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Geant4 TutorialEuropean Medical Physics School,
Archamps, France
Overview of the contents
Software process
Geant4 advanced example brachytherapy
Integration of the brachytherapy application
in a distributed computing environment
Run the brachytherapy example
Software Process
How to develop a rigorous and reliable
software application
Documentation: http://www.ge.infn.it/geant4 link: training, software engineering documentation
Software process
User Requirements Define the software functionality
Design Project of the software structure
Implementation
Test
For example, a process model is theUnified Software Development Process (USDP)
Iterative-incremental method
Concepts:
Capture User RequirementsCapture User Requirements
Define the scope of the software system to be built (“what it should do”)
How to collect User Requirements
•Study of the experimental set-up: involved particles, involved physics, detectors•What is the scope of the simulation
Example of User Requirement
UR1. The user shall be able to define electromagnetic processes for gammaNeed: EssentialPriority: HighSource: ESA
User Requirements
1. General UR 1.1 Configure the Run UR 1.2 Configure the Event Loop
2. Description of the experimental set-up UR 2.1 Describe a geometrical set-up: a Si-W tracker, a
CsI calorimeter and an anti-coincidence system made out of plastic scintillators.
UR 2.2 Record the coordinates of impact of tracks in the layers of the tracker. Record the energy release in the strips of the tracker.
UR 2.3 Record the energy deposited in each element of the calorimeter at every event.
UR 2.4 Record the energy deposited in each element of the anticoincidence at every event.
UR 2.5 Digitise the hits, setting a threshold for the energy deposit in the tracker.
UR 2.6 Generate a trigger signal combining signals from different detectors.
3. Physics UR 3.1 Generate primary events according to various
distributions relevant to gamma astrophysics UR 3.2 Activate electromagnetic processes appropriate
to the energy range of the experiment. UR 3.3 Activate hadronic processes appropriate to the
energy range of the experiment.
4. Analysis UR 4.1 Plot the x-y distribution of impact of the track. UR 4.2 Plot histograms during the simulation execution. UR 4.3 Store significant quantities in a ntuple (energy
release in the strips, hit strips) for further analysis. UR 4.4 Plot the energy distribution in the calorimeter.
5. Visualisation UR 5.1 Visualise the experimental set-up. UR 5.2 Visualise tracks in the experimental set-up. UR 5.3 Visualise hits in the experimental set-up.
6. User Interface UR 6.1 Configure the tracker, by modifying the number
of active planes, the pitch of the strips, the area of silicon tiles, the material of the converter
UR 6.2 Configure the calorimeter, by modifying the number of active elements, the number of layers.
UR 6.3 Configure the source. UR 6.4 Configure digitisation by modifying threshold UR 6.5 Configure the histograms
7. Persistency UR 7.1 Produce an intermediate output of the simulation
at the level of hits in the tracker. UR 7.2 Store significant results in FITS format. UR 7.3 Read in an intermediate output for further
elaboration.
Collect User Requirements in proper domains
DesignDesign
Define the structure of the software by a
software engineering point of view
OOAD Primaryparticles
Analysis
Detector
Visualisation
Run
Physics
Event
Design
Software development
UR1
design
implementation
test
Test phase is crucial and extremelyimportant
Test
Important and crucial issue
Always in respect to experimental dataexperimental data
Comparisons in respect to other MC toolkit are just
curiosity
Levels of tests:Microscopic test
Test on components of the application (i.e. Physics models adopted)Macroscopic test Test on the experimental set-up (physics, geometry, etc. together)
Iterative, incremental method
UR1
UR2
UR3
UR1 design implementation
test
UR2designimplementationtest
UR3 design implementation
test…..
Gain feedback on the developed software:Examples: - Is the UR satisfied? - Do we need new UR? - How can we improve the software ?
Documentation
User Requirement document
Design
Traceability documents
How to use the software application
Comments in the code
Software process and documentation are important for:Develop a rigorous and reliable softwareDevelop clear and clean softwareLimit the possibility of introducing bugsHelp other people to understand the software application
Geant4 brachytherapy advanced Geant4 brachytherapy advanced exampleexample
F. Foppiano3, S.Guatelli2,J.Moscicki1, M.G. Pia2
CERN1 ,INFN Genova2, National Institute for Cancer Research, IST
Genova3
www.ge.infn.it/geant4, advanced examples
Brachytherapy is a medical therapy used for cancer treatment
Radioactive sources are used to deposit therapeutic doses near tumors, while preserving surrounding healthy tissues
BrachytherapyEndocavitarybrachytherapy(lungs, uterus)
Interstitial brachytherapy (prostate)
Superficial brachytherapy(skin) Software is used to define patient’s treatment planning
It calculates the dose in the patient
Treatment planning: how to set (where?, how long?)radioactive sources in treatment’s target area
Commercial software for brachytherapy
Various commercial software products for treatment planning
No commercial software available for superficial brachytherapy with Leipzig applicators
PrecisionPrecision
CostCost
Based on approximated analytical methods,approximated analytical methods, because of speed constraints Uniform materialUniform material: water
Each software is specific to one techniquespecific to one technique Treatment planning software is expensiveexpensive (~ hundreds K $/euro)
Develop a Develop a general purposegeneral purpose
precise precise dosimetric system
with the capability of
Patient’s anatomy Patient’s anatomy modelingmodeling
interface to CT imagesinterface to CT images
with a user-friendly interfaceuser-friendly interface
adequate adequate speedspeed for clinical usage for clinical usageperforming atperforming at
PrecisionPrecision
Accurate model of the real experimental set-upAccurate model of the
real experimental set-up
Easy configuration for hospital usage
Easy configuration for hospital usage
SpeedSpeed
Calculation of 3-D dose distribution3-D dose distribution in the treatment area
Determination of isodose isodose curves
Based on Monte CarloMonte Carlo methodsAccurate description of physicsphysics interactions
Realistic description of geometrygeometry and tissuetissuePossibility to interface to CT images
Simple user interface + Graphic visualisation Elaboration of dose distributionsdose distributions and isodosesisodoses
ParallelisationParallelisationAccess to distributed computing resourcesdistributed computing resources
Other requirementsOther requirementsTransparentTransparentOpen to extension extension and new functionalityPublicly accessiblePublicly accessible
RequirementsRequirements
User Requirements
1.The user shall be able to visualise the geometry involved and the trajectories of the particles
The application provides the simulation of energy deposit of brachytherapic sources in a phantom
Geometry
Physics
Analysis
Visualisation
1.The phantom is a box 2.The user shall be able to change the absorber material of the phantom 3.The user shall be able to model patient anatomy 4.The dose should be collected in 1. mm wide voxels
1. Particles: e+,e-, gamma 2. Low Energy electromagnetic processes
1. The user shall be able to calculate the total absorbed energy in the phantom:
3D distribution in the volume2D distribution in the plain containing the source
PrecisionPrecisionPrecisionPrecision
Based on Monte Carlo methodsMonte Carlo methods
Microscopic validation of the physics modelsMicroscopic validation of the physics modelsComparison Comparison with experimental data experimental data
specific to the brachytherapic practice
Experimental validationvalidation of physics involved
Low Energy Package
Validity range: 250 eV – 100 GeV250 eV – 100 GeV– 250 eV is a “suggested” lower limit – data libraries down to 10 eV– 1 < Z < 100
Exploit evaluated data librariesevaluated data libraries (from LLNL): EADL (Evaluated Atomic Data Library) EEDL (Evaluated Electron Data Library) EPDL97 (Evaluated Photon Data Library)
for the calculation of total cross section and generation of the final state
Photon transmission, 1m Pb
shell effects
Compton scattering Rayleigh scattering Photoelectric effect Pair production Bremsstrahlung Ionisation
+ atomic relaxationshell effects
Photon transmission, 1m Al
Al
NISTGeant4-LowEGeant4-Standard
Stopping power
Photons and
electron physics
processes
2N-L=13.1 – =20 - p=0.87
NISTGeant4-LowEGeant4-Standard
Photon attenuation coefficient
Al
2N-S=23.2 – =15 - p=0.08
0 10 20 30 40 500,0
0,2
0,4
0,6
0,8
1,0
1,2 Simulazione Nucletron Misure
Dos
e %
Distanza lungo Z (mm)Distance along Z (mm)
SimulationNucletronDataF. Foppiano et al., IST
Genova
Comparison to protocol data,
original experimental
data
Dosimetric validation
Dosimetric validation
Microscopic validation
Microscopic validation
General purpose systemGeneral purpose systemGeneral purpose systemGeneral purpose system
Object Oriented technologySoftware system designed in terms of Abstract Interfaces
Abstract Factory design patternSource spectrum and geometry transparently interchangeableSource spectrum and geometry transparently interchangeable
For any brachytherapy technique
For any source type
Flexibility of modeling
CT DICOM interface
through Geant4 parameterised volumesGeant4 parameterised volumes parameterisation function: materialparameterisation function: material
Abstract Factory
Configuration of
any brachytherapy technique any brachytherapy technique
any source type any source type
through an Abstract FactoryAbstract Factory to define geometry, primary geometry, primary spectrumspectrum
Phantom
various materialsvarious materials water, soft tissue, bone, muscle etc.
General purpose software system for brachytherapy
No commercial general software exists!
Realistic model Realistic model of the experimental set-upof the experimental set-up
Realistic model Realistic model of the experimental set-upof the experimental set-up
Spectrum (192IrIr, 125II)Geometry
Phantom with realistic material modelPhantom with realistic material modelPossibility to interface the system to CT imagesPossibility to interface the system to CT images
Radioactive source
Patient
Titanium capsule tipsTitanium tube
Iodium core:Inner radius :0Outer radius: 0.30mmHalf length:1.75mm
Air:Outer radius:0.35mm half length:1.84mm
Titanium tube:Outer radius:0.40mmHalf length:1.84mm
Titanium capsule tip:Semisphereradius:0.40mm
Model of a I-125 brachytherapic sourcegeometry and materials
Model the source geometry
Air
Iodium core
Golden marker
Golden marker:Inner radius :0Outer radius: 0.085 mmHalf length:1.75mm
Precise geometry and material model of any type of source
Ir-192 source + applicator for superficial brachytherapy
3 m m ste e l c a b le
5.0 m m
0.6 m m
3.5 m m
1.1 m m
Ac tive Ir-192 C o re
Ir-192
Effects of source anisotropyEffects of source anisotropy
LongitudinalLongitudinal axis of the source axis of the sourceDifficult to make direct measurements
TransverseTransverse axis of the source axis of the sourceComparison with experimental data
Plato-BPS treatment planning algorithm makes some crude
approximation ( dependence,
no radial dependence)
-40 -30 -20 -10 0 10 20 30 400,0
0,5
1,0
1,5
2,0
2,5
Simulazioni Plato Misure
Dose %
Distanza lungo X (mm)Distance along X (mm)
SimulationSimulationPlatoPlatoDataData
-40 -30 -20 -10 0 10 20 30 400,0
0,5
1,0
1,5
2,0
2,5 Simulazioni Plato
Dose %
Distanza lungo Z (mm)
Distance along Z (mm)
Effects of source
anisotropySimulationSimulation
PlatoPlato
Rely on simulation for better accuracy than
conventional treatment planning software
Modeling the patient
source
Modeling a phantomModeling a phantom
of any material (water, tissue, bone, muscle etc.)
thanks to the flexibility of Geant4 materials package
Modeling geometry Modeling geometry and materials from and materials from
CT dataCT data
DICOMDICOM
Acquisition of CT image 3D patient anatomy
Computerized Tomography allows to reproduce the real 3D geometry of the patient
file
Pixels
grey tone proportional to material density
Digital Imaging and COmunication in Medicine
DICOM is the universal standard for sharing resources between heterogeneous and
multi-vendor equipment
Geant4-DICOM interface
Developed by L. Archambault, L. Beaulieu, V.-H. Tremblay (Univ. Laval and l'Hôtel-Dieu, Québec)
Donated to Geant4 for the common profit of the scientific community– under the condition that further improvements and developments are made
publicly available to the community
Released with Geant4 5.2, June 2003 in an extended example– with some software improvement by S. Guatelli and M.G. Pia
First implementation, further improvements foreseen
User-friendly interfaceUser-friendly interfaceto facilitate the usage in hospitalsto facilitate the usage in hospitals
User-friendly interfaceUser-friendly interfaceto facilitate the usage in hospitalsto facilitate the usage in hospitals
Store simulation information in histograms and ntuples
Graphic visualisation of dose distributions
Application configurationApplication configurationJob submissionJob submission
Dosimetric analysis
Web interface
AIDA + Anaphe
DosimetryDosimetry
AIDA + Anaphe
Analysis of the energy deposit in the phantom resulting from the simulation
Dose distribution
Isodose curves
for analysis
Simulation of energy deposit through Geant4 Low Energy Electromagnetic package
to obtain accurate dose distributionProduction threshold: 100 m
AIDAHistograms
NtuplesData vectors
FitVisualisation of
results
Abstract Interfaces for Data Analysis
Data Analysis
Primary particlesEnergy Spectrum(1D histogram)
Energy deposit(2D histogram)
http://aida.freehep.org
source
Bebig Isoseed I-125 source
0.16 mGy =100%
Isodose curvesIsodose curves
MicroSelectron-HDR source
Leipzig applicator
Interstitial brachytherapy
Superficialbrachytherapy
EndocavitaryBrachytherapy
DosimetryDosimetryDosimetryDosimetry
Application configuration
Fully configurable from the web
Type of source
Phantom configuration
# events
Run modes:
demo
parallel on a cluster (under test)
on the GRID (under development)
Speed adequate for clinic useSpeed adequate for clinic useSpeed adequate for clinic useSpeed adequate for clinic use
Transparent configuration in sequential or parallel mode
Transparent access to the GRID through an Transparent access to the GRID through an intermediate software layerintermediate software layer
Parallelisation
Access to distributed computing resources
Performance
Endocavitary brachytherapy
1M events
61 minutes
Interstitial brachytherapy
1M events
67 minutes
Superficial brachytherapy
1M events
65 minutes
on an “average” PIII machine, as an “average” hospital may own
Monte Carlo simulation is not practically conceivable for clinical application, even if more precise
Performance: parallel mode
1M events
4 minutes 34’’
1M events
4 minutes 36’’
1M events
4 minutes 25’’
on up to 50 workers, LSF at CERN, PIII machine, 500-1000 MHz
Performance adequate for clinical application, but…
it is not realistic to expect any hospital to own and maintain a PC farm
Endocavitary brachytherapy
Interstitial brachytherapy
Superficial brachytherapy
preliminary: further optimisation in progress
prototype for an intermediate layer between applications and
the GRID
Diane has been developed by J. MoscickiE-mail: [email protected] http://www.cern.ch/diane
Running on the GRID
Via DIANE
Same application code as running on a sequential machine or on a dedicated cluster
– completely transparent to the user
A hospital is not required to own and maintain extensive computing resources to exploit the scientific advantages of Monte Carlo simulation for radiotherapy
Any hospital
– even small ones, or in less wealthy countries, that cannot even small ones, or in less wealthy countries, that cannot afford expensive commercial software systemsafford expensive commercial software systems –
may have access to advanced software technologies and tools for radiotherapy
Distributed Geant4 application
Traceback from a run on CrossGrid testbed
Current #Grid setup (computing elements):5000 events, 2 workers, 10 tasks (500 events each)
- aocegrid.uab.es:2119/jobmanager-pbs-workq- bee001.ific.uv.es:2119/jobmanager-pbs-qgrid- cgnode00.di.uoa.gr:2119/jobmanager-pbs-workq- cms.fuw.edu.pl:2119/jobmanager-pbs-workq- grid01.physics.auth.gr:2119/jobmanager-pbs-workq- xg001.inp.demokritos.gr:2119/jobmanager-pbs-workq- xgrid.icm.edu.pl:2119/jobmanager-pbs-workq- zeus24.cyf-kr.edu.pl:2119/jobmanager-pbs-infinite- zeus24.cyf-kr.edu.pl:2119/jobmanager-pbs-long- zeus24.cyf-kr.edu.pl:2119/jobmanager-pbs-medium- zeus24.cyf-kr.edu.pl:2119/jobmanager-pbs-short- ce01.lip.pt:2119/jobmanager-pbs-qgrid
Spain
Poland
Greece
Portugal
Resource broker running in Portugal
matchmaking CrossGrid computing elements
Summary
A precise dosimetric system, based on Geant4– Accurate physics, geometry and material modeling, CT interface
Full dosimetric analysis– AIDA + Anaphe
Simple interface– configuration from WWW
Fast performance– parallel processing
Access to distributed computing resources– GRID
Beware: R&D prototype!Beware: R&D prototype!
General dosimetric system for radiotherapy
The system was developed for endocavitary brachytherapy
It has been extended to all the brachytherapic techniques
It is possible to generalise the system to other radiotherapic techniques
Plug-in system under development
Thanks to Object Orientedtechnique
Run Geant4 brachytherapy Run Geant4 brachytherapy advanced exampleadvanced example
Structure of the brachytherapy example
Brachytherapy exampleheader files in include/*.hh, source code in src/ *.ccmain in Brachy.ccmacro: VisualisationMacro.mac
ClassesBrachyAnalysisManagerBrachyDetectorConstructionBrachyDetectorMessengerBrachyEventActionBrachyMaterialBrachyPhantomHitBrachyPhantomROGeometry
BrachyPhantomSD BrachyPrimaryGeneratorAction BrachyPhysicsList BrachyRunAction BrachyEventAction BrachyVisManager
How to run
Define necessary environment variablessource geant4/env.csh
How to compile and linkgmake
How to run$G4WORKDIR/bin/Linux-g++/Brachy
Details on the brachytherapy Details on the brachytherapy
advanced example implementationadvanced example implementation
Mandatory user classes
PhysicsPrimary events
Detector
Abstract FactoriesConfiguration of
any brachytherapy technique any brachytherapy technique
any source type any source type
through an Abstract FactoryAbstract Factory to define geometry, primary geometry, primary spectrumspectrum
Titanium capsule tipsTitanium tubeIodium core:
Inner radius :0Outer radius: 0.30mmHalf length:1.75mm
Air:Outer radius:0.35mm half length:1.84mm
Titanium tube:Outer radius:0.40mmHalf length:1.84mm
Titanium capsule tip:Semisphereradius:0.40mm
Model of a I-125 brachytherapic sourcegeometry and materials
BrachyDetectorConstruction
Air
Iodium core
Golden marker
Golden marker:Inner radius :0Outer radius: 0.085 mmHalf length:1.75mm
BrachyDetectorConstruction::BrachyDetectorConstruction{}
BrachyDetectorConstruction::~BrachyDetectorConstruction{}
G4VPhysicalVolume* BrachyDetectorConstruction::Construct()
{
pMaterial-> DefineMaterials();
ConstructSource();
ConstructPhantom();
ConstructSensitiveDetector();
return WorldPhys;
}
BrachyDetectorConstruction
ConstructSource()
// source Bebig Isoseed I-125 ...// source Bebig Isoseed I-125 ...
// Iodium core
iodiumCore = new new G4TubsG4Tubs("ICore",0.085*mm,0.35*mm,1.75*mm,0.*deg,360.*deg);
iodiumCoreLog = new G4LogicalVolumenew G4LogicalVolume(iodiumCore,iodium,"iodiumCoreLog");
iodiumCorePhys = new G4PVPlacementnew G4PVPlacement(0, G4ThreeVector(0.,0.,0.), "iodiumCorePhys",
iodiumCoreLog, defaultTubPhys, false, 0);
// Golden marker
marker = new new G4TubsG4Tubs("GoldenMarker",0.*mm,0.085*mm,1.75*mm,0.*deg,360.*deg);
markerLog = new G4LogicalVolumenew G4LogicalVolume(marker,gold,"MarkerLog");
markerPhys = new G4PVPlacementnew G4PVPlacement(0, G4ThreeVector(0.,0.,0.), "MarkerPhys", markerLog,
defaultTubPhys, false, 0);
…. construct iodium core and golden marker…Air the mother volume is an air tube
BrachyPhysicsListBrachyPhysicsList::BrachyPhysicsList():
G4VUserPhysicsList()G4VUserPhysicsList()
{
defaultCutValue = 0.1*mm;
…..}
BrachyPhysicsList::~BrachyPhysicsList(){}void BrachyPhysicsList::ConstructParticle()ConstructParticle()
{
ConstructBosons();
ConstructLeptons();
}void BrachyPhysicsList::ConstructBosons(){ G4Gamma::GammaDefinition();}
void BrachyPhysicsList::ConstructLeptons(){ G4Electron::ElectronDefinition(); G4Positron::PositronDefinition();}
void BrachyPhysicsList::ConstructProceConstructProcess()ss()
{
AddTransportation();
ConstructEM();
}
BrachyPhysicsList Set the EM processes
void BrachyPhysicsList::ConstructEM()
{ theParticleIterator->reset();
while( (*theParticleIterator)() ){
G4ParticleDefinition* particle = theParticleIterator->value();
G4ProcessManager* pmanager = particle->GetProcessManager();
G4String particleName = particle->GetParticleName();
if (particleName == "gamma") {
lowePhot = new G4LowEnergyPhotoElectric("LowEnPhotoElec");
pmanager->AddDiscreteProcess(new G4LowEnergyRayleigh);
pmanager->AddDiscreteProcess(lowePhot);
pmanager->AddDiscreteProcess(new G4LowEnergyCompton);
pmanager->AddDiscreteProcess(new G4LowEnergyGammaConversion);
} else if (particleName == "e-") {
loweIon = new G4LowEnergyIonisation("LowEnergyIoni");
loweBrem = new G4LowEnergyBremsstrahlung("LowEnBrem");
pmanager->AddProcess(new G4MultipleScattering, -1, 1,1);
pmanager->AddProcess(loweIon, -1, 2,2);
pmanager->AddProcess(loweBrem, -1,-1,3);
} else if (particleName == "e+"){…}
…
}
Set EM processesfor e-, e+, gamma
BrachyPrimaryGeneratorAction
Energy(keV) Probability
27.4 0.783913
31.4 0.170416
35.5 0.045671
I-125 delivers gamma
•Gamma Energy Spectrum
•Random direction
•Random position inside the iodium core
void BrachyPrimaryGeneratorAction::GeneratePrimaries(G4Event* anEvent)GeneratePrimaries(G4Event* anEvent)
{…..particleGun->SetParticlePosition(position);particleGun -> SetParticleDirection(direction);particleGun -> SetParticleEnergy(energy);particleGun->GeneratePrimaryVertex(anEvent);}
Energy deposit
How to retrieve the energy deposit in the phantom
Concepts:
–Sensitive Detector
–Readout Geometry
–Hits
Set Sensitive Detector and RO Geometry
void BrachyDetectorConstruction::ConstructSensitiveDetector()
{
G4SDManager* pSDManager = G4SDManager::GetSDMpointer();G4SDManager* pSDManager = G4SDManager::GetSDMpointer();
if(!phantomSD){
phantomSD = new phantomSD = new BrachyPhantomSDBrachyPhantomSD(sensitiveDetectorName,numberOfVoxelsAlongX,
numberOfVoxelsAlongZ);
G4String ROGeometryName = "PhantomROGeometry";
phantomROGeometry = newBrachyPhantomROGeometryphantomROGeometry = newBrachyPhantomROGeometry(ROGeometryName,
phantomDimensionX,phantomDimensionZ,numberOfVoxelsAlongX,numberOfVoxelsAlongZ);
phantomROGeometry->BuildROGeometry();phantomROGeometry->BuildROGeometry();
phantomSD->SetROgeometry(phantomROGeometry);phantomSD->SetROgeometry(phantomROGeometry);
pSDManager->AddNewDetector(phantomSD);pSDManager->AddNewDetector(phantomSD);
PhantomLog->SetSensitiveDetector(phantomSD);PhantomLog->SetSensitiveDetector(phantomSD);
}
BrachyPhantomROGeometry::BrachyPhantomROGeometry() {}
BrachyROGeometry::~BrachyROGeometry() {}
G4VPhysicalVolume* BrachyPhantomROGeometry :: Build()Build(){ // example : X division ROPhantomXDivision = new G4Box( ….);
ROPhantomXDivisionLog = newG4LogicalVolume(….);
ROPhantomXDivisionPhys = new G4PVReplica(….);……..}
x
Readout Geometry
Store the energy deposit in one hit
Sensitive DetectorG4bool BrachyPhantomSD::ProcessHits
(G4Step* aStep, G4TouchableHistory* ROhist)
{….
G4double energyDeposit = aStep->GetTotalEnergyDeposit();
….
G4VPhysicalVolume* physVol = ROhist->GetVolume();
// Read Voxel indexes: i is the x index, k is the z index
G4int k = ROhist->GetReplicaNumber(1);
G4int i = ROhist->GetReplicaNumber(2);
G4int j= ROhist->GetReplicaNumber();
…..
BrachyPhantomHit* PhantomHit = new BrachyPhantomHit(
physVol ->GetLogicalVolume(), i,j,k)
PhantomHit->SetEdep(energyDeposit);
PhantomHit->SetPos(physVol->GetTranslation());
… }
HitsHit is a user-defined class derived from G4VHit
You can store various types information by implementing your own concrete Hit class:
position and time of the step momentum and energy of the track energy deposit of the step geometrical information etc.
Hit objects of a concrete hit class must be stored in a dedicated collection, which is instantiated from G4THitsCollection template G4THitsCollection template classclass
BrachyPhantomHit (header file)class BrachyPhantomHit : public G4VHitpublic G4VHit
{
public:
BrachyPhantomHit(G4LogicalVolume* ,G4int ,G4int ,G4int );
~BrachyPhantomHit();
…..
inline void SetCellID(G4int XID,G4int YID,G4int ZID) // Set Hit position
{xHitPosition = XID; zHitPosition = ZID; yHitPosition = YID; }
inline void SetEdep(G4double edep) {energyDeposit = edep;} //Set hit energy deposit
inline void SetPos(G4ThreeVector xyz) {hitPosition = xyz;} // Set hit position
inline G4int GetXID() {return xHitPosition;} //Get hit x coordinate
inline G4int GetZID() {return zHitPosition;} // Get hit z coordinate
inline G4int GetYID() {return yHitPosition;} // Get hit y coordinate
inline G4double GetEdep() {return energyDeposit;} // Get energy deposit
….}
BrachyEventAction
Retrieve energy deposit in the phantom
void BrachyEventAction::EndOfEventAction(const G4Event* evt)
{….
G4HCofThisEvent* HCE = evt->GetHCofThisEvent();
BrachyPhantomHitsCollection* CHC = NULL;
if(HCE)
CHC = (BrachyPhantomHitsCollection*)(HCE->GetHC(hitsCollectionID));
if(CHC)
{
G4int hitCount = CHC->entries();
for (G4int h = 0; h < hitCount; h++)
{
G4int i=((*CHC)[h])->GetZID();
G4int k=((*CHC)[h])->GetXID();
G4int j=((*CHC)[h])->GetYID();
G4double EnergyDep=((*CHC)[h]->GetEdep());
…}
…}
…}
Initialisationmain Run manager user detector
const ructionuser physics
list
1: initialize2 : const ruct
3: material const ruct ion
4: geometry construct ion5: world volume
6 : const ruct
7 : physics process const ruction
8: set cuts
Describe the geometrical set-up
Activate electromagnetic/hadronic
processes appropriate to the energy range of the experiment
Beam On
main Run Manager Geometry manager
Event generator
EventManager
1: Beam On2: close
3: generate one event
4: process one event
5: open
Generate primary events
Event processing
Event manager
Stacking manager
Tracking manager
Stepping manager
User sensitive detector
1: pop
2: process one track3: Stepping
4: generate hits
5: secondaries
6: push
Record the energy deposit and the position associated
How to produce •1D histograms•2D histograms•Ntuple
Analysis Tool•AIDA 3.0•Anaphe 5.0.5
BrachyAnalysisManagerBrachyAnalysisManager::BrachyAnalysisManager() :
….
{
//build up the factories
aFact = AIDA_createAnalysisFactory();
AIDA::ITreeFactory *treeFact = aFact->createTreeFactory();
theTree = treeFact->create(fileName,"hbook",false, true);
….
histFact = aFact->createHistogramFactory( *theTree );
tupFact = aFact->createTupleFactory ( *theTree );
}
void BrachyAnalysisManager::finish()
{
theTree->commit(); // write all histograms to file ...
theTree->close(); // close (will again commit) ...
}
Create the .hbk file…
Close the .hbk file
BrachyAnalysisManager
void BrachyAnalysisManager::book()
{
//creating a 2D histogram ...
h1 = histFact->createHistogram2D("10","Energy, pos",
300 ,-150.,150., //bins'number,xmin,xmax
300,-150.,150. );//bins'number,ymin,ymax
//creating a 1D histogram ...
h2 = histFact->createHistogram1D("20","Initial Energy", 500,0.,50.);
//creating a ntuple ...
if (tupFact) ntuple = tupFact->create("1","1",columnNames, options);
….}
BrachyAnalysisManager
void BrachyAnalysisManager::FillHistogramWithEnergyFillHistogramWithEnergy (G4double x, G4double z, G4float energyDeposit)
{
//2DHistogram: energy deposit in a voxel which center is fixed in position (x,z)
h1->fill(x,z,energyDeposit);
}
void BrachyAnalysisManager::PrimaryParticleEnergySpectrumPrimaryParticleEnergySpectrum
(G4double primaryParticleEnergy)
{
//1DHisotgram: energy spectrum of primary particles
h2->fill(primaryParticleEnergy);
}
How to fill histograms….
BrachyAnalysisManager
void BrachyAnalysisManager::FillNtupleWithEnergyFillNtupleWithEnergy(G4double xx,G4double yy, G4double zz, G4float en)
{…..
G4int indexX = ntuple->findColumn( "x" );
G4int indexY = ntuple->findColumn( "y" );
G4int indexZ = ntuple->findColumn( "z" );
G4int indexEnergy = ntuple->findColumn( "energy" );
ntuple->fill(indexEnergy, en);
ntuple->fill(indexX, xx);
ntuple->fill(indexY, yy);
ntuple->fill(indexZ, zz);
ntuple ->addRow();
}
How to fill Ntuples….
Analysis management
In the BrachyRunAction
void BrachyRunAction::BeginOfRunAction(const G4Run*)
{
….
BrachyAnalysisManager* analysis = BrachyAnalysisManager::getInstance();
analysis->book();
….
}
void BrachyRunAction::EndOfRunAction(const G4Run* aRun)
{
…..
BrachyAnalysisManager* analysis = BrachyAnalysisManager::getInstance()
…..
analysis->finish();
….
}
Booking histograms and ntuple …
…Closing the hbook file
Energy deposit
In the BrachyEventAction
void BrachyEventAction::EndOfEventAction(const G4Event* evt)
{
…. // here the energy deposit information is retrieved
//Store information about energy deposit in a 2DHistogram and in a ntuple ...
BrachyAnalysisManager* analysis = BrachyAnalysisManager::getInstance
analysis->FillHistogramWithEnergy(x,z,EnergyDep/MeV);}}
analysis->FillNtupleWithEnergy(x,y,z,EnergyDep/MeV);
…
}
Gamma energy spectrum
BrachyPrimaryGeneratorAction:: GeneratePrimaries(G4Event* anEvent)
{
//Store the initial energy in a 1D histogram
analysis-> PrimaryParticleEnergySpectrum(primaryParticleEnergy/keV);
// generate primary particle
…
}
In the BrachyPrimaryGeneratorAction
Analysis dynamic flow
Some Results
Primary particlesEnergy Spectrum(1D histogram)
Energy deposit(2D histogram)
Control, monitor the simulation
BrachyDetectorMessenger
BrachyDetectorMessenger::BrachyDetectorMessenger( BrachyDetectorConstruction* Det): detector(Det)
{ detectorDir = new G4UIdirectory("/phantom/");
detectorDir->SetGuidance(" phantom control.");
phantomMaterialCmd = new G4UIcmdWithAString("/phantom/selectMaterial",this);
phantomMaterialCmd->SetGuidance("Select Material of the detector.");
phantomMaterialCmd->SetParameterName("choice",false);
phantomMaterialCmd->AvailableForStates(G4State_Idle);
}
void BrachyDetectorMessenger::SetNewValue(G4UIcommand* command,G4String newValue)
{
if( command == phantomMaterialCmd )
{ detector->SetPhantomMaterial(newValue);}
}
(G)UIHow to change the phantom absorber material
• Run $G4WORKDIR/bin/Linux-g++/Brachy
• (G)UI session : interactive session
• Type /phantom/selectMaterial Lead
The phantom absorber material now is lead
Macro
A macro is an ASCII file containing UI commandsAll commands must be given with their full-path directories
A macro can be executed by /control/execute /control/loop /control/foreach
in UI session
/control/verbose 1/run/verbose 1/event /verbose 1/phantom/selectMaterial Lead
# run 10 events/run/beamOn 10
A macro can be executed also typing: $G4WORKDIR/bin/Linux-g++/Brachy macro.mac
Visualisation
Control of several kinds of visualisation
detector geometry particle trajectories hits in the detectors
In the Brachytherapy Example OGLIX, DAWN
VisualisationMacro.mac
# Macro file for the visualisation
# create empty scene
#
/vis/scene/create
#/vis/open OGLIX
/vis/open DAWN
/vis/viewer/flush
# for drawing the tracks
/tracking/storeTrajectory 1
/vis/scene/endOfEventAction accumulate
/vis/viewer/update
/run/initialize
/run/beamOn 10
