void Svtx_Reco(int verbosity = 0)
{
  //---------------
  // Load libraries
  //---------------

  gSystem->Load("libfun4all.so");
  gSystem->Load("libg4hough.so");

  //---------------
  // Fun4All server
  //---------------

  Fun4AllServer* se = Fun4AllServer::instance();

  //----------------------------------
  // Digitize the cell energy into ADC
  //----------------------------------
  PHG4SvtxDigitizer* digi = new PHG4SvtxDigitizer();
  digi->Verbosity(0);
  for (int i = 0; i < n_maps_layer; ++i)
  {
    digi->set_adc_scale(i, 255, 0.4e-6);  // reduced by a factor of 2.5 when going from maps thickess of 50 microns to 18 microns
  }

  if (n_intt_layer > 0)
  {
    // INTT

    // Load pre-defined deadmaps
    PHG4SvtxDeadMapLoader* deadMapINTT = new PHG4SvtxDeadMapLoader("SILICON_TRACKER");
    for (int i = 0; i < n_intt_layer; i++)
    {
      string DeadMapConfigName = Form("LadderType%d_RndSeed%d/", laddertype[i], i);
      string DeadMapPath = string(getenv("CALIBRATIONROOT")) + string("/Tracking/INTT/DeadMap_4Percent/"); //4% of dead/masked area (2% sensor + 2% chip) as a typical FVTX Run14 production run.
//      string DeadMapPath = string(getenv("CALIBRATIONROOT")) + string("/Tracking/INTT/DeadMap_8Percent/"); // 8% dead/masked area (6% sensor + 2% chip) as threshold of operational
      DeadMapPath +=  DeadMapConfigName;
      deadMapINTT->deadMapPath(n_maps_layer + i, DeadMapPath);
    }
//    se->registerSubsystem(deadMapINTT);

    std::vector<double> userrange;  // 3-bit ADC threshold relative to the mip_e at each layer.
    // these should be used for the INTT
    userrange.push_back(0.05);
    userrange.push_back(0.10);
    userrange.push_back(0.15);
    userrange.push_back(0.20);
    userrange.push_back(0.25);
    userrange.push_back(0.30);
    userrange.push_back(0.35);
    userrange.push_back(0.40);

    PHG4SiliconTrackerDigitizer* digiintt = new PHG4SiliconTrackerDigitizer();
    digiintt->Verbosity(verbosity);
    for (int i = 0; i < n_intt_layer; i++)
    {
      digiintt->set_adc_scale(n_maps_layer + i, userrange);
    }
    se->registerSubsystem(digiintt);

//    digiintt->Verbosity(1);
  }

  // TPC layers use the Svtx digitizer
  digi->SetTPCMinLayer(n_maps_layer + n_intt_layer);
  double ENC = 670.0;  // standard
  digi->SetENC(ENC);  
  double ADC_threshold = 4.0*ENC; 
  digi->SetADCThreshold(ADC_threshold);  // 4 * ENC seems OK
    cout << " TPC digitizer: Setting ENC to " << ENC << " ADC threshold to " << ADC_threshold 
       << " maps+INTT layers set to " << n_maps_layer + n_intt_layer << endl;
 
  se->registerSubsystem(digi);
  
  //-------------------------------------
  // Apply Live Area Inefficiency to Hits
  // This is obsolete, please use PHG4SvtxDeadMapLoader instead for pre-defined deadmap
  //-------------------------------------
  // defaults to 1.0 (fully active)

//  PHG4SvtxDeadArea* deadarea = new PHG4SvtxDeadArea();
//
//  for (int i = 0; i < n_maps_layer; i++)
//  {
//    deadarea->Verbosity(verbosity);
//    //deadarea->set_hit_efficiency(i,0.99);
//    deadarea->set_hit_efficiency(i, 1.0);
//  }
//  for (int i = n_maps_layer; i < n_maps_layer + n_intt_layer; i++)
//  {
//    //deadarea->set_hit_efficiency(i,0.99);
//    deadarea->set_hit_efficiency(i, 1.0);
//  }
//  se->registerSubsystem(deadarea);

  //-----------------------------
  // Apply MIP thresholds to Hits
  //-----------------------------

  PHG4SvtxThresholds* thresholds = new PHG4SvtxThresholds();
  thresholds->Verbosity(verbosity);

  // maps
  for (int i = 0; i < n_maps_layer; i++)
  {
    // reduced by x2.5 when going from cylinder maps with 50 microns thickness to actual maps with 18 microns thickness
    // Note the non-use of set_using_thickness here, this is so that the shortest dimension of the cell sets the mip energy loss
    thresholds->set_threshold(i, 0.1);
  }
  // INTT
  for (int i = n_maps_layer; i < n_maps_layer + n_intt_layer; i++)
  {
    thresholds->set_threshold(i, 0.1);
    thresholds->set_use_thickness_mip(i, true);
  }

  se->registerSubsystem(thresholds);

  //-------------
  // Cluster Hits
  //-------------

  PHG4SvtxClusterizer* clusterizer = new PHG4SvtxClusterizer("PHG4SvtxClusterizer", 0, n_maps_layer + n_intt_layer - 1);
  clusterizer->Verbosity(verbosity);
  // Reduced by 2 relative to the cylinder cell maps macro. I found this necessary to get full efficiency
  // Many hits in the present simulation are single cell hits, so it is not clear why the cluster threshold should be higher than the cell threshold
  clusterizer->set_threshold(0.1);  // fraction of a mip

  // no Z clustering for INTT type 1 layers (we DO want Z clustering for type 0 layers)
  // turning off phi clustering for type 0 layers is not necessary, there is only one strip per sensor in phi
  for (int i = n_maps_layer; i < n_maps_layer + n_intt_layer; i++)
  {
    if(laddertype[i-n_maps_layer] == 1)
      clusterizer->set_z_clustering(i, false);
  }

  se->registerSubsystem(clusterizer);

  PHG4TPCClusterizer* tpcclusterizer = new PHG4TPCClusterizer();
  tpcclusterizer->Verbosity(0);
  tpcclusterizer->setRangeLayers(n_maps_layer + n_intt_layer, Max_si_layer);
  tpcclusterizer->setEnergyCut(15 /*adc*/);
  tpcclusterizer->setFitWindowSigmas(0.0150, 0.0160);  // should be changed when TPC cluster resolution changes
  tpcclusterizer->setFitWindowMax(5 /*rphibins*/, 5 /*zbins*/);
  se->registerSubsystem(tpcclusterizer);

  // This should be true for everything except testing!
  const bool use_kalman_pat_rec = true;
  if (use_kalman_pat_rec)
  {
    //---------------------
    // PHG4KalmanPatRec
    //---------------------

    PHG4KalmanPatRec* kalman_pat_rec = new PHG4KalmanPatRec("PHG4KalmanPatRec", n_maps_layer, n_intt_layer, n_gas_layer);
    kalman_pat_rec->Verbosity(0);
    
    for(int i = 0;i<n_intt_layer;i++)
      {
	if(laddertype[i] == PHG4SiliconTrackerDefs::SEGMENTATION_Z)
	  {
	    // strip length is along phi
	    kalman_pat_rec->set_max_search_win_theta_intt(i, 0.010);
	    kalman_pat_rec->set_min_search_win_theta_intt(i, 0.00);
	    kalman_pat_rec->set_max_search_win_phi_intt(i, 0.20);
	    kalman_pat_rec->set_min_search_win_phi_intt(i, 0.20);
	  }
	else
	  {
	    // strip length is along theta
	    kalman_pat_rec->set_max_search_win_theta_intt(i, 0.200);
	    kalman_pat_rec->set_min_search_win_theta_intt(i, 0.200);
	    kalman_pat_rec->set_max_search_win_phi_intt(i, 0.0050);
	    kalman_pat_rec->set_min_search_win_phi_intt(i, 0.000);
	  }
      }
    
    se->registerSubsystem(kalman_pat_rec);
  }
  else
  {
    //---------------------
    // Truth Pattern Recognition
    //---------------------
    PHG4TruthPatRec* pat_rec = new PHG4TruthPatRec();
    se->registerSubsystem(pat_rec);
  }

  //---------------------
  // Kalman Filter
  //---------------------

  PHG4TrackKalmanFitter* kalman = new PHG4TrackKalmanFitter();
  kalman->Verbosity(0);
  if (use_primary_vertex)
    kalman->set_fit_primary_tracks(true);  // include primary vertex in track fit if true
  se->registerSubsystem(kalman);

  //------------------
  // Track Projections
  //------------------
  PHG4GenFitTrackProjection* projection = new PHG4GenFitTrackProjection();
  projection->Verbosity(verbosity);
  se->registerSubsystem(projection);

  /*  
  //----------------------
  // Beam Spot Calculation
  //----------------------
  PHG4SvtxBeamSpotReco* beamspot = new PHG4SvtxBeamSpotReco();
  beamspot->Verbosity(verbosity);
  se->registerSubsystem( beamspot );
  */

  return;
}
Ejemplo n.º 2
0
void Svtx_Reco(int verbosity = 0)
{
  // reconstructs the Svtx with ITS innner detector (7 layers)

  // requires Svtx setup and Svtx cell routines
  // prefers calorimeter reconstruction prior (once projections are working)

  //---------------
  // Load libraries
  //---------------

  gSystem->Load("libfun4all.so");
  gSystem->Load("libg4hough.so");

  //---------------
  // Fun4All server
  //---------------

  Fun4AllServer *se = Fun4AllServer::instance();

  //----------------------------------
  // Digitize the cell energy into ADC
  //----------------------------------
  // defaults to 8-bit ADC with MIP at 0.25% dynamic range
  PHG4SvtxDigitizer* digi = new PHG4SvtxDigitizer();
  digi->Verbosity(verbosity);
  digi->set_adc_scale(0, 255, 1.0e-6); // 1.0 keV / bit
  digi->set_adc_scale(1, 255, 1.0e-6); // 1.0 keV / bit
  digi->set_adc_scale(2, 255, 1.6e-6); // 1.6 keV / bit
  digi->set_adc_scale(3, 255, 1.6e-6); // 1.6 keV / bit
  digi->set_adc_scale(4, 255, 1.6e-6); // 1.6 keV / bit
  digi->set_adc_scale(5, 255, 1.6e-6); // 1.6 keV / bit
  digi->set_adc_scale(6, 255, 1.6e-6); // 1.6 keV / bit
  se->registerSubsystem( digi );
  
  //------------------------------------------
  // Apply Live Area Inefficiency to Hit Cells
  //------------------------------------------
  // defaults to 1.0 (fully active)
  PHG4SvtxDeadArea* deadarea = new PHG4SvtxDeadArea();
  deadarea->Verbosity(verbosity);
  deadarea->set_hit_efficiency(0,0.99); // Leo says use 1% inefficiency
  deadarea->set_hit_efficiency(1,0.99);
  deadarea->set_hit_efficiency(2,0.99);
  deadarea->set_hit_efficiency(3,0.99);
  deadarea->set_hit_efficiency(4,0.99);
  deadarea->set_hit_efficiency(5,0.99);
  deadarea->set_hit_efficiency(6,0.99);
  se->registerSubsystem( deadarea );
  
  //----------------------------------
  // Apply MIP thresholds to Hit Cells
  //----------------------------------
  PHG4SvtxThresholds* thresholds = new PHG4SvtxThresholds();
  thresholds->Verbosity(verbosity);
  thresholds->set_threshold(0,0.25);
  thresholds->set_threshold(1,0.25);
  thresholds->set_threshold(2,0.25);
  thresholds->set_threshold(3,0.25);
  thresholds->set_threshold(4,0.25);
  thresholds->set_threshold(5,0.25);
  thresholds->set_threshold(6,0.25);
  //thresholds->set_use_thickness_mip(0, true);
  se->registerSubsystem( thresholds );

  //---------------------
  // Make SVTX clusters
  //---------------------
  PHG4SvtxClusterizer* clusterizer = new PHG4SvtxClusterizer();
  clusterizer->Verbosity(verbosity);
  clusterizer->set_threshold(0.33);
  se->registerSubsystem( clusterizer );

  //---------------------
  // Track reconstruction
  //---------------------
  PHG4HoughTransform* hough = new PHG4HoughTransform(7,7);
  hough->set_mag_field(1.4);
  hough->Verbosity(verbosity);
  // ALICE ITS upgrade values for total thickness in X_0
  hough->set_material(0, 0.003);
  hough->set_material(1, 0.003);
  hough->set_material(2, 0.003);
  hough->set_material(3, 0.008);
  hough->set_material(4, 0.008);
  hough->set_material(5, 0.008);
  hough->set_material(6, 0.008);
  hough->setPtRescaleFactor(0.9972/1.00117);
  hough->set_chi2_cut_init(5.0);
  //hough->set_chi2_cut_fast(60.0,0.0,100.0); // 10.0, 50.0, 75.0
  hough->set_chi2_cut_fast(10.0,50.0,75.0); // 10.0, 50.0, 75.0
  hough->set_chi2_cut_full(5.0);
  hough->set_ca_chi2_cut(5.0);
  //hough->setMaxClusterError(3.0);
  hough->setRejectGhosts(false);
  hough->setRemoveHits(false);
  hough->setCutOnDCA(true);
  se->registerSubsystem( hough );

  //---------------------
  // Ghost rejection
  //---------------------
  PHG4TrackGhostRejection* rejection = new PHG4TrackGhostRejection(7);
  rejection->Verbosity(verbosity);
  rejection->set_max_shared_hits(3);
  se->registerSubsystem( rejection );

  //------------------
  // Track Projections
  //------------------
  PHG4SvtxTrackProjection* projection = new PHG4SvtxTrackProjection();
  projection->Verbosity(verbosity);
  se->registerSubsystem( projection );

  //----------------------
  // Beam Spot Calculation
  //----------------------
  PHG4SvtxBeamSpotReco* beamspot = new PHG4SvtxBeamSpotReco();
  beamspot->Verbosity(verbosity);
  se->registerSubsystem( beamspot );

  return;
}
Ejemplo n.º 3
0
void Svtx_Reco(int verbosity = 0)
{
  // reconstructs the MIE Svtx v2 detector (7 layers)

  // requires Svtx setup and Svtx cell routines
  // prefers calorimeter reconstruction prior (once projections are working)

  //---------------
  // Load libraries
  //---------------

  gSystem->Load("libfun4all.so");
  gSystem->Load("libg4hough.so");

  //---------------
  // Fun4All server
  //---------------

  Fun4AllServer *se = Fun4AllServer::instance();

  //----------------------------------
  // Digitize the cell energy into ADC
  //----------------------------------
  // defaults to 8-bit ADC with MIP at 0.25% dynamic range
  PHG4SvtxDigitizer* digi = new PHG4SvtxDigitizer();
  digi->Verbosity(verbosity);
  digi->set_adc_scale(0, 255, 1.0e-6); // 1.0 keV / bit
  digi->set_adc_scale(1, 255, 1.0e-6); // 1.0 keV / bit
  digi->set_adc_scale(2, 255, 1.6e-6); // 1.6 keV / bit
  digi->set_adc_scale(3, 255, 1.6e-6); // 1.6 keV / bit
  digi->set_adc_scale(4, 255, 1.6e-6); // 1.6 keV / bit
  digi->set_adc_scale(5, 255, 1.6e-6); // 1.6 keV / bit
  digi->set_adc_scale(6, 255, 1.6e-6); // 1.6 keV / bit
  se->registerSubsystem( digi );
  
  //-------------------------------------
  // Apply Live Area Inefficiency to Hits
  //-------------------------------------
  // defaults to 1.0 (fully active)
  PHG4SvtxDeadArea* deadarea = new PHG4SvtxDeadArea();
  deadarea->Verbosity(verbosity);
  // deadarea->set_hit_efficiency(0,0.90);
  // deadarea->set_hit_efficiency(1,0.90);
  // deadarea->set_hit_efficiency(2,0.98);
  // deadarea->set_hit_efficiency(3,0.98);
  // deadarea->set_hit_efficiency(4,0.98);
  // deadarea->set_hit_efficiency(5,0.98);
  // deadarea->set_hit_efficiency(6,0.98);
  se->registerSubsystem( deadarea );

  //-----------------------------
  // Apply MIP thresholds to Hits
  //-----------------------------
  PHG4SvtxThresholds* thresholds = new PHG4SvtxThresholds();
  thresholds->Verbosity(verbosity);
  thresholds->set_threshold(0,0.33);
  thresholds->set_threshold(1,0.33);
  thresholds->set_threshold(2,0.33);
  thresholds->set_threshold(3,0.33);
  thresholds->set_threshold(4,0.33);
  thresholds->set_threshold(5,0.33);
  thresholds->set_threshold(6,0.33);
  thresholds->set_use_thickness_mip(0, true);
  se->registerSubsystem( thresholds );

  //-------------
  // Cluster Hits
  //-------------
  // needs to have clusters hold hit ids not cell ids
  // will require changes to evaluation
  PHG4SvtxClusterizer* clusterizer = new PHG4SvtxClusterizer();
  clusterizer->Verbosity(verbosity);
  clusterizer->set_threshold(0.33);
  clusterizer->set_z_clustering(2, false);
  clusterizer->set_z_clustering(3, false);
  clusterizer->set_z_clustering(4, false);
  clusterizer->set_z_clustering(5, false);
  clusterizer->set_z_clustering(6, false);
  // clusterizer->set_energy_weighting(2, true);
  // clusterizer->set_energy_weighting(3, true);
  // clusterizer->set_energy_weighting(4, true);
  // clusterizer->set_energy_weighting(5, true);
  // clusterizer->set_energy_weighting(6, true);
  se->registerSubsystem( clusterizer );

  //---------------------
  // Track reconstruction
  //---------------------
  PHG4HoughTransform* hough = new PHG4HoughTransform(7,7);
  hough->Verbosity(verbosity);
  hough->set_mag_field(1.4);
  hough->set_material(0, 0.013);
  hough->set_material(1, 0.013);
  hough->set_material(2, 0.013);
  hough->set_material(3, 0.013);
  hough->set_material(4, 0.010);
  hough->set_material(5, 0.010);
  hough->set_material(6, 0.020);
  hough->setPtRescaleFactor(0.9972);
  hough->set_chi2_cut_init(3.0);
  hough->set_chi2_cut_full(3.0);
  hough->set_ca_chi2_cut(3.0);
  hough->setCutOnDCA(true);
  hough->setDCACut(0.1);
  hough->setDCAZCut(0.1);
  hough->setRejectGhosts(false);
  hough->setRemoveHits(false);
  se->registerSubsystem( hough );

  //---------------------
  // Ghost rejection
  //---------------------
  // needs updates to merge split tracks when possible
  PHG4TrackGhostRejection* rejection = new PHG4TrackGhostRejection(7); 
  rejection->Verbosity(verbosity);
  rejection->set_max_shared_hits(3);
  se->registerSubsystem( rejection );

  //------------------------
  // Final Track Refitting
  //------------------------
  // PHG4TrackKalmanFitter *kalman = new PHG4TrackKalmanFitter
  // we need a module to redo the Kalman fit with G4 material and real mag field
  // to update the track container

  //------------------------
  // Primary Track Refitting
  //------------------------
  // PHG4TrackKalmanFitter *kalman = new PHG4TrackKalmanFitter
  // we need a module to redo the Kalman fit including the vertex position
  // and create a separate stream of output tracks
  
  //------------------
  // Track Projections
  //------------------
  PHG4SvtxTrackProjection* projection = new PHG4SvtxTrackProjection();
  projection->Verbosity(verbosity);
  se->registerSubsystem( projection );

  //----------------------
  // Beam Spot Calculation
  //----------------------
  PHG4SvtxBeamSpotReco* beamspot = new PHG4SvtxBeamSpotReco();
  beamspot->Verbosity(verbosity);
  se->registerSubsystem( beamspot );

  return;
}
Ejemplo n.º 4
0
void Svtx_Reco(int verbosity = 0)
{
  //---------------
  // Load libraries
  //---------------

  gSystem->Load("libfun4all.so");
  gSystem->Load("libg4hough.so");

  //---------------
  // Fun4All server
  //---------------

  Fun4AllServer *se = Fun4AllServer::instance();

  //----------------------------------
  // Digitize the cell energy into ADC
  //----------------------------------
  PHG4SvtxDigitizer* digi = new PHG4SvtxDigitizer();
  digi->Verbosity(0);
  for (int i=0;i<n_svx_layer;++i) {
    digi->set_adc_scale(i, 255, 1.0e-6);
  }
  for (int i=n_svx_layer;i<63;++i) {
    digi->set_adc_scale(i, 10000, 1.0e-1);
  }
  se->registerSubsystem( digi );
  
  //-------------------------------------
  // Apply Live Area Inefficiency to Hits
  //-------------------------------------
  // defaults to 1.0 (fully active)
  
  PHG4SvtxDeadArea* deadarea = new PHG4SvtxDeadArea();
  deadarea->Verbosity(verbosity);
  deadarea->set_hit_efficiency(0,0.998);
  deadarea->set_hit_efficiency(1,0.998);
  deadarea->set_hit_efficiency(2,0.998);
  se->registerSubsystem( deadarea );

  //-----------------------------
  // Apply MIP thresholds to Hits
  //-----------------------------

  PHG4SvtxThresholds* thresholds = new PHG4SvtxThresholds();
  thresholds->Verbosity(verbosity);
  thresholds->set_threshold(0,0.33);
  thresholds->set_threshold(1,0.33);
  thresholds->set_threshold(2,0.33);
  thresholds->set_use_thickness_mip(0, true);
  se->registerSubsystem( thresholds );

  //-------------
  // Cluster Hits
  //------------- 
  PHG4TPCClusterizer* clusterizer = new PHG4TPCClusterizer("PHG4SvtxClusterizer",4,1);;
  se->registerSubsystem( clusterizer );

  //---------------------
  // Track reconstruction
  //---------------------
  PHG4HoughTransformTPC* hough = new PHG4HoughTransformTPC(63,56);
  hough->set_mag_field(1.4);
  hough->set_use_vertex(true);
  hough->setRemoveHits(true);
  hough->setRejectGhosts(true);
  hough->set_min_pT(0.2);
  hough->set_chi2_cut_full( 3.0 );
  hough->set_chi2_cut_init( 3.0 );

  hough->setBinScale(1.0);
  hough->setZBinScale(1.0);

  hough->Verbosity(0);
  double mat_scale = 1.0;
  hough->set_material(0, mat_scale*0.003);
  hough->set_material(1, mat_scale*0.003);
  hough->set_material(2, mat_scale*0.003);
  for (int i=3;i<63;++i) {
    hough->set_material(i, mat_scale*0.06/60.);
  }
  hough->setUseCellSize(false);
  
  for (int i=3;i<63;++i) {
    hough->setFitErrorScale(i, 1./sqrt(12.));
  }
  for (int i=3;i<63;++i) {
    hough->setVoteErrorScale(i, 0.2);
  }
  
  se->registerSubsystem( hough );
 
  //------------------
  // Track Projections
  //------------------
  PHG4SvtxTrackProjection* projection = new PHG4SvtxTrackProjection();
  projection->Verbosity(verbosity);
  se->registerSubsystem( projection );

  //----------------------
  // Beam Spot Calculation
  //----------------------
  PHG4SvtxBeamSpotReco* beamspot = new PHG4SvtxBeamSpotReco();
  beamspot->Verbosity(verbosity);
  se->registerSubsystem( beamspot );

  return;
}
Ejemplo n.º 5
0
void Svtx_Reco(int verbosity = 0)
{
  // reconstructs the MIE Svtx v2 detector (7 layers)

  // requires Svtx setup and Svtx cell routines
  // prefers calorimeter reconstruction prior (once projections are working)

  //---------------
  // Load libraries
  //---------------

  gSystem->Load("libfun4all.so");
  gSystem->Load("libg4hough.so");

  //---------------
  // Fun4All server
  //---------------

  Fun4AllServer *se = Fun4AllServer::instance();

  //----------------------------------
  // Digitize the cell energy into ADC
  //----------------------------------
  // defaults to 8-bit ADC with MIP at 0.25% dynamic range
  PHG4SvtxDigitizer* digi = new PHG4SvtxDigitizer();
  digi->Verbosity(verbosity);
  // digi->set_adc_scale(0,   1, 6.40e-6); // 6.4 keV / bit
  // digi->set_adc_scale(1,   1, 6.40e-6); // 6.4 keV / bit
  // digi->set_adc_scale(2, 255, 0.36e-6); // 0.36 keV / bit
  // digi->set_adc_scale(3, 255, 1.45e-6); // 1.45 keV / bit
  // digi->set_adc_scale(4, 255, 0.36e-6); // 0.36 keV / bit
  // digi->set_adc_scale(5, 255, 1.45e-6); // 1.45 keV / bit
  // digi->set_adc_scale(6, 255, 0.36e-6); // 0.36 keV / bit
  se->registerSubsystem( digi );
  
  //-------------------------------------
  // Apply Live Area Inefficiency to Hits
  //-------------------------------------
  // defaults to 1.0 (fully active)
  PHG4SvtxDeadArea* deadarea = new PHG4SvtxDeadArea();
  deadarea->Verbosity(verbosity);
  // deadarea->set_hit_efficiency(0,0.995);
  // deadarea->set_hit_efficiency(1,0.995);
  // deadarea->set_hit_efficiency(2,0.995);
  // deadarea->set_hit_efficiency(3,0.995);
  // deadarea->set_hit_efficiency(4,0.995);
  // deadarea->set_hit_efficiency(5,0.995);
  // deadarea->set_hit_efficiency(6,0.995);
  se->registerSubsystem( deadarea );

  //-----------------------------
  // Apply MIP thresholds to Hits
  //-----------------------------
  PHG4SvtxThresholds* thresholds = new PHG4SvtxThresholds();
  thresholds->Verbosity(verbosity);
  thresholds->set_threshold(0,0.25);
  thresholds->set_threshold(1,0.25);
  thresholds->set_threshold(2,0.25);
  thresholds->set_threshold(3,0.25);
  thresholds->set_threshold(4,0.25);
  thresholds->set_threshold(5,0.25);
  thresholds->set_threshold(6,0.25);
  se->registerSubsystem( thresholds );
 
  //---------------------
  // Make SVTX clusters
  //---------------------
  PHG4SvtxClusterizer* clusterizer = new PHG4SvtxClusterizer();
  clusterizer->Verbosity(verbosity);
  clusterizer->set_threshold(0.25);
  clusterizer->set_z_clustering(2, false);
  clusterizer->set_z_clustering(3, false);
  clusterizer->set_z_clustering(4, false);
  clusterizer->set_z_clustering(5, false);
  clusterizer->set_z_clustering(6, false);
  se->registerSubsystem( clusterizer );
 
  //---------------------
  // Track reconstruction
  //---------------------
  PHG4HoughTransform* hough = new PHG4HoughTransform(7,7);
  hough->set_mag_field(1.4);
  hough->Verbosity(verbosity);
  hough->set_material(0, 0.013);
  hough->set_material(1, 0.013);
  hough->set_material(2, 0.013);
  hough->set_material(3, 0.013);
  hough->set_material(4, 0.010);
  hough->set_material(5, 0.010);
  hough->set_material(6, 0.020);
  hough->setPtRescaleFactor(0.9972);
  hough->set_chi2_cut_init(3.0);
  hough->set_chi2_cut_full(3.0);
  hough->set_ca_chi2_cut(3.0);
  hough->setCutOnDCA(true);
  hough->setDCACut(0.1);
  hough->setDCAZCut(0.1);
  hough->setRejectGhosts(false);
  hough->setRemoveHits(false);
  se->registerSubsystem( hough );

  //---------------------
  // Ghost rejection
  //---------------------
  PHG4TrackGhostRejection* rejection = new PHG4TrackGhostRejection(7);
  rejection->Verbosity(verbosity);
  rejection->set_max_shared_hits(3);
  se->registerSubsystem( rejection );

  //------------------
  // Track Projections
  //------------------
  PHG4SvtxTrackProjection* projection = new PHG4SvtxTrackProjection();
  projection->Verbosity(verbosity);
  se->registerSubsystem( projection );

  //----------------------
  // Beam Spot Calculation
  //----------------------
  PHG4SvtxBeamSpotReco* beamspot = new PHG4SvtxBeamSpotReco();
  beamspot->Verbosity(verbosity);
  se->registerSubsystem( beamspot );

  return;
}