
///\file "B3/.README.txt"
///\brief Example B3 README page

/*! \page ExampleB3 Example %B3

 This example simulates schematically a Positron Emitted Tomography system.

\section B3_s1 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().

\section B3_s2 PHYSICS LIST

   The physics list contains standard electromagnetic processes and the
   radioactiveDecay module for GenericIon. It is defined in the B3::PhysicsList
   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
   - data files for 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
   <a href="http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides
                                         /InstallationGuide/html/ch03s03.html">
   Geant4 Installation Guide, Chapter 3.3: Note On Geant4 Datasets </a>.

\section B3_s3  ACTION INITALIZATION

   B3a::ActionInitialization class (see also B3b::ActionInitialization) 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:
      B3a::ActionInitialization::Build()
      (see also B3b::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
      B3a::ActionInitialization::BuildForMaster()
      (see also B3b::ActionInitialization::Build)
   which is invoked only in multi-threading mode.

\section B3_s4 PRIMARY GENERATOR

   The default particle beam is an ion (F18), at rest, randomly distributed
   within a zone inside a patient and is defined in
   B3::PrimaryGeneratorAction::GeneratePrimaries().
   The type of a primary particle can be changed with G4ParticleGun commands
   (see run2.mac).

\section B3_s5 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 B3::DetectorConstruction::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
   G4TScoreNtupleWriter.

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

   %B3a:

   At the end of event, the values acummulated in B3a::EventAction are passed
   in B3a::RunAction and summed over the whole run (see B3a::EventAction::EndOfevent()).
   In multi-threading mode the data accumulated in G4Accumulable objects per
   workers is merged to the master in B3a::RunAction::EndOfRunAction() and the final
   result is printed on the screen.

   G4Accumulable<> type instead of G4double and G4int types is used for the B3a::RunAction
   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:

   B3b::Run::RecordEvent(), called at end of event, collects informations
   event per event from the hits collections, and accumulates statistic for
   B3b::RunAction::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 B3b::Run::Merge().

\section B3_s6 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 B3::StackingAction::ClassifyNewTrack() is invoked by G4 kernel
   each time a new particle is created.

<hr>

The following paragraphs are common to all basic examples

\section B3_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
\verbatim
/vis/open DAWNFILE
\endverbatim
   then to get the same view
\verbatim
/vis/viewer/copyView viewer-0
\endverbatim
   or to get the same view *plus* scene-modifications
\verbatim
/vis/viewer/set/all viewer-0
\endverbatim
   then to see the result
\verbatim
/vis/viewer/flush
\endverbatim

   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,\n
   - <a href="http://geant4.slac.stanford.edu/Presentations/vis/G4OpenGLTutorial/G4OpenGLTutorial.html">
     OpenGL Tutorial </a>
   - <a href="http://geant4.slac.stanford.edu/Presentations/vis/G4DAWNTutorial/G4DAWNTutorial.html">
     DAWN Tutorial </a>
   - <a href="http://geant4.slac.stanford.edu/Presentations/vis/G4HepRAppTutorial/G4HepRAppTutorial.html">
     HepRApp Tutorial </a>

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

\section B3_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).

\section B3_C HOW TO RUN

   - Execute exampleB3a in the 'interactive mode' with visualization
\verbatim
% ./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
\endverbatim
      or
\verbatim
Idle> /control/execute run1.mac
....
Idle> exit
\endverbatim

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

*/
