KalmanFitter.cxx

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/*
  Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
*/
 
#include "KalmanFitter.h"
 
// ATHENA
#include "GaudiKernel/ListItem.h"
#include "TrkMeasurementBase/MeasurementBase.h"
#include "TrkParameters/TrackParameters.h"
#include "TrkSurfaces/PerigeeSurface.h"
#include "TrkTrackSummary/TrackSummary.h"
#include "GaudiKernel/EventContext.h"
#include "TrkRIO_OnTrack/RIO_OnTrack.h" 
#include "TrkPrepRawData/PrepRawData.h"
#include "TrkTrack/Track.h"
 
// ACTS
#include "Acts/Definitions/TrackParametrization.hpp"
#include "Acts/Definitions/Units.hpp"
#include "Acts/Propagator/EigenStepper.hpp"
#include "Acts/Propagator/Navigator.hpp"
#include "Acts/Propagator/Propagator.hpp"
#include "Acts/Surfaces/PerigeeSurface.hpp"
#include "Acts/Surfaces/Surface.hpp"
#include "Acts/TrackFitting/KalmanFitter.hpp"
#include "Acts/Utilities/Helpers.hpp"
#include "Acts/Utilities/Logger.hpp"
#include "Acts/Utilities/CalibrationContext.hpp"
#include "Acts/EventData/VectorTrackContainer.hpp"
 
#include "InDetPrepRawData/SCT_Cluster.h"
#include "InDetPrepRawData/PixelCluster.h"
#include "InDetRIO_OnTrack/SCT_ClusterOnTrack.h"
#include "InDetRIO_OnTrack/PixelClusterOnTrack.h"
 
#include "ActsEvent/TrackContainer.h"
// PACKAGE
#include "ActsGeometry/ATLASMagneticFieldWrapper.h"
#include "ActsGeometryInterfaces/ActsGeometryContext.h"
#include "ActsGeometry/ATLASSourceLink.h"
#include "ActsGeometry/ATLASSourceLinkSurfaceAccessor.h"
#include "ActsInterop/Logger.h"
 
#include "Acts/Propagator/DirectNavigator.hpp"
 
// STL
#include <vector>
 
namespace ActsTrk {
 
/*
The following is the implementation of the PRDSourceLinkCalibrator.
To use this implementation, the flag for a refitting from PRD measurment has to be turned on in the appropriate Acts config.
*/
template <typename trajectory_t>
void PRDSourceLinkCalibrator::calibrate(const Acts::GeometryContext& gctx,
    const Acts::CalibrationContext& /*cctx*/,
    const Acts::SourceLink& sl,
    typename trajectory_t::TrackStateProxy trackState) const {
    
    const Trk::PrepRawData* prd = sl.template get<PRDSourceLink>().prd;
    trackState.setUncalibratedSourceLink(sl);
 
    const Acts::BoundTrackParameters actsParam(trackState.referenceSurface().getSharedPtr(),
             trackState.predicted(),
             trackState.predictedCovariance(),
             Acts::ParticleHypothesis::pion());
    std::unique_ptr<const Trk::TrackParameters> trkParam = converterTool->actsTrackParametersToTrkParameters(actsParam, gctx);
    
    //RIO_OnTrack creation from the PrepRawData
    const Trk::Surface & prdsurf = prd->detectorElement()->surface(prd->identify());
    const Trk::RIO_OnTrack *rot = nullptr;
    const Trk::PlaneSurface *plsurf = nullptr;
    if (prdsurf.type() == Trk::SurfaceType::Plane)
      plsurf = static_cast < const Trk::PlaneSurface *>(&prdsurf);
 
    const Trk::StraightLineSurface *slsurf = nullptr;
        
    if (prdsurf.type() == Trk::SurfaceType::Line)
      slsurf = static_cast < const Trk::StraightLineSurface *>(&prdsurf);
 
    //@TODO, there is no way to put a MSG in this framework yet. So the next 3 lines are commented
    //if ((slsurf == nullptr) && (plsurf == nullptr)) {
      //msg(MSG::ERROR) << "Surface is neither PlaneSurface nor StraightLineSurface!" << endmsg; //ATH_MSG_ERROR doesn't work here because (ActsTrk::PRDSourceLinkCalibrator' has no member named 'msg')
    // }
    if (slsurf != nullptr) {
      Trk::AtaStraightLine atasl(
        slsurf->center(), 
        trackState.predicted()[Trk::phi],
        trackState.predicted()[Trk::theta],
        trackState.predicted()[Trk::qOverP], 
        *slsurf
       );
      if(broadRotCreator){
        rot = broadRotCreator->correct(*prd, atasl); 
        }
      else{
        rot = rotCreator->correct(*prd, atasl); 
        }
     } else if (plsurf != nullptr) {
      if ((trkParam.get())->covariance() != nullptr) { 
        Trk::AtaPlane atapl(
          plsurf->center(), 
          trackState.predicted()[Trk::phi],
          trackState.predicted()[Trk::theta],
          trackState.predicted()[Trk::qOverP], 
          *plsurf,
          AmgSymMatrix(5)(*trkParam.get()->covariance()) 
        );
        rot = rotCreator->correct(*prd, atapl);
      } else {
        Trk::AtaPlane atapl(
          plsurf->center(), 
          trackState.predicted()[Trk::phi],
          trackState.predicted()[Trk::theta],
          trackState.predicted()[Trk::qOverP], 
          *plsurf
        );
        rot = rotCreator->correct(*prd, atapl); 
      }
    } // End of RIO_OnTrack creation from the PrepRawData
 
    int dim = (*rot).localParameters().dimension();
    trackState.allocateCalibrated(dim);
    
    //Writting the calibrated ROT measurment into the trackState
    if (dim == 0)
      {
        throw std::runtime_error("Cannot create dim 0 measurement");
      } else if (dim == 1) {
        trackState.template calibrated<1>() = (*rot).localParameters().template head<1>(); 
        trackState.template calibratedCovariance<1>() = (*rot).localCovariance().template topLeftCorner<1, 1>(); 
        // Create a projection matrix onto 1D measurement 
        Acts::ActsMatrix<Acts::MultiTrajectoryTraits::MeasurementSizeMax, 2> proj;
        proj.setZero();
        if ((*rot).associatedSurface().bounds().type() == Trk::SurfaceBounds::Annulus) { 
          proj(Acts::eBoundLoc0, Acts::eBoundLoc1) = 1; // transforms predicted[1] -> calibrated[0] in Acts::MeasurementSelector::calculateChi2()
        } else {
          proj(Acts::eBoundLoc0, Acts::eBoundLoc0) = 1;
        }
        trackState.setProjector(proj);
      }
      else if (dim == 2)
        {
          trackState.template calibrated<2>() = (*rot).localParameters().template head<2>();
          trackState.template calibratedCovariance<2>() = (*rot).localCovariance().template topLeftCorner<2, 2>();
          // Create a 2D projection matrix
          Acts::ActsMatrix<Acts::MultiTrajectoryTraits::MeasurementSizeMax, 2> proj;
          proj.setZero();
          proj(Acts::eBoundLoc0, Acts::eBoundLoc0) = 1;
          proj(Acts::eBoundLoc1, Acts::eBoundLoc1) = 1;
          trackState.setProjector(proj);
        }
      else
      {
        throw std::runtime_error("Dim " + std::to_string(dim) +
                                " currently not supported.");
      }
    delete rot; //Delete rot as a precaution
 
}
 
const Acts::Surface* PRDSourceLinkSurfaceAccessor::operator()(const Acts::SourceLink& sourceLink) const {
  const auto& sl = sourceLink.get<PRDSourceLink>();
  const auto& trkSrf = sl.prd->detectorElement()->surface(sl.prd->identify());
  const auto& actsSrf = converterTool->trkSurfaceToActsSurface(trkSrf);
  return &actsSrf;
}
 
KalmanFitter::KalmanFitter(const std::string& t,const std::string& n,
               const IInterface* p) :
  base_class(t,n,p)
{}
 
StatusCode KalmanFitter::initialize() {
 
  ATH_MSG_DEBUG(name() << "::" << __FUNCTION__);
  ATH_CHECK(m_trackingGeometryTool.retrieve());
  ATH_CHECK(m_extrapolationTool.retrieve());
  ATH_CHECK(m_ATLASConverterTool.retrieve());
  ATH_CHECK(m_trkSummaryTool.retrieve());
  if(m_doReFitFromPRD){
  ATH_CHECK(m_ROTcreator.retrieve()); 
  ATH_CHECK(m_broadROTcreator.retrieve());
  }
 
  m_logger = makeActsAthenaLogger(this, "KalmanRefit");
 
  auto field = std::make_shared<ATLASMagneticFieldWrapper>();
 
  // Fitter
  Acts::EigenStepper<> stepper(field, m_overstepLimit);
  Acts::Navigator navigator( Acts::Navigator::Config{ m_trackingGeometryTool->trackingGeometry() },
                 logger().cloneWithSuffix("Navigator"));
  Acts::Propagator<Acts::EigenStepper<>, Acts::Navigator> propagator(stepper, 
                     std::move(navigator),
                     logger().cloneWithSuffix("Prop"));
 
  m_fitter = std::make_unique<Fitter>(std::move(propagator),
              logger().cloneWithSuffix("KalmanFitter"));
 
  // Direct Fitter
  Acts::DirectNavigator directNavigator( logger().cloneWithSuffix("DirectNavigator") );
  Acts::Propagator<Acts::EigenStepper<>, Acts::DirectNavigator> directPropagator(std::move(stepper),
                                         std::move(directNavigator),
                                         logger().cloneWithSuffix("DirectPropagator"));
 
  m_directFitter = std::make_unique<DirectFitter>(std::move(directPropagator),
                          logger().cloneWithSuffix("DirectKalmanFitter"));
 
  m_calibrator = std::make_unique<TrkMeasurementCalibrator>(*m_ATLASConverterTool);
  m_outlierFinder.StateChiSquaredPerNumberDoFCut = m_option_outlierChi2Cut;
  m_reverseFilteringLogic.momentumMax = m_option_ReverseFilteringPt;
 
  m_kfExtensions.outlierFinder.connect<&ActsTrk::FitterHelperFunctions::ATLASOutlierFinder::operator()<ActsTrk::MutableTrackStateBackend>>(&m_outlierFinder);
  m_kfExtensions.reverseFilteringLogic.connect<&ActsTrk::FitterHelperFunctions::ReverseFilteringLogic::operator()<ActsTrk::MutableTrackStateBackend>>(&m_reverseFilteringLogic);
  m_kfExtensions.updater.connect<&ActsTrk::FitterHelperFunctions::gainMatrixUpdate<ActsTrk::MutableTrackStateBackend>>();
  m_kfExtensions.smoother.connect<&ActsTrk::FitterHelperFunctions::gainMatrixSmoother<ActsTrk::MutableTrackStateBackend>>();
  m_kfExtensions.calibrator.connect<&TrkMeasurementCalibrator::calibrate<ActsTrk::MutableTrackStateBackend>>(m_calibrator.get());
 
  return StatusCode::SUCCESS;
}
 
// refit a track
// -------------------------------------------------------
std::unique_ptr<Trk::Track>
KalmanFitter::fit(const EventContext& ctx,
          const Trk::Track& inputTrack,
          const Trk::RunOutlierRemoval /*runOutlier*/,
          const Trk::ParticleHypothesis /*prtHypothesis*/) const
{
  std::unique_ptr<Trk::Track> track = nullptr;
  ATH_MSG_VERBOSE ("--> enter KalmanFitter::fit(Track,,)    with Track from author = "
       << inputTrack.info().dumpInfo());
 
  // protection against not having measurements on the input track
  if (!inputTrack.measurementsOnTrack() || inputTrack.measurementsOnTrack()->size() < 2) {
    ATH_MSG_DEBUG("called to refit empty track or track with too little information, reject fit");
    return nullptr;
  }
 
  // protection against not having track parameters on the input track
  if (!inputTrack.trackParameters() || inputTrack.trackParameters()->empty()) {
    ATH_MSG_DEBUG("input fails to provide track parameters for seeding the KF, reject fit");
    return nullptr;
  }
 
  // Construct a perigee surface as the target surface
  auto pSurface = Acts::Surface::makeShared<Acts::PerigeeSurface>(
      Acts::Vector3{0., 0., 0.});
  
  Acts::GeometryContext tgContext = m_trackingGeometryTool->getGeometryContext(ctx).context();
  Acts::MagneticFieldContext mfContext = m_extrapolationTool->getMagneticFieldContext(ctx);
  // CalibrationContext converter not implemented yet.
  Acts::CalibrationContext calContext = Acts::CalibrationContext();
 
  Acts::KalmanFitterExtensions<ActsTrk::MutableTrackStateBackend> kfExtensions = m_kfExtensions;
 
  ATLASSourceLinkSurfaceAccessor surfaceAccessor{&(*m_ATLASConverterTool)};
  kfExtensions.surfaceAccessor.connect<&ATLASSourceLinkSurfaceAccessor::operator()>(&surfaceAccessor);
 
  Acts::PropagatorPlainOptions propagationOption;
  propagationOption.maxSteps = m_option_maxPropagationStep;
  // Set the KalmanFitter options
  Acts::KalmanFitterOptions
      kfOptions(tgContext, mfContext, calContext,
                kfExtensions,
                propagationOption,
                &(*pSurface));
 
  std::vector<Acts::SourceLink> trackSourceLinks = m_ATLASConverterTool->trkTrackToSourceLinks(tgContext,inputTrack);
  // protection against error in the conversion from Atlas masurement to Acts source link
  if (trackSourceLinks.empty()) {
    ATH_MSG_DEBUG("input contain measurement but no source link created, probable issue with the converter, reject fit ");
    return track;
  }
 
  const auto& initialParams = m_ATLASConverterTool->trkTrackParametersToActsParameters((*inputTrack.perigeeParameters()), tgContext);
 
  // The covariance from already fitted track are too small and would result an incorect smoothing.
  // We scale up the input covaraiance to avoid this.
  Acts::BoundSquareMatrix scaledCov = Acts::BoundSquareMatrix::Identity();
  for (int i=0; i<6; ++i) {
    double scale = m_option_seedCovarianceScale;
    (scaledCov)(i,i) = scale * initialParams.covariance().value()(i,i);
  }
 
  // @TODO: Synchronize with prtHypothesis
  Acts::ParticleHypothesis hypothesis = Acts::ParticleHypothesis::pion();
 
  const Acts::BoundTrackParameters scaledInitialParams(initialParams.referenceSurface().getSharedPtr(),
                                                       initialParams.parameters(),
                                                       scaledCov,
                                                       hypothesis);
 
  ActsTrk::MutableTrackContainer tracks;
  
  // Perform the fit
  auto result = m_fitter->fit(trackSourceLinks.begin(), trackSourceLinks.end(),
    scaledInitialParams, kfOptions, tracks);
  if (result.ok()) {
    track = makeTrack(ctx, tgContext, tracks, result);
  }
  return track;
}
 
// fit a set of MeasurementBase objects
// --------------------------------
std::unique_ptr<Trk::Track>
KalmanFitter::fit(const EventContext& ctx,
          const Trk::MeasurementSet& inputMeasSet,
          const Trk::TrackParameters& estimatedStartParameters,
          const Trk::RunOutlierRemoval /*runOutlier*/,
          const Trk::ParticleHypothesis /*matEffects*/) const
{
  std::unique_ptr<Trk::Track> track = nullptr;
 
  // protection against not having measurements on the input track
  if (inputMeasSet.size() < 2) {
    ATH_MSG_DEBUG("called to refit empty measurement set or a measurement set with too little information, reject fit");
    return nullptr;
  }
 
  // Construct a perigee surface as the target surface
  auto pSurface = Acts::Surface::makeShared<Acts::PerigeeSurface>(
      Acts::Vector3{0., 0., 0.});
  
  Acts::GeometryContext tgContext = m_trackingGeometryTool->getGeometryContext(ctx).context();
  Acts::MagneticFieldContext mfContext = m_extrapolationTool->getMagneticFieldContext(ctx);
  // CalibrationContext converter not implemented yet.
  Acts::CalibrationContext calContext = Acts::CalibrationContext();
 
  Acts::KalmanFitterExtensions<ActsTrk::MutableTrackStateBackend> kfExtensions = m_kfExtensions;
 
  ATLASSourceLinkSurfaceAccessor surfaceAccessor{&(*m_ATLASConverterTool)};
  kfExtensions.surfaceAccessor.connect<&ATLASSourceLinkSurfaceAccessor::operator()>(&surfaceAccessor);
 
  Acts::PropagatorPlainOptions propagationOption;
  propagationOption.maxSteps = m_option_maxPropagationStep;
  // Set the KalmanFitter options
  Acts::KalmanFitterOptions
      kfOptions(tgContext, mfContext, calContext,
                kfExtensions,
                propagationOption,
                &(*pSurface));
 
  std::vector<Acts::SourceLink> trackSourceLinks;
  trackSourceLinks.reserve(inputMeasSet.size());
 
  for (auto it = inputMeasSet.begin(); it != inputMeasSet.end(); ++it){
   trackSourceLinks.push_back(m_ATLASConverterTool->trkMeasurementToSourceLink(tgContext, **it));
  }
  // protection against error in the conversion from Atlas masurement to Acts source link
  if (trackSourceLinks.empty()) {
    ATH_MSG_DEBUG("input contain measurement but no source link created, probable issue with the converter, reject fit ");
    return track;
  }
 
  const auto& initialParams = m_ATLASConverterTool->trkTrackParametersToActsParameters(estimatedStartParameters, tgContext); 
 
  ActsTrk::MutableTrackContainer tracks;
 
  // Perform the fit
  auto result = m_fitter->fit(trackSourceLinks.begin(), trackSourceLinks.end(),
    initialParams, kfOptions, tracks);
  if (result.ok()) {
    track = makeTrack(ctx, tgContext, tracks, result);
  }
  return track;
}
 
// fit a set of PrepRawData objects
// --------------------------------
std::unique_ptr<Trk::Track>
KalmanFitter::fit(const EventContext& ctx,
          const Trk::PrepRawDataSet& inputPRDColl,
          const Trk::TrackParameters& estimatedStartParameters,
          const Trk::RunOutlierRemoval /*runOutlier*/,
          const Trk::ParticleHypothesis /*prtHypothesis*/) const
{
    ATH_MSG_DEBUG("--> entering KalmanFitter::fit(PRDS,TP,)");
    
  
    std::unique_ptr<Trk::Track> track = nullptr;
 
    // Construct a perigee surface as the target surface
    auto pSurface = Acts::Surface::makeShared<Acts::PerigeeSurface>(
        Acts::Vector3{0., 0., 0.}); 
    
    Acts::GeometryContext tgContext = m_trackingGeometryTool->getGeometryContext(ctx).context();
    Acts::MagneticFieldContext mfContext = m_extrapolationTool->getMagneticFieldContext(ctx);
    // CalibrationContext converter not implemented yet.
    Acts::CalibrationContext calContext = Acts::CalibrationContext();
 
    Acts::KalmanFitterExtensions<ActsTrk::MutableTrackStateBackend> kfExtensions = m_kfExtensions;
 
    PRDSourceLinkCalibrator calibrator{}; // @TODO: Set tool pointers
    calibrator.rotCreator =m_ROTcreator.get();
    calibrator.broadRotCreator = m_broadROTcreator.get();
    calibrator.converterTool = m_ATLASConverterTool.get();
    kfExtensions.calibrator.connect<&PRDSourceLinkCalibrator::calibrate<ActsTrk::MutableTrackStateBackend>>(&calibrator);
 
    PRDSourceLinkSurfaceAccessor surfaceAccessor{m_ATLASConverterTool.get()};
    kfExtensions.surfaceAccessor.connect<&PRDSourceLinkSurfaceAccessor::operator()>(&surfaceAccessor);
 
    Acts::PropagatorPlainOptions propagationOption;
    propagationOption.maxSteps = m_option_maxPropagationStep;
    // Set the KalmanFitter options
    Acts::KalmanFitterOptions
        kfOptions(tgContext, mfContext, calContext,
                  kfExtensions,
                  propagationOption,
                  &(*pSurface));
 
 
    std::vector<Acts::SourceLink> trackSourceLinks; 
    trackSourceLinks.reserve(inputPRDColl.size());
 
    for(const Trk::PrepRawData* prd : inputPRDColl) {
      trackSourceLinks.push_back(Acts::SourceLink{PRDSourceLink{prd}});
    }
    // protection against error in the conversion from Atlas masurement to Acts source link
    if (trackSourceLinks.empty()) {
      ATH_MSG_WARNING("input contain measurement but no source link created, probable issue with the converter, reject fit ");
      return track;
    }
    //
 
    const auto& initialParams = m_ATLASConverterTool->trkTrackParametersToActsParameters(estimatedStartParameters, tgContext); 
 
 
    ActsTrk::MutableTrackContainer tracks;
    // Perform the fit
    auto result = m_fitter->fit(trackSourceLinks.begin(), trackSourceLinks.end(),
      initialParams, kfOptions, tracks);
    if (result.ok()) {
      track = makeTrack(ctx, tgContext, tracks, result, true);
    }
    return track; 
}
 
// fit a set of PrepRawData objects
// --------------------------------
std::unique_ptr< ActsTrk::MutableTrackContainer >
KalmanFitter::fit(const EventContext& ,
      const std::vector< ActsTrk::ATLASUncalibSourceLink> & clusterList,
      const Acts::BoundTrackParameters& initialParams,
      const Acts::GeometryContext& tgContext,
      const Acts::MagneticFieldContext& mfContext,
      const Acts::CalibrationContext& calContext,
      const TrackingSurfaceHelper &tracking_surface_helper,
      const Acts::Surface* targetSurface) const{
  ATH_MSG_DEBUG("--> entering KalmanFitter::fit(xAODMeasure...things,TP,)");
       
  std::vector<Acts::SourceLink> sourceLinks;
  sourceLinks.reserve(clusterList.size()); 
 
  std::vector<const Acts::Surface*> surfaces;
  surfaces.reserve(clusterList.size());
   
  for (const ActsTrk::ATLASUncalibSourceLink& el : clusterList) {
    sourceLinks.emplace_back( el );
    surfaces.push_back(&tracking_surface_helper.associatedActsSurface( getUncalibratedMeasurement(el) ));
  }
 
  Acts::KalmanFitterExtensions<ActsTrk::MutableTrackStateBackend> kfExtensions = m_kfExtensions;
  
  ActsTrk::ATLASUncalibSourceLinkSurfaceAccessor surfaceAccessor{ &(*m_ATLASConverterTool), &tracking_surface_helper };
  kfExtensions.surfaceAccessor.connect<&ActsTrk::ATLASUncalibSourceLinkSurfaceAccessor::operator()>(&surfaceAccessor);
 
  OnTrackCalibrator calibrator = OnTrackCalibrator<ActsTrk::MutableTrackStateBackend>
      ::NoCalibration(*m_ATLASConverterTool, tracking_surface_helper);
 
  kfExtensions.calibrator.connect<&OnTrackCalibrator<ActsTrk::MutableTrackStateBackend>::calibrate>(&calibrator);
   
  Acts::PropagatorPlainOptions propagationOption;
  propagationOption.maxSteps = m_option_maxPropagationStep;
 
  // Construct a perigee surface as the target surface if none is provided
  std::shared_ptr<Acts::Surface> pSurface{nullptr};
  if (!targetSurface){
    pSurface = Acts::Surface::makeShared<Acts::PerigeeSurface>(Acts::Vector3{0., 0., 0.});
    targetSurface = pSurface.get();
  }
 
  // Set the KalmanFitter options
  Acts::KalmanFitterOptions<ActsTrk::MutableTrackStateBackend>
    kfOptions(tgContext, mfContext, calContext,
          kfExtensions,
          propagationOption,
        targetSurface); 
  
  std::unique_ptr< ActsTrk::MutableTrackContainer > tracks = std::make_unique< ActsTrk::MutableTrackContainer >();
 
  
  auto result = m_directFitter->fit(sourceLinks.begin(),
                    sourceLinks.end(),
                    initialParams,
                    kfOptions,
                    surfaces,
                    *tracks.get());
   
  if (not result.ok()) {
    ATH_MSG_VERBOSE("Kalman Fitter on Seed has failed");
    return nullptr;
  } 
  return tracks; 
}
 
// extend a track fit to include an additional set of MeasurementBase objects
// re-implements the TrkFitterUtils/TrackFitter.cxx general code in a more
// mem efficient and stable way
// --------------------------------
std::unique_ptr<Trk::Track>
KalmanFitter::fit(const EventContext& ctx,
          const Trk::Track& inputTrack,
          const Trk::MeasurementSet& addMeasColl,
          const Trk::RunOutlierRemoval /*runOutlier*/,
          const Trk::ParticleHypothesis /*matEffects*/) const
{
  ATH_MSG_VERBOSE ("--> enter KalmanFitter::fit(Track,Meas'BaseSet,,)");
  ATH_MSG_VERBOSE ("    with Track from author = " << inputTrack.info().dumpInfo());
 
  // protection, if empty MeasurementSet
  if (addMeasColl.empty()) {
    ATH_MSG_DEBUG( "client tries to add an empty MeasurementSet to the track fit." );
    return fit(ctx,inputTrack);
  }
 
  // protection against not having measurements on the input track
  if (!inputTrack.measurementsOnTrack() || (inputTrack.measurementsOnTrack()->size() < 2 && addMeasColl.empty())) {
    ATH_MSG_DEBUG("called to refit empty track or track with too little information, reject fit");
    return nullptr;
  }
 
  // protection against not having track parameters on the input track
  if (!inputTrack.trackParameters() || inputTrack.trackParameters()->empty()) {
    ATH_MSG_DEBUG("input fails to provide track parameters for seeding the KF, reject fit");
    return nullptr;
  }
 
   std::unique_ptr<Trk::Track> track = nullptr;
 
  // Construct a perigee surface as the target surface
  auto pSurface = Acts::Surface::makeShared<Acts::PerigeeSurface>(
      Acts::Vector3{0., 0., 0.});
  
  Acts::GeometryContext tgContext = m_trackingGeometryTool->getGeometryContext(ctx).context();
  Acts::MagneticFieldContext mfContext = m_extrapolationTool->getMagneticFieldContext(ctx);
  // CalibrationContext converter not implemented yet.
  Acts::CalibrationContext calContext = Acts::CalibrationContext();
 
  Acts::KalmanFitterExtensions<ActsTrk::MutableTrackStateBackend> kfExtensions = m_kfExtensions;
 
  Acts::PropagatorPlainOptions propagationOption;
  propagationOption.maxSteps = m_option_maxPropagationStep;
  // Set the KalmanFitter options
  Acts::KalmanFitterOptions
      kfOptions(tgContext, mfContext, calContext,
                kfExtensions,
                propagationOption,
                &(*pSurface));
 
  std::vector<Acts::SourceLink> trackSourceLinks = m_ATLASConverterTool->trkTrackToSourceLinks(tgContext, inputTrack);
  const auto& initialParams = m_ATLASConverterTool->trkTrackParametersToActsParameters(*(inputTrack.perigeeParameters()), tgContext);
 
  for (auto it = addMeasColl.begin(); it != addMeasColl.end(); ++it)
  {
    trackSourceLinks.push_back(m_ATLASConverterTool->trkMeasurementToSourceLink(tgContext, **it));
  }
  // protection against error in the conversion from Atlas masurement to Acts source link
  if (trackSourceLinks.empty()) {
    ATH_MSG_DEBUG("input contain measurement but no source link created, probable issue with the converter, reject fit ");
    return track;
  }
 
  ActsTrk::MutableTrackContainer tracks;
  // Perform the fit
  auto result = m_fitter->fit(trackSourceLinks.begin(), trackSourceLinks.end(),
    initialParams, kfOptions, tracks);
  if (result.ok()) {
    track = makeTrack(ctx, tgContext, tracks, result);
  }
  return track;
}
 
// extend a track fit to include an additional set of PrepRawData objects
// --------------------------------
std::unique_ptr<Trk::Track>
KalmanFitter::fit(const EventContext& /*ctx*/,
          const Trk::Track& /*inputTrack*/,
          const Trk::PrepRawDataSet& /*addPrdColl*/,
          const Trk::RunOutlierRemoval /*runOutlier*/,
          const Trk::ParticleHypothesis /*matEffects*/) const
{
  ATH_MSG_DEBUG("Fit of Track with additional PrepRawDataSet not yet implemented");
  return nullptr;
}
 
// combined fit of two tracks
// --------------------------------
std::unique_ptr<Trk::Track>
KalmanFitter::fit(const EventContext& ctx,
          const Trk::Track& intrk1,
          const Trk::Track& intrk2,
          const Trk::RunOutlierRemoval /*runOutlier*/,
          const Trk::ParticleHypothesis /*matEffects*/) const
{
  ATH_MSG_VERBOSE ("--> enter KalmanFitter::fit(Track,Track,)");
  ATH_MSG_VERBOSE ("    with Tracks from #1 = " << intrk1.info().dumpInfo()
                   << " and #2 = " << intrk2.info().dumpInfo());
 
  // protection, if empty track2
  if (!intrk2.measurementsOnTrack()) {
    ATH_MSG_DEBUG( "input #2 is empty try to fit track 1 alone" );
    return fit(ctx,intrk1);
  }
 
  // protection, if empty track1
  if (!intrk1.measurementsOnTrack()) {
    ATH_MSG_DEBUG( "input #1 is empty try to fit track 2 alone" );
    return fit(ctx,intrk2);
  }
 
  // protection against not having track parameters on the input track
  if (!intrk1.trackParameters() || intrk1.trackParameters()->empty()) {
    ATH_MSG_DEBUG("input #1 fails to provide track parameters for seeding the KF, reject fit");
    return nullptr;
  }
 
   std::unique_ptr<Trk::Track> track = nullptr;
 
  // Construct a perigee surface as the target surface
  auto pSurface = Acts::Surface::makeShared<Acts::PerigeeSurface>(
      Acts::Vector3{0., 0., 0.});
  
  Acts::GeometryContext tgContext = m_trackingGeometryTool->getGeometryContext(ctx).context();
  Acts::MagneticFieldContext mfContext = m_extrapolationTool->getMagneticFieldContext(ctx);
  // CalibrationContext converter not implemented yet.
  Acts::CalibrationContext calContext = Acts::CalibrationContext();
 
  Acts::KalmanFitterExtensions<ActsTrk::MutableTrackStateBackend> kfExtensions = m_kfExtensions;
 
  Acts::PropagatorPlainOptions propagationOption;
  propagationOption.maxSteps = m_option_maxPropagationStep;
  // Set the KalmanFitter options
  Acts::KalmanFitterOptions
      kfOptions(tgContext, mfContext, calContext,
                kfExtensions,
                propagationOption,
                &(*pSurface));
 
  std::vector<Acts::SourceLink> trackSourceLinks = m_ATLASConverterTool->trkTrackToSourceLinks(tgContext, intrk1);
  std::vector<Acts::SourceLink> trackSourceLinks2 = m_ATLASConverterTool->trkTrackToSourceLinks(tgContext, intrk2);
  trackSourceLinks.insert(trackSourceLinks.end(), trackSourceLinks2.begin(), trackSourceLinks2.end());
  // protection against error in the conversion from Atlas masurement to Acts source link
  if (trackSourceLinks.empty()) {
    ATH_MSG_DEBUG("input contain measurement but no source link created, probable issue with the converter, reject fit ");
    return track;
  }
 
  const auto &initialParams = m_ATLASConverterTool->trkTrackParametersToActsParameters(*(intrk1.perigeeParameters()), tgContext);
 
  // The covariance from already fitted track are too small and would result an incorect smoothing.
  // We scale up the input covaraiance to avoid this.
  Acts::BoundSquareMatrix scaledCov = Acts::BoundSquareMatrix::Identity();
  for (int i=0; i<6; ++i) {
    double scale = m_option_seedCovarianceScale;
    (scaledCov)(i,i) = scale * initialParams.covariance().value()(i,i);
  }
 
  const Acts::BoundTrackParameters scaledInitialParams(initialParams.referenceSurface().getSharedPtr(),
                                                       initialParams.parameters(),
                                                       scaledCov,
                                                       Acts::ParticleHypothesis::pion());
 
 
  ActsTrk::MutableTrackContainer tracks;
  // Perform the fit
  auto result = m_fitter->fit(trackSourceLinks.begin(), trackSourceLinks.end(),
    scaledInitialParams, kfOptions, tracks);
  if (result.ok()) {
    track = makeTrack(ctx, tgContext, tracks, result);
  }
  return track;
}
 
std::unique_ptr<Trk::Track>
KalmanFitter::makeTrack(const EventContext& ctx,
            Acts::GeometryContext& tgContext,
            ActsTrk::MutableTrackContainer& tracks,
            Acts::Result<ActsTrk::MutableTrackContainer::TrackProxy, std::error_code>& fitResult, bool SourceLinkType) const {
  
  if (not fitResult.ok()) 
    return nullptr;    
 
  std::unique_ptr<Trk::Track> newtrack = nullptr;
  // Get the fit output object
  const auto& acts_track = fitResult.value();
  auto finalTrajectory = std::make_unique<Trk::TrackStates>();
  // initialise the number of dead Pixel and Acts strip
  int numberOfDeadPixel = 0;
  int numberOfDeadSCT = 0;
 
  std::vector<std::unique_ptr<const Acts::BoundTrackParameters>> actsSmoothedParam;
  // Loop over all the output state to create track state
  tracks.trackStateContainer().visitBackwards(acts_track.tipIndex(), 
                [&] (const auto &state) -> void
  {
    // First only concider state with an associated detector element not in the TRT
    auto flag = state.typeFlags();
    const auto* associatedDetEl = state.referenceSurface().associatedDetectorElement();
    if (not associatedDetEl) 
      return;
    
    const auto* actsElement = dynamic_cast<const ActsDetectorElement*>(associatedDetEl);
    if (not actsElement) 
      return;
 
    const auto* upstreamDetEl = actsElement->upstreamDetectorElement();
    if (not upstreamDetEl) 
      return;
 
    ATH_MSG_VERBOSE("Try casting to TRT for if");    
    if (dynamic_cast<const InDetDD::TRT_BaseElement*>(upstreamDetEl))
      return;
 
    const auto* trkDetElem = dynamic_cast<const Trk::TrkDetElementBase*>(upstreamDetEl);
    if (not trkDetElem)
      return;
 
    ATH_MSG_VERBOSE("trkDetElem type: " << static_cast<std::underlying_type_t<Trk::DetectorElemType>>(trkDetElem->detectorType()));
 
    ATH_MSG_VERBOSE("Try casting to SiDetectorElement");
    const auto* detElem = dynamic_cast<const InDetDD::SiDetectorElement*>(upstreamDetEl);
    if (not detElem)
      return;
    ATH_MSG_VERBOSE("detElem = " << detElem);
 
    // We need to determine the type of state 
    std::bitset<Trk::TrackStateOnSurface::NumberOfTrackStateOnSurfaceTypes> typePattern;
    std::unique_ptr<Trk::TrackParameters> parm;
 
    // State is a hole (no associated measurement), use predicted parameters   
    if (flag.test(Acts::TrackStateFlag::HoleFlag)){
      ATH_MSG_VERBOSE("State is a hole (no associated measurement), use predicted parameters");
      const Acts::BoundTrackParameters actsParam(state.referenceSurface().getSharedPtr(),
             state.predicted(),
             state.predictedCovariance(),
             acts_track.particleHypothesis());
      parm = m_ATLASConverterTool->actsTrackParametersToTrkParameters(actsParam, tgContext);
      auto boundaryCheck = m_boundaryCheckTool->boundaryCheck(*parm);
      
      // Check if this is a hole, a dead sensors or a state outside the sensor boundary
      ATH_MSG_VERBOSE("Check if this is a hole, a dead sensors or a state outside the sensor boundary");
      if(boundaryCheck == Trk::BoundaryCheckResult::DeadElement){
        if (detElem->isPixel()) {
          ++numberOfDeadPixel;
        }
        else if (detElem->isSCT()) {
          ++numberOfDeadSCT;
        }
        // Dead sensors states are not stored              
        return;
            } else if (boundaryCheck != Trk::BoundaryCheckResult::Candidate){
        // States outside the sensor boundary are ignored
        return;
      }
      typePattern.set(Trk::TrackStateOnSurface::Hole);
    }
    // The state was tagged as an outlier or was missed in the reverse filtering, use filtered parameters
    else if (flag.test(Acts::TrackStateFlag::OutlierFlag) or !state.hasSmoothed()) {
      ATH_MSG_VERBOSE("The state was tagged as an outlier or was missed in the reverse filtering, use filtered parameters");
      const Acts::BoundTrackParameters actsParam(state.referenceSurface().getSharedPtr(),
             state.filtered(),
             state.filteredCovariance(),
             acts_track.particleHypothesis());
      parm = m_ATLASConverterTool->actsTrackParametersToTrkParameters(actsParam, tgContext);
      typePattern.set(Trk::TrackStateOnSurface::Outlier);
    }
    // The state is a measurement state, use smoothed parameters 
    else{
      ATH_MSG_VERBOSE("The state is a measurement state, use smoothed parameters");
 
      const Acts::BoundTrackParameters actsParam(state.referenceSurface().getSharedPtr(),
             state.smoothed(),
             state.smoothedCovariance(),
             acts_track.particleHypothesis());
      
      actsSmoothedParam.push_back(std::make_unique<const Acts::BoundTrackParameters>(Acts::BoundTrackParameters(actsParam)));
      parm = m_ATLASConverterTool->actsTrackParametersToTrkParameters(actsParam, tgContext);
      typePattern.set(Trk::TrackStateOnSurface::Measurement);                                         
    }
    std::unique_ptr<Trk::MeasurementBase> measState;
    if (state.hasUncalibratedSourceLink() && !SourceLinkType){
      auto sl = state.getUncalibratedSourceLink().template get<ATLASSourceLink>();
      assert(sl);
      measState = sl->uniqueClone();
    }
    else if (state.hasUncalibratedSourceLink() && SourceLinkType){ //If the SourceLink is of type PRDSourceLink, we need to create the RIO_OnTrack here.
      auto sl = state.getUncalibratedSourceLink().template get<PRDSourceLink>().prd;
 
      //ROT creation
      const IdentifierHash idHash = sl->detectorElement()->identifyHash();
      int dim = state.calibratedSize();
      std::unique_ptr<Trk::RIO_OnTrack> rot;
      if (dim == 1) {
        const InDet::SCT_Cluster* sct_Cluster = dynamic_cast<const InDet::SCT_Cluster*>(sl);
        if(!sct_Cluster){
          ATH_MSG_ERROR("ERROR could not cast PRD to SCT_Cluster");
          return;
        }
        rot = std::make_unique<InDet::SCT_ClusterOnTrack>(sct_Cluster,Trk::LocalParameters(Trk::DefinedParameter(state.template calibrated<1>()[0], Trk::loc1)), state.template calibratedCovariance<1>(),idHash);
        } 
      else if (dim == 2) {
        const InDet::PixelCluster* pixelCluster = dynamic_cast<const InDet::PixelCluster*>(sl);
        if(!pixelCluster){ 
          //sometimes even with dim=2, only the SCT_Cluster implementation work for RIO_OnTrack creation
          ATH_MSG_VERBOSE("Dimension is 2 but we need SCT_Cluster for this measurment");
          const InDet::SCT_Cluster* sct_Cluster = dynamic_cast<const InDet::SCT_Cluster*>(sl);
          rot = std::make_unique<InDet::SCT_ClusterOnTrack>(sct_Cluster,Trk::LocalParameters(Trk::DefinedParameter(state.template calibrated<1>()[0], Trk::loc1)), state.template calibratedCovariance<1>(),idHash);
          }
        else{
        rot = std::make_unique<InDet::PixelClusterOnTrack>(pixelCluster,Trk::LocalParameters(state.template calibrated<2>()),state.template calibratedCovariance<2>(),idHash);
          }
        } 
      else {
          throw std::domain_error("Cannot handle measurement dim>2");
        }
      measState = rot->uniqueClone();
    }
    double nDoF = state.calibratedSize();
    auto quality =Trk::FitQualityOnSurface(state.chi2(), nDoF);
    const Trk::TrackStateOnSurface *perState = new Trk::TrackStateOnSurface(quality, std::move(measState), std::move(parm), nullptr, typePattern);
    // If a state was succesfully created add it to the trajectory 
    if (perState) {
      ATH_MSG_VERBOSE("State succesfully creates, adding it to the trajectory");
      finalTrajectory->insert(finalTrajectory->begin(), perState);
    }
  });
  // Convert the perigee state and add it to the trajectory
  const Acts::BoundTrackParameters actsPer(acts_track.referenceSurface().getSharedPtr(), 
                                          acts_track.parameters(), 
                                          acts_track.covariance(),
                                          acts_track.particleHypothesis());
  std::unique_ptr<Trk::TrackParameters> per = m_ATLASConverterTool->actsTrackParametersToTrkParameters(actsPer, tgContext);
  std::bitset<Trk::TrackStateOnSurface::NumberOfTrackStateOnSurfaceTypes> typePattern;
  typePattern.set(Trk::TrackStateOnSurface::Perigee);
  const Trk::TrackStateOnSurface *perState = new Trk::TrackStateOnSurface(nullptr, std::move(per), nullptr, typePattern);
  if (perState) finalTrajectory->insert(finalTrajectory->begin(), perState);
 
  // Create the track using the states
  Trk::TrackInfo newInfo(Trk::TrackInfo::TrackFitter::KalmanFitter, Trk::noHypothesis);
  newInfo.setTrackFitter(Trk::TrackInfo::TrackFitter::KalmanFitter); //Mark the fitter as KalmanFitter
  newtrack = std::make_unique<Trk::Track>(newInfo, std::move(finalTrajectory), nullptr);
  if (newtrack) {
    // Create the track summary and update the holes information
    if (!newtrack->trackSummary()) {
      newtrack->setTrackSummary(std::make_unique<Trk::TrackSummary>());
      newtrack->trackSummary()->update(Trk::numberOfPixelHoles, 0);
      newtrack->trackSummary()->update(Trk::numberOfSCTHoles, 0);
      newtrack->trackSummary()->update(Trk::numberOfTRTHoles, 0);
      newtrack->trackSummary()->update(Trk::numberOfPixelDeadSensors, numberOfDeadPixel);
      newtrack->trackSummary()->update(Trk::numberOfSCTDeadSensors, numberOfDeadSCT);
    }
    m_trkSummaryTool->updateTrackSummary(ctx, *newtrack, true);
  }
  return newtrack;
}
 
std::unique_ptr< ActsTrk::MutableTrackContainer >
KalmanFitter::fit(const EventContext& ctx,
          const ActsTrk::Seed &seed,
          const Acts::BoundTrackParameters& initialParams,
          const Acts::GeometryContext& tgContext,
          const Acts::MagneticFieldContext& mfContext,
          const Acts::CalibrationContext& calContext,
          const TrackingSurfaceHelper &tracking_surface_helper) const 
{
  std::vector<ActsTrk::ATLASUncalibSourceLink> sourceLinks;
  sourceLinks.reserve(6);
 
  std::vector<const Acts::Surface*> surfaces;
  surfaces.reserve(6);
  
  const auto& sps = seed.sp();
  for (const xAOD::SpacePoint* sp : sps) {
    const auto& measurements = sp->measurements();
    for (const xAOD::UncalibratedMeasurement *umeas : measurements) {
      ActsTrk::ATLASUncalibSourceLink el(makeATLASUncalibSourceLink(umeas));
      sourceLinks.emplace_back( el );
      surfaces.push_back(&tracking_surface_helper.associatedActsSurface(*umeas));
    }
  }
  return fit(ctx, sourceLinks, initialParams, tgContext, mfContext, calContext, tracking_surface_helper, surfaces.front()); 
}
  
}