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examples/advanced/hadrontherapy/README
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Text version of the Hadrontherapy README file
=========================================================
Last revsion: G.A.P.Cirrone, November 20010;
Released with the Geant4 9.4 version (December 2011)
Last revsion: F.Romano, 3 November 2012;
Released with the Geant4 9.6 version (December 2012)
------------------------------------------------------------------------------------------------
ADVERTISEMENT: this is the text version of the README file of the 'basic' hadrontherapy,
as it has been released in the official Geant4 9.4 release
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) are supported by the Italian INFN
Hadrontherapy (both basic and full version) is supported by the Italian INFN
Institute in the framework of the MC-INFN Group
A more complete and updated version of this file is published inside the web pages of Hadrontherapy:
http://g4advancedexamples.lngs.infn.it/Examples/hadrontherapy
Please refer to the web-published version to know the last and future developments of hadrontherapy
-------------------------------------------------------------------------------------------------
=========================================================
@@ -26,56 +22,67 @@ Please refer to the web-published version to know the last and future developmen
=========================================================
Code developed by:
G.A.P. Cirrone(a)°, G.Cuttone(a), F.Di Rosa(a), S.E.Mazzaglia(a), F.Romano(a)
R. Calcagno(a), G.A.P. Cirrone(a)*, G.Cuttone(a), F.Romano(a,b)*, A.Varisano(a)
Contributor authors:
P.Kaitaniemi(d), A.Heikkinen(d), G.Danielsen (d)
Past authors:
M.G.Pia(b), S.Guatelli(c), G.Russo(a), M.Russo(a), A.Lechner(e)
F.Di Rosa(a), S.Guatelli(d), A.Lechner(e), S.E.Mazzaglia(a), M.G.Pia(c), 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
(b) Centro Studi e Ricerche e Museo Storico della Fisica E.Fermi, Roma, Italy
(d) Helsinki Institute of Physics, Helsinki, Finland
(c) INFN Section of Genova, Italy
(d) University of Wallongong, Australia
(e) CERN, (CH)
*Corresponding author, email to cirrone@lns.infn.it
*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
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.
It 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.
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.
In the actual version two geometrical configuration are available: the 'passive beam line'
and the 'IAEA Benchmark' geometry. See the paragraph Geometry set-up for more information.
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;
The configuration 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 two macro files are actually provided for the use of hadrontherapy with proton and carbon beams: proton_therapy.mac and ion_therapy.mac.
The proton_therapy.mac permits to run a simulation with the whole passive beam line installed in Catania.
The carbon_therapy.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.
The macro iaea.mac uses an alternative geometry that was created for the IAEA benchmark. It features a geometry with water target, aluminum beam window, and a particle detector behind the target.
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
@@ -88,100 +95,16 @@ A complete guide for the Geant4 installation in different operating systems can
If you have troubles with the Geant4 installation please send an e-mail to us.
SISTEM SET-UP: enviroment variables
A CMakeLists.txt file is provided together with a standard GNUmakefile for compilation.
A standard Geant4 example GNUmakefile is provided
The following section reports the environment variables that are necessary for the run of Hadrontherapy.
#-------------------------------------
# SET UP LINUX GCC
#-------------------------------------
VERSION="geant4-09-03"
# Path to the directory in which you have put data files and CLHEP
LIBPATH=$HOME/Geant4Library
export G4SYSTEM=Linux-g++
# Path to the directory in which you put your Geant4 installation
export G4INSTALL=$HOME/${VERSION}
export G4LIB=$G4INSTALL/lib
export G4WORKDIR=$G4INSTALL/workdir
export G4EXE=$G4WORKDIR/bin/$G4SYSTEM
export CLHEP_BASE_DIR=$LIBPATH/CLHEP2.0.4.5
export G4LEDATA=$LIBPATH/G4EMLOW6.9
export G4LEVELGAMMADATA=$LIBPATH/PhotonEvaporation2.0
export G4NEUTRONHPDATA=$LIBPATH/G4NDL3.13
export G4RADIOACTIVEDATA=$LIBPATH/RadioactiveDecay3.2
export G4ABLADATA=$LIBPATH/G4ABLA3.0
export LD_LIBRARY_PATH=$CLHEP_BASE_DIR/lib:$LD_LIBRARY_PATH
# For the generation .root file directly using the ROOT (if ROOT is
# instaled in you machine)
export G4ANALYSIS_USE_ROOT=1
export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
#-------------------------------------
# SET UP VRML VIEW
#-------------------------------------
export G4VIS_BUILD_VRML_DRIVER=1
export G4VIS_USE_VRML=1
export G4VIS_USE_VRMLFILE=1
export G4VRMLFILE_MAX_FILE_NUM=100
export G4VRMLFILE_VIEWER=vrmlview #if installed
# Add path to your VRML installation
export PATH=$PATH:~/VRML
#-------------------------------------
# SET UP OpenGL o Mesa
#-------------------------------------
export G4VIS_BUILD_OPENGLX_DRIVER=1
export G4VIS_USE_OPENGLX=1
# Add path to your OpenGL installation
#export OGLHOME=/usr/lib
#-------------------------------------
# SET UP DAWN (if installed)
#-------------------------------------
export G4VIS_BUILD_DAWN_DRIVER=1
export G4VIS_BUILD_DOWNFILE_DRIVER=1
export G4VIS_USE_DAWN=1
export G4VIS_USE_DAWNFILE=1
# Add path to your DAWN installation
# export PATH=$PATH:~/dawn_3_86a
# VARIOUS USER INTERFACES
export G4UI_USE_XM=1
export G4UI_USE_TCSH=1
export G4UI_BUILD_QT_SESSION=1
export G4UI_USE_QT=1
# VARIOUS GRPHICAL USER INTERFACES
export G4VIS_BUILD_QT_SESSION=1
export G4VIS_BUILD_OPENGLQT_DRIVER=1
export G4VIS_USE_OPENGLQT=1
# If the QT libraries want be used for the User interfaces than the
# correct path must be addressed
export QTHOME=/usr/lib/qt-3.3
export PATH=$PATH:/usr/lib/qt-3.3/include/
export PATH=$PATH:/usr/lib/qt-3.3/
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 moment the Hadrontherapy include the simulation of the proton beam line for eye-treatments installed at the INFN-LNS facility in Catania. This is a passive beam line and it is simulated in the file PassiveProtonBeamLine.cc.
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.
@@ -189,29 +112,33 @@ 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 "IAEA" for the IAEA benchmark geometry. Both geometries are described below. By default the standard "default" geometry is used.
The water phantom to collect informations
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 the G4ANALYSIS_USE variable is defined and the AIDA interface is activated).
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 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.).
@@ -228,47 +155,51 @@ The elements simulated in the PassiveBeamLine.cc file are:
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).
Geometry for the IAEA benchmark
Simple geometry for benchmark purposes contains water phantom (thickness can be set using a macro command), an aluminum beam window and Plexi-glass. Behind the phantom we have a detector that records outcoming particles. The IAEA geometry can be activated by using the command:
/geometrySetup/selectGeometry IAEA
Example IAEA benchmark run can be done as follows:
run: Hadrontherapy macro/iaea.mac
analysis: root RootScripts/iaeaBenchmark/fragmentEnergy.C
PHYSICS PROCESSES AND PHYSICS MODELS IMPLEMENTATION
Physics models in Hadrontherapy, following the Geant4 organisation, can be definided using three different approaches:
Physics models in Hadrontherapy, following the Geant4 organisation, can be definided using four different approaches:
Activating one of the 'Reference Physics Lists' that are already prepared by the Geant4 Collaboration and are contained in the $G4INSTALL/source/physics_lists/lists folderlist.
The 'Reference Physics Lists' can be activated setting a specific enviroment variable to the name of the physics. For example if the QGSP_BIC Reference Physics Lists must be activated the User must set export PHYSLIST=QGSP_BIC (or setenv PHYSLIST QGSP_BIC). A 'Reference Physics Lists' contains all the physics process necessary to a particle transport.
If the User set the PHYSLIST variable, Hadrontherapy will start with the defaultMacroWithReferencePhysicsList.mac macro. See this macro file for more details.
Activating the 'Builders' already prepared by the Geant4 Collaboration and contained in the $G4INSTALL/source/physics_lists/builder folder.
Each builder is specific of a given model. There are builders for the electromagnetic processes, for the hadronic one, etc.
If the PHYSLIST variable is not defined Hadrontherapy starts with the defaultMacro.mac where the single builders are activated for the various processes of interest.
Each builder is activated with the /Physics/addPhysics <nome builder> command.
Defining a specific 'local' physics list. In Hadrontherapy two local physics list are defined (LocalINCLIonIonInelasticPhysic.cc and LocalIonIonInelasticPhysic.cc) where models for the ion-ion interactions are activated.
'Local' physics can be activated using the /Physics/addPhysics <nome builder> command (see the defaultMacro.mac to se an example).
****** SUGGESTED PHYSICS *********
AT MOMENT, IF ACCURATE RESULTS ARE NEDED, WE STRONGLY RECOMMEND:
1. The use of the macro 'hadron_therapy.mac', or
2. the QGSP_BIC_EMY Reference Physics Lists (define the PHYSLIST eviroment variable):
export PHYSLIST=QGSP_BIC_EMY
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 end user to change phantom and detector geometries and voxelization, some interactive commands have been provided. All parameters are mandatory, except those inside square brackets.
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
@@ -281,12 +212,9 @@ 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:
Command synopsis:
/changeDetector/size <dimX> <dimY> <dimZ> <[unit]>
/changeDetector/size <dimX> <dimY> <dimZ> <[unit]>
/changeDetector/voxelSize <dimX> <dimY> <dimZ> <[unit]>
/changeDetector/displacement <dispX> <dispY> <dispZ> <[unit]>
@@ -333,6 +261,7 @@ Obviously all the previous sizes must be set in order to maintain the detector f
/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).
@@ -348,22 +277,19 @@ 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 give them to the particle gun, for example issuing the macro commands:
/gun/particle ion
/gun/ion <Z> <A> <[charge]>
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
# and for C12 ion:
/gun/particle ion
/gun/ion 6 12 6
/parameter/getstopping G4_H 0.001 150 15 C12[0.0]
GEANT4 GENERAL PARTICLE SOURCE
# Value inside square brackets is the excitation energy of the ion (ground state in this case).
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.
HOW RUN HADRONTHERAPY
@@ -380,17 +306,7 @@ Hadrontherapy can be launched using a macro file:
> $G4WORDIR/bin/Linux-g++/Hadrontherapy macroFile.mac
The defaultMacro.mac file is contained in the main directory of Hadrontherapy and is automatically readed in case the user launch the executable without a parameter. A big number of other macro are inside the /macro folder.
Example use of command based scoring
In the IAEA geometry it is possible to collect the energy deposition data using the Geant4 command based scoring feature. This allows the users to define scorers interactively in the user interface without writing a single line of C++. Below is listed an example usage of command based scoring:
/score/create/boxMesh boxMesh_1
#Box size is the radius of the box ie 20x20x20 gives 40x40x40 outer dimensions
/score/mesh/boxSize 13.95 16. 16. cm
/score/mesh/translate/xyz 69 0.0 0.0 cm
/score/mesh/nBin 400 1 1 # 400 bins in x-direction, 1 in y and z directions
The defaultMacro.mac file is contained in the main directory of Hadrontherapy and is automatically read in case the user launch the executable without a parameter. Several macro files are inside the /macro folder.
SIMULATION OUTPUT
@@ -429,17 +345,18 @@ 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.
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.
Modules for LET and RBE (Relative Biological Effectiveness) calculation. The Catania Group in Collaboration with the Turin one is working on this.
Hadrontherapy will permit the simulation of a 'basic' experiment usefull in hadrontherapy applications. User will be able to simulate thin/thick target configuration to calculate quantities like double differential cross sections of secondaries produces, or fluence and yelds of primary and secondaries in a thick block. This work is maily discussed with P. Kaitaniemi and the Group from the Helsinki Institute of Physics.
What is requested from Users
Dicom interface
Please contact cirrone@lns.infn.it for more details or suggestions and feedbacks on this document
- Modules for LET and RBE (Relative Biological Effectiveness) calculation. The Catania Group in Collaboration with the Turin one is working on this. Both the two modules are already implemented (in a preliminary version) in an internal version of Hadrontherapy and can be provided, if requested. Please, contact us.
What is requested from Users:
- Dicom interface
Please contact cirrone@lns.infn.it or francesco.romano@lns.infn.it for more details or suggestions and feedbacks on this document.