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 		      Geant4 - Brachytherapy example
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                             README
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The brachytherapy example is currently maintained and upgraded by Susanna Guatelli (1), with the support of
Pablo Cirrone(2), Luciano Pandola (3), Dean Cutajar (1) and Stuart P. George (1)

1. Centre For Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia.
2. LNS, INFN, Catania, Italy.
3. LNGS, INFN, Gran Sasso, Italy
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Contact: susanna@uow.edu.au
         geant4-advanced-examples@cern.ch
        
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List of authors: 
S. Agostinelli, F. Foppiano, S. Garelli, S. Guatelli, M. G. Pia, M. Tropeano

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----> Introduction.                                                     
                                                                       
Brachytherapy example simulates  the energy deposit in a water phantom, produced by: 
1) Iridium source (endocavitary brachytherapy).                         
2) Iodium  source (interstitial brachytherapy).                         
3) Leipzig Applicator (superficial brachytherapy).   

In particular in this example it is shown how to:
- model a radioactive source  in terms of radiation field and geometry
- model the radiation field with the General Particle Source   
- calculate the energy deposition in a phantom by means of the G4 scoring mesh
- define the physics by means of a Geant4 Modular Physics List
- switch different physics approaches to model electromagnetic physics
- save results in an analysis ROOT file using the Geant4 analysis component.               

The example can be executed in multithreading mode

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----> 1.Experimental set-up.                                            

The default source is an Ir-131 source set in the center of the phantom.
The phantom is a box with size 30 cm. The phantom is set in the World volume filled 
with air.



The primary radiation field is defined by means of the GeneralParticleSource                           
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----> 2.SET-UP 
                                          
A standard Geant4 example CMakeLists.txt is provided.                   

Setup for analysis:
By default, the example has no analysis component. 

To compile and use the application with the analysis on, build the example with the following command:
cmake -DWITH_ANALYSIS_USE=ON -DGeant4_DIR=/path/to/Geant4_installation /path/to/brachytherapy_example                                                     
          
The installation of ROOT is required (http://root.cern.ch/drupal/).

macro.C and plot_primary.C are provided to plot the results of the simulation, contained
in the brachytherapy.root file. 

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----> 3.How to run the example.                                         

- Batch mode:
  $G4WORKDIR/bin/Linux-g++/Brachy IridiumSourceMacro.mac                
  $G4WORKDIR/bin/Linux-g++/Brachy IodiumSourceMacro.mac       
  $G4WORKDIR/bin/Linux-g++/Brachy LeipzigSourceMacro.mac  
                                                                        
- Interative mode:                                                      
  3) $G4WORKDIR/bin/Linux-g++/Brachy
     VisualisationMacro.mac is loaded automatically.         
                                                                         
* How to change the absorber material of the phantom:                                                                 
idle>/phantom/selectMaterial  materialName

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----> 4. Primary radiation Field

The radiation field is defined with the General Particle Source.

Two alternative options are offered:
1) Define gamma as primary radiation field. The gamma are originated from the radioactive core.
This radiation field is defined in:
iodine_source_primary.mac and iridium_source_primary.mac

2) Model the radioactive Decay. The primary particle is the radionuclide.
This option is modelled in iodine_decay.mac and iridium_decay.mac

The GPS macros are executed in IridiumSourceMacro.mac, IodiumSourceMacro.mac, LeipzigSourceMacro.mac
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----> 5. Scoring mesh

The scoring mesh is used to calculate the energy deposition in the voxels of the phantom,
integrated over the whole run. The scoring mesh is defined in the input macro file (see IridiumSourceMacro.mac for example).
The user can change the default output format of the scoring in the class BrachyUserScoreWriter.
                                                                         
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----> 6. Simulation output                                               

The output is:

- ASCII file EnergyDeposition.out, with xx (mm), yy(mm), zz(mm), and energy deposition (keV), in the phantom.
  By default:
  EnergyDeposition_iodine.out contains the Edep when Iodine source is selected
  EnergyDeposition_iridium.out contains the Edep when Iridium source is selected
  EnergyDeposition_Leipzig.out contains the Edep when the Iridium source with Leipzig applicator is selected

- brachytherapy.root, containing 
  - an ntuple with the 3D energy deposition in the phantom. The macro macro.C is provided as example 
    to open brachytherapy.root in ROOT interactive session and to plot the results of the simulation. 
    The ROOT file will be created if the example is built with the WITH_ANALYSIS_USE=ON option (see section 2).                   
  - 1D histogram withe the plot of energy spectrum of gamma emitted by the radioactive decay when the Ir or I decay is modelled
   (see section 4). plot_primary.C is provided as example to open brachytherapy.root and to plot the energy    spectra                                                                

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----> 7.Visualisation                                                     

a macro is provided ad example of visualisation:  VisualisationMacro.mac 


