]> git.uio.no Git - u/mrichter/AliRoot.git/blobdiff - STEER/AliReconstruction.cxx
Using the new AliGeomManager functionality. Inside RunLocalReconstruction - unload...
[u/mrichter/AliRoot.git] / STEER / AliReconstruction.cxx
index d18e8bcde108189878f17b007179826a44625126..cd33f80b43b7c55feab8777a753fe6b5a624efcf 100644 (file)
 // The index -1 (default) can be used for the last event to indicate no      //
 // upper limit of the event range.                                           //
 //                                                                           //
+// In case of raw-data reconstruction the user can modify the default        //
+// number of events per digits/clusters/tracks file. In case the option      //
+// is not used the number is set 1. In case the user provides 0, than        //
+// the number of events is equal to the number of events inside the          //
+// raw-data file (i.e. one digits/clusters/tracks file):                     //
+//                                                                           //
+//   rec.SetNumberOfEventsPerFile(...);                                      //
+//                                                                           //
+//                                                                           //
 // The name of the galice file can be changed from the default               //
 // "galice.root" by passing it as argument to the AliReconstruction          //
 // constructor or by                                                         //
 #include "AliTracker.h"
 #include "AliVertexer.h"
 #include "AliVertexerTracks.h"
+#include "AliV0vertexer.h"
+#include "AliCascadeVertexer.h"
 #include "AliHeader.h"
 #include "AliGenEventHeader.h"
 #include "AliPID.h"
 #include "AliDetectorTag.h"
 #include "AliEventTag.h"
 
+#include "AliGeomManager.h"
 #include "AliTrackPointArray.h"
 #include "AliCDBManager.h"
 #include "AliCDBEntry.h"
 #include "AliCentralTrigger.h"
 #include "AliCTPRawStream.h"
 
+#include "AliAODEvent.h"
+#include "AliAODHeader.h"
+#include "AliAODTrack.h"
+#include "AliAODVertex.h"
+#include "AliAODCluster.h"
+
+
 ClassImp(AliReconstruction)
 
 
 //_____________________________________________________________________________
-const char* AliReconstruction::fgkDetectorName[AliReconstruction::fgkNDetectors] = {"ITS", "TPC", "TRD", "TOF", "PHOS", "RICH", "EMCAL", "MUON", "FMD", "ZDC", "PMD", "START", "VZERO", "CRT", "HLT"};
+const char* AliReconstruction::fgkDetectorName[AliReconstruction::fgkNDetectors] = {"ITS", "TPC", "TRD", "TOF", "PHOS", "HMPID", "EMCAL", "MUON", "FMD", "ZDC", "PMD", "T0", "VZERO", "ACORDE", "HLT"};
 
 //_____________________________________________________________________________
 AliReconstruction::AliReconstruction(const char* gAliceFilename, const char* cdbUri,
@@ -162,9 +181,11 @@ AliReconstruction::AliReconstruction(const char* gAliceFilename, const char* cdb
   fUniformField(kTRUE),
   fRunVertexFinder(kTRUE),
   fRunHLTTracking(kFALSE),
+  fRunMuonTracking(kFALSE),
   fStopOnError(kFALSE),
   fWriteAlignmentData(kFALSE),
   fWriteESDfriend(kFALSE),
+  fWriteAOD(kFALSE),
   fFillTriggerESD(kTRUE),
 
   fRunLocalReconstruction("ALL"),
@@ -175,10 +196,12 @@ AliReconstruction::AliReconstruction(const char* gAliceFilename, const char* cdb
   fEquipIdMap(""),
   fFirstEvent(0),
   fLastEvent(-1),
+  fNumberOfEventsPerFile(1),
   fCheckPointLevel(0),
   fOptions(),
   fLoadAlignFromCDB(kTRUE),
   fLoadAlignData("ALL"),
+  fESDPar(""),
 
   fRunLoader(NULL),
   fRawReader(NULL),
@@ -207,9 +230,11 @@ AliReconstruction::AliReconstruction(const AliReconstruction& rec) :
   fUniformField(rec.fUniformField),
   fRunVertexFinder(rec.fRunVertexFinder),
   fRunHLTTracking(rec.fRunHLTTracking),
+  fRunMuonTracking(rec.fRunMuonTracking),
   fStopOnError(rec.fStopOnError),
   fWriteAlignmentData(rec.fWriteAlignmentData),
   fWriteESDfriend(rec.fWriteESDfriend),
+  fWriteAOD(rec.fWriteAOD),
   fFillTriggerESD(rec.fFillTriggerESD),
 
   fRunLocalReconstruction(rec.fRunLocalReconstruction),
@@ -220,10 +245,12 @@ AliReconstruction::AliReconstruction(const AliReconstruction& rec) :
   fEquipIdMap(rec.fEquipIdMap),
   fFirstEvent(rec.fFirstEvent),
   fLastEvent(rec.fLastEvent),
+  fNumberOfEventsPerFile(rec.fNumberOfEventsPerFile),
   fCheckPointLevel(0),
   fOptions(),
   fLoadAlignFromCDB(rec.fLoadAlignFromCDB),
   fLoadAlignData(rec.fLoadAlignData),
+  fESDPar(rec.fESDPar),
 
   fRunLoader(NULL),
   fRawReader(NULL),
@@ -356,6 +383,9 @@ void AliReconstruction::SetSpecificStorage(const char* calibType, const char* ur
 
 }
 
+
+
+
 //_____________________________________________________________________________
 Bool_t AliReconstruction::SetRunNumber()
 {
@@ -393,72 +423,6 @@ Bool_t AliReconstruction::SetRunNumber()
   return kTRUE;
 }
 
-//_____________________________________________________________________________
-Bool_t AliReconstruction::ApplyAlignObjsToGeom(TObjArray* alObjArray)
-{
-  // Read collection of alignment objects (AliAlignObj derived) saved
-  // in the TClonesArray ClArrayName and apply them to the geometry
-  // manager singleton.
-  //
-  alObjArray->Sort();
-  Int_t nvols = alObjArray->GetEntriesFast();
-
-  Bool_t flag = kTRUE;
-
-  for(Int_t j=0; j<nvols; j++)
-    {
-      AliAlignObj* alobj = (AliAlignObj*) alObjArray->UncheckedAt(j);
-      if (alobj->ApplyToGeometry() == kFALSE) flag = kFALSE;
-    }
-
-  if (AliDebugLevelClass() >= 1) {
-    gGeoManager->GetTopNode()->CheckOverlaps(20);
-    TObjArray* ovexlist = gGeoManager->GetListOfOverlaps();
-    if(ovexlist->GetEntriesFast()){  
-      AliError("The application of alignment objects to the geometry caused huge overlaps/extrusions!");
-   }
-  }
-
-  return flag;
-
-}
-
-//_____________________________________________________________________________
-Bool_t AliReconstruction::SetAlignObjArraySingleDet(const char* detName)
-{
-  // Fills array of single detector's alignable objects from CDB
-  
-  AliDebug(2, Form("Loading alignment data for detector: %s",detName));
-  
-  AliCDBEntry *entry;
-       
-  AliCDBPath path(detName,"Align","Data");
-       
-  entry=AliCDBManager::Instance()->Get(path.GetPath());
-  if(!entry){ 
-       AliDebug(2,Form("Couldn't load alignment data for detector %s",detName));
-       return kFALSE;
-  }
-  entry->SetOwner(1);
-  TClonesArray *alignArray = (TClonesArray*) entry->GetObject();       
-  alignArray->SetOwner(0);
-  AliDebug(2,Form("Found %d alignment objects for %s",
-                       alignArray->GetEntries(),detName));
-
-  AliAlignObj *alignObj=0;
-  TIter iter(alignArray);
-       
-  // loop over align objects in detector
-  while( ( alignObj=(AliAlignObj *) iter.Next() ) ){
-       fAlignObjArray->Add(alignObj);
-  }
-  // delete entry --- Don't delete, it is cached!
-       
-  AliDebug(2, Form("fAlignObjArray entries: %d",fAlignObjArray->GetEntries() ));
-  return kTRUE;
-
-}
-
 //_____________________________________________________________________________
 Bool_t AliReconstruction::MisalignGeometry(const TString& detectors)
 {
@@ -472,51 +436,36 @@ Bool_t AliReconstruction::MisalignGeometry(const TString& detectors)
 
   // Load alignment data from CDB and fill fAlignObjArray 
   if(fLoadAlignFromCDB){
-       if(!fAlignObjArray) fAlignObjArray = new TObjArray();
        
-       //fAlignObjArray->RemoveAll(); 
-       fAlignObjArray->Clear();        
-       fAlignObjArray->SetOwner(0);
-       TString detStr = detectors;
-       TString dataNotLoaded="";
-       TString dataLoaded="";
-  
-       for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
-         if (!IsSelected(fgkDetectorName[iDet], detStr)) continue;
-         if(!SetAlignObjArraySingleDet(fgkDetectorName[iDet])){
-           dataNotLoaded += fgkDetectorName[iDet];
-           dataNotLoaded += " ";
-         } else {
-           dataLoaded += fgkDetectorName[iDet];
-           dataLoaded += " ";
-         }
-       } // end loop over detectors
-  
-       if ((detStr.CompareTo("ALL") == 0)) detStr = "";
-       dataNotLoaded += detStr;
-       if(!dataLoaded.IsNull()) AliInfo(Form("Alignment data loaded for: %s",
-                         dataLoaded.Data()));
-       if(!dataNotLoaded.IsNull()) AliInfo(Form("Didn't/couldn't load alignment data for: %s",
-                         dataNotLoaded.Data()));
-  } // fLoadAlignFromCDB flag
-  // Check if the array with alignment objects was
-  // provided by the user. If yes, apply the objects
-  // to the present TGeo geometry
-  if (fAlignObjArray) {
-    if (gGeoManager && gGeoManager->IsClosed()) {
-      if (ApplyAlignObjsToGeom(fAlignObjArray) == kFALSE) {
-       AliError("The misalignment of one or more volumes failed!"
-                "Compare the list of simulated detectors and the list of detector alignment data!");
+    TString detStr = detectors;
+    TString loadAlObjsListOfDets = "";
+    
+    for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
+      if (!IsSelected(fgkDetectorName[iDet], detStr)) continue;
+      loadAlObjsListOfDets += fgkDetectorName[iDet];
+      loadAlObjsListOfDets += " ";
+    } // end loop over detectors
+    AliGeomManager::ApplyAlignObjsFromCDB(loadAlObjsListOfDets.Data());
+  }else{
+    // Check if the array with alignment objects was
+    // provided by the user. If yes, apply the objects
+    // to the present TGeo geometry
+    if (fAlignObjArray) {
+      if (gGeoManager && gGeoManager->IsClosed()) {
+       if (AliGeomManager::ApplyAlignObjsToGeom(*fAlignObjArray) == kFALSE) {
+         AliError("The misalignment of one or more volumes failed!"
+                  "Compare the list of simulated detectors and the list of detector alignment data!");
+         return kFALSE;
+       }
+      }
+      else {
+       AliError("Can't apply the misalignment! gGeoManager doesn't exist or it is still opened!");
        return kFALSE;
       }
     }
-    else {
-      AliError("Can't apply the misalignment! gGeoManager doesn't exist or it is still opened!");
-      return kFALSE;
-    }
   }
+  
+  delete fAlignObjArray; fAlignObjArray=0;
 
   return kTRUE;
 }
@@ -541,8 +490,7 @@ void AliReconstruction::SetOption(const char* detector, const char* option)
 
 
 //_____________________________________________________________________________
-Bool_t AliReconstruction::Run(const char* input,
-                             Int_t firstEvent, Int_t lastEvent)
+Bool_t AliReconstruction::Run(const char* input)
 {
 // run the reconstruction
 
@@ -574,9 +522,11 @@ Bool_t AliReconstruction::Run(const char* input,
   if (!gGeoManager) {
     TString geom(gSystem->DirName(fGAliceFileName));
     geom += "/geometry.root";
-    TGeoManager::Import(geom.Data());
+    AliGeomManager::LoadGeometry(geom.Data());
     if (!gGeoManager) if (fStopOnError) return kFALSE;
   }
+
+  AliCDBManager* man = AliCDBManager::Instance();
   if (!MisalignGeometry(fLoadAlignData)) if (fStopOnError) return kFALSE;
 
   // local reconstruction
@@ -609,7 +559,7 @@ Bool_t AliReconstruction::Run(const char* input,
   stopwatch.Start();
 
   // get the possibly already existing ESD file and tree
-  AliESD* esd = new AliESD; AliESD* hltesd = new AliESD;
+  AliESD* esd = new AliESD(); AliESD* hltesd = new AliESD();
   TFile* fileOld = NULL;
   TTree* treeOld = NULL; TTree *hlttreeOld = NULL;
   if (!gSystem->AccessPathName("AliESDs.root")){
@@ -617,39 +567,54 @@ Bool_t AliReconstruction::Run(const char* input,
     fileOld = TFile::Open("AliESDs.old.root");
     if (fileOld && fileOld->IsOpen()) {
       treeOld = (TTree*) fileOld->Get("esdTree");
-      if (treeOld) treeOld->SetBranchAddress("ESD", &esd);
+      if (treeOld)esd->ReadFromTree(treeOld);
       hlttreeOld = (TTree*) fileOld->Get("HLTesdTree");
-      if (hlttreeOld) hlttreeOld->SetBranchAddress("ESD", &hltesd);
+      if (hlttreeOld)  hltesd->ReadFromTree(hlttreeOld);
     }
   }
 
   // create the ESD output file and tree
   TFile* file = TFile::Open("AliESDs.root", "RECREATE");
+  file->SetCompressionLevel(2);
   if (!file->IsOpen()) {
     AliError("opening AliESDs.root failed");
     if (fStopOnError) {CleanUp(file, fileOld); return kFALSE;}    
   }
+
   TTree* tree = new TTree("esdTree", "Tree with ESD objects");
-  tree->Branch("ESD", "AliESD", &esd);
+  esd = new AliESD();
+  esd->CreateStdContent();
+  esd->WriteToTree(tree);
+
   TTree* hlttree = new TTree("HLTesdTree", "Tree with HLT ESD objects");
-  hlttree->Branch("ESD", "AliESD", &hltesd);
+  hltesd = new AliESD();
+  hltesd->CreateStdContent();
+  hltesd->WriteToTree(hlttree);
+
+  /* CKB Why?
   delete esd; delete hltesd;
   esd = NULL; hltesd = NULL;
-
-  // create the file and tree with ESD additions
-  TFile *filef=0; TTree *treef=0; AliESDfriend *esdf=0;
+  */
+  // create the branch with ESD additions
+  AliESDfriend *esdf = 0; 
   if (fWriteESDfriend) {
-     filef = TFile::Open("AliESDfriends.root", "RECREATE");
-     if (!filef->IsOpen()) {
-        AliError("opening AliESDfriends.root failed");
-     }
-     treef = new TTree("esdFriendTree", "Tree with ESD friends");
-     treef->Branch("ESDfriend", "AliESDfriend", &esdf);
+    esdf = new AliESDfriend();
+    TBranch *br=tree->Branch("ESDfriend.","AliESDfriend", &esdf);
+    br->SetFile("AliESDfriends.root");
+    esd->AddObject(esdf);
+  }
+  
+  // Get the diamond profile from OCDB
+  AliCDBEntry* entry = AliCDBManager::Instance()
+       ->Get("GRP/Calib/MeanVertex");
+       
+  if(entry) {
+       fDiamondProfile = dynamic_cast<AliESDVertex*> (entry->GetObject());  
+  } else {
+       AliError("No diamond profile found in OCDB!");
   }
 
-  gROOT->cd();
-
-  AliVertexerTracks tVertexer;
+  AliVertexerTracks tVertexer(AliTracker::GetBz());
   if(fDiamondProfile) tVertexer.SetVtxStart(fDiamondProfile);
 
   // loop over events
@@ -657,29 +622,29 @@ Bool_t AliReconstruction::Run(const char* input,
   
   for (Int_t iEvent = 0; iEvent < fRunLoader->GetNumberOfEvents(); iEvent++) {
     if (fRawReader) fRawReader->NextEvent();
-    if ((iEvent < firstEvent) || ((lastEvent >= 0) && (iEvent > lastEvent))) {
+    if ((iEvent < fFirstEvent) || ((fLastEvent >= 0) && (iEvent > fLastEvent))) {
       // copy old ESD to the new one
       if (treeOld) {
-       treeOld->SetBranchAddress("ESD", &esd);
+       esd->ReadFromTree(treeOld);
        treeOld->GetEntry(iEvent);
       }
       tree->Fill();
       if (hlttreeOld) {
-       hlttreeOld->SetBranchAddress("ESD", &hltesd);
+       esd->ReadFromTree(hlttreeOld);
        hlttreeOld->GetEntry(iEvent);
       }
       hlttree->Fill();
       continue;
     }
-
+    
     AliInfo(Form("processing event %d", iEvent));
     fRunLoader->GetEvent(iEvent);
 
-    char fileName[256];
-    sprintf(fileName, "ESD_%d.%d_final.root", 
+    char aFileName[256];
+    sprintf(aFileName, "ESD_%d.%d_final.root", 
            fRunLoader->GetHeader()->GetRun(), 
            fRunLoader->GetHeader()->GetEventNrInRun());
-    if (!gSystem->AccessPathName(fileName)) continue;
+    if (!gSystem->AccessPathName(aFileName)) continue;
 
     // local reconstruction
     if (!fRunLocalReconstruction.IsNull()) {
@@ -688,16 +653,21 @@ Bool_t AliReconstruction::Run(const char* input,
       }
     }
 
-    esd = new AliESD; hltesd = new AliESD;
+  
     esd->SetRunNumber(fRunLoader->GetHeader()->GetRun());
     hltesd->SetRunNumber(fRunLoader->GetHeader()->GetRun());
-    esd->SetEventNumber(fRunLoader->GetHeader()->GetEventNrInRun());
-    hltesd->SetEventNumber(fRunLoader->GetHeader()->GetEventNrInRun());
-
+    esd->SetEventNumberInFile(fRunLoader->GetHeader()->GetEventNrInRun());
+    hltesd->SetEventNumberInFile(fRunLoader->GetHeader()->GetEventNrInRun());
+    
     // Set magnetic field from the tracker
     esd->SetMagneticField(AliTracker::GetBz());
     hltesd->SetMagneticField(AliTracker::GetBz());
 
+    
+    
+    // Fill raw-data error log into the ESD
+    if (fRawReader) FillRawDataErrorLog(iEvent,esd);
+
     // vertex finder
     if (fRunVertexFinder) {
       if (!ReadESD(esd, "vertex")) {
@@ -718,6 +688,15 @@ Bool_t AliReconstruction::Run(const char* input,
       }
     }
 
+    // Muon tracking
+    if (!fRunTracking.IsNull()) {
+      if (fRunMuonTracking) {
+       if (!RunMuonTracking(esd)) {
+         if (fStopOnError) {CleanUp(file, fileOld); return kFALSE;}
+       }
+      }
+    }
+
     // barrel tracking
     if (!fRunTracking.IsNull()) {
       if (!ReadESD(esd, "tracking")) {
@@ -750,42 +729,93 @@ Bool_t AliReconstruction::Run(const char* input,
       }
     }
 
-    esd->SetPrimaryVertex(tVertexer.FindPrimaryVertex(esd));
+    //Try to improve the reconstructed primary vertex position using the tracks
+    AliESDVertex *pvtx=0;
+    Bool_t dovertex=kTRUE;
+    TObject* obj = fOptions.FindObject("ITS");
+    if (obj) {
+      TString optITS = obj->GetTitle();
+      if (optITS.Contains("cosmics") || optITS.Contains("COSMICS")) 
+       dovertex=kFALSE;
+    }
+    if(dovertex) pvtx=tVertexer.FindPrimaryVertex(esd);
+    if(fDiamondProfile) esd->SetDiamond(fDiamondProfile);
+    
+    if (pvtx)
+    if (pvtx->GetStatus()) {
+       // Store the improved primary vertex
+       esd->SetPrimaryVertex(pvtx);
+       // Propagate the tracks to the DCA to the improved primary vertex
+       Double_t somethingbig = 777.;
+       Double_t bz = esd->GetMagneticField();
+       Int_t nt=esd->GetNumberOfTracks();
+       while (nt--) {
+        AliESDtrack *t = esd->GetTrack(nt);
+         t->RelateToVertex(pvtx, bz, somethingbig);
+       } 
+    }
+
+    {
+    // V0 finding
+    AliV0vertexer vtxer;
+    vtxer.Tracks2V0vertices(esd);
 
+    // Cascade finding
+    AliCascadeVertexer cvtxer;
+    cvtxer.V0sTracks2CascadeVertices(esd);
+    }
     // write ESD
+    if (fWriteESDfriend) {
+      new (esdf) AliESDfriend(); // Reset...
+      esd->GetESDfriend(esdf);
+    }
     tree->Fill();
+
     // write HLT ESD
     hlttree->Fill();
 
-    // write ESD friend
-    if (fWriteESDfriend) {
-       esdf=new AliESDfriend();
-       esd->GetESDfriend(esdf);
-       treef->Fill();  
-    }
-
     if (fCheckPointLevel > 0)  WriteESD(esd, "final"); 
-    delete esd; delete hltesd;
-    esd = NULL; hltesd = NULL;
+    esd->Reset();
+    hltesd->Reset();
+    // esdf->Reset();
+    // delete esdf; esdf = 0;
+  } 
+
+
+  tree->GetUserInfo()->Add(esd);
+  hlttree->GetUserInfo()->Add(hltesd);
+
+
+
+  if(fESDPar.Contains("ESD.par")){
+    AliInfo("Attaching ESD.par to Tree");
+    TNamed *fn = CopyFileToTNamed(fESDPar.Data(),"ESD.par");
+    tree->GetUserInfo()->Add(fn);
   }
 
+
   AliInfo(Form("Execution time for filling ESD : R:%.2fs C:%.2fs",
               stopwatch.RealTime(),stopwatch.CpuTime()));
 
   file->cd();
+  if (fWriteESDfriend)
+    tree->SetBranchStatus("ESDfriend*",0);
   tree->Write();
   hlttree->Write();
 
-  if (fWriteESDfriend) {
-     filef->cd();
-     treef->Write(); delete treef; filef->Close(); delete filef; 
+  if (fWriteAOD) {
+    TFile *aodFile = TFile::Open("AliAOD.root", "RECREATE");
+    ESDFile2AODFile(file, aodFile);
+    aodFile->Close();
   }
 
+  gROOT->cd();
   // Create tags for the events in the ESD tree (the ESD tree is always present)
   // In case of empty events the tags will contain dummy values
   CreateTag(file);
-  CleanUp(file, fileOld);
+
+ CleanUp(file, fileOld);
 
   return kTRUE;
 }
@@ -799,6 +829,9 @@ Bool_t AliReconstruction::RunLocalReconstruction(const TString& detectors)
   TStopwatch stopwatch;
   stopwatch.Start();
 
+  AliCDBManager* man = AliCDBManager::Instance();
+  Bool_t origCache = man->GetCacheFlag();
+
   TString detStr = detectors;
   for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
     if (!IsSelected(fgkDetectorName[iDet], detStr)) continue;
@@ -809,6 +842,13 @@ Bool_t AliReconstruction::RunLocalReconstruction(const TString& detectors)
     AliInfo(Form("running reconstruction for %s", fgkDetectorName[iDet]));
     TStopwatch stopwatchDet;
     stopwatchDet.Start();
+
+    AliInfo(Form("Loading calibration data from OCDB for %s", fgkDetectorName[iDet]));
+
+    man->SetCacheFlag(kTRUE);
+    TString calibPath = Form("%s/Calib/*", fgkDetectorName[iDet]);
+    man->GetAll(calibPath); // entries are cached!
+
     if (fRawReader) {
       fRawReader->RewindEvents();
       reconstructor->Reconstruct(fRunLoader, fRawReader);
@@ -818,8 +858,14 @@ Bool_t AliReconstruction::RunLocalReconstruction(const TString& detectors)
     AliInfo(Form("Execution time for %s: R:%.2fs C:%.2fs",
                 fgkDetectorName[iDet],
                 stopwatchDet.RealTime(),stopwatchDet.CpuTime()));
+
+    // unload calibration data
+    man->UnloadFromCache(calibPath);
+    //man->ClearCache();
   }
 
+  man->SetCacheFlag(origCache);
+
   if ((detStr.CompareTo("ALL") != 0) && !detStr.IsNull()) {
     AliError(Form("the following detectors were not found: %s",
                   detStr.Data()));
@@ -889,9 +935,9 @@ Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
     }
     loader->WriteRecPoints("OVERWRITE");
     loader->UnloadRecPoints();
-    AliDebug(1,Form("Execution time for %s: R:%.2fs C:%.2fs",
-                   fgkDetectorName[iDet],
-                   stopwatchDet.RealTime(),stopwatchDet.CpuTime()));
+    AliInfo(Form("Execution time for %s: R:%.2fs C:%.2fs",
+                fgkDetectorName[iDet],
+                stopwatchDet.RealTime(),stopwatchDet.CpuTime()));
   }
 
   if ((detStr.CompareTo("ALL") != 0) && !detStr.IsNull()) {
@@ -924,6 +970,7 @@ Bool_t AliReconstruction::RunVertexFinder(AliESD*& esd)
   }
 
   if (fVertexer) {
+    if(fDiamondProfile) fVertexer->SetVtxStart(fDiamondProfile);
     AliInfo("running the ITS vertex finder");
     if (fLoader[0]) fLoader[0]->LoadRecPoints();
     vertex = fVertexer->FindVertexForCurrentEvent(fRunLoader->GetEventNumber());
@@ -934,7 +981,6 @@ Bool_t AliReconstruction::RunVertexFinder(AliESD*& esd)
       vertex->SetName("default");
     }
     else {
-      vertex->SetTruePos(vtxPos);  // store also the vertex from MC
       vertex->SetName("reconstructed");
     }
 
@@ -952,7 +998,7 @@ Bool_t AliReconstruction::RunVertexFinder(AliESD*& esd)
   }
   esd->SetVertex(vertex);
   // if SPD multiplicity has been determined, it is stored in the ESD
-  AliMultiplicity *mult= fVertexer->GetMultiplicity();
+  AliMultiplicity *mult = fVertexer->GetMultiplicity();
   if(mult)esd->SetMultiplicity(mult);
 
   for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
@@ -1026,6 +1072,70 @@ Bool_t AliReconstruction::RunHLTTracking(AliESD*& esd)
   return kTRUE;
 }
 
+//_____________________________________________________________________________
+Bool_t AliReconstruction::RunMuonTracking(AliESD*& esd)
+{
+// run the muon spectrometer tracking
+
+  TStopwatch stopwatch;
+  stopwatch.Start();
+
+  if (!fRunLoader) {
+    AliError("Missing runLoader!");
+    return kFALSE;
+  }
+  Int_t iDet = 7; // for MUON
+
+  AliInfo("is running...");
+
+  // Get a pointer to the MUON reconstructor
+  AliReconstructor *reconstructor = GetReconstructor(iDet);
+  if (!reconstructor) return kFALSE;
+
+  
+  TString detName = fgkDetectorName[iDet];
+  AliDebug(1, Form("%s tracking", detName.Data()));
+  AliTracker *tracker =  reconstructor->CreateTracker(fRunLoader);
+  if (!tracker) {
+    AliWarning(Form("couldn't create a tracker for %s", detName.Data()));
+    return kFALSE;
+  }
+     
+  // create Tracks
+  fLoader[iDet]->LoadTracks("update");
+  fLoader[iDet]->CleanTracks();
+  fLoader[iDet]->MakeTracksContainer();
+
+  // read RecPoints
+  fLoader[iDet]->LoadRecPoints("read");  
+  tracker->LoadClusters(fLoader[iDet]->TreeR());
+  
+  Int_t rv = tracker->Clusters2Tracks(esd);
+  
+  fLoader[iDet]->UnloadRecPoints();
+  
+  if ( rv )
+  {
+    AliError(Form("%s Clusters2Tracks failed", fgkDetectorName[iDet]));
+    return kFALSE;
+  }
+  
+  tracker->UnloadClusters();
+  
+  fLoader[iDet]->UnloadRecPoints();
+
+  fLoader[iDet]->WriteTracks("OVERWRITE");
+  fLoader[iDet]->UnloadTracks();
+
+  delete tracker;
+  
+  AliInfo(Form("Execution time: R:%.2fs C:%.2fs",
+              stopwatch.RealTime(),stopwatch.CpuTime()));
+
+  return kTRUE;
+}
+
+
 //_____________________________________________________________________________
 Bool_t AliReconstruction::RunTracking(AliESD*& esd)
 {
@@ -1036,6 +1146,10 @@ Bool_t AliReconstruction::RunTracking(AliESD*& esd)
 
   AliInfo("running tracking");
 
+  //Fill the ESD with the T0 info (will be used by the TOF) 
+  if (fReconstructor[11])
+      GetReconstructor(11)->FillESD(fRunLoader, esd);
+
   // pass 1: TPC + ITS inwards
   for (Int_t iDet = 1; iDet >= 0; iDet--) {
     if (!fTracker[iDet]) continue;
@@ -1086,7 +1200,7 @@ Bool_t AliReconstruction::RunTracking(AliESD*& esd)
     // run tracking
     if (fTracker[iDet]->PropagateBack(esd) != 0) {
       AliError(Form("%s backward propagation failed", fgkDetectorName[iDet]));
-      return kFALSE;
+      //      return kFALSE;
     }
     if (fCheckPointLevel > 1) {
       WriteESD(esd, Form("%s.back", fgkDetectorName[iDet]));
@@ -1118,7 +1232,7 @@ Bool_t AliReconstruction::RunTracking(AliESD*& esd)
     // run tracking
     if (fTracker[iDet]->RefitInward(esd) != 0) {
       AliError(Form("%s inward refit failed", fgkDetectorName[iDet]));
-      return kFALSE;
+      //      return kFALSE;
     }
     if (fCheckPointLevel > 1) {
       WriteESD(esd, Form("%s.refit", fgkDetectorName[iDet]));
@@ -1270,12 +1384,21 @@ Bool_t AliReconstruction::FillRawEventHeaderESD(AliESD*& esd)
   // 
 
   AliInfo("Filling information from RawReader Header");
+  esd->SetBunchCrossNumber(0);
+  esd->SetOrbitNumber(0);
+  esd->SetPeriodNumber(0);
   esd->SetTimeStamp(0);
   esd->SetEventType(0);
   const AliRawEventHeaderBase * eventHeader = fRawReader->GetEventHeader();
   if (eventHeader){
+
+    const UInt_t *id = eventHeader->GetP("Id");
+    esd->SetBunchCrossNumber((id)[1]&0x00000fff);
+    esd->SetOrbitNumber((((id)[0]<<20)&0xf00000)|(((id)[1]>>12)&0xfffff));
+    esd->SetPeriodNumber(((id)[0]>>4)&0x0fffffff);
+
     esd->SetTimeStamp((eventHeader->Get("Timestamp")));  
-    esd->SetEventType((eventHeader->Get("Type")));  
+    esd->SetEventType((eventHeader->Get("Type")));
   }
 
   return kTRUE;
@@ -1378,6 +1501,10 @@ Bool_t AliReconstruction::InitRunLoader()
       iEvent++;
     }
     fRawReader->RewindEvents();
+    if (fNumberOfEventsPerFile > 0)
+      fRunLoader->SetNumberOfEventsPerFile(fNumberOfEventsPerFile);
+    else
+      fRunLoader->SetNumberOfEventsPerFile(iEvent);
     fRunLoader->WriteHeader("OVERWRITE");
     fRunLoader->CdGAFile();
     fRunLoader->Write(0, TObject::kOverwrite);
@@ -1402,10 +1529,10 @@ AliReconstructor* AliReconstruction::GetReconstructor(Int_t iDet)
 
   if (detName == "HLT") {
     if (!gROOT->GetClass("AliLevel3")) {
-      gSystem->Load("libAliL3Src.so");
-      gSystem->Load("libAliL3Misc.so");
-      gSystem->Load("libAliL3Hough.so");
-      gSystem->Load("libAliL3Comp.so");
+      gSystem->Load("libAliHLTSrc.so");
+      gSystem->Load("libAliHLTMisc.so");
+      gSystem->Load("libAliHLTHough.so");
+      gSystem->Load("libAliHLTComp.so");
     }
   }
 
@@ -1445,7 +1572,7 @@ AliReconstructor* AliReconstruction::GetReconstructor(Int_t iDet)
        ->CreateDetectorFolders(fRunLoader->GetEventFolder(), 
                                detName, detName);
       // first check if a plugin is defined for the loader
-      TPluginHandler* pluginHandler = 
+      pluginHandler = 
        pluginManager->FindHandler("AliLoader", detName);
       // if not, add a plugin for it
       if (!pluginHandler) {
@@ -1512,6 +1639,11 @@ Bool_t AliReconstruction::CreateTrackers(const TString& detectors)
       fRunHLTTracking = kTRUE;
       continue;
     }
+    if (detName == "MUON") {
+      fRunMuonTracking = kTRUE;
+      continue;
+    }
+
 
     fTracker[iDet] = reconstructor->CreateTracker(fRunLoader);
     if (!fTracker[iDet] && (iDet < 7)) {
@@ -1566,7 +1698,7 @@ Bool_t AliReconstruction::ReadESD(AliESD*& esd, const char* recStep) const
   if (!esd) return kFALSE;
   char fileName[256];
   sprintf(fileName, "ESD_%d.%d_%s.root", 
-         esd->GetRunNumber(), esd->GetEventNumber(), recStep);
+         esd->GetRunNumber(), esd->GetEventNumberInFile(), recStep);
   if (gSystem->AccessPathName(fileName)) return kFALSE;
 
   AliInfo(Form("reading ESD from file %s", fileName));
@@ -1594,7 +1726,7 @@ void AliReconstruction::WriteESD(AliESD* esd, const char* recStep) const
   if (!esd) return;
   char fileName[256];
   sprintf(fileName, "ESD_%d.%d_%s.root", 
-         esd->GetRunNumber(), esd->GetEventNumber(), recStep);
+         esd->GetRunNumber(), esd->GetEventNumberInFile(), recStep);
 
   AliDebug(1, Form("writing ESD to file %s", fileName));
   TFile* file = TFile::Open(fileName, "recreate");
@@ -1613,6 +1745,11 @@ void AliReconstruction::WriteESD(AliESD* esd, const char* recStep) const
 //_____________________________________________________________________________
 void AliReconstruction::CreateTag(TFile* file)
 {
+  //GRP
+  Float_t lhcLuminosity = 0.0;
+  TString lhcState = "test";
+  UInt_t detectorMask = 0;
+
   /////////////
   //muon code//
   ////////////
@@ -1660,17 +1797,17 @@ void AliReconstruction::CreateTag(TFile* file)
     delete file;
     return ;
   }  
-  Int_t firstEvent = 0,lastEvent = 0;
-  TTree *t = (TTree*) file->Get("esdTree");
-  TBranch * b = t->GetBranch("ESD");
-  AliESD *esd = 0;
-  b->SetAddress(&esd);
+  Int_t lastEvent = 0;
+  TTree *b = (TTree*) file->Get("esdTree");
+  AliESD *esd = new AliESD();
+  esd->ReadFromTree(b);
 
-  b->GetEntry(0);
+  b->GetEntry(fFirstEvent);
   Int_t iInitRunNumber = esd->GetRunNumber();
   
-  Int_t iNumberOfEvents = b->GetEntries();
-  for (Int_t iEventNumber = 0; iEventNumber < iNumberOfEvents; iEventNumber++) {
+  Int_t iNumberOfEvents = (Int_t)b->GetEntries();
+  if(fLastEvent != -1) iNumberOfEvents = fLastEvent + 1;
+  for (Int_t iEventNumber = fFirstEvent; iEventNumber < iNumberOfEvents; iEventNumber++) {
     ntrack = 0;
     nPos = 0;
     nNeg = 0;
@@ -1871,17 +2008,21 @@ void AliReconstruction::CreateTag(TFile* file)
     evTag->SetMeanPt(meanPt);
     evTag->SetMaxPt(maxPt);
     
+    tag->SetLHCTag(lhcLuminosity,lhcState);
+    tag->SetDetectorTag(detectorMask);
+
     tag->SetRunId(iInitRunNumber);
     tag->AddEventTag(*evTag);
   }
-  lastEvent = iNumberOfEvents;
+  if(fLastEvent == -1) lastEvent = (Int_t)b->GetEntries();
+  else lastEvent = fLastEvent;
        
   ttag.Fill();
   tag->Clear();
 
   char fileName[256];
   sprintf(fileName, "Run%d.Event%d_%d.ESD.tag.root", 
-         tag->GetRunId(),firstEvent,lastEvent );
+         tag->GetRunId(),fFirstEvent,lastEvent );
   AliInfo(Form("writing tags to file %s", fileName));
   AliDebug(1, Form("writing tags to file %s", fileName));
  
@@ -1894,6 +2035,690 @@ void AliReconstruction::CreateTag(TFile* file)
   delete evTag;
 }
 
+//_____________________________________________________________________________
+void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
+{
+  // write all files from the given esd file to an aod file
+  
+  // create an AliAOD object 
+  AliAODEvent *aod = new AliAODEvent();
+  aod->CreateStdContent();
+  
+  // go to the file
+  aodFile->cd();
+  
+  // create the tree
+  TTree *aodTree = new TTree("AOD", "AliAOD tree");
+  aodTree->Branch(aod->GetList());
+
+  // connect to ESD
+  TTree *t = (TTree*) esdFile->Get("esdTree");
+  AliESD *esd = new AliESD();
+  esd->ReadFromTree(t);
+
+  Int_t nEvents = t->GetEntries();
+
+  // set arrays and pointers
+  Float_t posF[3];
+  Double_t pos[3];
+  Double_t p[3];
+  Double_t covVtx[6];
+  Double_t covTr[21];
+  Double_t pid[10];
+
+  // loop over events and fill them
+  for (Int_t iEvent = 0; iEvent < nEvents; ++iEvent) {
+    t->GetEntry(iEvent);
+
+    // Multiplicity information needed by the header (to be revised!)
+    Int_t nTracks   = esd->GetNumberOfTracks();
+    Int_t nPosTracks = 0;
+    for (Int_t iTrack=0; iTrack<nTracks; ++iTrack) 
+      if (esd->GetTrack(iTrack)->GetSign()> 0) nPosTracks++;
+
+    // Update the header
+    AliAODHeader* header = aod->GetHeader();
+    
+    header->SetRunNumber       (esd->GetRunNumber()       );
+    header->SetBunchCrossNumber(esd->GetBunchCrossNumber());
+    header->SetOrbitNumber     (esd->GetOrbitNumber()     );
+    header->SetPeriodNumber    (esd->GetPeriodNumber()    );
+    header->SetTriggerMask     (esd->GetTriggerMask()     ); 
+    header->SetTriggerCluster  (esd->GetTriggerCluster()  );
+    header->SetEventType       (esd->GetEventType()       );
+    header->SetMagneticField   (esd->GetMagneticField()   );
+    header->SetZDCN1Energy     (esd->GetZDCN1Energy()     );
+    header->SetZDCP1Energy     (esd->GetZDCP1Energy()     );
+    header->SetZDCN2Energy     (esd->GetZDCN2Energy()     );
+    header->SetZDCP2Energy     (esd->GetZDCP2Energy()     );
+    header->SetZDCEMEnergy     (esd->GetZDCEMEnergy()     );
+    header->SetRefMultiplicity   (nTracks);
+    header->SetRefMultiplicityPos(nPosTracks);
+    header->SetRefMultiplicityNeg(nTracks - nPosTracks);
+    header->SetMuonMagFieldScale(-999.); // FIXME
+    header->SetCentrality(-999.);        // FIXME
+//
+//
+
+    Int_t nV0s      = esd->GetNumberOfV0s();
+    Int_t nCascades = esd->GetNumberOfCascades();
+    Int_t nKinks    = esd->GetNumberOfKinks();
+    Int_t nVertices = nV0s + nCascades + nKinks;
+    
+    aod->ResetStd(nTracks, nVertices);
+    AliAODTrack *aodTrack;
+    
+
+    // Array to take into account the tracks already added to the AOD
+    Bool_t * usedTrack = NULL;
+    if (nTracks>0) {
+      usedTrack = new Bool_t[nTracks];
+      for (Int_t iTrack=0; iTrack<nTracks; ++iTrack) usedTrack[iTrack]=kFALSE;
+    }
+    // Array to take into account the V0s already added to the AOD
+    Bool_t * usedV0 = NULL;
+    if (nV0s>0) {
+      usedV0 = new Bool_t[nV0s];
+      for (Int_t iV0=0; iV0<nV0s; ++iV0) usedV0[iV0]=kFALSE;
+    }
+    // Array to take into account the kinks already added to the AOD
+    Bool_t * usedKink = NULL;
+    if (nKinks>0) {
+      usedKink = new Bool_t[nKinks];
+      for (Int_t iKink=0; iKink<nKinks; ++iKink) usedKink[iKink]=kFALSE;
+    }
+
+    // Access to the AOD container of vertices
+    TClonesArray &vertices = *(aod->GetVertices());
+    Int_t jVertices=0;
+
+    // Access to the AOD container of tracks
+    TClonesArray &tracks = *(aod->GetTracks());
+    Int_t jTracks=0; 
+  
+    // Add primary vertex. The primary tracks will be defined
+    // after the loops on the composite objects (V0, cascades, kinks)
+    const AliESDVertex *vtx = esd->GetPrimaryVertex();
+      
+    vtx->GetXYZ(pos); // position
+    vtx->GetCovMatrix(covVtx); //covariance matrix
+
+    AliAODVertex * primary = new(vertices[jVertices++])
+      AliAODVertex(pos, covVtx, vtx->GetChi2toNDF(), NULL, AliAODVertex::kPrimary);
+         
+    // Create vertices starting from the most complex objects
+      
+    // Cascades
+    for (Int_t nCascade = 0; nCascade < nCascades; ++nCascade) {
+      AliESDcascade *cascade = esd->GetCascade(nCascade);
+      
+      cascade->GetXYZ(pos[0], pos[1], pos[2]);
+      cascade->GetPosCovXi(covVtx);
+     
+      // Add the cascade vertex
+      AliAODVertex * vcascade = new(vertices[jVertices++]) AliAODVertex(pos,
+                                                                       covVtx,
+                                                                       cascade->GetChi2Xi(), // = chi2/NDF since NDF = 2*2-3
+                                                                       primary,
+                                                                       AliAODVertex::kCascade);
+
+      primary->AddDaughter(vcascade);
+
+      // Add the V0 from the cascade. The ESD class have to be optimized...
+      // Now we have to search for the corresponding Vo in the list of V0s
+      // using the indeces of the positive and negative tracks
+
+      Int_t posFromV0 = cascade->GetPindex();
+      Int_t negFromV0 = cascade->GetNindex();
+
+
+      AliESDv0 * v0 = 0x0;
+      Int_t indV0 = -1;
+
+      for (Int_t iV0=0; iV0<nV0s; ++iV0) {
+
+       v0 = esd->GetV0(iV0);
+       Int_t posV0 = v0->GetPindex();
+       Int_t negV0 = v0->GetNindex();
+
+       if (posV0==posFromV0 && negV0==negFromV0) {
+         indV0 = iV0;
+         break;
+       }
+      }
+
+      AliAODVertex * vV0FromCascade = 0x0;
+
+      if (indV0>-1 && !usedV0[indV0] ) {
+       
+       // the V0 exists in the array of V0s and is not used
+
+       usedV0[indV0] = kTRUE;
+       
+       v0->GetXYZ(pos[0], pos[1], pos[2]);
+       v0->GetPosCov(covVtx);
+       
+       vV0FromCascade = new(vertices[jVertices++]) AliAODVertex(pos,
+                                                                covVtx,
+                                                                v0->GetChi2V0(), // = chi2/NDF since NDF = 2*2-3
+                                                                vcascade,
+                                                                AliAODVertex::kV0);
+      } else {
+
+       // the V0 doesn't exist in the array of V0s or was used
+       cerr << "Error: event " << iEvent << " cascade " << nCascade
+            << " The V0 " << indV0 
+            << " doesn't exist in the array of V0s or was used!" << endl;
+
+       cascade->GetXYZ(pos[0], pos[1], pos[2]);
+       cascade->GetPosCov(covVtx);
+      
+       vV0FromCascade = new(vertices[jVertices++]) AliAODVertex(pos,
+                                                                covVtx,
+                                                                v0->GetChi2V0(), // = chi2/NDF since NDF = 2*2-3
+                                                                vcascade,
+                                                                AliAODVertex::kV0);
+       vcascade->AddDaughter(vV0FromCascade);
+      }
+
+      // Add the positive tracks from the V0
+
+      if (! usedTrack[posFromV0]) {
+
+       usedTrack[posFromV0] = kTRUE;
+
+       AliESDtrack *esdTrack = esd->GetTrack(posFromV0);
+       esdTrack->GetPxPyPz(p);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+       
+       vV0FromCascade->AddDaughter(aodTrack =
+                                   new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(), 
+                                          p, 
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->GetSign(),
+                                          esdTrack->GetITSClusterMap(), 
+                                          pid,
+                                          vV0FromCascade,
+                                          kTRUE,  // check if this is right
+                                          kFALSE, // check if this is right
+                                          AliAODTrack::kSecondary)
+               );
+       aodTrack->ConvertAliPIDtoAODPID();
+      }
+      else {
+       cerr << "Error: event " << iEvent << " cascade " << nCascade
+            << " track " << posFromV0 << " has already been used!" << endl;
+      }
+
+      // Add the negative tracks from the V0
+
+      if (!usedTrack[negFromV0]) {
+       
+       usedTrack[negFromV0] = kTRUE;
+       
+       AliESDtrack *esdTrack = esd->GetTrack(negFromV0);
+       esdTrack->GetPxPyPz(p);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+       
+       vV0FromCascade->AddDaughter(aodTrack =
+                new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(),
+                                          p,
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->GetSign(),
+                                          esdTrack->GetITSClusterMap(), 
+                                          pid,
+                                          vV0FromCascade,
+                                          kTRUE,  // check if this is right
+                                          kFALSE, // check if this is right
+                                          AliAODTrack::kSecondary)
+               );
+       aodTrack->ConvertAliPIDtoAODPID();
+      }
+      else {
+       cerr << "Error: event " << iEvent << " cascade " << nCascade
+            << " track " << negFromV0 << " has already been used!" << endl;
+      }
+
+      // Add the bachelor track from the cascade
+
+      Int_t bachelor = cascade->GetBindex();
+      
+      if(!usedTrack[bachelor]) {
+      
+       usedTrack[bachelor] = kTRUE;
+       
+       AliESDtrack *esdTrack = esd->GetTrack(bachelor);
+       esdTrack->GetPxPyPz(p);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+
+       vcascade->AddDaughter(aodTrack =
+               new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(),
+                                          p,
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->GetSign(),
+                                          esdTrack->GetITSClusterMap(), 
+                                          pid,
+                                          vcascade,
+                                          kTRUE,  // check if this is right
+                                          kFALSE, // check if this is right
+                                          AliAODTrack::kSecondary)
+               );
+       aodTrack->ConvertAliPIDtoAODPID();
+     }
+      else {
+       cerr << "Error: event " << iEvent << " cascade " << nCascade
+            << " track " << bachelor << " has already been used!" << endl;
+      }
+
+      // Add the primary track of the cascade (if any)
+
+    } // end of the loop on cascades
+    
+    // V0s
+        
+    for (Int_t nV0 = 0; nV0 < nV0s; ++nV0) {
+
+      if (usedV0[nV0]) continue; // skip if aready added to the AOD
+
+      AliESDv0 *v0 = esd->GetV0(nV0);
+      
+      v0->GetXYZ(pos[0], pos[1], pos[2]);
+      v0->GetPosCov(covVtx);
+
+      AliAODVertex * vV0 = 
+       new(vertices[jVertices++]) AliAODVertex(pos,
+                                               covVtx,
+                                               v0->GetChi2V0(), // = chi2/NDF since NDF = 2*2-3
+                                               primary,
+                                               AliAODVertex::kV0);
+      primary->AddDaughter(vV0);
+
+      Int_t posFromV0 = v0->GetPindex();
+      Int_t negFromV0 = v0->GetNindex();
+      
+      // Add the positive tracks from the V0
+
+      if (!usedTrack[posFromV0]) {
+       
+       usedTrack[posFromV0] = kTRUE;
+
+       AliESDtrack *esdTrack = esd->GetTrack(posFromV0);
+       esdTrack->GetPxPyPz(p);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+       
+       vV0->AddDaughter(aodTrack =
+               new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(), 
+                                          p, 
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->GetSign(),
+                                          esdTrack->GetITSClusterMap(), 
+                                          pid,
+                                          vV0,
+                                          kTRUE,  // check if this is right
+                                          kFALSE, // check if this is right
+                                          AliAODTrack::kSecondary)
+               );
+       aodTrack->ConvertAliPIDtoAODPID();
+      }
+      else {
+       cerr << "Error: event " << iEvent << " V0 " << nV0
+            << " track " << posFromV0 << " has already been used!" << endl;
+      }
+
+      // Add the negative tracks from the V0
+
+      if (!usedTrack[negFromV0]) {
+
+       usedTrack[negFromV0] = kTRUE;
+
+       AliESDtrack *esdTrack = esd->GetTrack(negFromV0);
+       esdTrack->GetPxPyPz(p);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+
+       vV0->AddDaughter(aodTrack =
+                new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(),
+                                          p,
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->GetSign(),
+                                          esdTrack->GetITSClusterMap(), 
+                                          pid,
+                                          vV0,
+                                          kTRUE,  // check if this is right
+                                          kFALSE, // check if this is right
+                                          AliAODTrack::kSecondary)
+               );
+       aodTrack->ConvertAliPIDtoAODPID();
+      }
+      else {
+       cerr << "Error: event " << iEvent << " V0 " << nV0
+            << " track " << negFromV0 << " has already been used!" << endl;
+      }
+
+    } // end of the loop on V0s
+    
+    // Kinks: it is a big mess the access to the information in the kinks
+    // The loop is on the tracks in order to find the mother and daugther of each kink
+
+
+    for (Int_t iTrack=0; iTrack<nTracks; ++iTrack) {
+
+
+      AliESDtrack * esdTrack = esd->GetTrack(iTrack);
+
+      Int_t ikink = esdTrack->GetKinkIndex(0);
+
+      if (ikink) {
+       // Negative kink index: mother, positive: daughter
+
+       // Search for the second track of the kink
+
+       for (Int_t jTrack = iTrack+1; jTrack<nTracks; ++jTrack) {
+
+         AliESDtrack * esdTrack1 = esd->GetTrack(jTrack);
+
+         Int_t jkink = esdTrack1->GetKinkIndex(0);
+
+         if ( TMath::Abs(ikink)==TMath::Abs(jkink) ) {
+
+           // The two tracks are from the same kink
+         
+           if (usedKink[TMath::Abs(ikink)-1]) continue; // skip used kinks
+
+           Int_t imother = -1;
+           Int_t idaughter = -1;
+
+           if (ikink<0 && jkink>0) {
+
+             imother = iTrack;
+             idaughter = jTrack;
+           }
+           else if (ikink>0 && jkink<0) {
+
+             imother = jTrack;
+             idaughter = iTrack;
+           }
+           else {
+             cerr << "Error: Wrong combination of kink indexes: "
+             << ikink << " " << jkink << endl;
+             continue;
+           }
+
+           // Add the mother track
+
+           AliAODTrack * mother = NULL;
+
+           if (!usedTrack[imother]) {
+       
+             usedTrack[imother] = kTRUE;
+       
+             AliESDtrack *esdTrack = esd->GetTrack(imother);
+             esdTrack->GetPxPyPz(p);
+             esdTrack->GetXYZ(pos);
+             esdTrack->GetCovarianceXYZPxPyPz(covTr);
+             esdTrack->GetESDpid(pid);
+
+             mother = 
+               new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(),
+                                          p,
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->GetSign(),
+                                          esdTrack->GetITSClusterMap(), 
+                                          pid,
+                                          primary,
+                                          kTRUE, // check if this is right
+                                          kTRUE, // check if this is right
+                                          AliAODTrack::kPrimary);
+             primary->AddDaughter(mother);
+             mother->ConvertAliPIDtoAODPID();
+           }
+           else {
+             cerr << "Error: event " << iEvent << " kink " << TMath::Abs(ikink)-1
+             << " track " << imother << " has already been used!" << endl;
+           }
+
+           // Add the kink vertex
+           AliESDkink * kink = esd->GetKink(TMath::Abs(ikink)-1);
+
+           AliAODVertex * vkink = 
+           new(vertices[jVertices++]) AliAODVertex(kink->GetPosition(),
+                                                   NULL,
+                                                   0.,
+                                                   mother,
+                                                   AliAODVertex::kKink);
+           // Add the daughter track
+
+           AliAODTrack * daughter = NULL;
+
+           if (!usedTrack[idaughter]) {
+       
+             usedTrack[idaughter] = kTRUE;
+       
+             AliESDtrack *esdTrack = esd->GetTrack(idaughter);
+             esdTrack->GetPxPyPz(p);
+             esdTrack->GetXYZ(pos);
+             esdTrack->GetCovarianceXYZPxPyPz(covTr);
+             esdTrack->GetESDpid(pid);
+
+             daughter = 
+               new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(),
+                                          p,
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->GetSign(),
+                                          esdTrack->GetITSClusterMap(), 
+                                          pid,
+                                          vkink,
+                                          kTRUE, // check if this is right
+                                          kTRUE, // check if this is right
+                                          AliAODTrack::kPrimary);
+             vkink->AddDaughter(daughter);
+             daughter->ConvertAliPIDtoAODPID();
+           }
+           else {
+             cerr << "Error: event " << iEvent << " kink " << TMath::Abs(ikink)-1
+             << " track " << idaughter << " has already been used!" << endl;
+           }
+
+
+         }
+       }
+
+      }      
+
+    }
+
+    
+    // Tracks (primary and orphan)
+      
+    for (Int_t nTrack = 0; nTrack < nTracks; ++nTrack) {
+       
+
+      if (usedTrack[nTrack]) continue;
+
+      AliESDtrack *esdTrack = esd->GetTrack(nTrack);
+      esdTrack->GetPxPyPz(p);
+      esdTrack->GetXYZ(pos);
+      esdTrack->GetCovarianceXYZPxPyPz(covTr);
+      esdTrack->GetESDpid(pid);
+
+      Float_t impactXY, impactZ;
+
+      esdTrack->GetImpactParameters(impactXY,impactZ);
+
+      if (impactXY<3) {
+       // track inside the beam pipe
+      
+       primary->AddDaughter(aodTrack =
+           new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                        esdTrack->GetLabel(),
+                                        p,
+                                        kTRUE,
+                                        pos,
+                                        kFALSE,
+                                        covTr, 
+                                        (Short_t)esdTrack->GetSign(),
+                                        esdTrack->GetITSClusterMap(), 
+                                        pid,
+                                        primary,
+                                        kTRUE, // check if this is right
+                                        kTRUE, // check if this is right
+                                        AliAODTrack::kPrimary)
+           );
+       aodTrack->ConvertAliPIDtoAODPID();
+      }
+      else {
+       // outside the beam pipe: orphan track
+           aodTrack =
+           new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                        esdTrack->GetLabel(),
+                                        p,
+                                        kTRUE,
+                                        pos,
+                                        kFALSE,
+                                        covTr, 
+                                        (Short_t)esdTrack->GetSign(),
+                                        esdTrack->GetITSClusterMap(), 
+                                        pid,
+                                        NULL,
+                                        kFALSE, // check if this is right
+                                        kFALSE, // check if this is right
+                                        AliAODTrack::kOrphan);
+           aodTrack->ConvertAliPIDtoAODPID();
+      }        
+    } // end of loop on tracks
+
+    // muon tracks
+    Int_t nMuTracks = esd->GetNumberOfMuonTracks();
+    for (Int_t nMuTrack = 0; nMuTrack < nMuTracks; ++nMuTrack) {
+      
+      AliESDMuonTrack *esdMuTrack = esd->GetMuonTrack(nMuTrack);     
+      p[0] = esdMuTrack->Px(); 
+      p[1] = esdMuTrack->Py(); 
+      p[2] = esdMuTrack->Pz();
+      pos[0] = primary->GetX(); 
+      pos[1] = primary->GetY(); 
+      pos[2] = primary->GetZ();
+      
+      // has to be changed once the muon pid is provided by the ESD
+      for (Int_t i = 0; i < 10; pid[i++] = 0.); pid[AliAODTrack::kMuon]=1.;
+      
+      primary->AddDaughter(
+         new(tracks[jTracks++]) AliAODTrack(0, // no ID provided
+                                            0, // no label provided
+                                            p,
+                                            kTRUE,
+                                            pos,
+                                            kFALSE,
+                                            NULL, // no covariance matrix provided
+                                            (Short_t)-99, // no charge provided
+                                            0, // no ITSClusterMap
+                                            pid,
+                                            primary,
+                                            kTRUE,  // check if this is right
+                                            kTRUE,  // not used for vertex fit
+                                            AliAODTrack::kPrimary)
+         );
+    }
+    
+    // Access to the AOD container of clusters
+    TClonesArray &clusters = *(aod->GetClusters());
+    Int_t jClusters=0;
+
+    // Calo Clusters
+    Int_t nClusters    = esd->GetNumberOfCaloClusters();
+
+    for (Int_t iClust=0; iClust<nClusters; ++iClust) {
+
+      AliESDCaloCluster * cluster = esd->GetCaloCluster(iClust);
+
+      Int_t id = cluster->GetID();
+      Int_t label = -1;
+      Float_t energy = cluster->E();
+      cluster->GetPosition(posF);
+      AliAODVertex *prodVertex = primary;
+      AliAODTrack *primTrack = NULL;
+      Char_t ttype=AliAODCluster::kUndef;
+      
+      if (cluster->IsPHOS()) ttype=AliAODCluster::kPHOSNeutral;
+      else if (cluster->IsEMCAL()) {
+       
+       if (cluster->GetClusterType() == AliESDCaloCluster::kPseudoCluster)
+         ttype = AliAODCluster::kEMCALPseudoCluster;
+       else
+         ttype = AliAODCluster::kEMCALClusterv1;
+       
+      }
+      
+      new(clusters[jClusters++]) AliAODCluster(id,
+                                              label,
+                                              energy,
+                                              pos,
+                                              NULL, // no covariance matrix provided
+                                              NULL, // no pid for clusters provided
+                                              prodVertex,
+                                              primTrack,
+                                              ttype);
+      
+    } // end of loop on calo clusters
+    
+    delete [] usedTrack;
+    delete [] usedV0;
+    delete [] usedKink;
+    
+    // fill the tree for this event
+    aodTree->Fill();
+  } // end of event loop
+  
+  aodTree->GetUserInfo()->Add(aod);
+  
+  // close ESD file
+  esdFile->Close();
+  
+  // write the tree to the specified file
+  aodFile = aodTree->GetCurrentFile();
+  aodFile->cd();
+  aodTree->Write();
+  
+  return;
+}
+
 void AliReconstruction::WriteAlignmentData(AliESD* esd)
 {
   // Write space-points which are then used in the alignment procedures
@@ -1945,3 +2770,72 @@ void AliReconstruction::WriteAlignmentData(AliESD* esd)
     fLoader[3]->UnloadRecPoints();
   }
 }
+
+//_____________________________________________________________________________
+void AliReconstruction::FillRawDataErrorLog(Int_t iEvent, AliESD* esd)
+{
+  // The method reads the raw-data error log
+  // accumulated within the rawReader.
+  // It extracts the raw-data errors related to
+  // the current event and stores them into
+  // a TClonesArray inside the esd object.
+
+  if (!fRawReader) return;
+
+  for(Int_t i = 0; i < fRawReader->GetNumberOfErrorLogs(); i++) {
+
+    AliRawDataErrorLog *log = fRawReader->GetErrorLog(i);
+    if (!log) continue;
+    if (iEvent != log->GetEventNumber()) continue;
+
+    esd->AddRawDataErrorLog(log);
+  }
+
+}
+
+TNamed* AliReconstruction::CopyFileToTNamed(TString fPath,TString fName){
+  // Dump a file content into a char in TNamed
+  ifstream in;
+  in.open(fPath.Data(),ios::in | ios::binary|ios::ate);
+  Int_t kBytes = (Int_t)in.tellg();
+  printf("Size: %d \n",kBytes);
+  TNamed *fn = 0;
+  if(in.good()){
+    char* memblock = new char [kBytes];
+    in.seekg (0, ios::beg);
+    in.read (memblock, kBytes);
+    in.close();
+    TString fData(memblock,kBytes);
+    fn = new TNamed(fName,fData);
+    printf("fData Size: %d \n",fData.Sizeof());
+    printf("fName Size: %d \n",fName.Sizeof());
+    printf("fn    Size: %d \n",fn->Sizeof());
+    delete[] memblock;
+  }
+  else{
+    AliInfo(Form("Could not Open %s\n",fPath.Data()));
+  }
+
+  return fn;
+}
+
+void AliReconstruction::TNamedToFile(TTree* fTree, TString fName){
+  // This is not really needed in AliReconstruction at the moment
+  // but can serve as a template
+
+  TList *fList = fTree->GetUserInfo();
+  TNamed *fn = (TNamed*)fList->FindObject(fName.Data());
+  printf("fn Size: %d \n",fn->Sizeof());
+
+  TString fTmp(fn->GetName()); // to be 100% sure in principle fName also works
+  const char* cdata = fn->GetTitle();
+  printf("fTmp Size %d\n",fTmp.Sizeof());
+
+  int size = fn->Sizeof()-fTmp.Sizeof()-sizeof(UChar_t)-sizeof(Int_t); // see dfinition of TString::SizeOf()...
+  printf("calculated size %d\n",size);
+  ofstream out(fName.Data(),ios::out | ios::binary);
+  out.write(cdata,size);
+  out.close();
+
+}
+