/**************************************************************************
* Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
*                                                                        *
* Author: The ALICE Off-line Project.                                    *
* Contributors are mentioned in the code where appropriate.              *
*                                                                        *
* Permission to use, copy, modify and distribute this software and its   *
* documentation strictly for non-commercial purposes is hereby granted   *
* without fee, provided that the above copyright notice appears in all   *
* copies and that both the copyright notice and this permission notice   *
* appear in the supporting documentation. The authors make no claims     *
* about the suitability of this software for any purpose. It is          *
* provided "as is" without express or implied warranty.                  *
**************************************************************************/
//
// PID Response class for the TRD detector
// Based on 1D Likelihood approach
// Calculation of probabilities using Bayesian approach
// Attention: This method is only used to separate electrons from pions
//
// Authors:
//  Markus Fasel <M.Fasel@gsi.de>
//  Anton Andronic <A.Andronic@gsi.de>
//
#include <TAxis.h>
#include <TClass.h>
#include <TDirectory.h>
#include <TFile.h>
#include <TH1.h>
#include <TKey.h>
#include <TMath.h>
#include <TObjArray.h>
#include <TROOT.h> 
#include <TString.h>
#include <TSystem.h>

#include "AliLog.h"
 
#include "AliVTrack.h"

#include "AliTRDPIDResponseObject.h"
#include "AliTRDPIDResponse.h"
//#include "AliTRDTKDInterpolator.h"
#include "AliTRDNDFast.h"
#include "AliTRDdEdxParams.h"

ClassImp(AliTRDPIDResponse)

//____________________________________________________________
AliTRDPIDResponse::AliTRDPIDResponse():
  TObject()
  ,fkPIDResponseObject(NULL)
  ,fkTRDdEdxParams(NULL)
  ,fGainNormalisationFactor(1.)
{
  //
  // Default constructor
  //
}

//____________________________________________________________
AliTRDPIDResponse::AliTRDPIDResponse(const AliTRDPIDResponse &ref):
  TObject(ref)
  ,fkPIDResponseObject(NULL)
  ,fkTRDdEdxParams(NULL)
  ,fGainNormalisationFactor(ref.fGainNormalisationFactor)
{
  //
  // Copy constructor
  //
}

//____________________________________________________________
AliTRDPIDResponse &AliTRDPIDResponse::operator=(const AliTRDPIDResponse &ref){
  //
  // Assignment operator
  //
  if(this == &ref) return *this;
  
  // Make copy
  TObject::operator=(ref);
  fGainNormalisationFactor = ref.fGainNormalisationFactor;
  fkPIDResponseObject = ref.fkPIDResponseObject;
  fkTRDdEdxParams = ref.fkTRDdEdxParams;

  return *this;
}

//____________________________________________________________
AliTRDPIDResponse::~AliTRDPIDResponse(){
  //
  // Destructor
  //
  if(IsOwner()) {
    delete fkPIDResponseObject;
    delete fkTRDdEdxParams;
  }
}

//____________________________________________________________
Bool_t AliTRDPIDResponse::Load(const Char_t * filename){
  //
  // Load References into the toolkit
  //
  AliDebug(1, "Loading reference histos from root file");
  TDirectory *owd = gDirectory;// store old working directory
  
  if(!filename)
    filename = Form("%s/STEER/LQ1dRef_v1.root",gSystem->ExpandPathName("$ALICE_ROOT"));
  TFile *in = TFile::Open(filename);
  if(!in){
    AliError("Ref file not available.");
    return kFALSE;
  }
  
  gROOT->cd();
  fkPIDResponseObject = dynamic_cast<const AliTRDPIDResponseObject *>(in->Get("TRDPIDResponse")->Clone());
  in->Close(); delete in;
  owd->cd();
  SetBit(kIsOwner, kTRUE);
  AliDebug(2, Form("Successfully loaded References for %d Momentum bins", fkPIDResponseObject->GetNumberOfMomentumBins()));
  return kTRUE;
}



//____________________________________________________________
Double_t AliTRDPIDResponse::GetNumberOfSigmas(const AliVTrack *track, AliPID::EParticleType type) const
{
  //
  //calculate the TRD nSigma
  //

  const Double_t badval = -9999;
  Double_t info[5]; for(int i=0; i<5; i++){info[i]=badval;}

  const Double_t delta = GetSignalDelta(track, type, kFALSE, info);

  const Double_t mean = info[0];
  const Double_t res = info[1];
  if(res<0){
    return badval;
  }

  const Double_t sigma = mean*res;
  const Double_t eps = 1e-12;
  return delta/(sigma + eps);
}

//____________________________________________________________
Double_t AliTRDPIDResponse::GetSignalDelta( const AliVTrack* track, AliPID::EParticleType type, Bool_t ratio/*=kFALSE*/, Double_t *info/*=0x0*/) const
{
  //
  //calculate the TRD signal difference w.r.t. the expected
  //output other information in info[]
  //

  const Double_t badval = -9999;

  //cut on number of chambers
  const Double_t cutch = 6;

  //cut on mean number of clusters per chamber
  const Double_t cutclsperch = 18;

  const Double_t nch = track->GetTRDNchamberdEdx();
  if(nch < cutch){
    return badval;
  }

  const Double_t ncls = track->GetTRDNclusterdEdx();
  if( ncls/nch < cutclsperch){
    return badval;
  }

  Double_t pTRD = -999;
  for(Int_t ich=0; ich<6; ich++){
    pTRD = track->GetTRDmomentum(ich);
    if(pTRD>0)
      break;
  }
  if(pTRD<0){
    return badval;
  }

  if(!fkTRDdEdxParams){
    AliError("AliTRDPIDResponse::GetSignalDelta fkTRDdEdxParams null");
    return -99999;
  }

  TVectorF meanvec = fkTRDdEdxParams->GetMeanParameter(type);
  TVectorF resvec  = fkTRDdEdxParams->GetSigmaParameter(type);

  Double_t meanpar[meanvec.GetNrows()];
  Double_t respar[resvec.GetNrows()];

  for(Int_t ii=0; ii<meanvec.GetNrows(); ii++){
    meanpar[ii]=meanvec[ii];
  }
  for(Int_t ii=0; ii<resvec.GetNrows(); ii++){
    respar[ii]=resvec[ii];
  }

  //============================================================================================<<<<<<<<<<<<<

  const Double_t bg = pTRD/AliPID::ParticleMass(type);
  const Double_t expsig = MeandEdxTR(&bg, meanpar);

  if(info){
    info[0]= expsig;
    info[1]= ResolutiondEdxTR(&ncls, respar);
  }

  const Double_t eps = 1e-10;

  if(ratio){
    return track->GetTRDsignal()/(expsig +  eps);
  }
  else{
    return track->GetTRDsignal() - expsig;
  }
}


Double_t AliTRDPIDResponse::ResolutiondEdxTR(const Double_t * xx,  const Double_t * par)
{
  //
  //resolution 
  //npar=3
  //

  const Double_t ncls = xx[0];

  return par[0]+par[1]*TMath::Power(ncls, par[2]);
}

Double_t AliTRDPIDResponse::MeandEdxTR(const Double_t * xx,  const Double_t * pin)
{
  //
  //ALEPH+LOGISTIC parametrization for dEdx+TR, in unit of MIP
  //npar = 8 = 3+5
  //

  Double_t ptr[4]={0};
  for(int ii=0; ii<3; ii++){
    ptr[ii+1]=pin[ii];
  }
  return MeanTR(xx,ptr) + MeandEdx(xx,&(pin[3]));
}

Double_t AliTRDPIDResponse::MeanTR(const Double_t * xx,  const Double_t * par)
{
  //
  //LOGISTIC parametrization for TR, in unit of MIP
  //npar = 4
  //
                                                                                                                                                                                                                                                        
  const Double_t bg = xx[0];
  const Double_t gamma = sqrt(1+bg*bg);

  const Double_t p0 = TMath::Abs(par[1]);
  const Double_t p1 = TMath::Abs(par[2]);
  const Double_t p2 = TMath::Abs(par[3]);

  const Double_t zz = TMath::Log(gamma);
  const Double_t tryield = p0/( 1 + TMath::Exp(-p1*(zz-p2)) );

  return par[0]+tryield;
}

Double_t AliTRDPIDResponse::MeandEdx(const Double_t * xx,  const Double_t * par)
{
  //
  //ALEPH parametrization for dEdx
  //npar = 5
  //

  const Double_t bg = xx[0];
  const Double_t beta = bg/TMath::Sqrt(1.+ bg*bg);

  const Double_t p0 = TMath::Abs(par[0]);
  const Double_t p1 = TMath::Abs(par[1]);

  const Double_t p2 = TMath::Abs(par[2]);

  const Double_t p3 = TMath::Abs(par[3]);
  const Double_t p4 = TMath::Abs(par[4]);

  const Double_t aa = TMath::Power(beta, p3);

  const Double_t bb = TMath::Log( p2 + TMath::Power(1./bg, p4) );

  return (p1-aa-bb)*p0/aa;

}


//____________________________________________________________
Int_t AliTRDPIDResponse::GetResponse(Int_t n, const Double_t * const dedx, const Float_t * const p, Double_t prob[AliPID::kSPECIES],ETRDPIDMethod PIDmethod,Bool_t kNorm) const
{
  //
  // Calculate TRD likelihood values for the track based on dedx and 
  // momentum values. The likelihoods are calculated by query the 
  // reference data depending on the PID method selected
  //
  // Input parameter :
  //   n - number of dedx slices/chamber
  //   dedx - array of dedx slices organized layer wise
  //   p - array of momentum measurements organized layer wise
  // 
  // Return parameters
  //   prob - probabilities allocated by TRD for particle specis
  //   kNorm - switch to normalize probabilities to 1. By default true. If false return not normalized prob.
  // 
  // Return value
  //   number of tracklets used for PID, 0 if no PID
    //
    AliDebug(3,Form(" Response for PID method: %d",PIDmethod));


    if(!fkPIDResponseObject){
	AliDebug(3,"Missing reference data. PID calculation not possible.");
	return 0;
    }

    for(Int_t is(AliPID::kSPECIES); is--;) prob[is]=.2;
    Double_t prLayer[AliPID::kSPECIES];
    Double_t dE[10], s(0.);
    Int_t ntrackletsPID=0;
    for(Int_t il(kNlayer); il--;){
	memset(prLayer, 0, AliPID::kSPECIES*sizeof(Double_t));
	if(!CookdEdx(n, &dedx[il*n], &dE[0],PIDmethod)) continue;
        s=0.;
        Bool_t filled=kTRUE;
	for(Int_t is(AliPID::kSPECIES); is--;){
	    //if((PIDmethod==kLQ2D)&&(!(is==0||is==2)))continue;
	    if((dE[0] > 0.) && (p[il] > 0.)) prLayer[is] = GetProbabilitySingleLayer(is, p[il], &dE[0],PIDmethod);
	    AliDebug(3, Form("Probability for Species %d in Layer %d: %e", is, il, prLayer[is]));
	    if(prLayer[is]<1.e-30){
		AliDebug(2, Form("Null for species %d species prob layer[%d].",is,il));
		filled=kFALSE;
		break;
	    }
	    s+=prLayer[is];
	}
	if(!filled){
	    continue;
	}
	if(s<1.e-30){
	    AliDebug(2, Form("Null all species prob layer[%d].", il));
	    continue;
	}
	for(Int_t is(AliPID::kSPECIES); is--;){
	    if(kNorm) prLayer[is] /= s;
	    prob[is] *= prLayer[is];
	}
	ntrackletsPID++;
    }
    if(!kNorm) return ntrackletsPID;

    s=0.;
    for(Int_t is(AliPID::kSPECIES); is--;) s+=prob[is];
    if(s<1.e-30){
	AliDebug(2, "Null total prob.");
	return 0;
    }
    for(Int_t is(AliPID::kSPECIES); is--;) prob[is]/=s;
    return ntrackletsPID;
}

//____________________________________________________________
Double_t AliTRDPIDResponse::GetProbabilitySingleLayer(Int_t species, Double_t plocal, Double_t *dEdx,ETRDPIDMethod PIDmethod) const {
  //
  // Get the non-normalized probability for a certain particle species as coming
  // from the reference histogram
  // Interpolation between momentum bins
  //
  AliDebug(1, Form("Make Probability for Species %d with Momentum %f", species, plocal));

  Double_t probLayer = 0.;

  Float_t pLower, pUpper;
	
  AliTRDNDFast *refUpper = dynamic_cast<AliTRDNDFast *>(fkPIDResponseObject->GetUpperReference((AliPID::EParticleType)species, plocal, pUpper,PIDmethod)),
      *refLower = dynamic_cast<AliTRDNDFast *>(fkPIDResponseObject->GetLowerReference((AliPID::EParticleType)species, plocal, pLower,PIDmethod));

  // Do Interpolation exept for underflow and overflow
  if(refLower && refUpper){
      Double_t probLower = refLower->Eval(dEdx);
      Double_t probUpper = refUpper->Eval(dEdx);

      probLayer = probLower + (probUpper - probLower)/(pUpper-pLower) * (plocal - pLower);
  } else if(refLower){
     // underflow
      probLayer = refLower->Eval(dEdx);
  } else if(refUpper){
      // overflow
      probLayer = refUpper->Eval(dEdx);
  } else {
      AliError("No references available");
  }
  AliDebug(1, Form("Eval 1D dEdx %f Probability %e", dEdx[0],probLayer));

  return probLayer;

/* old implementation

switch(PIDmethod){
case kNN: // NN
      break;
  case kLQ2D: // 2D LQ
      {
	  if(species==0||species==2){ // references only for electrons and pions
	      Double_t error = 0.;
	      Double_t point[kNslicesLQ2D];
	      for(Int_t idim=0;idim<kNslicesLQ2D;idim++){point[idim]=dEdx[idim];}

	      AliTRDTKDInterpolator *refUpper = dynamic_cast<AliTRDTKDInterpolator *>(fkPIDResponseObject->GetUpperReference((AliPID::EParticleType)species, plocal, pUpper,kLQ2D)),
	      *refLower = dynamic_cast<AliTRDTKDInterpolator *>(fkPIDResponseObject->GetLowerReference((AliPID::EParticleType)species, plocal, pLower,kLQ2D));
	      // Do Interpolation exept for underflow and overflow
	      if(refLower && refUpper){
                  Double_t probLower=0,probUpper=0;
		  refLower->Eval(point,probLower,error);
                  refUpper->Eval(point,probUpper,error);
		  probLayer = probLower + (probUpper - probLower)/(pUpper-pLower) * (plocal - pLower);
	      } else if(refLower){
		  // underflow
		  refLower->Eval(point,probLayer,error);
		  } else if(refUpper){
		  // overflow
		  refUpper->Eval(point,probLayer,error);
	      } else {
		  AliError("No references available");
	      }
	      AliDebug(2,Form("Eval 2D Q0 %f Q1 %f P %e Err %e",point[0],point[1],probLayer,error));
	  }
      }
      break;
  case kLQ1D: // 1D LQ
      {
	  TH1 *refUpper = dynamic_cast<TH1 *>(fkPIDResponseObject->GetUpperReference((AliPID::EParticleType)species, plocal, pUpper,kLQ1D)),
	      *refLower = dynamic_cast<TH1 *>(fkPIDResponseObject->GetLowerReference((AliPID::EParticleType)species, plocal, pLower,kLQ1D));
	  // Do Interpolation exept for underflow and overflow
	  if(refLower && refUpper){
	      Double_t probLower = refLower->GetBinContent(refLower->GetXaxis()->FindBin(dEdx[0]));
	      Double_t probUpper = refUpper->GetBinContent(refUpper->GetXaxis()->FindBin(dEdx[0]));

	      probLayer = probLower + (probUpper - probLower)/(pUpper-pLower) * (plocal - pLower);
	  } else if(refLower){
	      // underflow
	      probLayer = refLower->GetBinContent(refLower->GetXaxis()->FindBin(dEdx[0]));
	  } else if(refUpper){
	      // overflow
	      probLayer = refUpper->GetBinContent(refUpper->GetXaxis()->FindBin(dEdx[0]));
	  } else {
	      AliError("No references available");
	  }
	  AliDebug(1, Form("Eval 1D dEdx %f Probability %e", dEdx[0],probLayer));
      }
      break;
  default:
      break;
      }
      return probLayer;
      */

}

//____________________________________________________________
void AliTRDPIDResponse::SetOwner(){
  //
  // Make Deep Copy of the Reference Histograms
  //
    if(!fkPIDResponseObject || IsOwner()) return;
    const AliTRDPIDResponseObject *tmp = fkPIDResponseObject;
    fkPIDResponseObject = dynamic_cast<const AliTRDPIDResponseObject *>(tmp->Clone());
    SetBit(kIsOwner, kTRUE);
}

//____________________________________________________________
Bool_t AliTRDPIDResponse::CookdEdx(Int_t nSlice, const Double_t * const in, Double_t *out,ETRDPIDMethod PIDmethod) const
{
    //
    // Recalculate dE/dx
    //
  switch(PIDmethod){
  case kNN: // NN 
      break;
  case kLQ2D: // 2D LQ
      out[0]=0;
      out[1]=0;
      for(Int_t islice = 0; islice < nSlice; islice++){
	  if(in[islice]<=0){out[0]=0;out[1]=0;return kFALSE;}  // Require that all slices are filled
	  if(islice<fkPIDResponseObject->GetNSlicesQ0())out[0]+= in[islice];
	  else out[1]+= in[islice];
      }
      // normalize signal to number of slices
      out[0]*=1./Double_t(fkPIDResponseObject->GetNSlicesQ0());
      out[1]*=1./Double_t(nSlice-fkPIDResponseObject->GetNSlicesQ0());
      if(out[0] < 1e-6) return kFALSE;
      AliDebug(3,Form("CookdEdx Q0 %f Q1 %f",out[0],out[1]));
      break;
  case kLQ1D: // 1D LQ
      out[0]= 0.;
      for(Int_t islice = 0; islice < nSlice; islice++)
	  if(in[islice] > 0) out[0] += in[islice] * fGainNormalisationFactor;   // Protect against negative values for slices having no dE/dx information
      out[0]*=1./Double_t(nSlice);
      if(out[0] < 1e-6) return kFALSE;
      AliDebug(3,Form("CookdEdx dEdx %f",out[0]));
      break;

  default:
      return kFALSE;
  }
  return kTRUE;
}

//____________________________________________________________
Bool_t AliTRDPIDResponse::IdentifiedAsElectron(Int_t nTracklets, const Double_t *like, Double_t p, Double_t level,Double_t centrality,ETRDPIDMethod PIDmethod) const {
    //
    // Check whether particle is identified as electron assuming a certain electron efficiency level
    // Only electron and pion hypothesis is taken into account
    //
    // Inputs:
    //         Number of tracklets
    //         Likelihood values
    //         Momentum
    //         Electron efficiency level
    //
    // If the function fails when the params are not accessible, the function returns true
    //
  if(!fkPIDResponseObject){
    AliDebug(3,"No PID Param object available");
    return kTRUE;
  } 
  Double_t probEle = like[AliPID::kElectron]/(like[AliPID::kElectron] + like[AliPID::kPion]);
  Double_t params[4];
  if(!fkPIDResponseObject->GetThresholdParameters(nTracklets, level, params,centrality,PIDmethod)){
    AliError("No Params found for the given configuration");
    return kTRUE;
  }
  Double_t threshold = 1. - params[0] - params[1] * p - params[2] * TMath::Exp(-params[3] * p);
  if(probEle > TMath::Max(TMath::Min(threshold, 0.99), 0.2)) return kTRUE; // truncate the threshold upperwards to 0.999 and lowerwards to 0.2 and exclude unphysical values
  return kFALSE;
}

//____________________________________________________________
Bool_t AliTRDPIDResponse::SetPIDResponseObject(const AliTRDPIDResponseObject * obj){

    fkPIDResponseObject = obj;
    if((AliLog::GetDebugLevel("",IsA()->GetName()))>0)fkPIDResponseObject->Print("");
    return kTRUE;
}


//____________________________________________________________    
Bool_t AliTRDPIDResponse::SetdEdxParams(const AliTRDdEdxParams * par)
{
  fkTRDdEdxParams = par;
  return kTRUE;
}