-------------------------------------------------------------------

     =========================================================
     Geant4 - an Object-Oriented Toolkit for Simulation in HEP
     =========================================================

                            Example B3
                            ----------

 This example simulates schematically a Positron Emitted Tomography system.
	
 1- GEOMETRY DEFINITION

   The support of gamma detection are scintillating crystals. A small number
   of such crystals are optically grouped in a matrix of crystals. In
   this example, individual crystals are not described; only the matrix of
   crystals is and it is still called 'Crystal' hereafter.

   Crystals are circularly arranged to form a ring. Few rings make up the full
   detector (gamma camera). This is done by positionning Crystals in 
   Ring with an appropriate rotation matrix. Several copies of Ring are 
   then placed in the full detector.  

   The head of a patient is schematised as a homogeneous cylinder of brain
   tissue, placed at the center of full detector.
	
   The Crystal material, Lu2SiO5, is not included in the G4Nist database. 
   Therefore, it is explicitly built in DefineMaterials().
 	
 2- PHYSICS LIST

   The physics list contains standard electromagnetic processes and the
   radioactiveDecay module for GenericIon. It is defined in the B3PhysicsList 
   class as a Geant4 modular physics list with registered physics builders 
   provided in Geant4:
   - G4DecayPhysics - defines all particles and their decay processes
   - G4RadioactiveDecayPhysics - defines radioactiveDecay for GenericIon
   - G4EmStandardPhysics - defines all EM standard processes
 	 
   This physics list requires data files for:
   - low energy electromagnetic processes which path is defined via 
     the G4LEDATA envirnoment variable
   - nuclides properties which path is defined via 
     the G4ENSDFSTATEDATA envirnoment variable
   - radioactive decay hadronic processes which path is defined via 
     the G4RADIOACTIVEDATA envirnoment variable.
   
   See more on installation of the datasets in Geant4 Installation Guide,
   Chapter 3.3: Note On Geant4 Datasets:
   http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides
                                          /InstallationGuide/html/ch03s03.html
 3- ACTION INITALIZATION

   B3[a,b]ActionInitialization class instantiates and registers to Geant4 kernel 
   all user action classes.

   While in sequential mode the action classes are instatiated just once,
   via invoking the method:
      B3[a,b]ActionInitialization::Build() 
   in multi-threading mode the same method is invoked for each thread worker
   and so all user action classes are defined thread-local.

   A run action class is instantiated both thread-local 
   and global that's why its instance is created also in the method
      B3[a,b]ActionInitialization::BuildForMaster() 
   which is invoked only in multi-threading mode.
    	 
 4- PRIMARY GENERATOR
  
   The default particle beam is an ion (F18), at rest, randomly distributed 
   within a zone inside a patient and is defined in 
   B3PrimaryGeneratorAction::GeneratePrimaries().
   The type of a primary particle can be changed with G4ParticleGun commands 
   (see run2.mac).
   
 5- DETECTOR RESPONSE:  scorers

   A 'good' event is an event in which an identical energy of 511 keV is 
   deposited in two separate Crystals. A count of the number of such events 
   corresponds to a measure of the efficiency of the PET system. 
   The total dose deposited in a patient during a run is also computed. 
   
   Scorers are defined in B3DetectorConstruction::ConstructSDandField(). There are
   two G4MultiFunctionalDetector objects: one for the Crystal (EnergyDeposit), 
   and one for the Patient (DoseDeposit)

   The scorers hits are saved in form of ntuples in a Root file using Geant4 
   analysis tools. This feature is activated in the main () function with instantiating
   G4ScoreNtupleWriter. 

   Two variants of accumulation event statistics in a run are demonstrated 
   in this example:

   B3a:
   
   At the end of event, the values acummulated in B3aEventAction are passed 
   in B3aRunAction and summed over the whole run (see B3aEventAction::EndOfevent()). 
   In multi-threading mode the data accumulated in G4Accumulable objects per
   workers is merged to the master in B3aRunAction::EndOfRunAction() and the final
   result is printed on the screen.
   
   G4Accumulable<> type instead of G4double and G4int types is used for the B3aRunAction
   data members in order to facilitate merging of the values accumulated on workers 
   to the master.  Currently the accumulables have to be registered to G4AccumulablesManager
   and G4AccumulablesManager::Merge() has to be called from the users code. This is planned
   to be further simplified with a closer integration of G4Accumulable classes in
   the Geant4 kernel next year.

   B3b:

   B3bRun::RecordEvent(), called at end of event, collects informations 
   event per event from the hits collections, and accumulates statistic for 
   B3bRunAction::EndOfRunAction().	
   In addition, results for dose are accumulated in a
   standard floating-point summation and using a new lightweight statistical
   class called G4StatAnalysis. The G4StatAnalysis class records four values:
   (1) the sum, (2) sum^2, (3) number of entries, and (4) the number of entries
   less than mean * machine-epsilon (the machine epsilon is the difference
   between 1.0 and the next value representable by the floating-point type).
   From these 4 values, G4StatAnalysis provides the mean, FOM, relative error,
   standard deviation, variance, coefficient of variation, efficiency, r2int,
   and r2eff.
   
   In multi-threading mode the statistics accumulated per workers is merged 
   to the master in B3bRun::Merge().
   		
 6- STACKING ACTION
 
   Beta decay of Fluor generates a neutrino. One wishes not to track this
   neutrino; therefore one kills it immediately, before created particles
   are put in a stack.
   The function B3StackingAction::ClassifyNewTrack() is invoked by G4 kernel
   each time a new particle is created.       

 The following paragraphs are common to all basic examples

 A- VISUALISATION

   The visualization manager is set via the G4VisExecutive class
   in the main() function in exampleB3.cc.    
   The initialisation of the drawing is done via a set of /vis/ commands
   in the macro vis.mac. This macro is automatically read from
   the main function when the example is used in interactive running mode.

   By default, vis.mac opens an OpenGL viewer (/vis/open OGL).
   The user can change the initial viewer by commenting out this line
   and instead uncommenting one of the other /vis/open statements, such as
   HepRepFile or DAWNFILE (which produce files that can be viewed with the
   HepRApp and DAWN viewers, respectively).  Note that one can always
   open new viewers at any time from the command line.  For example, if
   you already have a view in, say, an OpenGL window with a name
   "viewer-0", then
      /vis/open DAWNFILE
   then to get the same view
      /vis/viewer/copyView viewer-0
   or to get the same view *plus* scene-modifications
      /vis/viewer/set/all viewer-0
   then to see the result
      /vis/viewer/flush

   The DAWNFILE, HepRepFile drivers are always available
   (since they require no external libraries), but the OGL driver requires
   that the Geant4 libraries have been built with the OpenGL option.

   For more information on visualization, including information on how to
   install and run DAWN, OpenGL and HepRApp, see the visualization tutorials,
   for example,
   http://geant4.slac.stanford.edu/Presentations/vis/G4[VIS]Tutorial/G4[VIS]Tutorial.html
   (where [VIS] can be replaced by DAWN, OpenGL and HepRApp)

   The tracks are automatically drawn at the end of each event, accumulated
   for all events and erased at the beginning of the next run.

 B- USER INTERFACES
 
   The user command interface is set via the G4UIExecutive class
   in the main() function in exampleB3.cc 
   The selection of the user command interface is then done automatically 
   according to the Geant4 configuration or it can be done explicitly via 
   the third argument of the G4UIExecutive constructor (see exampleB4a.cc). 
 
C- HOW TO RUN

    - Execute exampleB3a in the 'interactive mode' with visualization
        % ./exampleB3a
      and type in the commands from run1.mac line by line:  
        Idle> /control/verbose 2
        Idle> /tracking/verbose 2
        Idle> /run/beamOn 1 
        Idle> ...
        Idle> exit
      or
        Idle> /control/execute run1.mac
        ....
        Idle> exit

    - Execute exampleB3a in the 'batch' mode from macro files 
     (without visualization)
        % ./exampleB3a run2.mac
        % ./exampleB3a exampleB3.in > exampleB3.out

	
