////////////////////////////////////////////////////////////////////////
/// \class RAT::Classifiers::BiPoLikelihoodDiff
///
/// \brief:  Classifies post-reconstruction as In-Window BiPo-Coincidence
///
/// \author name:  Krish Majumdar <Krishanu.Majumdar@physics.ox.ac.uk>
///
/// REVISION HISTORY:
///     29/11/2013 : Krish Majumdar - New file
///     30/01/2014 : Krish Majumdar - added parameters to plot the distributions
///     13/02/2014 : Krish Majumdar - changes as requested for Pull Request
///     20/03/2014 : Krish Majumdar - changed classifier to be an Optimised Classifier
///     24/04/2015 : Matt Mottram - updated initialisation to dynamically load material
///     30/04/2015 : Matt Mottram - added failover to default material PDF
///     09/02/2015 : Matt Mottram - update default material
///     01/09/2020 : Logan Lebanowski - Properly account for partial fill
///
/// \details  Uses the Log-Likelihood Difference from comparing Time Residual
///           distributions to classify events as either pileup 212/214BiPo
///           coincidence events or not.  The classifier returns the difference
///           between the Log-Likelihood values of 130Te and BiPo distributions.
///
////////////////////////////////////////////////////////////////////////

#ifndef __RAT_Classifiers_BiPoLikelihoodDiff_
#define __RAT_Classifiers_BiPoLikelihoodDiff_

#include <string>
#include <vector>
#include <RAT/SeededClassifier.hh>
#include <RAT/OptimisedClassifier.hh>
#include <RAT/DU/TimeResidualCalculator.hh>

class G4PhysicsOrderedFreeVector;

namespace RAT
{
  namespace DS
  {
    class FitResult;
  }

  namespace Classifiers
  {
    class BiPoLikelihoodDiff : public SeededClassifier, public OptimisedClassifier
    {

    public:
      virtual std::string GetName() const { return BiPoLikelihoodDiff::Name(); }
      static std::string Name() { return std::string("BiPoLikelihoodDiff"); }
      void Initialise(const std::string&);
      void BeginOfRun(DS::Run& run);
      void EndOfRun(DS::Run&);
      void DefaultSeed();
      void SetSeed(const DS::FitResult& seed);
      virtual std::vector<double> GetParams() const;
      virtual std::vector<double> GetPositiveErrors() const;
      virtual std::vector<double> GetNegativeErrors() const;
      virtual void SetParams(const std::vector<double>& params);
      virtual void SetPositiveErrors(const std::vector<double>& errors);
      virtual void SetNegativeErrors(const std::vector<double>& errors);
      virtual DS::ClassifierResult GetClassification();

      /// Calculate the log-likelihood value of an event being a BiPo pileup, using the event's Time Residual PDF and the given value of deltaTime and Bi/Po Time Residual PDFs
      ///
      /// @param[in] params A vector of starting values for the optimisation of deltaTime: [starting value, minimum value, maximum value]
      /// @returns The log-likelihood value from comparing the event time residuals PDF to that of Bi and Po events combined for a SINGLE value of deltaTime
      virtual double operator() (const std::vector<double>& params);

      /// Calculate the log-likelihood value of an event being a 130Te NDBD, using the event's Time Residual PDF and the 130Te Time Residual PDF
      ///
      /// @returns The log-likelihood value from comparing the event time residuals PDF to that of 130Te events
      double logLikelihoodTe();

    private:
      std::string fIndex; ///< The required database index
      std::vector<double> fTimes; ///< A vector of time residual values to be used to create the time residual PDFs
      std::vector<double> fProbabilityTe; ///< A vector of probability values for Te events (1 for each time residual value in fTimes), to be used to create the Te time residual PDF
      std::vector<double> fProbabilityBi; ///< A vector of probability values for Bismuth Beta events (1 for each time residual value in fTimes), to be used to create the Bismuth Beta time residual PDF
      std::vector<double> fProbabilityPo; ///< A vector of probability values for Polonium Alpha events (1 for each time residual value in fTimes), to be used to create the Polonium Alpha time residual PDF
      G4PhysicsOrderedFreeVector* fBasePDFTe; ///< The time residuals PDF for Te events
      G4PhysicsOrderedFreeVector* fBasePDFBi; ///< The time residuals PDF for Bismuth Beta decay events (either 212 or 214)
      G4PhysicsOrderedFreeVector* fBasePDFPo; ///< The time residuals PDF for Polonium Alpha decay events (either 212 or 214)
      int fMeanPoAlphaNhits; ///< The mean Nhits of a Polonium Alpha decay (either 212 or 214)
      double fTriggerWindowStart; ///< The time (in ns) of the start of the trigger window with respect to the event's time
      double fTriggerWindowEnd; ///< The time (in ns) of the end of the trigger window with respect to the event's time
      DU::Point3D fEventPosition; ///< The fitted event position, used for calculating the event's time residuals
      double fEventTime; ///< The fitted event time, used for calculating the event's time residuals
      std::vector<double> fTimeResiduals; ///< A vector of time residuals offset by the 10th earliest time residual (is filled within the GetClassification function)
      double fNHitsWithinWindow; ///< The number of hit PMTs that have a raw time residual in the time window between fTriggerWindowStart and fTriggerWindowEnd (is calculated within the GetClassification function)
      std::vector<double> fParams;
      std::vector<double> fPositiveErrors;
      std::vector<double> fNegativeErrors;
      DU::TimeResidualCalculator fTRCalc; ///< Time residual calculator for a given run
      size_t fPSUPSystemId; // coordinate system id for Point3D
    };
  } //::Classifier
} //::RAT

#endif