emcalReclusterize.C

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//--------------------------------------------------
// Example macro to do Calorimeters filtering
// copy ESDs into AODs
//
// Pay attention to the options and definitions
// set in the lines below
//
//  Author : Gustavo Conesa Balbastre (INFN-LNF)
//
//-------------------------------------------------
//--------------------------------------------------
//
//-------------------------------------------------

enum anaModes {mLocal, mLocalCAF,mPROOF,mGRID};
//mLocal: Analyze locally files in your computer
//mLocalCAF: Analyze locally CAF files
//mPROOF: Analyze CAF files with PROOF

//---------------------------------------------------------------------------
//Settings to read locally several files, only for "mLocal" mode
//The different values are default, they can be set with environmental 
//variables: INDIR, PATTERN, NFILES, respectivelly
char * kInDir = "/Users/Gustavo/Work/data/134908/pass1"; 
//char * kInDir = "/Users/Gustavo/Work/data/137366/";
char * kPattern = ""; // Data are in files kInDir/kPattern+i 
Int_t kFile = 1; // Number of files
//---------------------------------------------------------------------------
//Collection file for grid analysis
char * kXML = "collection.xml";
//---------------------------------------------------------------------------

TString kInputData = "AOD"; //ESD, AOD, MC
TString kTreeName = "esdTree";
Bool_t kUsePhysSel = kFALSE;
Bool_t kEmbed = kTRUE;

void emcalReclusterize(Int_t mode=mLocal)
{
  // Main
  //char cmd[200] ; 
  //sprintf(cmd, ".! rm -rf outputAOD.root") ; 
  //gROOT->ProcessLine(cmd) ; 
  //--------------------------------------------------------------------
  // Load analysis libraries
  // Look at the method below, 
  // change whatever you need for your analysis case
  // ------------------------------------------------------------------
  LoadLibraries(mode) ;
  
  //-------------------------------------------------------------------------------------------------
  //Create chain from ESD and from cross sections files, look below for options.
  //-------------------------------------------------------------------------------------------------
  if(kInputData == "ESD")      kTreeName = "esdTree" ;
  else if(kInputData == "AOD") kTreeName = "aodTree" ;
  else {
    cout<<"Wrong  data type "<<kInputData<<endl;
    break;
  }
  
  TChain *chain       = new TChain(kTreeName) ;
  CreateChain(mode, chain);  
  
  if(chain){
    AliLog::SetGlobalLogLevel(AliLog::kError);//Minimum prints on screen
    
    //--------------------------------------
    // Make the analysis manager
    //-------------------------------------
    AliAnalysisManager *mgr  = new AliAnalysisManager("Manager", "Manager");
    
    // AOD output handler
    AliAODHandler* aodoutHandler   = new AliAODHandler();
    aodoutHandler->SetOutputFileName("outputAOD.root");
    if(kEmbed){
      aodoutHandler->SetCreateNonStandardAOD();
      kInputData = "AOD";
    }
    mgr->SetOutputEventHandler(aodoutHandler);
    

    //input
    if(kInputData == "ESD")
    {
      // ESD handler
      AliESDInputHandler *esdHandler = new AliESDInputHandler();
      mgr->SetInputEventHandler(esdHandler);
      esdHandler->SetReadFriends(kFALSE);
      cout<<"ESD handler "<<mgr->GetInputEventHandler()<<endl;
    }
    if(kInputData == "AOD")
    {
      // AOD handler
      AliAODInputHandler *aodHandler = new AliAODInputHandler();
      mgr->SetInputEventHandler(aodHandler);
      if(kEmbed){
        aodHandler->SetMergeEvents(kTRUE);
        aodHandler->AddFriend("AliAOD.root");
      }
      
      cout<<"AOD handler "<<mgr->GetInputEventHandler()<<endl;
      
    }
    
    //mgr->SetDebugLevel(1);
    
    //-------------------------------------------------------------------------
    //Define task, put here any other task that you want to use.
    //-------------------------------------------------------------------------
    AliAnalysisDataContainer *cinput1  = mgr->GetCommonInputContainer();
    AliAnalysisDataContainer *coutput1 = mgr->GetCommonOutputContainer();
    
    // ESD physics selection task
    if(kInputData == "ESD" && kUsePhysSel){
      gROOT->LoadMacro("AddTaskPhysicsSelection.C");
      AliPhysicsSelectionTask* physSelTask = AddTaskPhysicsSelection();
    }
    
    gROOT->LoadMacro("$ALICE_PHYSICS/PWGPP/EMCAL/macros/AddTaskEMCALClusterize.C");
    
    Bool_t kMC = kFALSE; // extra checks in case of MC analysis
    Bool_t outAOD = kFALSE ; // Generate output AOD with new clusters
    Bool_t calibEE = kTRUE; // It is set automatically, but here we force to use it or not in any case
    Bool_t calibTT = kTRUE; // It is set automatically, but here we force to use it or not in any case
    if(kRun < 122195 || (kRun > 126437 && kRun < 136851) || kMC) calibTT=kFALSE ; // Recalibration parameters not available for LHC10a,b,c,e,f,g
    Bool_t badMap  = kTRUE; // It is set automatically, but here we force to use it or not in any case  
    Bool_t  clTM      = kTRUE;
    Bool_t  exo       = kTRUE;  // Remove exotic cells
    Bool_t  clnonlin  = kTRUE;  // Apply non linearity (clusterization)
    Int_t   minEcell  = 50;     // 50  MeV (10 MeV used in reconstruction)
    Int_t   minEseed  = 100;    // 100 MeV
    Int_t   dTime     = 0;      // default, 250 ns
    Int_t   wTime     = 0;      // default 425 < T < 825 ns, careful if time calibration is on
    Int_t   unfMinE   = 15;     // Remove cells with less than 15 MeV from cluster after unfolding
    Int_t   unfFrac   = 1;      // Remove cells with less than 1% of cluster energy after unfolding
    
    TString arrayName = "";
    TString clusterzerName = "V1"; // "V2", "NxN","V1Unfold"
    
    AliAnalysisTaskEMCALClusterize * clv1 = AddTaskEMCALClusterize(arrayNameV1,outAOD,kMC,exo,clusterizerName,clTrigger, clTM,
                                                                   minEcell,minEseed,dTime,wTime,unfMinE,unfFrac,
                                                                   calibEnergy,badMap,calibTime,nonlinear);
    
    //    AliAnalysisTaskEMCALClusterize * clusterize = new AliAnalysisTaskEMCALClusterize();
//    clusterize->SetConfigFileName("ConfigEMCALClusterize.C");
//    clusterize->SetOCDBPath("local://$ALICE_ROOT/OCDB");
//    mgr->AddTask(clusterize);
//    
//    // Create containers for input/output
//    AliAnalysisDataContainer *cinput1  = mgr->GetCommonInputContainer()  ;
//    AliAnalysisDataContainer *coutput1 = mgr->GetCommonOutputContainer() ;
//    
//    mgr->ConnectInput  (clusterize, 0,  cinput1 );
//    mgr->ConnectOutput (clusterize, 0, coutput1 );
    
    //-----------------------
    // Run the analysis
    //-----------------------    
    TString smode = "";
    if (mode==mLocal || mode == mLocalCAF) 
      smode = "local";
    else if (mode==mPROOF) 
      smode = "proof";
    else if (mode==mGRID) 
      smode = "local";
    
    mgr->InitAnalysis();
    mgr->PrintStatus();
    mgr->StartAnalysis(smode.Data(),chain);
    
    cout <<" Analysis ended sucessfully "<< endl ;
    
  }
  else cout << "Chain was not produced ! "<<endl;
  
}

void  LoadLibraries(const anaModes mode) {
  
  //--------------------------------------
  // Load the needed libraries most of them already loaded by aliroot
  //--------------------------------------
  gSystem->Load("libTree");
  gSystem->Load("libGeom");
  gSystem->Load("libVMC");
  gSystem->Load("libXMLIO");
  gSystem->Load("libMatrix");
  gSystem->Load("libPhysics");

  //----------------------------------------------------------
  // >>>>>>>>>>> Local mode <<<<<<<<<<<<<< 
  //----------------------------------------------------------
  if (mode==mLocal || mode == mLocalCAF || mode == mGRID) {
    //--------------------------------------------------------
    // If you want to use already compiled libraries 
    // in the aliroot distribution
    //--------------------------------------------------------

    gSystem->Load("libSTEERBase");
    gSystem->Load("libESD");
    gSystem->Load("libAOD");
    gSystem->Load("libANALYSIS");
    gSystem->Load("libANALYSISalice");
    gSystem->Load("libANALYSISalice");

    //SetupPar("EMCALUtils"); 
    //SetupPar("PWGPPEMCAL"); 
    
    gSystem->Load("libEMCALUtils");
    gSystem->Load("libPWGPPEMCAL");
   
  }

  //---------------------------------------------------------
  // <<<<<<<<<< PROOF mode >>>>>>>>>>>>
  //---------------------------------------------------------
  else if (mode==mPROOF) {
    //
    // Connect to proof
    // Put appropriate username here
    // TProof::Reset("proof://mgheata@lxb6046.cern.ch"); 
    TProof::Open("proof://mgheata@lxb6046.cern.ch");
    
    //    gProof->ClearPackages();
    //    gProof->ClearPackage("ESD");
    //    gProof->ClearPackage("AOD");
    //    gProof->ClearPackage("ANALYSIS");   
    
    // Enable the STEERBase Package
    gProof->UploadPackage("STEERBase.par");
    gProof->EnablePackage("STEERBase");
    // Enable the ESD Package
    gProof->UploadPackage("ESD.par");
    gProof->EnablePackage("ESD");
    // Enable the AOD Package
    gProof->UploadPackage("AOD.par");
    gProof->EnablePackage("AOD");
    // Enable the Analysis Package
    gProof->UploadPackage("ANALYSIS.par");
    gProof->EnablePackage("ANALYSIS");
    // Enable the PHOS geometry Package
    //gProof->UploadPackage("PHOSUtils.par");
    //gProof->EnablePackage("PHOSUtils");
    gProof->ShowEnabledPackages();
  }  
  
}

void SetupPar(char* pararchivename)
{
  //Load par files, create analysis libraries
  //For testing, if par file already decompressed and modified
  //classes then do not decompress.
 
  TString cdir(Form("%s", gSystem->WorkingDirectory() )) ; 
  TString parpar(Form("%s.par", pararchivename)) ; 
  if ( gSystem->AccessPathName(parpar.Data()) ) {
    gSystem->ChangeDirectory(gSystem->Getenv("ALICE_PHYSICS")) ;
    TString processline(Form(".! make %s", parpar.Data())) ; 
    gROOT->ProcessLine(processline.Data()) ;
    gSystem->ChangeDirectory(cdir) ; 
    processline = Form(".! mv $ALICE_PHYSICS/%s .", parpar.Data()) ;
    gROOT->ProcessLine(processline.Data()) ;
  } 
  if ( gSystem->AccessPathName(pararchivename) ) {  
    TString processline = Form(".! tar xvzf %s",parpar.Data()) ;
    gROOT->ProcessLine(processline.Data());
  }
  
  TString ocwd = gSystem->WorkingDirectory();
  gSystem->ChangeDirectory(pararchivename);
  
  // check for BUILD.sh and execute
  if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) {
    printf("*******************************\n");
    printf("*** Building PAR archive    ***\n");
    cout<<pararchivename<<endl;
    printf("*******************************\n");
    
    if (gSystem->Exec("PROOF-INF/BUILD.sh")) {
      Error("runProcess","Cannot Build the PAR Archive! - Abort!");
      return -1;
    }
  }
  // check for SETUP.C and execute
  if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) {
    printf("*******************************\n");
    printf("*** Setup PAR archive       ***\n");
    cout<<pararchivename<<endl;
    printf("*******************************\n");
    gROOT->Macro("PROOF-INF/SETUP.C");
  }
  
  gSystem->ChangeDirectory(ocwd.Data());
  printf("Current dir: %s\n", ocwd.Data());
}



void CreateChain(const anaModes mode, TChain * chain){
  //Fills chain with data
  TString ocwd = gSystem->WorkingDirectory();
  
  //-----------------------------------------------------------
  //Analysis of CAF data locally and with PROOF
  //-----------------------------------------------------------
  if(mode ==mPROOF || mode ==mLocalCAF){
    // Chain from CAF
    gROOT->LoadMacro("$ALICE_PHYSICS/PWG/EMCAL/macros/CreateESDChain.C");
    // The second parameter is the number of input files in the chain
    chain = CreateESDChain("ESD12001.txt", 5);  
  }
  
  //---------------------------------------
  //Local files analysis
  //---------------------------------------
  else if(mode == mLocal){    
    //If you want to add several ESD files sitting in a common directory INDIR
    //Specify as environmental variables the directory (INDIR), the number of files 
    //to analyze (NFILES) and the pattern name of the directories with files (PATTERN)

    if(gSystem->Getenv("INDIR"))  
      kInDir = gSystem->Getenv("INDIR") ; 
    else cout<<"INDIR not set, use default: "<<kInDir<<endl;  
    
    if(gSystem->Getenv("PATTERN"))   
      kPattern = gSystem->Getenv("PATTERN") ; 
    else  cout<<"PATTERN not set, use default: "<<kPattern<<endl;
    
    if(gSystem->Getenv("NFILES"))
      kFile = atoi(gSystem->Getenv("NFILES")) ;
    else cout<<"NFILES not set, use default: "<<kFile<<endl;
    
    //Check if env variables are set and are correct
    if ( kInDir  && kFile) {
      printf("Get %d files from directory %s\n",kFile,kInDir);
      if ( ! gSystem->cd(kInDir) ) {//check if ESDs directory exist
  printf("%s does not exist\n", kInDir) ;
  return ;
      }

  
      cout<<"INDIR   : "<<kInDir<<endl;
      cout<<"NFILES  : "<<kFile<<endl;
      cout<<"PATTERN : " <<kPattern<<endl;

      TString datafile="";
      if(kInputData == "ESD") datafile = "AliESDs.root" ;
      else if(kInputData == "AOD") datafile = "AliAODs.root" ;
      else if(kInputData == "MC")  datafile = "galice.root" ;
      
      //Loop on ESD files, add them to chain
      Int_t event =0;
      Int_t skipped=0 ; 
      char file[120] ;
      
      for (event = 0 ; event < kFile ; event++) {
  sprintf(file, "%s/%s%d/%s", kInDir,kPattern,event,datafile.Data()) ; 
  TFile * fESD = 0 ; 
  //Check if file exists and add it, if not skip it
  if ( fESD = TFile::Open(file)) {
    if ( fESD->Get(kTreeName) ) { 
      printf("++++ Adding %s\n", file) ;
      chain->AddFile(file);
    }
  }
  else { 
    printf("---- Skipping %s\n", file) ;
    skipped++ ;
  }
      }
      printf("number of entries # %lld, skipped %d\n", chain->GetEntries(), skipped*100) ;  
    }
    else {
      TString input = "AliESDs.root" ;
      cout<<">>>>>> No list added, take a single file <<<<<<<<< "<<input<<endl;
      chain->AddFile(input);
    }
    
  }// local files analysis
  
  //------------------------------
  //GRID xml files
  //-----------------------------
  else if(mode == mGRID){
    //Get colection file. It is specified by the environmental
    //variable XML

    if(gSystem->Getenv("XML") )
      kXML = gSystem->Getenv("XML");
    else
      sprintf(kXML, "collection.xml") ; 
    
    if (!TFile::Open(kXML)) {
      printf("No collection file with name -- %s -- was found\n",kXML);
      return ;
    }
    else cout<<"XML file "<<kXML<<endl;

    //Load necessary libraries and connect to the GRID
    gSystem->Load("libNetx") ;
    gSystem->Load("libRAliEn");
    TGrid::Connect("alien://") ;

    //Feed Grid with collection file
    //TGridCollection * collection =  (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"%s\", 0)", kXML));
    TGridCollection * collection = (TGridCollection*) TAlienCollection::Open(kXML);
    if (! collection) {
      AliError(Form("%s not found", kXML)) ; 
      return kFALSE ; 
    }
    TGridResult* result = collection->GetGridResult("",0 ,0);
   
    // Makes the ESD chain 
    printf("*** Getting the Chain       ***\n");
    for (Int_t index = 0; index < result->GetEntries(); index++) {
      TString alienURL = result->GetKey(index, "turl") ; 
      cout << "================== " << alienURL << endl ; 
      chain->Add(alienURL) ; 
    }
  }// xml analysis
  
  gSystem->ChangeDirectory(ocwd.Data());
}