/**************************************************************************
 * 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.                  *
 **************************************************************************/
 

//---------------------------------------------------------------------
// FastJet v2.3.4 finder algorithm interface
// Last modification: Neutral cell energy included in the jet reconstruction
//
// Authors: Rafael.Diaz.Valdes@cern.ch
//          Magali.estienne@subatech.in2p3.fr (neutral part + bg subtraction option)
//
//---------------------------------------------------------------------


#include <Riostream.h>
#include <TLorentzVector.h>
#include <TFile.h>
#include <TH1F.h>
#include <TH2F.h>
#include <TArrayF.h>
#include <TClonesArray.h>

#include "AliFastJetFinder.h"
#include "AliFastJetHeaderV1.h"
#include "AliJetReaderHeader.h"
#include "AliJetReader.h"
#include "AliJetUnitArray.h"
#include "AliFastJetInput.h"
#include "AliJetBkg.h"
#include "AliAODJetEventBackground.h"
#include "AliAODTrack.h"

#include "fastjet/PseudoJet.hh"
#include "fastjet/ClusterSequenceArea.hh"
#include "fastjet/AreaDefinition.hh"
#include "fastjet/JetDefinition.hh"
// get info on how fastjet was configured
#include "fastjet/config.h"

#ifdef ENABLE_PLUGIN_SISCONE
#include "fastjet/SISConePlugin.hh"
#endif

#include<sstream>  // needed for internal io
#include<vector> 
#include <cmath> 

using namespace std;


ClassImp(AliFastJetFinder)


//____________________________________________________________________________

AliFastJetFinder::AliFastJetFinder():
  AliJetFinder(),
  fInputFJ(new AliFastJetInput()),
  fJetBkg(new  AliJetBkg())
{
  // Constructor
}

//____________________________________________________________________________

AliFastJetFinder::~AliFastJetFinder()
{
  // destructor
  delete  fInputFJ; fInputFJ = 0;
  delete  fJetBkg; fJetBkg = 0;
}

//______________________________________________________________________________
void AliFastJetFinder::FindJets()
{

  //pick up fastjet header
  AliFastJetHeaderV1 *header = (AliFastJetHeaderV1*)fHeader;
  Int_t  debug  = header->GetDebug();     // debug option
  Bool_t bgMode = header->GetBGMode();    // choose to subtract BG or not
  if(debug)cout<<"----------in AliFastJetFinder::FindJets() ------------------"<<endl;

  // check if we are reading AOD jets
  TRefArray *refs = 0;
  Bool_t fromAod = !strcmp(fReader->ClassName(),"AliJetAODReader");
  if (fromAod) { refs = fReader->GetReferences(); }

  // RUN ALGORITHM  
  // read input particles -----------------------------

  vector<fastjet::PseudoJet> inputParticles=fInputFJ->GetInputParticles();
  if(inputParticles.size()==0){
    if(debug)Printf("%s:%d No input particles found, skipping event",(char*)__FILE__,__LINE__);
    return;
  }

  // create an object that represents your choice of jet algorithm, and 
  // the associated parameters
  double rParam = header->GetRparam();
  double rBkgParam = header->GetRparamBkg();
  fastjet::Strategy strategy = header->GetStrategy();
  fastjet::RecombinationScheme recombScheme = header->GetRecombScheme();
  fastjet::JetAlgorithm algorithm = header->GetAlgorithm(); 
  fastjet::JetDefinition jetDef(algorithm, rParam, recombScheme, strategy);

  // create an object that specifies how we to define the area
  fastjet::AreaDefinition areaDef;
  double ghostEtamax = header->GetGhostEtaMax(); 
  double ghostArea   = header->GetGhostArea(); 
  int    activeAreaRepeats = header->GetActiveAreaRepeats(); 
  
  // now create the object that holds info about ghosts
  fastjet::GhostedAreaSpec ghostSpec(ghostEtamax, activeAreaRepeats, ghostArea);
  // and from that get an area definition
  fastjet::AreaType areaType = header->GetAreaType();
  areaDef = fastjet::AreaDefinition(areaType,ghostSpec);
  
  //***************************** JETS FINDING
  // run the jet clustering with the above jet definition
  fastjet::ClusterSequenceArea clust_seq(inputParticles, jetDef, areaDef);

  vector<fastjet::PseudoJet> jets;

  if(bgMode) // Do BG subtraction directly with the same algorithm (cambridge or kt) for jet signal and background
    {
      //***************************** CLUSTER JETS FINDING FOR RHO ESTIMATION
      // run the jet clustering with the above jet definition
	  fastjet::JetAlgorithm algorithmBkg = header->GetBGAlgorithm();
	  fastjet::JetDefinition jetDefBkg(algorithmBkg, rBkgParam, recombScheme, strategy);
      fastjet::ClusterSequenceArea clust_seq_bkg(inputParticles, jetDefBkg, areaDef);

      // save a comment in the header
      TString comment = "Running FastJet algorithm with the following setup. ";
      comment+= "Jet definition: ";
      comment+= TString(jetDef.description());
      comment+= "Jet bckg definition: ";
      comment+= TString(jetDefBkg.description());
      comment+= ". Area definition: ";
      comment+= TString(areaDef.description());
      comment+= ". Strategy adopted by FastJet and bkg: ";
      comment+= TString(clust_seq.strategy_string());
      header->SetComment(comment);
      if(debug){
          cout << "--------------------------------------------------------" << endl;
          cout << comment << endl;
          cout << "--------------------------------------------------------" << endl;
      }
      //header->PrintParameters();
      
      // extract the inclusive jets with pt > ptmin, sorted by pt
      double ptmin = header->GetPtMin(); 
      vector<fastjet::PseudoJet> inclusiveJets = clust_seq.inclusive_jets();

      //subtract background // ===========================================
      // set the rapididty , phi range within which to study the background 
      double rapMax = header->GetRapMax(); 
      double rapMin = header->GetRapMin();
      double phiMax = header->GetPhiMax();
      double phiMin = header->GetPhiMin();
      fastjet::RangeDefinition range(rapMin, rapMax, phiMin, phiMax);
      
      // Extract rho and sigma
      Double_t rho = 0.;
      Double_t sigma = 0.;
      Double_t meanarea = 0.;
      Bool_t Use4VectorArea = header->Use4VectorArea();
      vector<fastjet::PseudoJet> bkgJets = clust_seq_bkg.inclusive_jets();
      clust_seq_bkg.get_median_rho_and_sigma(bkgJets,range, Use4VectorArea, rho, sigma, meanarea, false);

	  // subtract background and extract jets bkg subtracted
      vector<fastjet::PseudoJet> subJets = clust_seq.subtracted_jets(rho,ptmin);

	  // print out
      //cout << "Printing inclusive sub jets with pt > "<< ptmin<<" GeV\n";
      //cout << "---------------------------------------\n";
      //cout << endl;
      //printf(" ijet   rap      phi        Pt         area  +-   err\n");
      
      // sort jets into increasing pt
      jets = sorted_by_pt(subJets);  

    }
  else { // No BG subtraction!!!!!!!! Default header is bgmode=0.

	  // save a comment in the header
	  TString comment = "Running FastJet algorithm with the following setup. ";
	  comment+= "Jet definition: ";
	  comment+= TString(jetDef.description());
	  comment+= ". Strategy adopted by FastJet: ";
	  comment+= TString(clust_seq.strategy_string());
	  header->SetComment(comment);
	  if(debug){
		  cout << "--------------------------------------------------------" << endl;
		  cout << comment << endl;
		  cout << "--------------------------------------------------------" << endl;
	  }
	  //header->PrintParameters();

	  // extract the inclusive jets with pt > ptmin, sorted by pt
	  double ptmin = header->GetPtMin();
	  vector<fastjet::PseudoJet> inclusiveJets = clust_seq.inclusive_jets(ptmin);

	  jets = sorted_by_pt(inclusiveJets); // Added by me

  }

  for (size_t j = 0; j < jets.size(); j++) { // loop for jets

	  double area      = clust_seq.area(jets[j]);
	  double areaError = clust_seq.area_error(jets[j]);

	  if(debug) printf("Jet found %5d %9.5f %8.5f %10.3f %8.3f +- %6.3f\n", (Int_t)j,jets[j].rap(),jets[j].phi(),jets[j].perp(), area, areaError);

      vector<fastjet::PseudoJet> constituents = clust_seq.constituents(jets[j]);
      int nCon= constituents.size();
      TArrayI ind(nCon);
      
      if ((jets[j].eta() > (header->GetJetEtaMax())) ||
          (jets[j].eta() < (header->GetJetEtaMin())) ||
          (jets[j].phi() > (header->GetJetPhiMax())) ||
          (jets[j].phi() < (header->GetJetPhiMin())) ||
          (jets[j].perp() < header->GetPtMin())) continue; // acceptance eta range and etmin

	  // go to write AOD  info
	  AliAODJet aodjet (jets[j].px(), jets[j].py(), jets[j].pz(), jets[j].E());
      aodjet.SetEffArea(area,areaError);
	  //cout << "Printing jet " << endl;
	  if(debug) aodjet.Print("");

	  Int_t count=0;
	  for (int i=0; i < nCon; i++)
	  {
		  fastjet::PseudoJet mPart=constituents[i];
		  ind[i]=mPart.user_index();
		  //	cout<<i<<"  index="<<ind[i]<<endl;

		  if(fromAod)
		  {
			  if(fReader->GetReaderHeader()->GetDetector()==0)
			  {
				  for (Int_t iref = 0; iref < refs->GetEntries(); iref++)
				  {
					  if(iref==ind[i]){
						  AliAODTrack * track = (AliAODTrack*)refs->At(iref);
						  aodjet.AddTrack(track);
					  }
				  }

			  } else {

				  TClonesArray* fUnit = fReader->GetUnitArray(); //Big mmentum array
				  if(fUnit == 0) { cout << "Could not get the momentum array" << endl; return; }
				  Int_t         nIn = fUnit->GetEntries();

				  //internal loop over all the unit cells
				  Int_t ipart = 0;

				  for(Int_t ii=0; ii<nIn; ii++)
				  {
					  AliJetUnitArray *uArray = (AliJetUnitArray*)fUnit->At(ii);
					  if(uArray->GetUnitEnergy()>0.){
						  uArray->SetUnitTrackID(ipart);//used to have the index available in AliJEtBkg
						  if(ipart==ind[i]){
							  TRefArray* trackArray = (TRefArray*)uArray->GetUnitTrackRef();
							  Int_t tracksInCell = trackArray->GetEntries();
							  for(int ji = 0; ji < tracksInCell; ji++){
								  AliAODTrack * track = (AliAODTrack*)trackArray->At(ji);
								  aodjet.AddTrack(track);
							  }

							  count++;
						  }
						  ipart++;
					  }
				  }
			  }
		  }
	 } 

 AddJet(aodjet);


  } // End loop on jets

}

//____________________________________________________________________________
void AliFastJetFinder::RunTest(const char* datafile)

{

   // This simple test run the kt algorithm for an ascii file testdata.dat
   // read input particles -----------------------------
  vector<fastjet::PseudoJet> inputParticles;
  Float_t px,py,pz,en;
  ifstream in;
  Int_t nlines = 0;
  // we assume a file basic.dat in the current directory
  // this file has 3 columns of float data
  in.open(datafile);
  while (1) {
      in >> px >> py >> pz >> en;
      if (!in.good()) break;
      //printf("px=%8f, py=%8f, pz=%8fn",px,py,pz);
      nlines++;
      inputParticles.push_back(fastjet::PseudoJet(px,py,pz,en)); 
   }
   //printf(" found %d pointsn",nlines);
   in.close();
   //////////////////////////////////////////////////
 
  // create an object that represents your choice of jet algorithm, and 
  // the associated parameters
  double rParam = 1.0;
  fastjet::Strategy strategy = fastjet::Best;
  fastjet::RecombinationScheme recombScheme = fastjet::BIpt_scheme;
  fastjet::JetDefinition jetDef(fastjet::kt_algorithm, rParam, recombScheme, strategy);
  
  
 
  // create an object that specifies how we to define the area
  fastjet::AreaDefinition areaDef;
  double ghostEtamax = 7.0;
  double ghostArea    = 0.05;
  int    activeAreaRepeats = 1;
  

  // now create the object that holds info about ghosts
  fastjet::GhostedAreaSpec ghostSpec(ghostEtamax, activeAreaRepeats, ghostArea);
  // and from that get an area definition
  areaDef = fastjet::AreaDefinition(fastjet::active_area,ghostSpec);
  

  // run the jet clustering with the above jet definition
  fastjet::ClusterSequenceArea clust_seq(inputParticles, jetDef, areaDef);
  
  
  // tell the user what was done
  cout << "--------------------------------------------------------" << endl;
  cout << "Jet definition was: " << jetDef.description() << endl;
  cout << "Area definition was: " << areaDef.description() << endl;
  cout << "Strategy adopted by FastJet was "<< clust_seq.strategy_string()<<endl<<endl;
  cout << "--------------------------------------------------------" << endl;
 
  
  // extract the inclusive jets with pt > 5 GeV, sorted by pt
  double ptmin = 5.0;
  vector<fastjet::PseudoJet> inclusiveJets = clust_seq.inclusive_jets(ptmin);
  
  cout << "Number of unclustered particles: " << clust_seq.unclustered_particles().size() << endl;
 
 
  //subtract background // ===========================================
  // set the rapididty range within which to study the background 
  double rapMax = ghostEtamax - rParam;
  fastjet::RangeDefinition range(rapMax);
  // subtract background
  vector<fastjet::PseudoJet> subJets =  clust_seq.subtracted_jets(range,ptmin);  
  
  // print them out //================================================
  cout << "Printing inclusive jets  after background subtraction \n";
  cout << "------------------------------------------------------\n";
  // sort jets into increasing pt
  vector<fastjet::PseudoJet> jets = sorted_by_pt(subJets);  

  printf(" ijet   rap      phi        Pt         area  +-   err\n");
  for (size_t j = 0; j < jets.size(); j++) {

    double area     = clust_seq.area(jets[j]);
    double areaError = clust_seq.area_error(jets[j]);

    printf("%5d %9.5f %8.5f %10.3f %8.3f +- %6.3f\n",(Int_t)j,jets[j].rap(),
	   jets[j].phi(),jets[j].perp(), area, areaError);
  }
  cout << endl;
  // ================================================================

  
 
}

//____________________________________________________________________________

void AliFastJetFinder::WriteJHeaderToFile() const
{
  fHeader->Write();
}

//____________________________________________________________________________

Float_t  AliFastJetFinder::EtaToTheta(Float_t arg)
{
  //  return (180./TMath::Pi())*2.*atan(exp(-arg));
  return 2.*atan(exp(-arg));


}

//____________________________________________________________________________

void AliFastJetFinder::InitTask(TChain *tree)
{

  printf("Fast jet finder initialization ******************");
  fReader->CreateTasks(tree);

}


Bool_t AliFastJetFinder::ProcessEvent()
{
  //
  // Process one event
  // from meomntum array

  Bool_t ok = fReader->FillMomentumArray();

  if (!ok) return kFALSE;
  fInputFJ->SetHeader(fHeader);
  fInputFJ->SetReader(fReader);
  fInputFJ->FillInput();
  // Jets
  FindJets(); 


  if( fAODEvBkg){
    fJetBkg->SetHeader(fHeader);
    fJetBkg->SetReader(fReader);
    Double_t sigma1 = 0,meanarea1= 0,sigma2 = 0,meanarea2 = 0;
    Double_t bkg1 = 0,bkg2 = 0;
    
    fJetBkg->SetFastJetInput(fInputFJ);
    fJetBkg->BkgFastJetb(bkg1,sigma1,meanarea1);
    fJetBkg->BkgFastJetWoHardest(bkg2,sigma2,meanarea2);
    fAODEvBkg->SetBackground(0,bkg1,sigma1,meanarea1);
    fAODEvBkg->SetBackground(1,bkg2,sigma2,meanarea2);
  }




  /*
  fJetBkg->SetFastJetInput(fInputFJ);
  Double_t bkg1=fJetBkg->BkgFastJet();
  Double_t bkg2=fJetBkg->BkgChargedFastJet();
  Double_t bkg3=fJetBkg->BkgFastJetCone(fAODjets);
  Double_t bkg4=fJetBkg->BkgRemoveJetLeading(fAODjets);
  
  fAODEvBkg->SetBackground(0,bkg1);
  fAODEvBkg->SetBackground(1,bkg2);
  fAODEvBkg->SetBackground(2,bkg3);
  fAODEvBkg->SetBackground(3,bkg4);
  */
  Reset();  
  return kTRUE;

}

Bool_t AliFastJetFinder::ProcessEvent2()
{
  //
  // Process one event
  // Charged only or charged+neutral jets
  //

  TRefArray* ref = new TRefArray();
  Bool_t procid = kFALSE;
  Bool_t ok = fReader->ExecTasks(procid,ref);

  // Delete reference pointer  
  if (!ok) {delete ref; return kFALSE;}
  
  // Leading particles
  fInputFJ->SetHeader(fHeader);
  fInputFJ->SetReader(fReader);
  fInputFJ->FillInput();
  
  // Jets
  FindJets();
  
  if( fAODEvBkg){
    fJetBkg->SetHeader(fHeader);
    fJetBkg->SetReader(fReader);
    fJetBkg->SetFastJetInput(fInputFJ);
    Double_t sigma1,meanarea1,sigma2,meanarea2;
    Double_t bkg1,bkg2;
    fJetBkg->BkgFastJetb(bkg1,sigma1,meanarea1);
    fJetBkg->BkgFastJetWoHardest(bkg2,sigma2,meanarea2);
    fAODEvBkg->SetBackground(0,bkg1,sigma1,meanarea1);
    fAODEvBkg->SetBackground(1,bkg2,sigma2,meanarea2);
  }


//  Double_t bkg1=fJetBkg->BkgFastJet();
//  Double_t bkg2=fJetBkg->BkgChargedFastJet();
//  Double_t bkg3=fJetBkg->BkgFastJetCone(fAODjets);
//  Double_t bkg4=fJetBkg->BkgRemoveJetLeading(fAODjets);
  
//  fAODEvBkg->SetBackground(0,bkg1);
//  fAODEvBkg->SetBackground(1,bkg2);
//  fAODEvBkg->SetBackground(2,bkg3);
//  fAODEvBkg->SetBackground(3,bkg4);
  
  Int_t nEntRef    = ref->GetEntries();

  for(Int_t i=0; i<nEntRef; i++)
    { 
      // Reset the UnitArray content which were referenced
      ((AliJetUnitArray*)ref->At(i))->SetUnitTrackID(0);
      ((AliJetUnitArray*)ref->At(i))->SetUnitEnergy(0.);
      ((AliJetUnitArray*)ref->At(i))->SetUnitCutFlag(kPtSmaller);
      ((AliJetUnitArray*)ref->At(i))->SetUnitCutFlag2(kPtSmaller);
      ((AliJetUnitArray*)ref->At(i))->SetUnitSignalFlag(kBad);
      ((AliJetUnitArray*)ref->At(i))->SetUnitSignalFlagC(kTRUE,kBad);
      ((AliJetUnitArray*)ref->At(i))->SetUnitDetectorFlag(kTpc);
      ((AliJetUnitArray*)ref->At(i))->SetUnitFlag(kOutJet);
      ((AliJetUnitArray*)ref->At(i))->ClearUnitTrackRef();

      // Reset process ID
      AliJetUnitArray* uA = (AliJetUnitArray*)ref->At(i);
      uA->ResetBit(kIsReferenced);
      uA->SetUniqueID(0);     
    }

  // Delete the reference pointer
  ref->Delete();
  delete ref;

  Reset();

  return kTRUE;
}