
	     =========================================================
                     Text version of the Hadrontherapy README file
             =========================================================

Last revision: F.Romano, 7 November 2013;
Released with the Geant4 10.0 version (December 2013)

------------------------------------------------------------------------------------------------
ADVERTISEMENT: this is the text version of the README file of the 'basic' hadrontherapy, 
as it has been released in the official Geant4 9.6 release

Visit the Hadrontherapy web site (http://www.lns.infn.it/link/Hadrontherapy) to request 
the complete version of this program, together with its documentation;
Hadrontherapy (both basic and full version) is supported by the Italian INFN
Institute in the framework of the MC-INFN Group

-------------------------------------------------------------------------------------------------

             =========================================================
                                HADRONTHERAPY
             =========================================================

 Code developed by:
 R. Calcagno(a), G.A.P. Cirrone(a)*, G.Cuttone(a), L. Pandola(a), F.Romano(a)*, A.Varisano(a)
 
 Past authors:
 F.Di Rosa(a), S.Guatelli(c), A.Lechner(d), S.E.Mazzaglia(a),  M.G.Pia(b), G.Russo(a), M.Russo(a)

 (a) Laboratori Nazionali del Sud 
     of the INFN, Catania, Italy

 (b) INFN Section of Genova, Italy
 
 (c) University of Wallongong, Australia

 (d) CERN, (CH)

  *Corresponding authors, email to: cirrone@lns.infn.it, francesco.romano@lns.infn.it
-------------------------------------------------------------------------------------------------
HADRONTHERAPY:
WHAT IT IS, WHAT IT DOES AND WHAT IT WILL PROVIDE
Hadrontherapy is a Geant4-based application specifically developed to address typical needs related to the proton and ion therapy. 
Its first release was in 2004. At that time Hadrontherapy was only capable to simulate a well specified proton therapy facility: the passive transport beam line installed at  Laboratori Nazionali del Sud (INFN) in Catania, Italy.

Today Hadrontontherapy, except that it is in continuous development, is more flexible and show many additional capabilities as respect the past.
Its geometrical set-up, for example, is now completely interchangeable permitting a simple switch between different geometrical configurations, which all share the same phantom (sensible detector) with the related features.
It is possible to do a simulation of a generic proton/ion transport beam line. In this new release, a module for dose average LET computations has been also included.
Deprecated ReadOutGeometry has been replaced by the use of Parallel World.

The configurations are:

	- Passive proton beam line, which is installed at the LNS-INFN facility in Catania for eye tumor treatment with protons at 62 MeV. It is simulated in PassiveProtonBeamLine.cc;

	- Passive carbon beam line, which is the simulation of the transport beam line at LNS-INFN of Catania for experiments with carbon ion beams. It is simulated in PassiveCarbonBeamLine.cc;
	
	both in PassiveProtonBeamLine.cc in PassiveCarbonBeamLine.cc the user can change the geometrical characteristics of beam line elements.
	Alternatively the user can use the macro file.


Folder structure of Hadrontherapy


Hadrontherapy distribution contain different sub-folders:

\src: where source .cc files are stored

\include: where header .hh files are stored

\macro: where a set of ready-to-use macro files are provided

\experimentalData: in this director a set of reference (both experimental and analithycal) data are stored. These data are then used to perform a direct comparison with simulation results that are stored in the simulationResults folder. Data stored are better described in the README file contained inside.

\SimulationOutputs: when one of the .mac file contained in the macro folder is used, simulation results are directly stored in this directory.

\RootScripts: if the ROOT program is installed the User can use the scripts contained in this directory to compare directly results from the his/her simulation with reference data provided inside the experimentalData folder.

Currently this folders structure is in development and reference data as well as ROOT scripts will be added in the meanwhile new features and capabilities will be added. Moreover some ROOT script can be missed. Apologize for this and contact author if you need more information, clarification or useful discussion. 

Description of the \macro folder

In the example directory, inside the "macro" folder different macro files are provided. In particular two macro files are related to the different beam lines with proton and carbon beams: hadron_therapy.mac and carbon_beamline.mac.
The hadron_therapy.mac permits to run a simulation with the whole proton passive beam line installed in Catania.
The carbon_beamline.mac excludes all the elements (moving the origin of the ion beam close to the water phantom) and reproduce a simple passive beam line for the use with carbon beams.

DOWNLOAD AND INSTALLATION

Hadrontherapy source code is actually released inside the official distribution of the Geant4 toolkit in the $G4INSTALL/examples/AdvancedExamples folder.

To run Hadrontherapy you must first install the Geant4 package. Once Geant4 is installed the example must be first compiled (with the command gmake inside the
../Hadrontherapy folder). When compilation is completed the program can be executed.

A complete guide for the Geant4 installation in different operating systems can be found inside the official installation Geant4 pages.

If you have troubles with the Geant4 installation please send an e-mail to us.

A CMakeLists.txt file is provided together with a standard GNUmakefile for compilation.                                                         


GEOMETRICAL SET-UP

The idea of Hadrontherapy is to provide a tool useful for Users interested in the field of proton and ion therapy. These can include the simple calculation of dose distribution curves in water or other materials, the derivation of important transport parameters (stopping powers, ranges, etc.) in different geometrical set-ups and for different materials, up to the complete simulation of a real transport beam line for therapy.

The main component of the simulation is the phantom, a box that can be filled with different material and where the score of different information (at moment  the dose deposited in voxels) can be performed. A more complete description of the phantom is given in the next subsection.

At the moment the Hadrontherapy example include the simulation of passive beam lines.
In the next future an ActiveProtonBeamLine.cc will be provided for the simulation of the active scanning treatment modality.
Moreover the possibility to add a very simple set-up (a beam, a phantom where collect the informations and some simple component) will be also provided.

All these configuration will be setted by macro commands.

There is also a facility that allows the user to make a choice between alternative geometry set-ups. This can be done by using command:
/geometrySetup/selectGeometry <name>
where <name> is either "default" for the standard hadrontherapy geometry or "Carbon" for INFN-LNS transport beam line, 
normally used for interdisciplinary researches at LNS-INFN in Catania with carbon and other ion beams.

At the end of the beam line a phantom (a box of uniform material) is reproduced. Inside it, a user-defined region is divided (via the ROGeomtry classes of Geant4) in cubic and identical voxels. The voxels size can be varied as well as the voxelized region.
At the end of a simulation run, the dose deposited by primaries and secondaries in each voxel is collected. This information is available as an .out file or as a .root (if activated). 

The default sizes of the active voxelized region are 40x40x40 mm and actually the default voxel configuration is 200 x 1 x 1, which means 200 slices with 0.2 mm of thickness.
Of course this default can be modified in order to obtain, for example, a matrix of 80x80x80 cubic voxels each with a lateral dimension of 0.5 mm.

As concern the cut and stepMax values, the default configuration implies a cut value of 0.01 mm in the whole  world (use the command /physic/setCuts <length>  in order to set the cut for all, and the command /physic/setDetectorCuts <length> to set the cut for the detector only)  and a stepMax of 0.01 mm just in the phantom (use the command /Step/waterPhantomStepMax 0.01 mm).
In any case it is strongly recommended to use a stepMax value not bigger than 5% of the dose slice thickness.

The Proton passive beam line class file

The following is the description of the elements of the passive proton beam line of the Laboratori Nazionali del Sud in Catania (I). This line is completely simulated inside this class.

The main elements are:

    * The SCATTERING SYSTEM: to transversally enlarge the original beam
    * The COLLIMATORS: placed along the beam line to collimate the beam;
    * The RANGE SHIFTERS: to decrease the energy of the primary proton beam to a specific value;
    * The MODULATOR WHEEL: to modulate the energy of the primary and mono-energetic beam in to a wide spectrum. The energy modulation is necessary to   
      homogeneously irradiate a tumour volume that can extends in depth up to 20 mm;
    * The MONITOR CHAMBERS: very thin ionisation chamber that permit the dose monitoring during the patient irradiation;
    * The MOPI detector: microstrips, air free detector utilised for the check of the beam symmetry during the treatment;
    * The PATIENT COLLIMATOR: a brass, tumour-shaped collimator able to  confine the proton irradiation field in order to irradiate just the tumour 
      mass in the transverse direction;

The user has the possibility to vary, via messenger, almost all the geometrical characteristics of the beam line elements (i.e. their position along the beam line, their thickness, etc.).

The elements simulated in the PassiveBeamLine.cc file are:

1. A scattering system, to spread geometrically the beam;

2. A system of collimators, to avoid the scattering radiation;

3. A modulation system that spreads the beam in energy and produces the so-called spread out Bragg peak; It is constituted by a rotating wheel of different thicknesses. The wheel  rotates around its axis (parallel to the proton beam axis) and its movement can be obtained by means of a messenger between runs.

4. A set of monitor chambers (special transmission ionisation chambers used to control the particle flux during the irradiation);

5. A final long collimator and a patient collimator defining the final shape of the beam before reaching the patient.

6. A water phantom: it is a box of water where the dose deposit is calculated. The use of  the water phantom is required by the international protocol on the measure of dose in the case of proton and ion beams (IAEA 398, 2000).         

PHYSICS PROCESSES AND PHYSICS MODELS IMPLEMENTATION

 Physics models in Hadrontherapy, following the Geant4 organisation, can be definided using four different approaches:

A particular care is addressed to the simulation of the physic processes.
Three different approaches can be used for the choose of the physic models.

Approach 1:
Using the macro command:
/physic/addPhysics/<physics List name>.

In this case the models (for electromagnetic, hadronic elastic and hadronic inelastic) can be
activated directly calling the name of the Physics Lists that are available inside the
Geant4 kernel in the directory:

$G4INSTALL/source/physics_lists/builders/include

An example of the use of the Physics List can be found in the macro files:
hadron_therapy.mac and carbon_beamline.mac

Approach 2:
A set of built-in physic models are also contained inside the Hadrontherapy directory. These
are called Local*.cc and Local*.hh and can be activated using the macro command:
/physic/addPhysics/<name>.

NOTE: we do not recommend the use of local physics lists while we recommend the use of the Physics Lists or of the Reference Physics Lists (Approach 1 or 3)

Approach 3:
We developed this approach in order to simplify the choice of the physic models to
be used in the application.
With this approach the user must only insert a command line in his/her .mac file using the: /physics/addPackage <PACKAGE_NAME>
This permits to switch-on an already build physic package.
Various packages are already present in the Geant4 tree: they are in the directory: geant4/source/physics_lists/lists/include

Approach 4:
Directly call a reference physics list by setting the variable PHYSLIST. Ex.:
 export PHYSLIST=QGSP_BIC_EMY 
and the export QGSP_BIC_EMY refernce physics list will be setted


INTERACTIVE COMMANDS
How to change Phantom and Detector geometries

In order to let the user to change phantom and detector geometries and voxelization, some interactive commands have been provided. All parameters are mandatory, except those inside square brackets.

Detector geometry 

The user can change:

(1) The detector (box) size.
 
(2) The voxels sizes. Changing this parameters, and/or the detector sizes, user should choose values in order to be divisors of the detector correspondent sizes.
For both above commands, zero or negative values mean << don't change it >>

(3) The displacement between the phantom and the detector.  Displacement parameters refer to the lower left corner of the detector respect to that of the phantom, by the point of view of the beam. In this case zero or positive values are allowed, while the negatives ones mean: << don't change it>>.

Command synopsis: 

/changeDetector/size <dimX> <dimY> <dimZ> <[unit]> 
/changeDetector/voxelSize <dimX> <dimY> <dimZ> <[unit]> 
/changeDetector/displacement <dispX> <dispY> <dispZ> <[unit]> 

Default size values are 4x4x4 cm for the detector, 0.2x40x40 mm for any voxel and 0x18x18 cm
for the displacement.    
where the X dimension is that along the beam direction

Phantom geometry

(1) The phantom size. As usually, zero or negatives values mean: <<don't change it>>.
(2) The phantom position respect to the world. In this case specified values refer to the three components of the position of the phantom's center respect to the world's.

Command synopsis:

/changePhantom/size <dimX> <dimY> <dimZ> <[unit]> # 40 40 40 cm
/changePhantom/position <posX> <posY> <posZ> <[unit]> # 20 0 0 cm

All   these    commands    must be   followed   by the  command  /changePhantom/update
in order to check and eventually apply changes to the real geometry.
Moreover  they  must   be    issued  between   runs  (so   where you   want but   after  the /run/initialize initialization command, or the G4State_Idle Geant4 state machine).
Obviously all the previous sizes must be set in order to maintain the detector fully inside the phantom, otherwise system complains.

 Some examples follow:

/changeDetector/size 40 0 0 cm 
# Will extend detector X size to cover in full the phantom X size   

/changeDetector/size 0 4.5 0 cm
# Will extend the Y size to 4.5 cm (note that voxel size Y is automatically
#  rounded to 4.5 cm because the default value along Y is 4 cm)
/changePhantom/update
# Remember to always update the geometry before the beamOn command!!

/changeDetector/size 0 8 0 cm
# Will extend the Y size to 8 cm. In this case voxel size Y doesn't change, but 
# the number of voxel along Y doubles.
/changePhantom/update

/changeDetector/voxelSize 100 0 0 um 
# 100 um should be a divisor of detector size X
# Will change only slabs X size to 100 um, without affecting the other.
/changePhantom/update

/changeDetector/displacement 0 0 0 # default unit mm
# Will place the detector in the left lower corner (from the point of view of the beam) of #the  phantom.
/changePhantom/update

Stopping powers calculation

It is possible for the end-user to calculate, via macro command, stopping powers only for those materials inserted into G4NistMaterialBuilder class (about 300).
To get stopping powers user must provide this command line on the idle interactive terminal (or into a macro file) :

/parameter/getstopping <G4_material> <Emin> <Emax> <nPoints> <[particle]> <[output_filename]>

All parameters are mandatory except those inside square brackets [].
Default values for parameters inside square brackets are respectively proton and standard output (usually the user console terminal).

Parameters are respectively:

The material (NIST) name (something like G4_..., the complete list of elements and materials is available into the G4NistMaterialBuilder class and can be printed  to the terminal screen via the macro command: /parameter/nist )
Kinetic energy range in MeV and the number of data points to be retrieved (in a logarithmically uniform space)
The particle name (proton, e+, e-, He3, neutron,... a full list can be gotten via the macro command: /particle/list).
 Only for ions, user must firstly select the particles (Z and A).
The output filename: if users leave this blank then the standard output is used.

Below is an example in order to calculate the stopping power for alphas into Hydrogen between 1 keV to 150 MeV for 15 points:

/parameter/getstopping G4_H 0.001 150 15 alpha 


GEANT4 GENERAL PARTICLE SOURCE

The General Particle Source (GPS, G4 class name: G4GeneralParticleSource) is used since this versione of Hadrontherapy: it enables the user to use standard energy, angular and spatial distributions. The GPS includes also methods to bias the sampling distribution.

The G4GeneralParticleSource can be utilised by typing commands from the /gps command directory, or include the /gps commands in a g4macro file.


LET calculation

Hadrontherapy application simulates and calculates the averaged dose LET.
At run time, data needed to calculate LET are collected. At the end of simulation, LET mean values are calculated and stored into a file.

The Let.out file will be produced at the end of a run, where you can
find the dose average LET for each tracked particles (both primary and
secondary ones) and the total mean LET. 
The file is structured as follows:
	- The first three columns contains the voxel indexes (first index "i" refers to the beam direction);
	- The fourth and fifth columns contain respectively total mean dose LET and primary mean dose LET;
	- The rest of columns contain LET Dose for each single ion (whose name is in the top row of the file).

To activate the LET computation (HadrontherapyLet.cc), you have to execute
the following command:

/analysis/computeLet



SIMULATION OUTPUT

Store results in an ASCII file

A .out ASCII file is generated at the end of each run, Dose.out is its default name that can be changed in the HadrontherapyMatrix.cc file.
The file contains four columns; the first three columns represent the voxel indexes (that univocally identify the voxel volume), while the last column represents the dose deposited in that given voxel.
Alternatively, user can force store of data to a given filename, after any BeamOn command and before the program end, by the macro command /analysis/writeDoseFile <myfile.out>.

Moreover, if the macro command /analysis/secondary <true> is given, before the BeamOn command, ordinated dose and fluence, for every secondary produced, is added to the file.
If the macro command /analysis/computeLet is given, an the ascii file Let.out is written, with the dose average LET computations.

User must take care that any change of the phantom geometry will clear all dose data.

Setting the name of the ROOT output file

By default the name of the ROOT output file is DoseDistribution.root. The name of the file can be set by using the macro command: analysis/setAnalysisFile <filename>

It is also possible to create multiple new output files in the same simulation session. For example:

/beam/energy/meanEnergy 4800 MeV
/analysis/setAnalysisFile firstRun.root
/run/beamOn 1000
/analysis/writeDoseFile firstRun.out # this will write both the .root and the .out file!

/beam/energy/meanEnergy 3000 MeV
/analysis/setAnalysisFile secondRun.root # this
/run/beamOn 1000
/analysis/writeDoseFile secondRun.out

Use of the ROOT analysis

It is possible to use ROOT data analysis package directly for the production of output files.
In the last version, anyway, this functionality must be implemented by User. This can be accomplished by setting an ad-hoc environment variable (i.e. G4ANALYSIS_USE_ROOT) to 1, adding in the code lines to create outputs with the ROOT libraries and recompiling the application.
In this case you must have the ROOT framework installed in your machine.

FUTURE CHALLENGES AND USERS' REQUESTS

This is a list of future components that will be added in Hadrontherapy and of main Users requests that we hope to fulfill in the next future.

What is in progress:

- A module for the simulation of an active beam line will be provided.
The Korean Group of the Proton therapy center, National Cancer Center is developing this.

- A module for the RBE (Relative Biological Effectiveness) calculation will be also delivered. The Catania Group in Collaboration with the Turin one is working on this. This module is already implemented (in a preliminary version) in an internal version of Hadrontherapy and can be provided, if requested. Please, contact us.

Please contact cirrone@lns.infn.it or francesco.romano@lns.infn.it for more details or suggestions and feedbacks on this document.


