Track3DKalman_module.cc

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//
// \file Track3DKalman.cxx
//
// \author echurch@fnal.gov
//
//  This algorithm is designed to reconstruct 3D tracks through  
//  GENFIT's Kalman filter.

// C++ includes
#include <math.h>
#include <algorithm>
#include <iostream>
#include <fstream>

#include "art/Framework/Core/ModuleMacros.h" 


// Framework includes
#include "canvas/Persistency/Common/FindManyP.h"
#include "art/Framework/Principal/Event.h" 
#include "fhiclcpp/ParameterSet.h" 
#include "art/Framework/Principal/Handle.h" 
#include "canvas/Persistency/Common/Ptr.h" 
#include "canvas/Persistency/Common/PtrVector.h" 
#include "art/Framework/Services/Registry/ServiceHandle.h" 
#include "art/Framework/Services/Optional/TFileService.h" 
#include "art/Framework/Services/Optional/TFileDirectory.h" 
#include "messagefacility/MessageLogger/MessageLogger.h" 

// art extensions
#include "nutools/RandomUtils/NuRandomService.h"

// LArSoft includes

#include "larcore/Geometry/Geometry.h"
#include "lardataobj/RecoBase/Cluster.h"
#include "lardataobj/RecoBase/Hit.h"
#include "lardataobj/RecoBase/Track.h"
#include "lardataobj/RecoBase/SpacePoint.h"
#include "lardata/Utilities/AssociationUtil.h"
#include "nusimdata/SimulationBase/MCTruth.h"
#include "lardataobj/Simulation/sim.h"


// ROOT includes
#include "TVectorD.h"
#include "TFile.h"
#include "TGeoManager.h"
#include "TF1.h"
#include "TGraph.h"
#include "TMath.h"

// GENFIT includes
#include "larreco/Genfit/GFException.h"
#include "larreco/Genfit/GFAbsTrackRep.h"
#include "larreco/Genfit/GeaneTrackRep2.h"
#include "larreco/Genfit/RKTrackRep.h"
#include "larreco/Genfit/GFConstField.h"
#include "larreco/Genfit/GFFieldManager.h"
#include "larreco/Genfit/PointHit.h"
#include "larreco/Genfit/GFTrack.h"
#include "larreco/Genfit/GFKalman.h"
#include "larreco/Genfit/GFDaf.h"

#include "art/Framework/Core/EDProducer.h"
#include <TTree.h>
#include <TMatrixT.h>

#include "larreco/Genfit/GFAbsTrackRep.h"

#include "CLHEP/Random/RandFlat.h"
#include "CLHEP/Random/RandGaussQ.h"

#include <vector>
#include <string>

//#include "RecoBase/SpacePoint.h"

namespace trkf {

  class Track3DKalman : public art::EDProducer {
    
  public:
    
    explicit Track3DKalman(fhicl::ParameterSet const& pset);
    ~Track3DKalman();
    
    void produce(art::Event& evt); 
    void beginJob();
    void endJob();
    void reconfigure(fhicl::ParameterSet const& p);

  private:
        
    std::string     fSpacePtsModuleLabel;// label for input collection
    std::string     fGenieGenModuleLabel;// label for input MC single particle generator
    std::string     fG4ModuleLabel;// label for input MC single particle generator
    bool fGenfPRINT;
      
  //  TFile *fileGENFIT;
    TTree *tree;

    TMatrixT<Double_t> *stMCT;
    TMatrixT<Double_t> *covMCT;
    TMatrixT<Double_t> *stREC;
    TMatrixT<Double_t> *covREC;
    Float_t chi2;
    Float_t chi2ndf;
    
    Float_t *fpRECt3D;    
    Float_t *fpRECL;
    Float_t *fpREC;
    Float_t *fpMCT;
    int nfail;
    int ndf;
    unsigned int evtt;
    unsigned int nTrks;
    unsigned int fptsNo;
    Float_t *fshx;
    Float_t *fshy;
    Float_t *fshz;
    unsigned int fDimSize; // if necessary will get this from pset in constructor.
  
    std::vector<double> fPosErr;
    std::vector<double> fMomErr;
    std::vector<double> fMomStart;
    genf::GFAbsTrackRep *repMC;
    genf::GFAbsTrackRep *rep;

  
  }; // class Track3DKalman

} // end namespace

static bool sp_sort_3dz(const art::Ptr<recob::SpacePoint>& h1, const art::Ptr<recob::SpacePoint>& h2)
{
  const double* xyz1 = h1->XYZ();
  const double* xyz2 = h2->XYZ();
  return xyz1[2] < xyz2[2];
}

namespace trkf {

//-------------------------------------------------
Track3DKalman::Track3DKalman(fhicl::ParameterSet const& pset) 
{

  this->reconfigure(pset);
  
  // create a default random engine; obtain the random seed from NuRandomService,
  // unless overridden in configuration with key "Seed"
  art::ServiceHandle<rndm::NuRandomService>()->createEngine(*this, pset, "Seed");
  
  produces< std::vector<recob::Track> >();
  produces< std::vector<recob::SpacePoint>              >();
  produces< art::Assns<recob::Track, recob::Cluster>    >();
  produces< art::Assns<recob::Track, recob::SpacePoint> >();
  produces< art::Assns<recob::Track, recob::Hit>        >();
}

//-------------------------------------------------
void Track3DKalman::reconfigure(fhicl::ParameterSet const& pset) 
{

  fSpacePtsModuleLabel   = pset.get< std::string >("SpacePtsModuleLabel");
  fGenieGenModuleLabel   = pset.get< std::string >("GenieGenModuleLabel");
  fG4ModuleLabel         = pset.get< std::string >("G4ModuleLabel");
  
  fPosErr                = pset.get< std::vector < double >  >("PosErr3");   // resolution. cm
  fMomErr                = pset.get< std::vector < double >  >("MomErr3");   // GeV
  fMomStart              = pset.get< std::vector < double >  >("MomStart3"); // Will be unit norm'd.
  fGenfPRINT             = pset.get< bool >("GenfPRINT");
  
}

//-------------------------------------------------
Track3DKalman::~Track3DKalman()
{

  /*
    delete stMCT ;
    delete covMCT;
    delete stREC;
    delete covREC;
    
    delete fpMCT;
    delete fpREC;
    delete fpRECL;
    delete fpRECt3D;
  */
}

//-------------------------------------------------
void Track3DKalman::beginJob()
{


  art::ServiceHandle<art::TFileService> tfs;
  
  stMCT  = new TMatrixT<Double_t>(5,1);
  covMCT = new TMatrixT<Double_t>(5,5);
  stREC  = new TMatrixT<Double_t>(5,1);
  covREC = new TMatrixT<Double_t>(5,5);
  
  fpMCT = new Float_t[4];
  fpREC = new Float_t[4];
  fpRECL = new Float_t[4];
  fpRECt3D = new Float_t[4];
  fDimSize = 400; // if necessary will get this from pset in constructor.

  fshx = new Float_t[fDimSize];
  fshy = new Float_t[fDimSize];
  fshz = new Float_t[fDimSize];

//   //TFile fileGENFIT("GENFITout.root","RECREATE");

  
  tree = tfs->make<TTree>("GENFITttree","GENFITttree");
  //tree->Branch("stMCT",&stMCT,"stMCT[5]/F"); // "TMatrixT<Double_t>"

  tree->Branch("stMCT","TMatrixD",&stMCT,64000,0);
  //tree->Branch("covMCT",&covMCT,"covMCT[25]/F");
  tree->Branch("covMCT","TMatrixD",&covMCT,64000,0);
  //tree->Branch("stREC",&stREC,"stREC[5]/F");
  tree->Branch("stREC","TMatrixD",&stREC,64000,0);
  //tree->Branch("covREC",&covREC,"covREC[25]/F");
  tree->Branch("covREC","TMatrixD",&covREC,64000,0);
  
  
  tree->Branch("chi2",&chi2,"chi2/F");
  tree->Branch("nfail",&nfail,"nfail/I");
  tree->Branch("ndf",&ndf,"ndf/I");
  tree->Branch("evtNo",&evtt,"evtNo/I");
  tree->Branch("chi2ndf",&chi2ndf,"chi2ndf/F");

  tree->Branch("trkNo",&nTrks,"trkNo/I");
  tree->Branch("ptsNo",&fptsNo,"ptsNo/I");
  tree->Branch("shx",fshx,"shx[ptsNo]/F");
  tree->Branch("shy",fshy,"shy[ptsNo]/F");
  tree->Branch("shz",fshz,"shz[ptsNo]/F");

  tree->Branch("pMCT",fpMCT,"pMCT[4]/F");
  tree->Branch("pRECKalF",fpREC,"pRECKalF[4]/F");
  tree->Branch("pRECKalL",fpRECL,"pRECKalL[4]/F");
  tree->Branch("pRECt3D",fpRECt3D,"pRECt3D[4]/F");
  

  //TGeoManager* geomGENFIT = new TGeoManager("Geometry", "Geane geometry");
  //TGeoManager::Import("config/genfitGeom.root");
  //  gROOT->Macro("config/Geane.C"); 
 
}

//-------------------------------------------------
void Track3DKalman::endJob()
{
  if (!rep) delete rep;
  if (!repMC) delete repMC;
}


//------------------------------------------------------------------------------------//
void Track3DKalman::produce(art::Event& evt)
{ 

  rep=0;
  repMC=0;

  // get services
  art::ServiceHandle<geo::Geometry> geom;
  // get the random number generator service and make some CLHEP generators
  art::ServiceHandle<art::RandomNumberGenerator> rng;
  CLHEP::HepRandomEngine &engine = rng->getEngine();
  CLHEP::RandGaussQ gauss(engine);

  // Make a std::unique_ptr<> for the thing you want to put into the event
  // because that handles the memory management for you
  std::unique_ptr<std::vector<recob::Track> > tcol(new std::vector<recob::Track>);
  std::unique_ptr< std::vector<recob::SpacePoint> >              spcol  (new std::vector<recob::SpacePoint>);
  std::unique_ptr< art::Assns<recob::Track, recob::SpacePoint> > tspassn(new art::Assns<recob::Track, recob::SpacePoint>);
  std::unique_ptr< art::Assns<recob::Track, recob::Cluster> >    tcassn (new art::Assns<recob::Track, recob::Cluster>);
  std::unique_ptr< art::Assns<recob::Track, recob::Hit> >        thassn (new art::Assns<recob::Track, recob::Hit>);

  // define TPC parameters
  TString tpcName = geom->GetLArTPCVolumeName();


  // get input Hit object(s).
  art::Handle< std::vector<recob::Track> > trackListHandle;
  evt.getByLabel(fSpacePtsModuleLabel,trackListHandle);

  art::PtrVector<simb::MCTruth> mclist;

  if (!evt.isRealData())
    {

      //      std::cout << "Track3DKalman: This is MC." << std::endl;
      // std::cout<<"Run "<<evt.run()<<" Event "<<evt.id().event()<<std::endl;

      art::Handle< std::vector<simb::MCTruth> > mctruthListHandle;
      evt.getByLabel(fGenieGenModuleLabel,mctruthListHandle);

      for (unsigned int ii = 0; ii <  mctruthListHandle->size(); ++ii)
        {
          art::Ptr<simb::MCTruth> mctparticle(mctruthListHandle,ii);
          mclist.push_back(mctparticle);
        }

    }

  //create collection of spacepoints that will be used when creating the Track object
  std::vector< art::Ptr<recob::SpacePoint> > spacepoints;
  art::PtrVector<recob::Track> trackIn;
  // std::cout<<"Run "<<evt.run()<<" Event "<<evt.id().event()<<std::endl;
  mf::LogInfo("Track3DKalman: ") << "There are " <<  trackListHandle->size() << " Track3Dreco/SpacePt tracks/groups (whichever) in this event.";

  art::FindManyP<recob::SpacePoint> fmsp(trackListHandle, evt, fSpacePtsModuleLabel);
  art::FindManyP<recob::Cluster>    fmc (trackListHandle, evt, fSpacePtsModuleLabel);
  art::FindManyP<recob::Hit>        fmh (trackListHandle, evt, fSpacePtsModuleLabel);

  for(unsigned int ii = 0; ii < trackListHandle->size(); ++ii)
    {
      art::Ptr<recob::Track> track(trackListHandle, ii);
      trackIn.push_back(track);
      
    }
      
      TVector3 MCOrigin;
      TVector3 MCMomentum;
      // TVector3 posErr(.05,.05,.05); // resolution. 0.5mm
      // TVector3 momErr(.1,.1,0.2);   // GeV
      TVector3 posErr(fPosErr[0],fPosErr[1],fPosErr[2]); // resolution. 0.5mm
      TVector3 momErr(fMomErr[0],fMomErr[1],fMomErr[2]);   // GeV

      // This is strictly for MC
      if (!evt.isRealData())
        {
          // Below breaks are stupid, I realize. But rather than keep all the MC
          // particles I just take the first primary, e.g., muon and only keep its
          // info in the branches of the Ttree. I could generalize later, ...
          for( unsigned int ii = 0; ii < mclist.size(); ++ii )
            {
            //art::Ptr<const simb::MCTruth> mc(mctruthListHandle,i);
            art::Ptr<simb::MCTruth> mc(mclist[ii]);
            for(int jj = 0; jj < mc->NParticles(); ++jj)
              {
                simb::MCParticle part(mc->GetParticle(jj));
                mf::LogInfo("Track3DKalman: ") << "FROM MC TRUTH, the particle's pdg code is: "<<part.PdgCode()<< " with energy = "<<part.E() <<", with energy = "<<part.E()<< " and vtx and momentum in Global (not volTPC) coords are " ;
                MCOrigin.SetXYZ(part.Vx(),part.Vy(),part.Vz()); // V for Vertex
                MCMomentum.SetXYZ(part.Px(),part.Py(),part.Pz());
                MCOrigin.Print();
                MCMomentum.Print();
                repMC = new genf::RKTrackRep(MCOrigin,
                                             MCMomentum,
                                             posErr,
                                             momErr,
                                             part.PdgCode());  
                break;
              }
            break;
          }
          //for saving of MC truth    
          stMCT->ResizeTo(repMC->getState());
          *stMCT = repMC->getState();
          covMCT-> ResizeTo(repMC->getCov());
          *covMCT = repMC->getCov();
          mf::LogInfo("Track3DKalman: ") <<" repMC, covMC are ... " ;
          repMC->getState().Print();
          repMC->getCov().Print();

        } // !isRealData
      
      art::PtrVector<recob::Track>::const_iterator trackIter = trackIn.begin();
      
      nTrks=0;
      while(trackIter!=trackIn.end()) {
        spacepoints.clear();
        spacepoints = fmsp.at(nTrks);
        
        mf::LogInfo("Track3DKalman: ") << "found "<< spacepoints.size() <<" 3D spacepoint(s).";
        
        // Add the 3D track to the vector of the reconstructed tracks
        if(spacepoints.size()>0){
          // Insert the GENFIT/Kalman stuff here then make the tracks. Units are cm, GeV.
          const double resolution = 0.5; // dunno, 5 mm
          const int numIT = 3; // 3->1, EC, 6-Jan-2011. Back, 7-Jan-2011.
          
          
          //TVector3 mom(0.0,0.0,2.0);
          TVector3 mom(fMomStart[0],fMomStart[1],fMomStart[2]);
          //mom.SetMag(1.);
          TVector3 momM(mom);
          momM.SetX(gauss.fire(momM.X(),momErr.X()/* *momM.X() */));
          momM.SetY(gauss.fire(momM.Y(),momErr.Y()/* *momM.Y() */));
          momM.SetZ(gauss.fire(momM.Z(),momErr.Z()/* *momM.Z() */));
          //std::cout << "Track3DKalman: sort spacepoints by z
          
          std::sort(spacepoints.begin(), spacepoints.end(), sp_sort_3dz);
          
          //std::sort(spacepoints.begin(), spacepoints.end(), sp_sort_3dx); // Reverse sort!
          
          genf::GFFieldManager::getInstance()->init(new genf::GFConstField(0.,0.,0.0));
          genf::GFDetPlane planeG((TVector3)(spacepoints[0]->XYZ()),momM);
          
          
          //      std::cout<<"Track3DKalman about to do GAbsTrackRep."<<std::endl;
          // Initialize with 1st spacepoint location and a guess at the momentum.
          rep = new genf::RKTrackRep(//posM-.5/momM.Mag()*momM,
                                     (TVector3)(spacepoints[0]->XYZ()),
                                     momM,
                                     posErr,
                                     momErr,
                                     13);  // mu- hypothesis
          //      std::cout<<"Track3DKalman: about to do GFTrack. repDim is " << rep->getDim() <<std::endl;
          
          
          genf::GFTrack fitTrack(rep);//initialized with smeared rep
          // Gonna sort in x cuz I want to essentially transform here to volTPC coords.
          // volTPC coords, cuz that's what the Geant3/Geane stepper wants, as that's its understanding
          // from the Geant4 geometry, which it'll use. EC, 7-Jan-2011.
          int ihit = 0;
          fptsNo = 0;
          for (unsigned int point=0;point<spacepoints.size();++point)
            {
              
              TVector3 spt3(spacepoints[point]->XYZ());
                if (point > 0 )
                  {
                    double eps (0.1);
                    TVector3 magNew(spt3[0],spt3[1],spt3[2]);
                    TVector3 magLast(spacepoints.back()->XYZ()[0],
                                     spacepoints.back()->XYZ()[1],
                                     spacepoints.back()->XYZ()[2]
                                     );
                    if (!(magNew.Mag()>=magLast.Mag()+eps || 
                          magNew.Mag()<=magLast.Mag()-eps)
                        )
                      continue;
                  }

              if (point%20) // Jump out of loop except on every 20th pt.
                {
                  //continue;
                  // Icarus paper suggests we may wanna decimate our data in order to give
                  // trackfitter a better idea of multiple-scattering. EC, 7-Jan-2011.
                  //if (std::abs(spt3[0]-spacepoints.at(point-1).XYZ()[0]) < 2) continue;
                }
              if (fptsNo<fDimSize)
                {
                  fshx[fptsNo] = spt3[0];
                  fshy[fptsNo] = spt3[1];
                  fshz[fptsNo] = spt3[2];
                }
                fptsNo++;
                
                
                LOG_DEBUG("Track3DKalman: ") << "ihit xyz..." << spt3[0]<<","<< spt3[1]<<","<< spt3[2];
                fitTrack.addHit(new genf::PointHit(spt3,resolution),
                                1,//dummy detector id
                                ihit++
                                );
            }
          
          //      std::cout<<"Track3DKalman about to do GFKalman."<<std::endl;
          genf::GFKalman k;
          //k.setBlowUpFactor(500); // Instead of 500 out of box. EC, 6-Jan-2011.
          //k.setInitialDirection(+1); // Instead of 1 out of box. EC, 6-Jan-2011.
          k.setNumIterations(numIT);
          //      std::cout<<"Track3DKalman back from setNumIterations."<<std::endl;
          try{
            //  std::cout<<"Track3DKalman about to processTrack."<<std::endl;
            k.processTrack(&fitTrack);
            //std::cout<<"Track3DKalman back from processTrack."<<std::endl;
          }
          catch(GFException& e){
            mf::LogError("Track3DKalman: ") << "just caught a GFException."<<std::endl;
            e.what();
            mf::LogError("Track3DKalman: ") << "Exceptions won't be further handled ->exit(1) "<<__LINE__;
            
            //  exit(1);
          }
          
          if(rep->getStatusFlag()==0) // 0 is successful completion
            {
              LOG_DEBUG("Track3DKalman: ") << __FILE__ << " " << __LINE__ ;
              LOG_DEBUG("Track3DKalman: ") << "Track3DKalman.cxx: Original plane:";
              
              if(fGenfPRINT) planeG.Print();
              LOG_DEBUG("Track3DKalman: ") << "Current (fit) reference Plane:";
              if(fGenfPRINT) rep->getReferencePlane().Print();
              
              LOG_DEBUG("Track3DKalman: ") << "Track3DKalman.cxx: Last reference Plane:";
              if(fGenfPRINT) rep->getLastPlane().Print();
              
              if(fGenfPRINT) 
                {
                  if(planeG!=rep->getReferencePlane()) 
                    LOG_DEBUG("Track3DKalman: ") <<"Track3DKalman: Original hit plane (not surprisingly) not current reference Plane!"<<std::endl;
                }
              
              stREC->ResizeTo(rep->getState());
              *stREC = rep->getState();
              covREC->ResizeTo(rep->getCov());
              *covREC = rep->getCov();
              if(fGenfPRINT)
                {
                  LOG_DEBUG("Track3DKalman: ") << " Final State and Cov:";
                  stREC->Print();
                  covREC->Print();
                }
              chi2 = rep->getChiSqu();
              ndf = rep->getNDF();
              nfail = fitTrack.getFailedHits();
              chi2ndf = chi2/ndf;
              double dircoss[3],dircose[3];
              (*trackIter)->Direction(dircoss,dircose);      
              
              for (int ii=0;ii<3;++ii)
                {
                  fpMCT[ii] = MCMomentum[ii]/MCMomentum.Mag();
                  fpREC[ii] = rep->getReferencePlane().getNormal()[ii];
                  fpRECL[ii] = rep->getLastPlane().getNormal()[ii];
                  fpRECt3D[ii] = dircoss[ii];
                }
              fpMCT[3] = MCMomentum.Mag();
              fpREC[3] = -1.0/(*stREC)[0][0];
              
              evtt = (unsigned int) evt.id().event();
              mf::LogInfo("Track3DKalman: ") << "Track3DKalman about to do tree->Fill(). Chi2/ndf is " << chi2/ndf << ". All in volTPC coords .... pMCT[0-3] is " << fpMCT[0] << ", " << fpMCT[1] << ", " << fpMCT[2] << ", " << fpMCT[3] << ". pREC[0-3] is " << fpREC[0] << ", "<< fpREC[1] << ", " << fpREC[2] << ", " << fpREC[3] << ".";
              
              tree->Fill();
              
              // Get the clusters associated to each track in induction and collection view
              std::vector< art::Ptr<recob::Cluster> > clusters = fmc.at(nTrks);
              std::vector< art::Ptr<recob::Hit> > hits = fmh.at(nTrks);

              // Use new Track constructor... EC, 21-Apr-2011.  
              std::vector<TVector3> dircos(spacepoints.size());
              dircos[0] = TVector3(fpREC);
              dircos.back() = TVector3(fpRECL);
              
              // fill a vector of TVector3 with the space points used to make this track
              std::vector<TVector3> xyz(spacepoints.size());
              size_t spStart = spcol->size();
              for(size_t tv = 0; tv < spacepoints.size(); ++tv){
                xyz[tv] = TVector3(spacepoints[tv]->XYZ());
                spcol->push_back(*(spacepoints[tv].get()));
              }
              size_t spEnd = spcol->size();

              tcol->push_back(recob::Track(xyz, dircos, std::vector< std::vector<double> >(0), 
                                           std::vector<double>(2, util::kBogusD), tcol->size()-1));

              // associate the track with its clusters and tracks
              util::CreateAssn(*this, evt, *tcol, clusters, *tcassn);
              util::CreateAssn(*this, evt, *tcol, hits,     *thassn);
              
              // associate the track to the space points
              util::CreateAssn(*this, evt, *tcol, *spcol, *tspassn, spStart, spEnd);

            } // getStatusFlag 
        } // spacepoints.size()>0
        
        //
        //std::cout<<"Track3DKalman found "<< tcol->size() <<" 3D track(s)"<<std::endl;
        if(trackIter!=trackIn.end()) trackIter++;
        
        nTrks++;
        
      } // end loop over Track3Dreco/SpacePt tracks/groups (whichever) we brought into this event.
      
      evt.put(std::move(tcol));
      evt.put(std::move(spcol));
      evt.put(std::move(tcassn));
      evt.put(std::move(thassn));
      evt.put(std::move(tspassn));

} // end method

  DEFINE_ART_MODULE(Track3DKalman)



} // end namespace trkf