Additional protection

[u/mrichter/AliRoot.git] / RICH / api.txt

How to open session:
	use static method  AliRunLoader::Open("galice.root","AlicE","update")
How to get total number of events in galice.root:
	use AliRun::GetEventsPerRun()  or AliRunLoader::GetNumberOfEvents()      
How to avoid using gAlice:
	detector->GetLoader()->GetRunLoader()->GetAliRun() returns gAlice global pointer.
How to retrieve pointer to alice run loader:
        use pRICH->GetLoader()->GetRunLoader() (all detector classes inherit from AliDetector which has GetLoader())
	use method AliRun::GetRunLoader for gAlice (deprecated)
How to get pointers to different root trees:
	TreeE belongs to AliRunLoader, available after AliRunLoader::LoadHeader()
	TreeK belongs to AliRunLoader, available after AliRunLoader::LoadKinematics()
	TreeH belongs to AliLoader   , available after AliLoader::LoadHits()
	TreeS belongs to AliLoader   , available after AliLoader::LoadSDigits()
	TreeD belongs to AliLoader   , available after AliLoader::LoadDigits()
	TreeR belongs to AliLoader   , available after AliLoader::LoadRecPoints()
        all methods return 0 on success. 
How to get event of interest:
	AliRunLoader::GetEvent(event_number) returns 0 on success
How to deal with the stack of particles?
        - first of all, the stack includes primary as well as secondary particles
	- pointer to the stack is taken:
         	AliRun::Stack() (global gAlice of type AliRun - deprecated way to do)
          	AliRunLoader::Stack() but before one needs to load event header by AliRunLoader::LoadHeader() otherwise both methods return 0.
          	Moreover loading header gives the information about number of particles only. 
          	To retrieve the list of particle one also needs to load kinematics by AliRunLoader::LoadKinematics()        
	- total amount of particles in stack for a given event:        
         	AliStack::GetNtrack() 
                AliRun::GetEvent() (after LoadHeader())
	- total amount of primary particles in stack for a given event (after LoadHeader()): 
        	AliStack::GetNprimary() 
How to retrieve hits:
	Hits are stored on primary by primary basis. Hits for the given primary is TClonesArray.
   	To retrieve all hits one needs to do:
     	-initialize the root tree and containers:   pRich->GetLoader()->LoadHits();  (AliLoader::LoadHits() returns 0 on success)
     	-read number of entries in TreeH:           pRich->GetLoader()->TreeH()->GetEntries()
     	-then for each entry:                       pRich->GetLoader()->TreeH()->GetEntry(i)
How to retrieve sdigits? 
	Sdigits stored in tree S with the branch of TClonesArray, all sdigits in a single TClonesArray
	So the tree has only one entry.
	One needs to say:
	-pRich->GetLoader()->LoadSDigits(); this one open file, get the tree and invoke AliRICH::SetTreeAddress()    
How to retrieve digits? 
	Digits stored in tree D with the 7 branches of TClonesArray, one per chamber, all digits of a given chamber in a single TClonesArray
	So the tree has only one entry.
	-One needs to say:
	  pRich->GetLoader()->LoadDigits(); this one opens file, gets the tree and invoke AliRICH::SetTreeAddress() which in turn corresponds 
          branches of the tree to the digits containers in memory. There are 7 containers, one per chamber, all of them belong to AliRICH.
	-Then one needs to take the tree entry (only one) to the memory:
          pRich->GetLoader()->TreeD()->GetEntry(0) 
	-Finally pRich->Digits(chamber_number) returns the pointer to TClonesArray of AliRICHdigit          
What are the debug methods avail:
        AliLog::SetGlobalDebugLevel(AliLog::kDebug)
How to get info for a given particle number:
	Header and Kinematics trees must be loaded, then possible to retrieve pointer to Stack of particles
	Int_t AliRunLoader::LoadHeader(); Int_t AliRunLoader::LoadKinematics()
	AliStack *AliRunLoader::Stack()
	TParticle *AliStack::Particle(tid)
	TParticle::Print()
How to deal with AliRunDigitizer:
	AliRunDigitizer::Exec() just call AliRunDigitizer::Digitize()	
What are the meanings of different VMC flags:         
	gMC->IsTrackAlive()
	gMC->IsTrackStop()
	gMC->IsTrackDisappeared()
How to get pad number for a local position:
	use static TVector AliRICHParam::Loc2Pad(TVector2 position);
Why list of chambers belongs to AliRICHParam:

How to check if a given stack particle is primary:
	Stack is TClonesArray of TParticle. TParticle::GetMother(0) returns -1 if it's primary (no mother)         
How to loop over all possible object:         
  for(Int_t iEventN=0;iEventN < GetLoader()->GetRunLoader()->GetAliRun()->GetEventsPerRun();iEventN++){//events loop
    for(Int_t iEntryN=0;iEntryN < GetLoader()->TreeH()->GetEntries();iEntryN++){//TreeH loop
      GetLoader()->TreeH()->GetEntry(iEntryN);//get current entry (prim)  
      for(Int_t iHitN=0;iHitN<Hits()->GetEntries();iHitN++){//hits loop
        AliVHMPIDHit *pHit=(AliVHMPIDHit*)Hits()->At(iHitN);//get current hit 
        
      }//hits loop
    }//TreeH loop
  }//events loop


RICH full simulation-reconstruction sequence

hits->sdigit:
	Responsible method is AliRICH::Hits2SDigits
	One hit may affect one or more pads.
        Hit position is taken on the anode wires plane as the most of avalanche is developed there.
        This position is not directly available, track intersections with entrance and exit of amplification gap are only stored.
        So the position in the middle of the gap is calculated as average out of pHit->In() and pHit->Out() positions.
        Then, total charge collected for this hit is calculated by AliRICHParam::Hit2Qdc.    
        Area of disintegration is a list of pads affected by current hit. This is a parameter of Mathienson    
sdigits->digits:
	The necessety of sdigits is dictated by the fact that trasport engine transports tracks in a continious sequence track by track. 
  It means that it may happen that the same pad is affected by few tracks. But this might be known only after the trasport of full event is finished. 

digits->clusters
	A set of neighbouring digits compose cluster. The aim of this trasformation is to construct a list of clusters out of digits list.
  The calling sequence is:
  AliReconstruction::Run()
  
  	AliRICHReconstructor::Reconstruct() creates an empty clusters list,  loops on chambers, retrives a list of digits for a given chamber, gives it to the methode Dig2Clu() and finally serializes
                                        the list 
                                        
    	AliRICHReconstructor::Dig2Clu() which knows no details about 


clusters+tracks->theta cerenkov 

	
	
	







Generalized structure of AliReconstruction:

Run()
{
  if(there is galice.root)                                        <-|
    AliRunLoader::Open(....)                                        | 
  else                                                              | this is done in InitRunLoader()
    if(raw data process requested)                                  |
      create galice.root on the base of AliRawReader::NextEvent   <-|   
  
  for(all detectors){                                             <-|
   if(detector not selected to run) skip this detector              | this is done in RunLocalReconstruction()
   reconstructor=get detector's reconstructor                       | 
                                                                    |   
   if(detector HasLocalReconstruction) skip this detector           | IMPORTANT! if HasLocalReconstruction() returns YES use RunLocalEventReconstruction instead
   if(run upon raw data)                                            |  
     reconstructor->Reconstruct(fRunLoader, fRawReader);            |   
   else                                                             | <- this approach is currently used by RICH as all branches are mounted in AliRICH.cxx
     reconstructor->Reconstruct(fRunLoader);                        |
  }                                                               <-|  

  for(all events){                                                      
  
    for(all detectors){                                                 |            
      if(detector not selected to run) skip this detector               |
      reconstructor=get detector's reconstructor                        | 
      loader=get detector's loader                                      | this is done in RunLocalEventReconstruction()
      if(raw data process requested and detector HasDigitConversion){   | 
        loader->LoadDigits("update");                                   | open file and invoke  detector->SetTreeAddress();
        loader->CleanDigits();                                          |   
        loader->MakeDigitsContainer();                                  | create tree
        reconstructor->Reconstruct(fRawReader,loader->TreeD());         | expected to fill TreeD out of raw reader
        loader->WriteDigits("overwrite");                               | 
        loader->UnloadDigits();                                         |  
      }                                                                 |
      if(detector do not HasLocalReconstruction) skip this detector     | IMPORTANT! assumed that this detector is already processed in RunLocalReconstruction()
      loader->LoadRecPoints("update");                                  |
      loader->CleanRecPoints();                                         |
      loader->MakeRecPointsContainer();                                 | 
      if(fRawReader && reconstructor do not HasDigitConversion()){      | 
        reconstructor->Reconstruct(fRawReader, loader->TreeR());        | expected to fill TreeR out of raw reader
      }else{                                                            |
        loader->LoadDigits("read");                                     |
        reconstructor->Reconstruct(loader->TreeD(),loader->TreeR());    | the only operations inside are pDigTree->GetEntry(0) and pCluTree->Fill();
        loader->UnloadDigits();                                         | 
      }                                                                 |
      loader->WriteRecPoints("OVERWRITE");                              |
      loader->UnloadRecPoints();                                        |
    }//detectors loop                                                   |
    
  }//events loop 
}


RICH calibration and alignment.

Abstract
RICH calibrartion and alignment strategy is described with emphasis put on those aspects of the procedure which are relevant for reconstruction and thus the final detector
figure of merit. In particulare, the refractive index calibration tecknique based on mass plot shifts analisys and chamber alignment with respect to core detectors 
are explained in details. External sources of calibration and alignment data are aslo mentioned as well as the way RICH intends to handle those data, including initial CDB
creater. 

Calibration. 
Looking on RICH chamber structure, full description of which is availbale elsewhere (ref RichTDR), easy to compile the table of all possible parameters affecting reconstruction.
The first one of major importance is a freon refractive index. Although the full optical path visiable by photons includes freon vessel, proximity and amplification gaps filled 
with methane and quartz window seperating above mentioned volumes, only freon refractive index is subject for calibration.  Refractive index of SiO2 window is not practically 
affected by any external parameters, while influence of methane temperature to it's refractive index is negligable. So it's enough to measure there optical curves just once.
In the rest, the only changable parameter is refractive index of freon. Temperature influence on freon refractive index was measured experimentally. The parametrization 
found to be:
  n=n0-0.0005(T-20)                        where T is freon temperature in degrees Celsius
  n0=Sqrt(1+ 0.554*lamda^2/(lamda^2-5796)) where lamda is photon wavelength in nm taken at 20 degress Celsius
Preliminary, the parametrization itself is considered to be permamnent one. The only parameter to store and retrieve is freon temperature. Since this value is available from
DCS DB and expected to be served by a SHUTTLE program which is not yet ready, the following temporaroly solution has been adopted.
In local CDB storage (deafult directory is $ALICE_ROOT) two versions of freon refractive index are written by external macro RichCdb.C :
Run0_0_v0_s0.root contains DiMauro's parametrization and the temperature is set to 20 degrees. To be used as default for simulation and reconstruction.
Run0_0_v0_s1.root contains DiMauro's parametrization and the temperature is set to 50 degrees. To be used in special uncalibrated reconstruction to test calibration procedure. 
Both of them are valid in run range from run number 0 to run number 0, thus in no way affecting any normal operations.   

Refractive index of freon (C6F14) is taken in AliRICHRecon for 3 different photon energies by means of 2 methodes: Set



Alignment.
Information about detector position and orientation is needed during reconstruction phase. This information affects track-cluster matching procedure, the relevant peace of 
code comes to AliRICHTracker::PropogateBack(). Matching precedure consists in prolongation of the track reconstructed in core detectores up to each RICH chamber plane in 
a sequenmce. The plane used is the entrance to RICH radiators. If the intersection exists and inside the sensitive area, the point of intersection is to be tranformed to RICH
local reference system. Note, that in this check, the dead zones inbetween radiators are not taken into account. This operation requiring MARS to LORS transformations is done
in AliRICHHelix::RichIntersection(). Plane to be intersected is defined by a point beloging to that plane served by AliRICHParam::Center(ChamberNumber) and a vector normal 
to the plane served by AliRICHParam::Norm(ChamberNumber). Transformations itself are done in AliRICHParam::Mars2Lors() and AliRICHParam::Lors2Mars(). Internaly in AliRICHParam, 
each chamber is reresented by TGeoHMatrix. It's worth to stress again that geometry related operations are needed to be done for 3 different planes per chamber, namly entrance 
to radiator, anod wires plane and photocathode plane. So AliRICHParam sustains 7*3=21 planes. Also important to say, that direct usage of TGeoHMatrix::MasterToLocal() 
and virce versa is not possible due to special nature of RICH LORS. According to the decision made about 3 years ago, RICH local reference system is centered in low left
hand corner of the chamber if one looks from outside to direction pointing to interection point.
So the most obvious candidate for alignable objects to be stored are thess 21 TGeoHMatrix objects. 
The approach suggested in AliAlignObj is not quite feasable mainly due to the fact it relays on incrementing procedure using import from geometry.root. RICH geometry is defined 
in a way that there is no volumes exactly corresponding to the RICH planes. 

Geometry of RICH chambers.
After the decision to rotate the whole RICH setup from 12 o'clock position to 2 o'clock position we have the following situtation:

Theta = 109.5 degress for chambers 1,3
Theta =  90.0 degress for chambers 2,4,6
Theta =  70.5 degress for chambers 5,7

Phi   =  50.0 degress for chambers 6,7 
Phi   =  30.0 degress for chambers 3,4,5 
Phi   =  10.0 degress for chambers 1,2 


Old parametrisation by AliRICHChamber:
RICH chamber 1 (454.877118 ,  80.207109 , -163.565361)(rho,theta,phi)=(490.0,109.5,10.0)
RICH chamber 2 (482.555799 ,  85.087607 ,    0.000000)(rho,theta,phi)=(490.0, 90.0,10.0)
RICH chamber 3 (400.012224 , 230.947165 , -163.565361)(rho,theta,phi)=(490.0,109.5,30.0)
RICH chamber 4 (424.352448 , 245.000000 ,    0.000000)(rho,theta,phi)=(490.0, 90.0,30.0)
RICH chamber 5 (400.012224 , 230.947165 ,  163.565361)(rho,theta,phi)=(490.0, 70.5,30.0)
RICH chamber 6 (314.965929 , 375.361777 ,    0.000000)(rho,theta,phi)=(490.0, 90.0,50.0)
RICH chamber 7 (296.899953 , 353.831585 ,  163.565361)(rho,theta,phi)=(490.0, 70.5,50.0)

New parametrization by TGeoHMatrix: 
RICH 1
 -0.328736   -0.173648    0.928321    Tx = 454.877118
 -0.057965    0.984808    0.163688    Ty =  80.207109
 -0.942641    0.000000   -0.333807    Tz = -163.565361
RICH 2
  0.000000   -0.173648    0.984808    Tx = 482.555799
  0.000000    0.984808    0.173648    Ty =  85.087607
 -1.000000    0.000000    0.000000    Tz =   0.000000
RICH 3
 -0.289085   -0.500000    0.816351    Tx = 400.012224
 -0.166903    0.866025    0.471321    Ty = 230.947165
 -0.942641    0.000000   -0.333807    Tz = -163.565361
RICH 4
  0.000000   -0.500000    0.866025    Tx = 424.352448
  0.000000    0.866025    0.500000    Ty = 245.000000
 -1.000000    0.000000    0.000000    Tz =   0.000000
RICH 5
  0.289085   -0.500000    0.816351    Tx = 400.012224
  0.166903    0.866025    0.471321    Ty = 230.947165
 -0.942641    0.000000    0.333807    Tz = 163.565361
RICH 6
  0.000000   -0.766044    0.642788    Tx = 314.965929
  0.000000    0.642788    0.766044    Ty = 375.361777
 -1.000000    0.000000    0.000000    Tz =   0.000000
RICH 7
  0.214567   -0.766044    0.605918    Tx = 296.899953
  0.255711    0.642788    0.722105    Ty = 353.831585
 -0.942641    0.000000    0.333807    Tz = 163.565361