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examples/basic/B3/.README.txt
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///\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
*/
examples/basic/B3/README
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-------------------------------------------------------------------
=========================================================
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 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
- 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
B3::PrimaryGeneratorAction::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 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().
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 B3::StackingAction::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