]> git.uio.no Git - u/mrichter/AliRoot.git/blobdiff - STEER/AliReconstruction.cxx
Call to fRunLoader->LoadHeader(); added in InitRunLoader(). In this way the run header
[u/mrichter/AliRoot.git] / STEER / AliReconstruction.cxx
index a552c84978a3f540f32b29d57648c468a8716c20..33ade2a548118c2535ea119c95d47a3bdd1b174f 100644 (file)
 #include <TSystem.h>
 #include <TROOT.h>
 #include <TPluginManager.h>
-#include <TStopwatch.h>
 #include <TGeoManager.h>
 #include <TLorentzVector.h>
+#include <TArrayS.h>
+#include <TArrayD.h>
 
 #include "AliReconstruction.h"
+#include "AliCodeTimer.h"
 #include "AliReconstructor.h"
 #include "AliLog.h"
 #include "AliRunLoader.h"
 #include "AliRawReaderDate.h"
 #include "AliRawReaderRoot.h"
 #include "AliRawEventHeaderBase.h"
-#include "AliESD.h"
+#include "AliESDEvent.h"
+#include "AliESDMuonTrack.h"
 #include "AliESDfriend.h"
 #include "AliESDVertex.h"
+#include "AliESDcascade.h"
+#include "AliESDkink.h"
+#include "AliESDtrack.h"
+#include "AliESDCaloCluster.h"
 #include "AliMultiplicity.h"
 #include "AliTracker.h"
 #include "AliVertexer.h"
 #include "AliPID.h"
 #include "AliESDpid.h"
 #include "AliESDtrack.h"
+#include "AliESDPmdTrack.h"
 
-#include "AliRunTag.h"
-#include "AliDetectorTag.h"
-#include "AliEventTag.h"
+#include "AliESDTagCreator.h"
+#include "AliAODTagCreator.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 "AliAODv0.h"
+#include "AliAODJet.h"
+#include "AliAODCaloCells.h"
+#include "AliAODCaloCluster.h"
+#include "AliAODPmdCluster.h"
+#include "AliAODFmdCluster.h"
+#include "AliAODTracklets.h"
+
+#include "AliQADataMaker.h" 
+
+#include "AliSysInfo.h" // memory snapshots
+
+
 ClassImp(AliReconstruction)
 
 
@@ -174,15 +199,22 @@ AliReconstruction::AliReconstruction(const char* gAliceFilename, const char* cdb
   fRunVertexFinder(kTRUE),
   fRunHLTTracking(kFALSE),
   fRunMuonTracking(kFALSE),
+  fRunV0Finder(kTRUE),
+  fRunCascadeFinder(kTRUE),
   fStopOnError(kFALSE),
   fWriteAlignmentData(kFALSE),
   fWriteESDfriend(kFALSE),
   fWriteAOD(kFALSE),
   fFillTriggerESD(kTRUE),
 
+  fCleanESD(kTRUE),
+  fDmax(50.),
+  fZmax(50.),
+
   fRunLocalReconstruction("ALL"),
   fRunTracking("ALL"),
   fFillESD("ALL"),
+  fUseTrackingErrorsForAlignment(""),
   fGAliceFileName(gAliceFilename),
   fInput(""),
   fEquipIdMap(""),
@@ -193,6 +225,7 @@ AliReconstruction::AliReconstruction(const char* gAliceFilename, const char* cdb
   fOptions(),
   fLoadAlignFromCDB(kTRUE),
   fLoadAlignData("ALL"),
+  fESDPar(""),
 
   fRunLoader(NULL),
   fRawReader(NULL),
@@ -202,6 +235,7 @@ AliReconstruction::AliReconstruction(const char* gAliceFilename, const char* cdb
 
   fAlignObjArray(NULL),
   fCDBUri(cdbUri),
+  fRemoteCDBUri(""),
   fSpecCDBUri()
 {
 // create reconstruction object with default parameters
@@ -210,6 +244,8 @@ AliReconstruction::AliReconstruction(const char* gAliceFilename, const char* cdb
     fReconstructor[iDet] = NULL;
     fLoader[iDet] = NULL;
     fTracker[iDet] = NULL;
+    fQADataMaker[iDet] = NULL;
+       fQACycles[iDet] = 999999;       
   }
   AliPID pid;
 }
@@ -222,15 +258,22 @@ AliReconstruction::AliReconstruction(const AliReconstruction& rec) :
   fRunVertexFinder(rec.fRunVertexFinder),
   fRunHLTTracking(rec.fRunHLTTracking),
   fRunMuonTracking(rec.fRunMuonTracking),
+  fRunV0Finder(rec.fRunV0Finder),
+  fRunCascadeFinder(rec.fRunCascadeFinder),
   fStopOnError(rec.fStopOnError),
   fWriteAlignmentData(rec.fWriteAlignmentData),
   fWriteESDfriend(rec.fWriteESDfriend),
   fWriteAOD(rec.fWriteAOD),
   fFillTriggerESD(rec.fFillTriggerESD),
 
+  fCleanESD(rec.fCleanESD),
+  fDmax(rec.fDmax),
+  fZmax(rec.fZmax),
+
   fRunLocalReconstruction(rec.fRunLocalReconstruction),
   fRunTracking(rec.fRunTracking),
   fFillESD(rec.fFillESD),
+  fUseTrackingErrorsForAlignment(rec.fUseTrackingErrorsForAlignment),
   fGAliceFileName(rec.fGAliceFileName),
   fInput(rec.fInput),
   fEquipIdMap(rec.fEquipIdMap),
@@ -241,6 +284,7 @@ AliReconstruction::AliReconstruction(const AliReconstruction& rec) :
   fOptions(),
   fLoadAlignFromCDB(rec.fLoadAlignFromCDB),
   fLoadAlignData(rec.fLoadAlignData),
+  fESDPar(rec.fESDPar),
 
   fRunLoader(NULL),
   fRawReader(NULL),
@@ -250,6 +294,7 @@ AliReconstruction::AliReconstruction(const AliReconstruction& rec) :
 
   fAlignObjArray(rec.fAlignObjArray),
   fCDBUri(rec.fCDBUri),
+  fRemoteCDBUri(rec.fRemoteCDBUri),
   fSpecCDBUri()
 {
 // copy constructor
@@ -261,6 +306,8 @@ AliReconstruction::AliReconstruction(const AliReconstruction& rec) :
     fReconstructor[iDet] = NULL;
     fLoader[iDet] = NULL;
     fTracker[iDet] = NULL;
+    fQADataMaker[iDet] = NULL;
+       fQACycles[iDet] = rec.fQACycles[iDet];  
   }
   for (Int_t i = 0; i < rec.fSpecCDBUri.GetEntriesFast(); i++) {
     if (rec.fSpecCDBUri[i]) fSpecCDBUri.Add(rec.fSpecCDBUri[i]->Clone());
@@ -285,6 +332,8 @@ AliReconstruction::~AliReconstruction()
   CleanUp();
   fOptions.Delete();
   fSpecCDBUri.Delete();
+
+  AliCodeTimer::Instance()->Print();
 }
 
 //_____________________________________________________________________________
@@ -310,6 +359,24 @@ void AliReconstruction::InitCDBStorage()
     man->SetDefaultStorage(fCDBUri);
   }
 
+  // Remote storage (the Grid storage) is used if it is activated
+  // and if the object is not found in the default storage
+  // OBSOLETE: Removed
+  //  if (man->IsRemoteStorageSet())
+  //  {
+  //   AliWarning("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!");
+  //   AliWarning("Remote CDB storage has been already set !");
+  //   AliWarning(Form("Ignoring the remote storage declared in AliReconstruction: %s",fRemoteCDBUri.Data()));
+  //   AliWarning("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!");
+  //   fRemoteCDBUri = "";
+  //  }
+  //  else {
+  //   AliDebug(2,"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!");
+  //   AliDebug(2, Form("Remote CDB storage is set to: %s",fRemoteCDBUri.Data()));
+  //   AliDebug(2, "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!");
+  //   man->SetRemoteStorage(fRemoteCDBUri);
+  //  }
+
   // Now activate the detector specific CDB storage locations
   for (Int_t i = 0; i < fSpecCDBUri.GetEntriesFast(); i++) {
     TObject* obj = fSpecCDBUri[i];
@@ -331,6 +398,17 @@ void AliReconstruction::SetDefaultStorage(const char* uri) {
 
 }
 
+//_____________________________________________________________________________
+void AliReconstruction::SetRemoteStorage(const char* uri) {
+// Store the desired remote CDB storage location
+// Activate it later within the Run() method
+// Remote storage (the Grid storage) is used if it is activated
+// and if the object is not found in the default storage
+
+  fRemoteCDBUri = uri;
+
+}
+
 //_____________________________________________________________________________
 void AliReconstruction::SetSpecificStorage(const char* calibType, const char* uri) {
 // Store a detector-specific CDB storage location
@@ -352,20 +430,20 @@ void AliReconstruction::SetSpecificStorage(const char* calibType, const char* ur
        }
   }
 
-  // check that calibType refers to a "valid" detector name
-  Bool_t isDetector = kFALSE;
-  for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
-    TString detName = fgkDetectorName[iDet];
-    if(aPath.GetLevel0() == detName) {
-       isDetector = kTRUE;
-       break;
-    }
-  }
-
-  if(!isDetector) {
-       AliError(Form("Not a valid detector: %s", aPath.GetLevel0().Data()));
-       return;
-  }
+//  // check that calibType refers to a "valid" detector name
+//  Bool_t isDetector = kFALSE;
+//  for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
+//    TString detName = fgkDetectorName[iDet];
+//    if(aPath.GetLevel0() == detName) {
+//     isDetector = kTRUE;
+//     break;
+//    }
+//  }
+//
+//  if(!isDetector) {
+//     AliError(Form("Not a valid detector: %s", aPath.GetLevel0().Data()));
+//     return;
+//  }
 
   TObject* obj = fSpecCDBUri.FindObject(aPath.GetPath().Data());
   if (obj) fSpecCDBUri.Remove(obj);
@@ -373,6 +451,9 @@ void AliReconstruction::SetSpecificStorage(const char* calibType, const char* ur
 
 }
 
+
+
+
 //_____________________________________________________________________________
 Bool_t AliReconstruction::SetRunNumber()
 {
@@ -388,7 +469,7 @@ Bool_t AliReconstruction::SetRunNumber()
     }
     // read run number from gAlice
     if(fRunLoader->GetAliRun())
-      AliCDBManager::Instance()->SetRun(fRunLoader->GetAliRun()->GetRunNumber());
+      AliCDBManager::Instance()->SetRun(fRunLoader->GetHeader()->GetRun());
     else {
       if(fRawReader) {
        if(fRawReader->NextEvent()) {
@@ -410,72 +491,6 @@ 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)
 {
@@ -489,53 +504,38 @@ 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
+    loadAlObjsListOfDets.Prepend("GRP "); //add alignment objects for non-sensitive modules
+    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;
 }
 
@@ -563,6 +563,8 @@ Bool_t AliReconstruction::Run(const char* input)
 {
 // run the reconstruction
 
+  AliCodeTimerAuto("")
+  
   // set the input
   if (!input) input = fInput.Data();
   TString fileName(input);
@@ -577,12 +579,14 @@ Bool_t AliReconstruction::Run(const char* input)
   if (!fEquipIdMap.IsNull() && fRawReader)
     fRawReader->LoadEquipmentIdsMap(fEquipIdMap);
 
-
+   AliSysInfo::AddStamp("Start");
   // get the run loader
   if (!InitRunLoader()) return kFALSE;
+   AliSysInfo::AddStamp("LoadLoader");
 
   // Initialize the CDB storage
   InitCDBStorage();
+   AliSysInfo::AddStamp("LoadCDB");
 
   // Set run number in CDBManager (if it is not already set by the user)
   if (!SetRunNumber()) if (fStopOnError) return kFALSE;
@@ -591,12 +595,12 @@ 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;
+   AliSysInfo::AddStamp("LoadGeom");
 
   // local reconstruction
   if (!fRunLocalReconstruction.IsNull()) {
@@ -614,6 +618,7 @@ Bool_t AliReconstruction::Run(const char* input)
       return kFALSE;
     }
   }
+   AliSysInfo::AddStamp("Vertexer");
 
   // get trackers
   if (!fRunTracking.IsNull() && !CreateTrackers(fRunTracking)) {
@@ -622,13 +627,10 @@ Bool_t AliReconstruction::Run(const char* input)
       return kFALSE;
     }      
   }
-
-
-  TStopwatch stopwatch;
-  stopwatch.Start();
+   AliSysInfo::AddStamp("LoadTrackers");
 
   // get the possibly already existing ESD file and tree
-  AliESD* esd = new AliESD; AliESD* hltesd = new AliESD;
+  AliESDEvent* esd = new AliESDEvent(); AliESDEvent* hltesd = new AliESDEvent();
   TFile* fileOld = NULL;
   TTree* treeOld = NULL; TTree *hlttreeOld = NULL;
   if (!gSystem->AccessPathName("AliESDs.root")){
@@ -636,55 +638,89 @@ 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 AliESDEvent();
+  esd->CreateStdContent();
+  esd->WriteToTree(tree);
+
   TTree* hlttree = new TTree("HLTesdTree", "Tree with HLT ESD objects");
-  hlttree->Branch("ESD", "AliESD", &hltesd);
+  hltesd = new AliESDEvent();
+  hltesd->CreateStdContent();
+  hltesd->WriteToTree(hlttree);
+
+  /* CKB Why?
   delete esd; delete hltesd;
   esd = NULL; hltesd = NULL;
-
+  */
   // create the branch with ESD additions
-  AliESDfriend *esdf=0;
+
+
+
+  AliESDfriend *esdf = 0; 
   if (fWriteESDfriend) {
-     TBranch *br=tree->Branch("ESDfriend.", "AliESDfriend", &esdf);
-     br->SetFile("AliESDfriends.root");
+    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!");
   }
 
-  AliVertexerTracks tVertexer;
+  AliVertexerTracks tVertexer(AliTracker::GetBz());
   if(fDiamondProfile) tVertexer.SetVtxStart(fDiamondProfile);
 
   // loop over events
   if (fRawReader) fRawReader->RewindEvents();
+   TString detStr(fFillESD) ; 
+
+  ProcInfo_t ProcInfo;
+  gSystem->GetProcInfo(&ProcInfo);
+  AliInfo(Form("Current memory usage %d %d", ProcInfo.fMemResident, ProcInfo.fMemVirtual));
+  
+  // checking the QA of previous steps
+  CheckQA() ; 
   
   for (Int_t iEvent = 0; iEvent < fRunLoader->GetNumberOfEvents(); iEvent++) {
     if (fRawReader) fRawReader->NextEvent();
     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);
 
@@ -701,16 +737,21 @@ Bool_t AliReconstruction::Run(const char* input)
       }
     }
 
-    esd = new AliESD; hltesd = new AliESD;
+  
     esd->SetRunNumber(fRunLoader->GetHeader()->GetRun());
     hltesd->SetRunNumber(fRunLoader->GetHeader()->GetRun());
     esd->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")) {
@@ -734,7 +775,7 @@ Bool_t AliReconstruction::Run(const char* input)
     // Muon tracking
     if (!fRunTracking.IsNull()) {
       if (fRunMuonTracking) {
-       if (!RunMuonTracking()) {
+       if (!RunMuonTracking(esd)) {
          if (fStopOnError) {CleanUp(file, fileOld); return kFALSE;}
        }
       }
@@ -742,21 +783,24 @@ Bool_t AliReconstruction::Run(const char* input)
 
     // barrel tracking
     if (!fRunTracking.IsNull()) {
-      if (!fRunMuonTracking) {
-       if (!ReadESD(esd, "tracking")) {
-         if (!RunTracking(esd)) {
-           if (fStopOnError) {CleanUp(file, fileOld); return kFALSE;}
-         }
-         if (fCheckPointLevel > 0) WriteESD(esd, "tracking");
+      if (!ReadESD(esd, "tracking")) {
+       if (!RunTracking(esd)) {
+         if (fStopOnError) {CleanUp(file, fileOld); return kFALSE;}
        }
+       if (fCheckPointLevel > 0) WriteESD(esd, "tracking");
       }
     }
+
     // fill ESD
     if (!fFillESD.IsNull()) {
       if (!FillESD(esd, fFillESD)) {
        if (fStopOnError) {CleanUp(file, fileOld); return kFALSE;}
       }
     }
+  
+    if (!fFillESD.IsNull()) 
+    RunQA(fFillESD.Data(), esd);
+
     // fill Event header information from the RawEventHeader
     if (fRawReader){FillRawEventHeaderESD(esd);}
 
@@ -773,8 +817,20 @@ Bool_t AliReconstruction::Run(const char* input)
       }
     }
 
+    file->cd();
+
     //Try to improve the reconstructed primary vertex position using the tracks
-    AliESDVertex *pvtx=tVertexer.FindPrimaryVertex(esd);
+    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
@@ -789,20 +845,24 @@ Bool_t AliReconstruction::Run(const char* input)
        } 
     }
 
-    {
-    // V0 finding
-    AliV0vertexer vtxer;
-    vtxer.Tracks2V0vertices(esd);
+    if (fRunV0Finder) {
+       // V0 finding
+       AliV0vertexer vtxer;
+       vtxer.Tracks2V0vertices(esd);
 
-    // Cascade finding
-    AliCascadeVertexer cvtxer;
-    cvtxer.V0sTracks2CascadeVertices(esd);
+       if (fRunCascadeFinder) {
+          // Cascade finding
+          AliCascadeVertexer cvtxer;
+          cvtxer.V0sTracks2CascadeVertices(esd);
+       }
     }
  
     // write ESD
+    if (fCleanESD) CleanESD(esd);
     if (fWriteESDfriend) {
-       esdf=new AliESDfriend();
-       esd->GetESDfriend(esdf);
+      esdf->~AliESDfriend();
+      new (esdf) AliESDfriend(); // Reset...
+      esd->GetESDfriend(esdf);
     }
     tree->Fill();
 
@@ -810,28 +870,69 @@ Bool_t AliReconstruction::Run(const char* input)
     hlttree->Fill();
 
     if (fCheckPointLevel > 0)  WriteESD(esd, "final"); 
+    esd->Reset();
+    hltesd->Reset();
+    if (fWriteESDfriend) {
+      esdf->~AliESDfriend();
+      new (esdf) AliESDfriend(); // Reset...
+    }
+    // esdf->Reset();
+    // delete esdf; esdf = 0;
+  // ESD QA 
  
-    delete esd; delete esdf; delete hltesd;
-    esd = NULL; esdf=NULL; hltesd = NULL;
+    gSystem->GetProcInfo(&ProcInfo);
+    AliInfo(Form("Event %d -> Current memory usage %d %d",iEvent, ProcInfo.fMemResident, ProcInfo.fMemVirtual));
+  }
+  
+  detStr = fFillESD ; 
+  // write quality assurance ESDs data (one entry for all events)
+  for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
+       if (!IsSelected(fgkDetectorName[iDet], detStr)) 
+               continue;
+    AliQADataMaker * qadm = GetQADataMaker(iDet);
+    if (!qadm) continue;
+    qadm->EndOfCycle(AliQA::kRECPOINTS);
+    qadm->EndOfCycle(AliQA::kESDS);
+    qadm->Finish(AliQA::kRECPOINTS);
+    qadm->Finish(AliQA::kESDS) ; 
+  }
+
+  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();
+  // we want to have only one tree version number
+  tree->Write(tree->GetName(),TObject::kOverwrite);
   hlttree->Write();
 
   if (fWriteAOD) {
-    CreateAOD(file);
+    TFile *aodFile = TFile::Open("AliAOD.root", "RECREATE");
+    ESDFile2AODFile(file, aodFile);
+    aodFile->Close();
   }
 
+  gROOT->cd();
+  CleanUp(file, fileOld);
+  
   // 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);
+  AliESDTagCreator *esdtagCreator = new AliESDTagCreator();
+  esdtagCreator->CreateESDTags(fFirstEvent,fLastEvent);
+  if (fWriteAOD) {
+    AliAODTagCreator *aodtagCreator = new AliAODTagCreator();
+    aodtagCreator->CreateAODTags(fFirstEvent,fLastEvent);
+  }
 
   return kTRUE;
 }
@@ -841,55 +942,55 @@ Bool_t AliReconstruction::Run(const char* input)
 Bool_t AliReconstruction::RunLocalReconstruction(const TString& detectors)
 {
 // run the local reconstruction
+  static Int_t eventNr=0;
+  AliCodeTimerAuto("")
 
 TStopwatch stopwatch;
-  stopwatch.Start();
//  AliCDBManager* man = AliCDBManager::Instance();
+//   Bool_t origCache = man->GetCacheFlag();
 
-  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;
+//     AliReconstructor* reconstructor = GetReconstructor(iDet);
+//     if (!reconstructor) continue;
+//     if (reconstructor->HasLocalReconstruction()) continue;
 
-  TString detStr = detectors;
-  for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
-    if (!IsSelected(fgkDetectorName[iDet], detStr)) continue;
-    AliReconstructor* reconstructor = GetReconstructor(iDet);
-    if (!reconstructor) continue;
-    if (reconstructor->HasLocalReconstruction()) continue;
-
-    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!
+//     AliCodeTimerStart(Form("running reconstruction for %s", fgkDetectorName[iDet]));
+//     AliInfo(Form("running reconstruction for %s", fgkDetectorName[iDet]));
+    
+//     AliCodeTimerStart(Form("Loading calibration data from OCDB for %s", fgkDetectorName[iDet]));                          
+//     AliInfo(Form("Loading calibration data from OCDB for %s", fgkDetectorName[iDet]));
 
-    if (fRawReader) {
-      fRawReader->RewindEvents();
-      reconstructor->Reconstruct(fRunLoader, fRawReader);
-    } else {
-      reconstructor->Reconstruct(fRunLoader);
-    }
-    AliInfo(Form("Execution time for %s: R:%.2fs C:%.2fs",
-                fgkDetectorName[iDet],
-                stopwatchDet.RealTime(),stopwatchDet.CpuTime()));
+//     man->SetCacheFlag(kTRUE);
+//     TString calibPath = Form("%s/Calib/*", fgkDetectorName[iDet]);
+//     man->GetAll(calibPath); // entries are cached!
 
-    // unload calibration data
-    man->ClearCache();
-  }
+//     AliCodeTimerStop(Form("Loading calibration data from OCDB for %s", fgkDetectorName[iDet]));
+     
+//     if (fRawReader) {
+//       fRawReader->RewindEvents();
+//       reconstructor->Reconstruct(fRunLoader, fRawReader);
+//     } else {
+//       reconstructor->Reconstruct(fRunLoader);
+//     }
+     
+//      AliCodeTimerStop(Form("running reconstruction for %s", fgkDetectorName[iDet]));
+    // AliSysInfo::AddStamp(Form("LRec%s_%d",fgkDetectorName[iDet],eventNr));
 
-  man->SetCacheFlag(origCache);
+//     // unload calibration data
+//     man->UnloadFromCache(calibPath);
+//     //man->ClearCache();
+//   }
 
-  if ((detStr.CompareTo("ALL") != 0) && !detStr.IsNull()) {
-    AliError(Form("the following detectors were not found: %s",
-                  detStr.Data()));
-    if (fStopOnError) return kFALSE;
-  }
+//   man->SetCacheFlag(origCache);
 
-  AliInfo(Form("Execution time: R:%.2fs C:%.2fs",
-              stopwatch.RealTime(),stopwatch.CpuTime()));
+//   if ((detStr.CompareTo("ALL") != 0) && !detStr.IsNull()) {
+//     AliError(Form("the following detectors were not found: %s",
+//                   detStr.Data()));
+//     if (fStopOnError) return kFALSE;
+//   }
 
+         eventNr++;
   return kTRUE;
 }
 
@@ -897,9 +998,8 @@ Bool_t AliReconstruction::RunLocalReconstruction(const TString& detectors)
 Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
 {
 // run the local reconstruction
-
-  TStopwatch stopwatch;
-  stopwatch.Start();
+  static Int_t eventNr=0;
+  AliCodeTimerAuto("")
 
   TString detStr = detectors;
   for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
@@ -907,13 +1007,17 @@ Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
     AliReconstructor* reconstructor = GetReconstructor(iDet);
     if (!reconstructor) continue;
     AliLoader* loader = fLoader[iDet];
+    if (!loader) {
+      AliWarning(Form("No loader is defined for %s!",fgkDetectorName[iDet]));
+      continue;
+    }
 
     // conversion of digits
     if (fRawReader && reconstructor->HasDigitConversion()) {
       AliInfo(Form("converting raw data digits into root objects for %s", 
                   fgkDetectorName[iDet]));
-      TStopwatch stopwatchDet;
-      stopwatchDet.Start();
+      AliCodeTimerAuto(Form("converting raw data digits into root objects for %s", 
+                            fgkDetectorName[iDet]));
       loader->LoadDigits("update");
       loader->CleanDigits();
       loader->MakeDigitsContainer();
@@ -921,16 +1025,11 @@ Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
       reconstructor->ConvertDigits(fRawReader, digitsTree);
       loader->WriteDigits("OVERWRITE");
       loader->UnloadDigits();
-      AliInfo(Form("Execution time for %s: R:%.2fs C:%.2fs",
-                  fgkDetectorName[iDet],
-                  stopwatchDet.RealTime(),stopwatchDet.CpuTime()));
     }
 
     // local reconstruction
-    if (!reconstructor->HasLocalReconstruction()) continue;
     AliInfo(Form("running reconstruction for %s", fgkDetectorName[iDet]));
-    TStopwatch stopwatchDet;
-    stopwatchDet.Start();
+    AliCodeTimerAuto(Form("running reconstruction for %s", fgkDetectorName[iDet]));
     loader->LoadRecPoints("update");
     loader->CleanRecPoints();
     loader->MakeRecPointsContainer();
@@ -948,11 +1047,25 @@ Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
       }
       loader->UnloadDigits();
     }
+
+    AliQADataMaker * qadm = GetQADataMaker(iDet);
+    if (qadm) {
+      AliCodeTimerStart(Form("running quality assurance data maker for %s", fgkDetectorName[iDet]));
+      AliInfo(Form("running quality assurance data maker for %s", fgkDetectorName[iDet]));
+         
+     if (qadm->IsCycleDone() ) {
+      qadm->EndOfCycle(AliQA::kRECPOINTS) ; 
+         qadm->EndOfCycle(AliQA::kESDS) ; 
+      qadm->StartOfCycle(AliQA::kRECPOINTS) ; 
+         qadm->StartOfCycle(AliQA::kESDS, "same") ; 
+     }
+      qadm->Exec(AliQA::kRECPOINTS, clustersTree) ; 
+      AliCodeTimerStop(Form("running quality assurance data maker for %s", fgkDetectorName[iDet]));
+    }
+
     loader->WriteRecPoints("OVERWRITE");
     loader->UnloadRecPoints();
-    AliDebug(1,Form("Execution time for %s: R:%.2fs C:%.2fs",
-                   fgkDetectorName[iDet],
-                   stopwatchDet.RealTime(),stopwatchDet.CpuTime()));
+    AliSysInfo::AddStamp(Form("LRec%s_%d",fgkDetectorName[iDet],eventNr), iDet,1,eventNr);
   }
 
   if ((detStr.CompareTo("ALL") != 0) && !detStr.IsNull()) {
@@ -960,20 +1073,16 @@ Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
                   detStr.Data()));
     if (fStopOnError) return kFALSE;
   }
-  
-  AliInfo(Form("Execution time: R:%.2fs C:%.2fs",
-              stopwatch.RealTime(),stopwatch.CpuTime()));
-
+  eventNr++;
   return kTRUE;
 }
 
 //_____________________________________________________________________________
-Bool_t AliReconstruction::RunVertexFinder(AliESD*& esd)
+Bool_t AliReconstruction::RunVertexFinder(AliESDEvent*& esd)
 {
 // run the barrel tracking
 
-  TStopwatch stopwatch;
-  stopwatch.Start();
+  AliCodeTimerAuto("")
 
   AliESDVertex* vertex = NULL;
   Double_t vtxPos[3] = {0, 0, 0};
@@ -985,6 +1094,7 @@ 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());
@@ -995,7 +1105,6 @@ Bool_t AliReconstruction::RunVertexFinder(AliESD*& esd)
       vertex->SetName("default");
     }
     else {
-      vertex->SetTruePos(vtxPos);  // store also the vertex from MC
       vertex->SetName("reconstructed");
     }
 
@@ -1013,7 +1122,7 @@ 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++) {
@@ -1021,19 +1130,15 @@ Bool_t AliReconstruction::RunVertexFinder(AliESD*& esd)
   }  
   delete vertex;
 
-  AliInfo(Form("Execution time: R:%.2fs C:%.2fs",
-              stopwatch.RealTime(),stopwatch.CpuTime()));
-
   return kTRUE;
 }
 
 //_____________________________________________________________________________
-Bool_t AliReconstruction::RunHLTTracking(AliESD*& esd)
+Bool_t AliReconstruction::RunHLTTracking(AliESDEvent*& esd)
 {
 // run the HLT barrel tracking
 
-  TStopwatch stopwatch;
-  stopwatch.Start();
+  AliCodeTimerAuto("")
 
   if (!fRunLoader) {
     AliError("Missing runLoader!");
@@ -1051,7 +1156,7 @@ Bool_t AliReconstruction::RunHLTTracking(AliESD*& esd)
     TString detName = fgkDetectorName[iDet];
     AliDebug(1, Form("%s HLT tracking", detName.Data()));
     reconstructor->SetOption(detName.Data());
-    AliTracker *tracker = reconstructor->CreateTracker(fRunLoader);
+    AliTracker *tracker = reconstructor->CreateTracker();
     if (!tracker) {
       AliWarning(Form("couldn't create a HLT tracker for %s", detName.Data()));
       if (fStopOnError) return kFALSE;
@@ -1081,19 +1186,15 @@ Bool_t AliReconstruction::RunHLTTracking(AliESD*& esd)
     delete tracker;
   }
 
-  AliInfo(Form("Execution time: R:%.2fs C:%.2fs",
-              stopwatch.RealTime(),stopwatch.CpuTime()));
-
   return kTRUE;
 }
 
 //_____________________________________________________________________________
-Bool_t AliReconstruction::RunMuonTracking()
+Bool_t AliReconstruction::RunMuonTracking(AliESDEvent*& esd)
 {
 // run the muon spectrometer tracking
 
-  TStopwatch stopwatch;
-  stopwatch.Start();
+  AliCodeTimerAuto("")
 
   if (!fRunLoader) {
     AliError("Missing runLoader!");
@@ -1110,7 +1211,7 @@ Bool_t AliReconstruction::RunMuonTracking()
   
   TString detName = fgkDetectorName[iDet];
   AliDebug(1, Form("%s tracking", detName.Data()));
-  AliTracker *tracker =  reconstructor->CreateTracker(fRunLoader);
+  AliTracker *tracker =  reconstructor->CreateTracker();
   if (!tracker) {
     AliWarning(Form("couldn't create a tracker for %s", detName.Data()));
     return kFALSE;
@@ -1122,12 +1223,21 @@ Bool_t AliReconstruction::RunMuonTracking()
   fLoader[iDet]->MakeTracksContainer();
 
   // read RecPoints
-  fLoader[iDet]->LoadRecPoints("read");
-
-  if (!tracker->Clusters2Tracks(0x0)) {
+  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");
@@ -1135,24 +1245,26 @@ Bool_t AliReconstruction::RunMuonTracking()
 
   delete tracker;
   
-
-  AliInfo(Form("Execution time: R:%.2fs C:%.2fs",
-              stopwatch.RealTime(),stopwatch.CpuTime()));
-
   return kTRUE;
 }
 
 
 //_____________________________________________________________________________
-Bool_t AliReconstruction::RunTracking(AliESD*& esd)
+Bool_t AliReconstruction::RunTracking(AliESDEvent*& esd)
 {
 // run the barrel tracking
-
-  TStopwatch stopwatch;
-  stopwatch.Start();
+  static Int_t eventNr=0;
+  AliCodeTimerAuto("")
 
   AliInfo("running tracking");
 
+  //Fill the ESD with the T0 info (will be used by the TOF) 
+  if (fReconstructor[11] && fLoader[11]) {
+    fLoader[11]->LoadRecPoints("READ");
+    TTree *treeR = fLoader[11]->TreeR();
+    GetReconstructor(11)->FillESD((TTree *)NULL,treeR,esd);
+  }
+
   // pass 1: TPC + ITS inwards
   for (Int_t iDet = 1; iDet >= 0; iDet--) {
     if (!fTracker[iDet]) continue;
@@ -1160,13 +1272,14 @@ Bool_t AliReconstruction::RunTracking(AliESD*& esd)
 
     // load clusters
     fLoader[iDet]->LoadRecPoints("read");
+    AliSysInfo::AddStamp(Form("RLoadCluster%s_%d",fgkDetectorName[iDet],eventNr),iDet,1, eventNr);
     TTree* tree = fLoader[iDet]->TreeR();
     if (!tree) {
       AliError(Form("Can't get the %s cluster tree", fgkDetectorName[iDet]));
       return kFALSE;
     }
     fTracker[iDet]->LoadClusters(tree);
-
+    AliSysInfo::AddStamp(Form("TLoadCluster%s_%d",fgkDetectorName[iDet],eventNr), iDet,2, eventNr);
     // run tracking
     if (fTracker[iDet]->Clusters2Tracks(esd) != 0) {
       AliError(Form("%s Clusters2Tracks failed", fgkDetectorName[iDet]));
@@ -1177,10 +1290,10 @@ Bool_t AliReconstruction::RunTracking(AliESD*& esd)
     }
     // preliminary PID in TPC needed by the ITS tracker
     if (iDet == 1) {
-      GetReconstructor(1)->FillESD(fRunLoader, esd);
       GetReconstructor(1)->FillESD((TTree*)NULL, (TTree*)NULL, esd);
       AliESDpid::MakePID(esd);
-    }
+    } 
+    AliSysInfo::AddStamp(Form("Tracking0%s_%d",fgkDetectorName[iDet],eventNr), iDet,3,eventNr);
   }
 
   // pass 2: ALL backwards
@@ -1192,18 +1305,20 @@ Bool_t AliReconstruction::RunTracking(AliESD*& esd)
     if (iDet > 1) {     // all except ITS, TPC
       TTree* tree = NULL;
       fLoader[iDet]->LoadRecPoints("read");
+      AliSysInfo::AddStamp(Form("RLoadCluster0%s_%d",fgkDetectorName[iDet],eventNr), iDet,1, eventNr);
       tree = fLoader[iDet]->TreeR();
       if (!tree) {
        AliError(Form("Can't get the %s cluster tree", fgkDetectorName[iDet]));
        return kFALSE;
       }
-      fTracker[iDet]->LoadClusters(tree);
+      fTracker[iDet]->LoadClusters(tree); 
+      AliSysInfo::AddStamp(Form("TLoadCluster0%s_%d",fgkDetectorName[iDet],eventNr), iDet,2, eventNr);
     }
 
     // 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]));
@@ -1216,10 +1331,10 @@ Bool_t AliReconstruction::RunTracking(AliESD*& esd)
     }
     // updated PID in TPC needed by the ITS tracker -MI
     if (iDet == 1) {
-      GetReconstructor(1)->FillESD(fRunLoader, esd);
       GetReconstructor(1)->FillESD((TTree*)NULL, (TTree*)NULL, esd);
       AliESDpid::MakePID(esd);
     }
+    AliSysInfo::AddStamp(Form("Tracking1%s_%d",fgkDetectorName[iDet],eventNr), iDet,3, eventNr);
   }
 
   // write space-points to the ESD in case alignment data output
@@ -1235,15 +1350,17 @@ 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]));
     }
-
+    AliSysInfo::AddStamp(Form("Tracking2%s_%d",fgkDetectorName[iDet],eventNr), iDet,3, eventNr);
     // unload clusters
     fTracker[iDet]->UnloadClusters();
+    AliSysInfo::AddStamp(Form("TUnloadCluster%s_%d",fgkDetectorName[iDet],eventNr), iDet,4, eventNr);
     fLoader[iDet]->UnloadRecPoints();
+    AliSysInfo::AddStamp(Form("RUnloadCluster%s_%d",fgkDetectorName[iDet],eventNr), iDet,5, eventNr);
   }
   //
   // Propagate track to the vertex - if not done by ITS
@@ -1257,25 +1374,39 @@ Bool_t AliReconstruction::RunTracking(AliESD*& esd)
     AliESDtrack * track = esd->GetTrack(itrack);
     if (!track) continue;
     if (track->IsOn(AliESDtrack::kITSrefit)) continue;
-    track->PropagateTo(kRadius, fieldZ, track->GetMass(),kMaxStep,kTRUE);
+   AliTracker::PropagateTrackTo(track,kRadius,track->GetMass(),kMaxStep,kTRUE);
     track->RelateToVertex(esd->GetVertex(),fieldZ, kMaxD);
   }
-  
-  AliInfo(Form("Execution time: R:%.2fs C:%.2fs",
-              stopwatch.RealTime(),stopwatch.CpuTime()));
-
+  eventNr++;
   return kTRUE;
 }
 
 //_____________________________________________________________________________
-Bool_t AliReconstruction::FillESD(AliESD*& esd, const TString& detectors)
+Bool_t AliReconstruction::CleanESD(AliESDEvent *esd){
+  //
+  // Remove the data which are not needed for the physics analysis.
+  //
+
+  AliInfo("Cleaning the ESD...");
+  Int_t nTracks=esd->GetNumberOfTracks();
+  AliInfo(Form("Number of ESD tracks before cleaning %d",nTracks));
+
+  Float_t cleanPars[]={fDmax,fZmax};
+  Bool_t rc=esd->Clean(cleanPars);
+
+  nTracks=esd->GetNumberOfTracks();
+  AliInfo(Form("Number of ESD tracks after cleaning %d",nTracks));
+
+  return rc;
+}
+
+//_____________________________________________________________________________
+Bool_t AliReconstruction::FillESD(AliESDEvent*& esd, const TString& detectors)
 {
 // fill the event summary data
 
-  TStopwatch stopwatch;
-  stopwatch.Start();
-  AliInfo("filling ESD");
-
+  AliCodeTimerAuto("")
+    static Int_t eventNr=0; 
   TString detStr = detectors;
   for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
     if (!IsSelected(fgkDetectorName[iDet], detStr)) continue;
@@ -1285,7 +1416,7 @@ Bool_t AliReconstruction::FillESD(AliESD*& esd, const TString& detectors)
     if (!ReadESD(esd, fgkDetectorName[iDet])) {
       AliDebug(1, Form("filling ESD for %s", fgkDetectorName[iDet]));
       TTree* clustersTree = NULL;
-      if (reconstructor->HasLocalReconstruction() && fLoader[iDet]) {
+      if (fLoader[iDet]) {
        fLoader[iDet]->LoadRecPoints("read");
        clustersTree = fLoader[iDet]->TreeR();
        if (!clustersTree) {
@@ -1310,15 +1441,10 @@ Bool_t AliReconstruction::FillESD(AliESD*& esd, const TString& detectors)
        reconstructor->FillESD(digitsTree, clustersTree, esd);
        if (fLoader[iDet]) fLoader[iDet]->UnloadDigits();
       }
-      if (reconstructor->HasLocalReconstruction() && fLoader[iDet]) {
+      if (fLoader[iDet]) {
        fLoader[iDet]->UnloadRecPoints();
       }
 
-      if (fRawReader) {
-        reconstructor->FillESD(fRunLoader, fRawReader, esd);
-      } else {
-        reconstructor->FillESD(fRunLoader, esd);
-      }
       if (fCheckPointLevel > 2) WriteESD(esd, fgkDetectorName[iDet]);
     }
   }
@@ -1328,20 +1454,20 @@ Bool_t AliReconstruction::FillESD(AliESD*& esd, const TString& detectors)
                   detStr.Data()));
     if (fStopOnError) return kFALSE;
   }
-
-  AliInfo(Form("Execution time: R:%.2fs C:%.2fs",
-              stopwatch.RealTime(),stopwatch.CpuTime()));
-
+  AliSysInfo::AddStamp(Form("FillESD%d",eventNr), 0,1, eventNr);
+  eventNr++;
   return kTRUE;
 }
 
 //_____________________________________________________________________________
-Bool_t AliReconstruction::FillTriggerESD(AliESD*& esd)
+Bool_t AliReconstruction::FillTriggerESD(AliESDEvent*& esd)
 {
   // Reads the trigger decision which is
   // stored in Trigger.root file and fills
   // the corresponding esd entries
 
+  AliCodeTimerAuto("")
+  
   AliInfo("Filling trigger information into the ESD");
 
   if (fRawReader) {
@@ -1380,7 +1506,7 @@ Bool_t AliReconstruction::FillTriggerESD(AliESD*& esd)
 
 
 //_____________________________________________________________________________
-Bool_t AliReconstruction::FillRawEventHeaderESD(AliESD*& esd)
+Bool_t AliReconstruction::FillRawEventHeaderESD(AliESDEvent*& esd)
 {
   // 
   // Filling information from RawReader Header
@@ -1389,12 +1515,17 @@ 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){
-    esd->SetBunchCrossNumber((eventHeader->GetP("Id")[0]));
-    esd->SetOrbitNumber((eventHeader->GetP("Id")[1]));
+
+    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")));
   }
@@ -1473,6 +1604,11 @@ Bool_t AliReconstruction::InitRunLoader()
       return kFALSE;
     }
 
+    //PH This is a temporary fix to give access to the kinematics
+    //PH that is needed for the labels of ITS clusters
+    fRunLoader->LoadHeader();
+    fRunLoader->LoadKinematics();
+
   } else {               // galice.root does not exist
     if (!fRawReader) {
       AliError(Form("the file %s does not exist", fGAliceFileName.Data()));
@@ -1525,15 +1661,6 @@ AliReconstructor* AliReconstruction::GetReconstructor(Int_t iDet)
   TString recName = "Ali" + detName + "Reconstructor";
   if (gAlice && !gAlice->GetDetector(detName) && (detName != "HLT")) return NULL;
 
-  if (detName == "HLT") {
-    if (!gROOT->GetClass("AliLevel3")) {
-      gSystem->Load("libAliHLTSrc.so");
-      gSystem->Load("libAliHLTMisc.so");
-      gSystem->Load("libAliHLTHough.so");
-      gSystem->Load("libAliHLTComp.so");
-    }
-  }
-
   AliReconstructor* reconstructor = NULL;
   // first check if a plugin is defined for the reconstructor
   TPluginHandler* pluginHandler = 
@@ -1558,7 +1685,7 @@ AliReconstructor* AliReconstruction::GetReconstructor(Int_t iDet)
   if (reconstructor) {
     TObject* obj = fOptions.FindObject(detName.Data());
     if (obj) reconstructor->SetOption(obj->GetTitle());
-    reconstructor->Init(fRunLoader);
+    reconstructor->Init();
     fReconstructor[iDet] = reconstructor;
   }
 
@@ -1612,7 +1739,7 @@ Bool_t AliReconstruction::CreateVertexer()
   fVertexer = NULL;
   AliReconstructor* itsReconstructor = GetReconstructor(0);
   if (itsReconstructor) {
-    fVertexer = itsReconstructor->CreateVertexer(fRunLoader);
+    fVertexer = itsReconstructor->CreateVertexer();
   }
   if (!fVertexer) {
     AliWarning("couldn't create a vertexer for ITS");
@@ -1643,11 +1770,12 @@ Bool_t AliReconstruction::CreateTrackers(const TString& detectors)
     }
 
 
-    fTracker[iDet] = reconstructor->CreateTracker(fRunLoader);
+    fTracker[iDet] = reconstructor->CreateTracker();
     if (!fTracker[iDet] && (iDet < 7)) {
       AliWarning(Form("couldn't create a tracker for %s", detName.Data()));
       if (fStopOnError) return kFALSE;
     }
+    AliSysInfo::AddStamp(Form("LTracker%s",fgkDetectorName[iDet]), iDet,0);
   }
 
   return kTRUE;
@@ -1664,6 +1792,8 @@ void AliReconstruction::CleanUp(TFile* file, TFile* fileOld)
     fLoader[iDet] = NULL;
     delete fTracker[iDet];
     fTracker[iDet] = NULL;
+    delete fQADataMaker[iDet];
+    fQADataMaker[iDet] = NULL;
   }
   delete fVertexer;
   fVertexer = NULL;
@@ -1687,9 +1817,9 @@ void AliReconstruction::CleanUp(TFile* file, TFile* fileOld)
   }
 }
 
-
 //_____________________________________________________________________________
-Bool_t AliReconstruction::ReadESD(AliESD*& esd, const char* recStep) const
+
+Bool_t AliReconstruction::ReadESD(AliESDEvent*& esd, const char* recStep) const
 {
 // read the ESD event from a file
 
@@ -1710,14 +1840,17 @@ Bool_t AliReconstruction::ReadESD(AliESD*& esd, const char* recStep) const
 
   gROOT->cd();
   delete esd;
-  esd = (AliESD*) file->Get("ESD");
+  esd = (AliESDEvent*) file->Get("ESD");
   file->Close();
   delete file;
   return kTRUE;
+
 }
 
+
+
 //_____________________________________________________________________________
-void AliReconstruction::WriteESD(AliESD* esd, const char* recStep) const
+void AliReconstruction::WriteESD(AliESDEvent* esd, const char* recStep) const
 {
 // write the ESD event to a file
 
@@ -1740,302 +1873,753 @@ void AliReconstruction::WriteESD(AliESD* esd, const char* recStep) const
 
 
 
+
 //_____________________________________________________________________________
-void AliReconstruction::CreateTag(TFile* file)
+void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
 {
-  /////////////
-  //muon code//
-  ////////////
-  Double_t fMUONMASS = 0.105658369;
-  //Variables
-  Double_t fX,fY,fZ ;
-  Double_t fThetaX, fThetaY, fPyz, fChisquare;
-  Double_t fPxRec,fPyRec, fPzRec, fEnergy;
-  Int_t fCharge;
-  TLorentzVector fEPvector;
-
-  Float_t fZVertexCut = 10.0; 
-  Float_t fRhoVertexCut = 2.0; 
-
-  Float_t fLowPtCut = 1.0;
-  Float_t fHighPtCut = 3.0;
-  Float_t fVeryHighPtCut = 10.0;
-  ////////////
-
-  Double_t partFrac[5] = {0.01, 0.01, 0.85, 0.10, 0.05};
-
-  // Creates the tags for all the events in a given ESD file
-  Int_t ntrack;
-  Int_t nProtons, nKaons, nPions, nMuons, nElectrons;
-  Int_t nPos, nNeg, nNeutr;
-  Int_t nK0s, nNeutrons, nPi0s, nGamas;
-  Int_t nCh1GeV, nCh3GeV, nCh10GeV;
-  Int_t nMu1GeV, nMu3GeV, nMu10GeV;
-  Int_t nEl1GeV, nEl3GeV, nEl10GeV;
-  Float_t maxPt = .0, meanPt = .0, totalP = .0;
-  Int_t fVertexflag;
-  Int_t iRunNumber = 0;
-  TString fVertexName("default");
-
-  AliRunTag *tag = new AliRunTag();
-  AliEventTag *evTag = new AliEventTag();
-  TTree ttag("T","A Tree with event tags");
-  TBranch * btag = ttag.Branch("AliTAG", &tag);
-  btag->SetCompressionLevel(9);
-  
-  AliInfo(Form("Creating the tags......."));   
+  // write all files from the given esd file to an aod file
+
+  // create an AliAOD object 
+  AliAODEvent *aod = new AliAODEvent();
+  aod->CreateStdContent();
   
-  if (!file || !file->IsOpen()) {
-    AliError(Form("opening failed"));
-    delete file;
-    return ;
-  }  
-  Int_t lastEvent = 0;
-  TTree *t = (TTree*) file->Get("esdTree");
-  TBranch * b = t->GetBranch("ESD");
-  AliESD *esd = 0;
-  b->SetAddress(&esd);
-
-  b->GetEntry(fFirstEvent);
-  Int_t iInitRunNumber = esd->GetRunNumber();
+  // go to the file
+  aodFile->cd();
   
-  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;
-    nNeutr =0;
-    nK0s = 0;
-    nNeutrons = 0;
-    nPi0s = 0;
-    nGamas = 0;
-    nProtons = 0;
-    nKaons = 0;
-    nPions = 0;
-    nMuons = 0;
-    nElectrons = 0;      
-    nCh1GeV = 0;
-    nCh3GeV = 0;
-    nCh10GeV = 0;
-    nMu1GeV = 0;
-    nMu3GeV = 0;
-    nMu10GeV = 0;
-    nEl1GeV = 0;
-    nEl3GeV = 0;
-    nEl10GeV = 0;
-    maxPt = .0;
-    meanPt = .0;
-    totalP = .0;
-    fVertexflag = 0;
-
-    b->GetEntry(iEventNumber);
-    iRunNumber = esd->GetRunNumber();
-    if(iRunNumber != iInitRunNumber) AliFatal("Inconsistency of run numbers in the AliESD!!!");
-    const AliESDVertex * vertexIn = esd->GetVertex();
-    if (!vertexIn) AliError("ESD has not defined vertex.");
-    if (vertexIn) fVertexName = vertexIn->GetName();
-    if(fVertexName != "default") fVertexflag = 1;
-    for (Int_t iTrackNumber = 0; iTrackNumber < esd->GetNumberOfTracks(); iTrackNumber++) {
-      AliESDtrack * esdTrack = esd->GetTrack(iTrackNumber);
-      UInt_t status = esdTrack->GetStatus();
+  // create the tree
+  TTree *aodTree = new TTree("aodTree", "AliAOD tree");
+  aodTree->Branch(aod->GetList());
+
+  // connect to ESD
+  TTree *t = (TTree*) esdFile->Get("esdTree");
+  AliESDEvent *esd = new AliESDEvent();
+  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 p_pos[3];
+  Double_t p_neg[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) {
+    //cout << "event: " << iEvent << endl;
+    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)->Charge()> 0) nPosTracks++;
+
+    // Access the header
+    AliAODHeader *header = aod->GetHeader();
+
+    // fill the header
+    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 + 1 /* = prim. vtx*/;
+    Int_t nJets     = 0;
+    Int_t nCaloClus = esd->GetNumberOfCaloClusters();
+    Int_t nFmdClus  = 0;
+    Int_t nPmdClus  = esd->GetNumberOfPmdTracks();
+   
+    aod->ResetStd(nTracks, nVertices, nV0s+nCascades, nJets, nCaloClus, nFmdClus, nPmdClus);
+    
+    // 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; 
+   
+    // Access to the AOD container of V0s
+    TClonesArray &V0s = *(aod->GetV0s());
+    Int_t jV0s=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();
       
-      //select only tracks with ITS refit
-      if ((status&AliESDtrack::kITSrefit)==0) continue;
-      //select only tracks with TPC refit
-      if ((status&AliESDtrack::kTPCrefit)==0) continue;
+    vtx->GetXYZ(pos); // position
+    vtx->GetCovMatrix(covVtx); //covariance matrix
+
+    AliAODVertex * primary = new(vertices[jVertices++])
+      AliAODVertex(pos, covVtx, vtx->GetChi2toNDF(), NULL, -1, AliAODVertex::kPrimary);
+         
+
+    AliAODTrack *aodTrack = 0x0;
+    
+    // Create vertices starting from the most complex objects
+
+    // Cascades
+    for (Int_t nCascade = 0; nCascade < nCascades; ++nCascade) {
+      AliESDcascade *cascade = esd->GetCascade(nCascade);
       
-      //select only tracks with the "combined PID"
-      if ((status&AliESDtrack::kESDpid)==0) continue;
-      Double_t p[3];
-      esdTrack->GetPxPyPz(p);
-      Double_t momentum = sqrt(pow(p[0],2) + pow(p[1],2) + pow(p[2],2));
-      Double_t fPt = sqrt(pow(p[0],2) + pow(p[1],2));
-      totalP += momentum;
-      meanPt += fPt;
-      if(fPt > maxPt) maxPt = fPt;
+      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,
+                                                                       nCascade,
+                                                                       AliAODVertex::kCascade);
+
+      primary->AddDaughter(vcascade); // the cascade 'particle' (represented by a vertex) is added as a daughter to the primary vertex
+
+      // Add the V0 from the cascade. The ESD class have to be optimized...
+      // Now we have to search for the corresponding V0 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,
+                                                                indV0,
+                                                                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);
       
-      if(esdTrack->GetSign() > 0) {
-       nPos++;
-       if(fPt > fLowPtCut) nCh1GeV++;
-       if(fPt > fHighPtCut) nCh3GeV++;
-       if(fPt > fVeryHighPtCut) nCh10GeV++;
+       vV0FromCascade = new(vertices[jVertices++]) AliAODVertex(pos,
+                                                                covVtx,
+                                                                v0->GetChi2V0(), // = chi2/NDF since NDF = 2*2-3
+                                                                vcascade,
+                                                                indV0,
+                                                                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_pos);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+       
+       vV0FromCascade->AddDaughter(aodTrack =
+                                   new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(), 
+                                          p_pos, 
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->Charge(),
+                                          esdTrack->GetITSClusterMap(), 
+                                          pid,
+                                          vV0FromCascade,
+                                          kTRUE,  // check if this is right
+                                          kFALSE, // check if this is right
+                                          AliAODTrack::kSecondary)
+               );
+       aodTrack->ConvertAliPIDtoAODPID();
       }
-      if(esdTrack->GetSign() < 0) {
-       nNeg++;
-       if(fPt > fLowPtCut) nCh1GeV++;
-       if(fPt > fHighPtCut) nCh3GeV++;
-       if(fPt > fVeryHighPtCut) nCh10GeV++;
+      else {
+       cerr << "Error: event " << iEvent << " cascade " << nCascade
+            << " track " << posFromV0 << " has already been used!" << endl;
       }
-      if(esdTrack->GetSign() == 0) nNeutr++;
-      
-      //PID
-      Double_t prob[5];
-      esdTrack->GetESDpid(prob);
-      
-      Double_t rcc = 0.0;
-      for(Int_t i = 0; i < AliPID::kSPECIES; i++) rcc += prob[i]*partFrac[i];
-      if(rcc == 0.0) continue;
-      //Bayes' formula
-      Double_t w[5];
-      for(Int_t i = 0; i < AliPID::kSPECIES; i++) w[i] = prob[i]*partFrac[i]/rcc;
-      
-      //protons
-      if ((w[4]>w[3])&&(w[4]>w[2])&&(w[4]>w[1])&&(w[4]>w[0])) nProtons++;
-      //kaons
-      if ((w[3]>w[4])&&(w[3]>w[2])&&(w[3]>w[1])&&(w[3]>w[0])) nKaons++;
-      //pions
-      if ((w[2]>w[4])&&(w[2]>w[3])&&(w[2]>w[1])&&(w[2]>w[0])) nPions++; 
-      //electrons
-      if ((w[0]>w[4])&&(w[0]>w[3])&&(w[0]>w[2])&&(w[0]>w[1])) {
-       nElectrons++;
-       if(fPt > fLowPtCut) nEl1GeV++;
-       if(fPt > fHighPtCut) nEl3GeV++;
-       if(fPt > fVeryHighPtCut) nEl10GeV++;
-      }          
-      ntrack++;
-    }//track loop
-    
-    /////////////
-    //muon code//
-    ////////////
-    Int_t nMuonTracks = esd->GetNumberOfMuonTracks();
-    // loop over all reconstructed tracks (also first track of combination)
-    for (Int_t iTrack = 0; iTrack <  nMuonTracks;  iTrack++) {
-      AliESDMuonTrack* muonTrack = esd->GetMuonTrack(iTrack);
-      if (muonTrack == 0x0) continue;
+
+      // Add the negative tracks from the V0
+
+      if (!usedTrack[negFromV0]) {
+       
+       usedTrack[negFromV0] = kTRUE;
+       
+       AliESDtrack *esdTrack = esd->GetTrack(negFromV0);
+       esdTrack->GetPxPyPz(p_neg);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+       
+       vV0FromCascade->AddDaughter(aodTrack =
+                new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(),
+                                          p_neg,
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->Charge(),
+                                          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 it to the V0 array as well
+      Double_t d0[2] = { -999., -99.};
+      // counting is probably wrong
+      new(V0s[jV0s++]) AliAODv0(vV0FromCascade, -999., -99., p_pos, p_neg, d0); // to be refined
+
+      // Add the bachelor track from the cascade
+
+      Int_t bachelor = cascade->GetBindex();
       
-      // Coordinates at vertex
-      fZ = muonTrack->GetZ(); 
-      fY = muonTrack->GetBendingCoor();
-      fX = muonTrack->GetNonBendingCoor(); 
+      if(!usedTrack[bachelor]) {
       
-      fThetaX = muonTrack->GetThetaX();
-      fThetaY = muonTrack->GetThetaY();
+       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->Charge(),
+                                          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;
+      }
       
-      fPyz = 1./TMath::Abs(muonTrack->GetInverseBendingMomentum());
-      fPzRec = - fPyz / TMath::Sqrt(1.0 + TMath::Tan(fThetaY)*TMath::Tan(fThetaY));
-      fPxRec = fPzRec * TMath::Tan(fThetaX);
-      fPyRec = fPzRec * TMath::Tan(fThetaY);
-      fCharge = Int_t(TMath::Sign(1.,muonTrack->GetInverseBendingMomentum()));
+      // Add the primary track of the cascade (if any)
       
-      //ChiSquare of the track if needed
-      fChisquare = muonTrack->GetChi2()/(2.0 * muonTrack->GetNHit() - 5);
-      fEnergy = TMath::Sqrt(fMUONMASS * fMUONMASS + fPxRec * fPxRec + fPyRec * fPyRec + fPzRec * fPzRec);
-      fEPvector.SetPxPyPzE(fPxRec, fPyRec, fPzRec, fEnergy);
+    } // 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,
+                                               nV0,
+                                               AliAODVertex::kV0);
+      primary->AddDaughter(vV0);
+
+      Int_t posFromV0 = v0->GetPindex();
+      Int_t negFromV0 = v0->GetNindex();
       
-      // total number of muons inside a vertex cut 
-      if((TMath::Abs(fZ)<fZVertexCut) && (TMath::Sqrt(fY*fY+fX*fX)<fRhoVertexCut)) {
-       nMuons++;
-       if(fEPvector.Pt() > fLowPtCut) {
-         nMu1GeV++; 
-         if(fEPvector.Pt() > fHighPtCut) {
-           nMu3GeV++; 
-           if (fEPvector.Pt() > fVeryHighPtCut) {
-             nMu10GeV++;
+      // Add the positive tracks from the V0
+
+      if (!usedTrack[posFromV0]) {
+       
+       usedTrack[posFromV0] = kTRUE;
+
+       AliESDtrack *esdTrack = esd->GetTrack(posFromV0);
+       esdTrack->GetPxPyPz(p_pos);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+       
+       vV0->AddDaughter(aodTrack =
+               new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(), 
+                                          p_pos, 
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->Charge(),
+                                          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_neg);
+       esdTrack->GetXYZ(pos);
+       esdTrack->GetCovarianceXYZPxPyPz(covTr);
+       esdTrack->GetESDpid(pid);
+
+       vV0->AddDaughter(aodTrack =
+                new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
+                                          esdTrack->GetLabel(),
+                                          p_neg,
+                                          kTRUE,
+                                          pos,
+                                          kFALSE,
+                                          covTr, 
+                                          (Short_t)esdTrack->Charge(),
+                                          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;
+      }
+
+      // add it to the V0 array as well
+      Double_t d0[2] = { 999., 99.};
+      new(V0s[jV0s++]) AliAODv0(vV0, 999., 99., p_pos, p_neg, d0); // to be refined
+    } // 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->Charge(),
+                                          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,
+                                                   esdTrack->GetID(), // This is the track ID of the mother's track!
+                                                   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->Charge(),
+                                          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;
            }
          }
        }
       }
-    }//muon track loop
-    
-    // Fill the event tags 
-    if(ntrack != 0)
-      meanPt = meanPt/ntrack;
-    
-    evTag->SetEventId(iEventNumber+1);
-    if (vertexIn) {
-      evTag->SetVertexX(vertexIn->GetXv());
-      evTag->SetVertexY(vertexIn->GetYv());
-      evTag->SetVertexZ(vertexIn->GetZv());
-      evTag->SetVertexZError(vertexIn->GetZRes());
-    }  
-    evTag->SetVertexFlag(fVertexflag);
-
-    evTag->SetT0VertexZ(esd->GetT0zVertex());
-    
-    evTag->SetTriggerMask(esd->GetTriggerMask());
-    evTag->SetTriggerCluster(esd->GetTriggerCluster());
-    
-    evTag->SetZDCNeutron1Energy(esd->GetZDCN1Energy());
-    evTag->SetZDCProton1Energy(esd->GetZDCP1Energy());
-    evTag->SetZDCNeutron2Energy(esd->GetZDCN2Energy());
-    evTag->SetZDCProton2Energy(esd->GetZDCP2Energy());
-    evTag->SetZDCEMEnergy(esd->GetZDCEMEnergy());
-    evTag->SetNumOfParticipants(esd->GetZDCParticipants());
-    
-    
-    evTag->SetNumOfTracks(esd->GetNumberOfTracks());
-    evTag->SetNumOfPosTracks(nPos);
-    evTag->SetNumOfNegTracks(nNeg);
-    evTag->SetNumOfNeutrTracks(nNeutr);
-    
-    evTag->SetNumOfV0s(esd->GetNumberOfV0s());
-    evTag->SetNumOfCascades(esd->GetNumberOfCascades());
-    evTag->SetNumOfKinks(esd->GetNumberOfKinks());
-    evTag->SetNumOfPMDTracks(esd->GetNumberOfPmdTracks());
-    
-    evTag->SetNumOfProtons(nProtons);
-    evTag->SetNumOfKaons(nKaons);
-    evTag->SetNumOfPions(nPions);
-    evTag->SetNumOfMuons(nMuons);
-    evTag->SetNumOfElectrons(nElectrons);
-    evTag->SetNumOfPhotons(nGamas);
-    evTag->SetNumOfPi0s(nPi0s);
-    evTag->SetNumOfNeutrons(nNeutrons);
-    evTag->SetNumOfKaon0s(nK0s);
-    
-    evTag->SetNumOfChargedAbove1GeV(nCh1GeV);
-    evTag->SetNumOfChargedAbove3GeV(nCh3GeV);
-    evTag->SetNumOfChargedAbove10GeV(nCh10GeV);
-    evTag->SetNumOfMuonsAbove1GeV(nMu1GeV);
-    evTag->SetNumOfMuonsAbove3GeV(nMu3GeV);
-    evTag->SetNumOfMuonsAbove10GeV(nMu10GeV);
-    evTag->SetNumOfElectronsAbove1GeV(nEl1GeV);
-    evTag->SetNumOfElectronsAbove3GeV(nEl3GeV);
-    evTag->SetNumOfElectronsAbove10GeV(nEl10GeV);
-    
-    evTag->SetNumOfPHOSClusters(esd->GetNumberOfPHOSClusters());
-    evTag->SetNumOfEMCALClusters(esd->GetNumberOfEMCALClusters());
-    
-    evTag->SetTotalMomentum(totalP);
-    evTag->SetMeanPt(meanPt);
-    evTag->SetMaxPt(maxPt);
-    
-    tag->SetRunId(iInitRunNumber);
-    tag->AddEventTag(*evTag);
-  }
-  if(fLastEvent == -1) lastEvent = (Int_t)b->GetEntries();
-  else lastEvent = fLastEvent;
+    }
+
+    // Tracks (primary and orphan)
+    for (Int_t nTrack = 0; nTrack < nTracks; ++nTrack) {
        
-  ttag.Fill();
-  tag->Clear();
 
-  char fileName[256];
-  sprintf(fileName, "Run%d.Event%d_%d.ESD.tag.root", 
-         tag->GetRunId(),fFirstEvent,lastEvent );
-  AliInfo(Form("writing tags to file %s", fileName));
-  AliDebug(1, Form("writing tags to file %s", fileName));
+      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->Charge(),
+                                        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
+       // Don't write them anymore!
+       continue;
+      }        
+    } // 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(aodTrack =
+         new(tracks[jTracks++]) AliAODTrack(0, // no ID provided
+                                            0, // no label provided
+                                            p,
+                                            kTRUE,
+                                            pos,
+                                            kFALSE,
+                                            NULL, // no covariance matrix provided
+                                            esdMuTrack->Charge(),
+                                            0, // ITSClusterMap is set below
+                                            pid,
+                                            primary,
+                                            kFALSE,  // muon tracks are not used to fit the primary vtx
+                                            kFALSE,  // not used for vertex fit
+                                            AliAODTrack::kPrimary)
+         );
+
+      aodTrack->SetHitsPatternInTrigCh(esdMuTrack->GetHitsPatternInTrigCh());
+      Int_t track2Trigger = esdMuTrack->GetMatchTrigger();
+      aodTrack->SetMatchTrigger(track2Trigger);
+      if (track2Trigger) 
+       aodTrack->SetChi2MatchTrigger(esdMuTrack->GetChi2MatchTrigger());
+      else 
+       aodTrack->SetChi2MatchTrigger(0.);
+    }
+   
+    // Access to the AOD container of PMD clusters
+    TClonesArray &pmdClusters = *(aod->GetPmdClusters());
+    Int_t jPmdClusters=0;
+  
+    for (Int_t iPmd = 0; iPmd < nPmdClus; ++iPmd) {
+      // file pmd clusters, to be revised!
+      AliESDPmdTrack *pmdTrack = esd->GetPmdTrack(iPmd);
+      Int_t nLabel = 0;
+      Int_t *label = 0x0;
+      Double_t pos[3] = { pmdTrack->GetClusterX(), pmdTrack->GetClusterY(), pmdTrack->GetClusterZ() };
+      Double_t pid[9] = { 0., 0., 0., 0., 0., 0., 0., 0., 0. }; // to be revised!
+      // type not set!
+      // assoc cluster not set
+      new(pmdClusters[jPmdClusters++]) AliAODPmdCluster(iPmd, nLabel, label, pmdTrack->GetClusterADC(), pos, pid);
+    }
+
+    // Access to the AOD container of clusters
+    TClonesArray &caloClusters = *(aod->GetCaloClusters());
+    Int_t jClusters=0;
+
+    // Calo Clusters
+    TArrayS EMCCellNumber(15000);
+    TArrayD EMCCellAmplitude(15000);
+    Int_t nEMCCells = 0;
+    const Float_t fEMCAmpScale = 1./500;
  
-  TFile* ftag = TFile::Open(fileName, "recreate");
-  ftag->cd();
-  ttag.Write();
-  ftag->Close();
-  file->cd();
-  delete tag;
-  delete evTag;
-}
+    for (Int_t iClust=0; iClust<nCaloClus; ++iClust) {
+
+      AliESDCaloCluster * cluster = esd->GetCaloCluster(iClust);
+
+      Int_t id = cluster->GetID();
+      Int_t nLabel = 0;
+      Int_t *label = 0x0;
+      Float_t energy = cluster->E();
+      cluster->GetPosition(posF);
+      Char_t ttype=AliAODCluster::kUndef;
+
+      if (cluster->GetClusterType() == AliESDCaloCluster::kPHOSCluster) {
+       ttype=AliAODCluster::kPHOSNeutral;
+      } 
+      else if (cluster->GetClusterType() == AliESDCaloCluster::kEMCALClusterv1) {
+       ttype = AliAODCluster::kEMCALClusterv1;
+      }
+      else if (cluster->GetClusterType() == AliESDCaloCluster::kEMCALPseudoCluster) {
+       // Collect raw tower info
+       for (Int_t iDig = 0; iDig < cluster->GetNumberOfDigits(); iDig++) {
+         EMCCellNumber[nEMCCells] = cluster->GetDigitIndex()->At(iDig);
+         EMCCellAmplitude[nEMCCells] = fEMCAmpScale*cluster->GetDigitAmplitude()->At(iDig);
+         nEMCCells++;
+       }
+       // don't write cluster data (it's just a pseudo cluster, holding the tower information)
+       continue; 
+      }
+      
+      AliAODCaloCluster *caloCluster = new(caloClusters[jClusters++]) AliAODCaloCluster(id,
+                                                                                       nLabel,
+                                                                                       label,
+                                                                                       energy,
+                                                                                       pos,
+                                                                                       NULL,
+                                                                                       ttype);
+      
+      caloCluster->SetCaloCluster(); // to be refined!
 
-//_____________________________________________________________________________
-void AliReconstruction::CreateAOD(TFile* esdFile)
-{
-  // do nothing for now
+    } // end of loop on calo clusters
+
+    // fill EMC cell info
+    AliAODCaloCells &EMCCells = *(aod->GetCaloCells());
+    EMCCells.CreateContainer(nEMCCells);
+    EMCCells.SetType(AliAODCaloCells::kEMCAL);
+    for (Int_t iCell = 0; iCell < nEMCCells; iCell++) {      
+      EMCCells.SetCell(iCell,EMCCellNumber[iCell],EMCCellAmplitude[iCell]);
+    }
+    EMCCells.Sort();
+
+    // tracklets    
+    AliAODTracklets &SPDTracklets = *(aod->GetTracklets());
+    const AliMultiplicity *mult = esd->GetMultiplicity();
+    if (mult) {
+      if (mult->GetNumberOfTracklets()>0) {
+       SPDTracklets.CreateContainer(mult->GetNumberOfTracklets());
+
+       for (Int_t n=0; n<mult->GetNumberOfTracklets(); n++) {
+         SPDTracklets.SetTracklet(n, mult->GetTheta(n), mult->GetPhi(n), mult->GetDeltaPhi(n), mult->GetLabel(n));
+       }
+      }
+    } else {
+      Printf("ERROR: AliMultiplicity could not be retrieved from ESD");
+    }
+
+    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)
+void AliReconstruction::WriteAlignmentData(AliESDEvent* esd)
 {
   // Write space-points which are then used in the alignment procedures
   // For the moment only ITS, TRD and TPC
@@ -2072,7 +2656,13 @@ void AliReconstruction::WriteAlignmentData(AliESD* esd)
          Int_t isp = 0;
          Int_t isp2 = 0;
          while (isp < nspdet) {
-           Bool_t isvalid = tracker->GetTrackPoint(idx[isp2],p); isp2++;
+           Bool_t isvalid;
+           if(IsSelected(fgkDetectorName[iDet],fUseTrackingErrorsForAlignment)) {
+             isvalid = tracker->GetTrackPointTrackingError(idx[isp2],p,track);
+           } else {
+             isvalid = tracker->GetTrackPoint(idx[isp2],p); 
+           } 
+           isp2++;
            const Int_t kNTPCmax = 159;
            if (iDet==1 && isp2>kNTPCmax) break;   // to be fixed
            if (!isvalid) continue;
@@ -2086,3 +2676,200 @@ void AliReconstruction::WriteAlignmentData(AliESD* esd)
     fLoader[3]->UnloadRecPoints();
   }
 }
+
+//_____________________________________________________________________________
+void AliReconstruction::FillRawDataErrorLog(Int_t iEvent, AliESDEvent* 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();
+
+}
+  
+
+
+//_____________________________________________________________________________
+AliQADataMaker * AliReconstruction::GetQADataMaker(Int_t iDet)
+{
+// get the quality assurance data maker object and the loader for a detector
+
+  if (fQADataMaker[iDet]) 
+    return fQADataMaker[iDet];
+
+  // load the QA data maker object
+  TPluginManager* pluginManager = gROOT->GetPluginManager();
+  TString detName = fgkDetectorName[iDet];
+  TString qadmName = "Ali" + detName + "QADataMaker";
+  if (gAlice && !gAlice->GetDetector(detName) && (detName != "HLT")) 
+    return NULL;
+
+  AliQADataMaker * qadm = NULL;
+  // first check if a plugin is defined for the quality assurance data maker
+  TPluginHandler* pluginHandler = pluginManager->FindHandler("AliQADataMaker", detName);
+  // if not, add a plugin for it
+  if (!pluginHandler) {
+    AliDebug(1, Form("defining plugin for %s", qadmName.Data()));
+    TString libs = gSystem->GetLibraries();
+    if (libs.Contains("lib" + detName + "base.so") ||
+       (gSystem->Load("lib" + detName + "base.so") >= 0)) {
+      pluginManager->AddHandler("AliQADataMaker", detName, 
+                               qadmName, detName + "qadm", qadmName + "()");
+    } else {
+      pluginManager->AddHandler("AliQADataMaker", detName, 
+                               qadmName, detName, qadmName + "()");
+    }
+    pluginHandler = pluginManager->FindHandler("AliQADataMaker", detName);
+  }
+  if (pluginHandler && (pluginHandler->LoadPlugin() == 0)) {
+    qadm = (AliQADataMaker *) pluginHandler->ExecPlugin(0);
+  }
+  if (qadm) {
+    AliInfo(Form("Initializing quality assurance data maker for %s", fgkDetectorName[iDet]));
+    qadm->Init(AliQA::kRECPOINTS, AliCDBManager::Instance()->GetRun(), GetQACycles(fgkDetectorName[iDet]));
+    qadm->StartOfCycle(AliQA::kRECPOINTS);
+    qadm->Init(AliQA::kESDS, AliCDBManager::Instance()->GetRun());
+    qadm->StartOfCycle(AliQA::kESDS, "same") ;         
+    fQADataMaker[iDet] = qadm;
+  }
+
+  return qadm;
+}
+
+//_____________________________________________________________________________
+Bool_t AliReconstruction::RunQA(const char* detectors, AliESDEvent *& esd)
+{
+  // run the Quality Assurance data producer
+
+  AliCodeTimerAuto("")
+  TString detStr = detectors;
+  for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
+   if (!IsSelected(fgkDetectorName[iDet], detStr)) 
+     continue;
+   AliQADataMaker * qadm = GetQADataMaker(iDet);
+   if (!qadm) 
+     continue;
+   AliCodeTimerStart(Form("running quality assurance data maker for %s", fgkDetectorName[iDet]));
+   AliInfo(Form("running quality assurance data maker for %s", fgkDetectorName[iDet]));
+    
+   qadm->Exec(AliQA::kESDS, esd) ; 
+   qadm->Increment() ; 
+
+   AliCodeTimerStop(Form("running quality assurance data maker for %s", fgkDetectorName[iDet]));
+ }
+ if ((detStr.CompareTo("ALL") != 0) && !detStr.IsNull()) {
+   AliError(Form("the following detectors were not found: %s",
+                detStr.Data()));
+   if (fStopOnError) 
+     return kFALSE;
+ }
+ return kTRUE;
+  
+}
+
+
+//_____________________________________________________________________________
+void AliReconstruction::CheckQA()
+{
+// check the QA of SIM for this run and remove the detectors 
+// with status Fatal
+  
+       TString newDetList ; 
+       for (Int_t iDet = 0; iDet < AliQA::kNDET; iDet++) {
+               TString detName(AliQA::GetDetName(iDet)) ;
+               if ( fRunLocalReconstruction.Contains(AliQA::GetDetName(iDet)) || 
+                       fRunLocalReconstruction.Contains("ALL") )  {
+                       AliQA * qa = AliQA::Instance(AliQA::DETECTORINDEX(iDet)) ; 
+                       if ( qa->IsSet(AliQA::DETECTORINDEX(iDet), AliQA::kSIM, AliQA::kFATAL)) {
+                               AliInfo(Form("QA status for %s in Hits and/or SDIGITS  and/or Digits was Fatal; No reconstruction performed", detName.Data())) ;
+                       } else if ( qa->IsSet(AliQA::DETECTORINDEX(iDet), AliQA::kSIM, AliQA::kERROR)) {
+                               AliError(Form("QA status for %s in Hits and/or SDIGITS  and/or Digits was ERROR", detName.Data())) ;
+                               newDetList += detName ; 
+                               newDetList += " " ; 
+                       } else if ( qa->IsSet(AliQA::DETECTORINDEX(iDet), AliQA::kSIM, AliQA::kWARNING) ) {
+                               AliWarning(Form("QA status for %s in Hits and/or SDIGITS  and/or Digits was WARNING", detName.Data())) ;
+                               newDetList += detName ; 
+                               newDetList += " " ; 
+                       } else if ( qa->IsSet(AliQA::DETECTORINDEX(iDet), AliQA::kSIM, AliQA::kINFO) ) {
+                               AliInfo(Form("QA status for %s in Hits and/or SDIGITS  and/or Digits was INFO", detName.Data())) ;
+                               newDetList += detName ; 
+                               newDetList += " " ; 
+                       } else {
+                               newDetList += detName ; 
+                               newDetList += " " ;                     
+                       }
+               }
+       }
+       fRunLocalReconstruction = newDetList ; 
+}
+
+//_____________________________________________________________________________
+Int_t AliReconstruction::GetDetIndex(const char* detector)
+{
+  // return the detector index corresponding to detector
+  Int_t index = -1 ; 
+  for (index = 0; index < fgkNDetectors ; index++) {
+    if ( strcmp(detector, fgkDetectorName[index]) == 0 )
+       break ; 
+  }    
+  return index ; 
+}