GATE documentation

Contents:

• 1. User guide
  • 1.1. Introduction & installation
    • 1.1.1. Why this new project ?
    • 1.1.2. Goals and features
    • 1.1.3. Installation (for users, not for developers)
    • 1.1.4. Additional command lines tools
    • 1.1.5. Teaching resources and examples
  • 1.2. Simulation
    • 1.2.1. Units values
    • 1.2.2. Main Simulation object
      • 1.2.2.1. Random Number Generator
      • 1.2.2.2. Run and timing
      • 1.2.2.3. Verbosity (for debug)
      • 1.2.2.4. Visualisation
      • 1.2.2.5. Multithreading
    • 1.2.3. Starting and SimulationEngine
    • 1.2.4. After the simulation
      • 1.2.4.1. Multiprocessing (advanced use)
  • 1.3. Geometry and volumes
    • 1.3.1. Overview: Volumes
    • 1.3.2. Volume hierarchy
    • 1.3.3. Common parameters
    • 1.3.4. Utility properties
    • 1.3.5. Materials
    • 1.3.6. Image volumes
    • 1.3.7. Tesselated (STL) volumes
    • 1.3.8. Repeated volumes
    • 1.3.9. Repeat Parametrised Volumes
    • 1.3.10. Boolean volumes
    • 1.3.11. Examples of complex geometries: Linac, SPECT, PET, phantoms
    • 1.3.12. Parallel worlds
  • 1.4. Sources
    • 1.4.1. Generic sources
    • 1.4.2. Voxelized sources
    • 1.4.3. Phase-Space sources
    • 1.4.4. GAN sources (Generative Adversarial Network)
    • 1.4.5. PHID source (Photon from Ion Decay)
    • 1.4.6. Pencil Beam sources
  • 1.5. Physics
    • 1.5.1. Physics list and decay
    • 1.5.2. Optical Physics Processes
      • 1.5.2.1. G4OpticalPhysics physics list
      • 1.5.2.2. Optical Physics Properties
      • 1.5.2.3. Scintillation
      • 1.5.2.4. Cerenkov photons
      • 1.5.2.5. Absorption
      • 1.5.2.6. Mie/Rayleigh Scattering
      • 1.5.2.7. Fluorescence
      • 1.5.2.8. Boundary Processes
    • 1.5.3. Defining Surfaces
      • 1.5.3.1. EXAMPLES -
      • 1.5.3.2. LUT Davis Model
      • 1.5.3.3. UNIFIED Model
    • 1.5.4. Electromagnetic parameters
    • 1.5.5. Managing the cuts and limits
  • 1.6. Actors and Filters
    • 1.6.1. SimulationStatisticsActor
    • 1.6.2. DoseActor
    • 1.6.3. PhaseSpaceActor
    • 1.6.4. Hits-related actors (digitizer)
      • 1.6.4.1. DigitizerHitsCollectionActor
      • 1.6.4.2. DigitizerHitsAdderActor
      • 1.6.4.3. DigitizerReadoutActor
      • 1.6.4.4. DigitizerGaussianBlurringActor
      • 1.6.4.5. DigitizerSpatialBlurringActor
      • 1.6.4.6. DigitizerEnergyWindowsActor
      • 1.6.4.7. DigitizerProjectionActor
      • 1.6.4.8. DigitizerEfficiencyActor
    • 1.6.5. Coincidences Sorter
    • 1.6.6. MotionVolumeActor
    • 1.6.7. ARFActor (and ARFTrainingDatasetActor)
    • 1.6.8. LETActor
    • 1.6.9. ComptonSplittingActor
  • 1.7. Additional functionalities
  • 1.8. Contributions
    • 1.8.1. Dose rate computation
    • 1.8.2. Phantoms
      • 1.8.2.1. Phantom: IEC 6 spheres NEMA phantom
      • 1.8.2.2. Phantom: cylinder phantom for PET NECR
    • 1.8.3. Radiation therapy linac
      • 1.8.3.1. LINACs reference systems :
      • 1.8.3.2. LINACs source types :
      • 1.8.3.3. Phase space plan
      • 1.8.3.4. Empty LINAC box
      • 1.8.3.5. Collimation systems
      • 1.8.3.6. Reproduction of a radiotherapy plan irradiation
    • 1.8.4. SPECT imaging systems
    • 1.8.5. PET imaging systems
• 2. Developer guide
  • 2.1. Installation for developers
    • 2.1.1. STEP 1 - Geant4 and Qt
    • 2.1.2. STEP 2 - ITK
    • 2.1.3. STEP 3 - opengate_core module (cpp bindings)
    • 2.1.4. STEP 4 - opengate module (python)
    • 2.1.5. STEP 5 - Before running
  • 2.2. How to contribute (for developers)
    • 2.2.1. Propose a pull request:
    • 2.2.2. Tests and documentation
    • 2.2.3. Code formatting
  • 2.3. GATE architecture: Managers and Engines
    • 2.3.1. References among managers and engines
  • 2.4. Geant4 bindings
    • 2.4.1. How to add a Geant4 bindings ?
    • 2.4.2. Misc
  • 2.5. Philosophy behind objects implemented as GateObject
  • 2.6. How a class in GATE 10 is (usually) set up:
    • 2.6.1. Naming convention
    • 2.6.2. __init__() method
    • 2.6.3. User info: handling parameters set by the user
    • 2.6.4. Initialization of Geant4 objects
    • 2.6.5. Implement a close() method if needed
    • 2.6.6. Implement a __getstate__() method if needed.
    • 2.6.7. Optional: Implement a __str__() method
  • 2.7. Helpers
  • 2.8. Engines
    • 2.8.1. SimulationEngine
    • 2.8.2. VolumeEngine
    • 2.8.3. PhysicsEngine
    • 2.8.4. ActorEngine
    • 2.8.5. SourceEngine
    • 2.8.6. ActionEngine
  • 2.9. OPENGATE elements: volumes, physic, sources, actors
    • 2.9.1. UserInfo (before initialisation)
  • 2.10. OPENGATE Geometry
  • 2.11. OPENGATE Physics
  • 2.12. OPENGATE Source
  • 2.13. OPENGATE Actors
    • 2.13.1. Hits collections
    • 2.13.2. How to develop a new Actor ?
      • 2.13.2.1. 1 - Create a c++ class GateMyActor
      • 2.13.2.2. 2 - Expose this class to python side
      • 2.13.2.3. 3 - Create a python file MyActor.py with the corresponding python class
      • 2.13.2.4. 4 - Conclusion
  • 2.14. SimulationEngine
  • 2.15. Documentation for the documentation
  • 2.16. Notes for developers
    • 2.16.1. Pybind11 hints
    • 2.16.2. Memory managment between Python and Geant4 - Why is there a segmentation fault?
    • 2.16.3. ITK
    • 2.16.4. Geant4 seems to be frozen/sleeping - the GIL is to blame - here is why
• 3. API Reference
  • 3.1. C11
  • 3.2. F18
  • 3.3. N13
  • 3.4. O15
  • 3.5. Ga68
  • 3.6. Na22
  • 3.7. Zr89
  • 3.8. Rb82
  • 3.9. setup
    • 3.9.1. Attributes
    • 3.9.2. Classes
    • 3.9.3. Functions
    • 3.9.4. Module Contents
      • warning()
      • get_cmake_dir()
      • get_base_dir()
      • version
      • CMakeExtension
      • CMakeBuild
      • package_data
  • 3.10. opengate
    • 3.10.1. Submodules
      • 3.10.1.1. opengate.actions
      • 3.10.1.2. opengate.actors
      • 3.10.1.3. opengate.base
      • 3.10.1.4. opengate.bin
      • 3.10.1.5. opengate.contrib
      • 3.10.1.6. opengate.decorators
      • 3.10.1.7. opengate.definitions
      • 3.10.1.8. opengate.element
      • 3.10.1.9. opengate.engines
      • 3.10.1.10. opengate.exception
      • 3.10.1.11. opengate.geometry
      • 3.10.1.12. opengate.image
      • 3.10.1.13. opengate.logger
      • 3.10.1.14. opengate.mac
      • 3.10.1.15. opengate.managers
      • 3.10.1.16. opengate.physics
      • 3.10.1.17. opengate.processing
      • 3.10.1.18. opengate.runtiming
      • 3.10.1.19. opengate.serialization
      • 3.10.1.20. opengate.sources
      • 3.10.1.21. opengate.tests
      • 3.10.1.22. opengate.uisessions
      • 3.10.1.23. opengate.userelement
      • 3.10.1.24. opengate.userhooks
      • 3.10.1.25. opengate.userinfo
      • 3.10.1.26. opengate.utility
    • 3.10.2. Attributes
    • 3.10.3. Classes
    • 3.10.4. Package Contents
      • Simulation
      • g4_units
  • 3.11. opengate_core
    • 3.11.1. Submodules
      • 3.11.1.1. opengate_core.g4DataSetup
      • 3.11.1.2. opengate_core.g4_bindings
      • 3.11.1.3. opengate_core.opengate_lib
      • 3.11.1.4. opengate_core.qt5Setup
      • 3.11.1.5. opengate_core.testsDataSetup
    • 3.11.2. Attributes
    • 3.11.3. Functions
    • 3.11.4. Package Contents
      • get_site_packages_dir()
      • get_libG4_path()
      • pathCurrentFile
      • reloadPython
      • data_packages
      • check_G4_data()
      • download_G4_data()
      • check_for_non_required_files_folders()
      • check_consistency_g4_data_folders()
      • get_G4_data_folder()
      • get_G4_data_paths()
      • set_G4_data_path()
      • set_qt5_path()
      • data_packages
      • check_G4_data()
      • download_G4_data()
      • check_for_non_required_files_folders()
      • check_consistency_g4_data_folders()
      • get_G4_data_folder()
      • get_G4_data_paths()
      • set_G4_data_path()

Indices and tables

• Index

• Module Index

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