]> 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 73ed864739a5eac301c85cfad0c327a3216215ad..33ade2a548118c2535ea119c95d47a3bdd1b174f 100644 (file)
 #include <TPluginManager.h>
 #include <TGeoManager.h>
 #include <TLorentzVector.h>
+#include <TArrayS.h>
+#include <TArrayD.h>
 
 #include "AliReconstruction.h"
 #include "AliCodeTimer.h"
 #include "AliRawReaderRoot.h"
 #include "AliRawEventHeaderBase.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 "AliTagCreator.h"
+#include "AliESDTagCreator.h"
+#include "AliAODTagCreator.h"
 
 #include "AliGeomManager.h"
 #include "AliTrackPointArray.h"
 #include "AliAODHeader.h"
 #include "AliAODTrack.h"
 #include "AliAODVertex.h"
-#include "AliAODCluster.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)
@@ -180,15 +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(""),
@@ -209,6 +235,7 @@ AliReconstruction::AliReconstruction(const char* gAliceFilename, const char* cdb
 
   fAlignObjArray(NULL),
   fCDBUri(cdbUri),
+  fRemoteCDBUri(""),
   fSpecCDBUri()
 {
 // create reconstruction object with default parameters
@@ -217,6 +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;
 }
@@ -229,15 +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),
@@ -258,6 +294,7 @@ AliReconstruction::AliReconstruction(const AliReconstruction& rec) :
 
   fAlignObjArray(rec.fAlignObjArray),
   fCDBUri(rec.fCDBUri),
+  fRemoteCDBUri(rec.fRemoteCDBUri),
   fSpecCDBUri()
 {
 // copy constructor
@@ -269,6 +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());
@@ -320,6 +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];
@@ -341,6 +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
@@ -362,20 +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);
@@ -401,7 +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()) {
@@ -445,6 +513,7 @@ Bool_t AliReconstruction::MisalignGeometry(const TString& detectors)
       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
@@ -510,12 +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;
@@ -528,8 +599,8 @@ Bool_t AliReconstruction::Run(const char* input)
     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()) {
@@ -547,6 +618,7 @@ Bool_t AliReconstruction::Run(const char* input)
       return kFALSE;
     }
   }
+   AliSysInfo::AddStamp("Vertexer");
 
   // get trackers
   if (!fRunTracking.IsNull() && !CreateTrackers(fRunTracking)) {
@@ -555,6 +627,7 @@ Bool_t AliReconstruction::Run(const char* input)
       return kFALSE;
     }      
   }
+   AliSysInfo::AddStamp("LoadTrackers");
 
   // get the possibly already existing ESD file and tree
   AliESDEvent* esd = new AliESDEvent(); AliESDEvent* hltesd = new AliESDEvent();
@@ -620,7 +693,16 @@ Bool_t AliReconstruction::Run(const char* input)
   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();
@@ -715,6 +797,10 @@ Bool_t AliReconstruction::Run(const char* input)
        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);}
 
@@ -731,6 +817,8 @@ Bool_t AliReconstruction::Run(const char* input)
       }
     }
 
+    file->cd();
+
     //Try to improve the reconstructed primary vertex position using the tracks
     AliESDVertex *pvtx=0;
     Bool_t dovertex=kTRUE;
@@ -757,18 +845,22 @@ 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->~AliESDfriend();
       new (esdf) AliESDfriend(); // Reset...
       esd->GetESDfriend(esdf);
     }
@@ -781,14 +873,29 @@ Bool_t AliReconstruction::Run(const char* input)
     esd->Reset();
     hltesd->Reset();
     if (fWriteESDfriend) {
+      esdf->~AliESDfriend();
       new (esdf) AliESDfriend(); // Reset...
     }
     // esdf->Reset();
     // delete esdf; esdf = 0;
-  } 
-
-
-
+  // ESD QA 
+    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);
@@ -805,7 +912,8 @@ Bool_t AliReconstruction::Run(const char* input)
   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) {
@@ -819,9 +927,12 @@ Bool_t AliReconstruction::Run(const char* input)
   
   // 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
-  AliTagCreator *tagCreator = new AliTagCreator();
-  tagCreator->CreateESDTags(fFirstEvent,fLastEvent);
-  if (fWriteAOD) tagCreator->CreateAODTags(fFirstEvent,fLastEvent);
+  AliESDTagCreator *esdtagCreator = new AliESDTagCreator();
+  esdtagCreator->CreateESDTags(fFirstEvent,fLastEvent);
+  if (fWriteAOD) {
+    AliAODTagCreator *aodtagCreator = new AliAODTagCreator();
+    aodtagCreator->CreateAODTags(fFirstEvent,fLastEvent);
+  }
 
   return kTRUE;
 }
@@ -831,53 +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("")
 
-  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;
 
-    AliCodeTimerStart(Form("running reconstruction for %s", fgkDetectorName[iDet]));
-    AliInfo(Form("running reconstruction for %s", fgkDetectorName[iDet]));
+//     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]));
+//     AliCodeTimerStart(Form("Loading calibration data from OCDB for %s", fgkDetectorName[iDet]));                          
+//     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!
+//     man->SetCacheFlag(kTRUE);
+//     TString calibPath = Form("%s/Calib/*", fgkDetectorName[iDet]);
+//     man->GetAll(calibPath); // entries are cached!
 
-    AliCodeTimerStop(Form("Loading calibration data from OCDB for %s", fgkDetectorName[iDet]));
+//     AliCodeTimerStop(Form("Loading calibration data from OCDB for %s", fgkDetectorName[iDet]));
      
-    if (fRawReader) {
-      fRawReader->RewindEvents();
-      reconstructor->Reconstruct(fRunLoader, fRawReader);
-    } else {
-      reconstructor->Reconstruct(fRunLoader);
-    }
+//     if (fRawReader) {
+//       fRawReader->RewindEvents();
+//       reconstructor->Reconstruct(fRunLoader, fRawReader);
+//     } else {
+//       reconstructor->Reconstruct(fRunLoader);
+//     }
      
-     AliCodeTimerStop(Form("running reconstruction for %s", fgkDetectorName[iDet]));
+//      AliCodeTimerStop(Form("running reconstruction for %s", fgkDetectorName[iDet]));
+    // AliSysInfo::AddStamp(Form("LRec%s_%d",fgkDetectorName[iDet],eventNr));
 
-    // unload calibration data
-    man->UnloadFromCache(calibPath);
-    //man->ClearCache();
-  }
+//     // unload calibration data
+//     man->UnloadFromCache(calibPath);
+//     //man->ClearCache();
+//   }
 
-  man->SetCacheFlag(origCache);
+//   man->SetCacheFlag(origCache);
 
-  if ((detStr.CompareTo("ALL") != 0) && !detStr.IsNull()) {
-    AliError(Form("the following detectors were not found: %s",
-                  detStr.Data()));
-    if (fStopOnError) return kFALSE;
-  }
+//   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;
 }
 
@@ -885,7 +998,7 @@ Bool_t AliReconstruction::RunLocalReconstruction(const TString& detectors)
 Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
 {
 // run the local reconstruction
-
+  static Int_t eventNr=0;
   AliCodeTimerAuto("")
 
   TString detStr = detectors;
@@ -894,6 +1007,10 @@ 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()) {
@@ -911,7 +1028,6 @@ Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
     }
 
     // local reconstruction
-    if (!reconstructor->HasLocalReconstruction()) continue;
     AliInfo(Form("running reconstruction for %s", fgkDetectorName[iDet]));
     AliCodeTimerAuto(Form("running reconstruction for %s", fgkDetectorName[iDet]));
     loader->LoadRecPoints("update");
@@ -931,8 +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();
+    AliSysInfo::AddStamp(Form("LRec%s_%d",fgkDetectorName[iDet],eventNr), iDet,1,eventNr);
   }
 
   if ((detStr.CompareTo("ALL") != 0) && !detStr.IsNull()) {
@@ -940,7 +1073,7 @@ Bool_t AliReconstruction::RunLocalEventReconstruction(const TString& detectors)
                   detStr.Data()));
     if (fStopOnError) return kFALSE;
   }
-  
+  eventNr++;
   return kTRUE;
 }
 
@@ -1023,7 +1156,7 @@ Bool_t AliReconstruction::RunHLTTracking(AliESDEvent*& 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;
@@ -1078,7 +1211,7 @@ Bool_t AliReconstruction::RunMuonTracking(AliESDEvent*& esd)
   
   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;
@@ -1120,14 +1253,17 @@ Bool_t AliReconstruction::RunMuonTracking(AliESDEvent*& esd)
 Bool_t AliReconstruction::RunTracking(AliESDEvent*& esd)
 {
 // run the barrel tracking
-
+  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])
-      GetReconstructor(11)->FillESD(fRunLoader, esd);
+  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--) {
@@ -1136,13 +1272,14 @@ Bool_t AliReconstruction::RunTracking(AliESDEvent*& 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]));
@@ -1153,10 +1290,10 @@ Bool_t AliReconstruction::RunTracking(AliESDEvent*& 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
@@ -1168,12 +1305,14 @@ Bool_t AliReconstruction::RunTracking(AliESDEvent*& 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
@@ -1192,10 +1331,10 @@ Bool_t AliReconstruction::RunTracking(AliESDEvent*& 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
@@ -1216,10 +1355,12 @@ Bool_t AliReconstruction::RunTracking(AliESDEvent*& esd)
     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
@@ -1233,20 +1374,39 @@ Bool_t AliReconstruction::RunTracking(AliESDEvent*& 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);
   }
-  
+  eventNr++;
   return kTRUE;
 }
 
+//_____________________________________________________________________________
+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
 
   AliCodeTimerAuto("")
-
+    static Int_t eventNr=0; 
   TString detStr = detectors;
   for (Int_t iDet = 0; iDet < fgkNDetectors; iDet++) {
     if (!IsSelected(fgkDetectorName[iDet], detStr)) continue;
@@ -1256,7 +1416,7 @@ Bool_t AliReconstruction::FillESD(AliESDEvent*& 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) {
@@ -1281,15 +1441,10 @@ Bool_t AliReconstruction::FillESD(AliESDEvent*& 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]);
     }
   }
@@ -1299,7 +1454,8 @@ Bool_t AliReconstruction::FillESD(AliESDEvent*& esd, const TString& detectors)
                   detStr.Data()));
     if (fStopOnError) return kFALSE;
   }
-
+  AliSysInfo::AddStamp(Form("FillESD%d",eventNr), 0,1, eventNr);
+  eventNr++;
   return kTRUE;
 }
 
@@ -1448,6 +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()));
@@ -1500,15 +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 = 
@@ -1533,7 +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;
   }
 
@@ -1587,7 +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");
@@ -1618,11 +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;
@@ -1639,6 +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;
@@ -1662,7 +1817,6 @@ void AliReconstruction::CleanUp(TFile* file, TFile* fileOld)
   }
 }
 
-
 //_____________________________________________________________________________
 
 Bool_t AliReconstruction::ReadESD(AliESDEvent*& esd, const char* recStep) const
@@ -1724,7 +1878,7 @@ void AliReconstruction::WriteESD(AliESDEvent* esd, const char* recStep) const
 void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
 {
   // write all files from the given esd file to an aod file
-  
+
   // create an AliAOD object 
   AliAODEvent *aod = new AliAODEvent();
   aod->CreateStdContent();
@@ -1733,7 +1887,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
   aodFile->cd();
   
   // create the tree
-  TTree *aodTree = new TTree("AOD", "AliAOD tree");
+  TTree *aodTree = new TTree("aodTree", "AliAOD tree");
   aodTree->Branch(aod->GetList());
 
   // connect to ESD
@@ -1747,23 +1901,27 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
   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)->GetSign()> 0) nPosTracks++;
+      if (esd->GetTrack(iTrack)->Charge()> 0) nPosTracks++;
 
-    // Update the header
-    AliAODHeader* header = aod->GetHeader();
-    
+    // Access the header
+    AliAODHeader *header = aod->GetHeader();
+
+    // fill the header
     header->SetRunNumber       (esd->GetRunNumber()       );
     header->SetBunchCrossNumber(esd->GetBunchCrossNumber());
     header->SetOrbitNumber     (esd->GetOrbitNumber()     );
@@ -1782,18 +1940,18 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
     header->SetRefMultiplicityNeg(nTracks - nPosTracks);
     header->SetMuonMagFieldScale(-999.); // FIXME
     header->SetCentrality(-999.);        // FIXME
-//
-//
 
     Int_t nV0s      = esd->GetNumberOfV0s();
     Int_t nCascades = esd->GetNumberOfCascades();
     Int_t nKinks    = esd->GetNumberOfKinks();
-    Int_t nVertices = nV0s + nCascades + nKinks;
-    
-    aod->ResetStd(nTracks, nVertices);
-    AliAODTrack *aodTrack;
+    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) {
@@ -1812,7 +1970,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
       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;
@@ -1820,7 +1978,11 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
     // 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();
@@ -1829,10 +1991,13 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
     vtx->GetCovMatrix(covVtx); //covariance matrix
 
     AliAODVertex * primary = new(vertices[jVertices++])
-      AliAODVertex(pos, covVtx, vtx->GetChi2toNDF(), NULL, AliAODVertex::kPrimary);
+      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);
@@ -1845,12 +2010,13 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                                                        covVtx,
                                                                        cascade->GetChi2Xi(), // = chi2/NDF since NDF = 2*2-3
                                                                        primary,
+                                                                       nCascade,
                                                                        AliAODVertex::kCascade);
 
-      primary->AddDaughter(vcascade);
+      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 Vo in the list of V0s
+      // 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();
@@ -1874,7 +2040,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
 
       AliAODVertex * vV0FromCascade = 0x0;
 
-      if (indV0>-1 && !usedV0[indV0] ) {
+      if (indV0>-1 && !usedV0[indV0]) {
        
        // the V0 exists in the array of V0s and is not used
 
@@ -1887,6 +2053,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                                                 covVtx,
                                                                 v0->GetChi2V0(), // = chi2/NDF since NDF = 2*2-3
                                                                 vcascade,
+                                                                indV0,
                                                                 AliAODVertex::kV0);
       } else {
 
@@ -1902,8 +2069,10 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                                                 covVtx,
                                                                 v0->GetChi2V0(), // = chi2/NDF since NDF = 2*2-3
                                                                 vcascade,
+                                                                indV0,
                                                                 AliAODVertex::kV0);
        vcascade->AddDaughter(vV0FromCascade);
+
       }
 
       // Add the positive tracks from the V0
@@ -1913,7 +2082,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        usedTrack[posFromV0] = kTRUE;
 
        AliESDtrack *esdTrack = esd->GetTrack(posFromV0);
-       esdTrack->GetPxPyPz(p);
+       esdTrack->GetPxPyPz(p_pos);
        esdTrack->GetXYZ(pos);
        esdTrack->GetCovarianceXYZPxPyPz(covTr);
        esdTrack->GetESDpid(pid);
@@ -1921,12 +2090,12 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        vV0FromCascade->AddDaughter(aodTrack =
                                    new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
                                           esdTrack->GetLabel(), 
-                                          p, 
+                                          p_pos
                                           kTRUE,
                                           pos,
                                           kFALSE,
                                           covTr, 
-                                          (Short_t)esdTrack->GetSign(),
+                                          (Short_t)esdTrack->Charge(),
                                           esdTrack->GetITSClusterMap(), 
                                           pid,
                                           vV0FromCascade,
@@ -1948,7 +2117,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        usedTrack[negFromV0] = kTRUE;
        
        AliESDtrack *esdTrack = esd->GetTrack(negFromV0);
-       esdTrack->GetPxPyPz(p);
+       esdTrack->GetPxPyPz(p_neg);
        esdTrack->GetXYZ(pos);
        esdTrack->GetCovarianceXYZPxPyPz(covTr);
        esdTrack->GetESDpid(pid);
@@ -1956,12 +2125,12 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        vV0FromCascade->AddDaughter(aodTrack =
                 new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
                                           esdTrack->GetLabel(),
-                                          p,
+                                          p_neg,
                                           kTRUE,
                                           pos,
                                           kFALSE,
                                           covTr, 
-                                          (Short_t)esdTrack->GetSign(),
+                                          (Short_t)esdTrack->Charge(),
                                           esdTrack->GetITSClusterMap(), 
                                           pid,
                                           vV0FromCascade,
@@ -1976,6 +2145,11 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
             << " 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();
@@ -1998,7 +2172,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                           pos,
                                           kFALSE,
                                           covTr, 
-                                          (Short_t)esdTrack->GetSign(),
+                                          (Short_t)esdTrack->Charge(),
                                           esdTrack->GetITSClusterMap(), 
                                           pid,
                                           vcascade,
@@ -2012,19 +2186,19 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        cerr << "Error: event " << iEvent << " cascade " << nCascade
             << " track " << bachelor << " has already been used!" << endl;
       }
-
+      
       // Add the primary track of the cascade (if any)
-
+      
     } // end of the loop on cascades
-    
     // V0s
         
     for (Int_t nV0 = 0; nV0 < nV0s; ++nV0) {
 
       if (usedV0[nV0]) continue; // skip if aready added to the AOD
 
-      AliESDv0 *v0 = esd->GetV0(nV0);
-      
+      AliESDv0 *v0 = esd->GetV0(nV0); 
+     
       v0->GetXYZ(pos[0], pos[1], pos[2]);
       v0->GetPosCov(covVtx);
 
@@ -2033,6 +2207,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                                covVtx,
                                                v0->GetChi2V0(), // = chi2/NDF since NDF = 2*2-3
                                                primary,
+                                               nV0,
                                                AliAODVertex::kV0);
       primary->AddDaughter(vV0);
 
@@ -2046,7 +2221,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        usedTrack[posFromV0] = kTRUE;
 
        AliESDtrack *esdTrack = esd->GetTrack(posFromV0);
-       esdTrack->GetPxPyPz(p);
+       esdTrack->GetPxPyPz(p_pos);
        esdTrack->GetXYZ(pos);
        esdTrack->GetCovarianceXYZPxPyPz(covTr);
        esdTrack->GetESDpid(pid);
@@ -2054,12 +2229,12 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        vV0->AddDaughter(aodTrack =
                new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
                                           esdTrack->GetLabel(), 
-                                          p, 
+                                          p_pos
                                           kTRUE,
                                           pos,
                                           kFALSE,
                                           covTr, 
-                                          (Short_t)esdTrack->GetSign(),
+                                          (Short_t)esdTrack->Charge(),
                                           esdTrack->GetITSClusterMap(), 
                                           pid,
                                           vV0,
@@ -2081,7 +2256,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        usedTrack[negFromV0] = kTRUE;
 
        AliESDtrack *esdTrack = esd->GetTrack(negFromV0);
-       esdTrack->GetPxPyPz(p);
+       esdTrack->GetPxPyPz(p_neg);
        esdTrack->GetXYZ(pos);
        esdTrack->GetCovarianceXYZPxPyPz(covTr);
        esdTrack->GetESDpid(pid);
@@ -2089,12 +2264,12 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
        vV0->AddDaughter(aodTrack =
                 new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
                                           esdTrack->GetLabel(),
-                                          p,
+                                          p_neg,
                                           kTRUE,
                                           pos,
                                           kFALSE,
                                           covTr, 
-                                          (Short_t)esdTrack->GetSign(),
+                                          (Short_t)esdTrack->Charge(),
                                           esdTrack->GetITSClusterMap(), 
                                           pid,
                                           vV0,
@@ -2109,6 +2284,9 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
             << " 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
@@ -2117,7 +2295,6 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
 
     for (Int_t iTrack=0; iTrack<nTracks; ++iTrack) {
 
-
       AliESDtrack * esdTrack = esd->GetTrack(iTrack);
 
       Int_t ikink = esdTrack->GetKinkIndex(0);
@@ -2180,7 +2357,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                           pos,
                                           kFALSE,
                                           covTr, 
-                                          (Short_t)esdTrack->GetSign(),
+                                          (Short_t)esdTrack->Charge(),
                                           esdTrack->GetITSClusterMap(), 
                                           pid,
                                           primary,
@@ -2203,6 +2380,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                                    NULL,
                                                    0.,
                                                    mother,
+                                                   esdTrack->GetID(), // This is the track ID of the mother's track!
                                                    AliAODVertex::kKink);
            // Add the daughter track
 
@@ -2226,7 +2404,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                           pos,
                                           kFALSE,
                                           covTr, 
-                                          (Short_t)esdTrack->GetSign(),
+                                          (Short_t)esdTrack->Charge(),
                                           esdTrack->GetITSClusterMap(), 
                                           pid,
                                           vkink,
@@ -2240,18 +2418,12 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
              cerr << "Error: event " << iEvent << " kink " << TMath::Abs(ikink)-1
              << " track " << idaughter << " has already been used!" << endl;
            }
-
-
          }
        }
-
-      }      
-
+      }
     }
 
-    
     // Tracks (primary and orphan)
-      
     for (Int_t nTrack = 0; nTrack < nTracks; ++nTrack) {
        
 
@@ -2267,7 +2439,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
 
       esdTrack->GetImpactParameters(impactXY,impactZ);
 
-      if (impactXY<3) {
+      if (impactXY<3.) {
        // track inside the beam pipe
       
        primary->AddDaughter(aodTrack =
@@ -2278,7 +2450,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                         pos,
                                         kFALSE,
                                         covTr, 
-                                        (Short_t)esdTrack->GetSign(),
+                                        (Short_t)esdTrack->Charge(),
                                         esdTrack->GetITSClusterMap(), 
                                         pid,
                                         primary,
@@ -2290,25 +2462,11 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
       }
       else {
        // outside the beam pipe: orphan track
-           aodTrack =
-           new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
-                                        esdTrack->GetLabel(),
-                                        p,
-                                        kTRUE,
-                                        pos,
-                                        kFALSE,
-                                        covTr, 
-                                        (Short_t)esdTrack->GetSign(),
-                                        esdTrack->GetITSClusterMap(), 
-                                        pid,
-                                        NULL,
-                                        kFALSE, // check if this is right
-                                        kFALSE, // check if this is right
-                                        AliAODTrack::kOrphan);
-           aodTrack->ConvertAliPIDtoAODPID();
+       // 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) {
@@ -2324,7 +2482,7 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
       // 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(
+      primary->AddDaughter(aodTrack =
          new(tracks[jTracks++]) AliAODTrack(0, // no ID provided
                                             0, // no label provided
                                             p,
@@ -2332,75 +2490,132 @@ void AliReconstruction::ESDFile2AODFile(TFile* esdFile, TFile* aodFile)
                                             pos,
                                             kFALSE,
                                             NULL, // no covariance matrix provided
-                                            (Short_t)-99, // no charge provided
-                                            0, // no ITSClusterMap
+                                            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
+                                            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 &clusters = *(aod->GetClusters());
+    TClonesArray &caloClusters = *(aod->GetCaloClusters());
     Int_t jClusters=0;
 
     // Calo Clusters
-    Int_t nClusters    = esd->GetNumberOfCaloClusters();
-
-    for (Int_t iClust=0; iClust<nClusters; ++iClust) {
+    TArrayS EMCCellNumber(15000);
+    TArrayD EMCCellAmplitude(15000);
+    Int_t nEMCCells = 0;
+    const Float_t fEMCAmpScale = 1./500;
+    for (Int_t iClust=0; iClust<nCaloClus; ++iClust) {
 
       AliESDCaloCluster * cluster = esd->GetCaloCluster(iClust);
 
       Int_t id = cluster->GetID();
-      Int_t label = -1;
+      Int_t nLabel = 0;
+      Int_t *label = 0x0;
       Float_t energy = cluster->E();
       cluster->GetPosition(posF);
-      AliAODVertex *prodVertex = primary;
-      AliAODTrack *primTrack = NULL;
       Char_t ttype=AliAODCluster::kUndef;
-      
-      if (cluster->IsPHOS()) ttype=AliAODCluster::kPHOSNeutral;
-      else if (cluster->IsEMCAL()) {
-       
-       if (cluster->GetClusterType() == AliESDCaloCluster::kPseudoCluster)
-         ttype = AliAODCluster::kEMCALPseudoCluster;
-       else
-         ttype = AliAODCluster::kEMCALClusterv1;
-       
+
+      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; 
       }
       
-      new(clusters[jClusters++]) AliAODCluster(id,
-                                              label,
-                                              energy,
-                                              pos,
-                                              NULL, // no covariance matrix provided
-                                              NULL, // no pid for clusters provided
-                                              prodVertex,
-                                              primTrack,
-                                              ttype);
+      AliAODCaloCluster *caloCluster = new(caloClusters[jClusters++]) AliAODCaloCluster(id,
+                                                                                       nLabel,
+                                                                                       label,
+                                                                                       energy,
+                                                                                       pos,
+                                                                                       NULL,
+                                                                                       ttype);
       
+      caloCluster->SetCaloCluster(); // to be refined!
+
     } // 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;
 }
 
@@ -2441,7 +2656,13 @@ void AliReconstruction::WriteAlignmentData(AliESDEvent* 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;
@@ -2523,4 +2744,132 @@ void AliReconstruction::TNamedToFile(TTree* fTree, TString fName){
   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 ; 
+}