15/jul/054th workshop on geant4 bio-medical developments and physics validation 1 python interface...

15/Jul/05 4th Workshop on Geant4 Bio-medical Developments and Physics Validation

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Python Interface forPython Interface forGeant4 Medical Geant4 Medical

ApplicationsApplications

K.Murakami

(KEK)

15/Jul/05


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IntroductionIntroduction Missing functionalities of current Geant4 command-line interface

more powerful scripting environment only simple flow control is available, but not enough. flow control, variables, arithmetic operation

direct handling each object of G4XXX only limited manager-like classes can be exposed via G4UIcommand.

Python is believed to be the most promising technological choice in terms of Python as a powerful scripting language

Python can work as front-end of a light framework modularization of user classes with dynamic loading scheme

DetectorConstruction, PhysicsList, PrimaryGeneratorAction, UserAction-s It helps avoid code duplication.

Python as “Software Component Bus” C++ objects can be exposed to python. interconnectivity with many Python external modules,

analysis tools (ROOT/AIDA), web interface,...


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Project Aim of Geant4PyProject Aim of Geant4Py

Generic and straight forward approach of Pythonization of Geant4 not specific to particular applications minimal dependencies of external packages

only depending on Boost-Python, which is a common, well-established and freely available library.


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Use-Case of Medical Use-Case of Medical ApplicationApplication System integration of developed components...

geometry modeling (DICOM, DICOM-RT, beam line, ...) physics list (EM, Hadron, Ion [BC, JQMD], ...) MPI parallelization (MPICH2) Analysis packages (ROOT, HBOOK, AIDA, ...) Visualization (Real Intage, DoctorView, AVS, ...) Web applications (mod-python, CherryPy) (G)UI (Java, Python, Web App., Qt, Tk, ...) Grid service (LCG, Clarens)

Interconnectivity with these items can be realized via Python interface.


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Software StructureSoftware Structure Applications

C++ application, Python scripts, Web applications, ...

Component Implementation geometry modeling physics list scoring, ...

Simulation Framework component models plug-in management scripting parallelization

Other Frameworks analysis (ROOT) visualization, ...

Software Component Bus Python, API, original interface

Applications

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FoundationLibraries

OptionalLibraries

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Software Component Bus

Foundation Libraries Geant4, JQMD, ... MPICH, ... LCG Python, Boost-Python CLHEP ...

Optional Libraries ROOT, CERNLIB, ... JAVA, Qt, Tk ...

Components Implementation


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Tools for Geant4/Python interfaceTools for Geant4/Python interface There are several activities; SWIG

supports for multiple languages Implementation of G4/Python interface can be found in advanced

examples (Tiara).

LCG Python Geant4 interface using PyReflex tool

Boost-Python a part of comprehensive Boost C++ library, but independent from

other components focused to C++/python interface, so performance loss is not so m

uch.


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What is/isnot ExposedWhat is/isnot ExposedWhat is exposed: Classes for main Geant4 flow control

G4RunManager, G4UImanager, G4UIterminal Some Utility classes

G4String, G4ThreeVector, G4RotationMatrix, ... Classes of base classes of user actions

G4UserDetetorConstruction, G4UserPhysicsList, G4UserXXXAction (PrimaryGenerator, Run, Event, Stepping,...) can be inherited in Python side

Classes having information to be analyzed G4Step, G4Track, G4StepPoint, G4ParticleDefinition, ...

Classes for construction user inputs G4ParticleGun, G4Box, G4PVPlacement, ...

What is not exposed: NOT all methods are exposed.

only safe methods (getting internal information) are exposed. Out of Scope

implementation of physics processes implementation of internal control flows It just ends in deterioration of performance.


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Module StructureModule Structure

Python module name : “Geant4” including CLHEP components typedef-ed as G4XXX, like

G4ThreeVector, G4RotationMatrix, ... Units definition (“HEPUnit” as namespace)

From users side,>>> import Geant4

>>> from Geant4 import * “Geant4” module consists of a collection of submodu

les same as Geant4 directory structure. run/event/particle/geometry/track/...


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Name Policy in Python sideName Policy in Python side

Names of classes as well as methods are same as used in Geant4.

>>> gRunManager= Geant4.G4RunManager()>>> gRunManager.BeamOn(10)

This makes it easy to translate from C++ to Python, and vice versa.

As an exception, pure singleton class, which has no public constructor, like G4UImanager, can not be exposed in Boost-Python. So, necessary members of such classes are exposed directly in Geant4 namespace.

>>> Geant4.gApplyUIcommand(“/run/beamOn”)>>> Geant4.gGetCurrentValues(“/run/verbose”) >>> Geant4.gStartUISession()


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Global Variables/FunctionsGlobal Variables/Functions Some global variables/functions starting with "g“ are predefined.

gRunManager gVisManager gApplyUIcommand() gGetCurrentValues() gStartUISession()

gRunManager and gVisManager are taken care not so as to be doubly instantiated, so that users do not have to take any more care about the timing of object instantiation in python side.

All of visualization drivers (OpenGL, VRML, DAWN, ...) are automatically registered. So users are now free from implementation of VisManager.

Note that care from C++ side is of course in need!if(G4RunManager::GetRunManager() ==0 ) G4RunManager* runManager= new G4RunManager();


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List of Current Exposed ClassesList of Current Exposed Classes global

G4String G4ThreeVector

interface G4UImanager G4UIterminal

run G4RunManager G4VUserDetectorConstruction G4VUserPhysicsList G4UserRunAction G4VUserPrimaryGeneratorAction G4Run

event G4Event G4ParticleGun G4UserEventAction

tracking G4UserSteppingAction

track G4Step G4Track G4StepPoint G4StepStatus G4TrackStatus

particles G4ParticleDefinition G4DynamicParticle G4PrimaryParticle G4PrimaryVertex

geometry G4VTouchable G4TouchableHistotry G4VPhysicalVolume

material G4Material

visualization G4VisManager G4VGraphicSystem G4OpenGLStoredX ...


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Various Levels of PythonizationVarious Levels of Pythonization

Various level of pythonized application can be realized. It is completely up to users!

Two metrics Execution Speed

just wrapping current existing applications Interactivity

interactive analysis rapid prototyping educational use for G4 primer


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Use-case of PythonizationUse-case of PythonizationExecution Speed

Interactivity/Pythonization

large scale of mass production

a collection of short productionswith various running conditions

applications having interconnections with other software components

interactive analysis

free from compilation- rapid prototyping- educational uses


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An Example of Exposure of Users’ An Example of Exposure of Users’ ApplicationApplication

Uses’ existing applications are easily exposed to python following a simple prescription of Boost-Python manner.

BOOST_PYTHON_MODULE(demo_wp){ class_<MyApplication>("MyApplication", "my application") .def("Configure", &MyApplication::Configure) ; class_<MyMaterials>("MyMaterials", "my material") .def("Construct", &MyMaterials::Construct) ; class_<MyDetectorConstruction, MyDetectorConstruction*, b

ases<G4VUserDetectorConstruction> > ("MyDetectorConstruction", "my detector")

; class_<MyPhysicsList, MyPhysicsList*, bases<G4VUserPhy

sicsList> > ("MyPhysicsList", "my physics list") ;}


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A Medical Application ExampleA Medical Application Example Several examples of using Python interface are/will be pr

esented. An example of “water phantom dosimetry”

This demo program shows that a Geant4 applicationwell coworks with ROOT on Python front end.VisManager, PrimaryGeneratorAction, UserAction-s, histogramming with ROOT are implemented in Python.

dose calculation in a water phantom Python overloading of user actions on-line histogramming with ROOT visualization


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Example of A Python ScriptExample of A Python Scriptfrom Geant4 import *import demo_wp # module of a user G4 applicationimport ROOT

# -------------------------------------------------------------class MyRunAction(G4UserRunAction): # Python inheritance "My Run Action“def EndOfRunAction(self, run): # method override print "*** End of Run“ print "- Run sammary : (id= %d, #events= %d)" \ % (run.runID, run.numberOfEventToBeProcessed)

# -------------------------------------------------------------class MyPrimaryGeneratorAction(G4VUserPrimaryGeneratorAction): "My Primary Generator Action“ def __init__(self): G4VUserPrimaryGeneratorAction.__init__(self) self.particleGun= G4ParticleGun(1)

def GeneratePrimaries(self, event): self.particleGun.GeneratePrimaryVertex(event)


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# user detector construction (C++)myDC= demo_wp.MyDetectorConstruction() gRunManager.SetUserInitialization(myDC)

# user physics list (C++)myPL= demo_wp.MyPhysicsList()gRunManager.SetUserInitialization(myPL)

# user P.G.A (Python)myPGA= MyPrimaryGeneratorAction()gRunManager.SetUserAction(myPGA)

...# setting particle gunpg= myPGA.particleGunpg.SetParticleByName("proton")pg.SetParticleEnergy(230.*HEPUnit.MeV)pg.SetParticleMomentumDirection(G4ThreeVector(0., 0., 1.))pg.SetParticlePosition(G4ThreeVector(0.,0.,-20.)*HEPUnit.cm)

gRunManager.Initialize()

gApplyUICommand("/control/execute vis.mac")gRunManager.BeamOn(100)


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Further to go...Further to go...

Making rapid progress for implementation of missing elements

Realize interconnection with various software components; example of using AIDA example of using GDML multi-thread and parallelization web application GUI support in specific application contexts GRID service ...


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Software RequirementsSoftware Requirements All libraries should be compiled in shared libraries. Python BOOST-Python

1.32, latest Geant4

7.0 or later - should be built in "global" and "shared" libraries. - All header files should be collected into $(G4INSTALL)/include by "make

includes" CLHEP

1.9.1.1 or later - building shared objects is supported since version 1.9.

Platforms SUSE Linux 9.3 is a development environment.

It is the easiest way to go, because Boost C++ library is preinstalled. Scientific Linux 3 (SL3) is checked for well working. SL4 will be checked as well.


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SummarySummary Python Interface of Geant4 (Geant4Py) has been well designed a

nd implementation is now rapidly on-going. Python as a powerful scripting language

much better interactivity configuration rapid prototyping

Python as “Software Component Bus” interconnectivity with various kind of software components.

histogramming with ROOT system integration

We have a plan to commit the package into the next December release. “environments/” directory is a suitable position

GUIPython

math...shell

GRIDGUI

PyROOT

RootClasses

MPI

Geant4Py

Geat4Classes


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ResourcesResources

Project Home Page http://www-geant4.kek.jp/projects/Geant4Py/

CVS view http://www-geant4.kek.jp/projects/Geant4Py/cvs/

Wiki Technical notes for the developers http://www-geant4.kek.jp/projects/Geant4Py/puki

wiki/

15/jul/054th workshop on geant4 bio-medical developments and physics validation 1 python interface...

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