Welcome to GAMOS’s documentation!

• 1   Introduction
  • 1.1   About this document
  • 1.2   Introduction to GAMOS
  • 1.3   Structure of GAMOS
  • 1.4   The plug-in concept
• 2   Getting started
  • 2.1   Getting the code and installing it
    • 2.1.1   Installing in Linux and Mac OS
    • 2.1.2   Installing in Windows
  • 2.2   Running an example in Linux or Mac OS
  • 2.3   Running an example in Windows
    • 2.3.1   GAMOS Graphical User Interface
  • 2.4   Compiling GAMOS
    • 2.4.1   Compiling your new code
• 3   Geometry
  • 3.1   Building your geometry with a text file
    • 3.1.1   Description of geometry text file format
    • 3.1.2   Dumping your Geant4 geometry in text file format
    • 3.1.3   Adding new tags to your input text file
    • 3.1.4   Parallel geometries
  • 3.2   Building complex geometries in a simple way
  • 3.3   Building a simple geometry with one material
  • 3.4   Building your geometry with C++ code
  • 3.5   Phantom geometries
    • 3.5.1   Simple phantom geometries
    • 3.5.2   Reading DICOM files
    • 3.5.3   Setting off visualization of phantom geometries
  • 3.6   Movements
  • 3.7   Geometry utilities
  • 3.8   Magnetic and electric fields
• 4   Visualization
  • 4.1   3D Geant4 visualization
  • 4.2   2D visualization
• Generator
  • Using GAMOS generator
    • Introduction
    • Particle sources
    • Distributions of energy, position, direction and time
  • Reading your generator particles from a text file
  • Reading your generator particles from a binary file
  • Event generator changing energy and material
  • Event generator histograms
  • Biasing generator distributions
  • Building your generator with C++
  • Using ions
• 6   Physics
  • 6.1   GAMOS electromagnetic physics lists
    • 6.1.1   Basic electromagnetic physics list
    • 6.1.2   GAMOS extended electromagnetic physics list
    • 6.1.3   Geant4 electromagnetic physics list options
    • 6.1.4   Multiple scattering models
    • 6.1.5   Bremsstrahlung angular distributions
  • 6.2   GAMOS hadrontherapy physics list
  • 6.3   Microdosimetry physics list
  • 6.4   Other physics lists
  • 6.5   Optical photons
    • 6.5.1   Using optical photons as primary generator
  • 6.6   X-ray refraction
  • 6.7   Coulomb scattering
  • 6.8   Atomic deexcitation processes
  • 6.9   Decay process
  • 6.10   Radioactive decay process
  • 6.11   Cerenkov process
  • 6.12   Coulomb scattering
  • 6.13   Nuclear processes of electromagnetic particles
  • 6.14   Replacing electromagnetic process models
    • 6.14.1   Replacing a set of process models
    • 6.14.2   Replacing one process model
  • 6.15   Removing a process from a physics list
  • 6.16   Production thresholds (cuts)
    • 6.16.1   Production cuts by region
    • 6.16.2   Energy cuts to range cuts conversion
    • 6.16.3   Minimum and maximum production cuts
    • 6.16.4   Apply cuts for all processes
  • 6.17   User limits
  • 6.18   Automatic optimisation of cuts
    • 6.18.1   Range rejection
  • 6.19   Building your physics list with C++ code
• 7   User Actions
  • 7.1   Geant4 and GAMOS user actions
  • 7.2   Adding a filter
  • 7.3   Adding a classifier
  • 7.4   User action name, including filters and classifiers
  • 7.5   Creating your GAMOS user action with C++ code
• 8   Sensitive Detector and Hits
  • 8.1   Sensitive detectors
    • 8.1.1   Attaching a sensitive detector to a volume
    • 8.1.2   Building your sensitive detector with C++ code
  • 8.2   Hits
  • 8.3   Hits digitization and reconstruction
    • 8.3.1   Hits digitization
    • 8.3.2   Hits and digits reconstruction
    • 8.3.3   Examples of reconstructed hit builders
  • 8.4   Detector effects
    • 8.4.1   Energy resolution
    • 8.4.2   Time resolution
    • 8.4.3   Detector measuring time
    • 8.4.4   Detector dead time
    • 8.4.5   Minimum hit energy
  • 8.5   Identifying each sensitive detector copy
  • 8.6   Storing and retrieving hits
    • 8.6.1   Storing and retrieving simulated hits
    • 8.6.2   File format
    • 8.6.3   Storing reconstructed hits
  • 8.7   Hits histograms
• 9   Scoring
  • 9.1   Creating a scorer
  • 9.2   Scorer classes
    • 9.2.1   Scoring in voxelised phantoms
  • 9.3   Compound scorer
    • 9.3.1   Linear Energy Transfer (LET) scorer classes
  • 9.4   Filters
  • 9.5   Scorer printers
  • 9.6   Classifiers
  • 9.7   Multiplying by data
  • 9.8   Multiplying by a distribution
  • 9.9   Convergence testing
  • 9.10   Point detector scorer
    • 9.10.1   Theoretical basis
    • 9.10.2   GAMOS implementation
    • 9.10.3   Variance reduction techniques
    • 9.10.4   Sum scoring results and plot them
• 10   Variance reduction techniques
  • 10.1   Introduction
  • 10.2   Importance sampling
  • 10.3   Geometrical biasing
  • 10.4   Biasing operations
    • 10.4.1   Cross section biasing
    • 10.4.2   Force collision
    • 10.4.3   Uniform bremsstrahlung splitting
    • 10.4.4   Directional bremsstrahlung splitting
    • 10.4.5   Equal weight bremsstrahlung splitting
• 11   Histogramming
  • 11.1   Histogram formats
  • 11.2   Histograms in CSV format
  • 11.3   Histograms in TXT format
  • 11.4   Normalize histograms
  • 11.5   Changing histogram minimum, maximum and number of bins
  • 11.6   Histograms name separator
  • 11.7   Output files name
  • 11.8   Analysing your histograms with ROOT
    • 11.8.1   Printing the histograms in graphics files
    • 11.8.2   Comparing histograms in two files
  • 11.9   Creating your own histogram with C++ code
• 12   Analysis of data output
  • 12.1   Introduction: GAMOS data
  • 12.2   Data users
    • 12.2.1   Behaviour as a function of information object
    • 12.2.2   Behaviour as a function of output format
    • 12.2.3   Selection of data list for a data user
    • 12.2.4   Saving GAMOS data in a ROOT TTree
    • 12.2.5   Filter from data
    • 12.2.6   Classifier by data
    • 12.2.7   Primitive scorer from data
  • 12.3   List of available data
    • 12.3.1   Position data
    • 12.3.2   Direction data
    • 12.3.3   Momentum data
    • 12.3.4   Energy data
    • 12.3.5   Geometrical objects data
    • 12.3.6   Material data
    • 12.3.7   Particle and process data
    • 12.3.8   Secondary tracks data
    • 12.3.9   Ancestor data
    • 12.3.10   Other data
  • 12.4   Output file names
  • 12.5   Merging results from different jobs
    • 12.5.1   Example of Analysing text output files
• 13   Filters
  • 13.1   Introduction
  • 13.2   Simple filters
  • 13.3   Volume filters
  • 13.4   Filters of filters
  • 13.5   Applying filters to a user action
  • 13.6   Checking filters at a user action
  • 13.7   Filtering steps in the future
• 14   Classifiers
  • 14.1   Introduction
  • 14.2   Setting indices to classifiers
  • 14.3   Classifiying on secondary data
• 15   Distributions
  • 15.1   Introduction
  • 15.2   Creating a distribution
  • 15.3   Assigning a GAMOS data
  • 15.4   Reading values from a file
  • 15.5   Numeric distributions
  • 15.6   String distributions
    • 15.6.1   String data distribution
    • 15.6.2   Geometrical biasing distribution
  • 15.7   Ratio of distributions
• 16   Utility user actions
  • 16.1   Counting the number of tracks and events
  • 16.2   Counting the processes
  • 16.3   Shower shape studies
  • 16.4   Killing all tracks
  • 16.5   Table of tracks and steps
  • 16.6   Material budget studies
  • 16.7   Detailed report of where CPU time is spent
  • 16.8   Changing the weight using a distribution
  • 16.9   Copying the weight to the secondary particles
  • 16.10   Stopping run after a certain CPU time
  • 16.11   Visualising only a set of events
  • 16.12   Setting the correlation between the gammas of a radioactive decay chain
  • 16.13   Printing electromagnetic parameters
• 4   Visualization
  • 4.1   3D Geant4 visualization
  • 4.2   2D visualization
• 17   Managing the verbosity
  • 17.1   GAMOS verbosity managers
    • 17.1.1   Controlling GAMOS verbosity by event
  • 17.2   Using a GAMOS verbosity manager in your code
  • 17.3   Creating your own verbosity manager
  • 17.4   Controlling the Geant4 verbosity by event and track
  • 17.5   Dumping the standard output and error in log files
• 18   Nuclear Medicine Detector Applications
  • 18.1   Identifying Compton interactions
    • 18.1.1   Compton studies histograms
    • 18.1.2   Histograms of data about the interactions and the reconstructed hits
    • 18.1.3   Classification of good and bad identification histograms as a function of variable
  • 18.2   Histograms of gammas at sensitive detectors
  • 18.3   Automatic determination of production cuts for a detector
  • 18.4   Automatic determination of user limits for a detector
• 19   PET application
  • 19.1   PET geometry
  • 19.2   PET event classification
  • 19.3   PET histograms: event classification
  • 19.4   PET output for reconstruction
    • 19.4.1   List-mode binary file
    • 19.4.2   Projection data file
  • 19.5   PET histograms: positrons
  • 19.6   Detector histograms: distance between two gammas
• 20   SPECT application
  • 20.1   SPECT event classification
  • 20.2   SPECT histograms: event classification
  • 20.3   SPECT output for reconstruction
• 21   Compton camera application
  • 21.1   Compton camera geometry
  • 21.2   Compton camera Event Classification
  • 21.3   Compton camera histograms: event classification
  • 21.4   Compton camera output for reconstruction
• 22   Image reconstruction utilities
  • 22.1   List-mode to projection data
  • 22.2   Summing projection data files
  • 22.3   Analytic image reconstruction
  • 22.4   Visualization tools
  • 22.5   Stochastic Image Ensemble method
    • 22.5.1   Introduction
    • 22.5.2   Getting Started
    • 22.5.3   Program Parameters and Flags
    • 22.5.4   Analysis
• 23   Radiotherapy application
  • 23.1   Geometrical modules
    • 23.1.1   JAWS module
    • 23.1.2   MLC module
  • 23.2   Using phase spaces
    • 23.2.1   Writing phase spaces
    • 23.2.2   Phase space text file
    • 23.2.3   Phase space histograms
    • 23.2.4   Reading phase spaces
    • 23.2.5   Adding extra information to a phase space
    • 23.2.6   Reusing a particle at a phase space without writing the phase space file
  • 23.3   Optimisation of a linac simulation
    • 23.3.1   Cuts optimisation
    • 23.3.2   Electromagnetic parameters optimisation
    • 23.3.3   Particle splitting
    • 23.3.4   Killing particles at big X/Y
  • 23.4   Scoring dose in phantom
    • 23.4.1   Saving scores and scores squared in binary file
    • 23.4.2   Saving scores and score errors in text file
    • 23.4.3   Saving scores in histograms
  • 23.5   Analysis utilities
    • 23.5.1   Summing phase space files
    • 23.5.2   Making histograms out of a phase space file
    • 23.5.3   Merging ‘sqdose’ files
    • 23.5.4   Merging ‘3ddose’ files
    • 23.5.5   Making histograms out of a ‘sqdose’ file
    • 23.5.6   Automatic determination of production cuts for an accelerator simulation
    • 23.5.7   Automatic determination of production cuts for a dose in a phantom simulation
    • 23.5.8   Automatic determination of user limits for an accelerator simulation
    • 23.5.9   Automatic determination of user limits for a dose in phantom simulation
• 24   Shielding application
  • 24.1   Introduction
  • 24.2   Studying penetration
  • 24.3   Activation studies
    • 24.3.1   Sum activation results and plot them
  • 24.4   Correcting decay time to take into account isotope activity
  • 24.5   Print channel by channel hadronic cross sections
  • 24.6   Counting hadronic cross sections
  • 24.7   Make histograms of secondary particles from the neutron_hp or particle_hp databases
  • 24.8   Print yields of production of secondary particles from charged particles traversing a thick material
  • 24.9   Analysis utilities
    • 24.9.1   Summing scoring results
    • 24.9.2   Summing activation results
• 25   Managing DICOM files
  • 25.1   Managing DICOM CT geometry files
    • 25.1.1   Converting DICOM CT geometry files to GAMOS simulation files
    • 25.1.2   GAMOS CT geometry file format
    • 25.1.3   Reading a DICOM CT geometry file in a GAMOS job
  • 25.2   Managing DICOM CT structure files
    • 25.2.1   Converting a DICOM RTSTRUCT files to GAMOS simulation files
    • 25.2.2   Using files with CT structures in your GAMOS job
    • 25.2.3   Filtering on DICOM structures
  • 25.3   Managing DICOM PET image files
    • 25.3.1   Converting DICOM PET files to GAMOS simulation files
    • 25.3.2   Reading a DICOM PET image file in a GAMOS job
  • 25.4   Managing RT plan data
    • 25.4.1   Converting DICOM RT plan data to GAMOS ASCII format
    • 25.4.2   Using DICOM RT plan data in a GAMOS job
  • 25.5   Managing RTIon plan data
    • 25.5.1   Converting DICOM RTIon plan data to GAMOS ASCII format
    • 25.5.2   Using DICOM RTIon plan data in a GAMOS job
  • 25.6   Visualizing geometry superimposed to DICOM images
  • 25.7   Partial phantom geometries
  • 25.8   Visualizing all types of DICOM files
    • 25.8.1   Visualizing CT images
    • 25.8.2   Visualizing PET images
    • 25.8.3   Visualizing RT structures
    • 25.8.4   Visualizing Doses
    • 25.8.5   Drawing options
  • 25.9   Modifying the material indices of voxels inside a CT structure
  • 25.10   Use simple phantom geometries
• 26   Optimising the CPU time of your application
  • 26.1   Knowing where the time is spent
  • 26.2   Production cuts
  • 26.3   Killing particles of small energy
  • 26.4   Killing particles
  • 26.5   Optimising the particle generation
  • 26.6   Limiting the number of user actions
  • 26.7   Using variance reduction techniques
• Appendix A: Miscellaneous
  • Using parameters
    • Checking the usage of parameters
  • Managing the input data files
  • Random number seeds
    • Setting the initial random number seeds
    • Restoring the initial random number seeds
    • Changing the random engine
  • Sending several jobs in the same machine
  • Identifying touchables
  • Using asterisks to get volume, particle and material names
  • Using particle names
• Appendix B: Extending GAMOS functionality with C++ utilities
  • Converting a Geant4 example into a GAMOS example
  • Creating your plug-in
  • Using a parameter in your C++ code
  • Event classification by interaction types
  • Structure of GAMOS

Indices and tables

• Index
• Module Index
• Search Page