[u/mrichter/AliRoot.git] / JETAN / AliFastJetFinder.cxx

/**************************************************************************
 * 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();
  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);
  

  if(bgMode) // BG subtraction!!!!!!!!!! Not entering here
    {
      //***************************** JETS FINDING AND EXTRACTION
      // run the jet clustering with the above jet definition
      fastjet::ClusterSequenceArea clust_seq(inputParticles, jetDef, areaDef);

      // save a comment in the header
      
      TString comment = "Running FastJet algorithm with the following setup. ";
      comment+= "Jet definition: ";
      comment+= TString(jetDef.description());
      comment+= ". Area definition: ";
      comment+= TString(areaDef.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);
      
      //cout << "Number of unclustered particles: " << clust_seq.unclustered_particles().size() << endl;
      
      
      //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);
      
      // subtract background
      vector<fastjet::PseudoJet> subJets =  clust_seq.subtracted_jets(range,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
      vector<fastjet::PseudoJet> jets = sorted_by_pt(subJets);  
      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);
	
	// go to write AOD  info
	AliAODJet aodjet (jets[j].px(), jets[j].py(), jets[j].pz(), jets[j].E());
	//cout << "Printing jet " << endl;
	if(debug) aodjet.Print("");
	//cout << "Adding jet ... " ;
	AddJet(aodjet);
	//cout << "added \n" << endl;
	
      }
    }


  else { // No BG subtraction!!!!!!!! Default header is bgmode=0.
   
    TClonesArray* fUnit = fReader->GetUnitArray(); //Big mmentum array
    if(fUnit == 0) { cout << "Could not get the momentum array" << endl; return; }
    Int_t         nIn = fUnit->GetEntries();

 
    //fastjet::ClusterSequence clust_seq(inputParticles, jetDef); 
    fastjet::ClusterSequenceArea clust_seq(inputParticles, jetDef, areaDef);
   
    // 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);
    
    //cout << "Number of unclustered particles: " << clust_seq.unclustered_particles().size() << endl;
    
    vector<fastjet::PseudoJet> jets = sorted_by_pt(inclusiveJets); // Added by me
    for (size_t j = 0; j < jets.size(); j++) { // loop for jets     // Added by me
      
      if(debug) printf("Jet found %5d %9.5f %8.5f %10.3f \n",(Int_t)j,jets[j].rap(),jets[j].phi(),jets[j].perp());

      vector<fastjet::PseudoJet> constituents = clust_seq.constituents(jets[j]);
      int nCon= constituents.size();
      TArrayI ind(nCon);
      Double_t area=clust_seq.area(jets[j]);
      // go to write AOD  info
      AliAODJet aodjet (jets[j].px(), jets[j].py(), jets[j].pz(), jets[j].E());
      aodjet.SetEffArea(area,0);
      //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;
	
	//internal loop over all the unit cells
	Int_t ipart = 0;
	//	count=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 for 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(); 

  fJetBkg->SetHeader(fHeader);
  fJetBkg->SetReader(fReader);
  Double_t sigma1,meanarea1,sigma2,meanarea2;
  Double_t bkg1,bkg2;
  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();
  
  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;
}
Commit	Line	Data
	1	/**************************************************************************
	2	* Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
	3	* *
	4	* Author: The ALICE Off-line Project. *
	5	* Contributors are mentioned in the code where appropriate. *
	6	* *
	7	* Permission to use, copy, modify and distribute this software and its *
	8	* documentation strictly for non-commercial purposes is hereby granted *
	9	* without fee, provided that the above copyright notice appears in all *
	10	* copies and that both the copyright notice and this permission notice *
	11	* appear in the supporting documentation. The authors make no claims *
	12	* about the suitability of this software for any purpose. It is *
	13	* provided "as is" without express or implied warranty. *
	14	**************************************************************************/
	15
	16
	17	//---------------------------------------------------------------------
	18	// FastJet v2.3.4 finder algorithm interface
	19	// Last modification: Neutral cell energy included in the jet reconstruction
	20	//
	21	// Authors: Rafael.Diaz.Valdes@cern.ch
	22	// Magali.estienne@subatech.in2p3.fr (neutral part + bg subtraction option)
	23	//
	24	//---------------------------------------------------------------------
	25
	26
	27	#include <Riostream.h>
	28	#include <TLorentzVector.h>
	29	#include <TFile.h>
	30	#include <TH1F.h>
	31	#include <TH2F.h>
	32	#include <TArrayF.h>
	33	#include <TClonesArray.h>
	34
	35	#include "AliFastJetFinder.h"
	36	#include "AliFastJetHeaderV1.h"
	37	#include "AliJetReaderHeader.h"
	38	#include "AliJetReader.h"
	39	#include "AliJetUnitArray.h"
	40	#include "AliFastJetInput.h"
	41	#include "AliJetBkg.h"
	42	#include "AliAODJetEventBackground.h"
	43	#include "AliAODTrack.h"
	44
	45	#include "fastjet/PseudoJet.hh"
	46	#include "fastjet/ClusterSequenceArea.hh"
	47	#include "fastjet/AreaDefinition.hh"
	48	#include "fastjet/JetDefinition.hh"
	49	// get info on how fastjet was configured
	50	#include "fastjet/config.h"
	51
	52	#ifdef ENABLE_PLUGIN_SISCONE
	53	#include "fastjet/SISConePlugin.hh"
	54	#endif
	55
	56	#include<sstream> // needed for internal io
	57	#include<vector>
	58	#include <cmath>
	59
	60	using namespace std;
	61
	62
	63	ClassImp(AliFastJetFinder)
	64
	65
	66	//____________________________________________________________________________
	67
	68	AliFastJetFinder::AliFastJetFinder():
	69	AliJetFinder(),
	70	fInputFJ(new AliFastJetInput()),
	71	fJetBkg(new AliJetBkg())
	72	{
	73	// Constructor
	74	}
	75
	76	//____________________________________________________________________________
	77
	78	AliFastJetFinder::~AliFastJetFinder()
	79	{
	80	// destructor
	81	delete fInputFJ; fInputFJ = 0;
	82	delete fJetBkg; fJetBkg = 0;
	83	}
	84
	85	//______________________________________________________________________________
	86	void AliFastJetFinder::FindJets()
	87	{
	88
	89	//pick up fastjet header
	90	AliFastJetHeaderV1 header = (AliFastJetHeaderV1)fHeader;
	91	Int_t debug = header->GetDebug(); // debug option
	92	Bool_t bgMode = header->GetBGMode(); // choose to subtract BG or not
	93	if(debug)cout<<"----------in AliFastJetFinder::FindJets() ------------------"<<endl;
	94
	95	// check if we are reading AOD jets
	96	TRefArray *refs = 0;
	97	Bool_t fromAod = !strcmp(fReader->ClassName(),"AliJetAODReader");
	98	if (fromAod) { refs = fReader->GetReferences(); }
	99
	100	// RUN ALGORITHM
	101	// read input particles -----------------------------
	102
	103	vector<fastjet::PseudoJet> inputParticles=fInputFJ->GetInputParticles();
	104	if(inputParticles.size()==0){
	105	if(debug)Printf("%s:%d No input particles found, skipping event",(char*)__FILE__,__LINE__);
	106	return;
	107	}
	108
	109	// create an object that represents your choice of jet algorithm, and
	110	// the associated parameters
	111	double rParam = header->GetRparam();
	112	fastjet::Strategy strategy = header->GetStrategy();
	113	fastjet::RecombinationScheme recombScheme = header->GetRecombScheme();
	114	fastjet::JetAlgorithm algorithm = header->GetAlgorithm();
	115	fastjet::JetDefinition jetDef(algorithm, rParam, recombScheme, strategy);
	116
	117	// create an object that specifies how we to define the area
	118	fastjet::AreaDefinition areaDef;
	119	double ghostEtamax = header->GetGhostEtaMax();
	120	double ghostArea = header->GetGhostArea();
	121	int activeAreaRepeats = header->GetActiveAreaRepeats();
	122
	123	// now create the object that holds info about ghosts
	124	fastjet::GhostedAreaSpec ghostSpec(ghostEtamax, activeAreaRepeats, ghostArea);
	125	// and from that get an area definition
	126	fastjet::AreaType areaType = header->GetAreaType();
	127	areaDef = fastjet::AreaDefinition(areaType,ghostSpec);
	128
	129
	130
	131
	132
	133	if(bgMode) // BG subtraction!!!!!!!!!! Not entering here
	134	{
	135	//***************************** JETS FINDING AND EXTRACTION
	136	// run the jet clustering with the above jet definition
	137	fastjet::ClusterSequenceArea clust_seq(inputParticles, jetDef, areaDef);
	138
	139	// save a comment in the header
	140
	141	TString comment = "Running FastJet algorithm with the following setup. ";
	142	comment+= "Jet definition: ";
	143	comment+= TString(jetDef.description());
	144	comment+= ". Area definition: ";
	145	comment+= TString(areaDef.description());
	146	comment+= ". Strategy adopted by FastJet: ";
	147	comment+= TString(clust_seq.strategy_string());
	148	header->SetComment(comment);
	149	if(debug){
	150	cout << "--------------------------------------------------------" << endl;
	151	cout << comment << endl;
	152	cout << "--------------------------------------------------------" << endl;
	153	}
	154	//header->PrintParameters();
	155
	156
	157	// extract the inclusive jets with pt > ptmin, sorted by pt
	158	double ptmin = header->GetPtMin();
	159	vector<fastjet::PseudoJet> inclusiveJets = clust_seq.inclusive_jets(ptmin);
	160
	161	//cout << "Number of unclustered particles: " << clust_seq.unclustered_particles().size() << endl;
	162
	163
	164	//subtract background // ===========================================
	165	// set the rapididty , phi range within which to study the background
	166	double rapMax = header->GetRapMax();
	167	double rapMin = header->GetRapMin();
	168	double phiMax = header->GetPhiMax();
	169	double phiMin = header->GetPhiMin();
	170	fastjet::RangeDefinition range(rapMin, rapMax, phiMin, phiMax);
	171
	172	// subtract background
	173	vector<fastjet::PseudoJet> subJets = clust_seq.subtracted_jets(range,ptmin);
	174
	175	// print out
	176	//cout << "Printing inclusive sub jets with pt > "<< ptmin<<" GeV\n";
	177	//cout << "---------------------------------------\n";
	178	//cout << endl;
	179	//printf(" ijet rap phi Pt area +- err\n");
	180
	181	// sort jets into increasing pt
	182	vector<fastjet::PseudoJet> jets = sorted_by_pt(subJets);
	183	for (size_t j = 0; j < jets.size(); j++) { // loop for jets
	184
	185	double area = clust_seq.area(jets[j]);
	186	double areaError = clust_seq.area_error(jets[j]);
	187
	188	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);
	189
	190	// go to write AOD info
	191	AliAODJet aodjet (jets[j].px(), jets[j].py(), jets[j].pz(), jets[j].E());
	192	//cout << "Printing jet " << endl;
	193	if(debug) aodjet.Print("");
	194	//cout << "Adding jet ... " ;
	195	AddJet(aodjet);
	196	//cout << "added \n" << endl;
	197
	198	}
	199	}
	200
	201
	202
	203
	204
	205
	206	else { // No BG subtraction!!!!!!!! Default header is bgmode=0.
	207
	208	TClonesArray* fUnit = fReader->GetUnitArray(); //Big mmentum array
	209	if(fUnit == 0) { cout << "Could not get the momentum array" << endl; return; }
	210	Int_t nIn = fUnit->GetEntries();
	211
	212
	213	//fastjet::ClusterSequence clust_seq(inputParticles, jetDef);
	214	fastjet::ClusterSequenceArea clust_seq(inputParticles, jetDef, areaDef);
	215
	216	// save a comment in the header
	217
	218	TString comment = "Running FastJet algorithm with the following setup. ";
	219	comment+= "Jet definition: ";
	220	comment+= TString(jetDef.description());
	221	comment+= ". Strategy adopted by FastJet: ";
	222	comment+= TString(clust_seq.strategy_string());
	223	header->SetComment(comment);
	224	if(debug){
	225	cout << "--------------------------------------------------------" << endl;
	226	cout << comment << endl;
	227	cout << "--------------------------------------------------------" << endl;
	228	}
	229	//header->PrintParameters();
	230
	231	// extract the inclusive jets with pt > ptmin, sorted by pt
	232	double ptmin = header->GetPtMin();
	233	vector<fastjet::PseudoJet> inclusiveJets = clust_seq.inclusive_jets(ptmin);
	234
	235	//cout << "Number of unclustered particles: " << clust_seq.unclustered_particles().size() << endl;
	236
	237	vector<fastjet::PseudoJet> jets = sorted_by_pt(inclusiveJets); // Added by me
	238	for (size_t j = 0; j < jets.size(); j++) { // loop for jets // Added by me
	239
	240	if(debug) printf("Jet found %5d %9.5f %8.5f %10.3f \n",(Int_t)j,jets[j].rap(),jets[j].phi(),jets[j].perp());
	241
	242	vector<fastjet::PseudoJet> constituents = clust_seq.constituents(jets[j]);
	243	int nCon= constituents.size();
	244	TArrayI ind(nCon);
	245	Double_t area=clust_seq.area(jets[j]);
	246	// go to write AOD info
	247	AliAODJet aodjet (jets[j].px(), jets[j].py(), jets[j].pz(), jets[j].E());
	248	aodjet.SetEffArea(area,0);
	249	//cout << "Printing jet " << endl;
	250	if(debug) aodjet.Print("");
	251	Int_t count=0;
	252	for (int i=0; i < nCon; i++)
	253	{
	254	fastjet::PseudoJet mPart=constituents[i];
	255	ind[i]=mPart.user_index();
	256	// cout<<i<<" index="<<ind[i]<<endl;
	257
	258	//internal loop over all the unit cells
	259	Int_t ipart = 0;
	260	// count=0;
	261	for(Int_t ii=0; ii<nIn; ii++)
	262	{
	263	AliJetUnitArray uArray = (AliJetUnitArray)fUnit->At(ii);
	264	if(uArray->GetUnitEnergy()>0.){
	265	uArray->SetUnitTrackID(ipart);//used to have the index available in AliJEtBkg
	266	if(ipart==ind[i]){
	267	TRefArray* trackArray = (TRefArray*)uArray->GetUnitTrackRef();
	268	Int_t tracksInCell = trackArray->GetEntries();
	269	for(int ji = 0; ji < tracksInCell; ji++){
	270	AliAODTrack * track = (AliAODTrack*)trackArray->At(ji);
	271	aodjet.AddTrack(track);
	272	}
	273
	274	count++;
	275	}
	276	ipart++;
	277	}
	278	}
	279	}
	280
	281
	282
	283	AddJet(aodjet);
	284
	285	} // end loop for jets
	286	}
	287
	288	}
	289
	290	//____________________________________________________________________________
	291	void AliFastJetFinder::RunTest(const char* datafile)
	292
	293	{
	294
	295	// This simple test run the kt algorithm for an ascii file testdata.dat
	296	// read input particles -----------------------------
	297	vector<fastjet::PseudoJet> inputParticles;
	298	Float_t px,py,pz,en;
	299	ifstream in;
	300	Int_t nlines = 0;
	301	// we assume a file basic.dat in the current directory
	302	// this file has 3 columns of float data
	303	in.open(datafile);
	304	while (1) {
	305	in >> px >> py >> pz >> en;
	306	if (!in.good()) break;
	307	//printf("px=%8f, py=%8f, pz=%8fn",px,py,pz);
	308	nlines++;
	309	inputParticles.push_back(fastjet::PseudoJet(px,py,pz,en));
	310	}
	311	//printf(" found %d pointsn",nlines);
	312	in.close();
	313	//////////////////////////////////////////////////
	314
	315	// create an object that represents your choice of jet algorithm, and
	316	// the associated parameters
	317	double rParam = 1.0;
	318	fastjet::Strategy strategy = fastjet::Best;
	319	fastjet::RecombinationScheme recombScheme = fastjet::BIpt_scheme;
	320	fastjet::JetDefinition jetDef(fastjet::kt_algorithm, rParam, recombScheme, strategy);
	321
	322
	323
	324	// create an object that specifies how we to define the area
	325	fastjet::AreaDefinition areaDef;
	326	double ghostEtamax = 7.0;
	327	double ghostArea = 0.05;
	328	int activeAreaRepeats = 1;
	329
	330
	331	// now create the object that holds info about ghosts
	332	fastjet::GhostedAreaSpec ghostSpec(ghostEtamax, activeAreaRepeats, ghostArea);
	333	// and from that get an area definition
	334	areaDef = fastjet::AreaDefinition(fastjet::active_area,ghostSpec);
	335
	336
	337	// run the jet clustering with the above jet definition
	338	fastjet::ClusterSequenceArea clust_seq(inputParticles, jetDef, areaDef);
	339
	340
	341	// tell the user what was done
	342	cout << "--------------------------------------------------------" << endl;
	343	cout << "Jet definition was: " << jetDef.description() << endl;
	344	cout << "Area definition was: " << areaDef.description() << endl;
	345	cout << "Strategy adopted by FastJet was "<< clust_seq.strategy_string()<<endl<<endl;
	346	cout << "--------------------------------------------------------" << endl;
	347
	348
	349	// extract the inclusive jets with pt > 5 GeV, sorted by pt
	350	double ptmin = 5.0;
	351	vector<fastjet::PseudoJet> inclusiveJets = clust_seq.inclusive_jets(ptmin);
	352
	353	cout << "Number of unclustered particles: " << clust_seq.unclustered_particles().size() << endl;
	354
	355
	356	//subtract background // ===========================================
	357	// set the rapididty range within which to study the background
	358	double rapMax = ghostEtamax - rParam;
	359	fastjet::RangeDefinition range(rapMax);
	360	// subtract background
	361	vector<fastjet::PseudoJet> subJets = clust_seq.subtracted_jets(range,ptmin);
	362
	363	// print them out //================================================
	364	cout << "Printing inclusive jets after background subtraction \n";
	365	cout << "------------------------------------------------------\n";
	366	// sort jets into increasing pt
	367	vector<fastjet::PseudoJet> jets = sorted_by_pt(subJets);
	368
	369	printf(" ijet rap phi Pt area +- err\n");
	370	for (size_t j = 0; j < jets.size(); j++) {
	371
	372	double area = clust_seq.area(jets[j]);
	373	double areaError = clust_seq.area_error(jets[j]);
	374
	375	printf("%5d %9.5f %8.5f %10.3f %8.3f +- %6.3f\n",(Int_t)j,jets[j].rap(),
	376	jets[j].phi(),jets[j].perp(), area, areaError);
	377	}
	378	cout << endl;
	379	// ================================================================
	380
	381
	382
	383	}
	384
	385	//____________________________________________________________________________
	386
	387	void AliFastJetFinder::WriteJHeaderToFile() const
	388	{
	389	fHeader->Write();
	390	}
	391
	392	//____________________________________________________________________________
	393
	394	Float_t AliFastJetFinder::EtaToTheta(Float_t arg)
	395	{
	396	// return (180./TMath::Pi())2.atan(exp(-arg));
	397	return 2.*atan(exp(-arg));
	398
	399
	400	}
	401
	402	//____________________________________________________________________________
	403
	404	void AliFastJetFinder::InitTask(TChain *tree)
	405	{
	406
	407	printf("Fast jet finder initialization ******************");
	408	fReader->CreateTasks(tree);
	409
	410	}
	411
	412
	413	Bool_t AliFastJetFinder::ProcessEvent()
	414	{
	415	//
	416	// Process one event
	417	// from meomntum array
	418
	419	Bool_t ok = fReader->FillMomentumArray();
	420
	421	if (!ok) return kFALSE;
	422	fInputFJ->SetHeader(fHeader);
	423	fInputFJ->SetReader(fReader);
	424	fInputFJ->FillInput();
	425	// Jets
	426	FindJets();
	427
	428	fJetBkg->SetHeader(fHeader);
	429	fJetBkg->SetReader(fReader);
	430	Double_t sigma1,meanarea1,sigma2,meanarea2;
	431	Double_t bkg1,bkg2;
	432	fJetBkg->SetFastJetInput(fInputFJ);
	433	fJetBkg->BkgFastJetb(bkg1,sigma1,meanarea1);
	434	fJetBkg->BkgFastJetWoHardest(bkg2,sigma2,meanarea2);
	435	fAODEvBkg->SetBackground(0,bkg1,sigma1,meanarea1);
	436	fAODEvBkg->SetBackground(1,bkg2,sigma2,meanarea2);
	437
	438
	439
	440
	441
	442	/*
	443	fJetBkg->SetFastJetInput(fInputFJ);
	444	Double_t bkg1=fJetBkg->BkgFastJet();
	445	Double_t bkg2=fJetBkg->BkgChargedFastJet();
	446	Double_t bkg3=fJetBkg->BkgFastJetCone(fAODjets);
	447	Double_t bkg4=fJetBkg->BkgRemoveJetLeading(fAODjets);
	448
	449	fAODEvBkg->SetBackground(0,bkg1);
	450	fAODEvBkg->SetBackground(1,bkg2);
	451	fAODEvBkg->SetBackground(2,bkg3);
	452	fAODEvBkg->SetBackground(3,bkg4);
	453	*/
	454	Reset();
	455	return kTRUE;
	456
	457	}
	458
	459	Bool_t AliFastJetFinder::ProcessEvent2()
	460	{
	461	//
	462	// Process one event
	463	// Charged only or charged+neutral jets
	464	//
	465
	466	TRefArray* ref = new TRefArray();
	467	Bool_t procid = kFALSE;
	468	Bool_t ok = fReader->ExecTasks(procid,ref);
	469
	470	// Delete reference pointer
	471	if (!ok) {delete ref; return kFALSE;}
	472
	473	// Leading particles
	474	fInputFJ->SetHeader(fHeader);
	475	fInputFJ->SetReader(fReader);
	476	fInputFJ->FillInput();
	477
	478	// Jets
	479	FindJets();
	480
	481	fJetBkg->SetHeader(fHeader);
	482	fJetBkg->SetReader(fReader);
	483	fJetBkg->SetFastJetInput(fInputFJ);
	484	Double_t sigma1,meanarea1,sigma2,meanarea2;
	485	Double_t bkg1,bkg2;
	486	fJetBkg->BkgFastJetb(bkg1,sigma1,meanarea1);
	487	fJetBkg->BkgFastJetWoHardest(bkg2,sigma2,meanarea2);
	488	fAODEvBkg->SetBackground(0,bkg1,sigma1,meanarea1);
	489	fAODEvBkg->SetBackground(1,bkg2,sigma2,meanarea2);
	490
	491
	492
	493	// Double_t bkg1=fJetBkg->BkgFastJet();
	494	// Double_t bkg2=fJetBkg->BkgChargedFastJet();
	495	// Double_t bkg3=fJetBkg->BkgFastJetCone(fAODjets);
	496	// Double_t bkg4=fJetBkg->BkgRemoveJetLeading(fAODjets);
	497
	498	// fAODEvBkg->SetBackground(0,bkg1);
	499	// fAODEvBkg->SetBackground(1,bkg2);
	500	// fAODEvBkg->SetBackground(2,bkg3);
	501	// fAODEvBkg->SetBackground(3,bkg4);
	502
	503	Int_t nEntRef = ref->GetEntries();
	504
	505	for(Int_t i=0; i<nEntRef; i++)
	506	{
	507	// Reset the UnitArray content which were referenced
	508	((AliJetUnitArray*)ref->At(i))->SetUnitTrackID(0);
	509	((AliJetUnitArray*)ref->At(i))->SetUnitEnergy(0.);
	510	((AliJetUnitArray*)ref->At(i))->SetUnitCutFlag(kPtSmaller);
	511	((AliJetUnitArray*)ref->At(i))->SetUnitCutFlag2(kPtSmaller);
	512	((AliJetUnitArray*)ref->At(i))->SetUnitSignalFlag(kBad);
	513	((AliJetUnitArray*)ref->At(i))->SetUnitSignalFlagC(kTRUE,kBad);
	514	((AliJetUnitArray*)ref->At(i))->SetUnitDetectorFlag(kTpc);
	515	((AliJetUnitArray*)ref->At(i))->SetUnitFlag(kOutJet);
	516	((AliJetUnitArray*)ref->At(i))->ClearUnitTrackRef();
	517
	518	// Reset process ID
	519	AliJetUnitArray* uA = (AliJetUnitArray*)ref->At(i);
	520	uA->ResetBit(kIsReferenced);
	521	uA->SetUniqueID(0);
	522	}
	523
	524	// Delete the reference pointer
	525	ref->Delete();
	526	delete ref;
	527
	528	Reset();
	529
	530	return kTRUE;
	531	}