PWG/Tools/AliHelperPID.cxx

   1
   2 /**************************************************************************
   3  * Copyright(c) 1998-2009, ALICE Experiment at CERN, All rights reserved. *
   4  *                                                                        *
   5  * Author: The ALICE Off-line Project.                                    *
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  12  * appear in the supporting documentation. The authors make no claims     *
  13  * about the suitability of this software for any purpose. It is          *
  14  * provided "as is" without express or implied warranty.                  *
  15  **************************************************************************/
  16
  17 //-----------------------------------------------------------------
  18 //         AliHelperPID class
  19 //-----------------------------------------------------------------
  20
  21 #include "AliHelperPID.h"
  22 #include "AliVEvent.h"
  23 #include "AliAODEvent.h"
  24 #include "AliMCEvent.h"
  25 #include "AliMCEventHandler.h"
  26 #include "TH1F.h"
  27 #include "TH2F.h"
  28 #include "TList.h"
  29 #include "AliStack.h"
  30 #include "AliVTrack.h"
  31 #include "TParticle.h"
  32 #include "AliAODMCParticle.h"
  33 #include "AliPIDResponse.h"
  34 #include "AliPIDCombined.h"
  35 #include "AliAnalysisManager.h"
  36 #include "AliInputEventHandler.h"
  37
  38 using namespace AliHelperPIDNameSpace;
  39 using namespace std;
  40
  41 const char * kPIDTypeName[]={"TPC","TOF","TPC-TOF"} ;
  42 const char * kDetectorName[]={"ITS","TPC","TOF"} ;
  43 const char * kParticleSpeciesName[]={"Pions","Kaons","Protons","Undefined"} ;
  44
  45 ClassImp(AliHelperPID)
  46
  47 AliHelperPID::AliHelperPID() : TNamed("HelperPID", "PID object"),fisMC(0), fPIDType(kNSigmaTPCTOF), fNSigmaPID(3), fBayesCut(0.8), fPIDResponse(0), fPIDCombined(0),fOutputList(0),fRequestTOFPID(1),fRemoveTracksT0Fill(0),fUseExclusiveNSigma(0),fPtTOFPID(.6),fHasTOFPID(0){
  48
  49   for(Int_t ipart=0;ipart<kNSpecies;ipart++)
  50     for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++)
  51       fnsigmas[ipart][ipid]=999.;
  52
  53   for(Int_t ipart=0;ipart<kNSpecies;ipart++)fHasDoubleCounting[ipart]=kFALSE;
  54
  55   fOutputList = new TList;
  56   fOutputList->SetOwner();
  57   fOutputList->SetName("OutputList");
  58
  59   //nsigma plot
  60   for(Int_t ipart=0;ipart<kNSpecies;ipart++){
  61     for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
  62       Double_t miny=-30;
  63       Double_t maxy=30;
  64       if(ipid==kNSigmaTPCTOF){miny=0;maxy=50;}
  65       TH2F *fHistoNSigma=new TH2F(Form("NSigma_%d_%d",ipart,ipid),Form("n#sigma %s %s",kParticleSpeciesName[ipart],kPIDTypeName[ipid]),200,0,10,500,miny,maxy);
  66       fHistoNSigma->GetXaxis()->SetTitle("P_{T} (GeV / c)");
  67       fHistoNSigma->GetYaxis()->SetTitle(Form("n#sigma %s %s",kParticleSpeciesName[ipart],kPIDTypeName[ipid]));
  68       fOutputList->Add(fHistoNSigma);
  69     }
  70   }
  71
  72   //nsigmaRec plot
  73   for(Int_t ipart=0;ipart<kNSpecies;ipart++){
  74     for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
  75       Double_t miny=-10;
  76       Double_t maxy=10;
  77       if(ipid==kNSigmaTPCTOF){miny=0;maxy=20;}
  78       TH2F *fHistoNSigma=new TH2F(Form("NSigmaRec_%d_%d",ipart,ipid),
  79                                   Form("n#sigma for reconstructed %s %s",kParticleSpeciesName[ipart],kPIDTypeName[ipid]),200,0,10,500,miny,maxy);
  80       fHistoNSigma->GetXaxis()->SetTitle("P_{T} (GeV / c)");
  81       fHistoNSigma->GetYaxis()->SetTitle(Form("n#sigma %s %s",kParticleSpeciesName[ipart],kPIDTypeName[ipid]));
  82       fOutputList->Add(fHistoNSigma);
  83     }
  84   }
  85
  86   //BayesRec plot
  87   for(Int_t ipart=0;ipart<kNSpecies;ipart++){
  88     Double_t miny=0.;
  89     Double_t maxy=1;
  90     TH2F *fHistoBayes=new TH2F(Form("BayesRec_%d",ipart),
  91                                Form("probability for reconstructed %s",kParticleSpeciesName[ipart]),200,0,10,500,miny,maxy);
  92     fHistoBayes->GetXaxis()->SetTitle("P_{T} (GeV / c)");
  93     fHistoBayes->GetYaxis()->SetTitle(Form("Bayes prob %s",kParticleSpeciesName[ipart]));
  94     fOutputList->Add(fHistoBayes);
  95   }
  96
  97   //nsigmaDC plot
  98   for(Int_t ipart=0;ipart<kNSpecies;ipart++){
  99     for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 100       Double_t miny=-10;
 101       Double_t maxy=10;
 102       if(ipid==kNSigmaTPCTOF){miny=0;maxy=20;}
 103       TH2F *fHistoNSigma=new TH2F(Form("NSigmaDC_%d_%d",ipart,ipid),
 104                                   Form("n#sigma for double counting %s %s",kParticleSpeciesName[ipart],kPIDTypeName[ipid]),200,0,10,500,miny,maxy);
 105       fHistoNSigma->GetXaxis()->SetTitle("P_{T} (GeV / c)");
 106       fHistoNSigma->GetYaxis()->SetTitle(Form("n#sigma %s %s",kParticleSpeciesName[ipart],kPIDTypeName[ipid]));
 107       fOutputList->Add(fHistoNSigma);
 108     }
 109   }
 110
 111   //nsigmaMC plot
 112   for(Int_t ipart=0;ipart<kNSpecies;ipart++){
 113     for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 114       Double_t miny=-30;
 115       Double_t maxy=30;
 116       if(ipid==kNSigmaTPCTOF){miny=0;maxy=50;}
 117       TH2F *fHistoNSigma=new TH2F(Form("NSigmaMC_%d_%d",ipart,ipid),
 118                                   Form("n#sigma for MC %s %s",kParticleSpeciesName[ipart],kPIDTypeName[ipid]),200,0,10,500,miny,maxy);
 119       fHistoNSigma->GetXaxis()->SetTitle("P_{T} (GeV / c)");
 120       fHistoNSigma->GetYaxis()->SetTitle(Form("n#sigma %s %s",kParticleSpeciesName[ipart],kPIDTypeName[ipid]));
 121       fOutputList->Add(fHistoNSigma);
 122     }
 123   }
 124
 125   //PID signal plot
 126   for(Int_t idet=0;idet<kNDetectors;idet++){
 127     for(Int_t ipart=0;ipart<kNSpecies;ipart++){
 128       Double_t maxy=500;
 129       if(idet==kTOF)maxy=1.1;
 130       TH2F *fHistoPID=new TH2F(Form("PID_%d_%d",idet,ipart),Form("%s signal - %s",kDetectorName[idet],kParticleSpeciesName[ipart]),200,0,10,500,-maxy,maxy);
 131       fHistoPID->GetXaxis()->SetTitle("P (GeV / c)");
 132       fHistoPID->GetYaxis()->SetTitle(Form("%s signal",kDetectorName[idet]));
 133       fOutputList->Add(fHistoPID);
 134     }
 135   }
 136 }
 137
 138 //////////////////////////////////////////////////////////////////////////////////////////////////
 139
 140 TH2F* AliHelperPID::GetHistogram2D(const char * name){
 141   // returns histo named name
 142   return (TH2F*) fOutputList->FindObject(name);
 143 }
 144
 145 //////////////////////////////////////////////////////////////////////////////////////////////////
 146
 147 Int_t AliHelperPID::GetParticleSpecies(AliVTrack * trk, Bool_t FIllQAHistos){
 148   //return the specie according to the minimum nsigma value
 149   //no double counting, this has to be evaluated using CheckDoubleCounting()
 150
 151   Int_t ID=kSpUndefined;
 152
 153   //get the PID response
 154   if(!fPIDResponse) {
 155     AliAnalysisManager *man = AliAnalysisManager::GetAnalysisManager();
 156     AliInputEventHandler* inputHandler = (AliInputEventHandler*)(man->GetInputEventHandler());
 157     fPIDResponse = inputHandler->GetPIDResponse();
 158   }
 159   if(!fPIDResponse) {
 160     AliFatal("Cannot get pid response");
 161   }
 162
 163   //calculate nsigmas (used also by the bayesian)
 164   CalculateNSigmas(trk,FIllQAHistos);//fill the data member fnsigmas with the nsigmas value [ipart][iPID]
 165
 166   //Do PID
 167   if(fPIDType==kBayes){//use bayesianPID
 168
 169     if(!fPIDCombined) {
 170       AliFatal("PIDCombined object has to be set in the steering macro");
 171     }
 172
 173     ID = GetIDBayes(trk,FIllQAHistos);
 174
 175   }else{ //use nsigma PID
 176
 177     ID=FindMinNSigma(trk,FIllQAHistos);
 178
 179     if(fUseExclusiveNSigma){ //if one particle has double counting and exclusive nsigma is requested ID = kSpUndefined
 180       Bool_t *HasDC;
 181       HasDC=GetDoubleCounting(trk,FIllQAHistos);
 182       for(Int_t ipart=0;ipart<kNSpecies;ipart++){
 183         if(HasDC[ipart]==kTRUE)  ID = kSpUndefined;
 184       }
 185     }
 186   }
 187
 188   //Fill PID signal plot
 189   if(ID != kSpUndefined){
 190     for(Int_t idet=0;idet<kNDetectors;idet++){
 191       TH2F *h=GetHistogram2D(Form("PID_%d_%d",idet,ID));
 192       if(idet==kITS)h->Fill(trk->P(),trk->GetITSsignal()*trk->Charge());
 193       if(idet==kTPC)h->Fill(trk->P(),trk->GetTPCsignal()*trk->Charge());
 194       if(idet==kTOF && fHasTOFPID)h->Fill(trk->P(),TOFBetaCalc(trk)*trk->Charge());
 195     }
 196   }
 197   return ID;
 198 }
 199
 200 //////////////////////////////////////////////////////////////////////////////////////////////////
 201
 202 Int_t AliHelperPID::GetParticleSpecies(AliVParticle * part) {
 203   // return PID according to MC truth
 204   switch(TMath::Abs(part->PdgCode())){
 205   case 2212:
 206     return kSpProton;
 207     break;
 208   case 321:
 209     return kSpKaon;
 210     break;
 211   case 211:
 212     return kSpPion;
 213     break;
 214   default:
 215     return kSpUndefined;
 216   }
 217 }
 218
 219 //////////////////////////////////////////////////////////////////////////////////////////////////
 220
 221 Int_t AliHelperPID::GetIDBayes(AliVTrack * trk, Bool_t FIllQAHistos){
 222
 223   Bool_t *IDs=GetAllCompatibleIdentitiesNSigma(trk,FIllQAHistos);
 224
 225   Double_t probBayes[AliPID::kSPECIES];
 226
 227   UInt_t detUsed= 0;
 228   CheckTOF(trk);
 229   if(fHasTOFPID && trk->Pt()>fPtTOFPID){//use TOF information
 230     detUsed = CalcPIDCombined(trk, fPIDResponse, AliPIDResponse::kDetTOF|AliPIDResponse::kDetTPC, probBayes);
 231     if(detUsed != (AliPIDResponse::kDetTOF|AliPIDResponse::kDetTPC))return kSpUndefined;//check that TPC and TOF are used
 232   }else{
 233     detUsed = CalcPIDCombined(trk, fPIDResponse,AliPIDResponse::kDetTPC, probBayes);
 234     if(detUsed != AliPIDResponse::kDetTPC)return kSpUndefined;//check that TPC is used
 235   }
 236
 237   //the probability has to be normalized to one, we check it
 238   Double_t sump=0.;
 239   for(Int_t ipart=0;ipart<AliPID::kSPECIES;ipart++)sump+=probBayes[ipart];
 240   if(sump<.99 && sump>1.01){//FIXME precision problem in the sum, workaround
 241     AliFatal("Bayesian probability not normalized to one");
 242   }
 243
 244   //probabilities are normalized to one, if the cut is above .5 there is no problem
 245   if(probBayes[AliPID::kPion]>fBayesCut && IDs[kSpPion]==1){
 246     TH2F *h=GetHistogram2D(Form("BayesRec_%d",kSpPion));
 247     h->Fill(trk->Pt(),probBayes[AliPID::kPion]);
 248     return kSpPion;
 249   }
 250   else if(probBayes[AliPID::kKaon]>fBayesCut && IDs[kSpKaon]==1){
 251     TH2F *h=GetHistogram2D(Form("BayesRec_%d",kSpKaon));
 252     h->Fill(trk->Pt(),probBayes[AliPID::kKaon]);
 253     return kSpKaon;
 254   }
 255   else if(probBayes[AliPID::kProton]>fBayesCut && IDs[kSpProton]==1){
 256     TH2F *h=GetHistogram2D(Form("BayesRec_%d",kSpProton));
 257     h->Fill(trk->Pt(),probBayes[AliPID::kProton]);
 258     return kSpProton;
 259   }
 260   else{
 261     return kSpUndefined;
 262   }
 263 }
 264
 265 //////////////////////////////////////////////////////////////////////////////////////////////////
 266
 267 UInt_t AliHelperPID::CalcPIDCombined(const AliVTrack *track,const AliPIDResponse *PIDResponse, Int_t detMask, Double_t* prob) const{
 268   //
 269   // Bayesian PID calculation
 270   //
 271   for(Int_t i=0;i<AliPID::kSPECIES;i++)
 272     {
 273       prob[i]=0.;
 274     }
 275   fPIDCombined->SetDetectorMask(detMask);
 276
 277   return fPIDCombined->ComputeProbabilities((AliVTrack*)track, PIDResponse, prob);
 278 }
 279
 280 //////////////////////////////////////////////////////////////////////////////////////////////////
 281
 282 void AliHelperPID::CalculateNSigmas(AliVTrack * trk, Bool_t FIllQAHistos){
 283   //defines data member fnsigmas
 284
 285   // Compute nsigma for each hypthesis
 286   AliVParticle *inEvHMain = dynamic_cast<AliVParticle *>(trk);
 287   // --- TPC
 288   Double_t nsigmaTPCkProton = fPIDResponse->NumberOfSigmasTPC(inEvHMain, AliPID::kProton);
 289   Double_t nsigmaTPCkKaon   = fPIDResponse->NumberOfSigmasTPC(inEvHMain, AliPID::kKaon);
 290   Double_t nsigmaTPCkPion   = fPIDResponse->NumberOfSigmasTPC(inEvHMain, AliPID::kPion);
 291   // --- TOF
 292   Double_t nsigmaTOFkProton=999.,nsigmaTOFkKaon=999.,nsigmaTOFkPion=999.;
 293   Double_t nsigmaTPCTOFkProton=999.,nsigmaTPCTOFkKaon=999.,nsigmaTPCTOFkPion=999.;
 294
 295   CheckTOF(trk);
 296
 297   if(fHasTOFPID && trk->Pt()>fPtTOFPID){//use TOF information
 298     nsigmaTOFkProton = fPIDResponse->NumberOfSigmasTOF(inEvHMain, AliPID::kProton);
 299     nsigmaTOFkKaon   = fPIDResponse->NumberOfSigmasTOF(inEvHMain, AliPID::kKaon);
 300     nsigmaTOFkPion   = fPIDResponse->NumberOfSigmasTOF(inEvHMain, AliPID::kPion);
 301     Double_t d2Proton=nsigmaTPCkProton * nsigmaTPCkProton + nsigmaTOFkProton * nsigmaTOFkProton;
 302     Double_t d2Kaon=nsigmaTPCkKaon * nsigmaTPCkKaon + nsigmaTOFkKaon * nsigmaTOFkKaon;
 303     Double_t d2Pion=nsigmaTPCkPion * nsigmaTPCkPion + nsigmaTOFkPion * nsigmaTOFkPion;
 304     //commented, this is done in analogy with AliESDTrackCuts, nsigma combind according to the probability
 305     // --- combined
 306     // -----------------------------------
 307     // How to get to a n-sigma cut?
 308     //
 309     // The accumulated statistics from 0 to d is
 310     //
 311     // ->  Erf(d/Sqrt(2)) for a 1-dim gauss (d = n_sigma)
 312     // ->  1 - Exp(-d**2) for a 2-dim gauss (d*d = dx*dx + dy*dy != n_sigma)
 313     // It means that for a 2-dim gauss: n_sigma(d) = Sqrt(2)*ErfInv(1 - Exp((-d**2)/2)
 314     //
 315     // work around precision problem
 316     // if d is too big, TMath::Exp(...) gets 0, and TMath::ErfInverse(1) that should be infinite, gets 0 :(
 317     //if(TMath::Exp(- d2Proton / 2) > 1e-15)nsigmaTPCTOFkProton  =  TMath::Sqrt(2)*TMath::ErfInverse(1 - TMath::Exp(- d2Proton / 2));
 318     //if(TMath::Exp(- d2Kaon / 2) > 1e-15)nsigmaTPCTOFkKaon    = TMath::Sqrt(2)*TMath::ErfInverse(1 - TMath::Exp(- d2Kaon / 2));
 319     //if(TMath::Exp(- d2Pion / 2) > 1e-15)nsigmaTPCTOFkPion     = TMath::Sqrt(2)*TMath::ErfInverse(1 - TMath::Exp(- d2Pion / 2));
 320
 321     //used for the 2PC PID paper (circular cut)
 322     nsigmaTPCTOFkProton  =  TMath::Sqrt(d2Proton);
 323     nsigmaTPCTOFkKaon    =  TMath::Sqrt(d2Kaon);
 324     nsigmaTPCTOFkPion    =  TMath::Sqrt(d2Pion);
 325   }else{
 326     // --- combined
 327     // if TOF is missing and below fPtTOFPID only the TPC information is used
 328     nsigmaTPCTOFkProton = TMath::Abs(nsigmaTPCkProton);
 329     nsigmaTPCTOFkKaon   = TMath::Abs(nsigmaTPCkKaon);
 330     nsigmaTPCTOFkPion   = TMath::Abs(nsigmaTPCkPion);
 331   }
 332
 333   //set data member fnsigmas
 334   fnsigmas[kSpPion][kNSigmaTPC]=nsigmaTPCkPion;
 335   fnsigmas[kSpKaon][kNSigmaTPC]=nsigmaTPCkKaon;
 336   fnsigmas[kSpProton][kNSigmaTPC]=nsigmaTPCkProton;
 337   fnsigmas[kSpPion][kNSigmaTOF]=nsigmaTOFkPion;
 338   fnsigmas[kSpKaon][kNSigmaTOF]=nsigmaTOFkKaon;
 339   fnsigmas[kSpProton][kNSigmaTOF]=nsigmaTOFkProton;
 340   fnsigmas[kSpPion][kNSigmaTPCTOF]=nsigmaTPCTOFkPion;
 341   fnsigmas[kSpKaon][kNSigmaTPCTOF]=nsigmaTPCTOFkKaon;
 342   fnsigmas[kSpProton][kNSigmaTPCTOF]=nsigmaTPCTOFkProton;
 343
 344   if(FIllQAHistos){
 345     //Fill NSigma SeparationPlot
 346     for(Int_t ipart=0;ipart<kNSpecies;ipart++){
 347       for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 348         if((ipid!=kNSigmaTPC) && (!fHasTOFPID) && trk->Pt()<fPtTOFPID)continue;//not filling TOF and combined if no TOF PID
 349         TH2F *h=GetHistogram2D(Form("NSigma_%d_%d",ipart,ipid));
 350         h->Fill(trk->Pt(),fnsigmas[ipart][ipid]);
 351       }
 352     }
 353   }
 354 }
 355
 356 //////////////////////////////////////////////////////////////////////////////////////////////////
 357
 358 Int_t AliHelperPID::FindMinNSigma(AliVTrack * trk,Bool_t FillQAHistos){
 359
 360   CheckTOF(trk);
 361   if(fRequestTOFPID && (!fHasTOFPID) && trk->Pt()>fPtTOFPID)return kSpUndefined;
 362
 363   //get the identity of the particle with the minimum Nsigma
 364   Double_t nsigmaPion=999., nsigmaKaon=999., nsigmaProton=999.;
 365   switch (fPIDType){
 366   case kNSigmaTPC:
 367     nsigmaProton  =  TMath::Abs(fnsigmas[kSpProton][kNSigmaTPC]);
 368     nsigmaKaon    =  TMath::Abs(fnsigmas[kSpKaon][kNSigmaTPC])  ;
 369     nsigmaPion    =  TMath::Abs(fnsigmas[kSpPion][kNSigmaTPC])  ;
 370     break;
 371   case kNSigmaTOF:
 372     nsigmaProton  =  TMath::Abs(fnsigmas[kSpProton][kNSigmaTOF]);
 373     nsigmaKaon    =  TMath::Abs(fnsigmas[kSpKaon][kNSigmaTOF])  ;
 374     nsigmaPion    =  TMath::Abs(fnsigmas[kSpPion][kNSigmaTOF])  ;
 375     break;
 376   case kNSigmaTPCTOF://In case of no TOF matching the combined nsigma is the TPC one
 377     nsigmaProton  =  TMath::Abs(fnsigmas[kSpProton][kNSigmaTPCTOF]);
 378     nsigmaKaon    =  TMath::Abs(fnsigmas[kSpKaon][kNSigmaTPCTOF])  ;
 379     nsigmaPion    =  TMath::Abs(fnsigmas[kSpPion][kNSigmaTPCTOF])  ;
 380     break;
 381   case kBayes://the nsigma in the bayesian is used to clean with a very large n-sigma value
 382     nsigmaProton  =  TMath::Abs(fnsigmas[kSpProton][kNSigmaTPCTOF]);
 383     nsigmaKaon    =  TMath::Abs(fnsigmas[kSpKaon][kNSigmaTPCTOF])  ;
 384     nsigmaPion    =  TMath::Abs(fnsigmas[kSpPion][kNSigmaTPCTOF])  ;
 385     break;
 386   }
 387
 388   // guess the particle based on the smaller nsigma (within fNSigmaPID)
 389   if( ( nsigmaKaon==nsigmaPion ) && ( nsigmaKaon==nsigmaProton )) return kSpUndefined;//if is the default value for the three
 390
 391   if( ( nsigmaKaon   < nsigmaPion ) && ( nsigmaKaon < nsigmaProton ) && (nsigmaKaon   < fNSigmaPID)){
 392     if(FillQAHistos){
 393       for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 394         if((ipid!=kNSigmaTPC) && (!fHasTOFPID) && (trk->Pt()<fPtTOFPID))continue;//not filling TOF and combined if no TOF PID
 395         TH2F *h=GetHistogram2D(Form("NSigmaRec_%d_%d",kSpKaon,ipid));
 396         h->Fill(trk->Pt(),fnsigmas[kSpKaon][ipid]);
 397       }
 398     }
 399     return kSpKaon;
 400   }
 401   if( ( nsigmaPion   < nsigmaKaon ) && ( nsigmaPion < nsigmaProton ) && (nsigmaPion   < fNSigmaPID)){
 402     if(FillQAHistos){
 403       for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 404         if((ipid!=kNSigmaTPC) && (!fHasTOFPID) && (trk->Pt()<fPtTOFPID))continue;//not filling TOF and combined if no TOF PID
 405         TH2F *h=GetHistogram2D(Form("NSigmaRec_%d_%d",kSpPion,ipid));
 406         h->Fill(trk->Pt(),fnsigmas[kSpPion][ipid]);
 407       }
 408     }
 409     return kSpPion;
 410   }
 411   if( ( nsigmaProton < nsigmaKaon ) && ( nsigmaProton < nsigmaPion ) && (nsigmaProton < fNSigmaPID)){
 412     if(FillQAHistos){
 413       for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 414         if((ipid!=kNSigmaTPC) && (!fHasTOFPID) && (trk->Pt()<fPtTOFPID))continue;//not filling TOF and combined if no TOF PID
 415         TH2F *h=GetHistogram2D(Form("NSigmaRec_%d_%d",kSpProton,ipid));
 416         h->Fill(trk->Pt(),fnsigmas[kSpProton][ipid]);
 417       }
 418     }
 419     return kSpProton;
 420   }
 421   // else, return undefined
 422   return kSpUndefined;
 423 }
 424
 425 //////////////////////////////////////////////////////////////////////////////////////////////////
 426
 427 Bool_t* AliHelperPID::GetDoubleCounting(AliVTrack * trk,Bool_t FIllQAHistos){
 428   //if a particle has double counting set fHasDoubleCounting[ipart]=kTRUE
 429   //fill DC histos
 430   for(Int_t ipart=0;ipart<kNSpecies;ipart++)fHasDoubleCounting[ipart]=kFALSE;//array with kTRUE for second (or third) identity of the track
 431
 432   Int_t MinNSigma=FindMinNSigma(trk,kFALSE);//not filling the NSigmaRec histos
 433
 434   CheckTOF(trk);
 435
 436   if(MinNSigma==kSpUndefined)return fHasDoubleCounting;//in case of undefined no Double counting
 437
 438   Double_t nsigmaPion=999., nsigmaKaon=999., nsigmaProton=999.;
 439   switch (fPIDType) {
 440   case kNSigmaTPC:
 441     nsigmaProton  =  TMath::Abs(fnsigmas[kSpProton][kNSigmaTPC]);
 442     nsigmaKaon    =  TMath::Abs(fnsigmas[kSpKaon][kNSigmaTPC])  ;
 443     nsigmaPion    =  TMath::Abs(fnsigmas[kSpPion][kNSigmaTPC])  ;
 444     break;
 445   case kNSigmaTOF:
 446     nsigmaProton  =  TMath::Abs(fnsigmas[kSpProton][kNSigmaTOF]);
 447     nsigmaKaon    =  TMath::Abs(fnsigmas[kSpKaon][kNSigmaTOF])  ;
 448     nsigmaPion    =  TMath::Abs(fnsigmas[kSpPion][kNSigmaTOF])  ;
 449     break;
 450   case kNSigmaTPCTOF://In case of no TOF matching the combined nsigma is the TPC one
 451     nsigmaProton  =  TMath::Abs(fnsigmas[kSpProton][kNSigmaTPCTOF]);
 452     nsigmaKaon    =  TMath::Abs(fnsigmas[kSpKaon][kNSigmaTPCTOF])  ;
 453     nsigmaPion    =  TMath::Abs(fnsigmas[kSpPion][kNSigmaTPCTOF])  ;
 454     break;
 455   case kBayes://the nsigma in the bayesian is used to clean with a very large n-sigma value
 456     nsigmaProton  =  TMath::Abs(fnsigmas[kSpProton][kNSigmaTPCTOF]);
 457     nsigmaKaon    =  TMath::Abs(fnsigmas[kSpKaon][kNSigmaTPCTOF])  ;
 458     nsigmaPion    =  TMath::Abs(fnsigmas[kSpPion][kNSigmaTPCTOF])  ;
 459     break;
 460   }
 461   if(nsigmaPion<fNSigmaPID && MinNSigma!=kSpPion)fHasDoubleCounting[kSpPion]=kTRUE;
 462   if(nsigmaKaon<fNSigmaPID && MinNSigma!=kSpKaon)fHasDoubleCounting[kSpKaon]=kTRUE;
 463   if(nsigmaProton<fNSigmaPID && MinNSigma!=kSpProton)fHasDoubleCounting[kSpProton]=kTRUE;
 464
 465   if(FIllQAHistos){
 466     //fill NSigma distr for double counting
 467     for(Int_t ipart=0;ipart<kNSpecies;ipart++){
 468       if(fHasDoubleCounting[ipart]){
 469         for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 470           if((ipid!=kNSigmaTPC) && (!fHasTOFPID) && (trk->Pt()<fPtTOFPID))continue;//not filling TOF and combined if no TOF PID
 471           TH2F *h=GetHistogram2D(Form("NSigmaDC_%d_%d",ipart,ipid));
 472           h->Fill(trk->Pt(),fnsigmas[ipart][ipid]);
 473         }
 474       }
 475     }
 476   }
 477   return fHasDoubleCounting;
 478 }
 479
 480 //////////////////////////////////////////////////////////////////////////////////////////////////
 481
 482 Bool_t* AliHelperPID::GetAllCompatibleIdentitiesNSigma(AliVTrack * trk,Bool_t FIllQAHistos){
 483
 484   Bool_t *IDs=GetDoubleCounting(trk,FIllQAHistos);
 485   IDs[FindMinNSigma(trk,FIllQAHistos)]=kTRUE;
 486   return IDs;
 487
 488 }
 489
 490 //////////////////////////////////////////////////////////////////////////////////////////////////
 491
 492 Int_t AliHelperPID::GetMCParticleSpecie(AliVEvent* event, AliVTrack * trk, Bool_t FillQAHistos){
 493   //return the specie according to the MC truth
 494   CheckTOF(trk);
 495
 496   if(!fisMC)AliFatal("Error: AliHelperPID::GetMCParticleSpecie called on data\n");
 497
 498   Int_t code=999;
 499   Bool_t isAOD=kFALSE;
 500   Bool_t isESD=kFALSE;
 501   TString nameoftrack(event->ClassName());
 502   if(!nameoftrack.CompareTo("AliESDEvent"))isESD=kTRUE;
 503   else if(!nameoftrack.CompareTo("AliAODEvent"))isAOD=kTRUE;
 504   else AliFatal("Not processing AODs nor ESDs") ;
 505
 506   if(isAOD){
 507     TClonesArray *arrayMC = 0;
 508     arrayMC = (TClonesArray*) event->GetList()->FindObject(AliAODMCParticle::StdBranchName());
 509     if (!arrayMC)AliFatal("Error: MC particles branch not found!\n");
 510     AliAODMCParticle *partMC = (AliAODMCParticle*) arrayMC->At(TMath::Abs(trk->GetLabel()));
 511     if (!partMC){
 512       AliError("Cannot get MC particle");
 513       return kSpUndefined;
 514     }
 515     code=partMC->GetPdgCode();
 516   }
 517   if(isESD){
 518     AliStack* stack=0x0;
 519     AliMCEventHandler* eventHandler = dynamic_cast<AliMCEventHandler*> (AliAnalysisManager::GetAnalysisManager()->GetMCtruthEventHandler());
 520     if (!eventHandler) AliFatal("ERROR: Could not retrieve MC event handler");
 521     AliMCEvent* mcEvent = eventHandler->MCEvent();
 522     if (!mcEvent)AliFatal("ERROR: Could not retrieve MC event");
 523     stack = mcEvent->Stack();
 524     if (!stack) AliFatal("ERROR: stack not available\n");
 525     TParticle *part=0;
 526     part = (TParticle*)stack->Particle(TMath::Abs(trk->GetLabel()));
 527     if (!part){
 528       AliError("Cannot get MC particle");
 529       return kSpUndefined;
 530     }
 531     code = part->GetPdgCode();
 532   }
 533   switch(TMath::Abs(code)){
 534   case 2212:
 535     if(FillQAHistos){
 536       for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 537         if((ipid!=kNSigmaTPC) && (!fHasTOFPID) && (trk->Pt()<fPtTOFPID))continue;//not filling TOF and combined if no TOF PID
 538         TH2F *h=GetHistogram2D(Form("NSigmaMC_%d_%d",kSpProton,ipid));
 539         h->Fill(trk->Pt(),fnsigmas[kSpProton][ipid]);
 540       }
 541     }
 542     return kSpProton;
 543     break;
 544   case 321:
 545     if(FillQAHistos){
 546       for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 547         if((ipid!=kNSigmaTPC) && (!fHasTOFPID) && (trk->Pt()<fPtTOFPID))continue;//not filling TOF and combined if no TOF PID
 548         TH2F *h=GetHistogram2D(Form("NSigmaMC_%d_%d",kSpKaon,ipid));
 549         h->Fill(trk->Pt(),fnsigmas[kSpKaon][ipid]);
 550       }
 551     }
 552     return kSpKaon;
 553     break;
 554   case 211:
 555     if(FillQAHistos){
 556       for(Int_t ipid=0;ipid<=kNSigmaPIDType;ipid++){
 557         if((ipid!=kNSigmaTPC) && (!fHasTOFPID) && (trk->Pt()<fPtTOFPID))continue;//not filling TOF and combined if no TOF PID
 558         TH2F *h=GetHistogram2D(Form("NSigmaMC_%d_%d",kSpPion,ipid));
 559         h->Fill(trk->Pt(),fnsigmas[kSpPion][ipid]);
 560       }
 561     }
 562     return kSpPion;
 563     break;
 564   default:
 565     return kSpUndefined;
 566   }
 567
 568 }
 569
 570 //////////////////////////////////////////////////////////////////////////////////////////////////
 571
 572 void AliHelperPID::CheckTOF(AliVTrack * trk)
 573 {
 574   //check if the particle has TOF Matching
 575
 576   //get the PIDResponse
 577   if(fPIDResponse->CheckPIDStatus(AliPIDResponse::kTOF,trk)==0)fHasTOFPID=kFALSE;
 578   else fHasTOFPID=kTRUE;
 579
 580   //in addition to TOF status we look at the pt
 581   if(trk->Pt()<fPtTOFPID)fHasTOFPID=kFALSE;
 582
 583   if(fRemoveTracksT0Fill)
 584     {
 585       Int_t startTimeMask = fPIDResponse->GetTOFResponse().GetStartTimeMask(trk->P());
 586       if (startTimeMask < 0)fHasTOFPID=kFALSE;
 587     }
 588 }
 589
 590 //////////////////////////////////////////////////////////////////////////////////////////////////
 591
 592 Double_t AliHelperPID::TOFBetaCalc(AliVTrack *track) const{
 593   //TOF beta calculation
 594   Double_t tofTime=track->GetTOFsignal();
 595
 596   Double_t c=TMath::C()*1.E-9;// m/ns
 597   Float_t startTime = fPIDResponse->GetTOFResponse().GetStartTime(((AliVTrack*)track)->P());//in ps
 598   Double_t length= fPIDResponse->GetTOFResponse().GetExpectedSignal(track,AliPID::kElectron)*1E-3*c;
 599   tofTime -= startTime;      // subtract startTime to the signal
 600   Double_t tof= tofTime*1E-3; // ns, average T0 fill subtracted, no info from T0detector
 601   tof=tof*c;
 602   return length/tof;
 603 }
 604
 605 //////////////////////////////////////////////////////////////////////////////////////////////////
 606
 607 Double_t AliHelperPID::GetMass(AliHelperParticleSpecies_t id) const{
 608   //return Mass according to AliHelperParticleSpecies_t. If undefined return -999.
 609   Double_t mass=-999.;
 610   if (id == kSpProton) { mass=9.38271999999999995e-01; }
 611   if (id == kSpKaon)   { mass=4.93676999999999977e-01; }
 612   if (id == kSpPion)    { mass=1.39570000000000000e-01; }
 613   return mass;
 614 }
 615
 616 //////////////////////////////////////////////////////////////////////////////////////////////////
 617
 618 Long64_t AliHelperPID::Merge(TCollection* list)
 619 {
 620   // Merging interface.
 621   // Returns the number of merged objects (including this).
 622   Printf("Merging");
 623   if (!list)
 624     return 0;
 625   if (list->IsEmpty())
 626     return 1;
 627   TIterator* iter = list->MakeIterator();
 628   TObject* obj;
 629   // collections of TList with output histos
 630   TList collections;
 631   Int_t count = 0;
 632   while ((obj = iter->Next())) {
 633     AliHelperPID* entry = dynamic_cast<AliHelperPID*> (obj);
 634     if (entry == 0)
 635       continue;
 636     TList * outputlist = entry->GetOutputList();
 637     collections.Add(outputlist);
 638     count++;
 639   }
 640   fOutputList->Merge(&collections);
 641   delete iter;
 642   Printf("OK");
 643   return count+1;
 644 }