);
            } else {
              fvw = (et1 - ew1 * es1 - bt2 + bw2 * bs2) / dsl;
            }
            if(fvw > 0 && fvw < nwires) {
              // vertex wire in the detector
              vw = (0.5 + fvw);
              // require vtx US of cluster 1 End AND
              //         vtx DS of cluster 2 Begin
              if(fvw <= ew1 + 2  && fvw >= bw2 - 2) {
                fvt  = et1 + (vw - ew1) * es1;
                fvt += bt2 + (vw - bw2) * bs2;
                fvt /= 2;
                if(vtxprt) mf::LogVerbatim("CC")<<"Chk clusters topo2 "<<tcl[it1].ID<<" "<<tcl[it2].ID<<" vtx wire "<<vw<<" time "<<(int)fvt<<" dth "<<dth;
                if(fvt > 0. && fvt < maxtime) {
                  ChkVertex(fvw, fvt, it1, it2, 2);
                } // fvt in detector
              } // vw topo 2 check
            } // fvw in detector
          } // topo 2
  // topo 3: check for vtx DS of it1 and US of it2
          dth = std::abs(bth1 - eth2);
          if(tcl[it1].BeginVtx < 0 && tcl[it2].EndVtx < 0 && dth > angcut) {
            dsl = bs1 - es2;
            if(fabs(bw1 - ew2) < 3 && fabs(bt1 - et2) < 500) {
              fvw = 0.5 * (bw1 + ew2);
            } else {
              fvw = (et2 - ew2 * es2 - bt1 + bw1 * bs1) / dsl;
            }
            if(fvw > 0 && fvw < nwires) {
              vw = (0.5 + fvw);
              // require vtx US of cluster 2 Begin AND
              //         vtx DS of cluster 1 End
              if(fvw <= ew2 + 2 && fvw >= bw1 - 2) {
                fvt  = et2 + (fvw - ew2) * es2;
                fvt += bt1 + (fvw - bw1) * es1;
                fvt /= 2;
                if(vtxprt) mf::LogVerbatim("CC")<<"Chk clusters topo3 "<<tcl[it1].ID<<" "<<tcl[it2].ID<<" vtx wire "<<vw<<" time "<<(int)fvt<<" dth "<<dth;
                if(fvt > 0. && fvt < maxtime) {
                  ChkVertex(fvw, fvt, it1, it2, 3);
                } // fvt in detector
              } // vw topo 3 check
            } // fvw in detector
          } // topo 3
  // topo 4: check for vtx DS of it1 and DS of it2
          dth = std::abs(bth1 - bth2);
          if(tcl[it1].BeginVtx < 0 && tcl[it2].BeginVtx < 0 && dth > 0.1) {
            dsl = bs2 - bs1;
            // find vertex wire and vertex time in float precision (fvw, fvt)
            // convert to integer if within the detector (vw, vt)
            fvw = (bt1 - bw1 * bs1 - bt2 + bw2 * bs2) / dsl;
            if(vtxprt) mf::LogVerbatim("CC")<<"Chk clusters topo4 "<<bw1<<":"<<(int)bt1<<" "<<bw2<<":"<<(int)bt2<<" fvw "<<fvw<<" nwires "<<nwires;
            if(fvw > 0 && fvw < nwires) {
              // vertex wire in the detector
              vw = (0.5 + fvw);
              // require vtx in the range of wires with hits AND vtx DS of both clusters AND
              // vtx not too far DS of both clusters
              float dwcut = 10;
              if(tcl[it1].tclhits.size() < 2 * dwcut) dwcut = tcl[it1].tclhits.size()/2;
              if(tcl[it2].tclhits.size() < 2 * dwcut) dwcut = tcl[it2].tclhits.size()/2;
              if(fvw <= fLastWire + 1 &&
                 fvw >= bw1 - dwcut && fvw <= bw1 + dwcut &&
                 fvw >= bw2 - dwcut && fvw <= bw1 + dwcut) {
                fvt = bt1 + (fvw - bw1) * bs1;
                if(vtxprt) mf::LogVerbatim("CC")<<" vtx wire "<<vw<<" time "<<fvt<<" dth "<<dth<<" dwcut "<<dwcut;
                if(fvt > 0. && fvt < maxtime) {
                  // vertex wire US of cluster ends and time in the detector
                  // Check for signal at the vertex position and adjust the vertex by 1 wire
                  // if necessary
                  SigOK = ChkSignal(vw, fvt, vw, fvt);
                  if(!SigOK) {
                    fvw -= 1.;
                    vw = (0.5 + fvw);
                    SigOK = ChkSignal(vw, fvt, vw, fvt);
                  }
                  // Check this against existing vertices and update
                  if(SigOK) ChkVertex(fvw, fvt, it1, it2, 4);
                } // fvt in detector
              } // vw topo 4 check
            } // fvw in detector
          } // topo4
        } // it2
      } // it1

      // Fix vertices where both ends of a cluster are assigned to the 
      // same vertex. This can happen with short clusters
      for(unsigned short it = 0; it < tcl.size(); ++it) {
        if(tcl[it].ID < 0) continue;
        if(tcl[it].CTP != clCTP) continue;
        if(tcl[it].BeginVtx > -1 && tcl[it].BeginVtx == tcl[it].EndVtx ) {
          unsigned short iv = tcl[it].BeginVtx;
          float dwir = tcl[it].BeginWir - vtx[iv].Wire;
          float dtim = tcl[it].BeginTim - vtx[iv].Time;
          float rbeg = dwir * dwir + dtim * dtim;
          dwir = tcl[it].EndWir - vtx[iv].Wire;
          dtim = tcl[it].EndTim - vtx[iv].Time;
          float rend = dwir * dwir + dtim * dtim;
          if(rend < rbeg) {
            tcl[it].EndVtx = -99;
          } else {
            tcl[it].BeginVtx = -99;
          }
        } // tcl[it].BeginVtx == tcl[it].EndVtx
      } // it

      if(vtx.size() > vtxSizeIn) FitAllVtx(clCTP);
      
      // "delete" any vertices that have only one cluster
      for(unsigned short ivx = 0; ivx < vtx.size(); ++ivx) {
        if(vtx[ivx].CTP != clCTP) continue;
        if(vtx[ivx].NClusters == 1) {
          vtx[ivx].NClusters = 0;
          for(unsigned short icl = 0; icl < tcl.size(); ++icl) {
            if(tcl[icl].CTP != clCTP) continue;
            if(tcl[icl].BeginVtx == ivx) {
              tcl[icl].BeginVtx = -99;
              break;
            }
            if(tcl[icl].EndVtx == ivx) {
              tcl[icl].EndVtx = -99;
              break;
            }
          } // icl
        } // vtx[ivx].NClusters == 1
      } // ivx
      
      
    } // FindVertices()

void cluster::ClusterCrawlerAlg::FitAllVtx ( CTP_t  inCTP )

private

Definition at line 2153 of file ClusterCrawlerAlg.cxx.

      {

        for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
          if(vtx[iv].CTP != inCTP) continue;
          FitVtx(iv);
      }

    } // FitAllVtx

void cluster::ClusterCrawlerAlg::FitCluster ( )

private

Definition at line 4410 of file ClusterCrawlerAlg.cxx.

  {
    // Fits the hits on the US end of a cluster. This routine assumes that
    // wires are numbered from lower (upstream) to higher (downstream) and
    // that the hits in the fclhits vector are sorted so that upstream hits
    // are at the end of the vector


    clChisq = 999.;
    
    if(pass > fNumPass - 1) {
      mf::LogError("CC")<<"FitCluster called on invalid pass "<<pass;
      return;
    }

    unsigned short ii, nht = 0;
    // fit all hits or truncate?
    nht = fcl2hits.size();
    if(clLA) {
      // Fit large angle cluster
      if(nht > fLAClusMaxHitsFit) nht = fLAClusMaxHitsFit;
    } else {
      if(nht > fMaxHitsFit[pass]) nht = fMaxHitsFit[pass];
    }
    if(nht < 2) return;
    
    std::vector<float> xwir;
    std::vector<float> ytim;
    std::vector<float> ytimerr2;
    // apply an angle dependent scale factor.
    float angfactor = AngleFactor(clpar[1]);

    unsigned int wire;
    unsigned int wire0 = fHits[fcl2hits[fcl2hits.size()-1]].WireID().Wire;
    unsigned int ihit;
    float terr, qave = 0, qwt;
    for(ii = 0; ii < nht; ++ii) {
      ihit = fcl2hits[fcl2hits.size() - 1 - ii];
      qave += fHits[ihit].Integral();
    } // ii
    qave /= (float)nht;
    for(ii = 0; ii < nht; ++ii) {
      ihit = fcl2hits[fcl2hits.size() - 1 - ii];
      wire = fHits[ihit].WireID().Wire;
      xwir.push_back(wire - wire0);
      ytim.push_back(fHits[ihit].PeakTime());
      // Scale error by hit multiplicity to account for bias in hit
      // multiplet fitting
      terr = fHitErrFac * fHits[ihit].RMS() * fHits[ihit].Multiplicity();
      if(fAveChg > 0) {
        // increase the error for large charge hits
        qwt = (fHits[ihit].Integral() / qave) - 1;
        if(qwt < 1) qwt = 1;
        terr *= qwt;
      }
      if(terr < 0.01) terr = 0.01;
      ytimerr2.push_back(angfactor * terr * terr);
    }
    CalculateAveHitWidth();
    if(prt) {
      mf::LogVerbatim myprt("CC");
      myprt<<"FitCluster W:T ";
      unsigned short cnt = 0;
      for(std::vector<unsigned int>::reverse_iterator it = fcl2hits.rbegin(); it != fcl2hits.rend(); ++it) {
        unsigned int ihit = *it;
        unsigned short wire = fHits[ihit].WireID().Wire;
        myprt<<wire<<":"<<(short)fHits[ihit].PeakTime()<<" ";
        ++cnt;
        if(cnt == 8) {
          myprt<<" .... ";
          break;
        }
      }
    } // prt
    
    if(xwir.size() < 2) return;

    float intcpt = 0.;
    float slope = 0.;
    float intcpterr = 0.;
    float slopeerr = 0.;
    float chidof = 0.;
    fLinFitAlg.LinFit(xwir, ytim, ytimerr2, intcpt, slope, intcpterr, slopeerr, chidof);
    clChisq = chidof;
    if(chidof > fChiCut[0]) return;
    clpar[0] = intcpt;
    clpar[1] = slope;
    clpar[2] = wire0;
    clparerr[0] = intcpterr;
    clparerr[1] = slopeerr;

    if(prt) mf::LogVerbatim("CC")<<"nht "<<nht<<" fitpar "<<(int)clpar[0]<<"+/-"<<(int)intcpterr
      <<" "<<clpar[1]<<"+/-"<<slopeerr<<" clChisq "<<clChisq;
  
  }

void cluster::ClusterCrawlerAlg::FitClusterChg ( )

private

Definition at line 4528 of file ClusterCrawlerAlg.cxx.

  {
    // Fits the charge of hits on the fcl2hits vector to a line, or simply
    // uses the average of 1 or 2 hits as determined by NHitsAve

    if(fcl2hits.size() == 0) return;
    unsigned int ih0 = fcl2hits.size() - 1;
    
    if(pass >= fNumPass) {
      mf::LogError("CC")<<"FitClusterChg bad pass "<<pass;
      return;
    }
    
    // Handle Large Angle clusters
    if(clLA) {
      // simple average of the charge (and the hit width
      // while we are here)
      unsigned short nhave = fLAClusMaxHitsFit;
      if(nhave > fcl2hits.size()) nhave = fcl2hits.size();
      fAveChg = 0;
      fChgSlp = 0;
      fAveHitWidth = 0;
      unsigned int iht;
      for(unsigned short ii = 0; ii < nhave; ++ii) {
        iht = fcl2hits[fcl2hits.size() - 1 - ii];
        fAveChg += fHits[iht].Integral();
        fAveHitWidth += (fHits[iht].EndTick() - fHits[iht].StartTick());
      } // ii
      fAveChg /= (float)fcl2hits.size();
      fAveHitWidth /= (float)fcl2hits.size();
      return;
    } // clLA

    // number of hits at the leading edge that we will fit
    unsigned short fitLen = fNHitsAve[pass];
    // start fitting charge when there are at least 6 hits if we are tracking
    // long clusters
    if(fitLen > 5 &&  // Fit 6 hits when tracking long clusters AND
       fcl2hits.size() > 5 && // there are at least 6 hits AND
       fcl2hits.size() < fitLen) // there are less than fNHitsAve[pass]
        fitLen = 5;
    
    // don't find the average charge --> no charge cut is made
    if(fNHitsAve[pass] < 1) return;
    
    if(fNHitsAve[pass] == 1) {
      // simply use the charge and width the last hit
      fAveChg = fHits[fcl2hits[ih0]].Integral();
      fChgSlp = 0.;
    } else if(fNHitsAve[pass] == 2) {
      // average the last two points if requested
      fAveChg = (fHits[fcl2hits[ih0]].Integral() + 
                 fHits[fcl2hits[ih0 - 1]].Integral()) / 2.;
      fChgSlp = 0.;
    } else if((unsigned short)fcl2hits.size() > fitLen){
      // do a real fit
      std::vector<float> xwir;
      std::vector<float> ychg;
      std::vector<float> ychgerr2;
      // origin of the fit
      unsigned int wire0 = fHits[fcl2hits[fcl2hits.size()-1]].WireID().Wire;
      // find the mean and rms of the charge
      unsigned short npt = 0;
      unsigned short imlast = 0;
      float ave = 0.;
      float rms = 0.;
      // this loop intentionally ignores the Begin hit
      for(unsigned int ii = fcl2hits.size() - 1; ii > 0; --ii) {
        ++npt;
        float chg = fHits[fcl2hits[ii]].Integral();
        ave += chg;
        rms += chg * chg;
        if(npt == fitLen) {
          imlast = ii;
          break;
        }
      }
      float fnpt = npt;
      ave /= fnpt;
      rms = std::sqrt((rms - fnpt * ave * ave) / (fnpt - 1));
      float chgcut = ave + rms;
      float chg;
      unsigned int wire;
      for(unsigned short ii = fcl2hits.size() - 1; ii > imlast; --ii) {
        wire = fHits[fcl2hits[ii]].WireID().Wire;
        chg = fHits[fcl2hits[ii]].Integral();
        if(chg > chgcut) continue;
        xwir.push_back((float)(wire - wire0));
        ychg.push_back(chg);
        ychgerr2.push_back(chg);
      }
      if(ychg.size() < 3) return;
      float intcpt; float slope; float intcpterr;
      float slopeerr; float chidof;
      fLinFitAlg.LinFit(xwir, ychg, ychgerr2, intcpt, slope, intcpterr, slopeerr, chidof);
  if(prt) mf::LogVerbatim("CC")<<"FitClusterChg wire "<<wire0
    <<" chidof "<<(int)chidof<<" npt "<<xwir.size()
    <<" charge = "<<(int)intcpt<<" slope = "<<(int)slope
    <<" first ave "<<(int)ave<<" rms "<<(int)rms;
      if(chidof > 100.) return;
      // fit must have gone wrong if the fStepCrawlChgRatCut average is greater than
      // the average using all points
      if(intcpt > ave) return;
      // ensure that change does not exceed 30%
      if(fAveChg > 0) {
        ave = intcpt / fAveChg;
        if(ave > 1.3) return;
        if(ave < 0.77) return;
      }
      fAveChg = intcpt;
      fChgSlp = slope;
    }
  } // fitchg

void cluster::ClusterCrawlerAlg::FitClusterMid ( unsigned short  it1, unsigned int  iht, short  nhit  )

private

Definition at line 4304 of file ClusterCrawlerAlg.cxx.

  {
    FitClusterMid(tcl[it1].tclhits, ihtin, nhit);
  } // FitClusterMid

void cluster::ClusterCrawlerAlg::FitClusterMid ( std::vector< unsigned int > &  hitVec, unsigned int  iht, short  nhit  )

private

Definition at line 4310 of file ClusterCrawlerAlg.cxx.

  {
    // Fits hits on temp cluster it1 to a line starting at hit ihtin and including
    // nhit hits incrementing towards the hit vector End when nhit > 0 and
    // decrementing towards the hit vector Begin when nhit < 0.
    // The fit params are stashed in the clpar and clparerr arrays. 
    // fAveChg is re-calculated as well.
    
    
    // set chisq bad in case something doesn't work out
    clChisq = 99.;
    
    if(hitVec.size() < 3) return;
 
    std::vector<float> xwir;
    std::vector<float> ytim;
    std::vector<float> ytimerr2;
    
    unsigned short ii, hitcnt = 0, nht = 0, usnhit;
    float wire0 = 0;
    unsigned int iht;
    bool UseEm = false;
    fAveChg = 0.;
    fChgSlp = 0.;

    if(nhit > 0) {
      usnhit = nhit;
      // find the first desired hit and move towards the End
      for(ii = 0; ii < hitVec.size(); ++ii) {
        iht = hitVec[ii];
        if(iht > fHits.size()-1) {
          mf::LogError("CC")<<"FitClusterMid bad iht "<<iht;
          return;
        }
        // look for the desired first hit. Use this as the origin wire
        if(iht == ihtin) {
          UseEm = true;
          wire0 = fHits[iht].WireID().Wire;
        }
        // use hits after finding the first desired hit
        if(UseEm) {
          xwir.push_back((float)fHits[iht].WireID().Wire - wire0);
          ytim.push_back(fHits[iht].PeakTime());
          // pass the error^2 to the fitter
          float terr = fHitErrFac * fHits[iht].RMS();
          ytimerr2.push_back(terr * terr);
          fAveChg += fHits[iht].Integral();
          ++hitcnt;
          if(hitcnt == usnhit) break;
        }
      }    
      nht = hitcnt;
    } else {
      usnhit = -nhit;
      // find the first desired hit and move towards the Begin
      for(auto ii = hitVec.crbegin(); ii != hitVec.crend(); ++ii) {
        iht = *ii;
        if(iht > fHits.size()-1) {
          mf::LogVerbatim("CC")<<"FitClusterMid bad iht "<<iht;
          return;
        }
        // look for the desired first hit. Use this as the origin wire
        if(iht == ihtin) {
          UseEm = true;
          wire0 = fHits[iht].WireID().Wire;
        }
        // use hits after finding the first desired hit
        if(UseEm) {
          xwir.push_back((float)fHits[iht].WireID().Wire - wire0);
          ytim.push_back(fHits[iht].PeakTime());
          float terr = fHitErrFac * fHits[iht].RMS();
          ytimerr2.push_back(terr * terr);
          fAveChg += fHits[iht].Integral();
          ++hitcnt;
          if(hitcnt == usnhit) break;
        }
      }    
      nht = hitcnt;
    }
    
    if(nht < 2) return;
    fAveChg = fAveChg / (float)nht;
    fChgSlp = 0.;
    
    float intcpt = 0.;
    float slope = 0.;
    float intcpterr = 0.;
    float slopeerr = 0.;
    float chidof = 0.;
    fLinFitAlg.LinFit(xwir, ytim, ytimerr2, intcpt, slope, intcpterr, slopeerr, chidof);
    clChisq = chidof;
    if(clChisq > fChiCut[0]) return;
    clpar[0] = intcpt;
    clpar[1] = slope;
    clpar[2] = wire0;
    clparerr[0] = intcpterr;
    clparerr[1] = slopeerr;
  }

void cluster::ClusterCrawlerAlg::FitVtx ( unsigned short  iv )

private

Definition at line 5229 of file ClusterCrawlerAlg.cxx.

References geo::CryostatID::Cryostat, tca::DecodeCTP(), min, geo::PlaneID::Plane, geo::TPCID::TPC, x, and y.

    {
      std::vector<float> x;
      std::vector<float> y;
      std::vector<float> ey2;
      float arg;
      
      // don't fit fixed vertices
      if(vtx[iv].Fixed) return;

      // Set this large in case something bad happens
      vtx[iv].ChiDOF = 99;

      // make a list of clusters
      unsigned short icl;
      std::vector<unsigned short> vcl;
      for(icl = 0; icl < tcl.size(); ++icl) {
        if(tcl[icl].ID < 0) continue;
        if(tcl[icl].CTP != vtx[iv].CTP) continue;
        if(tcl[icl].EndVtx == iv) vcl.push_back(icl);
        if(tcl[icl].BeginVtx == iv) vcl.push_back(icl);
      }
      
      vtx[iv].NClusters = vcl.size();
      
      if(vcl.size() == 0) return;
      
      // don't let the time error be less than the expected
      // time error of hits on a cluster. This is crude by
      // probably good enough
      icl = vcl[0];
      unsigned short indx = tcl[icl].tclhits.size() - 1;
      unsigned int hit = tcl[icl].tclhits[indx];
      float minTimeErr = fHitErrFac * fHits[hit].RMS() * fHits[hit].Multiplicity();
      
      if(vcl.size() == 1) {
        icl = vcl[0];
        // Put the vertex at the appropriate end of the cluster
        if(tcl[icl].EndVtx == iv) {
          vtx[iv].Wire = tcl[icl].EndWir;
          vtx[iv].WireErr = 1;
          vtx[iv].Time = tcl[icl].EndTim;
          // set the vertex time error to the hit error used for fitting
          indx = tcl[icl].tclhits.size() - 1;
          hit = tcl[icl].tclhits[indx];
          vtx[iv].TimeErr = fHitErrFac * fHits[hit].RMS() * fHits[hit].Multiplicity();
          vtx[iv].ChiDOF = 0;
        }
        if(tcl[icl].BeginVtx == iv) {
          vtx[iv].Wire = tcl[icl].BeginWir;
          vtx[iv].WireErr = 1;
          vtx[iv].Time = tcl[icl].BeginTim;
          // set the vertex time error to the hit error used for fitting
          hit = tcl[icl].tclhits[0];
          vtx[iv].TimeErr = fHitErrFac * fHits[hit].RMS() * fHits[hit].Multiplicity();
          vtx[iv].ChiDOF = 0;
        }
        return;
      } // size 1

      std::vector<double> slps;
      std::vector<double> slperrs;
      for(unsigned short ii = 0; ii < vcl.size(); ++ii) {
        icl = vcl[ii];
        if(tcl[icl].EndVtx == iv) {
          x.push_back(tcl[icl].EndSlp);
          slps.push_back(tcl[icl].EndSlp);
          slperrs.push_back(tcl[icl].EndSlpErr);
          arg = tcl[icl].EndSlp * tcl[icl].EndWir - tcl[icl].EndTim;
          y.push_back(arg);
          if(tcl[icl].EndSlpErr > 0.) {
            arg = tcl[icl].EndSlpErr * tcl[icl].EndWir;
          } else {
            arg = .1 * tcl[icl].EndWir;
          }
          ey2.push_back(arg * arg);
        } else if(tcl[icl].BeginVtx == iv) {
          x.push_back(tcl[icl].BeginSlp);
          slps.push_back(tcl[icl].BeginSlp);
          slperrs.push_back(tcl[icl].BeginSlpErr);
          arg = tcl[icl].BeginSlp * tcl[icl].BeginWir - tcl[icl].BeginTim;
          y.push_back(arg);
          if(tcl[icl].BeginSlpErr > 0.) {
            arg = tcl[icl].BeginSlpErr * tcl[icl].BeginWir;
          } else {
            arg = .1 * tcl[icl].BeginWir;
          }
          ey2.push_back(arg * arg);
        }
      } // ii
      if(x.size() < 2) return;
      
      // calculate error
      double sumerr = 0, cnt = 0;
      for(unsigned short ii = 0; ii < slps.size() - 1; ++ii) {
        for(unsigned short jj = ii + 1; jj < slps.size(); ++jj) {
          arg = std::min(slperrs[ii], slperrs[jj]);
          arg /= (slps[ii] - slps[jj]);
          sumerr += arg * arg;
          ++cnt;
        } // jj
      } // ii
      sumerr /= cnt;
      
      float vTime = 0.;
      float vTimeErr = 0.;
      float vWire = 0.;
      float vWireErr = 0.;
      float chiDOF;
      fLinFitAlg.LinFit(x, y, ey2, vTime, vWire, vTimeErr, vWireErr, chiDOF);
      if(chiDOF > 900) return;
      vTime = -vTime;
      // a crazy time from the fit?
      if(vTime < 0 || vTime > fMaxTime) return;
      // a crazy wire from the fit?
      geo::PlaneID iplID = DecodeCTP(vtx[iv].CTP);
      if(vWire < 0 || vWire > geom->Nwires(iplID.Plane, iplID.TPC, iplID.Cryostat)) return;
      vtx[iv].ChiDOF = chiDOF;
      vtx[iv].Wire = vWire;
      vtx[iv].Time = vTime;
      vtx[iv].WireErr = vWire * sqrt(sumerr);
      vtx[iv].TimeErr = vTime * fabs(sumerr);
//      std::cout<<"vWire "<<vWire<<" Err "<<vtx[iv].WireErr<<" vTime "<<vTime<<" Err "<<vtx[iv].TimeErr
//      <<" sumerr "<<sumerr<<" nclusters "<<x.size()<<"\n";
      // set minimum wire error
      if(vtx[iv].WireErr < 1) vtx[iv].WireErr = 2;
      // set minimum time error
      if(vtx[iv].TimeErr < minTimeErr) vtx[iv].TimeErr = minTimeErr;
      
    } // FitVtx

void cluster::ClusterCrawlerAlg::FixMultipletLocalIndices ( size_t  begin, size_t  end, short int  multiplicity = -1  )

private

Resets the local index and multiplicity of all the hits in [begin;end[.

Definition at line 1859 of file ClusterCrawlerAlg.cxx.

References recob::Hit::Channel(), recob::Hit::DegreesOfFreedom(), evd::details::end(), recob::Hit::EndTick(), recob::Hit::GoodnessOfFit(), recob::Hit::Integral(), recob::Hit::PeakAmplitude(), recob::Hit::PeakTime(), recob::Hit::RMS(), recob::Hit::SigmaIntegral(), recob::Hit::SigmaPeakAmplitude(), recob::Hit::SigmaPeakTime(), recob::Hit::SignalType(), recob::Hit::StartTick(), recob::Hit::SummedADC(), recob::Hit::View(), and recob::Hit::WireID().

  {
    //
    // Resets multiplicity and local index of the hits in the range.
    // All hits are assumed to be in the same multiplet.
    // All hits that are not obsolete are given a multiplicity equal to the
    // number of non-obsolete hits in the multiplet, and the local index is
    // assigned as an increasing number starting from 0 with the first
    // non-obsolete hit on.
    //
    
    // first pass: determine the actual number of hits in the multiplet
    if (multiplicity < 0) {
      multiplicity = 0;
      for (size_t iHit = begin; iHit < end; ++iHit) {
        if(inClus[iHit] < 0) continue;
        //          if (!isHitPresent(iHit)) continue;
        ++multiplicity;
      } // for
    } // if no valid multiplicity is given
    
    // second pass: assign the correct multiplicity
    short int local_index = 0;
    for (size_t iHit = begin; iHit < end; ++iHit) {
      if(inClus[iHit] < 0) continue;
      //        if (!isHitPresent(iHit)) continue;
      
      // copy everything but overwrite the local index and multiplicity
      // TODO use a write wrapper!
      recob::Hit const& hit = fHits[iHit];
      fHits[iHit] = recob::Hit(
                               hit.Channel(),
                               hit.StartTick(),
                               hit.EndTick(),
                               hit.PeakTime(),
                               hit.SigmaPeakTime(),
                               hit.RMS(),
                               hit.PeakAmplitude(),
                               hit.SigmaPeakAmplitude(),
                               hit.SummedADC(),
                               hit.Integral(),
                               hit.SigmaIntegral(),
                               multiplicity,        // multiplicity
                               local_index,         // local index
                               hit.GoodnessOfFit(),
                               hit.DegreesOfFreedom(),
                               hit.View(),
                               hit.SignalType(),
                               hit.WireID()
                               );
      
      ++local_index;
    } // for
    
  } // FixMultipletLocalIndices()

std::vector<ClusterStore> const& cluster::ClusterCrawlerAlg::GetClusters ( ) const

inline

Returns a constant reference to the clusters found.

Definition at line 122 of file ClusterCrawlerAlg.h.

References tcl.

Referenced by cluster::ClusterCrawler::produce().

{ return tcl; }

std::vector<VtxStore> const& cluster::ClusterCrawlerAlg::GetEndPoints ( ) const

inline

Returns a constant reference to the 2D end points found.

Definition at line 125 of file ClusterCrawlerAlg.h.

References vtx.

{ return vtx; }

void cluster::ClusterCrawlerAlg::GetHitRange ( CTP_t  CTP )

private

Definition at line 6075 of file ClusterCrawlerAlg.cxx.

References geo::CryostatID::Cryostat, tca::DecodeCTP(), art::errors::LogicError, max, geo::PlaneID::Plane, and geo::TPCID::TPC.

    {
      // fills the WireHitRange vector for the supplied Cryostat/TPC/Plane code
      // Hits must have been sorted by increasing wire number
                        fFirstHit = 0;
      geo::PlaneID planeID = DecodeCTP(CTP);
      unsigned int nwires = geom->Nwires(planeID.Plane, planeID.TPC, planeID.Cryostat);
      WireHitRange.resize(nwires + 1);

      // These will be re-defined later
      fFirstWire = 0;
      fLastWire = 0;
      
      unsigned int wire, iht;
      unsigned int nHitInPlane;
      std::pair<int, int> flag;
      
       // Define the "no hits on wire" condition
      flag.first = -2; flag.second = -2;
      for(auto& apair : WireHitRange) apair = flag;

      nHitInPlane = 0;

      std::vector<bool> firsthit;
      firsthit.resize(nwires+1, true);
      bool firstwire = true;
      for(iht = 0; iht < fHits.size(); ++iht) {
        if(fHits[iht].WireID().TPC != planeID.TPC) continue;
        if(fHits[iht].WireID().Cryostat != planeID.Cryostat) continue;
        if(fHits[iht].WireID().Plane != planeID.Plane) continue;
        wire = fHits[iht].WireID().Wire;
        // define the first hit start index in this TPC, Plane
        if(firsthit[wire]) {
          WireHitRange[wire].first = iht;
          firsthit[wire] = false;
        }
        if(firstwire){
          fFirstWire = wire;
          firstwire = false;
        }
        WireHitRange[wire].second = iht+1;
        fLastWire = wire+1;
        ++nHitInPlane;
      }
      // overwrite with the "dead wires" condition
      lariov::ChannelStatusProvider const& channelStatus
        = art::ServiceHandle<lariov::ChannelStatusService>()->GetProvider();
      
      flag.first = -1; flag.second = -1;
      unsigned int nbad = 0;
      for(wire = 0; wire < nwires; ++wire) {
        raw::ChannelID_t chan = geom->PlaneWireToChannel((int)planeID.Plane,(int)wire,(int)planeID.TPC,(int)planeID.Cryostat);
        if(!channelStatus.IsGood(chan)) {
          WireHitRange[wire] = flag;
          ++nbad;
        }
      } // wire
//      std::cout<<nbad<<" bad wires in plane "<<planeID.Plane<<"\n";

      // define the MergeAvailable vector and check for errors
      if(mergeAvailable.size() < fHits.size()) throw art::Exception(art::errors::LogicError)
        <<"GetHitRange: Invalid mergeAvailable vector size "<<mergeAvailable.size()<<fHits.size();
      unsigned int firstHit, lastHit;
      unsigned int cnt;
      cnt = 0;
      float maxRMS, chiSep, peakCut;
      for(wire = 0; wire < nwires; ++wire) {
        // ignore dead wires and wires with no hits
        if(WireHitRange[wire].first < 0) continue;
        firstHit = WireHitRange[wire].first;
        lastHit = WireHitRange[wire].second;
        for(iht = firstHit; iht < lastHit; ++iht) {
          if(fHits[iht].WireID().Wire != wire)
            throw art::Exception(art::errors::LogicError)<<"Bad WireHitRange on wire "<<wire<<"\n";
          ++cnt;
          if(fHits[iht].Multiplicity() > 1) {
            peakCut = 0.6 * fHits[iht].PeakAmplitude();
            std::pair<size_t, size_t> MultipletRange = FindHitMultiplet(iht);
            for(size_t jht = MultipletRange.first; jht < MultipletRange.second; ++jht) {
              if(jht == iht) continue;
              // require that the j hit be similar in magnitude to the i hit
              if(fHits[jht].PeakAmplitude() < peakCut) continue;
              maxRMS = std::max(fHits[iht].RMS(), fHits[jht].RMS());
              chiSep = std::abs(fHits[iht].PeakTime() - fHits[jht].PeakTime()) / maxRMS;
              if(chiSep < fHitMergeChiCut) {
                mergeAvailable[iht] = true;
                break;
              }
            } // jht
          } // fHits[iht].Multiplicity() > 1
        } // iht
      } // wire
      if(cnt != nHitInPlane) mf::LogWarning("CC")<<"Bad WireHitRange count "<<cnt<<" "<<nHitInPlane<<"\n";

      if(!fMergeAllHits) return;
      
      // Merge all of the hits
      bool didMerge;
      for(wire = 0; wire < nwires; ++wire) {
        if(WireHitRange[wire].first < 0) continue;
        firstHit = WireHitRange[wire].first;
        lastHit = WireHitRange[wire].second;
        for(iht = firstHit; iht < lastHit; ++iht) {
          if(!mergeAvailable[iht]) continue;
          // already merged?
          if(fHits[iht].GoodnessOfFit() == 6666) continue;
          MergeHits(iht, didMerge);
          mergeAvailable[iht] = false;
        } // iht
      } // wire

    } // GetHitRange()

std::vector<short> const& cluster::ClusterCrawlerAlg::GetinClus ( ) const

inline

Returns (and loses) the collection of reconstructed hits.

Definition at line 116 of file ClusterCrawlerAlg.h.

References inClus.

Referenced by cluster::ClusterCrawler::produce().

{return inClus; }

std::vector<Vtx3Store> const& cluster::ClusterCrawlerAlg::GetVertices ( ) const

inline

Returns a constant reference to the 3D vertices found.

Definition at line 128 of file ClusterCrawlerAlg.h.

References ClearResults(), SortByMultiplet(), and vtx3.

Referenced by cluster::ClusterCrawler::produce().

{ return vtx3; }

void cluster::ClusterCrawlerAlg::KillGarbageClusters ( )

private

Definition at line 530 of file ClusterCrawlerAlg.cxx.

  {
    // Ghost Clusters:
    
    if(tcl.size() < 2) return;
    
    unsigned short icl, jcl;
    // This code preferentially selects icl clusters that were
    // reconstructed on an early pass (unless they were split)
    std::vector<float> iHits, jHits;
    unsigned int indx;
    // find the average hit width on the first pass and construct
    // a hit separation cut
    float sepcut = 0, iFrac, jFrac;
    bool first = true;
    unsigned short iLoIndx, jLoIndx, olapSize, iop, ii, jj;
    unsigned short nclose;
    float iChg, jChg;
    // vecrtor of clusters that will be killed after all is done
    std::vector<unsigned short> killMe;
    bool doKill;
    for(icl = 0; icl < tcl.size() - 1; ++icl) {
      if(tcl[icl].ID < 0) continue;
      if(tcl[icl].CTP != clCTP) continue;
//      if(tcl[icl].ProcCode < 300) continue;
      // put the hits into a wire ordered vector
      iHits.clear();
      // initialize to a large positive value
      iHits.resize(tcl[icl].BeginWir - tcl[icl].EndWir + 1, 1000);
      iChg = 0;
      for(auto iht : tcl[icl].tclhits) {
        indx = fHits[iht].WireID().Wire - tcl[icl].EndWir;
        if(indx > iHits.size() - 1) {
          mf::LogWarning("CC")<<"KillGarbageClusters: icl ID "<<tcl[icl].ID<<" Bad indx "<<indx<<" "<<iHits.size()<<"\n";
          continue;
        }
        iHits[indx] = fHits[iht].PeakTime();
        iChg += fHits[iht].Integral();
        if(first) sepcut += fHits[iht].RMS();
      } // iht
      if(first) {
        sepcut /= (float)tcl[icl].tclhits.size();
        // clusters are consider ghost candidates if many hits
        // are within sepcut of each other on the same wire
        sepcut *= 10;
        first = false;
      } // first
      for(jcl = icl + 1; jcl < tcl.size(); ++jcl) {
        if(tcl[jcl].ID < 0) continue;
        if(tcl[jcl].CTP != clCTP) continue;
//        if(tcl[jcl].ProcCode < 300) continue;
        // ignore if there is no overlap
        if(tcl[icl].BeginWir < tcl[jcl].EndWir) continue;
        if(tcl[icl].EndWir > tcl[jcl].BeginWir) continue;
        // require similar angle
        if(std::abs(tcl[icl].BeginAng - tcl[jcl].BeginAng) > fKillGarbageClusters) continue;
        // find the overlap region
        if(tcl[icl].EndWir < tcl[jcl].EndWir) {
          //  icl E-----------....
          //  jcl    E----------....
          // olap    xxxxxxxxxx...
          iLoIndx = tcl[jcl].EndWir - tcl[icl].EndWir;
          jLoIndx = 0;
          if(tcl[icl].BeginWir < tcl[jcl].BeginWir) {
            //  icl E-----------B
            //  jcl    E------------B
            // olap    xxxxxxxxxx
            olapSize = tcl[icl].BeginWir - tcl[jcl].EndWir + 1;
          } else {
            //  icl E-----------B
            //  jcl    E-----B
            // olap    xxxxxxx
            olapSize = tcl[jcl].BeginWir - tcl[jcl].EndWir + 1;
          } // iBegin
        } // iEnd < jEnd
        else {
          //  icl    E-----------....
          //  jcl E----------....
          // olap    xxxxxxxxxx...
          iLoIndx = 0;
          jLoIndx = tcl[icl].EndWir - tcl[icl].EndWir;
          if(tcl[icl].BeginWir < tcl[jcl].BeginWir) {
            //  icl    E-----B
            //  jcl E-----------B
            // olap    xxxxxxx
            olapSize = tcl[icl].BeginWir - tcl[icl].EndWir + 1;
          } else {
            //  icl    E-----------B
            //  jcl E----------B
            // olap    xxxxxxxxx
            olapSize = tcl[jcl].BeginWir - tcl[icl].EndWir + 1;
          }
        } // iEnd > jEnd
        jHits.clear();
        // initialize to a large negative value
        jHits.resize(tcl[jcl].BeginWir - tcl[jcl].EndWir + 1, -1000);
        jChg = 0;
        for(auto jht : tcl[jcl].tclhits) {
          indx = fHits[jht].WireID().Wire - tcl[jcl].EndWir;
          if(indx > jHits.size() - 1) {
            mf::LogWarning("CC")<<"KillGarbageClusters: jcl ID "<<tcl[jcl].ID<<" Bad indx "<<indx<<" "<<jHits.size()<<"\n";
            continue;
          }
          jHits[indx] = fHits[jht].PeakTime();
          jChg += fHits[jht].Integral();
        } // jht
/*
        mf::LogVerbatim myprt("CC");
        myprt<<"Check icl ID "<<tcl[icl].ID<<" size "<<iHits.size()<<" iLoIndx "<<iLoIndx;
        myprt<<" wire range "<<tcl[icl].EndWir<<"-"<<tcl[icl].BeginWir;
        myprt<<" jcl ID "<<tcl[jcl].ID<<" size "<<jHits.size()<<" jLoIndx "<<jLoIndx;
        myprt<<" wire range "<<tcl[jcl].EndWir<<"-"<<tcl[jcl].BeginWir;
        myprt<<" olapSize "<<olapSize;
*/
        // count the number of close hits
        nclose = 0;
        for(iop = 0; iop < olapSize; ++iop) {
          ii = iLoIndx + iop;
          if(ii > iHits.size() - 1) continue;
          jj = jLoIndx + iop;
          if(jj > jHits.size() - 1) continue;
          if(std::abs(iHits[ii] - jHits[jj]) < sepcut) ++nclose;
        } // iop
        iFrac = (float)nclose / (float)iHits.size();
        jFrac = (float)nclose / (float)jHits.size();
        if(iFrac < 0.5 && jFrac < 0.5) continue;
        doKill = (iFrac < jFrac && iChg > jChg);
/*
        mf::LogVerbatim myprt("CC");
        myprt<<"Check icl ID "<<tcl[icl].ID<<" size "<<iHits.size()<<" iFrac "<<iFrac<<" iChg "<<(int)iChg;
        myprt<<" jcl ID "<<tcl[jcl].ID<<" size "<<jHits.size()<<" jFrac "<<jFrac<<" jChg "<<(int)jChg<<" doKill? "<<doKill;
*/
        if(doKill) killMe.push_back(jcl);
      } // jcl
    } // icl
    
    if(killMe.size() == 0) return;
   for(auto icl : killMe) {
     // killing time
     if(tcl[icl].ID < 0) continue;
     tcl[icl].ProcCode = 666;
     MakeClusterObsolete(icl);
    } // icl
    
    
  } // KillGarbageClusters

void cluster::ClusterCrawlerAlg::LACrawlUS ( )

private

Definition at line 3736 of file ClusterCrawlerAlg.cxx.

                                    {
    // Crawl a large angle cluster upstream. Similar to CrawlUS but require
    // that a hit be added on each wire


    unsigned int dhit = fcl2hits[0];
    short dwir = fHits[dhit].WireID().Wire;
    clLA = true;
    prt = false;
    if(fDebugPlane == (short)plane && dwir == fDebugWire && fDebugHit > 0)
      prt = std::abs(fHits[dhit].PeakTime() - fDebugHit) < 40;

    if(prt) {
      mf::LogVerbatim myprt("CC");
      myprt<<"******************* LACrawlUS PASS "<<pass<<" Hits ";
      for(unsigned short ii = 0; ii < fcl2hits.size(); ++ii) {
        unsigned int iht = fcl2hits[fcl2hits.size() - 1 - ii];
        myprt<<fHits[iht].WireID().Wire<<":"<<(int)fHits[iht].PeakTime()<<" ";
      }
    }

    bool SigOK = true;
    bool HitOK = true;
    short nmissed = 0;
    // count the number of kinks encountered. Hits US of the kink are removed
    // and crawling continues unless another kink is encountered
    unsigned short kinkOnWire = 0;
    unsigned int it = fcl2hits.size() - 1;
    unsigned int lasthit = fcl2hits[it];
    unsigned int lastwire = fHits[lasthit].WireID().Wire;
    unsigned int prevHit, prevWire;
    bool ChkCharge = false;
    for(unsigned int nextwire = lastwire-1; nextwire >= fFirstWire; --nextwire) {
      if(prt) mf::LogVerbatim("CC")<<"LACrawlUS: next wire "<<nextwire<<" HitRange "<<WireHitRange[nextwire].first;
      // stop crawling if there is a nearby vertex
      if(CrawlVtxChk(nextwire)) {
        if(prt) mf::LogVerbatim("CC")<<"LACrawlUS: stop at vertex";
        clStopCode = 6;
        break;
      }
      // AddLAHit will merge the hit on nextwire if necessary
      AddLAHit(nextwire, ChkCharge, HitOK, SigOK);
      if(prt) mf::LogVerbatim("CC")<<"LACrawlUS: HitOK "<<HitOK<<" SigOK "<<SigOK<<" nmissed SigOK "<<nmissed<<" cut "<<fAllowNoHitWire;
      if(SigOK) nmissed = 0;
      if(!SigOK) {
        ++nmissed;
        if(nmissed > fAllowNoHitWire) {
          clStopCode = 1;
          break;
        }
        continue;
      }
      // If a hit was added after a gap, check to see if there is indeed
      // a wire signal in the gap
      if(HitOK) {
        prevHit = fcl2hits[fcl2hits.size() - 2];
        prevWire = fHits[prevHit].WireID().Wire;
        if(prevWire > nextwire + 2) {
          if(!ChkSignal(fcl2hits[fcl2hits.size()-1], fcl2hits[fcl2hits.size()-2])) {
            // no hit so trim the last hit and quit
            FclTrimUS(1);
            break;
          } // no signal
        } // prevWire > nextwire + 2
      } // HitOK
      // Merge all of the hit multiplets in the fcl2hits array into single
      // hits when enough hits have been found to call this a credible large
      // angle cluster. The last hit was already merged in AddHit
      if(fcl2hits.size() == 4) {
        bool didMerge;
        for(unsigned short kk = 0; kk< fcl2hits.size()-1; ++kk) {
          unsigned int hit = fcl2hits[kk];
          if(mergeAvailable[hit]) MergeHits(hit, didMerge);
        }
        // update the fit
        FitCluster();
        clBeginSlp = clpar[1];
        // start checking the charge ratio when adding new hits
        ChkCharge = true;
        continue;
      } // fcl2hits.size() == 4
      unsigned short chsiz = chifits.size()-1;
      // chsiz is fcl2hits.size() - 1...
      if(chsiz < 6) continue;
      if(fKinkChiRat[pass] <= 0) continue;
      if(chifits.size() != fcl2hits.size()) {
        mf::LogError("CC")
          <<"LACrawlUS: chifits size error "<<chifits.size()<<" "<<fcl2hits.size();
        return;
      }
      if(prt) mf::LogVerbatim("CC") <<"Kink chk "<<chifits[chsiz]<<" "<<chifits[chsiz-1]
        <<" "<<chifits[chsiz-2]<<" "<<chifits[chsiz-3];
      if( chifits[chsiz-1] > fKinkChiRat[pass] * chifits[chsiz-2] &&
          chifits[chsiz]   > fKinkChiRat[pass] * chifits[chsiz-1]) {
        // find the kink angle (crudely) from the 0th and 2nd hit
        unsigned int ih0 = fcl2hits.size() - 1;
        unsigned int hit0 = fcl2hits[ih0];
        unsigned int ih2 = ih0 - 2;
        unsigned int hit2 = fcl2hits[ih2];
        float dt02 = fHits[hit2].PeakTime() - fHits[hit0].PeakTime();
        float dw02 = fHits[hit2].WireID().Wire - fHits[hit0].WireID().Wire;
        float th02 = std::atan( fScaleF * dt02 / dw02);
        // and the 3rd and 5th hit
        unsigned int ih3 = ih2 - 1;
        unsigned int hit3 = fcl2hits[ih3];
        unsigned int ih5 = ih3 - 2;
        unsigned int hit5 = fcl2hits[ih5];
        float dt35 = fHits[hit5].PeakTime() - fHits[hit3].PeakTime();
        float dw35 = fHits[hit5].WireID().Wire - fHits[hit3].WireID().Wire;
        float th35 = std::atan(fScaleF * dt35 / dw35);
        float dth = std::abs(th02 - th35);
        if(prt) mf::LogVerbatim("CC")<<" Kink angle "<<std::setprecision(3)<<dth<<" cut "<<fKinkAngCut[pass];
        if(dth > fKinkAngCut[pass]) {
          // hit a kink. Lop of the first 3 hits, refit and keep crawling?
          FclTrimUS(3);
          FitCluster();
          // See if this is a second kink and it is close to the first
          // kink (which had hits removed).
          if(kinkOnWire > 0) {
            if(kinkOnWire - nextwire < 4) {
              if(prt) mf::LogVerbatim("CC") <<"Hit a second kink. kinkOnWire = "<<kinkOnWire<<" Stopping";
              // set the kink stop code
              clStopCode = 3;
              break;
            }
          }
          kinkOnWire = nextwire;
          if(prt) mf::LogVerbatim("CC")<<"Removed kink hits";
        } // kinkang check
      } // chifits test
    } // nextwire

    CheckClusterHitFrac(prt);

    clProcCode += 300;
    if(prt) mf::LogVerbatim("CC")<<"LACrawlUS done. Nhits = "<<fcl2hits.size();
    prt = false;
  } // LACrawlUS

void cluster::ClusterCrawlerAlg::MakeClusterObsolete ( unsigned short  icl )

private

Marks the cluster as obsolete and frees hits still associated with it.

Definition at line 854 of file ClusterCrawlerAlg.cxx.

                                                                {
    short& ID = tcl[icl].ID;
    if (ID <= 0) {
      mf::LogError("CC")<<"Trying to make already-obsolete cluster obsolete ID = "<<ID;
      return; // already obsolete
    }
    ID = -ID;                     // mark the cluster as obsolete
    
    // release the hits
    for(unsigned int iht = 0; iht < tcl[icl].tclhits.size(); ++iht) inClus[tcl[icl].tclhits[iht]] = 0;

  } // ClusterCrawlerAlg::MakeClusterObsolete()

void cluster::ClusterCrawlerAlg::MergeHits ( const unsigned int  theHit, bool &  didMerge  )

private

Definition at line 1654 of file ClusterCrawlerAlg.cxx.

References recob::Hit::Channel(), recob::Hit::DegreesOfFreedom(), recob::Hit::EndTick(), recob::Hit::Integral(), recob::Hit::Multiplicity(), recob::Hit::PeakAmplitude(), recob::Hit::PeakTime(), recob::Hit::PeakTimeMinusRMS(), recob::Hit::PeakTimePlusRMS(), geo::PlaneID::Plane, recob::Hit::RMS(), recob::Hit::SigmaIntegral(), recob::Hit::SigmaPeakAmplitude(), recob::Hit::SigmaPeakTime(), recob::Hit::SignalType(), recob::Hit::StartTick(), recob::Hit::SummedADC(), recob::Hit::View(), geo::WireID::Wire, and recob::Hit::WireID().

                                                                             {
    // Merge all unused separate hits in the multiplet of which
    // theHit is a member into one hit (= theHit).
    // Mark the merged hits other than theHit obsolete.
    // Hits in the multiplet that are associated with an existing cluster are
    // not affected.
    // Hit multiplicity is reworked (including all the hits in the multiplet).
    // Used hits have the multiplicity and index corrected too; the local
    // index reflects the peak time.
    // Note that theHit may or may not be marked free (usually, it is not)
    
    didMerge = false;
    
    if(theHit > fHits.size() - 1) {
//      mf::LogError("CC")<<"Bad theHit";
      return;
    }
    
    recob::Hit const& hit = fHits[theHit];
    
    // don't bother trying to merge an already merged hit
    if(fHits[theHit].GoodnessOfFit() == 6666) {
      if(prt) mf::LogVerbatim("CC")<<"MergeHits Trying to merge already merged hit "
        <<hit.WireID().Plane<<":"<<hit.WireID().Wire<<":"<<(int)hit.PeakTime()
        <<" Multiplicity "<<hit.Multiplicity()<<" theHit "<<theHit;
      return;
    }
    
    // don't merge if it isn't available
    if(!mergeAvailable[theHit]) {
//      if(prt) mf::LogVerbatim("CC")<<"MergeHits "<<hit.WireID().Plane<<":"<<hit.WireID().Wire<<":"<<(int)hit.PeakTime()<<" Multiplicity "<<hit.Multiplicity()<<" theHit "<<theHit<<" is not available";
      return;
    }
    
    if(hit.Multiplicity() < 2) return;
    
//    if(prt) mf::LogVerbatim("CC")<<"MergeHits "<<hit.WireID().Plane<<":"<<hit.WireID().Wire<<":"<<(int)hit.PeakTime()<<" Multiplicity "<<hit.Multiplicity()<<" theHit "<<theHit;
//    if(prt && fcl2hits.size() > 0)mf::LogVerbatim("CC")<<" Seed hit "<<fHits[fcl2hits[0]].WireID().Wire<<":"<<(int)fHits[fcl2hits[0]].PeakTime();
    
    // number of hits in this hit multiplet
    std::pair<size_t, size_t> MultipletRange = FindHitMultiplet(theHit);
    
    // ensure that this is a high multiplicity hit:
    if (MultipletRange.second <= MultipletRange.first) return;
    
    // do a quick check to see how many hits are available to be merged
    unsigned short nAvailable = 0;
    unsigned short nInClus = 0;
    for(size_t jht = MultipletRange.first; jht < MultipletRange.second; ++jht) {
      if(jht == theHit) continue;
      if(fHits[jht].GoodnessOfFit() == 6666) continue;
      if(inClus[jht] != 0) {
        ++nInClus;
        continue;
      }
      ++nAvailable;
    } // jht
    if(nAvailable == 0) return;
    // don't merge if any hit is used
    if(nInClus > 0) return;
    
    // calculate the Charge normalization factor using the hit information
    // instead of passing CCHitFinder ChgNorms all the way down here
    float chgNorm = 2.507 * hit.PeakAmplitude() * hit.RMS() / hit.Integral();
    
    short loTime = 9999;
    short hiTime = 0;
    unsigned short nGaus = 1;
    float hitSep;
    // number of hits that are close to theHit
    unsigned short nclose = 0;
    // find the time range for the hit multiplet
    for(size_t jht = MultipletRange.first; jht < MultipletRange.second; ++jht) {
      if(inClus[jht] < 0) continue;
      recob::Hit const& other_hit = fHits[jht];
/*
      if(prt) {
        mf::LogVerbatim("CC")
        <<" P:W:T "<<plane<<":"<<other_hit.WireID().Wire<<":"<<(int)other_hit.PeakTime()
        <<" Amp "<<(int)other_hit.PeakAmplitude()
        <<" RMS "<<other_hit.RMS()
        <<" Charge "<<(int)other_hit.Integral()
        <<" inClus "<<inClus[jht];
      }
*/
      // error checking
      if((other_hit.StartTick() != hit.StartTick())
         || (other_hit.WireID() != hit.WireID()))
      {
/*
        mf::LogError("CC")<<"Hit multiplet ID error "
        << other_hit.WireID() << " @" << other_hit.StartTick()
        << " " << other_hit.LocalIndex() << "/" << other_hit.Multiplicity()
        << " vs. " << hit.WireID() << " @" << hit.StartTick()
        << " " << hit.LocalIndex() << "/" << hit.Multiplicity()
        ;
*/
        return;
      }
      if (other_hit.Multiplicity() != hit.Multiplicity()) {
/*
        mf::LogError("CC")
        << " hit #" << jht << " in the same multiplet as #" << theHit
        << " has different multiplicity!"
        << "\n hit #" << theHit << ": " << hit
        << "\n hit #" << jht << ": " << other_hit;
*/
        return;
      }
      // hit is not used by another cluster
      if(inClus[jht] != 0) continue;
      short arg = (short)(other_hit.PeakTimeMinusRMS(3));
      if(arg < loTime) loTime = arg;
      arg = (short)(other_hit.PeakTimePlusRMS(3));
      if(arg > hiTime) hiTime = arg;
      if(jht != theHit) ++nGaus;
      hitSep = std::abs(other_hit.PeakTime() - hit.PeakTime()) / other_hit.RMS();
      if(jht != theHit && hitSep < 3) ++nclose;
    } // jht
    // all hits in the multiplet other than this one used?
    if(nGaus < 2) return;
    
    // the hits in this multiplet will have this multiplicity from now on
    const short int NewMultiplicity = hit.Multiplicity() + 1 - nGaus;
    
    if(loTime < 0) loTime = 0;
    ++hiTime;
    // define a signal shape, fill it with zeros
    std::vector<double> signal(hiTime - loTime, 0.);
    // now add the Gaussians for each hit
    double chgsum = 0.;
    for(size_t jht = MultipletRange.first; jht < MultipletRange.second; ++jht) {
      recob::Hit const& other_hit = fHits[jht];
      if(jht != theHit) {
        // hit used in another cluster
        if(inClus[jht] != 0) continue;
        // declare this hit obsolete
        inClus[jht] = -1;
      } // jht != theHit
      // add up the charge
      chgsum += other_hit.Integral();
      for(unsigned short time = loTime; time < hiTime; ++time) {
        unsigned short indx = time - loTime;
        double arg = (other_hit.PeakTime() - (double)time) / other_hit.RMS();
        signal[indx] += other_hit.PeakAmplitude() * exp(-0.5 * arg * arg);
      } // time
    } // jj
    // find the average weighted time
    double sigsum = 0.;
    double sigsumt = 0.;
    for(unsigned short time = loTime; time < hiTime; ++time) {
      sigsum  += signal[time - loTime];
      sigsumt += signal[time - loTime] * time;
    }
    if(sigsum == 0.) {
//      mf::LogError("CC")<<"MergeHits: bad sum";
      return;
    }
    double aveTime = sigsumt / sigsum;
    // find the RMS
    sigsumt = 0.;
    for(unsigned short time = loTime; time < hiTime; ++time) {
      double dtime = time - aveTime;
      sigsumt += signal[time - loTime] * dtime * dtime;
    }
    const float RMS = std::sqrt(sigsumt / sigsum);
    // find the amplitude from the integrated charge and the RMS
    const float amplitude = chgsum * chgNorm/ (2.507 * RMS);
    // modify the hit "in place" (actually completely overwrite it...)
    // TODO a lot of these quantities need revamp!!
    fHits[theHit] = recob::Hit(
                               hit.Channel(),
                               hit.StartTick(),
                               hit.EndTick(),
                               aveTime,                // peak_time
                               hit.SigmaPeakTime(),
                               RMS,                    // rms
                               amplitude,              // peak_amplitude
                               hit.SigmaPeakAmplitude(),
                               hit.SummedADC(),
                               chgsum,                 // hit_integral
                               hit.SigmaIntegral(),
                               NewMultiplicity,        // multiplicity
                               0,                      // local index
                               6666,                   // GoodnessOfFit (flag for merged hit)
                               hit.DegreesOfFreedom(),
                               hit.View(),
                               hit.SignalType(),
                               hit.WireID()
                               );
/*
    if(prt) {
      mf::LogVerbatim("CC")
      <<" theHit "<<fHits[theHit].WireID().Wire<<":"<<(int)aveTime
      <<" RMS "<<std::setprecision(1)<<fHits[theHit].RMS()
      <<" chg "<<(int)chgsum<<" Amp "<<(int)fHits[theHit].PeakAmplitude();
    }
*/
    FixMultipletLocalIndices(MultipletRange.first, MultipletRange.second);
    didMerge = true;
    
  } // MergeHits()

void cluster::ClusterCrawlerAlg::MergeOverlap ( )

private

Definition at line 679 of file ClusterCrawlerAlg.cxx.

References tca::PrintHit(), and cluster::SortByLowHit().

  {
    // Tries to merge overlapping clusters schematically shown below. The minimal condition is that both
    // clusters have a length of at least minLen wires with minOvrLap of the minLen wires in the overlap region
    //      End  Begin
    // icl  ------
    // jcl     ------
    //         End  Begin
    // This can occur when tracking cosmic rays through delta ray showers.
    // If successfull the hits in clusters icl and jcl are merged into one long cluster
    // and a short cluster if there are sufficient remaining hits.
    // This routine changes the "pass" variable to define cuts and should NOT be used inside any pass loops
    
    unsigned short icl, jcl;
    
    bool chkprt = (fDebugWire == 666);
    if(chkprt) mf::LogVerbatim("CC")<<"Inside MergeOverlap using clCTP "<<clCTP;
    
    unsigned short minLen = 6;
    unsigned short minOvrLap = 2;
    
    // use the loosest dTick cut which is probably the last one
    float maxDTick = fTimeDelta[fTimeDelta.size() - 1];
    
    unsigned int overlapSize, ii, indx, bWire, eWire;
    unsigned int iht, jht;
    float dang, prtime, dTick;
    for(icl = 0; icl < tcl.size(); ++icl) {
      if(tcl[icl].ID < 0) continue;
      if(tcl[icl].CTP != clCTP) continue;
      prt = chkprt && fDebugPlane == (int)clCTP;
      if(tcl[icl].BeginVtx >= 0) continue;
      if(tcl[icl].tclhits.size() < minLen) continue;
      for(jcl = 0; jcl < tcl.size(); ++jcl) {
        if(icl == jcl) continue;
        if(tcl[jcl].ID < 0) continue;
        if(tcl[jcl].CTP != clCTP) continue;
        if(tcl[jcl].EndVtx >= 0) continue;
        if(tcl[jcl].tclhits.size() < minLen) continue;
        // icl Begin is not far enough DS from the end of jcl
        if(tcl[icl].BeginWir < tcl[jcl].EndWir + minOvrLap) continue;
        // and it doesn't end within the wire boundaries of jcl
        if(tcl[icl].BeginWir > tcl[jcl].BeginWir - minOvrLap) continue;
        // jcl End isn't far enough US from the end of icl
        if(tcl[jcl].EndWir < tcl[icl].EndWir + minOvrLap) continue;
        dang = std::abs(tcl[icl].BeginAng - tcl[jcl].EndAng);
        if(prt) mf::LogVerbatim("CC")<<"MergeOverlap icl ID "<<tcl[icl].ID<<" jcl ID "<<tcl[jcl].ID<<" dang "<<dang;
        if(dang > 0.5) continue;
        overlapSize = tcl[icl].BeginWir - tcl[jcl].EndWir + 1;
        eWire = tcl[jcl].EndWir;
        bWire = tcl[icl].BeginWir;
        if(prt) mf::LogVerbatim("CC")<<" Candidate icl ID "<<tcl[icl].ID<<" "<<tcl[icl].EndWir<<"-"<<tcl[icl].BeginWir<<" jcl ID "<<tcl[jcl].ID<<" "<<tcl[jcl].EndWir<<"-"<<tcl[jcl].BeginWir<<" overlapSize "<<overlapSize<<" bWire "<<bWire<<" eWire "<<eWire;
        iht = 0; jht = 0;
        for(ii = 0; ii < tcl[icl].tclhits.size(); ++ii) {
          iht = tcl[icl].tclhits[ii];
          if(fHits[iht].WireID().Wire < eWire) break;
        } // ii
        // require that the ends be similar in time
        dTick = std::abs(fHits[iht].PeakTime() - tcl[jcl].EndTim);
        if(dTick > maxDTick) continue;
        if(prt) mf::LogVerbatim("CC")<<" dTick icl iht time "<<PrintHit(iht)<<" jcl EndTim "<<tcl[jcl].EndTim<<" dTick "<<dTick;
        for(ii = 0; ii < tcl[jcl].tclhits.size(); ++ii) {
          jht = tcl[jcl].tclhits[tcl[jcl].tclhits.size() - ii - 1];
          if(fHits[jht].WireID().Wire > bWire) break;
        } // ii
        dTick = std::abs(fHits[jht].PeakTime() - tcl[icl].BeginTim);
        if(dTick > maxDTick) continue;
        if(prt) mf::LogVerbatim("CC")<<" dTick jcl jht time "<<PrintHit(jht)<<" icl BeginTim "<<tcl[icl].BeginTim<<" dTick "<<dTick;
        // Calculate the line between iht and jht
        clpar[0] = fHits[iht].PeakTime();
        clpar[2] = fHits[iht].WireID().Wire;
        clpar[1] = (fHits[jht].PeakTime() - fHits[iht].PeakTime()) / ((float)fHits[jht].WireID().Wire - clpar[2]);
        // put the hits in the overlap region into a vector if they are close to the line
        std::vector<unsigned int> oWireHits(overlapSize, INT_MAX);
        std::vector<float> delta(overlapSize, maxDTick);
        for(ii = 0; ii < tcl[icl].tclhits.size(); ++ii) {
          iht = tcl[icl].tclhits[ii];
          if(fHits[iht].WireID().Wire < eWire) break;
          prtime = clpar[0] + clpar[1] * ((float)fHits[iht].WireID().Wire - clpar[2]);
          dTick = std::abs(fHits[iht].PeakTime() - prtime);
          indx = fHits[iht].WireID().Wire - eWire;
          if(dTick > delta[indx]) continue;
          delta[indx] = dTick;
          oWireHits[indx] = iht;
        } // ii
        // enter the second set of hits
        for(ii = 0; ii < tcl[jcl].tclhits.size(); ++ii) {
          jht = tcl[jcl].tclhits[tcl[jcl].tclhits.size() - ii - 1];
          if(fHits[jht].WireID().Wire > bWire) break;
          prtime = clpar[0] + clpar[1] * ((float)fHits[jht].WireID().Wire - clpar[2]);
          dTick = std::abs(fHits[jht].PeakTime() - prtime);
          indx = fHits[jht].WireID().Wire - eWire;
          if(dTick > delta[indx]) continue;
          delta[indx] = dTick;
          oWireHits[indx] = jht;
        } // ii
        // stuff them into fcl2hits
        fcl2hits.clear();
        for(ii = 0; ii < oWireHits.size(); ++ii) {
          if(oWireHits[ii] == INT_MAX) continue;
          iht = oWireHits[ii];
          fcl2hits.push_back(iht);
          if(prt) mf::LogVerbatim("CC")<<"hit "<<PrintHit(iht);
        } // ii
        if(fcl2hits.size() < 0.5 * overlapSize) continue;
        if(fcl2hits.size() < 3) continue;
        std::sort(fcl2hits.begin(), fcl2hits.end(), SortByLowHit);
        FitCluster();
        if(prt) mf::LogVerbatim("CC")<<" Overlap size "<<overlapSize<<" fit chisq "<<clChisq<<" nhits "<<fcl2hits.size();
        if(clChisq > 20) continue;
        // save these hits so we can paste them back on fcl2hits when merging
        std::vector<unsigned int> oHits = fcl2hits;
        // prepare to make a new cluster
        TmpGet(jcl);
        // resize it
        unsigned short jclNewSize;
        for(jclNewSize = 0; jclNewSize < fcl2hits.size(); ++jclNewSize) {
          iht = fcl2hits[jclNewSize];
          if(fHits[iht].WireID().Wire <= bWire) break;
        } // jclNewSize
        if(prt) {
          mf::LogVerbatim("CC")<<"jcl old size "<<fcl2hits.size()<<" newSize "<<jclNewSize;
          iht = fcl2hits[fcl2hits.size()-1];
          unsigned int iiht = fcl2hits[jclNewSize-1];
          mf::LogVerbatim("CC")<<"jcl old last wire "<<fHits[iht].WireID().Wire<<" After resize last wire "<<fHits[iiht].WireID().Wire;
        }
        fcl2hits.resize(jclNewSize);
        // append the hits in the overlap region
        fcl2hits.insert(fcl2hits.end(), oHits.begin(), oHits.end());
        // now paste in the icl hits that are US of the overlap region
        for(ii = 0; ii < tcl[icl].tclhits.size(); ++ii) {
          iht = tcl[icl].tclhits[ii];
          if((unsigned int)fHits[iht].WireID().Wire >= eWire) continue;
          fcl2hits.insert(fcl2hits.end(),tcl[icl].tclhits.begin()+ii, tcl[icl].tclhits.end());
          break;
        }
        clBeginSlp = tcl[jcl].BeginSlp;
        clBeginSlpErr = tcl[jcl].BeginSlpErr;
        clBeginAng = tcl[jcl].BeginAng;
        clBeginWir = tcl[jcl].BeginWir;
        clBeginTim = tcl[jcl].BeginTim;
        clBeginChg = tcl[jcl].BeginChg;
        clBeginChgNear = tcl[jcl].BeginChgNear;
        // End info from icl
        clEndSlp = tcl[icl].EndSlp;
        clEndSlpErr = tcl[icl].EndSlpErr;
        clEndAng = tcl[icl].EndAng;
        clEndWir = tcl[icl].EndWir;
        clEndTim = tcl[icl].EndTim;
        clEndChg = tcl[icl].EndChg;
        clEndChgNear = tcl[icl].EndChgNear;
        clStopCode = tcl[icl].StopCode;
        clProcCode = tcl[icl].ProcCode + 500;
        MakeClusterObsolete(icl);
        MakeClusterObsolete(jcl);
        if(!TmpStore()) {
          // Merged cluster is fubar. Try to recover
          RestoreObsoleteCluster(icl);
          RestoreObsoleteCluster(jcl);
          CheckHitClusterAssociations();
          continue;
        }
        CheckHitClusterAssociations();
        tcl[tcl.size() - 1].BeginVtx = tcl[jcl].BeginVtx;
        tcl[tcl.size() - 1].EndVtx = tcl[icl].BeginVtx;
        // after this point any failure should result in a jcl loop break
        if(prt) mf::LogVerbatim("CC")<<"MergeOverlap new long cluster ID "<<tcl[tcl.size()-1].ID<<" in clCTP "<<clCTP;
        // icl cluster made obsolete so we must have done something
        if(tcl[icl].ID < 0) break;
      } // jcl
    } // icl
    
  } // MergeOverlap()

float cluster::ClusterCrawlerAlg::PointVertexChi ( float  wire, float  tick, unsigned short  ivx  )

private

Definition at line 6383 of file ClusterCrawlerAlg.cxx.

  {
    // Returns the Chisq/DOF between a (Wire, Tick) point and a vertex
    
    if(ivx > vtx.size()) return 9999;
    
    float dW = wire - vtx[ivx].Wire;
    float chi = dW / vtx[ivx].WireErr;
    float totChi = chi * chi;
    float dT = tick - vtx[ivx].Time;
    chi = dT / vtx[ivx].TimeErr;
    totChi += chi * chi;
    
    return totChi;
    
  } // PointVertexChi

void cluster::ClusterCrawlerAlg::PrintClusters ( )

private

Definition at line 3499 of file ClusterCrawlerAlg.cxx.

References art::right().

  {

    // prints clusters to the screen for code development
    mf::LogVerbatim myprt("CC");
    
    PrintVertices();
    
    float aveRMS, aveRes;
    myprt<<"*************************************** Clusters *********************************************************************\n";
    myprt<<"  ID CTP nht Stop  Proc  beg_W:T    bAng  bSlp  Err  bChg end_W:T      eAng  eSlp  Err  eChg  bVx  eVx aveRMS Qual cnt\n";
    for(unsigned short ii = 0; ii < tcl.size(); ++ii) {
      // print clusters in all planes (fDebugPlane = 3) or in a selected plane
      if(fDebugPlane < 3 && fDebugPlane != (int)tcl[ii].CTP) continue;
      myprt<<std::right<<std::setw(4)<<tcl[ii].ID;
      myprt<<std::right<<std::setw(3)<<tcl[ii].CTP;
      myprt<<std::right<<std::setw(5)<<tcl[ii].tclhits.size();
      myprt<<std::right<<std::setw(4)<<tcl[ii].StopCode;
      myprt<<std::right<<std::setw(6)<<tcl[ii].ProcCode;
      unsigned int iTime = tcl[ii].BeginTim;
      myprt<<std::right<<std::setw(6)<<tcl[ii].BeginWir<<":"<<iTime;
      if(iTime < 10) {
        myprt<<"   ";
      } else if(iTime < 100) {
        myprt<<"  ";
      } else if(iTime < 1000) myprt<<" ";
      myprt<<std::right<<std::setw(7)<<std::fixed<<std::setprecision(2)<<tcl[ii].BeginAng;
      if(std::abs(tcl[ii].BeginSlp) < 100) {
        myprt<<std::right<<std::setw(6)<<std::fixed<<std::setprecision(2)<<tcl[ii].BeginSlp;
      } else {
        myprt<<std::right<<std::setw(6)<<(int)tcl[ii].BeginSlp;
      }
      myprt<<std::right<<std::setw(6)<<std::fixed<<std::setprecision(2)<<tcl[ii].BeginSlpErr;
      myprt<<std::right<<std::setw(5)<<(int)tcl[ii].BeginChg;
//      myprt<<std::right<<std::setw(5)<<std::fixed<<std::setprecision(1)<<tcl[ii].BeginChgNear;
      iTime = tcl[ii].EndTim;
      myprt<<std::right<<std::setw(6)<<tcl[ii].EndWir<<":"<<iTime;
      if(iTime < 10) {
        myprt<<"   ";
      } else if(iTime < 100) {
        myprt<<"  ";
      } else if(iTime < 1000) myprt<<" ";
      myprt<<std::right<<std::setw(7)<<std::fixed<<std::setprecision(2)<<tcl[ii].EndAng;
      if(std::abs(tcl[ii].EndSlp) < 100) {
        myprt<<std::right<<std::setw(6)<<std::fixed<<std::setprecision(2)<<tcl[ii].EndSlp;
      } else {
        myprt<<std::right<<std::setw(6)<<(int)tcl[ii].EndSlp;
      }
      myprt<<std::right<<std::setw(6)<<std::fixed<<std::setprecision(2)<<tcl[ii].EndSlpErr;
      myprt<<std::right<<std::setw(5)<<(int)tcl[ii].EndChg;
//      myprt<<std::right<<std::setw(5)<<std::fixed<<std::setprecision(1)<<tcl[ii].EndChgNear;
      myprt<<std::right<<std::setw(5)<<tcl[ii].BeginVtx;
      myprt<<std::right<<std::setw(5)<<tcl[ii].EndVtx;
      aveRMS = 0;
      unsigned int iht = 0;
      for(unsigned short jj = 0; jj < tcl[ii].tclhits.size(); ++jj) {
        iht = tcl[ii].tclhits[jj];
        aveRMS += fHits[iht].RMS();
      }
      aveRMS /= (float)tcl[ii].tclhits.size();
      myprt<<std::right<<std::setw(5)<<std::fixed<<std::setprecision(1)<<aveRMS;
      aveRes = 0;
      // find cluster tracking resolution
      unsigned int hit0, hit1, hit2, cnt = 0;
      float arg;
      for(unsigned short iht = 1; iht < tcl[ii].tclhits.size()-1; ++iht) {
        hit1 = tcl[ii].tclhits[iht];
        hit0 = tcl[ii].tclhits[iht-1];
        hit2 = tcl[ii].tclhits[iht+1];
        // require hits on adjacent wires
        if(fHits[hit1].WireID().Wire + 1 != fHits[hit0].WireID().Wire) continue;
        if(fHits[hit2].WireID().Wire + 1 != fHits[hit1].WireID().Wire) continue;
        arg = (fHits[hit0].PeakTime() + fHits[hit2].PeakTime())/2 - fHits[hit1].PeakTime();
        aveRes += arg * arg;
        ++cnt;
      }
      if(cnt > 1) {
        aveRes /= (float)cnt;
        aveRes = sqrt(aveRes);
        // convert to a quality factor
        aveRes /= (aveRMS * fHitErrFac);
        myprt<<std::right<<std::setw(6)<<std::fixed<<std::setprecision(1)<<aveRes;
        myprt<<std::right<<std::setw(5)<<std::fixed<<cnt;
      } else {
        myprt<<"    NA";
        myprt<<std::right<<std::setw(5)<<std::fixed<<cnt;
      }
       myprt<<"\n";
      // TEMP
//      if(tcl[ii].BeginVtx >= 0) myprt<<"Begin vtx Chi "<<ClusterVertexChi(ii, 0, tcl[ii].BeginVtx)<<"\n";
//      if(tcl[ii].EndVtx >= 0) myprt<<"End vtx Chi "<<ClusterVertexChi(ii, 1, tcl[ii].EndVtx)<<"\n";
    } // ii
    
  } // PrintClusters()

std::string cluster::ClusterCrawlerAlg::PrintHit ( unsigned int  iht )

private

Definition at line 6402 of file ClusterCrawlerAlg.cxx.

References util::flags::to_string().

  {
    
    if(iht > fHits.size() - 1) return "Bad Hit";
    return std::to_string(fHits[iht].WireID().Plane) + ":" +std::to_string(fHits[iht].WireID().Wire) + ":" + std::to_string((int)fHits[iht].PeakTime());
    
  } // PrintHit

void cluster::ClusterCrawlerAlg::PrintVertices ( )

private

Definition at line 3436 of file ClusterCrawlerAlg.cxx.

References art::right().

  {

    mf::LogVerbatim myprt("CC");
    
    if(vtx3.size() > 0) {
      // print out 3D vertices
      myprt<<"****** 3D vertices ******************************************__2DVtx_Indx__*******\n";
      myprt<<"Vtx  Cstat  TPC Proc     X       Y       Z    XEr  YEr  ZEr  pln0 pln1 pln2  Wire\n";
      for(unsigned short iv = 0; iv < vtx3.size(); ++iv) {
        myprt<<std::right<<std::setw(3)<<std::fixed<<iv<<std::setprecision(1);
        myprt<<std::right<<std::setw(7)<<vtx3[iv].CStat;
        myprt<<std::right<<std::setw(5)<<vtx3[iv].TPC;
        myprt<<std::right<<std::setw(5)<<vtx3[iv].ProcCode;
        myprt<<std::right<<std::setw(8)<<vtx3[iv].X;
        myprt<<std::right<<std::setw(8)<<vtx3[iv].Y;
        myprt<<std::right<<std::setw(8)<<vtx3[iv].Z;
        myprt<<std::right<<std::setw(5)<<vtx3[iv].XErr;
        myprt<<std::right<<std::setw(5)<<vtx3[iv].YErr;
        myprt<<std::right<<std::setw(5)<<vtx3[iv].ZErr;
        myprt<<std::right<<std::setw(5)<<vtx3[iv].Ptr2D[0];
        myprt<<std::right<<std::setw(5)<<vtx3[iv].Ptr2D[1];
        myprt<<std::right<<std::setw(5)<<vtx3[iv].Ptr2D[2];
        myprt<<std::right<<std::setw(5)<<vtx3[iv].Wire;
        if(vtx3[iv].Wire < 0) {
          myprt<<"    Matched in all planes";
        } else {
          myprt<<"    Incomplete";
        }
        myprt<<"\n";
      }
    } // vtx3.size
    
    if(vtx.size() > 0) {
      // print out 2D vertices
      myprt<<"************ 2D vertices ************\n";
      myprt<<"Vtx   CTP    wire     error   tick     error  ChiDOF  NCl  topo  cluster IDs\n";
      for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
        if(fDebugPlane < 3 && fDebugPlane != (int)vtx[iv].CTP) continue;
        myprt<<std::right<<std::setw(3)<<std::fixed<<iv<<std::setprecision(1);
        myprt<<std::right<<std::setw(6)<<vtx[iv].CTP;
        myprt<<std::right<<std::setw(8)<<vtx[iv].Wire<<" +/- ";
        myprt<<std::right<<std::setw(4)<<vtx[iv].WireErr;
        myprt<<std::right<<std::setw(8)<<vtx[iv].Time<<" +/- ";
        myprt<<std::right<<std::setw(4)<<vtx[iv].TimeErr;
        myprt<<std::right<<std::setw(8)<<vtx[iv].ChiDOF;
        myprt<<std::right<<std::setw(5)<<vtx[iv].NClusters;
        myprt<<std::right<<std::setw(6)<<vtx[iv].Topo;
        myprt<<"    ";
        // display the cluster IDs
        for(unsigned short ii = 0; ii < tcl.size(); ++ii) {
          if(fDebugPlane < 3 && fDebugPlane != (int)tcl[ii].CTP) continue;
          if(tcl[ii].ID < 0) continue;
          if(tcl[ii].BeginVtx == (short)iv) myprt<<std::right<<std::setw(4)<<tcl[ii].ID;
          if(tcl[ii].EndVtx == (short)iv) myprt<<std::right<<std::setw(4)<<tcl[ii].ID;
        }
        myprt<<"\n";
      } // iv
    } // vtx.size

  } // PrintVertices

void cluster::ClusterCrawlerAlg::reconfigure ( fhicl::ParameterSet const &  pset )

virtual

Definition at line 51 of file ClusterCrawlerAlg.cxx.

References art::errors::Configuration, fhicl::ParameterSet::get(), and fhicl::ParameterSet::has_key().

Referenced by cluster::ClusterCrawler::reconfigure().

  {
    
    fNumPass            = pset.get< unsigned short >("NumPass", 0);
    fMaxHitsFit         = pset.get< std::vector<unsigned short> >("MaxHitsFit");
    fMinHits            = pset.get< std::vector<unsigned short> >("MinHits");
    fNHitsAve           = pset.get< std::vector<unsigned short> >("NHitsAve");
    fChgCut             = pset.get< std::vector<float> >("ChgCut");
    fChiCut             = pset.get< std::vector<float> >("ChiCut");
    fMaxWirSkip         = pset.get< std::vector<unsigned short> >("MaxWirSkip");
    fMinWirAfterSkip    = pset.get< std::vector<unsigned short> >("MinWirAfterSkip");
    fKinkChiRat         = pset.get< std::vector<float> >("KinkChiRat");
    fKinkAngCut         = pset.get< std::vector<float> >("KinkAngCut");
    fDoMerge            = pset.get< std::vector<bool>  >("DoMerge");
    fTimeDelta          = pset.get< std::vector<float> >("TimeDelta");
    fMergeChgCut        = pset.get< std::vector<float> >("MergeChgCut");
    fFindVertices       = pset.get< std::vector<bool>  >("FindVertices");
    fLACrawl            = pset.get< std::vector<bool>  >("LACrawl");
    fMinAmp                                             = pset.get< std::vector<float> >("MinAmp", {5, 5, 5});
                fChgNearWindow                  = pset.get< float >("ChgNearWindow");
                fChgNearCut                             = pset.get< float >("ChgNearCut");

    fChkClusterDS       = pset.get< bool   >("ChkClusterDS",false);
    fVtxClusterSplit    = pset.get< bool   >("VtxClusterSplit", false);
    fFindStarVertices   = pset.get< bool   >("FindStarVertices", false);
    if(pset.has_key("HammerCluster")) {
      mf::LogWarning("CC")<<"fcl setting HammerCluster is replaced by FindHammerClusters. Ignoring...";
    }
    fFindHammerClusters = pset.get< bool   >("FindHammerClusters", false);
    fKillGarbageClusters = pset.get< float   >("KillGarbageClusters", 0);
    fRefineVertexClusters = pset.get< bool >("RefineVertexClusters", false);
    fHitErrFac          = pset.get< float  >("HitErrFac", 0.2);
    fHitMinAmp          = pset.get< float  >("HitMinAmp", 0.2);
    fClProjErrFac       = pset.get< float  >("ClProjErrFac", 4);
    fMinHitFrac         = pset.get< float  >("MinHitFrac", 0.6);
    
    fLAClusAngleCut     = pset.get< float  >("LAClusAngleCut", 45);
                fLAClusMaxHitsFit       = pset.get< unsigned short>("LAClusMaxHitsFit");
    fMergeAllHits       = pset.get< bool  >("MergeAllHits", false);
    fHitMergeChiCut     = pset.get< float  >("HitMergeChiCut", 2.5);
    fMergeOverlapAngCut = pset.get< float  >("MergeOverlapAngCut");
    fAllowNoHitWire     = pset.get< unsigned short  >("AllowNoHitWire", 0);
                fVertex2DCut                            = pset.get< float  >("Vertex2DCut", 5);
    fVertex2DWireErrCut = pset.get< float  >("Vertex2DWireErrCut", 5);
    fVertex3DCut        = pset.get< float  >("Vertex3DCut", 5);
    
    fDebugPlane         = pset.get< int  >("DebugPlane", -1);
    fDebugWire          = pset.get< int  >("DebugWire", -1);
    fDebugHit           = pset.get< int  >("DebugHit", -1);

    
    // some error checking
    bool badinput = false;
    if(fNumPass > fMaxHitsFit.size()) badinput = true;
    if(fNumPass > fMinHits.size()) badinput = true;
    if(fNumPass > fNHitsAve.size()) badinput = true;
    if(fNumPass > fChgCut.size()) badinput = true;
    if(fNumPass > fChiCut.size()) badinput = true;
    if(fNumPass > fMaxWirSkip.size()) badinput = true;
    if(fNumPass > fMinWirAfterSkip.size()) badinput = true;
    if(fNumPass > fKinkChiRat.size()) badinput = true;
    if(fNumPass > fKinkAngCut.size()) badinput = true;
    if(fNumPass > fDoMerge.size()) badinput = true;
    if(fNumPass > fTimeDelta.size()) badinput = true;
    if(fNumPass > fMergeChgCut.size()) badinput = true;
    if(fNumPass > fFindVertices.size()) badinput = true;
    if(fNumPass > fLACrawl.size()) badinput = true;

    if(badinput) throw art::Exception(art::errors::Configuration)
      << "ClusterCrawlerAlg: Bad input from fcl file";

    
  } // reconfigure

void cluster::ClusterCrawlerAlg::RefineVertexClusters ( unsigned short  ivx )

private

Definition at line 1366 of file ClusterCrawlerAlg.cxx.

  {
    
    // Try to attach or remove hits on the ends of vertex clusters
    
    std::vector<unsigned short> begClusters;
    std::vector<short> begdW;
    std::vector<unsigned short> endClusters;
    std::vector<short> enddW;

    unsigned int vWire = (unsigned int)(vtx[iv].Wire + 0.5);
    unsigned int vWireErr = (unsigned int)(2 * vtx[iv].WireErr);
    unsigned int vWireLo = vWire - vWireErr;
    unsigned int vWireHi = vWire + vWireErr;

    unsigned short icl, ii;
    short dW;
    bool needsWork = false;
    short maxdW = -100;
    short mindW = 100;
    for(icl = 0; icl < tcl.size(); ++icl) {
      if(tcl[icl].ID < 0) continue;
      if(tcl[icl].CTP != vtx[iv].CTP) continue;
      if(tcl[icl].BeginVtx == iv) {
        dW = vWire - tcl[icl].BeginWir;
        if(dW > maxdW) maxdW = dW;
        if(dW < mindW) mindW = dW;
        if(std::abs(dW) > 1) needsWork = true;
        // TODO: Check dTime also?
        begClusters.push_back(icl);
        begdW.push_back(dW);
      }
      if(tcl[icl].EndVtx == iv) {
        dW = vWire - tcl[icl].EndWir;
        if(dW > maxdW) maxdW = dW;
        if(dW < mindW) mindW = dW;
        if(std::abs(dW) > 1) needsWork = true;
        endClusters.push_back(icl);
        enddW.push_back(dW);
      }
    } // icl
    
    if(vtxprt) mf::LogVerbatim("CC")<<"RefineVertexClusters: vertex "<<iv<<" needsWork "<<needsWork
      <<" mindW "<<mindW<<" maxdW "<<maxdW<<" vWireErr "<<vWireErr;
    
    if(!needsWork) return;
    
    // See if we can move the vertex within errors to reconcile the differences
    // without altering the clusters
    if( ((unsigned int)std::abs(mindW) < vWireErr) && ((unsigned int)std::abs(maxdW) < vWireErr) && std::abs(maxdW - mindW) < 2) {
      if(vtxprt) mf::LogVerbatim("CC")<<" Move vtx wire "<<vtx[iv].Wire;
      vtx[iv].Wire -= (float)(maxdW + mindW)/2;
      if(vtxprt) mf::LogVerbatim("CC")<<" to "<<vtx[iv].Wire;
      // TODO: Fix the vertex time here if necessary
      vtx[iv].Fixed = true;
      // try to attach other clusters
      VertexCluster(iv);
      return;
    }

    // Check the vertex End clusters
    unsigned short newSize;
    for(ii = 0; ii < endClusters.size(); ++ii) {
      icl = endClusters[ii];
      if(vtxprt) mf::LogVerbatim("CC")<<" endCluster "<<tcl[icl].ID<<" dW "<<enddW[ii]<<" vWire "<<vWire;
      if(tcl[icl].EndWir < vWire) {
        // vertex is DS of the cluster end -> remove hits
        TmpGet(icl);
        newSize = fcl2hits.size();
        for(auto hiter = fcl2hits.rbegin(); hiter < fcl2hits.rend(); ++hiter) {
          if(fHits[*hiter].WireID().Wire > vWire) break;
          --newSize;
        }
        // release the hits
        for(auto hiter = fcl2hits.begin(); hiter < fcl2hits.end(); ++hiter) inClus[*hiter] = 0;
        // shorten the cluster
        fcl2hits.resize(newSize);
        MakeClusterObsolete(icl);
        // fit
        FitCluster();
        clProcCode += 700;
        // store it
        TmpStore();
        tcl[tcl.size()-1].EndVtx = iv;
        // update the vertex association
        if(vtxprt) mf::LogVerbatim("CC")<<" modified cluster "<<tcl[icl].ID<<" -> "<<tcl[tcl.size()-1].ID;
      } // tcl[icl].EndWir < vWire
      else if(tcl[icl].EndWir > vWire) {
        mf::LogVerbatim("CC")<<"RefineVertexClusters: Write some EndVtx code";
      } //
    } // ii endClusters
    
    if(begClusters.size() > 0) mf::LogVerbatim("CC")<<"RefineVertexClusters: Write some BeginVtx code";
    
    if(mindW < 0 && maxdW > 0) {
      // vertex wire is in between the ends of the clusters
      // inspect the hits on both clusters near the vertex. The vertex should probably be on the hit
      // with the highest charge
      int vtxHit = -1;
      unsigned short clsBigChg = 0;
      float bigChg = 0;
      unsigned int iht;
      unsigned int ihit;
      // check the begClusters
      for(ii = 0; ii < begClusters.size(); ++ii) {
        icl = begClusters[ii];
        for(iht = 0; iht < tcl[icl].tclhits.size(); ++iht) {
          ihit = tcl[icl].tclhits[iht];
          if(fHits[ihit].Integral() > bigChg) {
            bigChg = fHits[ihit].Integral();
            vtxHit = ihit;
            clsBigChg = icl;
          }
          if(fHits[ihit].WireID().Wire < vWireLo) break;
        } // iht
      } // ii
      // now check the endClusters
      for(ii = 0; ii < endClusters.size(); ++ii) {
        icl = endClusters[ii];
        for(iht = 0; iht < tcl[icl].tclhits.size(); ++iht) {
          ihit = tcl[icl].tclhits[tcl[icl].tclhits.size() - 1 - iht];
          if(fHits[ihit].Integral() > bigChg) {
            bigChg = fHits[ihit].Integral();
            vtxHit = ihit;
            clsBigChg = icl;
          }
          if(fHits[ihit].WireID().Wire > vWireHi) break;
        } // iht
      } // ii
      if(vtxHit > 0) {
        if(vtxprt) mf::LogVerbatim("CC")<<" moving vertex location to hit "
          <<fHits[vtxHit].WireID().Wire<<":"<<(int)fHits[vtxHit].PeakTime()<<" on cluster "<<tcl[clsBigChg].ID;
        vtx[iv].Wire = fHits[vtxHit].WireID().Wire;
        vtx[iv].Time = fHits[vtxHit].PeakTime();
        vtx[iv].Fixed = true;
      } // vtxHit > 0
    } // mindW < 0 && maxdW > 0
    
    FitVtx(iv);
    
  } // RefineVertexClusters

void cluster::ClusterCrawlerAlg::RemoveObsoleteHits ( )

private

Removes obsolete hits from hits, updating the indices.

Definition at line 1059 of file ClusterCrawlerAlg.cxx.

References hits().

                                             {
    
    unsigned int destHit = 0;
    
    if(fHits.size() != inClus.size()) {
      mf::LogError("CC")<<"RemoveObsoleteHits size mis-match "<<fHits.size()<<" "<<inClus.size();
      return;
    }
    
    unsigned short icl;
    for(unsigned int srcHit = 0; srcHit < fHits.size(); ++srcHit) {
      if(inClus[srcHit] < 0) continue;
      if(srcHit != destHit) {
        fHits[destHit] = std::move(fHits[srcHit]);
        inClus[destHit] = inClus[srcHit];
        if(inClus[destHit] > 0) {
          // hit is in a cluster. Find it and change the index
          icl = inClus[destHit] - 1;
          auto& hits = tcl[icl].tclhits;
          auto iHitIndex = std::find(hits.begin(), hits.end(), srcHit);
          if (iHitIndex == hits.end()) {
            mf::LogError("CC")<< "RemoveObsoleteHits: Hit #" << srcHit << " not found in cluster ID "<< inClus[destHit];
          } else {
            *iHitIndex = destHit; // update the index
          }
        } // inClus[destHit] > 0
      }
      ++destHit;
    } // srcHit
    
    fHits.resize(destHit);
    inClus.resize(destHit);
    
  } // RemoveObsoleteHits()

void cluster::ClusterCrawlerAlg::RestoreObsoleteCluster ( unsigned short  icl )

private

Restores an obsolete cluster.

Definition at line 868 of file ClusterCrawlerAlg.cxx.

                                                                   {
    short& ID = tcl[icl].ID;
    if(ID > 0) {
      mf::LogError("CC")<<"Trying to restore non-obsolete cluster ID = "<<ID;
      return;
    }
    ID = -ID;
    
    for(unsigned short iht = 0; iht < tcl[icl].tclhits.size(); ++iht) inClus[tcl[icl].tclhits[iht]] = ID;
    
  } // RestoreObsoleteCluster()

void cluster::ClusterCrawlerAlg::RunCrawler

(

std::vector< recob::Hit > const &

srchits

)

Definition at line 181 of file ClusterCrawlerAlg.cxx.

References detinfo::DetectorProperties::DriftVelocity(), detinfo::DetectorProperties::Efield(), tca::EncodeCTP(), geo::TPCGeo::Nplanes(), detinfo::DetectorProperties::NumberTimeSamples(), tca::PrintClusters(), detinfo::DetectorProperties::SamplingRate(), and detinfo::DetectorProperties::Temperature().

Referenced by cluster::ClusterCrawler::produce().

  {
    // Run the ClusterCrawler algorithm - creating seed clusters and crawling upstream.

    CrawlInit();
    
    fHits = srchits; // plain copy of the sources; it's the base of our hit result
    
    if(fHits.size() < 3) return;
    if(fHits.size() > UINT_MAX) {
      mf::LogWarning("CC")<<"Too many hits for ClusterCrawler "<<fHits.size();
      return;
    }
    
    // don't do anything...
    if(fNumPass == 0) return;
    
    // sort it as needed;
    // that is, sorted by wire ID number,
    // then by start of the region of interest in time, then by the multiplet
    std::sort(fHits.begin(), fHits.end(), &SortByMultiplet);
    
    inClus.resize(fHits.size());
    mergeAvailable.resize(fHits.size());
    for(unsigned int iht = 0; iht < inClus.size(); ++iht) {
      inClus[iht] = 0;
       mergeAvailable[iht] = false;
     }
    
    const detinfo::DetectorProperties* detprop = lar::providerFrom<detinfo::DetectorPropertiesService>();

    for (geo::TPCID const& tpcid: geom->IterateTPCIDs()) {
      geo::TPCGeo const& TPC = geom->TPC(tpcid);
      for(plane = 0; plane < TPC.Nplanes(); ++plane){
        WireHitRange.clear();
        // define a code to ensure clusters are compared within the same plane
        clCTP = EncodeCTP(tpcid.Cryostat, tpcid.TPC, plane);
        cstat = tpcid.Cryostat;
        tpc = tpcid.TPC;
        // fill the WireHitRange vector with first/last hit on each wire
        // dead wires and wires with no hits are flagged < 0
        GetHitRange(clCTP);

// sanity check
/*
  std::cout<<"Plane "<<plane<<" sanity check. Wire range "<<fFirstWire<<" "<<fLastWire;
  unsigned int nhts = 0;
  for(unsigned int wire = fFirstWire; wire < fLastWire; ++wire) {
    if(WireHitRange[wire].first < 0) continue;
    unsigned int fhit = WireHitRange[wire].first;
    unsigned int lhit = WireHitRange[wire].second;
    for(unsigned int hit = fhit; hit < lhit; ++hit) {
      ++nhts;
      if(fHits[hit].WireID().Wire != wire) {
        std::cout<<"Bad wire "<<hit<<" "<<fHits[hit].WireID().Wire<<" "<<wire<<"\n";
        return;
      } // check wire
      if(fHits[hit].WireID().Plane != plane) {
        std::cout<<"Bad plane "<<hit<<" "<<fHits[hit].WireID().Plane<<" "<<plane<<"\n";
        return;
      } // check plane
      if(fHits[hit].WireID().TPC != tpc) {
        std::cout<<"Bad tpc "<<hit<<" "<<fHits[hit].WireID().TPC<<" "<<tpc<<"\n";
        return;
      } // check tpc
    } // hit
  } // wire
  std::cout<<" is OK. nhits "<<nhts<<"\n";
*/
        if (WireHitRange.empty()||(fFirstWire == fLastWire)) continue;
        raw::ChannelID_t channel = fHits[fFirstHit].Channel();
        // get the scale factor to convert dTick/dWire to dX/dU. This is used
        // to make the kink and merging cuts
        float wirePitch = geom->WirePitch(geom->View(channel));
        float tickToDist = detprop->DriftVelocity(detprop->Efield(),detprop->Temperature());
        tickToDist *= 1.e-3 * detprop->SamplingRate(); // 1e-3 is conversion of 1/us to 1/ns
        fScaleF = tickToDist / wirePitch;
        // convert Large Angle Cluster crawling cut to a slope cut
        if(fLAClusAngleCut > 0) 
          fLAClusSlopeCut = std::tan(3.142 * fLAClusAngleCut / 180.) / fScaleF;
        fMaxTime = detprop->NumberTimeSamples();
        fNumWires = geom->Nwires(plane, tpc, cstat);
        // look for clusters
        if(fNumPass > 0) ClusterLoop();
      } // plane
      if(fVertex3DCut > 0) {
        // Match vertices in 3 planes
        VtxMatch(tpcid);
        Vtx3ClusterMatch(tpcid);
                                if(fFindHammerClusters) FindHammerClusters();
        // split clusters using 3D vertices
        Vtx3ClusterSplit(tpcid);
      }
      if(fDebugPlane >= 0) {
        mf::LogVerbatim("CC")<<"Clustering done in TPC ";
        PrintClusters();
      }
    } // for all tpcs
    
    // clean up
    WireHitRange.clear();
    fcl2hits.clear();
    chifits.clear();
    hitNear.clear();
    chgNear.clear();
    
/*
    // TEMP. Print out cluster info for tuning
    std::array<unsigned int, 3> ncl;
    std::array<unsigned int, 3> nht;
    std::array<unsigned int, 3> nhtTot;
    std::array<unsigned int, 3> nhtNotMerged;
    unsigned int ipl;
    for(ipl = 0; ipl < 3; ++ipl) {
      ncl[ipl] = 0;
      nht[ipl] = 0;
      nhtTot[ipl] = 0;
      nhtNotMerged[ipl] = 0;
    }
    // hits in clusters
    for(unsigned int icl = 0; icl < tcl.size(); ++icl) {
      if(tcl[icl].ID < 0) continue;
      geo::PlaneID iplID = DecodeCTP(tcl[icl].CTP);
      ipl = iplID.Plane;
      ++ncl[ipl];
      nht[ipl] += tcl[icl].tclhits.size();
    }
    // total number of hits
    for(unsigned int iht = 0; iht < fHits.size(); ++iht) {
      ipl = fHits[iht].WireID().Plane;
      ++nhtTot[ipl];
      if(inClus[iht] >= 0) ++nhtNotMerged[ipl];
    }
    int frc1, frc2;
    for(ipl = 0; ipl < 3; ++ipl) {
      frc1 = 0; frc2 = 0;
      if(nhtNotMerged[ipl] > 0) frc1 = 100 * (float)nht[ipl] / (float)nhtNotMerged[ipl];
      if(nhtTot[ipl] > 0) frc2 = 100 * (float)nhtNotMerged[ipl] / (float)nhtTot[ipl];
      frc2 = 100 - frc2;
      std::cout<<"plane "<<ipl<<" num clusters "<<ncl[ipl]<<" Hits in clusters "<<frc1<<"%. Hits merged "<<frc2<<"%\n";
    }
*/
    // remove the hits that have become obsolete
    RemoveObsoleteHits();
    
  } // RunCrawler

bool cluster::ClusterCrawlerAlg::SortByMultiplet ( recob::Hit const &  a, recob::Hit const &  b  )

static

Comparison for sorting hits by wire and hit multiplet.

Definition at line 129 of file ClusterCrawlerAlg.cxx.

References geo::WireID::cmp(), recob::Hit::LocalIndex(), recob::Hit::StartTick(), and recob::Hit::WireID().

Referenced by GetVertices().

  {
    // compare the wire IDs first:
    int cmp_res = a.WireID().cmp(b.WireID());
    if (cmp_res != 0) return cmp_res < 0; // order is decided, unless equal
    // decide by start time
    if (a.StartTick() != b.StartTick()) return a.StartTick() < b.StartTick();
    // if still undecided, resolve by local index
    return a.LocalIndex() < b.LocalIndex(); // if still unresolved, it's a bug!
  } // ClusterCrawlerAlg::SortByMultiplet()

bool cluster::ClusterCrawlerAlg::SplitCluster ( unsigned short  icl, unsigned short  pos, unsigned short  ivx  )

private

Definition at line 2838 of file ClusterCrawlerAlg.cxx.

    {
      // split cluster icl into two clusters

      if(tcl[icl].ID < 0) return false;

//      if(pos < 3 || pos > tcl[icl].tclhits.size() - 3) return false;
      
      // declare icl obsolete
      MakeClusterObsolete(icl);
      
      unsigned short ii, iclnew;
      unsigned int iht;

      if(pos > 2) {
        // Have enough hits to make a cluster at the Begin end
        // Create the first cluster (DS) using the Begin info
        clBeginSlp = tcl[icl].BeginSlp;
        clBeginSlpErr = tcl[icl].BeginSlpErr;
        clBeginAng = tcl[icl].BeginAng;
        clBeginWir = tcl[icl].BeginWir;
        clBeginTim = tcl[icl].BeginTim;
        clBeginChg = tcl[icl].BeginChg;
        clStopCode = 5;
        clProcCode = tcl[icl].ProcCode;
        fcl2hits.clear();
        chifits.clear();
        hitNear.clear();
        chgNear.clear();
        for(ii = 0; ii < pos; ++ii) {
          iht = tcl[icl].tclhits[ii];
          fcl2hits.push_back(iht);
        }
        // determine the pass in which this cluster was created
        pass = tcl[icl].ProcCode - 10 * (tcl[icl].ProcCode / 10);
        if(pass > fNumPass-1) pass = fNumPass-1;
        // fit the end hits
        FitCluster();
        clEndSlp = clpar[1];
        clEndSlpErr = clparerr[1];
        clEndAng = std::atan(fScaleF * clEndSlp);
        // find the charge at the end
        FitClusterChg();
        clEndChg = fAveChg;
        if(!TmpStore()) {
          RestoreObsoleteCluster(icl);
          return false;
        }
        // associate the End with the supplied vertex
        iclnew = tcl.size() - 1;
        tcl[iclnew].EndVtx = ivx;
        tcl[iclnew].BeginVtx = tcl[icl].BeginVtx;
        if(vtxprt) mf::LogVerbatim("CC")<<"SplitCluster made cluster "<<iclnew<<" attached to Begin vtx "<<ivx;
     } // pos > 2

      if(pos < tcl[icl].tclhits.size() - 3) {
        // have enough hits to make a cluster at the End
        // now create the second cluster (US)
        clEndSlp = tcl[icl].EndSlp;
        clEndSlpErr = tcl[icl].EndSlpErr;
        clEndAng = std::atan(fScaleF * clEndSlp);
        clEndWir = tcl[icl].EndWir;
        clEndTim = tcl[icl].EndTim;
        clEndChg = tcl[icl].EndChg;
        clStopCode = 5;
        clProcCode = tcl[icl].ProcCode;
        fcl2hits.clear();
        chifits.clear();
        hitNear.clear();
        chgNear.clear();
        bool didFit = false;
        for(ii = pos; ii < tcl[icl].tclhits.size(); ++ii) {
          iht = tcl[icl].tclhits[ii];
          if(inClus[iht] != 0) {
            RestoreObsoleteCluster(icl);
            return false;
          }
          fcl2hits.push_back(iht);
          // define the Begin parameters
          if(fcl2hits.size() == fMaxHitsFit[pass] ||
             fcl2hits.size() == fMinHits[pass]) {
            FitCluster();
            clBeginSlp = clpar[1];
            clBeginAng = std::atan(fScaleF * clBeginSlp);
            clBeginSlpErr = clparerr[1];
            didFit = true;
          }
          if((unsigned short)fcl2hits.size() == fNHitsAve[pass] + 1) {
            FitClusterChg();
            clBeginChg = fAveChg;
            didFit = true;
          }
        } // ii
        // do a fit using all hits if one wasn't done
        if(!didFit) {
          FitCluster();
          FitClusterChg();
          clBeginChg = fAveChg;
        }
        if(!TmpStore()) {
          // clobber the previously stored cluster
          MakeClusterObsolete(tcl.size() - 1);
          RestoreObsoleteCluster(icl);
          return false;
        }
        // associate the End with the supplied vertex
        iclnew = tcl.size() - 1;
        tcl[iclnew].BeginVtx = ivx;
        tcl[iclnew].EndVtx = tcl[icl].EndVtx;
        if(vtxprt) mf::LogVerbatim("CC")<<"SplitCluster made cluster "<<iclnew<<" attached to End vtx "<<ivx;
      }
      
                        return true;
    } // SplitCluster()

void cluster::ClusterCrawlerAlg::TmpGet ( unsigned short  it1 )

private

Definition at line 3595 of file ClusterCrawlerAlg.cxx.

    {
      // copies temp cluster it1 into the fcl2hits vector, etc. This is 
      // effectively the inverse of cl2TmpStore
      
      if(it1 > tcl.size()) return;


      clBeginSlp = tcl[it1].BeginSlp;
      clBeginSlpErr = tcl[it1].BeginSlpErr;
      clBeginAng = tcl[it1].BeginAng;
      clBeginWir = tcl[it1].BeginWir;
      clBeginTim = tcl[it1].BeginTim;
      clBeginChg = tcl[it1].BeginChg;
      clBeginChgNear = tcl[it1].BeginChgNear;
      clEndSlp = tcl[it1].EndSlp;
      clEndSlpErr = tcl[it1].EndSlpErr;
      clEndAng = tcl[it1].EndAng;
      clEndWir = tcl[it1].EndWir;
      clEndTim = tcl[it1].EndTim;
      clEndChg = tcl[it1].EndChg;
      clEndChgNear = tcl[it1].EndChgNear;
      clStopCode = tcl[it1].StopCode;
      clProcCode = tcl[it1].ProcCode;
      clCTP = tcl[it1].CTP;
      fcl2hits = tcl[it1].tclhits;
    }

bool cluster::ClusterCrawlerAlg::TmpStore ( )

private

Definition at line 3625 of file ClusterCrawlerAlg.cxx.

References cluster::ClusterCrawlerAlg::ClusterStore::BeginAng, cluster::ClusterCrawlerAlg::ClusterStore::BeginChg, cluster::ClusterCrawlerAlg::ClusterStore::BeginChgNear, cluster::ClusterCrawlerAlg::ClusterStore::BeginSlp, cluster::ClusterCrawlerAlg::ClusterStore::BeginSlpErr, cluster::ClusterCrawlerAlg::ClusterStore::BeginTim, cluster::ClusterCrawlerAlg::ClusterStore::BeginVtx, cluster::ClusterCrawlerAlg::ClusterStore::BeginWir, cluster::ClusterCrawlerAlg::ClusterStore::CTP, tca::EncodeCTP(), cluster::ClusterCrawlerAlg::ClusterStore::EndAng, cluster::ClusterCrawlerAlg::ClusterStore::EndChg, cluster::ClusterCrawlerAlg::ClusterStore::EndChgNear, cluster::ClusterCrawlerAlg::ClusterStore::EndSlp, cluster::ClusterCrawlerAlg::ClusterStore::EndSlpErr, cluster::ClusterCrawlerAlg::ClusterStore::EndTim, cluster::ClusterCrawlerAlg::ClusterStore::EndVtx, cluster::ClusterCrawlerAlg::ClusterStore::EndWir, cluster::ClusterCrawlerAlg::ClusterStore::ID, cluster::ClusterCrawlerAlg::ClusterStore::ProcCode, cluster::ClusterCrawlerAlg::ClusterStore::StopCode, and cluster::ClusterCrawlerAlg::ClusterStore::tclhits.

  {

    if(fcl2hits.size() < 2) return false;
    if(fcl2hits.size() > fHits.size()) return false;
    
    if(NClusters == SHRT_MAX) return false;
    
    ++NClusters;
    
    unsigned int hit0 = fcl2hits[0];
    unsigned int hit;
    unsigned int tCST = fHits[hit0].WireID().Cryostat;
    unsigned int tTPC = fHits[hit0].WireID().TPC;
    unsigned int tPlane = fHits[hit0].WireID().Plane;
    unsigned int lastWire = 0;
    
    for(unsigned short it = 0; it < fcl2hits.size(); ++it) {
      hit = fcl2hits[it];
      if(inClus[hit] != 0) {
/*
        mf::LogError("CC")<<"TmpStore: Trying to use obsolete/used hit "<<hit<<" inClus "<<inClus[hit]
          <<" on wire "<<fHits[hit].WireID().Wire<<" on cluster "<<NClusters
          <<" in plane "<<plane<<" ProcCode "<<clProcCode;
*/
        --NClusters;
        return false;
      }
      // check for WireID() consistency
      if(fHits[hit].WireID().Cryostat != tCST || fHits[hit].WireID().TPC != tTPC || fHits[hit].WireID().Plane != tPlane) {
/*
        mf::LogError("CC")<<"TmpStore: CTP mis-match "<<hit<<" WireID().TPC "<<fHits[hit].WireID().TPC
        <<" WireID().Plane "<<fHits[hit].WireID().Plane<<" tCST "<<tCST<<" tTPC "<<tTPC<<" tPlane "<<tPlane
        <<" on cluster "<<NClusters<<" ProcCode "<<clProcCode;
*/
        --NClusters;
        return false;
      }
      // check for decreasing wire number
      if(clProcCode < 900 && it > 0 && fHits[hit].WireID().Wire >= lastWire) {
/*
        mf::LogError("CC")<<"TmpStore: Hits not in correct wire order. Seed hit "<<fHits[fcl2hits[0]].WireID().Plane<<":"
          <<fHits[fcl2hits[0]].WireID().Wire<<":"<<(int)fHits[fcl2hits[0]].PeakTime()<<" it "<<it<<" hit wire "<<fHits[hit].WireID().Wire
          <<" ProcCode "<<clProcCode;
*/
        --NClusters;
/*
        for(unsigned short ii = 0; ii < fcl2hits.size(); ++ii) {
          mf::LogVerbatim("CC")<<ii<<" "<<fcl2hits[ii]<<" "<<fHits[fcl2hits[ii]].WireID().Plane<<":"<<fHits[fcl2hits[ii]].WireID().Wire<<":"<<(int)fHits[fcl2hits[ii]].PeakTime();
        }
*/
        return false;
      }
      lastWire = fHits[hit].WireID().Wire;
      inClus[hit] = NClusters;
    }
    
    // ensure that the cluster begin/end info is correct

    // define the begin/end charge if it wasn't done already
    if(clEndChg <= 0) {
      // use the next to the last two hits. The End hit may have low charge
      unsigned int ih0 = fcl2hits.size() - 2;
      hit = fcl2hits[ih0];
      clEndChg = fHits[hit].Integral();
      hit = fcl2hits[ih0 - 1];
      clEndChg += fHits[hit].Integral();
      clEndChg = clEndChg / 2.;
    }
    if(clBeginChg <= 0) {
      // use the 2nd and third hit. The Begin hit may have low charge
      hit = fcl2hits[1];
      clBeginChg = fHits[hit].Integral();
      hit = fcl2hits[2];
      clBeginChg += fHits[hit].Integral();
      clBeginChg = clBeginChg / 2.;
    }
    
    hit0 = fcl2hits[0];
    hit = fcl2hits[fcl2hits.size()-1];
    
    // store the cluster in the temporary ClusterStore struct
    ClusterStore clstr;
    
    clstr.ID = NClusters;
    clstr.BeginSlp    = clBeginSlp;
    clstr.BeginSlpErr = clBeginSlpErr;
    clstr.BeginAng    = std::atan(fScaleF * clBeginSlp);
    clstr.BeginWir    = fHits[hit0].WireID().Wire;
    clstr.BeginTim    = fHits[hit0].PeakTime();
    clstr.BeginChg    = clBeginChg;
    clstr.BeginChgNear = clBeginChgNear;
    clstr.EndSlp      = clEndSlp;
    clstr.EndSlpErr   = clEndSlpErr;
    clstr.EndAng      = std::atan(fScaleF * clEndSlp);
    clstr.EndWir      = fHits[hit].WireID().Wire;
    clstr.EndTim      = fHits[hit].PeakTime();
    clstr.EndChg      = clEndChg;
    clstr.EndChgNear  = clEndChgNear;
    clstr.StopCode    = clStopCode;
    clstr.ProcCode    = clProcCode;
    clstr.BeginVtx    = -99;
    clstr.EndVtx      = -99;
    clstr.CTP         = EncodeCTP(tCST, tTPC, tPlane);
    clstr.tclhits     = fcl2hits;
    tcl.push_back(clstr);

    return true;
  } // TmpStore()

void cluster::ClusterCrawlerAlg::VertexCluster ( unsigned short  ivx )

private

Definition at line 2083 of file ClusterCrawlerAlg.cxx.

    {
      // try to attach clusters to the specified vertex
      if(vtx[iv].NClusters == 0) return;

      short dwb, dwe, dtb, dte;
      bool sigOK;
      
//      vtxprt = (fDebugPlane >= 0 && fDebugWire == 3333);
      
      for(unsigned short icl = 0; icl < tcl.size(); ++icl) {
        if(tcl[icl].ID < 0) continue;
        if(tcl[icl].CTP != vtx[iv].CTP) continue;
        
        dwb = vtx[iv].Wire - tcl[icl].BeginWir;
        dtb = vtx[iv].Time - tcl[icl].BeginTim;
        dwe = vtx[iv].Wire - tcl[icl].EndWir;
        dte = vtx[iv].Time - tcl[icl].EndTim;
        
        float drb = dwb * dwb + dtb * dtb;
        float dre = dwe * dwe + dte * dte;
        
        bool bCloser = (drb < dre);
        
        // ignore clusters in showers
        if(bCloser) {
          if(tcl[icl].BeginChgNear > fChgNearCut) continue;
        } else {
          if(tcl[icl].EndChgNear > fChgNearCut) continue;
        }
        
        if(vtxprt) mf::LogVerbatim("CC")<<"VertexCluster: Try icl ID "<<tcl[icl].ID<<" w vtx "<<iv<<" dwb "<<dwb<<" dwe "<<dwe<<" drb "<<drb<<" dre "<<dre<<" Begin closer? "<<bCloser;
        
        if(tcl[icl].BeginVtx < 0 && bCloser && dwb > -3 && dwb < 3 && tcl[icl].EndVtx != iv) {
          sigOK = ChkSignal(tcl[icl].BeginWir, tcl[icl].BeginTim, vtx[iv].Wire, vtx[iv].Time);
          if(vtxprt) mf::LogVerbatim("CC")<<" Attach cluster Begin to vtx? "<<iv<<" sigOK "<<sigOK;
          if(sigOK) {
            if(vtxprt) mf::LogVerbatim("CC")<<" check ClusterVertexChi "<<ClusterVertexChi(icl, 0, iv);
            if(ClusterVertexChi(icl, 0, iv) < fVertex2DCut) {
              // do a fit and check the vertex error
              tcl[icl].BeginVtx = iv;
              FitVtx(iv);
              if(vtx[iv].ChiDOF > fVertex2DCut || vtx[iv].WireErr > fVertex2DWireErrCut) {
                tcl[icl].BeginVtx = -99;
                FitVtx(iv);
              }
            } // good DoCA
          } // sigOK
        } // check BEGIN
        
        if(tcl[icl].EndVtx < 0 && !bCloser && dwe > -3 && dwe < 3 && tcl[icl].BeginVtx != iv) {
          sigOK = ChkSignal(tcl[icl].EndWir, tcl[icl].EndTim, vtx[iv].Wire, vtx[iv].Time);
          if(vtxprt) mf::LogVerbatim("CC")<<" Attach cluster End to vtx? "<<iv<<" sigOK "<<sigOK;
          if(sigOK) {
            if(vtxprt) mf::LogVerbatim("CC")<<" check ClusterVertexChi "<<ClusterVertexChi(icl, 1, iv);
            if(ClusterVertexChi(icl, 1, iv) < 3) {
              // do a fit and check the vertex error
              tcl[icl].EndVtx = iv;
              FitVtx(iv);
              if(vtx[iv].ChiDOF > fVertex2DCut || vtx[iv].WireErr > fVertex2DWireErrCut) {
                tcl[icl].EndVtx = -99;
                FitVtx(iv);
              }
            } // good DoCA
          } // sigOK
        } // check END
      } // icl
    } // VertexCluster

void cluster::ClusterCrawlerAlg::Vtx3ClusterMatch ( geo::TPCID const &  tpcid )

private

Definition at line 5361 of file ClusterCrawlerAlg.cxx.

References util::absDiff(), detinfo::DetectorProperties::ConvertXToTicks(), geo::CryostatID::Cryostat, cluster::ClusterCrawlerAlg::VtxStore::CTP, tca::EncodeCTP(), cluster::ClusterCrawlerAlg::VtxStore::Fixed, cluster::ClusterCrawlerAlg::VtxStore::Time, cluster::ClusterCrawlerAlg::VtxStore::Topo, geo::TPCID::TPC, cluster::ClusterCrawlerAlg::VtxStore::Wire, and X.

      {
        // Look for clusters that end/begin near the expected wire/time
        // for incomplete 3D vertices
        if(vtx3.size() == 0) return;
        
        const unsigned int cstat = tpcid.Cryostat;
        const unsigned int tpc = tpcid.TPC;
        
        unsigned int thePlane, theWire;
        float theTime;
        int dwb, dwe;

        const detinfo::DetectorProperties* detprop = lar::providerFrom<detinfo::DetectorPropertiesService>();

        for(unsigned short ivx = 0; ivx < vtx3.size(); ++ivx) {
          // A complete 3D vertex with matching 2D vertices in all planes?
          if(vtx3[ivx].Wire < 0) continue;
          if(vtx3[ivx].CStat != cstat || vtx3[ivx].TPC != tpc) continue;
          // Find the plane that is missing a 2D vertex
          thePlane = 3;
          theWire = vtx3[ivx].Wire;
          for(plane = 0; plane < 3; ++plane) {
            if(vtx3[ivx].Ptr2D[plane] >= 0) continue;
            thePlane = plane;
            break;
          } // plane
          if(thePlane > 2) continue;
          theTime = detprop->ConvertXToTicks(vtx3[ivx].X, thePlane, tpc, cstat);
          clCTP = EncodeCTP(cstat, tpc, thePlane);
          // Create a new 2D vertex and see how many clusters we can attach to it
          VtxStore vnew;
          vnew.Wire = theWire;
          vnew.Time = theTime;
          vnew.CTP = clCTP;
          vnew.Topo = 7;
          vnew.Fixed = false;
          vtx.push_back(vnew);
          unsigned short ivnew = vtx.size() -1;
          std::vector<short> vclIndex;
          for(unsigned short icl = 0; icl < tcl.size(); ++icl) {
            if(tcl[icl].ID < 0) continue;
            if(tcl[icl].CTP != clCTP) continue;
            dwb = util::absDiff(theWire, tcl[icl].BeginWir);
            dwe = util::absDiff(theWire, tcl[icl].EndWir);
            // rough cut to start
            if(dwb > 10 && dwe > 10) continue;
            if(dwb < dwe && dwb < 10 && tcl[icl].BeginVtx < 0) {
              // cluster begin is closer
              if(theWire < tcl[icl].BeginWir + 5) continue;
              if(ClusterVertexChi(icl, 0, ivnew) > fVertex3DCut) continue;
              tcl[icl].BeginVtx = ivnew;
              vclIndex.push_back(icl);
            } else if(dwe < 10 && tcl[icl].EndVtx < 0) {
              // cluster end is closer
              if(theWire > tcl[icl].EndWir - 5) continue;
              if(ClusterVertexChi(icl, 1, ivnew) > fVertex3DCut) continue;
              tcl[icl].EndVtx = ivnew;
              vclIndex.push_back(icl);
            } // dwb/dwe check
          } // icl
          bool goodVtx = false;
          if(vclIndex.size() > 0) {
            FitVtx(ivnew);
            goodVtx = (vtx[ivnew].ChiDOF < fVertex3DCut);
            vtx3[ivx].Ptr2D[thePlane] = ivnew;
          }
          if(goodVtx) {
            vtx3[ivx].Ptr2D[thePlane] = ivnew;
            vtx3[ivx].Wire = -1;
          } else {
            // clobber the vertex
            vtx.pop_back();
            for(unsigned short ii = 0; ii < vclIndex.size(); ++ii) {
              unsigned short icl = vclIndex[ii];
              if(tcl[icl].BeginVtx == ivnew) tcl[icl].BeginVtx = -99;
              if(tcl[icl].EndVtx == ivnew) tcl[icl].EndVtx = -99;
            } // ii
          }
        } // ivx
      } // Vtx3ClusterMatch

void cluster::ClusterCrawlerAlg::Vtx3ClusterSplit ( geo::TPCID const &  tpcid )

private

Definition at line 5444 of file ClusterCrawlerAlg.cxx.

References detinfo::DetectorProperties::ConvertXToTicks(), geo::CryostatID::Cryostat, cluster::ClusterCrawlerAlg::VtxStore::CTP, tca::EncodeCTP(), cluster::ClusterCrawlerAlg::VtxStore::Fixed, cluster::ClusterCrawlerAlg::VtxStore::Time, cluster::ClusterCrawlerAlg::VtxStore::TimeErr, cluster::ClusterCrawlerAlg::VtxStore::Topo, geo::TPCID::TPC, cluster::ClusterCrawlerAlg::VtxStore::Wire, cluster::ClusterCrawlerAlg::VtxStore::WireErr, and X.

      {
        // Try to split clusters in a view in which there is no 2D vertex
        // assigned to a 3D vertex
        if(vtx3.size() == 0) return;
        const unsigned int cstat = tpcid.Cryostat;
        const unsigned int tpc = tpcid.TPC;
        
        vtxprt = (fDebugPlane >= 0) && (fDebugHit == 6666);
        
        unsigned int lastplane = 5, kcl, kclID;
        float dth, theTime;
        unsigned int thePlane, theWire, plane;
        unsigned int loWire, hiWire;

        const detinfo::DetectorProperties* detprop = lar::providerFrom<detinfo::DetectorPropertiesService>();

        for(unsigned short ivx = 0; ivx < vtx3.size(); ++ivx) {
          if(vtx3[ivx].CStat != cstat || vtx3[ivx].TPC != tpc) continue;
          // Complete 3D vertex with matching 2D vertices in all planes?
          if(vtxprt) mf::LogVerbatim("CC")<<"Vtx3ClusterSplit ivx "<<ivx<<" Ptr2D "<<vtx3[ivx].Ptr2D[0]<<" "<<vtx3[ivx].Ptr2D[1]<<" "<<vtx3[ivx].Ptr2D[2]<<" wire "<<vtx3[ivx].Wire;
          if(vtx3[ivx].Wire < 0) continue;
          // find the plane that needs to be studied
          thePlane = 3;
          theWire = vtx3[ivx].Wire;
          for(plane = 0; plane < 3; ++plane) {
            if(vtx3[ivx].Ptr2D[plane] >= 0) continue;
            thePlane = plane;
            break;
          } // plane
          if(thePlane > 2) continue;
          theTime = detprop->ConvertXToTicks((double)vtx3[ivx].X, 
            (int)thePlane, (int)tpcid.TPC, (int)tpcid.Cryostat);
          // get the hit range if necessary
          if(thePlane != lastplane) {
            clCTP = EncodeCTP(tpcid.Cryostat, tpcid.TPC, thePlane);
            GetHitRange(clCTP);
            lastplane = thePlane;
          }
          // make a list of clusters that have hits near this point on nearby wires
          std::vector<short> clIDs;
          if(theWire > fFirstWire + 5) { loWire = theWire - 5; } else { loWire = fFirstWire; }
          if(theWire < fLastWire  - 5) { hiWire = theWire + 5; } else { hiWire = fLastWire; }
          if(vtxprt) mf::LogVerbatim("CC")<<"3DVtx "<<ivx<<" look for cluster hits near P:W:T "<<thePlane<<":"<<theWire<<":"<<(int)theTime<<" Wire range "<<loWire<<" to "<<hiWire;
          for(unsigned int wire = loWire; wire < hiWire; ++wire) {
            // ignore dead wires or wires with no hits
            if(WireHitRange[wire].first < 0) continue;
            unsigned int firsthit = WireHitRange[wire].first;
            unsigned int lasthit = WireHitRange[wire].second;
            for(unsigned int khit = firsthit; khit < lasthit; ++khit) {
              // ignore obsolete and un-assigned hits
              if(inClus[khit] <= 0) continue;
              if((unsigned int)inClus[khit] > tcl.size() + 1) {
                mf::LogError("CC")<<"Invalid hit InClus. "<<khit<<" "<<inClus[khit];
                continue;
              }
              // check an expanded time range
              if(theTime < fHits[khit].StartTick() - 20) continue;
              if(theTime > fHits[khit].EndTick() + 20) continue;
              kclID = inClus[khit];
              kcl = kclID - 1;
              // ignore obsolete clusters
              if(tcl[kcl].ID < 0) continue;
              // ignore short clusters
              if(tcl[kcl].tclhits.size() < 6) continue;
              // ignore long straight clusters
              if(tcl[kcl].tclhits.size() > 100 && std::abs(tcl[kcl].BeginAng - tcl[kcl].EndAng) < 0.1) continue;
              // put the cluster in the list if it's not there already
              if(vtxprt) mf::LogVerbatim("CC")<<"Bingo "<<ivx<<" plane "<<thePlane<<" wire "<<wire<<" hit "<<fHits[khit].WireID().Wire<<":"<<(int)fHits[khit].PeakTime()<<" inClus "<<inClus[khit]<<" P:W:T "<<thePlane<<":"<<tcl[kcl].BeginWir<<":"<<(int)tcl[kcl].BeginTim;
              if(std::find(clIDs.begin(), clIDs.end(), kclID) == clIDs.end()) {
                clIDs.push_back(kclID);
              } // std::find
            } // khit
          } // wire
          if(clIDs.size() == 0) continue;
          if(vtxprt) for(unsigned int ii = 0; ii < clIDs.size(); ++ii) mf::LogVerbatim("CC")<<" clIDs "<<clIDs[ii];

          unsigned short ii, icl, jj;
          unsigned int iht;
          short nhitfit;
          bool didit;
          // find a reasonable time error using the 2D vertices that comprise this
          // incomplete 3D vertex
          float tErr = 1;
          unsigned short i2Dvx = 0;
          for(ii = 0; ii < 3; ++ii) {
            if(ii == thePlane) continue;
            i2Dvx = vtx3[ivx].Ptr2D[ii];
            if(i2Dvx > vtx.size() - 1) {
              mf::LogError("CC")<<"Vtx3ClusterSplit: Coding error";
              return;
            }
            if(vtx[i2Dvx].TimeErr > tErr) tErr = vtx[i2Dvx].TimeErr;
          } // ii -> plane

          // do a local fit near the crossing point and make a tighter cut
          for(ii = 0; ii < clIDs.size(); ++ii) {
            icl = clIDs[ii] - 1;
            didit = false;
            for(jj = 0; jj < tcl[icl].tclhits.size(); ++jj) {
              iht = tcl[icl].tclhits[jj];
              if(fHits[iht].WireID().Wire < theWire) {
                nhitfit = 3;
                if(jj > 3) nhitfit = -3;
                FitClusterMid(icl, iht, nhitfit);
                float doca = DoCA(-1, 1, theWire, theTime);
                if(vtxprt) mf::LogVerbatim("CC")<<" cls "<<icl<<" dth "<<dth<<" DoCA "<<doca<<" tErr "<<tErr;
                if((doca / tErr) > 2) clIDs[ii] = -1;
                didit = true;
                break;
              } // fHits[iht].WireID().Wire < theWire
              if(didit) break;
            } // jj
            if(didit) break;
          } // ii
          if(vtxprt) {
            mf::LogVerbatim("CC")<<"clIDs after fit "<<clIDs.size();
            for(ii = 0; ii < clIDs.size(); ++ii) mf::LogVerbatim("CC")<<" clIDs "<<clIDs[ii];
          }

          // see if any candidates remain
          unsigned short nok = 0;
          for(ii = 0; ii < clIDs.size(); ++ii) if(clIDs[ii] >= 0) ++nok;
          if(nok == 0) continue;

          // make a new 2D vertex
          VtxStore vnew;
          vnew.Wire = theWire;
          vnew.WireErr = 1;
          vnew.Time = theTime;
          vnew.TimeErr = 1;
          vnew.Topo = 8;
          vnew.CTP = clCTP;
          vnew.Fixed = false;
          vtx.push_back(vnew);
          // update the 2D -> 3D vertex pointer
          unsigned short ivnew = vtx.size() - 1;
          if(vtxprt) mf::LogVerbatim("CC")<<"Make new 2D vtx "<<ivnew<<" in plane "<<thePlane<<" from 3D vtx "<<ivx;
          vtx3[ivx].Ptr2D[thePlane] = ivnew;
          // either split or attach clusters to this vertex 
          for(ii = 0; ii < clIDs.size(); ++ii) {
            if(clIDs[ii] < 0) continue;
            icl = clIDs[ii] - 1;
            // find the split position
            // split the cluster. Find the split position
            unsigned short pos = 0;
            for(unsigned short jj = 0; jj < tcl[icl].tclhits.size(); ++jj) {
              iht = tcl[icl].tclhits[jj];
              if(fHits[iht].WireID().Wire < theWire) {
                pos = jj;
                break;
              }
            } // jj
            if(pos == 0) {
              // vertex is DS of the cluster Begin
              tcl[icl].BeginVtx = ivnew;
              if(vtxprt) mf::LogVerbatim("CC")<<"Attach to Begin "<<icl;
            } else if(pos > tcl[icl].tclhits.size()) {
              // vertex is US of the cluster Eend
              tcl[icl].EndVtx = ivnew;
              if(vtxprt) mf::LogVerbatim("CC")<<"Attach to End "<<icl;
            } else {
              // vertex is in the middle of the cluster
              if(vtxprt) mf::LogVerbatim("CC")<<"Split cluster "<<clIDs[ii]<<" at pos "<<pos;
              if(!SplitCluster(icl, pos, ivnew)) {
                if(vtxprt) mf::LogVerbatim("CC")<<"SplitCluster failed";
                continue;
              }
              tcl[icl].ProcCode += 10000;
              tcl[tcl.size()-1].ProcCode += 10000;
            } // pos check
          } // ii
          // Fit the vertex position
          FitVtx(ivnew);
          if(vtx[ivnew].ChiDOF < 5 && vtx[ivnew].WireErr < fVertex2DWireErrCut) {
            // mark the 3D vertex as complete
            vtx3[ivx].Wire = -1;
          } else {
            if(vtxprt) mf::LogVerbatim("CC")<<"Bad vtx fit "<<ivnew<<" ChiDOF "<<vtx[ivnew].ChiDOF<<" WireErr "<<vtx[ivnew].WireErr;
            // Recover (partially) from a bad fit. Leave the ProcCode as-is to trace this problem
            vtx.pop_back();
            vtx3[ivx].Ptr2D[thePlane] = -1;
            // find the cluster - vertex associations
            for(jj = 0; jj < tcl.size(); ++jj) {
              if(tcl[jj].BeginVtx == ivnew) tcl[jj].BeginVtx = -99;
              if(tcl[jj].EndVtx == ivnew) tcl[jj].EndVtx = -99;
            } // jj
          }
        } // ivx
        
      } // Vtx3ClusterSplit()

bool cluster::ClusterCrawlerAlg::VtxClusterSplit ( )

private

Definition at line 1509 of file ClusterCrawlerAlg.cxx.

    {

      // split clusters that cross vertices
      
      vtxprt = (fDebugPlane >= 0 && fDebugWire == 5555);

      if(vtxprt) mf::LogVerbatim("CC")<<"VtxClusterSplit ";

      if(vtx.size() == 0) return false;
      unsigned short tclsize = tcl.size();
      if(tclsize < 2) return false;
      
//      float dth;
      bool didit;
      bool didSomething = false;

      for(unsigned short icl = 0; icl < tclsize; ++icl) {
        if(tcl[icl].ID < 0) continue;
        if(tcl[icl].CTP != clCTP) continue;
        // ignore short clusters
        if(tcl[icl].tclhits.size() < 5) continue;
        // check vertices
        didit = false;
        for(unsigned short ivx = 0; ivx < vtx.size(); ++ivx) {
          if(vtx[ivx].CTP != clCTP) continue;
          // abandoned vertex?
          if(vtx[ivx].NClusters == 0) continue;
          // already assigned to this vertex?
          if(tcl[icl].BeginVtx == ivx) continue;
          if(tcl[icl].EndVtx == ivx) continue;
/*
          // long dead-straight cluster?
          if(tcl[icl].tclhits.size() > 100) { 
            dth = tcl[icl].BeginAng - tcl[icl].EndAng;
            if(fabs(dth) < 0.1) continue;
          }
*/
          // vertex wire in-between the cluster ends?
          if(vtx[ivx].Wire < tcl[icl].EndWir) continue;
          if(vtx[ivx].Wire > tcl[icl].BeginWir) continue;
          // vertex time in-between the cluster ends?
          float hiTime = tcl[icl].BeginTim;
          if(tcl[icl].EndTim > hiTime) hiTime = tcl[icl].EndTim;
          if(vtx[ivx].Time > hiTime + 5) continue;
          float loTime = tcl[icl].BeginTim;
          if(tcl[icl].EndTim < loTime) loTime = tcl[icl].EndTim;
          if(vtx[ivx].Time < loTime - 5) continue;
          // find the hit on the cluster that is closest to the vertex on the
          // DS side
          if(vtxprt) mf::LogVerbatim("CC")<<" Chk cluster ID "<<tcl[icl].ID<<" with vertex "<<ivx;
          short ihvx = -99;
          // nSplit is the index of the hit in the cluster where we will
          // split it if all requirements are met
          unsigned short nSplit = 0;
          unsigned short nLop = 0;
          unsigned int iht;
          for(unsigned short ii = tcl[icl].tclhits.size()-1; ii > 0 ; --ii) {
            iht = tcl[icl].tclhits[ii];
            ++nLop;
            if(fHits[iht].WireID().Wire >= vtx[ivx].Wire) {
              nSplit = ii;
  if(vtxprt) mf::LogVerbatim("CC")<<"Split cluster "<<tcl[icl].ID<<" at wire "<<fHits[iht].WireID().Wire
                <<" nSplit "<<nSplit;
              ihvx = iht;
              break;
            }
          } // ii
          // found the wire. Now make a rough time cut
          if(ihvx < 0) continue;
//          short dtime = std::abs(short(fHits[ihvx].PeakTime() - vtx[ivx].Time));
//  if(vtxprt) mf::LogVerbatim("CC")<<" Delta time "<<dtime;
          if(fabs(fHits[ihvx].PeakTime() - vtx[ivx].Time) > 10) continue;
          // check the angle between the crossing cluster icl and the
          // clusters that comprise the vertex. 
          // First decide which end of cluster icl to use to define the angle
          float iclAng = 0.;
          if(nSplit > tcl[icl].tclhits.size() / 2) {
            iclAng = tcl[icl].EndAng;
          } else {
            iclAng = tcl[icl].BeginAng;
          }
                                if(vtxprt) mf::LogVerbatim("CC")<<" iclAng "<<iclAng;
          // check angle wrt the the vertex clusters
          bool angOK = false;
          for(unsigned short jcl = 0; jcl < tclsize; ++jcl) {
            if(tcl[jcl].ID < 0) continue;
            if(tcl[jcl].CTP != clCTP) continue;
            if(tcl[jcl].BeginVtx == ivx) {
              if(fabs(tcl[jcl].BeginAng - iclAng) > 0.4) {
                // large angle difference. Set the flag
                angOK = true;
                break;
              }
            } // tcl[jcl].BeginVtx == ivx
            if(tcl[jcl].EndVtx == ivx) {
              if(fabs(tcl[jcl].EndAng - iclAng) > 0.4) {
                // large angle difference. Set the flag
                angOK = true;
                break;
              }
            } // tcl[jcl].EndVtx == ivx
          } // jcl
          // time to split or chop
          if(angOK) {
  if(vtxprt) mf::LogVerbatim("CC")<<"Split/Chop at pos "<<nLop;
            if(nLop < 3) {
              // lop off hits at the US end
              // Put the cluster in the local arrays
              TmpGet(icl);
              for(unsigned short ii = 0; ii < nLop; ++ii) {
                unsigned int iht = fcl2hits[fcl2hits.size()-1];
                inClus[iht] = 0;
                fcl2hits.pop_back();
              }
              // store it
              clProcCode += 1000;
              // declare this cluster obsolete
              MakeClusterObsolete(icl);
              // store the new one
              if(!TmpStore()) continue;
              unsigned short newcl = tcl.size() - 1;
              tcl[newcl].BeginVtx = tcl[icl].BeginVtx;
              tcl[newcl].EndVtx = ivx;
            } else {
              // split the cluster into two
              // correct the split position
              ++nSplit;
              if(SplitCluster(icl, nSplit, ivx)) {
                tcl[tcl.size()-1].ProcCode += 1000;
                tcl[tcl.size()-2].ProcCode += 1000;
              }
            }
            didit = true;
            didSomething = true;
          } // angOK
          if(didit) break;
        } // ivx
      } // icl
      
      return didSomething;
      
    } // VtxClusterSplit()

void cluster::ClusterCrawlerAlg::VtxConstraint ( unsigned int  iwire, unsigned int  ihit, unsigned int  jwire, unsigned int &  useHit, bool &  doConstrain  )

private

Definition at line 1322 of file ClusterCrawlerAlg.cxx.

References recob::Hit::PeakTime(), geo::WireID::Wire, and recob::Hit::WireID().

    {
      // checks hits on wire jwire to see if one is on a line between a US vertex
      // and the hit ihit on wire iwire. If one is found, doConstrain is set true
      // and the hit index is returned.
      doConstrain = false;
      if(vtx.size() == 0) return;
      // no vertices made yet on the first pass
      if(pass == 0) return;
      // skip if vertices were not requested to be made on the previous pass
      if( !fFindVertices[pass - 1] ) return;
      
      if(jwire > WireHitRange.size() - 1) {
        mf::LogError("CC")<<"VtxConstraint fed bad jwire "<<jwire<<" WireHitRange size "<<WireHitRange.size();
        return;
      }
      
      unsigned int jfirsthit = WireHitRange[jwire].first;
      unsigned int jlasthit = WireHitRange[jwire].second;
      for(unsigned short iv = 0; iv < vtx.size(); ++iv) {
        if(vtx[iv].CTP != clCTP) continue;
        // vertex must be US of the cluster
        if(vtx[iv].Wire > jwire) continue;
        // but not too far US
        if(vtx[iv].Wire < jwire - 10) continue;
        recob::Hit const& hit = fHits[ihit];
        clpar[0] = hit.PeakTime();
        clpar[1] = (vtx[iv].Time - hit.PeakTime()) / (vtx[iv].Wire - iwire);
        clpar[2] = hit.WireID().Wire;
        float prtime = clpar[0] + clpar[1] * (jwire - iwire);
        for(unsigned int jhit = jfirsthit; jhit < jlasthit; ++jhit) {
          if(inClus[jhit] != 0) continue;
          const float tdiff = std::abs(fHits[jhit].TimeDistanceAsRMS(prtime));
          if(tdiff < 2.5) {
            useHit = jhit;
            doConstrain = true;
            return;
          }
        } // jhit
      } // iv
    } // VtxConstraint()

void cluster::ClusterCrawlerAlg::VtxMatch ( geo::TPCID const &  tpcid )

private

Definition at line 5830 of file ClusterCrawlerAlg.cxx.

References detinfo::DetectorProperties::ConvertTicksToX(), geo::CryostatID::Cryostat, cluster::ClusterCrawlerAlg::Vtx3Store::CStat, tca::DecodeCTP(), e, evd::kWire, geo::kX, geo::TPCGeo::LocalToWorld(), geo::TPCGeo::Nplanes(), geo::PlaneID::Plane, cluster::ClusterCrawlerAlg::Vtx3Store::ProcCode, cluster::ClusterCrawlerAlg::Vtx3Store::Ptr2D, geo::InvalidWireError::suggestedWireID(), cluster::ClusterCrawlerAlg::Vtx3Store::TPC, geo::TPCID::TPC, cluster::ClusterCrawlerAlg::Vtx3Store::Wire, geo::WireID::Wire, cluster::ClusterCrawlerAlg::Vtx3Store::X, cluster::ClusterCrawlerAlg::Vtx3Store::XErr, y, cluster::ClusterCrawlerAlg::Vtx3Store::Y, cluster::ClusterCrawlerAlg::Vtx3Store::YErr, cluster::ClusterCrawlerAlg::Vtx3Store::Z, z, and cluster::ClusterCrawlerAlg::Vtx3Store::ZErr.

    {
      // Create 3D vertices from 2D vertices. 3D vertices that are matched
      // in all three planes have Ptr2D >= 0 for all planes
      
      
      geo::TPCGeo const& TPC = geom->TPC(tpcid);
      const detinfo::DetectorProperties* detprop = lar::providerFrom<detinfo::DetectorPropertiesService>();
      
      const unsigned int cstat = tpcid.Cryostat;
      const unsigned int tpc = tpcid.TPC;
      
      // Y,Z limits of the detector
      double local[3] = {0.,0.,0.};
      double world[3] = {0.,0.,0.};
      
      const geo::TPCGeo &thetpc = geom->TPC(tpc, cstat);
      thetpc.LocalToWorld(local,world);
      // reduce the active area of the TPC by 1 cm to prevent wire boundary issues
      float YLo = world[1]-geom->DetHalfHeight(tpc,cstat) + 1;
      float YHi = world[1]+geom->DetHalfHeight(tpc,cstat) - 1;
      float ZLo = world[2]-geom->DetLength(tpc,cstat)/2 + 1;
      float ZHi = world[2]+geom->DetLength(tpc,cstat)/2 - 1;
      
      vtxprt = (fDebugPlane >= 0) && (fDebugHit == 6666);
      
      if(vtxprt) {
        mf::LogVerbatim("CC")<<"Inside VtxMatch";
        PrintVertices();
      }
      
      // wire spacing in cm
      float wirePitch = geom->WirePitch(0, tpcid.TPC, tpcid.Cryostat);
      
      // fill temp vectors of 2D vertex X and X errors
      std::vector<float> vX(vtx.size());
      std::vector<float> vXsigma(vtx.size());
      float vXp;
      for(unsigned short ivx = 0; ivx < vtx.size(); ++ivx) {
        if(vtx[ivx].NClusters == 0) continue;
        geo::PlaneID iplID = DecodeCTP(vtx[ivx].CTP);
        if(iplID.TPC != tpc || iplID.Cryostat != cstat) continue;
        // Convert 2D vertex time error to X error
        vX[ivx]  = detprop->ConvertTicksToX((double)vtx[ivx].Time, (int)iplID.Plane, (int)tpc, (int)cstat);
        vXp = detprop->ConvertTicksToX((double)(vtx[ivx].Time + vtx[ivx].TimeErr), (int)iplID.Plane, (int)tpc, (int)cstat);
        vXsigma[ivx] = fabs(vXp - vX[ivx]);
      } // ivx
      
      // create a array/vector of 2D vertex indices in each plane
      std::array<std::vector<unsigned short>, 3> vIndex;
      unsigned short indx, ipl;
      for(unsigned short ivx = 0; ivx < vtx.size(); ++ivx) {
        if(vtx[ivx].NClusters == 0) continue;
        geo::PlaneID iplID = DecodeCTP(vtx[ivx].CTP);
        if(iplID.TPC != tpc || iplID.Cryostat != cstat) continue;
        ipl = iplID.Plane;
        if(ipl > 2) continue;
        indx = vIndex[ipl].size();
        vIndex[ipl].resize(indx + 1);
        vIndex[ipl][indx] = ivx;
      }
      
      // vector of 2D vertices -> 3D vertices.
      std::vector<short> vPtr;
      for(unsigned short ii = 0; ii < vtx.size(); ++ii) vPtr.push_back(-1);
      
      // temp vector of all 2D vertex matches
      std::vector<Vtx3Store> v3temp;
      
      double y = 0, z = 0;
      TVector3 WPos = {0, 0, 0};
      // i, j, k indicates 3 different wire planes
      unsigned short ii, jpl, jj, kpl, kk, ivx, jvx, kvx;
      unsigned int iWire, jWire;
      unsigned short v3dBest = 0;
      float xbest = 0, ybest = 0, zbest = 0;
      float kX, kWire;
      // compare vertices in each view
      bool gotit = false;
      for(ipl = 0; ipl < 2; ++ipl) {
        for(ii = 0; ii < vIndex[ipl].size(); ++ii) {
          ivx = vIndex[ipl][ii];
          if(ivx > vtx.size() - 1) {
            mf::LogError("CC")<<"VtxMatch: bad ivx "<<ivx;
            return;
          }
          // vertex has been matched already
          if(vPtr[ivx] >= 0) continue;
          iWire = vtx[ivx].Wire;
          float best = fVertex3DCut;
          // temp array of 2D vertex indices in each plane
          // BUG the double brace syntax is required to work around clang bug 21629
          // (https://bugs.llvm.org/show_bug.cgi?id=21629)
          std::array<short, 3> t2dIndex = {{-1, -1, -1}};
          std::array<short, 3> tmpIndex = {{-1, -1, -1}};
          for(jpl = ipl + 1; jpl < 3; ++jpl) {
            for(jj = 0; jj < vIndex[jpl].size(); ++jj) {
              jvx = vIndex[jpl][jj];
              if(jvx > vtx.size() - 1) {
                mf::LogError("CC")<<"VtxMatch: bad jvx "<<jvx;
                return;
              }
              // vertex has been matched already
              if(vPtr[jvx] >= 0) continue;
              jWire = vtx[jvx].Wire;
              // new stuff
              float dX = fabs(vX[ivx] - vX[jvx]);
              float dXSigma = sqrt(vXsigma[ivx] * vXsigma[ivx] + vXsigma[jvx] * vXsigma[jvx]);
              float dXChi = dX / dXSigma;
              
              if(vtxprt) mf::LogVerbatim("CC")<<"VtxMatch: ipl "<<ipl<<" ivx "<<ivx<<" ivX "<<vX[ivx]
                <<" jpl "<<jpl<<" jvx "<<jvx<<" jvX "<<vX[jvx]<<" W:T "<<(int)vtx[jvx].Wire<<":"<<(int)vtx[jvx].Time<<" dXChi "<<dXChi<<" fVertex3DCut "<<fVertex3DCut;
              
              if(dXChi > fVertex3DCut) continue;
              geom->IntersectionPoint(iWire, jWire, ipl, jpl, cstat, tpc, y, z);
              if(y < YLo || y > YHi || z < ZLo || z > ZHi) continue;
              WPos[1] = y;
              WPos[2] = z;
              kpl = 3 - ipl - jpl;
              kX = 0.5 * (vX[ivx] + vX[jvx]);
              kWire = -1;
              if(TPC.Nplanes() > 2){
                try{
                  kWire = geom->NearestWire(WPos, kpl, tpc, cstat);
                }
                catch(geo::InvalidWireError const& e) {
                  kWire = e.suggestedWireID().Wire; // pick the closest valid wire
                }
              }
              kpl = 3 - ipl - jpl;
              // save this incomplete 3D vertex
              Vtx3Store v3d;
              v3d.ProcCode = 1;
              tmpIndex[ipl] = ivx;
              tmpIndex[jpl] = jvx;
              tmpIndex[kpl] = -1;
              v3d.Ptr2D = tmpIndex;
              v3d.X = kX;
              v3d.XErr = dXSigma;
              v3d.Y = y;
              float yzSigma = wirePitch * sqrt(vtx[ivx].WireErr * vtx[ivx].WireErr + vtx[jvx].WireErr * vtx[jvx].WireErr);
              v3d.YErr = yzSigma;
              v3d.Z = z;
              v3d.ZErr = yzSigma;
              v3d.Wire = kWire;
              v3d.CStat = cstat;
              v3d.TPC = tpc;
              v3temp.push_back(v3d);

  if(vtxprt) mf::LogVerbatim("CC")
    <<"VtxMatch: 2 Plane match ivx "<<ivx<<" P:W:T "<<ipl<<":"<<(int)vtx[ivx].Wire<<":"<<(int)vtx[ivx].Time
    <<" jvx "<<jvx<<" P:W:T "<<jpl<<":"<<(int)vtx[jvx].Wire<<":"<<(int)vtx[jvx].Time<<" dXChi "<<dXChi<<" yzSigma "<<yzSigma;

              if(TPC.Nplanes() == 2) continue;
              // look for a 3 plane match
              best = fVertex3DCut;
              for(kk = 0; kk < vIndex[kpl].size(); ++kk) {
                kvx = vIndex[kpl][kk];
                if(vPtr[kvx] >= 0) continue;
//                float kvxX = detprop->ConvertTicksToX((double)vtx[kvx].Time, (int)kpl, (int)tpc, (int)cstat);
                // Wire difference error
                float dW = wirePitch * (vtx[kvx].Wire - kWire) / yzSigma;
                // X difference error
                float dX = (vX[kvx] - kX) / dXSigma;
                float kChi = 0.5 * sqrt(dW * dW + dX * dX);
                if(kChi < best) {
                  best = kChi;
                  xbest = (vX[kvx] + 2 * kX) / 3;
                  ybest = y;
                  zbest = z;
                  t2dIndex[ipl] = ivx;
                  t2dIndex[jpl] = jvx;
                  t2dIndex[kpl] = kvx;
                  v3dBest = v3temp.size() - 1;
                }

  if(vtxprt) mf::LogVerbatim("CC")<<" kvx "<<kvx<<" kpl "<<kpl
    <<" wire "<<(int)vtx[kvx].Wire<<" kTime "<<(int)vtx[kvx].Time<<" kChi "<<kChi<<" best "<<best<<" dW "<<vtx[kvx].Wire - kWire;

              } // kk
              if(vtxprt) mf::LogVerbatim("CC")<<" done best = "<<best<<" fVertex3DCut "<<fVertex3DCut;
              if(TPC.Nplanes() > 2 && best < fVertex3DCut) {
                // create a real 3D vertex using the previously entered incomplete 3D vertex as a template
                if(v3dBest > v3temp.size() - 1) {
                  mf::LogError("CC")<<"VtxMatch: bad v3dBest "<<v3dBest;
                  return;
                }
                Vtx3Store v3d = v3temp[v3dBest];
                v3d.Ptr2D = t2dIndex;
                v3d.Wire = -1;
                // TODO need to average ybest and zbest here with error weighting
                v3d.X = xbest;
                v3d.Y = ybest;
                v3d.Z = zbest;
                vtx3.push_back(v3d);
                gotit = true;
                // mark the 2D vertices as used
                for(unsigned short jj = 0; jj < 3; ++jj) if(t2dIndex[jj] >= 0) vPtr[t2dIndex[jj]] = vtx3.size() - 1;
                
                if(vtxprt) mf::LogVerbatim("CC")<<"New 3D vtx "<<vtx3.size()<<" X "<<v3d.X<<" Y "<<v3d.Y<<" Z "<<v3d.Z
                  <<" t2dIndex "<<t2dIndex[0]<<" "<<t2dIndex[1]<<" "<<t2dIndex[2]<<" best Chi "<<best;
                
              } // best < dRCut
              if(gotit) break;
            } // jj
            if(gotit) break;
          } // jpl
          if(gotit) break;
        } // ii
      } // ipl
      
      // Store incomplete 3D vertices but ignore those that are part of a complete 3D vertex
      unsigned short vsize = vtx3.size();
      for(unsigned short it = 0; it < v3temp.size(); ++it) {
        bool keepit = true;
        for(unsigned short i3d = 0; i3d < vsize; ++i3d) {
          for(unsigned short plane = 0; plane < 3; ++plane) {
            if(v3temp[it].Ptr2D[plane] == vtx3[i3d].Ptr2D[plane]) {
              keepit = false;
              break;
            }
          } // plane
          if(!keepit) break;
        } // i3d

        if(keepit) vtx3.push_back(v3temp[it]);
      } // it
      
      // Modify Ptr2D for 2-plane detector
      if(TPC.Nplanes() == 2) {
        for(unsigned short iv3 = 0; iv3 < vtx3.size(); ++iv3) {
          vtx3[iv3].Ptr2D[2] = 666;
        } //iv3
      } // 2 planes
      
  if(vtxprt) {
    for(unsigned short it = 0; it < vtx3.size(); ++it) {
      mf::LogVerbatim("CC")<<"vtx3 "<<it<<" Ptr2D "<<vtx3[it].Ptr2D[0]<<" "<<vtx3[it].Ptr2D[1]<<" "<<vtx3[it].Ptr2D[2]
        <<" wire "<<vtx3[it].Wire;
    }
  }

    } // VtxMatch

std::vector<recob::Hit>&& cluster::ClusterCrawlerAlg::YieldHits ( )

inline

Returns (and loses) the collection of reconstructed hits.

Definition at line 119 of file ClusterCrawlerAlg.h.

References fHits.

Referenced by cluster::ClusterCrawler::produce().

{ return std::move(fHits); }

Member Data Documentation

std::vector<float> cluster::ClusterCrawlerAlg::chgNear

private

charge near a cluster on each wire

Definition at line 284 of file ClusterCrawlerAlg.h.

std::vector<float> cluster::ClusterCrawlerAlg::chifits

private

fit chisq for monitoring kinks, etc

Definition at line 280 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clBeginAng

private

Definition at line 224 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clBeginChg

private

begin average charge

Definition at line 228 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clBeginChgNear

private

nearby charge

Definition at line 229 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clBeginSlp

private

begin slope (= DS end = high wire number)

Definition at line 223 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clBeginSlpErr

private

Definition at line 225 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clBeginTim

private

begin time

Definition at line 227 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::clBeginWir

private

begin wire

Definition at line 226 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clChisq

private

chisq of the current fit

Definition at line 202 of file ClusterCrawlerAlg.h.

CTP_t cluster::ClusterCrawlerAlg::clCTP

private

Cryostat/TPC/Plane code.

Definition at line 259 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clEndAng

private

Definition at line 231 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clEndChg

private

end average charge

Definition at line 235 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clEndChgNear

private

nearby charge

Definition at line 236 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clEndSlp

private

slope at the end (= US end = low wire number)

Definition at line 230 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clEndSlpErr

private

Definition at line 232 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clEndTim

private

begin time

Definition at line 234 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::clEndWir

private

begin wire

Definition at line 233 of file ClusterCrawlerAlg.h.

bool cluster::ClusterCrawlerAlg::clLA

private

using Large Angle crawling code

Definition at line 260 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clpar[3]

private

cluster parameters for the current fit with origin at the US wire on the cluster (in clpar[2])

Definition at line 199 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::clparerr[2]

private

cluster parameter errors

Definition at line 201 of file ClusterCrawlerAlg.h.

short cluster::ClusterCrawlerAlg::clProcCode

private

Processor code = pass number + 10 ChkMerge

• 20 ChkMerge with overlapping hits
• 100 ChkMerge12
• 200 ClusterFix
• 300 LACrawlUS
• 500 MergeOverlap
• 666 KillGarbageClusters
• 1000 VtxClusterSplit
• 2000 failed pass N cuts but passes pass N=1 cuts
• 5000 ChkClusterDS +10000 Vtx3ClusterSplit

Definition at line 247 of file ClusterCrawlerAlg.h.

short cluster::ClusterCrawlerAlg::clStopCode

private

8 = SPECIAL CODE FOR STEP CRAWLING

code for the reason for stopping cluster tracking 0 = no signal on the next wire 1 = skipped too many occupied/dead wires 2 = failed the fMinWirAfterSkip cut 3 = ended on a kink. Fails fKinkChiRat 4 = failed the fChiCut cut 5 = cluster split by VtxClusterSplit 6 = stop at a vertex 7 = LA crawl stopped due to slope cut

Definition at line 237 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::cstat

private

Definition at line 265 of file ClusterCrawlerAlg.h.

constexpr unsigned int cluster::ClusterCrawlerAlg::CTPpad = 1000

static

Definition at line 42 of file ClusterCrawlerAlg.h.

Referenced by DecodeCTP().

unsigned short cluster::ClusterCrawlerAlg::fAllowNoHitWire

private

Definition at line 186 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fAveChg

private

average charge at leading edge of cluster

Definition at line 203 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fAveHitWidth

private

average width (EndTick - StartTick) of hits

Definition at line 206 of file ClusterCrawlerAlg.h.

std::vector<float> cluster::ClusterCrawlerAlg::fChgCut

private

charge difference cut for adding a hit to a cluster

Definition at line 153 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fChgNearCut

private

to define a shower-like cluster

cut on ratio of nearby/cluster charge to

Definition at line 286 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fChgNearWindow

private

window (ticks) for finding nearby charge

Definition at line 285 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fChgSlp

private

slope of the charge vs wire

Definition at line 205 of file ClusterCrawlerAlg.h.

std::vector<float> cluster::ClusterCrawlerAlg::fChiCut

private

stop adding hits to clusters if chisq too high

Definition at line 149 of file ClusterCrawlerAlg.h.

bool cluster::ClusterCrawlerAlg::fChkClusterDS

private

Definition at line 169 of file ClusterCrawlerAlg.h.

std::vector<unsigned int> cluster::ClusterCrawlerAlg::fcl2hits

private

vector of hits used in the cluster

Definition at line 279 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fClProjErrFac

private

cluster projection error factor

Definition at line 177 of file ClusterCrawlerAlg.h.

int cluster::ClusterCrawlerAlg::fDebugHit

private

out detailed information while crawling

Definition at line 193 of file ClusterCrawlerAlg.h.

int cluster::ClusterCrawlerAlg::fDebugPlane

private

Definition at line 191 of file ClusterCrawlerAlg.h.

int cluster::ClusterCrawlerAlg::fDebugWire

private

set to the Begin Wire and Hit of a cluster to print

Definition at line 192 of file ClusterCrawlerAlg.h.

std::vector<bool> cluster::ClusterCrawlerAlg::fDoMerge

private

try to merge clusters?

Definition at line 157 of file ClusterCrawlerAlg.h.

std::vector<geo::WireID> cluster::ClusterCrawlerAlg::fFilteredWires

private

Definition at line 196 of file ClusterCrawlerAlg.h.

bool cluster::ClusterCrawlerAlg::fFindHammerClusters

private

look for hammer type clusters

Definition at line 162 of file ClusterCrawlerAlg.h.

bool cluster::ClusterCrawlerAlg::fFindStarVertices

private

Definition at line 171 of file ClusterCrawlerAlg.h.

std::vector<bool> cluster::ClusterCrawlerAlg::fFindVertices

private

run vertexing code after clustering?

Definition at line 160 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::fFirstHit

private

first hit used

Definition at line 263 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::fFirstWire

private

the first wire with a hit

Definition at line 262 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fHitErrFac

private

hit time error = fHitErrFac * hit RMS used for cluster fit

Definition at line 175 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fHitMergeChiCut

private

is < cut. Set < 0 for no merging

Merge cluster hit-multiplets if the separation chisq

Definition at line 183 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fHitMinAmp

private

< ignore hits with Amp < this value

Definition at line 176 of file ClusterCrawlerAlg.h.

std::vector<recob::Hit> cluster::ClusterCrawlerAlg::fHits

private

our version of the hits

Definition at line 214 of file ClusterCrawlerAlg.h.

Referenced by YieldHits().

std::string cluster::ClusterCrawlerAlg::fhitsModuleLabel

private

Definition at line 289 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fKillGarbageClusters

private

Definition at line 168 of file ClusterCrawlerAlg.h.

std::vector<float> cluster::ClusterCrawlerAlg::fKinkAngCut

private

kink angle cut made after fKinkChiRat

Definition at line 152 of file ClusterCrawlerAlg.h.

std::vector<float> cluster::ClusterCrawlerAlg::fKinkChiRat

private

Max consecutive chisq increase for the last 3 hits on the cluster

Definition at line 150 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fLAClusAngleCut

private

call Large Angle Clustering code if > 0

Definition at line 179 of file ClusterCrawlerAlg.h.

unsigned short cluster::ClusterCrawlerAlg::fLAClusMaxHitsFit

private

max hits fitted on a Large Angle cluster

Definition at line 180 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fLAClusSlopeCut

private

Definition at line 181 of file ClusterCrawlerAlg.h.

std::vector<bool> cluster::ClusterCrawlerAlg::fLACrawl

private

Crawl Large Angle clusters on pass?

Definition at line 161 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::fLastWire

private

the last wire with a hit

Definition at line 264 of file ClusterCrawlerAlg.h.

trkf::LinFitAlg cluster::ClusterCrawlerAlg::fLinFitAlg

private

Definition at line 221 of file ClusterCrawlerAlg.h.

std::vector<unsigned short> cluster::ClusterCrawlerAlg::fMaxHitsFit

private

Max number of hits fitted.

Definition at line 145 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::fMaxTime

private

Definition at line 269 of file ClusterCrawlerAlg.h.

std::vector<unsigned short> cluster::ClusterCrawlerAlg::fMaxWirSkip

private

max number of wires that can be skipped while crawling

Definition at line 154 of file ClusterCrawlerAlg.h.

bool cluster::ClusterCrawlerAlg::fMergeAllHits

private

Definition at line 182 of file ClusterCrawlerAlg.h.

std::vector<float> cluster::ClusterCrawlerAlg::fMergeChgCut

private

max charge ratio for matching

Definition at line 159 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fMergeOverlapAngCut

private

angle cut for merging overlapping clusters

Definition at line 185 of file ClusterCrawlerAlg.h.

std::vector<float> cluster::ClusterCrawlerAlg::fMinAmp

private

expected minimum signal in each wire plane

Definition at line 166 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fMinHitFrac

private

Definition at line 178 of file ClusterCrawlerAlg.h.

std::vector<unsigned short> cluster::ClusterCrawlerAlg::fMinHits

private

Min number of hits to make a cluster.

Definition at line 146 of file ClusterCrawlerAlg.h.

std::vector<unsigned short> cluster::ClusterCrawlerAlg::fMinWirAfterSkip

private

after skipping

minimum number of hits on consecutive wires

Definition at line 155 of file ClusterCrawlerAlg.h.

std::vector<unsigned short> cluster::ClusterCrawlerAlg::fNHitsAve

private

set to > 2 to do a charge fit using fNHitsAve hits

number of US hits used to compute fAveChg

Definition at line 147 of file ClusterCrawlerAlg.h.

unsigned short cluster::ClusterCrawlerAlg::fNumPass

private

number of passes over the hit collection

Definition at line 144 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::fNumWires

private

Definition at line 268 of file ClusterCrawlerAlg.h.

bool cluster::ClusterCrawlerAlg::fRefineVertexClusters

private

Definition at line 164 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fScaleF

private

scale factor from Tick/Wire to dx/du

Definition at line 270 of file ClusterCrawlerAlg.h.

std::vector<float> cluster::ClusterCrawlerAlg::fTimeDelta

private

max time difference for matching

Definition at line 158 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fVertex2DCut

private

2D vtx -> cluster matching cut (chisq/dof)

Definition at line 187 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fVertex2DWireErrCut

private

Definition at line 188 of file ClusterCrawlerAlg.h.

float cluster::ClusterCrawlerAlg::fVertex3DCut

private

2D vtx -> 3D vtx matching cut (chisq/dof)

Definition at line 189 of file ClusterCrawlerAlg.h.

bool cluster::ClusterCrawlerAlg::fVtxClusterSplit

private

Definition at line 170 of file ClusterCrawlerAlg.h.

art::ServiceHandle<geo::Geometry> cluster::ClusterCrawlerAlg::geom

private

Definition at line 212 of file ClusterCrawlerAlg.h.

std::vector<short> cluster::ClusterCrawlerAlg::hitNear

private

Number of nearby hits that were merged have hitnear < 0

Definition at line 281 of file ClusterCrawlerAlg.h.

std::vector<short> cluster::ClusterCrawlerAlg::inClus

private

Hit used in cluster (-1 = obsolete, 0 = free)

Definition at line 215 of file ClusterCrawlerAlg.h.

Referenced by GetinClus().

std::vector<bool> cluster::ClusterCrawlerAlg::mergeAvailable

private

set true if hit is with HitMergeChiCut of a neighbor hit

Definition at line 216 of file ClusterCrawlerAlg.h.

unsigned short cluster::ClusterCrawlerAlg::NClusters

private

Definition at line 210 of file ClusterCrawlerAlg.h.

unsigned short cluster::ClusterCrawlerAlg::pass

private

Definition at line 272 of file ClusterCrawlerAlg.h.

unsigned int cluster::ClusterCrawlerAlg::plane

private

Definition at line 267 of file ClusterCrawlerAlg.h.

Referenced by EncodeCTP().

bool cluster::ClusterCrawlerAlg::prt

private

Definition at line 208 of file ClusterCrawlerAlg.h.

std::vector< ClusterStore > cluster::ClusterCrawlerAlg::tcl

private

the clusters we are creating

Definition at line 217 of file ClusterCrawlerAlg.h.

Referenced by GetClusters().

unsigned int cluster::ClusterCrawlerAlg::tpc

private

Definition at line 266 of file ClusterCrawlerAlg.h.

std::vector< VtxStore > cluster::ClusterCrawlerAlg::vtx

private

the endpoints we are reconstructing

Definition at line 218 of file ClusterCrawlerAlg.h.

Referenced by GetEndPoints().

std::vector< Vtx3Store > cluster::ClusterCrawlerAlg::vtx3

private

the 3D vertices we are reconstructing

Definition at line 219 of file ClusterCrawlerAlg.h.

Referenced by GetVertices().

bool cluster::ClusterCrawlerAlg::vtxprt

private

Definition at line 209 of file ClusterCrawlerAlg.h.

std::vector< std::pair<int, int> > cluster::ClusterCrawlerAlg::WireHitRange

private

Definition at line 277 of file ClusterCrawlerAlg.h.

---

The documentation for this class was generated from the following files:

• larreco/v06_64_02/source/larreco/RecoAlg/ClusterCrawlerAlg.h
• larreco/v06_64_02/source/larreco/RecoAlg/ClusterCrawlerAlg.cxx