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This commit is contained in:
Gabriele Cosmo
2018-12-07 15:15:39 +01:00
parent 6aa23be517
commit db49709b53
11370 changed files with 187480 additions and 160142 deletions
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examples/advanced/iort_therapy/CMakeLists.txt
+24 -29
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@@ -3,16 +3,11 @@
cmake_minimum_required(VERSION 2.6 FATAL_ERROR)
project(iort_therapy)
#----------------------------------------------------------------------------
# Find Geant4 package, activating all available UI and Vis drivers by default
# You can set WITH_GEANT4_UIVIS to OFF via the command line or ccmake/cmake-gui
# to build a batch mode only executable
#
option(WITH_GEANT4_UIVIS "Build example with Geant4 UI and Vis drivers" ON)
if(WITH_GEANT4_UIVIS)
find_package(Geant4 REQUIRED ui_all vis_all)
else()
find_package(Geant4 REQUIRED)
option(WITH_GEANT4_UIVIS "Build example with Geant4 UI and Vis drivers" ON)
if(WITH_GEANT4_UIVIS)
find_package(Geant4 REQUIRED ui_all vis_all)
else()
find_package(Geant4 REQUIRED)
endif()
#----------------------------------------------------------------------------
@@ -23,19 +18,19 @@ include(${Geant4_USE_FILE})
#----------------------------------------------------------------------------
# Find ROOT (optional package)
#
find_package(ROOT QUIET)
if(ROOT_FOUND)
message(STATUS "G4 Examples: ROOT found. --> iort_therapy example with ROOT plotter enabled.")
# Uncomment this line if suitable (some customization may be needed)
add_definitions(-DG4ANALYSIS_USE_ROOT)
include_directories(${PROJECT_SOURCE_DIR}/include
${Geant4_INCLUDE_DIR}
${ROOT_INCLUDE_DIRS})
else()
message(STATUS "G4 Examples: ROOT not found. --> iort_therapy example with ROOT plotter disabled.")
include_directories(${PROJECT_SOURCE_DIR}/include
#find_package(ROOT QUIET)
#if(ROOT_FOUND)
# message(STATUS "G4 Examples: ROOT found. --> iort_therapy example with ROOT plotter enabled.")
# # Uncomment this line if suitable (some customization may be needed)
# add_definitions(-DG4ANALYSIS_USE_ROOT)
# include_directories(${PROJECT_SOURCE_DIR}/include
# ${Geant4_INCLUDE_DIR}
# ${ROOT_INCLUDE_DIRS})
#else()
#message(STATUS "G4 Examples: ROOT not found. --> iort_therapy example with ROOT plotter disabled.")
include_directories(${PROJECT_SOURCE_DIR}/include
${Geant4_INCLUDE_DIR})
endif()
#endif()
#----------------------------------------------------------------------------
# Locate sources and headers for this project
@@ -47,11 +42,12 @@ file(GLOB headers ${PROJECT_SOURCE_DIR}/include/*.hh)
# Add the executable, and link it to the Geant4 libraries
#
add_executable(iort_therapy iort_therapy.cc ${sources} ${headers})
if(ROOT_FOUND)
target_link_libraries(iort_therapy ${Geant4_LIBRARIES} ${ROOT_LIBRARIES})
else()
target_link_libraries(iort_therapy ${Geant4_LIBRARIES})
endif()
#if(ROOT_FOUND)
# target_link_libraries(iort_therapy ${Geant4_LIBRARIES} ${ROOT_LIBRARIES})
#else()
target_link_libraries(iort_therapy ${Geant4_LIBRARIES})
#endif()
#----------------------------------------------------------------------------
# Copy all scripts to the build directory, i.e. the directory in which we
@@ -59,8 +55,7 @@ endif()
# relies on these scripts being in the current working directory.
#
set(iort_therapy_SCRIPTS
batch.mac defaultMacro.mac defaultMacroWithReferencePhysicsList.mac macro/GUIPersonalisation.mac
)
batch.mac defaultMacro.mac)
foreach(_script ${iort_therapy_SCRIPTS})
configure_file(
examples/advanced/iort_therapy/GNUmakefile
-1
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@@ -1,4 +1,3 @@
# $Id: GNUmakefile 68009 2013-03-13 11:31:34Z gcosmo $
# --------------------------------------------------------------
# GNUmakefile for examples module. Gabriele Cosmo, 06/04/98.
# --------------------------------------------------------------
examples/advanced/iort_therapy/macro/GUIPersonalisation.mac → examples/advanced/iort_therapy/GUIPersonalisation.mac
View File
examples/advanced/iort_therapy/History
+30
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@@ -7,6 +7,36 @@ carlo.casarino@polooncologicocefalu.it
History file of the IORT application
====================================================
13.11.2018 - G. Cosmo tag iort_therapy-V10-04-06
IORTDetectorConstruction: fixed initialisation setting of inner
radius also for "DiscoIORT0" component.
12.11.2018 - G. Cosmo tag iort_therapy-V10-04-05
IORTDetectorConstruction: fixed initialisation setting of inner
radius for "DiscoIORT1" component.
09.11.2018 - G. Cosmo tag iort_therapy-V10-04-04
IORTDetectorConstruction: fixed typos in printout.
18.09.2018 - S. Guatelli tag iort_therapy-V10-04-03
unused variable deleted
17.09.2018 - S. Guatelli tag iort_therapy-V10-04-02
CMakeList.txt updated
17.09.2018 - S. Guatelli tag iort_therapy-V10-04-01
delete macro directory.
12.09.2018 - S. Guatelli tag iort_therapy-V10-04-00
removed RO geometry together with Hit class. Scoring mesh included.
G4_UI_USE and G4_VIS_USE removed.
How to delete the geometry of the disk has been changed (bug eliminated).
Analysis class deleted (no analysis directly connected with the IORT example)
G4Decay and IORTMatrix deleted as they are not needed.
Protontherapy removed as it is out of the scope.
G4SystemOfUnits.hh included
README updated accordingly to changes.
28.11.2017 - B.Morgan tag iort_therapy-V10-03-01
Replace ROOT_INCLUDE_DIR with ROOT_INCLUDE_DIRS
examples/advanced/iort_therapy/README
+10 -112
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@@ -3,16 +3,6 @@
Text version of the iort_therapy README file
=========================================================
Last revision: C.Casarino, October 2014;
Released with the Geant4 10.0 version (December 2013)
=========================================================
iort_therapy
=========================================================
Main Authors:
G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
@@ -30,7 +20,7 @@ Released with the Geant4 10.0 version (December 2013)
(d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
(e) University of Wallongong, Australia
(e) University of Wollongong, Australia
*Corresponding author, email to carlo.casarino@polooncologicocefalu.it
@@ -53,8 +43,6 @@ iort_therapy distribution contain these 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
Currently this folders structure is in development and in the meanwhile new features and capabilities will be added.
@@ -70,9 +58,6 @@ A CMakeLists.txt file is provided together with a standard GNUmakefile for compi
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.
GEOMETRICAL SET-UP
@@ -105,8 +90,6 @@ The applicator consists of a cylindrical PMMA tube (the final collimator). In th
IortBeamLineJunctions();
IortBeamLineFinalCollimator();
The user has now the possibility to vary, via messenger, the inner and outer radius of the final collimator.
@@ -118,7 +101,7 @@ At the end of a simulation run the dose deposited by primaries and secondaries i
THE DETECTOR
The default sizes of the sensible voxelized region (detector) are 7cmx15cmx15cm and actually the default voxel configuration is 0.5mm x 0.5mm x 0.5mm, which means a matrix of 140x300x300 cubic voxels each with a lateral dimension of 0.5 mm. Of course this default can be modified.
A scoring mesh is set to score the dose in the phantom (see defaultMacro.mac)
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.
@@ -127,38 +110,17 @@ In any case it is strongly recommended to use a stepMax value not bigger than 5%
SHIELDING DISC
Inside the detector is positioned a double layered shielding disc. For both layers it is possible via macro to change the outer and inner radius, the thickness, the position along the beam axis and the material.
ADVERTISEMENT: to delete the disc out the entire geometry the relative macro command must be used!!
ADVERTISEMENT: to re-insert the disc in the entire geometry the relative macro command must be used!!
NOTE 1: to delete the disc out the entire geometry the relative macro command must be used!!
NOTE 2: to re-insert the disc in the entire geometry the relative macro command must be used!!
PHYSICS PROCESSES AND PHYSICS MODELS IMPLEMENTATION
Physics models in iort_therapy, following the Geant4 organization, can be defined using two 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 environment 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, iort_therapy 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 iort_therapy 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.
****** SUGGESTED PHYSICS *********
AT MOMENT, IF ACCURATE RESULTS ARE NEDED, WE STRONGLY RECOMMEND:
1. The use of the emstandard_opt3, or
2. the QGSP_BIC_EMY Reference Physics Lists (define the PHYSLIST evironment variable):
export PHYSLIST=QGSP_BIC_EMY
A particular care is addressed to the simulation of the physic processes.
EM Standard option 4 is activated. The user can change the physics list interactively.
INTERACTIVE COMMANDS
How to change Phantom, Detector and Shielding Disc 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.
@@ -181,21 +143,13 @@ 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>>.
(2) 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 7x15x15 cm for the detector, 0.5x0.5x0.5 mm for any voxel. The default detector position is chosen so that the 15x15 detector face is aligned and centered respect the detector beam exposed face.
The user has to change the scoring mesh accordingly via UI commands.
Shielding Disc geometry
@@ -233,41 +187,7 @@ Command synopsis:
/InsertProtectionDisc/insert
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 give them to the particle gun, for example issuing the macro commands:
/gun/particle ion
/gun/ion <Z> <A> <[charge]>
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]
# Value inside square brackets is the excitation energy of the ion (ground state in this case).
To set initial beam features
**** To set initial beam features
By default, the beam propagates along the positive X direction with Gaussian momentum and Y-Z distributions.
It is possible to select: particle type, mean energy and relative standard deviation, X,Y and Z coordinates, Y and Z standard deviations and, finally, the beam spread along X direction (Theta).
@@ -284,8 +204,6 @@ Command synopsis:
/beam/position/Zposition/sigmaZ
/beam/momentum/Theta
HOW RUN iort_therapy
Run the example in interactive mode
@@ -308,28 +226,8 @@ 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 IORTMatrix.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.
A .out ASCII file is generated at the end of each run, Dose.out.
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 in Gray deposited in that given voxel.
FUTURE CHALLENGES
This is a list of future components that will be added in iort_therapy.
In the next future iort_therapy will be improved making it possible to simulate roto-translations of the collimator beam line respect the target thus reproducing the mobility characteristics of the linac.
Dicom Interface
A first work in progress version iort_therapy-DICOM is underdeveloped. This application imports in iort_therapy the main parts and facilities of the Dicom extended-medical example, so it permits to replace the water phantom with a voxellized phantom version of the dicom images.
Human-Phantom Interface
Also a second work in progress version iort_therapy-Human-Phantom is underdeveloped. It is based on the Human-Phantom advanced example. Thus there will be the possibility to replace the water phantom with the human phantom.
All these configuration will be set by macro commands.
Please contact carlo.casarino@polooncologicocefalu.it for more details or suggestions and feedbacks on this document.
examples/advanced/iort_therapy/batch.mac
+15 -13
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@@ -22,17 +22,7 @@
##########################
# Set of the physic models
#
/Physics/addPhysics emstandard_opt3 # Electromagnetic model
/Physics/addPhysics Em_extra_physics
#/Physics/addPhysics Elastic # Hadronic elastic model
#/Physics/addPhysics decay
#/Physics/addPhysics radioactive_decay
#/Physics/addPhysics Stopping_physics
#/Physics/addPhysics Neutron_tracking_cut
#/Physics/addPhysics binary # Hadronic inelastic model
#/Physics/addPhysics local_ion_ion_inelastic # Optional Hadronic inelastic model for ions (local physic list)
#/Physics/addPackage QGSP_BIC_EMY
/Physics/addPhysics standard_opt3 # Electromagnetic model
##########################
# Geometry #
@@ -102,7 +92,19 @@
#/InsertProtectionDisc/insert
#/changePhantom/update
# Scoring mesh is used to calculate
# the dose in the phantom
/score/create/boxMesh boxMesh_1
#
/score/mesh/boxSize 10. 10. 10. cm
/score/mesh/nBin 300 300 300
/score/mesh/translate/xyz 4.5 0. 0. cm
/score/quantity/doseDeposit dose Gy
#
/score/close
#
/score/list
/DeleteProtectionDisc/delete
/run/beamOn 2000
/score/dumpQuantityToFile boxMesh_1 dose dose.out
/run/beamOn 2
examples/advanced/iort_therapy/clean.sh
-9
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@@ -1,9 +0,0 @@
rm *.~
rm macro/*.~
rm include/*.~
rm src/*.~
rm *.out
rm *.root
rm currentRun.rndm
rm currentEvent.rndm
rm *.prim *.eps *.heprep
examples/advanced/iort_therapy/defaultMacro.mac
+16 -27
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@@ -1,16 +1,3 @@
# G.A.P.Cirrone and C.Casarino
#
# Default macro file. It is called if no argument is provided at run
#
# i.e. simply typing $G4WORKDIR/bin/Linux-++/Iort <no argument here!>
#
# This macro can be used for a proton or electron beam in water. Both electromagnetic and
# hadronic models may be swiched on
#/control/getEnv G4SYSTEM
#########################
# Set of the verboses
#
@@ -23,16 +10,6 @@
# Set of the physic models
#
/Physics/addPhysics standard_opt3 # Electromagnetic model
#/Physics/addPhysics Em_extra_physics
#/Physics/addPhysics Elastic # Hadronic elastic model
#/Physics/addPhysics decay
#/Physics/addPhysics radioactive_decay
#/Physics/addPhysics Stopping_physics
#/Physics/addPhysics Neutron_tracking_cut
#/Physics/addPhysics binary # Hadronic inelastic model
#/Physics/addPhysics local_ion_ion_inelastic # Optional Hadronic inelastic model for ions (local physic list)
#/Physics/addPackage QGSP_BIC_EMY
##########################
# Geometry #
@@ -66,7 +43,7 @@
# Definition of the GUI
# It will work only if the QT GUI interface is active
#
/control/execute macro/GUIPersonalisation.mac
#/control/execute macro/GUIPersonalisation.mac
##########################
# Set here the cut and the step max for the tracking.
# Suggested values of cut and step:
@@ -84,7 +61,6 @@
# Set the primary particle type,
# energy and position along the X direction and spread
#
#/gun/particle proton
/beam/energy/meanEnergy 9.9 MeV # 6.2 MeV old
/beam/energy/sigmaEnergy 500 keV # 400 keV old
/beam/position/Xposition -862.817 mm # coll40, coll50, coll60, coll70, coll80 -> -862.817 mm ; coll100 ->
@@ -124,7 +100,20 @@
#/InsertProtectionDisc/insert
#/changePhantom/update
#
# Scoring mesh is used to calculate
# the dose in the phantom
/score/create/boxMesh boxMesh_1
#
/score/mesh/boxSize 10. 10. 10. cm
/score/mesh/nBin 300 300 300
/score/mesh/translate/xyz 4.5 0. 0. cm
/score/quantity/doseDeposit dose Gy
#
/score/close
#
/score/list
/DeleteProtectionDisc/delete
/run/beamOn 100
/score/dumpQuantityToFile boxMesh_1 dose dose.out
/run/beamOn 2
examples/advanced/iort_therapy/defaultMacroWithReferencePhysicsList.mac
-132
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@@ -1,132 +0,0 @@
# G.A.P.Cirrone and C.Casarino
#
# Default macro file. It is called if no argument is provided at run
#
# i.e. simply typing $G4WORKDIR/bin/Linux-++/IORT <no argument here!>
#
# This macro can be used for a proton or electron beam in water. Both electromagnetic and
# hadronic models may be swiched on
#/control/getEnv G4SYSTEM
#########################
# Set of the verboses
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0
##########################
# Set of the physic models
#
#/Physics/addPhysics emstandard_opt3 # Electromagnetic model
#/Physics/addPhysics Em_extra_physics
#/Physics/addPhysics Elastic # Hadronic elastic model
#/Physics/addPhysics decay
#/Physics/addPhysics radioactive_decay
#/Physics/addPhysics Stopping_physics
#/Physics/addPhysics Neutron_tracking_cut
#/Physics/addPhysics binary # Hadronic inelastic model
#/Physics/addPhysics local_ion_ion_inelastic # Optional Hadronic inelastic model for ions (local physic list)
#/Physics/addPackage QGSP_BIC_EMY
##########################
# Geometry #
##########################
#/geometrySetup/selectGeometry coll50
##########################
# Initialisation procedure
#
/run/initialize
##########################
# Visualisation
#
/vis/scene/create
/vis/open OGL
/vis/viewer/flush
/vis/viewer/set/viewpointThetaPhi 30 140 deg
/vis/viewer/zoom 1
/vis/viewer/pan -10 0 cm
/vis/scene/add/trajectories
/vis/scene/endOfEventAction accumulate
#/vis/viewer/update # new
##########################
# Definition of the GUI
# It will work only if the QT GUI interface is active
#
/control/execute macro/GUIPersonalisation.mac
##########################
# Set here the cut and the step max for the tracking.
# Suggested values of cut and step:
#
# Set cuts ONLY inside the detector
#/Physics/setDetectorCuts 0.01 mm
# Definition of the production cuts
/run/setCut 0.01 mm
/run/setCutForAGivenParticle e- 1 mm
/run/setCutForAGivenParticle e+ 1 mm
/run/setCutForAGivenParticle gamma 1 mm
/run/setCutForAGivenParticle proton 1 mm
/run/setCutForRegion DetectorLog 0.01 mm
# Set cuts OUTSIDE the detector
#/Physics/setCuts 1. mm
#/Physics/setCuts 0.01 mm
#/Step/waterPhantomStepMax 0.01 mm
#########################
# Set the primary particle type,
# energy and position along the X direction
#
#/gun/particle proton
/beam/energy/meanEnergy 9.9 MeV # 6.2 MeV old
/beam/energy/sigmaEnergy 500 keV # 400 keV old
/beam/position/Xposition -862.817 mm # coll40, coll50, coll60, coll70, coll80 -> -862.817 mm ; coll100 ->
# -1062.817 mm ;
#########################
# Display the event number
# during the run
#
/event/printEventNumber 1000
#########################
# Start of the run
#
# If secondary particles dose & fluence are needed
#/analysis/secondary true
# Default material is water liquid
#/changePhantom/material G4_PLEXIGLASS
#/ProtectionDisc1/OuterRadiusDisc1 40 # default -> 40*mm ; 30(coll40);35(coll50);45(coll70);50(coll40);60(coll100)
#/ProtectionDisc1/InnerRadiusDisc1 # default -> 0*mm
#/ProtectionDisc1/HeightDisc1 # default -> 2*mm
#/ProtectionDisc1/XPositionDisc1 -11.0 # default -> -11*mm R90 (10.1 MeV) -> -10.68 mm da centro detector (24mm)
#/ProtectionDisc1/material G4_Al # default -> G4_WATER ;
#/ProtectionDisc2/OuterRadiusDisc2 40 # default -> 40*mm ; 30(coll40);35(coll50);45(coll70);50(coll40);60(coll100)
#/ProtectionDisc2/InnerRadiusDisc2 # default -> 0*mm
#/ProtectionDisc2/HeightDisc2 # default -> 1*mm
#/ProtectionDisc2/XPositionDisc2 -8.0 # default -> -8*mm
#/ProtectionDisc2/material G4_Pb # default -> G4_WATER ;
#/InsertProtectionDisc/insert
#/changePhantom/update
#/DeleteProtectionDisc/delete
/run/beamOn 10
examples/advanced/iort_therapy/include/Collimator100BeamLine.hh
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator100BeamLineMessenger.hh
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator40BeamLine.hh
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator40BeamLineMessenger.hh
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator50BeamLine.hh
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator50BeamLineMessenger.hh
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator60BeamLine.hh
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator60BeamLineMessenger.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator70BeamLine.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator70BeamLineMessenger.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator80BeamLine.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Collimator80BeamLineMessenger.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/Decay.hh
-67
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@@ -1,67 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
// ==============================
// PHYSICS PROCESSES:
// ==============================
// Decay process for:
// all considered, unstable particles
//
//
// ==============================
// COMMENTS:
// ==============================
// No comments
//
#ifndef DECAY_H
#define DECAY_H 1
#include "G4VPhysicsConstructor.hh"
#include "globals.hh"
class Decay : public G4VPhysicsConstructor
{
public:
Decay(const G4String& name = "UnstableParticles-Decay");
virtual ~Decay();
virtual void ConstructParticle() {};
virtual void ConstructProcess();
};
#endif
examples/advanced/iort_therapy/include/IORTAnalysisFileMessenger.hh
-86
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@@ -1,86 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTAnalysisFileMessenger_h
#define IORTAnalysisFileMessenger_h 1
#include "G4UImessenger.hh"
#include "globals.hh"
class IORTAnalysisManager; ///< Provides SetanalysisFileName()
class G4UIcmdWithAString;
class G4UIcmdWithABool;
/**
* A messenger object of this class is created by the AnalysisManager.
* The point of a messenger is to connect the G4UI with the simulation
* functionality.
* The messenger needs to contain a command object and to have SetValue
* method that is called once a command is set.
*
* @see IORTAnalysisManager
*/
class IORTAnalysisFileMessenger: public G4UImessenger
{
public:
IORTAnalysisFileMessenger(IORTAnalysisManager* amgr);
~IORTAnalysisFileMessenger();
/**
* Called when new command given.
* @param command is a pointer to the given command object
* @param newValue holds the argument given as a G4String
* @return is void
*/
void SetNewValue(G4UIcommand* command, G4String newValue);
private:
IORTAnalysisManager* AnalysisManager; ///< handle to AnalysisManager
/**
* G4 user interface command (that takes a string argument) object
* Constructor requires command name and messenger class(this).
*/
G4UIcmdWithABool *secondaryCmd;
G4UIcmdWithAString *DoseMatrixCmd;
G4UIcmdWithAString *FileNameCmd;
};
#endif
examples/advanced/iort_therapy/include/IORTAnalysisManager.hh
-185
View File
@@ -1,185 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c),
// G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTTHERAPYANALYSISMANAGER_HH
#define IORTTHERAPYANALYSISMANAGER_HH 1
#include "globals.hh"
#include "g4root.hh"
/**
* Messenger class for analysis-settings for HadronTherapyAnalysisManager
*/
class IORTAnalysisFileMessenger;
/**
* A class for connecting the simulation to an analysis package.
*/
class IORTAnalysisManager
{
private:
/**
* Analysis manager is a singleton object (there is only one instance).
* The pointer to this object is available through the use of the method GetInstance();
*
* @see GetInstance
*/
IORTAnalysisManager();
public:
~IORTAnalysisManager();
/**
* Get the pointer to the analysis manager.
*/
static IORTAnalysisManager* GetInstance();
/**
* Book the histograms and ntuples.
*/
void book();
/**
* Set name for the analysis file .root (used by macro)
*/
void SetAnalysisFileName(G4String);
/**
* Fill the ntuple with the energy deposit in the phantom
*/
void FillEnergyDeposit(G4int voxelXId, G4int voxelYId, G4int voxelZId,
G4double energyDeposit);
void BraggPeak(G4int, G4double); ///< Fill 1D histogram with the Bragg peak in the phantom
void SecondaryProtonEnergyDeposit(G4int slice, G4double energy);
///< Fill 1D histogram with the energy deposit of secondary protons
void SecondaryNeutronEnergyDeposit(G4int slice, G4double energy);
///< Fill 1D histogram with the energy deposit of secondary neutrons
void SecondaryAlphaEnergyDeposit(G4int slice, G4double energy);
///< Fill 1D histogram with the energy deposit of secondary alpha particles
void SecondaryGammaEnergyDeposit(G4int slice, G4double energy);
///< Fill 1D histogram with the energy deposit of secondary gamma
void SecondaryElectronEnergyDeposit(G4int slice, G4double energy);
///< Fill 1D histogram with the energy deposit of secondary electrons
void SecondaryTritonEnergyDeposit(G4int slice, G4double energy);
///< Fill 1D histogram with the energy deposit of secondary tritons
void SecondaryDeuteronEnergyDeposit(G4int slice, G4double energy);
///< Fill 1D histogram with the energy deposit of secondary deuterons
void SecondaryPionEnergyDeposit(G4int slice, G4double energy);
///< Fill 1D histogram with the energy deposit of secondary pions
void electronEnergyDistribution(G4double secondaryParticleKineticEnergy);
///< Energy distribution of secondary electrons originated in the phantom
void gammaEnergyDistribution(G4double secondaryParticleKineticEnergy);
///< Energy distribution of secondary gamma originated in the phantom
void deuteronEnergyDistribution(G4double secondaryParticleKineticEnergy);
///< Energy distribution of secondary deuterons originated in the phantom
void tritonEnergyDistribution(G4double secondaryParticleKineticEnergy);
///< Energy distribution of secondary tritons originated in the phantom
void alphaEnergyDistribution(G4double secondaryParticleKineticEnergy);
///< Energy distribution of secondary alpha originated in the phantom
void heliumEnergy(G4double secondaryParticleKineticEnergy);
///< Energy distribution of the helium (He3 and alpha) particles after the phantom
void hydrogenEnergy(G4double secondaryParticleKineticEnergy);
///< Energy distribution of the hydrogen (proton, d, t) particles after the phantom
//Kinetic energy by voxel, mass number A and atomic number Z.
void FillKineticFragmentTuple(G4int i, G4int j, G4int k, G4int A, G4double Z, G4double kinEnergy);
//Kinetic energy by voxel, mass number A and atomic number Z of only primary particles
void FillKineticEnergyPrimaryNTuple(G4int i, G4int j, G4int k, G4double kinEnergy);
///< Energy by voxel, mass number A and atomic number Z.
void FillVoxelFragmentTuple(G4int i, G4int j, G4int k, G4int A, G4double Z, G4double energy, G4double fluence);
void FillFragmentTuple(G4int A, G4double Z, G4double energy, G4double posX, G4double posY, G4double posZ);
///< Energy ntuple
void FillLetFragmentTuple(G4int i, G4int j, G4int k, G4int A, G4double Z, G4double letT, G4double letD);
///< let ntuple
void genericIonInformation(G4int, G4double, G4int, G4double);
void ThintargetBeamDisp(G4double,G4double);
void startNewEvent();
///< Tell the analysis manager that a new event is starting
void setGeometryMetaData(G4double, G4double, G4double);
///< from the detector construction information about the geometry can be written as metadata
void setBeamMetaData(G4double, G4double);
///< metadata about the beam can be written this way
void flush();
///< Close the .hbk file with the histograms and the ntuples
private:
static IORTAnalysisManager* instance;
IORTAnalysisFileMessenger* fMess;
G4String analysisFileName;
G4long eventCounter; // Simulation metadata
G4double detectorDistance;
G4double phantomDepth;
G4double beamEnergy;
G4double energyError;
G4double phantomCenterDistance;
};
#endif
examples/advanced/iort_therapy/include/IORTDetectorConstruction.hh
+6 -25
View File
@@ -32,7 +32,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
@@ -50,10 +50,7 @@
class G4VPhysicalVolume;
class G4LogicalVolume;
class IORTDetectorROGeometry;
class IORTDetectorMessenger;
class IORTDetectorSD;
class IORTMatrix;
class IORTDetectorConstruction
{
@@ -70,7 +67,7 @@ private:
void ConstructPhantom();
void ConstructDetector();
// void ConstructDisc();
void ConstructSensitiveDetector(G4ThreeVector positionToWORLD);
void ConstructSensitiveDetector();
void ParametersCheck();
public:
@@ -79,6 +76,7 @@ inline G4ThreeVector GetDetectorToWorldPosition()
{
return phantomPosition + detectorPosition;
}
/////////////////////////////////////////////////////////////////////////////
// Get displacement between phantom and detector by detector position (center of), phantom (center of) and detector sizes
inline G4ThreeVector GetDetectorToPhantomPosition()
@@ -116,7 +114,7 @@ inline bool IsInside(G4double detectorX,
{
if (detectorX > phantomX)
{
G4cout << "Error: Detector X dimension must be smaller or equal to the corrispondent of the phantom" << G4endl;
G4cout << "Error: Detector X dimension must be smaller or equal to the correspondent of the phantom" << G4endl;
return false;
}
if ( (phantomX - detectorX) < detToPhantomPosition.getX())
@@ -129,7 +127,7 @@ inline bool IsInside(G4double detectorX,
{
if (detectorY > phantomY)
{
G4cout << "Error: Detector Y dimension must be smaller or equal to the corrispondent of the phantom" << G4endl;
G4cout << "Error: Detector Y dimension must be smaller or equal to the correspondent of the phantom" << G4endl;
return false;
}
if ( (phantomY - detectorY) < detToPhantomPosition.getY())
@@ -142,7 +140,7 @@ inline bool IsInside(G4double detectorX,
{
if (detectorZ > phantomZ)
{
G4cout << "Error: Detector Z dimension must be smaller or equal to the corrispondent of the phantom" << G4endl;
G4cout << "Error: Detector Z dimension must be smaller or equal to the correspondent of the phantom" << G4endl;
return false;
}
if ( (phantomZ - detectorZ) < detToPhantomPosition.getZ())
@@ -192,10 +190,6 @@ private:
G4VPhysicalVolume* motherPhys;
IORTDetectorSD* detectorSD; // Pointer to sensitive detector
IORTDetectorROGeometry* detectorROGeometry; // Pointer to ROGeometry
IORTMatrix* matrix;
G4Box *phantom , *detector;
G4LogicalVolume *phantomLogicalVolume, *detectorLogicalVolume;
G4VPhysicalVolume *phantomPhysicalVolume, *detectorPhysicalVolume;
@@ -210,20 +204,8 @@ private:
G4ThreeVector phantomPosition, detectorPosition, detectorToPhantomPosition; // phantom center, detector center, detector to phantom relative position
G4double sizeOfVoxelAlongX;
G4double sizeOfVoxelAlongY;
G4double sizeOfVoxelAlongZ;
G4int numberOfVoxelsAlongX;
G4int numberOfVoxelsAlongY;
G4int numberOfVoxelsAlongZ;
G4double volumeOfVoxel, massOfVoxel;
G4Material *phantomMaterial, *detectorMaterial;
G4Region* aRegion;
//Disco0 IORT
G4Tubs* solidDiscoIORT0;
@@ -246,7 +228,6 @@ private:
G4VPhysicalVolume* physiDiscoIORT;
G4Material* DiscoMaterialIORT;
// Disco2 IORT
G4double innerRadiusDiscoIORT1;
examples/advanced/iort_therapy/include/IORTDetectorHit.hh
-113
View File
@@ -1,113 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTDetectorHit_h
#define IORTDetectorHit_h 1
#include "G4VHit.hh"
#include "G4THitsCollection.hh"
#include "G4Allocator.hh"
class IORTDetectorHit : public G4VHit
{
public:
IORTDetectorHit();
~IORTDetectorHit();
IORTDetectorHit(const IORTDetectorHit &right);
const IORTDetectorHit& operator = (const IORTDetectorHit &right);
int operator == (const IORTDetectorHit &right) const;
inline void *operator new(size_t);
inline void operator delete(void *aHit);
private:
G4int xHitID; // Hit x voxel
G4int zHitID; // Hit z voxel
G4int yHitID; // Hit y voxel
G4double energyDeposit; // Energy deposit associated with the hit
public:
// Methods to get the information - energy deposit and associated
// position in the phantom - of the hits stored in the hits collection
inline G4int GetXID() // Get x index of the voxel
{return xHitID;}
inline G4int GetZID() // Get y index of the voxel
{return zHitID;}
inline G4int GetYID() // Get z index of the voxel
{return yHitID;}
inline G4double GetEdep() // Get energy deposit
{return energyDeposit;}
// Methods to store the information of the hit ( energy deposit, position in the phantom )
// in the hits collection
inline void SetEdepAndPosition(G4int xx, G4int yy, G4int zz, G4double eDep)
{
xHitID = xx;
yHitID = yy;
zHitID = zz;
energyDeposit = eDep;
}
};
typedef G4THitsCollection<IORTDetectorHit> IORTDetectorHitsCollection;
extern G4Allocator<IORTDetectorHit> IORTDetectorHitAllocator;
inline void* IORTDetectorHit::operator new(size_t)
{
void *aHit;
aHit = (void *) IORTDetectorHitAllocator.MallocSingle();
return aHit;
}
inline void IORTDetectorHit::operator delete(void *aHit)
{
IORTDetectorHitAllocator.FreeSingle((IORTDetectorHit*) aHit);
}
#endif
examples/advanced/iort_therapy/include/IORTDetectorMessenger.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/IORTDetectorROGeometry.hh
-77
View File
@@ -1,77 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
//The detectior is devided in voxels.
//
//
#ifndef IORTDetectorROGeometry_h
#define IORTDetectorROGeometry_h
#include "G4VReadOutGeometry.hh"
class IORTDetectorROGeometry : public G4VReadOutGeometry
{
public:
IORTDetectorROGeometry(G4String aString,
G4ThreeVector detectorPos,
G4double detectorDimX,
G4double detectorDimY,
G4double detectorDimZ,
G4int numberOfVoxelsX,
G4int numberOfVoxelsY,
G4int numberOfVoxelsZ);
~IORTDetectorROGeometry();
private:
G4VPhysicalVolume* Build();
private:
const G4ThreeVector detectorToWorldPosition;
const G4double detectorSizeX;
const G4double detectorSizeY;
const G4double detectorSizeZ;
const G4int numberOfVoxelsAlongX;
const G4int numberOfVoxelsAlongY;
const G4int numberOfVoxelsAlongZ;
G4VPhysicalVolume *RODetectorZDivisionPhys;
};
#endif
examples/advanced/iort_therapy/include/IORTDetectorSD.hh
-69
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@@ -1,69 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTDetectorSD_h
#define IORTDetectorSD_h 1
#include "G4VSensitiveDetector.hh"
#include "IORTDetectorHit.hh"
#include "globals.hh"
class G4Step;
class G4HCofThisEvent;
class G4TouchableHistory;
class IORTDetectorSD : public G4VSensitiveDetector
{
public:
IORTDetectorSD(G4String name);
~IORTDetectorSD();
std::ofstream ofs;
void Initialize(G4HCofThisEvent*);
G4bool ProcessHits(G4Step*aStep,G4TouchableHistory*ROhist);
void EndOfEvent(G4HCofThisEvent*HCE);
private:
IORTDetectorHitsCollection *HitsCollection;
G4String sensitiveDetectorName;
};
#endif
examples/advanced/iort_therapy/include/IORTDummySD.hh
-62
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@@ -1,62 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTDummySD_h
#define IORTDummySD_h 1
#include "G4VSensitiveDetector.hh"
class G4Step;
class IORTDummySD : public G4VSensitiveDetector
{
public:
IORTDummySD();
~IORTDummySD() {};
void Initialize(G4HCofThisEvent* ) {};
G4bool ProcessHits(G4Step* ,G4TouchableHistory*) {return false;}
void EndOfEvent(G4HCofThisEvent*) {};
void clear() {};
void DrawAll() {};
void PrintAll() {};
};
IORTDummySD::IORTDummySD() : G4VSensitiveDetector("dummySD")
{}
#endif
examples/advanced/iort_therapy/include/IORTEventAction.hh
+1 -4
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
@@ -43,7 +43,6 @@
#include "G4UserEventAction.hh"
#include "globals.hh"
class IORTMatrix;
class IORTEventActionMessenger;
class IORTEventAction : public G4UserEventAction
@@ -68,8 +67,6 @@ public:
private:
G4String drawFlag; //Visualisation flag
G4int hitsCollectionID;
//IORTMatrix *matrix;
G4int printModulo;
IORTEventActionMessenger* pointerEventMessenger;
};
examples/advanced/iort_therapy/include/IORTEventActionMessenger.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/IORTGeometryController.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/IORTInteractionParameters.hh
-111
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@@ -1,111 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTInteractionParameters_H
#define IORTInteractionParameters_H 1
#include "G4EmCalculator.hh"
#include "G4NistMaterialBuilder.hh"
#include "G4NistElementBuilder.hh"
#ifdef G4ANALYSIS_USE_ROOT
#include "TROOT.h"
#include "TCanvas.h"
#include "TFile.h"
#include "TH1F.h"
#include "TH2F.h"
#include "TGraph.h"
#include "TLegend.h"
#include "TLegendEntry.h"
#include "TStyle.h"
#endif
class IORTDetectorConstruction;
class IORTParameterMessenger;
class G4ParticleDefinition;
class G4Material;
class IORTInteractionParameters : public G4EmCalculator
{
public:
IORTInteractionParameters(G4bool);
~IORTInteractionParameters();
// Get data for Mass SP
// G4NistMaterialBuilder class materials
// User must provide: material kinetic energy lower limit, kinetic energy upper limit, number of points to retrieve,
// [particle], [output filename].
G4bool GetStoppingTable (const G4String& vararg);
G4double GetStopping (G4double energy,
const G4ParticleDefinition*,
const G4Material*,
G4double density = 0.);
#ifdef G4ANALYSIS_USE_ROOT
void PlotStopping(const G4String&);
#endif
void ListOfNistMaterials (const G4String& vararg);
void BeamOn();
bool ParseArg (const G4String& vararg);
private:
G4Material* GetNistMaterial(G4String material);
G4NistElementBuilder* nistEle;
G4NistMaterialBuilder* nistMat;
std::ofstream outfile;
std::ostream data;
G4Material* Pmaterial;
IORTParameterMessenger* pMessenger;
bool beamFlag;
#ifdef G4ANALYSIS_USE_ROOT
TCanvas *theRootCanvas;
TGraph *theRootGraph;
TAxis *axisX, *axisY;
#endif
G4double kinEmin, kinEmax, npoints;
G4String particle, material, filename;
G4double dedxtot, density;
std::vector<G4double> energy;
std::vector<G4double> massDedx;
};
#endif
examples/advanced/iort_therapy/include/IORTMatrix.hh
-149
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@@ -1,149 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTMatrix_H
#define IORTMatrix_H 1
#include <G4ParticleDefinition.hh>
#include "globals.hh"
#include <vector>
#include <fstream>
// The information: energy deposit and position in the phantom
// is stored in a matrix
// type struct useful to store nucludes data
struct ion
{
G4bool isPrimary; // true if particle is primary
G4int PDGencoding; // Particle data group id for the particle
//G4String extName; // AZ[excitation energy]: like He3[1277.4], He4[0.0], Li7[231.4], ...
G4String name; // simple name without excitation energy: He3, He4, Li7, ...
std::string::size_type len; // name length
G4int Z; // atomic number
G4int A; // mass number
G4double *dose; // pointer to dose matrix
unsigned int *fluence; // pointer to fluence matrix
//friend bool operator<(const ion& a, const ion& b) {return (a.Z == b.Z) ? b.A < a.A : b.Z < a.Z ;}
G4bool operator<(const ion& a) const{return (this->Z == a.Z) ? this-> A < a.A : this->Z < a.Z ;}
};
class IORTMatrix
{
private:
IORTMatrix(G4int numberOfVoxelAlongX,
G4int numberOfVoxelAlongY,
G4int numberOfVoxelAlongZ,
G4double massOfVoxel); //< this is supposed to be a singleton
public:
~IORTMatrix();
// Get object instance only
static IORTMatrix* GetInstance();
// Make & Get instance
static IORTMatrix* GetInstance(G4int nX, G4int nY, G4int nZ, G4double mass);
static G4bool secondary;
// Full list of generated nuclides
void PrintNuclides();
// Hit array marker (useful to avoid multiple counts of fluence)
void ClearHitTrack();
G4int* GetHitTrack(G4int i, G4int j, G4int k);
// All the elements of the matrix are initialised to zero
void Initialize();
void Clear();
// Fill DOSE/fluence matrix for particle:
// if fluence parameter is true then fluence at voxel (i, j, k) is increased
// else energyDeposit fill the dose matrix for voxel (i,j,k)
G4bool Fill(G4int, G4ParticleDefinition* particleDef, G4int i, G4int j, G4int k, G4double energyDeposit, G4bool fluence=false);
// Fill TOTAL DOSE matrix for primary particles only
void Fill(G4int i, G4int j, G4int k, G4double energyDeposit);
// The matrix is filled with the energy deposit
// in the element corresponding to the voxel of the phantom where
// the energy deposit was registered
// Store the information of the matrix in a ntuple and in
// a 1D Histogram
void TotalEnergyDeposit();
// Store single matrix data to filename
void StoreMatrix(G4String file, void* data,size_t psize);
// Store all fluence data to filenames
void StoreFluenceData();
// Store all dose data to filenames
void StoreDoseData();
// Store all data (except the total dose) to ONE filename
void StoreDoseFluenceAscii(G4String filename = "");
void StoreDoseFluenceRoot();
inline G4int Index(G4int i, G4int j, G4int k) { return (i * numberOfVoxelAlongY + j) * numberOfVoxelAlongZ + k; }
// Get a unique index from a three dimensional one
G4double * GetMatrix(){return matrix;}
G4int GetNvoxel(){return numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;}
// Total number of voxels read only access
G4int GetNumberOfVoxelAlongX(){return numberOfVoxelAlongX;}
G4int GetNumberOfVoxelAlongY(){return numberOfVoxelAlongY;}
G4int GetNumberOfVoxelAlongZ(){return numberOfVoxelAlongZ;}
private:
static IORTMatrix* instance;
G4int numberOfVoxelAlongX;
G4int numberOfVoxelAlongY;
G4int numberOfVoxelAlongZ;
G4double massOfVoxel;
G4double* matrix;
G4int* hitTrack;
G4String stdFile, filename;
std::ofstream ofs;
// Dose&fluence data store
std::vector <ion> ionStore;
// want secondary particles?
G4double doseUnit;
};
#endif
examples/advanced/iort_therapy/include/IORTParameterMessenger.hh
-67
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@@ -1,67 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTParameterMessenger_h
#define IORTParameterMessenger_h 1
#include "globals.hh"
#include "G4UImessenger.hh"
class IORTInteractionParameters;
class G4UIdirectory;
//class G4UIcmdWithADoubleAndUnit;
class G4UIcmdWithAString;
class G4UIcmdWithoutParameter;
class IORTParameterMessenger : public G4UImessenger
{
public:
IORTParameterMessenger(IORTInteractionParameters* );
~IORTParameterMessenger();
void SetNewValue(G4UIcommand*, G4String);
private:
IORTInteractionParameters* pParam;
G4UIdirectory *paramDir;
G4UIcmdWithAString *dedxCmd, *listCmd;
};
#endif
examples/advanced/iort_therapy/include/IORTParticles.hh
-66
View File
@@ -1,66 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#ifndef IORTPARTICLES_HH
#define IORTPARTICLES_HH 1
#include "globals.hh"
#include "G4VPhysicsConstructor.hh"
class IORTParticles : public G4VPhysicsConstructor {
public:
IORTParticles(const G4String& name = "particles");
virtual ~IORTParticles();
virtual void ConstructParticle();
// This method is dummy
virtual void ConstructProcess() {};
};
#endif
examples/advanced/iort_therapy/include/IORTPhysicsList.hh
+4 -12
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
@@ -77,17 +77,9 @@ private:
G4double cutForElectron;
G4double cutForPositron;
G4bool helIsRegistered;
G4bool bicIsRegistered;
G4bool biciIsRegistered;
G4bool locIonIonInelasticIsRegistered;
G4bool radioactiveDecayIsRegistered;
G4String emName;
G4VPhysicsConstructor* emPhysicsList;
G4VPhysicsConstructor* decPhysicsList;
std::vector<G4VPhysicsConstructor*> hadronPhys;
G4String emName;
G4VPhysicsConstructor* emPhysicsList;
G4VPhysicsConstructor* decPhysicsList;
IORTStepMax* stepMaxProcess;
IORTPhysicsListMessenger* pMessenger;
examples/advanced/iort_therapy/include/IORTPhysicsListMessenger.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/IORTPrimaryGeneratorAction.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/IORTRunAction.hh
+1 -16
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
@@ -45,8 +45,6 @@
#include "globals.hh"
class G4Run;
class IORTAnalysisManager;
class IORTDetectorConstruction;
class IORTRunMessenger;
class IORTFactory;
@@ -59,19 +57,6 @@ public:
public:
void BeginOfRunAction(const G4Run*);
void EndOfRunAction(const G4Run* );
void SelectEnergy(G4int);
void AddEMProcess();
// Counts the number of electromagnetic processes
// of primary particles in the phantom
void AddHadronicProcess();
// Counts the number of hadronic processes
// of primary particles in the phantom
private:
G4int electromagnetic;
G4int hadronic;
};
#endif
examples/advanced/iort_therapy/include/IORTStepMax.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/IORTStepMaxMessenger.hh
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/include/IORTSteppingAction.hh
+1 -10
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
@@ -49,12 +49,6 @@
class IORTRunAction;
class IORTSteppingMessenger;
#ifndef G4NOHIST
class HepTupleManager;
class HepHistogram;
#endif
class IORTSteppingAction : public G4UserSteppingAction
{
public:
@@ -62,8 +56,5 @@ public:
~IORTSteppingAction();
void UserSteppingAction(const G4Step*);
private:
IORTRunAction* runAction;
};
#endif
examples/advanced/iort_therapy/iort_therapy.cc
+19 -89
View File
@@ -46,7 +46,7 @@
//
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
//
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
//
// *Corresponding Author, email to carlo.casarino@polooncologicocefalu.it
@@ -58,31 +58,20 @@
#include "G4VModularPhysicsList.hh"
#include "IORTEventAction.hh"
#include "IORTPhysicsList.hh"
#include "IORTDetectorSD.hh"
#include "IORTPrimaryGeneratorAction.hh"
#include "IORTRunAction.hh"
#include "IORTMatrix.hh"
#include "Randomize.hh"
#include "G4RunManager.hh"
#include "G4UImessenger.hh"
#include "globals.hh"
#include "IORTSteppingAction.hh"
#include "IORTAnalysisManager.hh"
#include "IORTGeometryController.hh"
#include "IORTGeometryMessenger.hh"
#include "IORTInteractionParameters.hh"
#include "G4VisExecutive.hh"
#include "G4UIExecutive.hh"
#include <ctime>
#include "G4ScoringManager.hh"
#ifdef G4VIS_USE
#include "G4VisExecutive.hh"
#endif
#ifdef G4UI_USE
#include "G4UIExecutive.hh"
#endif
#include <ctime>
//////////////////////////////////////////////////////////////////////////////////////////////
int main(int argc ,char ** argv)
@@ -90,12 +79,14 @@ int main(int argc ,char ** argv)
// Set the Random engine
CLHEP::HepRandom::setTheEngine(new CLHEP::RanecuEngine());
//imported from eliot_geant4.9.3p01// to create a different seed
G4int seed = time(NULL);
CLHEP::HepRandom::setTheSeed(seed);
//imported from eliot_geant4.9.3p01
G4RunManager* runManager = new G4RunManager;
// G4int seed = time(NULL);
// CLHEP::HepRandom::setTheSeed(seed);
G4RunManager* runManager = new G4RunManager;
G4ScoringManager::GetScoringManager();
// Scoring mesh
// Geometry controller is responsible for instantiating the
// geometries. All geometry specific setup tasks are now in class
// IORTGeometryController.
@@ -103,36 +94,11 @@ int main(int argc ,char ** argv)
// Connect the geometry controller to the G4 user interface
IORTGeometryMessenger *geometryMessenger = new IORTGeometryMessenger(geometryController);
G4ScoringManager *scoringManager = G4ScoringManager::GetScoringManager();
scoringManager->SetVerboseLevel(1);
// Initialize the default IORT geometry
geometryController->SetGeometry("default");
// Initialize command based scoring
G4ScoringManager::GetScoringManager();
// Initialize the physics
G4PhysListFactory factory;
G4VModularPhysicsList* phys = 0;
G4String physName = "";
geometryController->SetGeometry("default");
// Physics List name defined via environment variable
char* path = getenv("PHYSLIST");
if (path) { physName = G4String(path); }
if(factory.IsReferencePhysList(physName))
{
phys = factory.GetReferencePhysList(physName);
}
if(!phys) { phys = new IORTPhysicsList(); }
runManager->SetUserInitialization(phys);
// runManager -> SetUserInitialization(new IORTPhysicsList());
runManager->SetUserInitialization(new IORTPhysicsList());
// Initialize the primary particles
IORTPrimaryGeneratorAction *pPrimaryGenerator = new IORTPrimaryGeneratorAction();
@@ -147,20 +113,10 @@ int main(int argc ,char ** argv)
IORTSteppingAction* steppingAction = new IORTSteppingAction(pRunAction);
runManager -> SetUserAction(steppingAction);
// Interaction data: stopping powers
IORTInteractionParameters* pInteraction = new IORTInteractionParameters(true);
// Initialize analysis
IORTAnalysisManager* analysis = IORTAnalysisManager::GetInstance();
analysis -> book();
#ifdef G4VIS_USE
// Visualization manager
G4VisManager* visManager = new G4VisExecutive;
visManager -> Initialize();
#endif
G4UImanager* UImanager = G4UImanager::GetUIpointer();
if (argc!=1) // batch mode
@@ -171,47 +127,21 @@ int main(int argc ,char ** argv)
}
else
{ // interactive mode : define UI session
#ifdef G4UI_USE
G4UIExecutive* ui = new G4UIExecutive(argc, argv);
#ifdef G4VIS_USE
if(factory.IsReferencePhysList(physName))
{
UImanager->ApplyCommand("/control/execute defaultMacroWithReferencePhysicsList.mac");
}
else
{
UImanager->ApplyCommand("/control/execute defaultMacro.mac");
}
#endif
UImanager->ApplyCommand("/control/execute defaultMacro.mac");
if (ui->IsGUI())
ui->SessionStart();
delete ui;
#endif
}
// Job termination
// Store dose & fluence data to ASCII & ROOT files
if ( IORTMatrix * pMatrix = IORTMatrix::GetInstance() )
{
pMatrix -> TotalEnergyDeposit();
pMatrix -> StoreDoseFluenceAscii();
pMatrix -> StoreDoseFluenceRoot();
}
analysis -> flush(); // Finalize & write the root file
#ifdef G4VIS_USE
delete visManager;
#endif
delete visManager;
delete geometryMessenger;
delete geometryController;
delete pInteraction;
delete runManager;
return 0;
examples/advanced/iort_therapy/iort_therapy.out
+64 -127
View File
@@ -4,7 +4,7 @@
############################################
**************************************************************
Geant4 version Name: geant4-10-05-beta-01 (29-June-2018)
Geant4 version Name: geant4-10-05-ref-00 (7-December-2018)
Copyright : Geant4 Collaboration
References : NIM A 506 (2003), 250-303
: IEEE-TNS 53 (2006), 270-278
@@ -12,7 +12,6 @@
WWW : http://geant4.org/
**************************************************************
... open Root analysis file : DoseDistribution.root - done
Visualization Manager instantiating with verbosity "warnings (3)"...
Visualization Manager initialising...
Registering graphics systems...
@@ -63,44 +62,45 @@ Some /vis commands (optionally) take a string to specify colour.
/tracking/verbose 0
/run/verbose 1
/event/verbose 0
/Physics/addPhysics emstandard_opt3
/Physics/addPhysics Em_extra_physics
/Physics/addPhysics standard_opt3
THE FOLLOWING ELECTROMAGNETIC PHYSICS LIST HAS BEEN ACTIVATED: G4EmStandardPhysics_option3
/run/initialize
-------- WWWW ------- G4Exception-START -------- WWWW -------
*** G4Exception : DIGIHIT1001
issued by : G4VReadOutGeometry
The concept and the functionality of Readout Geometry has been merged
into Parallel World. This G4VReadOutGeometry is kept for the sake of
not breaking the commonly-used interface in the sensitive detector class.
But this functionality of G4VReadOutGeometry class is no longer tested
and thus may not be working well. We strongly recommend our customers to
migrate to Parallel World scheme.
*** This is just a warning message. ***
-------- WWWW -------- G4Exception-END --------- WWWW -------
Instantiating new Read Out Geometry "DetectorROGeometry"
Registering new DetectorSD "Detector"
IORTMatrix: Memory space to store physical dose into 12600000 voxels has been allocated
The Detector has been built --- Add a scoring mesh for it in the GUI if appropriate (similar to the phantom one)
/run/geometryModified
The (X,Y,Z) dimensions of the phantom are : (20 cm ,20 cm ,20 cm )
The (X,Y,Z) dimensions of the detector are : (7 cm ,15 cm ,15 cm )
Displacement between Phantom and World is: DX= 4.5 cm DY= 0 fm DZ= 0 fm
The (X,Y,Z) sizes of the Voxels are: (500 um ,500 um ,500 um )
The number of Voxels along (X,Y,Z) is: (140,300,300)
G4PhysicsListHelper::AddTransportation()--- G4CoupledTransportation is used
--- G4CoupledTransportation is used
### G4EmConfigurator::AddModels n= 0
PhysicsList::SetCuts:CutLength : 10 um
PhysicsList::SetCuts:CutLength : 100 um
/Physics/setDetectorCuts 0.01 mm
/Physics/setCuts 0.01 mm
/Step/waterPhantomStepMax 0.01 mm
/beam/energy/meanEnergy 9.9 MeV
The mean Kinetic energy of the incident beam has been changed to (MeV):9.9
/beam/energy/sigmaEnergy 500 keV
The sigma of the kinetic energy of the incident beam has been changed to (MeV):0.5
/beam/position/Xposition -862.817 mm
/event/printEventNumber 1000
/score/create/boxMesh boxMesh_1
/score/mesh/boxSize 10. 10. 10. cm
/score/mesh/nBin 300 300 300
.... G4ScoringMessenger::MeshBinCommand - G4ScoringBox
/score/mesh/translate/xyz 4.5 0. 0. cm
/score/quantity/doseDeposit dose Gy
/score/close
/score/list
G4ScoringManager has 1 scoring meshes.
G4ScoringBox : boxMesh_1 --- Shape: Box mesh
Size (x, y, z): (10, 10, 10) [cm]
# of segments: (300, 300, 300)
displacement: (4.5, 0, 0) [cm]
registered primitve scorers :
0 dose
/DeleteProtectionDisc/delete
/run/geometryModified
/run/beamOn 2
/run/beamOn 2000
/run/geometryModified
### === Deexcitation model UAtomDeexcitation is activated for 2 regions:
DefaultRegionForTheWorld 1 0 0
@@ -140,7 +140,7 @@ eIoni: for e- SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
MollerBhabha : Emin= 0 eV Emax= 100 TeV
MollerBhabha : Emin= 0 eV Emax= 100 TeV deltaVI
eBrem: for e- SubType= 3
dE/dx and range tables from 10 eV to 100 TeV in 260 bins
@@ -167,7 +167,7 @@ eIoni: for e+ SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
MollerBhabha : Emin= 0 eV Emax= 100 TeV
MollerBhabha : Emin= 0 eV Emax= 100 TeV deltaVI
eBrem: for e+ SubType= 3
dE/dx and range tables from 10 eV to 100 TeV in 260 bins
@@ -198,8 +198,8 @@ hIoni: for proton SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.05, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
Bragg : Emin= 0 eV Emax= 2 MeV
BetheBloch : Emin= 2 MeV Emax= 100 TeV
Bragg : Emin= 0 eV Emax= 2 MeV deltaVI
BetheBloch : Emin= 2 MeV Emax= 100 TeV deltaVI
hBrems: for proton SubType= 3
dE/dx and range tables from 10 eV to 100 TeV in 260 bins
@@ -244,8 +244,8 @@ ionIoni: for alpha SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.01, dRoverRange= 0.1, integral: 1, fluct: 1, linLossLimit= 0.02
===== EM models for the G4Region DefaultRegionForTheWorld ======
BraggIon : Emin= 0 eV Emax= 7.9452 MeV
BetheBloch : Emin= 7.9452 MeV Emax= 100 TeV
BraggIon : Emin= 0 eV Emax= 7.9452 MeV deltaVI
BetheBloch : Emin= 7.9452 MeV Emax= 100 TeV deltaVI
nuclearStopping: for alpha SubType= 8 BuildTable= 0
===== EM models for the G4Region DefaultRegionForTheWorld ======
@@ -261,8 +261,8 @@ hIoni: for anti_proton SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.05, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
ICRU73QO : Emin= 0 eV Emax= 2 MeV
BetheBloch : Emin= 2 MeV Emax= 100 TeV
ICRU73QO : Emin= 0 eV Emax= 2 MeV deltaVI
BetheBloch : Emin= 2 MeV Emax= 100 TeV deltaVI
hBrems: for anti_proton SubType= 3
dE/dx and range tables from 10 eV to 100 TeV in 260 bins
@@ -291,8 +291,8 @@ hIoni: for kaon+ SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.05, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
Bragg : Emin= 0 eV Emax= 1.05231 MeV
BetheBloch : Emin= 1.05231 MeV Emax= 100 TeV
Bragg : Emin= 0 eV Emax= 1.05231 MeV deltaVI
BetheBloch : Emin= 1.05231 MeV Emax= 100 TeV deltaVI
hBrems: for kaon+ SubType= 3
dE/dx and range tables from 10 eV to 100 TeV in 260 bins
@@ -317,8 +317,8 @@ hIoni: for kaon- SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.05, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
ICRU73QO : Emin= 0 eV Emax= 1.05231 MeV
BetheBloch : Emin= 1.05231 MeV Emax= 100 TeV
ICRU73QO : Emin= 0 eV Emax= 1.05231 MeV deltaVI
BetheBloch : Emin= 1.05231 MeV Emax= 100 TeV deltaVI
hBrems: for kaon- SubType= 3
dE/dx and range tables from 10 eV to 100 TeV in 260 bins
@@ -343,8 +343,8 @@ muIoni: for mu+ SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.05, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
Bragg : Emin= 0 eV Emax= 200 keV
BetheBloch : Emin= 200 keV Emax= 1 GeV
Bragg : Emin= 0 eV Emax= 200 keV deltaVI
BetheBloch : Emin= 200 keV Emax= 1 GeV deltaVI
MuBetheBloch : Emin= 1 GeV Emax= 100 TeV
muBrems: for mu+ SubType= 3
@@ -370,8 +370,8 @@ muIoni: for mu- SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.05, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
ICRU73QO : Emin= 0 eV Emax= 200 keV
BetheBloch : Emin= 200 keV Emax= 1 GeV
ICRU73QO : Emin= 0 eV Emax= 200 keV deltaVI
BetheBloch : Emin= 200 keV Emax= 1 GeV deltaVI
MuBetheBloch : Emin= 1 GeV Emax= 100 TeV
muBrems: for mu- SubType= 3
@@ -387,69 +387,6 @@ muPairProd: for mu- SubType= 4
===== EM models for the G4Region DefaultRegionForTheWorld ======
muPairProd : Emin= 0 eV Emax= 100 TeV
====================================================================
HADRONIC PROCESSES SUMMARY (verbose level 1)
---------------------------------------------------
Hadronic Processes for e+
Process: positronNuclear
Model: G4ElectroVDNuclearModel: 0 eV ---> 1 PeV
Cr_sctns: ElectroNuclearXS: 0 eV ---> 100 TeV
Cr_sctns: GheishaInelastic: 0 eV ---> 100 TeV
---------------------------------------------------
Hadronic Processes for e-
Process: electronNuclear
Model: G4ElectroVDNuclearModel: 0 eV ---> 1 PeV
Cr_sctns: ElectroNuclearXS: 0 eV ---> 100 TeV
Cr_sctns: GheishaInelastic: 0 eV ---> 100 TeV
---------------------------------------------------
Hadronic Processes for gamma
Process: photonNuclear
Model: BertiniCascade: 0 eV ---> 3.5 GeV
Model: TheoFSGenerator: 3 GeV ---> 100 TeV
Cr_sctns: PhotoNuclearXS: 0 eV ---> 100 TeV
Cr_sctns: GheishaInelastic: 0 eV ---> 100 TeV
---------------------------------------------------
Hadronic Processes for mu+
Process: muonNuclear
Model: G4MuonVDNuclearModel: 0 eV ---> 1 PeV
Cr_sctns: KokoulinMuonNuclearXS: 0 eV ---> 100 TeV
---------------------------------------------------
Hadronic Processes for mu-
Process: muonNuclear
Model: G4MuonVDNuclearModel: 0 eV ---> 1 PeV
Cr_sctns: KokoulinMuonNuclearXS: 0 eV ---> 100 TeV
================================================================
=======================================================================
====== Pre-compound/De-excitation Physics Parameters ========
=======================================================================
Type of pre-compound inverse x-section 3
Pre-compound model active 1
Pre-compound low energy (MeV) 0.1
Type of de-excitation inverse x-section 3
Type of de-excitation factory Evaporation
Number of de-excitation channels 8
Min excitation energy (keV) 0.01
Min energy per nucleon for multifragmentation (MeV) 1e+05
Level density (1/MeV) 0.1
Time limit for long lived isomeres (ns) 1e+12
Internal e- conversion flag 1
Store e- internal conversion data 0
Electron internal conversion ID 2
Correlated gamma emission flag 0
Max 2J for sampling of angular correlations 10
=======================================================================
msc: for pi+ SubType= 10
RangeFactor= 0.2, stepLimitType: 0, latDisplacement: 1
===== EM models for the G4Region DefaultRegionForTheWorld ======
@@ -460,8 +397,8 @@ hIoni: for pi+ SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.05, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
Bragg : Emin= 0 eV Emax= 297.505 keV
BetheBloch : Emin= 297.505 keV Emax= 100 TeV
Bragg : Emin= 0 eV Emax= 297.505 keV deltaVI
BetheBloch : Emin= 297.505 keV Emax= 100 TeV deltaVI
hBrems: for pi+ SubType= 3
dE/dx and range tables from 10 eV to 100 TeV in 260 bins
@@ -486,8 +423,8 @@ hIoni: for pi- SubType= 2
Lambda tables from threshold to 100 TeV, 20 bins per decade, spline: 1
finalRange(mm)= 0.05, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
ICRU73QO : Emin= 0 eV Emax= 297.505 keV
BetheBloch : Emin= 297.505 keV Emax= 100 TeV
ICRU73QO : Emin= 0 eV Emax= 297.505 keV deltaVI
BetheBloch : Emin= 297.505 keV Emax= 100 TeV deltaVI
hBrems: for pi- SubType= 3
dE/dx and range tables from 10 eV to 100 TeV in 260 bins
@@ -506,43 +443,43 @@ hPairProd: for pi- SubType= 4
Index : 0 used in the geometry : Yes
Material : G4_AIR
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 10 um
Energy thresholds : gamma 990 eV e- 990 eV e+ 990 eV proton 1 keV
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 100 um
Energy thresholds : gamma 990 eV e- 990 eV e+ 990 eV proton 10 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 1 used in the geometry : Yes
Material : G4_Galactic
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 10 um
Energy thresholds : gamma 990 eV e- 990 eV e+ 990 eV proton 1 keV
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 100 um
Energy thresholds : gamma 990 eV e- 990 eV e+ 990 eV proton 10 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 2 used in the geometry : Yes
Material : G4_Ti
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 10 um
Energy thresholds : gamma 1.28664 keV e- 42.9443 keV e+ 42.0872 keV proton 1 keV
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 100 um
Energy thresholds : gamma 1.28664 keV e- 42.9443 keV e+ 42.0872 keV proton 10 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 3 used in the geometry : Yes
Material : G4_PLEXIGLASS
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 10 um
Energy thresholds : gamma 990 eV e- 18.2368 keV e+ 17.8256 keV proton 1 keV
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 100 um
Energy thresholds : gamma 990 eV e- 18.2368 keV e+ 17.8256 keV proton 10 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 4 used in the geometry : Yes
Material : G4_Al
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 10 um
Energy thresholds : gamma 990 eV e- 34.1725 keV e+ 33.9436 keV proton 1 keV
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 100 um
Energy thresholds : gamma 990 eV e- 34.1725 keV e+ 33.9436 keV proton 10 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 5 used in the geometry : Yes
Material : G4_WATER
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 10 um
Energy thresholds : gamma 990 eV e- 14.0874 keV e+ 14.0874 keV proton 1 keV
Range cuts : gamma 10 um e- 10 um e+ 10 um proton 100 um
Energy thresholds : gamma 990 eV e- 14.0874 keV e+ 14.0874 keV proton 10 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
@@ -559,18 +496,18 @@ Index : 6 used in the geometry : Yes
Run 0 starts ...
---> Begin of Event: 0
---> Begin of Event: 1000
Run terminated.
Run Summary
Number of events processed : 2
User=0.050000s Real=0.049744s Sys=0.000000s
Dose is being written to Dose.out
... write Root file : DoseDistribution.root - done
... close Root file : DoseDistribution.root - done
Number of events processed : 2000
User=12.400000s Real=13.946527s Sys=0.180000s
/score/dumpQuantityToFile boxMesh_1 dose dose.out
Graphics systems deleted.
Visualization Manager deleting...
G4 kernel has come to Quit state.
================== Deleting memory pools ===================
Number of memory pools allocated: 12 of which, static: 1
Dynamic pools deleted: 11 / Total memory freed: 0.18 MB
Number of memory pools allocated: 11 of which, static: 0
Dynamic pools deleted: 11 / Total memory freed: 0.17 MB
============================================================
RunManagerKernel is deleted. Good bye :)
examples/advanced/iort_therapy/macro/GNUmakefile
-11
View File
@@ -1,11 +0,0 @@
# GNUmakefile for macro directory, Gillis Danielsen
all:
make doc
doc:
doxygen ./configureDoxygen
viewdoc:
make doc
firefox ../../hadrontherapyDoxygen/html/index.html
examples/advanced/iort_therapy/macro/detectorGeometry.mac
-149
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# S.E. Mazzaglia Nov 14, 2009
# Example macro file to show how to change geometric properties and voxelization of the phantom/detector
#######################
# Set of the verboses #
#######################
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0
##########################
# Set of the physic models
#
#/Physics/addPhysics standard_opt3 # Electromagnetic model
#/Physics/addPhysics elastic # Hadronic elastic model
#/Physics/addPhysics binary # Hadronic inelastic model
#/Physics/addPhysics local_ion_ion_inelastic # Hadronic inelastic model for ions (local physic list)
#/Physics/addPhysics radioactive_decay
#
# Or alternatively:
#
/Physics/addPhysics QGSP_BIC_EMY
/Physics/addPhysics radioactive_decay
# Initialize geometry and physic
/run/initialize
#############################
# Initialize graphic system #
#############################
#
/vis/scene/create
/vis/open OGL
/vis/viewer/flush
/vis/viewer/set/viewpointThetaPhi 30 140 deg
/vis/scene/add/trajectories
/vis/scene/endOfEventAction accumulate -1 # this accumulate infinite tracks
# zoom to phantom...
/vis/viewer/panTo 1.5 0.5
/vis/viewer/zoomTo 3
##########################
# Set here the cut and the step max for the tracking.
# Suggested values of cut and step:
#
/Physics/setCuts 0.01 mm
/Step/waterPhantomStepMax 0.01 mm
#########################
#########################
# Set the primary particle type,
# energy and position along the X direction
#
/gun/particle proton
/beam/energy/meanEnergy 62 MeV
/beam/energy/sigmaEnergy 400 keV
/beam/position/Xposition -2700 mm
# Copy & Paste in a new macro the previous and ONE of the following groups of commands
# in order to change the Phantom & Detector geometry!
############################
# Change Phantom geometry #
############################
# Move Phantom 10 cm forward the default position (20, 0 , 0 cm)
# Position refers to the center of the phantom box respect to the center of the World
/changePhantom/position 30. 0. 0. cm
/changePhantom/update
# Enlarge Phantom to (42, 40, 40 cm) respect to the default sizes (40, 40, 40 cm)
# Null or negative parameters mean "leave it unchanged"
/changePhantom/size 42. 0. 0. cm
/changePhantom/update
#
/run/beamOn 300
#
############################
# Change Detector geometry #
############################
# Change detector size along X dimension
# "0" parameter means "leave it unchanged"
/changeDetector/size 41. 0. 0. cm
# The following line moves the detector 1 cm forward (along the beam direction),
# respect to the default position inside the phantom (0, 18, 18 cm).
# 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.
# Negative parameters means "leave it unchanged"
/changeDetector/displacement 1. -1. -1. cm
#
/run/beamOn 300
#
###########################
# Change Detector Voxels #
###########################
#
# Use the following line if you need more slabs along the X direction, leaving unchanged the other sizes
# Null or negative parameters mean "leave it unchanged"
/changeDetector/voxelSize 100. 0. 0. um
/changePhantom/update
# StepMax SHOULD not be bigger than 5% of the dose slice thickness!
/Step/waterPhantomStepMax 0.005 mm
#################################################################################################
####################################
# Change Phantom/Detector geometry #
####################################
##########################################################################################
# Cut & paste the following commands in order to create, starting from the default sizes,
# an unique, 10 microns depth, slab in the detector,
# enlarging it to fit to the phantom Y and Z sizes
# Set voxel size along X to 10 microns
/changeDetector/voxelSize 10 0 0 um
# Put detector in the lower left corner of the phantom
/changeDetector/displacement 0 0 0
# Resize the detector to fit voxel X size and phantom Y and Z sizes
/changeDetector/size 0.01 400 400 mm
# Enlarge voxel Y and Z sizes to fit to that of the phantom (in order to have a simple slab)
/changeDetector/voxelSize 0 400 400 mm
# Optionally, fit completely the phantom to the detector
/changePhantom/size 0.01 0 0 mm
/changePhantom/update
#########################################################################################
##########################################################################################
# Cut & paste the following commands in order to create, starting from the default sizes,
# a full voxellized (200 by 200 by 200) detector
/changeDetector/voxelSize 0 200 200 um
/changeDetector/displacement 0 0 0
/changePhantom/size 4 4 4 cm
/changePhantom/update
##########################################################################################
examples/advanced/iort_therapy/macro/manySlabsPhantom.mac
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# S.E. Mazzaglia May 4 2010
# Example macro file to show how to change geometric properties and voxelization of the phantom/detector
#######################
# Set of the verboses #
#######################
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0
##########################
# Set of the Physic models
#
#/Physics/addPhysics standard_opt3 # Electromagnetic model
#/Physics/addPhysics elastic # Hadronic elastic model
#/Physics/addPhysics binary # Hadronic inelastic model
#/Physics/addPhysics local_ion_ion_inelastic # Hadronic inelastic model for ions (local Physic list)
#/Physics/addPhysics radioactive_decay
#
# Or alternatively:
#
/Physics/addPhysics QGSP_BIC_EMY
# Initialize geometry and Physics
/run/initialize
#############################
# Initialize graphic system #
#############################
#
/vis/scene/create
/vis/open OGL
/vis/viewer/flush
/vis/viewer/set/viewpointThetaPhi 30 140 deg
/tracking/storeTrajectory 1
/vis/scene/endOfEventAction accumulate -1 # this accumulate infinite tracks
# zoom to phantom...
/vis/viewer/panTo 1.5 0.5
/vis/viewer/zoomTo 3
##########################
# Set here the cut and the step max for the tracking.
# Suggested values of cut and step:
#
# Set cuts outside detector
/Physics/setCuts 0.01 mm
# Set cuts ONLY inside detector
/Physics/setDetectorCuts 0.01 mm
/Step/waterPhantomStepMax 0.01 mm
#########################
#########################
# Set the primary particle type,
# energy and position along the X direction
#
/gun/particle proton
/beam/energy/meanEnergy 62 MeV
/beam/energy/sigmaEnergy 400 keV
/beam/position/Xposition -2700 mm
# Copy & Paste in a new macro the previous and ONE of the following groups of commands
# in order to change the Phantom & Detector geometry!
######################################
# Change Phantom & Detector geometry #
######################################
##########################################################################################
# Cut & paste the following commands in order to create,
# a Phantom with a detector divided by 40 slabs
# Each slab is 0.1 mm along the X direction, 40 mm along the Y and Z.
#/changePhantom/material G4_PLEXIGLASS # in case you do not want the default phantom made of liquid water
/changePhantom/size 40 40 40 cm
/changeDetector/size 4 4 4 cm
/changeDetector/voxelSize 0.1 40 40 mm
/changePhantom/update # update geometry!
/run/beamOn 1000
examples/advanced/iort_therapy/macro/oneSlabPhantom.mac
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# S.E. Mazzaglia May 4 2010
# Example macro file to show how to change geometric properties and voxelization of the phantom/detector
#######################
# Set of the verboses #
#######################
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0
##########################
# Set of the physic models
#
#/physic/addPhysics standard_opt3 # Electromagnetic model
#/physic/addPhysics elastic # Hadronic elastic model
#/physic/addPhysics binary # Hadronic inelastic model
#/physic/addPhysics local_ion_ion_inelastic # Hadronic inelastic model for ions (local physic list)
#/Physics/addPhysics radioactive_decay
#
# Or alternatively:
#
/Physics/addPhysics QGSP_BIC_EMY
# Initialize geometry and physic
/run/initialize
#############################
# Initialize graphic system #
#############################
#
/vis/scene/create
/vis/open OGL
/vis/viewer/flush
/vis/viewer/set/viewpointThetaPhi 30 140 deg
/tracking/storeTrajectory 1
/vis/scene/endOfEventAction accumulate -1 # this accumulate infinite tracks
# zoom to phantom...
/vis/viewer/panTo 1.5 0.5
/vis/viewer/zoomTo 3
##########################
# Set here the cut and the step max for the tracking.
# Suggested values of cut and step:
#
# Set cuts outside detector
/Physics/setCuts 0.01 mm
# Set cuts ONLY inside detector
/Physics/setDetectorCuts 0.01 mm
/Step/waterPhantomStepMax 0.01 mm
#########################
#########################
# Set the primary particle type,
# energy and position along the X direction
#
/gun/particle proton
/beam/energy/meanEnergy 62 MeV
/beam/energy/sigmaEnergy 400 keV
/beam/position/Xposition -2700 mm
# Copy & Paste in a new macro the previous and ONE of the following groups of commands
# in order to change the Phantom & Detector geometry!
######################################
# Change Phantom & Detector geometry #
######################################
##########################################################################################
# Cut & paste the following commands in order to create,
# a Phantom with a detector divided by one only slab
# 1 mm along the X direction, 400 mm along the Y and Z.
#/changePhantom/material G4_PLEXIGLASS # in case you do not want the default phantom made of liquid water
/changeDetector/displacement 0 0 0 mm
/changePhantom/size 1 400 400 mm
/changeDetector/size 1 400 400 mm
/changeDetector/voxelSize 1 400 400 mm
/changePhantom/update # update geometry!
/run/beamOn 1000
examples/advanced/iort_therapy/macro/stoppingPowers.mac
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# S.E. Mazzaglia Nov 14, 2009
#
# Example macro file showing how to calculate stopping powers for particles and ions
#
#######################
# Set of the verboses #
#######################
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0
##########################
# Set of the physic models
#
#/Physics/addPhysics standard_opt3 # Electromagnetic model
#/Physics/addPhysics elastic # Hadronic elastic model
#/Physics/addPhysics binary # Hadronic inelastic model
#/Physics/addPhysics local_ion_ion_inelastic # Hadronic inelastic model for ions (local physic list)
#/Physics/addPhysics radioactive_decay
#
# Or alternatively:
#
/Physics/addPhysics QGSP_BIC_EMY
/Physics/addPhysics radioactive_decay
# Initialize geometry and physic
/run/initialize
#########################
###############################
# Stopping Powers calculation #
###############################
###############################
# List of available materials #
###############################
# Show all available materials (list with additional informations)
/parameter/nist all
# Show all available elements (list with additional informations)
#/parameter/nist simple
# Show all available elements and materials (simple full list)
#/parameter/nist
###############
# "Particles" #
###############
# Calculate stopping power for proton into liquid water at 1 MeV
/parameter/getstopping G4_WATER
# Calculate stopping powers for protons into Hydrogen from 1 keV up to 200 MeV with 100 data points
# Print data to user terminal
/parameter/getstopping G4_H 0.001 200 100
# Calculate stopping powers for alphas into Copper from 1 keV up to 200 MeV with 100 data points
/parameter/getstopping G4_Cu 0.001 200 100 alpha stopAlpha_Cu_1keV_200MeV.out
########
# Ions #
########
# First you need to define the ion
/gun/particle ion
/gun/ion 6 12 6
# This is non necessary if the ion is already into Geant4 database:
# /particle/list
/parameter/getstopping G4_WATER 1 150 200 C12[0.0] stopCarbon_Water_1MeV_150MeV.out
examples/advanced/iort_therapy/macro/visualisationMacro.mac
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# G.A.P.Cirrone
#
# Default macro file. It is called if no argument is provided at run
#
# i.e. simply typing $G4WORKDIR/bin/Linux-++/Hadrontherapy <no argument here!>
#
# This macro can be used for a proton beam in water. Both electrmagnetic and
# hadronic models are swiched on
#########################
# Set of the verboses
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0
##########################
# Set of the physic models
#
/Physics/addPhysics QGSP_BIC_EMY
/Physics/addPhysics radioactive_decay
##########################
# Initialisation procedure
#
/run/initialize
##########################
# Visualisation
#
/vis/scene/create
/vis/open OGL
#/vis/viewer/flush
/vis/viewer/set/viewpointThetaPhi 30 140 deg
/vis/viewer/zoom 1
/vis/viewer/pan -10 0 cm
/vis/scene/add/trajectories
/vis/scene/endOfEventAction accumulate
/vis/viewer/update
##########################
# Set here the cut and the step max for the tracking.
# Suggested values of cut and step:
#
/Physics/setCuts 0.01 mm
/Step/waterPhantomStepMax 0.01 mm
#########################
# Set the primary particle type,
# energy and position along the X direction
#
/gun/particle proton
/beam/energy/meanEnergy 62 MeV
/beam/energy/sigmaEnergy 400 keV
/beam/position/Xposition -2700 mm
#########################
# Display the event number
# during the run
#
/event/printEventNumber 10
#########################
# Start of the run
#
/run/beamOn 100
examples/advanced/iort_therapy/macro/voxellizedPhantom.mac
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# S.E. Mazzaglia May 4 2010
# Example macro file to show how to change geometric properties and voxelization of the phantom/detector
#######################
# Set of the verboses #
#######################
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0
##########################
# Set of the physic models
#
/Physics/addPhysics emstandard_opt3 # Electromagnetic model
/Physics/addPhysics Em_extra_physics
/Physics/addPhysics Elastic # Hadronic elastic model
/Physics/addPhysics decay
/Physics/addPhysics radioactive_decay
/Physics/addPhysics Stopping_physics
/Physics/addPhysics Neutron_tracking_cut
/Physics/addPhysics binary # Hadronic inelastic model
# Initialize geometry and physic
/run/initialize
#############################
# Initialize graphic system #
#############################
#
/vis/scene/create
/vis/open OGL
/vis/viewer/flush
/vis/viewer/set/viewpointThetaPhi 30 140 deg
/tracking/storeTrajectory 1
/vis/scene/endOfEventAction accumulate -1 # this accumulate infinite tracks
# zoom to phantom...
/vis/viewer/panTo 1.5 0.5
/vis/viewer/zoomTo 3
##########################
# Set here the cut and the step max for the tracking.
# Suggested values of cut and step:
#
# Set cuts outside detector
/Physics/setCuts 0.01 mm
# Set cuts ONLY inside detector
/Physics/setDetectorCuts 0.01 mm
/Step/waterPhantomStepMax 0.01 mm
#########################
#########################
# Set the primary particle type,
# energy and position along the X direction
#
/gun/particle proton
/beam/energy/meanEnergy 62 MeV
/beam/energy/sigmaEnergy 400 keV
/beam/position/Xposition -2700 mm
####################################
# Change Phantom/Detector geometry #
####################################
##########################################################################################
# Cut & paste the following commands in order to create, starting from the default sizes,
# a full voxellized (40 by 40 by 40) detector
/changePhantom/size 4 4 4 cm
/changeDetector/size 4 4 4 cm
/changeDetector/voxelSize 1 1 1 mm
# Put the detector in the lower left corner of the phantom
/changeDetector/displacement 0 0 0
/changePhantom/update
##########################################################################################
/run/beamOn 5000
examples/advanced/iort_therapy/src/Collimator100BeamLine.cc
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/Collimator100BeamLineMessenger.cc
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/Collimator40BeamLine.cc
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/Collimator40BeamLineMessenger.cc
+2 -2
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
@@ -45,7 +45,7 @@
#include "G4UIcmdWithAString.hh"
Collimator40BeamLineMessenger::Collimator40BeamLineMessenger(Collimator40BeamLine* beamLine)
Collimator40BeamLineMessenger::Collimator40BeamLineMessenger(Collimator40BeamLine* beamLine)
:collimator40(beamLine)
{
examples/advanced/iort_therapy/src/Collimator50BeamLine.cc
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/Collimator50BeamLineMessenger.cc
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
@@ -44,12 +44,9 @@
#include "G4UIcmdWithADoubleAndUnit.hh"
#include "G4UIcmdWithAString.hh"
Collimator50BeamLineMessenger::Collimator50BeamLineMessenger(Collimator50BeamLine* beamLine)
Collimator50BeamLineMessenger::Collimator50BeamLineMessenger(Collimator50BeamLine* beamLine)
:collimator50(beamLine)
{
beamLineDir = new G4UIdirectory("/beamLine/");
beamLineDir -> SetGuidance("set specification of range shifter");
examples/advanced/iort_therapy/src/Collimator60BeamLine.cc
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/Collimator80BeamLineMessenger.cc
+1 -1
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@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/IORTAnalysisFileMessenger.cc
-114
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@@ -1,114 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c),
// G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTAnalysisFileMessenger.hh"
#include "IORTAnalysisManager.hh"
#include "G4UIcmdWithAString.hh"
#include "G4UIcmdWithABool.hh"
#include "G4UIdirectory.hh"
#include "IORTMatrix.hh"
/////////////////////////////////////////////////////////////////////////////
IORTAnalysisFileMessenger::IORTAnalysisFileMessenger(IORTAnalysisManager* amgr) :
AnalysisManager(amgr)
{
secondaryCmd = new G4UIcmdWithABool("/analysis/secondary",this);
secondaryCmd -> SetParameterName("secondary", true);
secondaryCmd -> SetDefaultValue("true");
secondaryCmd -> SetGuidance("Set if dose/fluence for the secondary particles will be written"
"\n[usage]: /analysis/secondary [true/false]");
secondaryCmd -> AvailableForStates(G4State_Idle, G4State_PreInit);
DoseMatrixCmd = new G4UIcmdWithAString("/analysis/writeDoseFile",this);
DoseMatrixCmd->SetGuidance("Write the dose/fluence to an ASCII file");
DoseMatrixCmd->SetDefaultValue("Dose.out");
DoseMatrixCmd->SetParameterName("choice",true);
// With this messenger you can:
// give a name to the generated .root file
// One can use this messenger to define a different .root file name other then the default one
FileNameCmd = new G4UIcmdWithAString("/analysis/setAnalysisFile",this);
FileNameCmd->SetGuidance("Set the .root filename for the root-output");
FileNameCmd->SetDefaultValue("default.root");
FileNameCmd->SetParameterName("choice",true); ///<doc did not say what second boolean really does
FileNameCmd->AvailableForStates(G4State_Idle,G4State_PreInit);
}
/////////////////////////////////////////////////////////////////////////////
IORTAnalysisFileMessenger::~IORTAnalysisFileMessenger()
{
delete secondaryCmd;
delete DoseMatrixCmd;
delete FileNameCmd;
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisFileMessenger::SetNewValue(G4UIcommand* command, G4String newValue)
{
if (command == secondaryCmd)
{
if (IORTMatrix::GetInstance())
{
IORTMatrix::GetInstance() -> secondary = secondaryCmd -> GetNewBoolValue(newValue);
}
}
else if (command == DoseMatrixCmd) // Filename can be passed here TODO
{
if ( IORTMatrix * pMatrix = IORTMatrix::GetInstance() )
{
pMatrix -> TotalEnergyDeposit();
pMatrix -> StoreDoseFluenceAscii(newValue);
pMatrix -> StoreDoseFluenceRoot();
// Finalize & write output file
IORTAnalysisManager::GetInstance() -> flush();
}
}
else if (command == FileNameCmd)
{
AnalysisManager->SetAnalysisFileName(newValue);
IORTAnalysisManager::GetInstance() -> book(); // Book for a new output file
}
}
examples/advanced/iort_therapy/src/IORTAnalysisManager.cc
-458
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@@ -1,458 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c),
// G.A.P. Cirrone(d), F.Romano(d)
//
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTAnalysisManager.hh"
#include "IORTMatrix.hh"
#include "IORTAnalysisFileMessenger.hh"
#include <time.h>
IORTAnalysisManager* IORTAnalysisManager::instance = 0;
IORTAnalysisManager::IORTAnalysisManager() :
analysisFileName("DoseDistribution"),
eventCounter(0)
{
fMess = new IORTAnalysisFileMessenger(this);
}
/////////////////////////////////////////////////////////////////////////////
IORTAnalysisManager::~IORTAnalysisManager()
{
if (fMess)
delete fMess;
delete G4AnalysisManager::Instance();
}
/////////////////////////////////////////////////////////////////////////////
IORTAnalysisManager* IORTAnalysisManager::GetInstance()
{
if (instance == 0) instance = new IORTAnalysisManager;
return instance;
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SetAnalysisFileName(G4String aFileName)
{
analysisFileName = aFileName;
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::book()
{
// Create analysis manager
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->SetVerboseLevel(1);
man->SetFirstHistoId(1);
man->SetFirstNtupleId(1);
man->OpenFile(analysisFileName);
// Create the histograms with the energy deposit along the X axis
//ID=1 <different waterthicknesses are accoutned for in ROOT-analysis stage>
man->CreateH1("braggPeak","slice, energy", 400, 0., 80); //
//ID=2
man->CreateH1("h20","Secondary protons - slice, energy", 400, 0., 400.);
//ID=3
man->CreateH1("h30","Secondary neutrons - slice, energy", 400, 0., 400.);
//ID=4
man->CreateH1("h40","Secondary alpha - slice, energy", 400, 0., 400.);
//ID=5
man->CreateH1("h50","Secondary gamma - slice, energy", 400, 0., 400.);
//ID=6
man->CreateH1("h60","Secondary electron - slice, energy", 400, 0., 400.);
//ID=7
man->CreateH1("h70","Secondary triton - slice, energy", 400, 0., 400.);
//ID=8
man->CreateH1("h80","Secondary deuteron - slice, energy", 400, 0., 400.);
//ID=9
man->CreateH1("h90","Secondary pion - slice, energy", 400, 0., 400.);
//ID=10
man->CreateH1("h100","Energy distribution of secondary electrons", 70, 0., 70.);
//ID=11
man->CreateH1("h110","Energy distribution of secondary photons", 70, 0., 70.);
//ID=12
man->CreateH1("h120","Energy distribution of secondary deuterons", 70, 0., 70.);
//ID = 13
man->CreateH1("h130","Energy distribution of secondary tritons", 70, 0., 70.);
//ID = 14
man->CreateH1("h140","Energy distribution of secondary alpha particles", 70, 0., 70.);
//ID = 15
man->CreateH1("heliumEnergyAfterPhantom",
"Energy distribution of secondary helium fragments after the phantom",
70, 0., 500.);
//ID= 16
man->CreateH1("hydrogenEnergyAfterPhantom",
"Energy distribution of secondary helium fragments after the phantom",
70, 0., 500.);
//Now the ntuples
//ID = 1
man->CreateNtuple("kinFragNtuple",
"Kinetic energy by voxel & fragment");
man->CreateNtupleIColumn("i");
man->CreateNtupleIColumn("j");
man->CreateNtupleIColumn("k");
man->CreateNtupleIColumn("A");
man->CreateNtupleDColumn("Z");
man->CreateNtupleDColumn("kineticEnergy");
man->FinishNtuple();
//ID = 2
man->CreateNtuple("kineticEnergyPrimaryNtuple",
"Kinetic energy by voxel of primary");
man->CreateNtupleIColumn("i");
man->CreateNtupleIColumn("j");
man->CreateNtupleIColumn("k");
man->CreateNtupleDColumn("kineticEnergy");
man->FinishNtuple();
//ID = 3
man->CreateNtuple("doseFragNtuple",
"Energy deposit by voxel & fragment");
man->CreateNtupleIColumn("i");
man->CreateNtupleIColumn("j");
man->CreateNtupleIColumn("k");
man->CreateNtupleIColumn("A");
man->CreateNtupleDColumn("Z");
man->CreateNtupleDColumn("energy");
man->FinishNtuple();
// ID =4
man->CreateNtuple("fluenceFragNtuple",
"Fluence by voxel & fragment");
man->CreateNtupleIColumn("i");
man->CreateNtupleIColumn("j");
man->CreateNtupleIColumn("k");
man->CreateNtupleIColumn("A");
man->CreateNtupleDColumn("Z");
man->CreateNtupleDColumn("fluence");
man->FinishNtuple();
// ID=5
man->CreateNtuple("letFragNtuple",
"Let by voxel & fragment");
man->CreateNtupleIColumn("i");
man->CreateNtupleIColumn("j");
man->CreateNtupleIColumn("k");
man->CreateNtupleIColumn("A");
man->CreateNtupleDColumn("Z");
man->CreateNtupleDColumn("letT");
man->CreateNtupleDColumn("letD");
man->FinishNtuple();
//ID=6
man->CreateNtuple("theROOTNtuple",
"Energy deposit by slice");
man->CreateNtupleIColumn("i");
man->CreateNtupleIColumn("j");
man->CreateNtupleIColumn("k");
man->CreateNtupleDColumn("energy");
man->FinishNtuple();
//ID=7
man->CreateNtuple("theROOTIonTuple",
"Generic ion information");
man->CreateNtupleIColumn("a");
man->CreateNtupleDColumn("z");
man->CreateNtupleIColumn("occupancy");
man->CreateNtupleDColumn("energy");
man->FinishNtuple();
//ID=8
man->CreateNtuple("fragmentNtuple",
"Fragments");
man->CreateNtupleIColumn("A");
man->CreateNtupleDColumn("Z");
man->CreateNtupleDColumn("energy");
man->CreateNtupleDColumn("posX");
man->CreateNtupleDColumn("posY");
man->CreateNtupleDColumn("posZ");
man->FinishNtuple();
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::FillEnergyDeposit(G4int i,
G4int j,
G4int k,
G4double energy)
{
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->FillNtupleIColumn(6,0,i);
man->FillNtupleIColumn(6,1,j);
man->FillNtupleIColumn(6,2,k);
man->FillNtupleDColumn(6,3,energy);
man->AddNtupleRow(6);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::BraggPeak(G4int slice, G4double energy)
{
//FIXME
G4AnalysisManager::Instance()->FillH1(1,slice,energy);
//histo1->SetBinContent(slice, energy); //This uses setbincontent instead of fill to get labels correct
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SecondaryProtonEnergyDeposit(G4int slice, G4double energy)
{
G4AnalysisManager::Instance()->FillH1(2,slice,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SecondaryNeutronEnergyDeposit(G4int slice, G4double energy)
{
G4AnalysisManager::Instance()->FillH1(3,slice,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SecondaryAlphaEnergyDeposit(G4int slice, G4double energy)
{
G4AnalysisManager::Instance()->FillH1(4,slice,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SecondaryGammaEnergyDeposit(G4int slice, G4double energy)
{
G4AnalysisManager::Instance()->FillH1(5,slice,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SecondaryElectronEnergyDeposit(G4int slice, G4double energy)
{
G4AnalysisManager::Instance()->FillH1(6,slice,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SecondaryTritonEnergyDeposit(G4int slice, G4double energy)
{
G4AnalysisManager::Instance()->FillH1(7,slice,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SecondaryDeuteronEnergyDeposit(G4int slice, G4double energy)
{
G4AnalysisManager::Instance()->FillH1(8,slice,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::SecondaryPionEnergyDeposit(G4int slice, G4double energy)
{
G4AnalysisManager::Instance()->FillH1(9,slice,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::electronEnergyDistribution(G4double energy)
{
G4AnalysisManager::Instance()->FillH1(10,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::gammaEnergyDistribution(G4double energy)
{
G4AnalysisManager::Instance()->FillH1(11,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::deuteronEnergyDistribution(G4double energy)
{
G4AnalysisManager::Instance()->FillH1(12,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::tritonEnergyDistribution(G4double energy)
{
G4AnalysisManager::Instance()->FillH1(13,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::alphaEnergyDistribution(G4double energy)
{
G4AnalysisManager::Instance()->FillH1(14,energy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::heliumEnergy(G4double secondaryParticleKineticEnergy)
{
G4AnalysisManager::Instance()->FillH1(15,secondaryParticleKineticEnergy);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::hydrogenEnergy(G4double secondaryParticleKineticEnergy)
{
G4AnalysisManager::Instance()->FillH1(16,secondaryParticleKineticEnergy);
}
/////////////////////////////////////////////////////////////////////////////
// FillKineticFragmentTuple create an ntuple where the voxel indexs, the atomic number and mass and the kinetic
// energy of all the particles interacting with the phantom, are stored
void IORTAnalysisManager::FillKineticFragmentTuple(G4int i, G4int j, G4int k, G4int A, G4double Z, G4double kinEnergy)
{
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->FillNtupleIColumn(1,0,i);
man->FillNtupleIColumn(1,1,j);
man->FillNtupleIColumn(1,2,k);
man->FillNtupleIColumn(1,3,A);
man->FillNtupleDColumn(1,4,Z);
man->FillNtupleDColumn(1,5,kinEnergy);
man->AddNtupleRow(1);
}
/////////////////////////////////////////////////////////////////////////////
// FillKineticEnergyPrimaryNTuple creates a ntuple where the voxel indexs and the kinetic
// energies of ONLY primary particles interacting with the phantom, are stored
void IORTAnalysisManager::FillKineticEnergyPrimaryNTuple(G4int i, G4int j, G4int k, G4double kinEnergy)
{
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->FillNtupleIColumn(2,0,i);
man->FillNtupleIColumn(2,1,j);
man->FillNtupleIColumn(2,2,k);
man->FillNtupleDColumn(2,3,kinEnergy);
man->AddNtupleRow(2);
}
/////////////////////////////////////////////////////////////////////////////
// This function is called only if ROOT is activated.
// It is called by the IORTMatric.cc class file and it is used to create two ntuples containing
// the total energy deposited and the fluence values, in each voxel and per any particle (primary
// and secondary particles beam)
void IORTAnalysisManager::FillVoxelFragmentTuple(G4int i, G4int j, G4int k, G4int A, G4double Z,
G4double energy, G4double fluence)
{
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->FillNtupleIColumn(3,0,i);
man->FillNtupleIColumn(3,1,j);
man->FillNtupleIColumn(3,2,k);
man->FillNtupleIColumn(3,3,A);
man->FillNtupleDColumn(3,4,Z);
man->FillNtupleDColumn(3,5,energy);
man->AddNtupleRow(3);
// Fill the ntuple containing the voxel, mass and atomic number and the fluence
if (i==1 && Z==1) {
man->FillNtupleIColumn(4,0,i);
man->FillNtupleIColumn(4,1,j);
man->FillNtupleIColumn(4,2,k);
man->FillNtupleIColumn(4,3,A);
man->FillNtupleDColumn(4,4,Z);
man->FillNtupleDColumn(4,5,fluence);
man->AddNtupleRow(4);
}
}
void IORTAnalysisManager::FillLetFragmentTuple(G4int i, G4int j, G4int k, G4int A, G4double Z,
G4double letT, G4double letD)
{
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->FillNtupleIColumn(5,0,i);
man->FillNtupleIColumn(5,1,j);
man->FillNtupleIColumn(5,2,k);
man->FillNtupleIColumn(5,3,A);
man->FillNtupleDColumn(5,4,Z);
man->FillNtupleDColumn(5,5,letT);
man->FillNtupleDColumn(5,6,letD);
man->AddNtupleRow(5);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::FillFragmentTuple(G4int A, G4double Z, G4double energy,
G4double posX, G4double posY, G4double posZ)
{
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->FillNtupleIColumn(8,0,A);
man->FillNtupleDColumn(8,1,Z);
man->FillNtupleDColumn(8,2,energy);
man->FillNtupleDColumn(8,3,posX);
man->FillNtupleDColumn(8,4,posY);
man->FillNtupleDColumn(8,5,posZ);
man->AddNtupleRow(8);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::genericIonInformation(G4int a,
G4double z,
G4int electronOccupancy,
G4double energy)
{
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->FillNtupleIColumn(7,0,a);
man->FillNtupleDColumn(7,1,z);
man->FillNtupleIColumn(7,2,electronOccupancy);
man->FillNtupleDColumn(7,3,energy);
man->AddNtupleRow(7);
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::startNewEvent()
{
eventCounter++;
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::setGeometryMetaData(G4double endDetectorPosition, G4double waterThickness,
G4double phantomCenter)
{
detectorDistance = endDetectorPosition;
phantomDepth = waterThickness;
phantomCenterDistance = phantomCenter;
}
/////////////////////////////////////////////////////////////////////////////
void IORTAnalysisManager::setBeamMetaData(G4double meanKineticEnergy,G4double sigmaEnergy)
{
beamEnergy = meanKineticEnergy;
energyError = sigmaEnergy;
}
/////////////////////////////////////////////////////////////////////////////
// Flush data & close the file
void IORTAnalysisManager::flush()
{
// Save histograms
G4AnalysisManager* man = G4AnalysisManager::Instance();
man->Write();
man->CloseFile();
eventCounter = 0;
}
examples/advanced/iort_therapy/src/IORTDetectorConstruction.cc
+81 -186
View File
@@ -33,14 +33,13 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include <cmath>
#include <CLHEP/Units/SystemOfUnits.h>
#include "G4SystemOfUnits.hh"
#include "globals.hh"
#include "G4SDManager.hh"
#include "G4RunManager.hh"
@@ -60,17 +59,15 @@
#include "G4VisAttributes.hh"
#include "G4NistManager.hh"
#include "IORTDetectorConstruction.hh"
#include "IORTDetectorROGeometry.hh"
#include "IORTDetectorMessenger.hh"
#include "IORTDetectorSD.hh"
#include "IORTMatrix.hh"
#include "IORTAnalysisManager.hh"
#include "G4Tubs.hh"
#include "G4MultiFunctionalDetector.hh"
#include "G4VPrimitiveScorer.hh"
#include "G4PSDoseDeposit3D.hh"
#include "IORTDetectorMessenger.hh"
/////////////////////////////////////////////////////////////////////////////
IORTDetectorConstruction::IORTDetectorConstruction(G4VPhysicalVolume* physicalTreatmentRoom)
: motherPhys(physicalTreatmentRoom), // pointer to WORLD volume
detectorSD(0), detectorROGeometry(0), matrix(0),
phantom(0), detector(0),
phantomLogicalVolume(0), detectorLogicalVolume(0),
phantomPhysicalVolume(0), detectorPhysicalVolume(0),
@@ -89,7 +86,6 @@ IORTDetectorConstruction::IORTDetectorConstruction(G4VPhysicalVolume* physicalTr
physiDiscoIORT1(0)
{
IORTAnalysisManager::GetInstance();
/* NOTE! that the IORTDetectorConstruction class
* does NOT inherit from G4VUserDetectorConstruction G4 class
@@ -100,54 +96,58 @@ IORTDetectorConstruction::IORTDetectorConstruction(G4VPhysicalVolume* physicalTr
// Messenger to change parameters of the phantom/detector geometry
detectorMessenger = new IORTDetectorMessenger(this);
// Default detector voxels size
// 200 slabs along the beam direction (X)
sizeOfVoxelAlongX = 0.5 *CLHEP::mm; //
sizeOfVoxelAlongY = 0.5 *CLHEP::mm; //
sizeOfVoxelAlongZ = 0.5 *CLHEP::mm; //
// Define here the material of the water phantom and of the detector
SetPhantomMaterial("G4_WATER");
// Construct geometry (messenger commands)
SetDetectorSize(7.*CLHEP::cm, 15.*CLHEP::cm, 15.*CLHEP::cm);
SetPhantomSize(20. *CLHEP::cm, 20. *CLHEP::cm, 20. *CLHEP::cm);
SetPhantomPosition(G4ThreeVector(4.5 *CLHEP::cm, 0. *CLHEP::cm, 0. *CLHEP::cm));
SetDetectorToPhantomPosition(G4ThreeVector(0. *CLHEP::cm, 2.5 *CLHEP::cm, 2.5 *CLHEP::cm));
// Detector
// Default detector sizes
detectorSizeX = 7.* cm;
detectorSizeY = 15.* cm;
detectorSizeZ = 15.* cm;
SetDetectorSize(detectorSizeX, detectorSizeY, detectorSizeZ);
// Phantom
SetPhantomSize(20. *cm, 20. *cm, 20. *cm);
SetPhantomPosition(G4ThreeVector(4.5 *cm, 0. *cm, 0. *cm));
SetDetectorToPhantomPosition(G4ThreeVector(0. *cm, 2.5 *cm, 2.5 *cm));
// Default protection disc geometry and materials
SetOuterRadiusDiscoIORT (40. *CLHEP::mm);
SetinnerRadiusDiscoIORT (0.*CLHEP::mm);
SetheightDiscoIORT (2.0*CLHEP::mm);
SetDiscoXPositionIORT (-11.0*CLHEP::mm);
SetDiscoYPositionIORT (0.0*CLHEP::mm);
SetDiscoZPositionIORT (0.0*CLHEP::mm);
SetOuterRadiusDiscoIORT (40. *mm);
SetinnerRadiusDiscoIORT (0.*mm);
SetheightDiscoIORT (2.0*mm);
SetDiscoXPositionIORT (-11.0*mm);
SetDiscoYPositionIORT (0.0*mm);
SetDiscoZPositionIORT (0.0*mm);
SetDiscoMaterialIORT("G4_WATER");
SetOuterRadiusDiscoIORT1 (40. *CLHEP::mm);
SetinnerRadiusDiscoIORT1 (0.*CLHEP::mm);
SetheightDiscoIORT1 (1.0*CLHEP::mm);
SetDiscoXPositionIORT1 (-8.0*CLHEP::mm);
SetOuterRadiusDiscoIORT1 (40. *mm);
SetinnerRadiusDiscoIORT1 (0.*mm);
SetheightDiscoIORT1 (1.0*mm);
SetDiscoXPositionIORT1 (-8.0*mm);
SetDiscoMaterialIORT1("G4_WATER");
SetAngleDiscoIORT0 (90.0 *CLHEP::deg);
SetAngleDiscoIORT0 (90.0 *deg);
// Write virtual parameters to the real ones and check for consistency
UpdateGeometry();
UpdateGeometry();
}
/////////////////////////////////////////////////////////////////////////////
IORTDetectorConstruction::~IORTDetectorConstruction()
{
delete detectorROGeometry;
delete matrix;
delete detectorMessenger;
}
/////////////////////////////////////////////////////////////////////////////
// ConstructPhantom() is the method that reconstuct a water box (called phantom
// (or water phantom) in the usual Medical physicists slang).
// (or water phantom)).
// A water phantom can be considered a good
// approximation of a an human body.
////////////////////////////////////////////////////////////////////////////
void IORTDetectorConstruction::ConstructPhantom()
{
// Definition of the solid volume of the Phantom
@@ -201,6 +201,7 @@ void IORTDetectorConstruction::ConstructPhantom()
// The detector is the volume that can be dived in slices or voxelized
// and in it we can collect a number of usefull information:
// dose distribution, fluence distribution, LET and so on
void IORTDetectorConstruction::ConstructDetector()
{
@@ -224,19 +225,10 @@ void IORTDetectorConstruction::ConstructDetector()
false,0);
// Visualisation attributes of the detector
//skyBlue = new G4VisAttributes( G4Colour(135/255. , 206/255. , 235/255. ));
G4VisAttributes * skyBlue1 = new G4VisAttributes( G4Colour(135/255. , 206/255. , 235/255. ));
//skyBlue1 -> SetForceWireframe(true);
//skyBlue1 -> SetForceSolid(true);
//skyBlue -> SetVisibility(true);
//skyBlue -> SetForceSolid(true);
//skyBlue -> SetForceWireframe(false);
//detectorLogicalVolume -> SetVisAttributes(skyBlue);
detectorLogicalVolume -> SetVisAttributes(skyBlue1);
// detectorLogicalVolume -> SetVisAttributes(G4VisAttributes::GetInvisible());
// **************
// Cut per Region
// **************
@@ -249,7 +241,8 @@ void IORTDetectorConstruction::ConstructDetector()
detectorLogicalVolume -> SetRegion(aRegion);
aRegion -> AddRootLogicalVolume(detectorLogicalVolume);
}
G4cout << "The Detector has been built --- Add a scoring mesh for it in the GUI if appropriate (similar to the phantom one)" << G4endl;
}
void IORTDetectorConstruction::ConstructDisc()
@@ -257,10 +250,8 @@ void IORTDetectorConstruction::ConstructDisc()
// ---------------------------------------------------------------//
// 6.0 mm Protection Discs Volume //
// ---------------------------------------------------------------//
const G4double startAngleDiscoIORT0 = 0.*CLHEP::deg;
const G4double spanningAngleDiscoIORT0 = 360.*CLHEP::deg;
//G4double phi0 = 180. *CLHEP::deg; // messenger
const G4double startAngleDiscoIORT0 = 0.*deg;
const G4double spanningAngleDiscoIORT0 = 360.*deg;
// Matrix definition for a rotation (deg).
G4RotationMatrix rm0;
@@ -299,23 +290,16 @@ void IORTDetectorConstruction::ConstructDisc()
gray1-> SetVisibility(true);
//gray1 -> SetForceWireframe(true);
//gray1-> SetForceSolid(true);
// const G4double OuterRadiusDiscoIORT = 35. *CLHEP::mm; // messenger
// const G4double innerRadiusDiscoIORT = 0.*CLHEP::mm; // messenger
// const G4double heightDiscoIORT = 3.0*CLHEP::mm; // messenger
const G4double startAngleDiscoIORT = 0.*CLHEP::deg;
const G4double spanningAngleDiscoIORT = 360.*CLHEP::deg;
// const G4double DiscoXPositionIORT = -14.0*CLHEP::mm; // messenger
//G4Material* DiscoMaterialIORT = G4NistManager::Instance()->FindOrBuildMaterial("G4_PLEXIGLASS", isotopes);// messenger
const G4double startAngleDiscoIORT = 0.*deg;
const G4double spanningAngleDiscoIORT = 360.*deg;
G4double phi = 0. *CLHEP::deg;
G4double phi = 0. *deg;
// Matrix definition for a 90 deg rotation. Also used for other volumes
G4RotationMatrix rm;
rm.rotateY(phi);
solidDiscoIORT = new G4Tubs("DiscoIORT", innerRadiusDiscoIORT,
OuterRadiusDiscoIORT,
heightDiscoIORT,
@@ -334,16 +318,9 @@ void IORTDetectorConstruction::ConstructDisc()
// ---------------------------------------------------------------//
// 2.0 mm Lead Protection Disc //
// ---------------------------------------------------------------//
// const G4double OuterRadiusDiscoIORT1 = 35. *CLHEP::mm;
// const G4double innerRadiusDiscoIORT1 = 0.*CLHEP::mm;
// const G4double heightDiscoIORT1 = 0.5*CLHEP::mm;
const G4double startAngleDiscoIORT1 = 0.*CLHEP::deg;
const G4double spanningAngleDiscoIORT1 = 360.*CLHEP::deg;
// const G4double DiscoXPositionIORT1 = -10.5*CLHEP::mm; messenger
// G4Material* DiscoMaterialIORT1 = G4NistManager::Instance()->FindOrBuildMaterial("G4_Cu", isotopes);// messenger
const G4double startAngleDiscoIORT1 = 0.*deg;
const G4double spanningAngleDiscoIORT1 = 360.*deg;
solidDiscoIORT1 = new G4Tubs("DiscoIORT1", innerRadiusDiscoIORT1,
OuterRadiusDiscoIORT1,
@@ -364,47 +341,6 @@ void IORTDetectorConstruction::ConstructDisc()
}
/////////////////////////////////////////////////////////////////////////////
void IORTDetectorConstruction::ConstructSensitiveDetector(G4ThreeVector detectorToWorldPosition)
{
// Install new Sensitive Detector and ROGeometry
delete detectorROGeometry; // this should be safe in C++ also if we have a NULL pointer
//if (detectorSD) detectorSD->PrintAll();
//delete detectorSD;
// Sensitive Detector and ReadOut geometry definition
G4SDManager* sensitiveDetectorManager = G4SDManager::GetSDMpointer();
static G4String sensitiveDetectorName = "Detector";
if (!detectorSD)
{
// The sensitive detector is instantiated
detectorSD = new IORTDetectorSD(sensitiveDetectorName);
}
// The Read Out Geometry is instantiated
static G4String ROGeometryName = "DetectorROGeometry";
detectorROGeometry = new IORTDetectorROGeometry(ROGeometryName,
detectorToWorldPosition,
detectorSizeX/2, // controllare che sia necessario /2
detectorSizeY/2, // CONFERMATO!!! ci vuole!!!
detectorSizeZ/2,
numberOfVoxelsAlongX,
numberOfVoxelsAlongY,
numberOfVoxelsAlongZ);
G4cout << "Instantiating new Read Out Geometry \"" << ROGeometryName << "\""<< G4endl;
// This will invoke Build() IORTDetectorROGeometry virtual method
detectorROGeometry -> BuildROGeometry();
// Attach ROGeometry to SDetector
detectorSD -> SetROgeometry(detectorROGeometry);
//sensitiveDetectorManager -> Activate(sensitiveDetectorName, true);
if (!sensitiveDetectorManager -> FindSensitiveDetector(sensitiveDetectorName, false))
{
G4cout << "Registering new DetectorSD \"" << sensitiveDetectorName << "\""<< G4endl;
// Register user SD
sensitiveDetectorManager -> AddNewDetector(detectorSD);
// Attach SD to detector logical volume
detectorLogicalVolume -> SetSensitiveDetector(detectorSD);
}
}
void IORTDetectorConstruction::ParametersCheck()
{
// Check phantom/detector sizes & relative position
@@ -417,20 +353,8 @@ void IORTDetectorConstruction::ParametersCheck()
detectorToPhantomPosition
))
G4Exception("IORTDetectorConstruction::ParametersCheck()", "IORT0001", FatalException, "Error: Detector is not fully inside Phantom!");
// Check Detector sizes respect to the voxel ones
if ( detectorSizeX < sizeOfVoxelAlongX) {
G4Exception("IORTDetectorConstruction::ParametersCheck()", "IORT0002", FatalException, "Error: Detector X size must be bigger or equal than that of Voxel X");
}
if ( detectorSizeY < sizeOfVoxelAlongY) {
G4Exception("IORTDetectorConstruction::ParametersCheck()", "IORT0003", FatalException, "Error: Detector X size must be bigger or equal than that of Voxel Y");
}
if ( detectorSizeZ < sizeOfVoxelAlongZ) {
G4Exception("IORTDetectorConstruction::ParametersCheck()", "IORT0004", FatalException, "Error: Detector X size must be bigger or equal than that of Voxel Z");
}
}
/////////////////
// MESSENGERS //
////////////////
@@ -530,15 +454,12 @@ void IORTDetectorConstruction::SetDetectorSize(G4double sizeX, G4double sizeY, G
if (sizeX > 0.) {detectorSizeX = sizeX;}
if (sizeY > 0.) {detectorSizeY = sizeY;}
if (sizeZ > 0.) {detectorSizeZ = sizeZ;}
SetVoxelSize(sizeOfVoxelAlongX, sizeOfVoxelAlongY, sizeOfVoxelAlongZ);
}
/////////////////////////////////////////////////////////////////////////////
void IORTDetectorConstruction::SetVoxelSize(G4double sizeX, G4double sizeY, G4double sizeZ)
void IORTDetectorConstruction::SetVoxelSize(G4double , G4double , G4double)
{
if (sizeX > 0.) {sizeOfVoxelAlongX = sizeX;}
if (sizeY > 0.) {sizeOfVoxelAlongY = sizeY;}
if (sizeZ > 0.) {sizeOfVoxelAlongZ = sizeZ;}
G4cout<< "SetVoxelSize method is not needed anymore " << G4endl;
}
void IORTDetectorConstruction::SetPhantomPosition(G4ThreeVector pos)
{
@@ -560,7 +481,7 @@ void IORTDetectorConstruction::SetOuterRadiusDiscoIORT(G4double outerr)
void IORTDetectorConstruction::SetinnerRadiusDiscoIORT(G4double innerr)
{
if (innerr > 0.) {innerRadiusDiscoIORT = innerr;}
if (innerr >= 0.) {innerRadiusDiscoIORT = innerr;}
}
@@ -599,7 +520,7 @@ void IORTDetectorConstruction::SetOuterRadiusDiscoIORT1(G4double outerr)
void IORTDetectorConstruction::SetinnerRadiusDiscoIORT1(G4double innerr)
{
if (innerr > 0.) {innerRadiusDiscoIORT1 = innerr;}
if (innerr >= 0.) {innerRadiusDiscoIORT1 = innerr;}
}
@@ -654,38 +575,19 @@ void IORTDetectorConstruction::UpdateGeometry()
else ConstructDetector();
// update disc function
delete solidDiscoIORT0;
delete logicDiscoIORT0;
delete physiDiscoIORT0;
delete solidDiscoIORT;
delete logicDiscoIORT;
delete physiDiscoIORT;
delete solidDiscoIORT1;
delete logicDiscoIORT1;
delete physiDiscoIORT1;
if (physiDiscoIORT1) delete physiDiscoIORT1;
if (logicDiscoIORT1) delete logicDiscoIORT1;
if (solidDiscoIORT1) delete solidDiscoIORT1;
if (physiDiscoIORT) delete physiDiscoIORT;
if (logicDiscoIORT) delete logicDiscoIORT;
if (solidDiscoIORT) delete solidDiscoIORT;
if (physiDiscoIORT0) delete physiDiscoIORT0;
if (logicDiscoIORT0) delete logicDiscoIORT0;
if (solidDiscoIORT0) delete solidDiscoIORT0;
ConstructDisc();
// Round to nearest integer number of voxel
numberOfVoxelsAlongX = G4lrint(detectorSizeX / sizeOfVoxelAlongX);
sizeOfVoxelAlongX = ( detectorSizeX / numberOfVoxelsAlongX );
numberOfVoxelsAlongY = G4lrint(detectorSizeY / sizeOfVoxelAlongY);
sizeOfVoxelAlongY = ( detectorSizeY / numberOfVoxelsAlongY );
numberOfVoxelsAlongZ = G4lrint(detectorSizeZ / sizeOfVoxelAlongZ);
sizeOfVoxelAlongZ = ( detectorSizeZ / numberOfVoxelsAlongZ );
//G4cout << "*************** DetectorToWorldPosition " << GetDetectorToWorldPosition()/cm << "\n";
ConstructSensitiveDetector(GetDetectorToWorldPosition());
volumeOfVoxel = sizeOfVoxelAlongX * sizeOfVoxelAlongY * sizeOfVoxelAlongZ;
massOfVoxel = detectorMaterial -> GetDensity() * volumeOfVoxel;
// This will clear the existing matrix (together with all data inside it)!
matrix = IORTMatrix::GetInstance(numberOfVoxelsAlongX,
numberOfVoxelsAlongY,
numberOfVoxelsAlongZ,
massOfVoxel);
// Inform the kernel about the new geometry
G4RunManager::GetRunManager() -> GeometryHasBeenModified();
@@ -695,18 +597,21 @@ void IORTDetectorConstruction::UpdateGeometry()
}
void IORTDetectorConstruction::DeleteDisc()
{
delete solidDiscoIORT0;
delete logicDiscoIORT0;
delete physiDiscoIORT0;
delete solidDiscoIORT;
delete logicDiscoIORT;
delete physiDiscoIORT;
delete solidDiscoIORT1;
delete logicDiscoIORT1;
delete physiDiscoIORT1;
G4RunManager::GetRunManager() -> GeometryHasBeenModified();
G4RunManager::GetRunManager() -> PhysicsHasBeenModified();
{
if (physiDiscoIORT1) delete physiDiscoIORT1;
if (logicDiscoIORT1) delete logicDiscoIORT1;
if (solidDiscoIORT1) delete solidDiscoIORT1;
if (physiDiscoIORT) delete physiDiscoIORT;
if (logicDiscoIORT) delete logicDiscoIORT;
if (solidDiscoIORT) delete solidDiscoIORT;
if (physiDiscoIORT0) delete physiDiscoIORT0;
if (logicDiscoIORT0) delete logicDiscoIORT0;
if (solidDiscoIORT0) delete solidDiscoIORT0;
G4RunManager::GetRunManager() -> GeometryHasBeenModified();
G4RunManager::GetRunManager() -> PhysicsHasBeenModified();
}
@@ -727,15 +632,5 @@ void IORTDetectorConstruction::PrintParameters()
G4cout << "DX= "<< G4BestUnit(phantomPosition.getX(),"Length") <<
"DY= "<< G4BestUnit(phantomPosition.getY(),"Length") <<
"DZ= "<< G4BestUnit(phantomPosition.getZ(),"Length") << G4endl;
G4cout << "The (X,Y,Z) sizes of the Voxels are: (" <<
G4BestUnit(sizeOfVoxelAlongX, "Length") << ',' <<
G4BestUnit(sizeOfVoxelAlongY, "Length") << ',' <<
G4BestUnit(sizeOfVoxelAlongZ, "Length") << ')' << G4endl;
G4cout << "The number of Voxels along (X,Y,Z) is: (" <<
numberOfVoxelsAlongX << ',' <<
numberOfVoxelsAlongY <<',' <<
numberOfVoxelsAlongZ << ')' << G4endl;
}
examples/advanced/iort_therapy/src/IORTDetectorHit.cc
-77
View File
@@ -1,77 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTDetectorHit.hh"
G4Allocator<IORTDetectorHit> IORTDetectorHitAllocator;
IORTDetectorHit::IORTDetectorHit()
{
energyDeposit = 0;
}
IORTDetectorHit::~IORTDetectorHit()
{
}
IORTDetectorHit::IORTDetectorHit(const IORTDetectorHit &right)
: G4VHit()
{
xHitID = right.xHitID;
zHitID = right.zHitID;
yHitID = right.yHitID;
energyDeposit = right.energyDeposit;
}
const IORTDetectorHit& IORTDetectorHit::operator=(const IORTDetectorHit &right)
{
xHitID = right.xHitID;
zHitID = right.zHitID;
yHitID = right.yHitID;
energyDeposit = right.energyDeposit;
return *this;
}
int IORTDetectorHit::operator==(const IORTDetectorHit &right) const
{
return((xHitID==right.xHitID)&&(zHitID==right.zHitID)&&(yHitID==right.yHitID));
}
examples/advanced/iort_therapy/src/IORTDetectorMessenger.cc
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/IORTDetectorROGeometry.cc
-206
View File
@@ -1,206 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTDetectorROGeometry.hh"
#include "IORTDummySD.hh"
#include "G4SystemOfUnits.hh"
#include "G4LogicalVolume.hh"
#include "G4VPhysicalVolume.hh"
#include "G4PVPlacement.hh"
#include "G4PVReplica.hh"
#include "G4Box.hh"
#include "G4ThreeVector.hh"
#include "G4Material.hh"
/////////////////////////////////////////////////////////////////////////////
IORTDetectorROGeometry::IORTDetectorROGeometry(G4String aString, G4ThreeVector pos,
G4double detectorDimX,
G4double detectorDimY,
G4double detectorDimZ,
G4int numberOfVoxelsX,
G4int numberOfVoxelsY,
G4int numberOfVoxelsZ):
G4VReadOutGeometry(aString),
detectorToWorldPosition(pos),
detectorSizeX(detectorDimX),
detectorSizeY(detectorDimY),
detectorSizeZ(detectorDimZ),
numberOfVoxelsAlongX(numberOfVoxelsX),
numberOfVoxelsAlongY(numberOfVoxelsY),
numberOfVoxelsAlongZ(numberOfVoxelsZ)
{
}
/////////////////////////////////////////////////////////////////////////////
IORTDetectorROGeometry::~IORTDetectorROGeometry()
{
}
/////////////////////////////////////////////////////////////////////////////
G4VPhysicalVolume* IORTDetectorROGeometry::Build()
{
// A dummy material is used to fill the volumes of the readout geometry.
// (It will be allowed to set a NULL pointer in volumes of such virtual
// division in future, since this material is irrelevant for tracking.)
G4Material* dummyMat = new G4Material(name="dummyMat", 1., 1.*g/mole, 1.*g/cm3);
G4double worldSizeX = 400.0 *cm; // 200.0 *cm;
G4double worldSizeY = 400.0 *cm; // 200.0 *cm;
G4double worldSizeZ = 400.0 *cm; // 200.0 *cm;
G4double halfDetectorSizeX = detectorSizeX;
G4double halfDetectorSizeY = detectorSizeY;
G4double halfDetectorSizeZ = detectorSizeZ;
// World volume of ROGeometry ...
G4Box* ROWorld = new G4Box("ROWorld",
worldSizeX,
worldSizeY,
worldSizeZ);
G4LogicalVolume* ROWorldLog = new G4LogicalVolume(ROWorld, dummyMat,
"ROWorldLog", 0,0,0);
G4VPhysicalVolume* ROWorldPhys = new G4PVPlacement(0,G4ThreeVector(),
"ROWorldPhys",
ROWorldLog,
0,false,0);
// Detector ROGeometry
G4Box *RODetector = new G4Box("RODetector",
halfDetectorSizeX,
halfDetectorSizeY,
halfDetectorSizeZ);
G4LogicalVolume *RODetectorLog = new G4LogicalVolume(RODetector,
dummyMat,
"RODetectorLog",
0,0,0);
G4VPhysicalVolume *RODetectorPhys = new G4PVPlacement(0,
detectorToWorldPosition,
"DetectorPhys",
RODetectorLog,
ROWorldPhys,
false,0);
// Division along X axis: the detector is divided in slices along the X axis
G4double halfXVoxelSizeX = halfDetectorSizeX/numberOfVoxelsAlongX;
G4double halfXVoxelSizeY = halfDetectorSizeY;
G4double halfXVoxelSizeZ = halfDetectorSizeZ;
G4double voxelXThickness = 2*halfXVoxelSizeX;
G4Box *RODetectorXDivision = new G4Box("RODetectorXDivision",
halfXVoxelSizeX,
halfXVoxelSizeY,
halfXVoxelSizeZ);
G4LogicalVolume *RODetectorXDivisionLog = new G4LogicalVolume(RODetectorXDivision,
dummyMat,
"RODetectorXDivisionLog",
0,0,0);
G4VPhysicalVolume *RODetectorXDivisionPhys = new G4PVReplica("RODetectorXDivisionPhys",
RODetectorXDivisionLog,
RODetectorPhys,
kXAxis,
numberOfVoxelsAlongX,
voxelXThickness);
// Division along Y axis: the slices along the X axis are divided along the Y axis
G4double halfYVoxelSizeX = halfXVoxelSizeX;
G4double halfYVoxelSizeY = halfDetectorSizeY/numberOfVoxelsAlongY;
G4double halfYVoxelSizeZ = halfDetectorSizeZ;
G4double voxelYThickness = 2*halfYVoxelSizeY;
G4Box *RODetectorYDivision = new G4Box("RODetectorYDivision",
halfYVoxelSizeX,
halfYVoxelSizeY,
halfYVoxelSizeZ);
G4LogicalVolume *RODetectorYDivisionLog = new G4LogicalVolume(RODetectorYDivision,
dummyMat,
"RODetectorYDivisionLog",
0,0,0);
G4VPhysicalVolume *RODetectorYDivisionPhys = new G4PVReplica("RODetectorYDivisionPhys",
RODetectorYDivisionLog,
RODetectorXDivisionPhys,
kYAxis,
numberOfVoxelsAlongY,
voxelYThickness);
// Division along Z axis: the slices along the Y axis are divided along the Z axis
G4double halfZVoxelSizeX = halfXVoxelSizeX;
G4double halfZVoxelSizeY = halfYVoxelSizeY;
G4double halfZVoxelSizeZ = halfDetectorSizeZ/numberOfVoxelsAlongZ;
G4double voxelZThickness = 2*halfZVoxelSizeZ;
G4Box *RODetectorZDivision = new G4Box("RODetectorZDivision",
halfZVoxelSizeX,
halfZVoxelSizeY,
halfZVoxelSizeZ);
G4LogicalVolume *RODetectorZDivisionLog = new G4LogicalVolume(RODetectorZDivision,
dummyMat,
"RODetectorZDivisionLog",
0,0,0);
RODetectorZDivisionPhys = new G4PVReplica("RODetectorZDivisionPhys",
RODetectorZDivisionLog,
RODetectorYDivisionPhys,
kZAxis,
numberOfVoxelsAlongZ,
voxelZThickness);
IORTDummySD *dummySD = new IORTDummySD;
RODetectorZDivisionLog -> SetSensitiveDetector(dummySD);
return ROWorldPhys;
}
examples/advanced/iort_therapy/src/IORTDetectorSD.cc
-205
View File
@@ -1,205 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTDetectorSD.hh"
#include "IORTAnalysisManager.hh"
#include "IORTDetectorHit.hh"
#include "G4Step.hh"
#include "G4VTouchable.hh"
#include "G4TouchableHistory.hh"
#include "G4SDManager.hh"
#include "IORTMatrix.hh"
#include "G4SystemOfUnits.hh"
/////////////////////////////////////////////////////////////////////////////
IORTDetectorSD::IORTDetectorSD(G4String dname):
G4VSensitiveDetector(dname)
{
G4String HCname;
collectionName.insert(HCname="IORTDetectorHitsCollection");
HitsCollection = NULL;
sensitiveDetectorName = dname;
}
/////////////////////////////////////////////////////////////////////////////
IORTDetectorSD::~IORTDetectorSD()
{
}
/////////////////////////////////////////////////////////////////////////////
void IORTDetectorSD::Initialize(G4HCofThisEvent*)
{
HitsCollection = new IORTDetectorHitsCollection(sensitiveDetectorName,
collectionName[0]);
}
/////////////////////////////////////////////////////////////////////////////
G4bool IORTDetectorSD::ProcessHits(G4Step* aStep, G4TouchableHistory* ROhist)
{
//The code doesn't seem to get here if we use the IAEA geometry. FIXME
if(!ROhist)
return false;
if (aStep -> GetPreStepPoint() -> GetPhysicalVolume() -> GetName() != "DetectorPhys")
return false;
// Get kinetic energy
G4Track * theTrack = aStep -> GetTrack();
//G4double kineticEnergy = theTrack -> GetKineticEnergy();
G4ParticleDefinition *particleDef = theTrack -> GetDefinition();
//Get particle name
G4String particleName = particleDef -> GetParticleName();
// G4cout << particleDef -> GetParticleType() << '\n';
// Get unique track_id (in an event)
G4int trackID = theTrack -> GetTrackID();
G4double energyDeposit = aStep -> GetTotalEnergyDeposit();
G4int Z = particleDef-> GetAtomicNumber();
//G4int A = particleDef-> GetAtomicMass();
// Read voxel indexes: i is the x index, k is the z index
G4int k = ROhist -> GetReplicaNumber(0);
G4int i = ROhist -> GetReplicaNumber(2);
G4int j = ROhist -> GetReplicaNumber(1);
IORTAnalysisManager* analysis = IORTAnalysisManager::GetInstance();
IORTMatrix* matrix = IORTMatrix::GetInstance();
if (matrix)
{
// Increment Fluences & accumulate energy spectra
// Hit voxels are marked with track_id throught hitTrack matrix
G4int* hitTrack = matrix -> GetHitTrack(i,j,k); // hitTrack MUST BE cleared at every eventAction!
if ( *hitTrack != trackID )
{
*hitTrack = trackID;
/*
* Fill FLUENCE data for every single nuclide
* Exclude e-, neutrons, gamma, ...
*/
if ( Z >= 1)
matrix -> Fill(trackID, particleDef, i, j, k, 0, true);
/*
// Fragments kinetic energy (ntuple)
if (trackID !=1 && Z>=1)
{
// First step kinetic energy for every fragment
analysis -> FillKineticFragmentTuple(i, j, k, A, Z, kineticEnergy/MeV);
}
// Kinetic energy spectra for primary particles
if ( trackID == 1 && i == 0)
{
// First step kinetic energy for primaries only
analysis -> FillKineticEnergyPrimaryNTuple(i, j, k, kineticEnergy/MeV);
}
*/
}
if(energyDeposit != 0)
{
/*
* This method will fill a dose matrix for every single nuclide.
* A method of the IORTMatrix class (StoreDoseFluenceAscii())
* is called automatically at the end of main (or via the macro command /analysis/writeDoseFile.
* It permits to store all dose/fluence data into a single plane ASCII file.
*/
// if (A==1 && Z==1) // primary and sec. protons
if ( Z>=1 ) // exclude e-, neutrons, gamma, ...
matrix -> Fill(trackID, particleDef, i, j, k, energyDeposit);
/*
* Create a hit with the information of position is in the detector
*/
IORTDetectorHit* detectorHit = new IORTDetectorHit();
detectorHit -> SetEdepAndPosition(i, j, k, energyDeposit);
HitsCollection -> insert(detectorHit);
}
}
if(energyDeposit != 0)
{
if(trackID != 1)
{
if (particleName == "proton")
analysis -> SecondaryProtonEnergyDeposit(i, energyDeposit/MeV);
else if (particleName == "neutron")
analysis -> SecondaryNeutronEnergyDeposit(i, energyDeposit/MeV);
else if (particleName == "alpha")
analysis -> SecondaryAlphaEnergyDeposit(i, energyDeposit/MeV);
else if (particleName == "gamma")
analysis -> SecondaryGammaEnergyDeposit(i, energyDeposit/MeV);
else if (particleName == "e-")
analysis -> SecondaryElectronEnergyDeposit(i, energyDeposit/MeV);
else if (particleName == "triton")
analysis -> SecondaryTritonEnergyDeposit(i, energyDeposit/MeV);
else if (particleName == "deuteron")
analysis -> SecondaryDeuteronEnergyDeposit(i, energyDeposit/MeV);
else if (particleName == "pi+" || particleName == "pi-" ||
particleName == "pi0")
analysis -> SecondaryPionEnergyDeposit(i, energyDeposit/MeV);
}
}
return true;
}
/////////////////////////////////////////////////////////////////////////////
void IORTDetectorSD::EndOfEvent(G4HCofThisEvent* HCE)
{
static G4int HCID = -1;
if(HCID < 0)
{
HCID = GetCollectionID(0);
}
HCE -> AddHitsCollection(HCID,HitsCollection);
}
examples/advanced/iort_therapy/src/IORTEventAction.cc
+4 -49
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
@@ -41,33 +41,24 @@
#include "G4SystemOfUnits.hh"
#include "G4Event.hh"
#include "G4EventManager.hh"
#include "G4HCofThisEvent.hh"
#include "G4VHitsCollection.hh"
#include "G4SDManager.hh"
#include "G4VVisManager.hh"
#include "IORTEventAction.hh"
#include "IORTDetectorHit.hh"
#include "IORTDetectorSD.hh"
#include "IORTDetectorConstruction.hh"
#include "IORTMatrix.hh"
#include "IORTEventActionMessenger.hh"
/////////////////////////////////////////////////////////////////////////////
IORTEventAction::IORTEventAction() :
drawFlag("all" ),printModulo(1000), pointerEventMessenger(0)
{
hitsCollectionID = -1;
pointerEventMessenger = new IORTEventActionMessenger(this);
}
/////////////////////////////////////////////////////////////////////////////
IORTEventAction::~IORTEventAction()
{
delete pointerEventMessenger;
}
/////////////////////////////////////////////////////////////////////////////
void IORTEventAction::BeginOfEventAction(const G4Event* evt)
{
G4int evtNb = evt->GetEventID();
@@ -75,45 +66,9 @@ void IORTEventAction::BeginOfEventAction(const G4Event* evt)
//printing survey
if (evtNb%printModulo == 0)
G4cout << "\n---> Begin of Event: " << evtNb << G4endl;
G4SDManager* pSDManager = G4SDManager::GetSDMpointer();
if(hitsCollectionID == -1)
hitsCollectionID = pSDManager -> GetCollectionID("IORTDetectorHitsCollection");
}
/////////////////////////////////////////////////////////////////////////////
void IORTEventAction::EndOfEventAction(const G4Event* evt)
{
if(hitsCollectionID < 0)
return;
G4HCofThisEvent* HCE = evt -> GetHCofThisEvent();
// Clear voxels hit list
IORTMatrix* matrix = IORTMatrix::GetInstance();
if (matrix) matrix -> ClearHitTrack();
if(HCE)
{
IORTDetectorHitsCollection* CHC = (IORTDetectorHitsCollection*)(HCE -> GetHC(hitsCollectionID));
if(CHC)
{
if(matrix)
{
// Fill the matrix with the information: voxel and associated energy deposit
// in the detector at the end of the event
G4int HitCount = CHC -> entries();
for (G4int h=0; h<HitCount; h++)
{
G4int i = ((*CHC)[h]) -> GetXID();
G4int j = ((*CHC)[h]) -> GetYID();
G4int k = ((*CHC)[h]) -> GetZID();
G4double energyDeposit = ((*CHC)[h]) -> GetEdep();
matrix -> Fill(i, j, k, energyDeposit/MeV);
}
}
}
}
}
void IORTEventAction::EndOfEventAction(const G4Event*)
{}
examples/advanced/iort_therapy/src/IORTEventActionMessenger.cc
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/IORTGeometryController.cc
+1 -2
View File
@@ -33,14 +33,13 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTGeometryController.hh"
#include "IORTDetectorConstruction.hh"
#include "IORTInteractionParameters.hh"
#include "Collimator40BeamLine.hh"
#include "Collimator50BeamLine.hh"
#include "Collimator60BeamLine.hh"
examples/advanced/iort_therapy/src/IORTGeometryMessenger.cc
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/IORTInteractionParameters.cc
-295
View File
@@ -1,295 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include <fstream>
#include <iostream>
#include <sstream>
#include <cmath>
#include <vector>
#include "IORTInteractionParameters.hh"
#include "IORTParameterMessenger.hh"
#include "IORTDetectorConstruction.hh"
#include "globals.hh"
#include "G4SystemOfUnits.hh"
#include "G4UnitsTable.hh"
#include "G4UImanager.hh"
#include "G4RunManager.hh"
#include "G4LossTableManager.hh"
#include "G4Material.hh"
#include "G4MaterialCutsCouple.hh"
#include "G4ParticleDefinition.hh"
#include "G4ParticleTable.hh"
#include "G4NistManager.hh"
#include "G4Element.hh"
#include "G4StateManager.hh"
IORTInteractionParameters::IORTInteractionParameters(G4bool wantMessenger):
nistEle(new G4NistElementBuilder(0)),
nistMat(new G4NistMaterialBuilder(nistEle, 0)),
data(G4cout.rdbuf()),
pMessenger(0),
beamFlag(false)
#ifdef G4ANALYSIS_USE_ROOT
,theRootCanvas(0),
theRootGraph(0)
#endif
{
if (wantMessenger) pMessenger = new IORTParameterMessenger(this);
}
IORTInteractionParameters::~IORTInteractionParameters()
{
if (pMessenger) delete pMessenger;
delete nistMat;
delete nistEle;
}
G4double IORTInteractionParameters::GetStopping (G4double ene,
const G4ParticleDefinition* pDef,
const G4Material* pMat,
G4double dens)
{
if (dens) return ComputeTotalDEDX(ene, pDef, pMat)/dens;
return ComputeTotalDEDX(ene, pDef, pMat);
}
bool IORTInteractionParameters::GetStoppingTable(const G4String& vararg)
{
// Check arguments
if ( !ParseArg(vararg)) return false;
// Clear previous energy & mass sp vectors
energy.clear();
massDedx.clear();
// log scale
if (kinEmin != kinEmax && npoints >1)
{
G4double logmin = std::log10(kinEmin);
G4double logmax = std::log10(kinEmax);
G4double en;
// uniform log space
for (G4double c = 0.; c < npoints; c++)
{
en = std::pow(10., logmin + ( c*(logmax-logmin) / (npoints - 1.)) );
energy.push_back(en/MeV);
dedxtot = ComputeTotalDEDX (en, particle, material);
massDedx.push_back ( (dedxtot / density)/(MeV*cm2/g) );
}
}
else // one point only
{
energy.push_back(kinEmin/MeV);
dedxtot = ComputeTotalDEDX (kinEmin, particle, material);
massDedx.push_back ( (dedxtot / density)/(MeV*cm2/g) );
}
G4cout.precision(6);
data << "MeV " << "MeV*cm2/g " << particle << " (into " <<
material << ", density = " << G4BestUnit(density,"Volumic Mass") << ")" << G4endl;
data << G4endl;
data << std::left << std::setfill(' ');
for (size_t i=0; i<energy.size(); i++){
data << std::setw(16) << energy[i] << massDedx[i] << G4endl;
}
outfile.close();
// This will plot
#ifdef G4ANALYSIS_USE_ROOT
PlotStopping("pdf");
#endif
// Info to user
G4String ofName = (filename == "") ? "User terminal": filename;
G4cout << "User choice:\n";
G4cout << "Kinetic energy lower limit= "<< G4BestUnit(kinEmin,"Energy") <<
", Kinetic energy upper limit= " << G4BestUnit(kinEmax,"Energy") <<
", npoints= "<< npoints << ", particle= \"" << particle <<
"\", material= \"" << material << "\", filename= \""<<
ofName << "\"" << G4endl;
return true;
}
///////////////////////////////////////////////////////////////////////////////////
// Save Plot
#ifdef G4ANALYSIS_USE_ROOT
void IORTInteractionParameters::PlotStopping(const G4String& filetype)
{
if (!theRootCanvas)
{
gROOT->Reset();
gROOT->SetStyle("Plain");
theRootCanvas = new TCanvas("theRootCanvas","Interaction Parameters",200, 10, 600,400);
theRootCanvas -> SetFillColor(20);
theRootCanvas -> SetBorderMode(1);
theRootCanvas -> SetBorderSize(1);
theRootCanvas -> SetFrameBorderMode(0);
theRootCanvas -> SetGrid();
// Use global pad: root manual pgg 109,...
}
if (theRootGraph) delete theRootGraph;
theRootGraph = new TGraph(energy.size(), &energy[0], &massDedx[0]);
//theRootGraph = new TGraph();
axisX = theRootGraph -> GetXaxis(),
axisY = theRootGraph -> GetYaxis();
axisX -> SetTitle("MeV");
axisY -> SetTitle("Stopping Power (MeV cm2/g)");
//axisX -> SetNdivisions(500,kTRUE);
//axisX -> SetTickLength(0.03);
//axisX -> SetLabelOffset(2.005);
axisX -> SetAxisColor(2);
axisY -> SetAxisColor(2);
gPad -> SetLogx(1);
gPad -> SetLogy(1);
theRootGraph -> SetMarkerColor(4);
theRootGraph -> SetMarkerStyle(20);// circle
theRootGraph -> SetMarkerSize(.5);
G4String gName = particle.substr(0, particle.find("[") ); // cut excitation energy
gName = gName + "_" + material;
G4String fName = "./referenceData/interaction/" + gName + "." + filetype;
theRootGraph -> SetTitle(gName);
theRootGraph -> Draw("AP");
//theRootCanvas -> Update();
//theRootCanvas -> Draw();
theRootCanvas -> SaveAs(fName);
}
#endif
// Search for user material choice inside G4NistManager database
G4Material* IORTInteractionParameters::GetNistMaterial(G4String mat)
{
Pmaterial = G4NistManager::Instance()->FindOrBuildMaterial(mat);
if (Pmaterial) density = Pmaterial -> GetDensity();
return Pmaterial;
}
// Parse arguments line
bool IORTInteractionParameters::ParseArg(const G4String& vararg)
{
kinEmin = kinEmax = npoints = 0.;
particle = material = filename = "";
// set internal variables
std::istringstream strParam(vararg);
// TODO here check for number and parameters consistency
strParam >> std::skipws >> material >> kinEmin >> kinEmax >> npoints >> particle >> filename;
// npoints must be an integer!
npoints = std::floor(npoints);
// Check that kinEmax >= kinEmin > 0 && npoints >= 1
// TODO NIST points and linear scale
if (kinEmax == 0. && kinEmin > 0. ) kinEmax = kinEmin;
if (kinEmax == 0. && kinEmin == 0. ) kinEmax = kinEmin = 1.*MeV;
if (kinEmax < kinEmin)
{
G4cout << "WARNING: kinEmin must not exceed kinEmax!" << G4endl;
G4cout << "Usage: /parameter/command material kinetic Emin kinetic Emax nPoints [particle] [output filename]" << G4endl;
return false;
}
if (npoints < 1) npoints = 1;
// check if element/material is into database
if (!GetNistMaterial(material) )
{
G4cout << "WARNING: material \"" << material << "\" doesn't exist in NIST elements/materials"
" table [$G4INSTALL/source/materials/src/G4NistMaterialBuilder.cc]" << G4endl;
G4cout << "Use command \"/parameter/nist\" to see full materials list" << G4endl;
return false;
}
// Check for particle
if (particle == "") particle = "proton"; // default to "proton"
else if ( !FindParticle(particle) )
{
G4cout << "WARNING: Particle \"" << particle << "\" isn't supported." << G4endl;
G4cout << "Try the command \"/particle/list\" to get full supported particles list." << G4endl;
G4cout << "If you are interested in an ion that isn't in this list you must give it to the particle gun."
"\nTry the commands:\n/gun/particle ion"
"\n/gun/ion <atomic number> <mass number> <[charge]>" << G4endl << G4endl;
return false;
}
// start physics by forcing a G4RunManager::BeamOn():
BeamOn();
// Set output file
if( filename != "" )
{
outfile.open(filename,std::ios_base::trunc); // overwrite existing file
data.rdbuf(outfile.rdbuf());
}
else data.rdbuf(G4cout.rdbuf()); // output is G4cout!
return true;
}
// Force physics tables build
void IORTInteractionParameters::BeamOn()
{
// first check if RunManager is above G4State_Idle
G4StateManager* mState = G4StateManager::GetStateManager();
G4ApplicationState aState = mState -> GetCurrentState();
if ( aState <= G4State_Idle && beamFlag == false)
{
G4cout << "Issuing a G4RunManager::beamOn()... ";
G4cout << "Current Run State is " << mState -> GetStateString( aState ) << G4endl;
G4RunManager::GetRunManager() -> BeamOn(0);
beamFlag = true;
}
}
// print a list of Nist elements and materials
void IORTInteractionParameters::ListOfNistMaterials(const G4String& vararg)
{
/*
$G4INSTALL/source/materials/src/G4NistElementBuilder.cc
You can also construct a new material by the ConstructNewMaterial method:
see $G4INSTALL/source/materials/src/G4NistMaterialBuilder.cc
*/
// Get simplest full list
if (vararg =="list")
{
const std::vector<G4String>& vec = nistMat -> GetMaterialNames();
for (size_t i=0; i<vec.size(); i++)
{
G4cout << std::setw(12) << std::left << i+1 << vec[i] << G4endl;
}
G4cout << G4endl;
}
else if (vararg =="all" || vararg =="simple" ||
vararg =="compound" || vararg =="hep" )
{
nistMat -> ListMaterials(vararg);
}
}
examples/advanced/iort_therapy/src/IORTMatrix.cc
-403
View File
@@ -1,403 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include <fstream>
#include <iostream>
#include <sstream>
#include <iomanip>
#include "IORTMatrix.hh"
#include "IORTAnalysisManager.hh"
#include "IORTPrimaryGeneratorAction.hh"
#include "globals.hh"
#include "G4SystemOfUnits.hh"
#include "G4RunManager.hh"
#include "G4ParticleGun.hh"
// Units definition: CLHEP/Units/SystemOfUnits.h
//
IORTMatrix* IORTMatrix::instance = NULL;
G4bool IORTMatrix::secondary = false;
// Only return a pointer to matrix
IORTMatrix* IORTMatrix::GetInstance()
{
return instance;
}
// This STATIC method delete (!) the old matrix and rewrite a new object returning a pointer to it
// TODO A check on the parameters is required!
IORTMatrix* IORTMatrix::GetInstance(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass)
{
if (instance) delete instance;
instance = new IORTMatrix(voxelX, voxelY, voxelZ, mass);
instance -> Initialize();
return instance;
}
IORTMatrix::IORTMatrix(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass):
stdFile("Dose.out"),
doseUnit(MeV/g)
{
// Number of the voxels of the phantom
// For Y = Z = 1 the phantom is divided in slices (and not in voxels)
// orthogonal to the beam axis
numberOfVoxelAlongX = voxelX;
numberOfVoxelAlongY = voxelY;
numberOfVoxelAlongZ = voxelZ;
massOfVoxel = mass;
// Create the dose matrix
matrix = new G4double[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ];
if (matrix)
{
G4cout << "IORTMatrix: Memory space to store physical dose into " <<
numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ <<
" voxels has been allocated " << G4endl;
}
else G4Exception("IORTMatrix::IORTMatrix()", "IORT0005", FatalException, "Error: can't allocate memory to store physical dose!");
// Hit voxel (TrackID) marker
// This array mark the status of voxel, if a hit occur, with the trackID of the particle
// Must be initialized
hitTrack = new G4int[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ];
ClearHitTrack();
}
/////////////////////////////////////////////////////////////////////////////
IORTMatrix::~IORTMatrix()
{
delete[] matrix;
delete[] hitTrack;
// free fluences/dose data memory
Clear();
}
/////////////////////////////////////////////////////////////////////////////
void IORTMatrix::Clear()
{
for (size_t i=0; i<ionStore.size(); i++)
{
delete[] ionStore[i].dose;
delete[] ionStore[i].fluence;
}
ionStore.clear();
}
/////////////////////////////////////////////////////////////////////////////
// Initialise the elements of the matrix to zero
void IORTMatrix::Initialize()
{
// Clear ions store
Clear();
// Clear dose
for(int i=0;i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;i++)
{
matrix[i] = 0;
}
}
/////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////
// Print generated nuclides list
void IORTMatrix::PrintNuclides()
{
for (size_t i=0; i<ionStore.size(); i++)
{
G4cout << ionStore[i].name << G4endl;
}
}
/////////////////////////////////////////////////////////////////////////////
// Clear Hit voxel (TrackID) markers
void IORTMatrix::ClearHitTrack()
{
for(G4int i=0; i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; i++) hitTrack[i] = 0;
}
// Return Hit status
G4int* IORTMatrix::GetHitTrack(G4int i, G4int j, G4int k)
{
return &(hitTrack[Index(i,j,k)]);
}
/////////////////////////////////////////////////////////////////////////////
// Dose methods...
// Fill DOSE/fluence matrix for secondary particles:
// If fluence parameter is true (default value is FALSE) then fluence at voxel (i, j, k) is increased.
// The energyDeposit parameter fill the dose matrix for voxel (i,j,k)
/////////////////////////////////////////////////////////////////////////////
G4bool IORTMatrix::Fill(G4int trackID,
G4ParticleDefinition* particleDef,
G4int i, G4int j, G4int k,
G4double energyDeposit,
G4bool fluence)
{
if ( (energyDeposit <=0. && !fluence) || !secondary) return false;
// Get Particle Data Group particle ID
G4int PDGencoding = particleDef -> GetPDGEncoding();
PDGencoding -= PDGencoding%10;
// Search for already allocated data...
for (size_t l=0; l < ionStore.size(); l++)
{
if (ionStore[l].PDGencoding == PDGencoding )
{ // Is it a primary or a secondary particle?
if ( ((trackID == 1) && (ionStore[l].isPrimary)) || ((trackID !=1) && (!ionStore[l].isPrimary)))
{
if (energyDeposit > 0.) ionStore[l].dose[Index(i, j, k)] += energyDeposit/massOfVoxel;
// Fill a matrix per each ion with the fluence
if (fluence) ionStore[l].fluence[Index(i, j, k)]++;
return true;
}
}
}
G4int Z = particleDef-> GetAtomicNumber();
G4int A = particleDef-> GetAtomicMass();
G4String fullName = particleDef -> GetParticleName();
G4String name = fullName.substr (0, fullName.find("[") ); // cut excitation energy
// Let's put a new particle in our store...
ion newIon =
{
(trackID == 1) ? true:false,
PDGencoding,
name,
name.length(),
Z,
A,
new G4double[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ],
new unsigned int[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ]
};
// Initialize data
if (newIon.dose && newIon.fluence)
{
for(G4int q=0; q<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; q++)
{
newIon.dose[q] = 0.;
newIon.fluence[q] = 0;
}
if (energyDeposit > 0.) newIon.dose[Index(i, j, k)] += energyDeposit/massOfVoxel;
if (fluence) newIon.fluence[Index(i, j, k)]++;
ionStore.push_back(newIon);
// TODO Put some verbosity check
/*
G4cout << "Memory space to store the DOSE/FLUENCE into " <<
numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ <<
" voxels has been allocated for the nuclide " << newIon.name <<
" (Z = " << Z << ", A = " << A << ")" << G4endl ;
*/
return true;
}
else // XXX Out of memory! XXX
{
return false;
}
}
/////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////
// Methods to store data to filenames...
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////
//
// General method to store matrix data to filename
void IORTMatrix::StoreMatrix(G4String file, void* data, size_t psize)
{
if (data)
{
ofs.open(file, std::ios::out);
if (ofs.is_open())
{
for(G4int i = 0; i < numberOfVoxelAlongX; i++)
for(G4int j = 0; j < numberOfVoxelAlongY; j++)
for(G4int k = 0; k < numberOfVoxelAlongZ; k++)
{
G4int n = Index(i, j, k);
// Check for data type: u_int, G4double, XXX
if (psize == sizeof(unsigned int))
{
unsigned int* pdata = (unsigned int*)data;
if (pdata[n]) ofs << i << '\t' << j << '\t' <<
k << '\t' << pdata[n] << G4endl;
}
else if (psize == sizeof(G4double))
{
G4double* pdata = (G4double*)data;
if (pdata[n]) ofs << i << '\t' << j << '\t' <<
k << '\t' << pdata[n] << G4endl;
}
}
ofs.close();
}
}
}
// Store fluence per single ion in multiple files
void IORTMatrix::StoreFluenceData()
{
for (size_t i=0; i < ionStore.size(); i++){
StoreMatrix(ionStore[i].name + "_Fluence.out", ionStore[i].fluence, sizeof(unsigned int));
}
}
// Store dose per single ion in multiple files
void IORTMatrix::StoreDoseData()
{
for (size_t i=0; i < ionStore.size(); i++){
StoreMatrix(ionStore[i].name + "_Dose.out", ionStore[i].dose, sizeof(G4double));
}
}
/////////////////////////////////////////////////////////////////////////
// Store dose for all ions into a single file and into ntuples.
// Please note that this function is called via messenger commands
// defined in the IORTAnalysisFileMessenger.cc class file
void IORTMatrix::StoreDoseFluenceAscii(G4String file)
{
#define width 15L
filename = (file=="") ? stdFile:file;
// Sort like periodic table
std::sort(ionStore.begin(), ionStore.end());
G4cout << "Dose is being written to " << filename << G4endl;
ofs.open(filename, std::ios::out);
if (ofs.is_open())
{
// Write the voxels index and the list of particles/ions
ofs << std::setprecision(6) << std::left <<
"i\tj\tk\t";
// Total dose
ofs << std::setw(width) << "Dose(MeV/g)";
if (secondary)
{
for (size_t l=0; l < ionStore.size(); l++)
{
G4String a = (ionStore[l].isPrimary) ? "_1":""; // is it a primary?
ofs << std::setw(width) << ionStore[l].name + a <<
std::setw(width) << ionStore[l].name + a;
}
ofs << G4endl;
/*
* PDGencondig
*/
/*
ofs << std::setprecision(6) << std::left <<
"0\t0\t0\t";
// Total dose
ofs << std::setw(width) << '0';
for (size_t l=0; l < ionStore.size(); l++)
{
ofs << std::setw(width) << ionStore[l].PDGencoding <<
std::setw(width) << ionStore[l].PDGencoding;
}
ofs << G4endl;
*/
}
// Write data
for(G4int i = 0; i < numberOfVoxelAlongX; i++)
for(G4int j = 0; j < numberOfVoxelAlongY; j++)
for(G4int k = 0; k < numberOfVoxelAlongZ; k++)
{
G4int n = Index(i, j, k);
// Write only not identically null data lines
if (matrix[n])
{
ofs << G4endl;
ofs << i << '\t' << j << '\t' << k << '\t';
// Total dose
ofs << std::setw(width) << matrix[n]/massOfVoxel/doseUnit;
if (secondary)
{
for (size_t l=0; l < ionStore.size(); l++)
{
// Fill ASCII file rows
ofs << std::setw(width) << ionStore[l].dose[n]/massOfVoxel/doseUnit <<
std::setw(width) << ionStore[l].fluence[n];
}
}
}
}
ofs.close();
}
}
/////////////////////////////////////////////////////////////////////////////
void IORTMatrix::StoreDoseFluenceRoot()
{
IORTAnalysisManager* analysis = IORTAnalysisManager::GetInstance();
for(G4int i = 0; i < numberOfVoxelAlongX; i++)
for(G4int j = 0; j < numberOfVoxelAlongY; j++)
for(G4int k = 0; k < numberOfVoxelAlongZ; k++)
{
G4int n = Index(i, j, k);
for (size_t l=0; l < ionStore.size(); l++)
{
// Do the same work for .root file: fill dose/fluence ntuple
analysis -> FillVoxelFragmentTuple( i, j, k,
ionStore[l].A,
ionStore[l].Z,
ionStore[l].dose[n]/massOfVoxel/doseUnit,
ionStore[l].fluence[n] );
}
}
}
void IORTMatrix::Fill(G4int i, G4int j, G4int k,
G4double energyDeposit)
{
if (matrix)
matrix[Index(i,j,k)] += energyDeposit;
// Store the energy deposit in the matrix element corresponding
// to the phantom voxel
}
void IORTMatrix::TotalEnergyDeposit()
{
// Store the information of the matrix in a ntuple and in
// a 1D Histogram
}
examples/advanced/iort_therapy/src/IORTParameterMessenger.cc
-97
View File
@@ -1,97 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTParameterMessenger.hh"
#include "IORTInteractionParameters.hh"
#include "G4UIdirectory.hh"
#include "G4UIcmdWithAString.hh"
IORTParameterMessenger::IORTParameterMessenger(IORTInteractionParameters* param)
:pParam(param)
{
paramDir = new G4UIdirectory("/parameter/");
paramDir -> SetGuidance("Commands to generate stopping power and range");
dedxCmd = new G4UIcmdWithAString("/parameter/getstopping",this);
dedxCmd->SetGuidance("Get mass stopping powers"
"\n[usage]: /parameter/getstopping Material [Emin] [Emax] [N] [Particle] [File]"
"\n Material:(string) Material name, like G4_H, G4_WATER,..., look at /parameter/nist"
"\n Emin Emax:(double) minimum and maximum kinetic energy (MeV)"
"\n N:(double) [number of points]"
"\n Particle:(string) Particle name, look at /particle/list"
"\n File:(string) Name for the output file."
"\nDefault values for parameters inside [] are respectively:"
"\n \"1 MeV\", \"Emin\", \"1\", \"proton\", \"stdout\"");
dedxCmd->SetParameterName("inputData",false);
dedxCmd->AvailableForStates(G4State_Idle);
listCmd = new G4UIcmdWithAString("/parameter/nist",this);
listCmd -> SetGuidance("Print NIST elements/materials.\nParameters:"
"\n\t all: will print elements and compounds"
"\n\t simple: will print elements only"
"\n\t compound: will print compounds only"
"\n\t hep: will print hep compounds"
"\n\t list: will print a simple full list of all elements and compounds");
listCmd -> SetParameterName("String",true);
listCmd -> SetDefaultValue("list");
listCmd -> SetCandidates("all simple compound hep list");
listCmd ->AvailableForStates(G4State_Idle);
//Available G4 States (G4State_PreInit, G4State_Init, G4State_Idle,G4State_GeomClosed, G4State_EventProc);
}
IORTParameterMessenger::~IORTParameterMessenger()
{
delete paramDir;
delete dedxCmd;
delete listCmd;
}
void IORTParameterMessenger::SetNewValue(G4UIcommand* command, G4String vararg)
{
if (command == dedxCmd)
{
pParam -> GetStoppingTable(vararg);
}
else if (command == listCmd)
{
pParam -> ListOfNistMaterials(vararg);
}
}
examples/advanced/iort_therapy/src/IORTParticles.cc
-82
View File
@@ -1,82 +0,0 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//
// (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTParticles.hh"
#include "G4ParticleDefinition.hh"
#include "G4ParticleTypes.hh"
#include "G4ParticleTable.hh"
#include "G4LeptonConstructor.hh"
#include "G4BosonConstructor.hh"
#include "G4MesonConstructor.hh"
#include "G4BaryonConstructor.hh"
#include "G4ShortLivedConstructor.hh"
#include "G4IonConstructor.hh"
IORTParticles::IORTParticles(const G4String& name)
: G4VPhysicsConstructor(name)
{ }
IORTParticles::~IORTParticles()
{}
void IORTParticles::ConstructParticle()
{
//
// Define all the particles involved in the experimental set-up
//
G4LeptonConstructor lepton;
lepton.ConstructParticle();
G4BosonConstructor boson;
boson.ConstructParticle();
G4MesonConstructor meson;
meson.ConstructParticle();
G4BaryonConstructor baryon;
baryon.ConstructParticle();
G4ShortLivedConstructor shortLived;
shortLived.ConstructParticle();
G4IonConstructor ion;
ion.ConstructParticle();
}
examples/advanced/iort_therapy/src/IORTPhysicsList.cc
+26 -197
View File
@@ -33,36 +33,12 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
//
// Physics models in IORT, following the Geant4 organisation, can be definided using three different approaches:
// 1. 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 folder
// 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 IORT will start with the defaultMacroWithReferencePhysicsList.mac
// macro. See this macro file for more details
//
// 2. 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 IORT 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
//
// ****** SUGGESTED PHYSICS *********
//
// AT MOMENT, IF ACCURATE RESULTS ARE NEDED, WE STRONGLY RECOMMEND:
// 1. The use of the emstandard_opt3, or
// 2. the QGSP_BIC_EMY Reference Physics Lists (define the PHYSLIST eviroment variable):
// export PHYSLIST=QGSP_BIC_EMY
#include "G4SystemOfUnits.hh"
#include "G4RunManager.hh"
#include "G4Region.hh"
@@ -70,57 +46,32 @@
#include "IORTPhysicsList.hh"
#include "IORTPhysicsListMessenger.hh"
#include "IORTStepMax.hh"
#include "G4PhysListFactory.hh"
#include "G4VPhysicsConstructor.hh"
// Local physic directly implemented in the Hadronthrapy directory
//#include "LocalIonIonInelasticPhysic.hh" // Physic dedicated to the ion-ion inelastic processes
//#include "LocalINCLIonIonInelasticPhysic.hh" // Physic dedicated to the ion-ion inelastic processes using ////INCL/ABLA
// #include "LocalStandardICRU73EmPhysic.hh" // This permits the use of the ICRU73 tables for stopping powers of ions. AGGIUNTO da eliot_geant4.9.3p01_version
// Physic lists (contained inside the Geant4 source code, in the 'physicslists folder')
#include "G4EmStandardPhysics_option3.hh"
#include "G4EmStandardPhysics_option4.hh"
#include "G4EmLivermorePhysics.hh"
#include "G4EmPenelopePhysics.hh"
#include "G4EmExtraPhysics.hh"
#include "G4StoppingPhysics.hh"
#include "G4DecayPhysics.hh"
#include "G4HadronElasticPhysics.hh"
#include "G4HadronElasticPhysicsHP.hh"
#include "G4HadronDElasticPhysics.hh"
#include "G4HadronHElasticPhysics.hh"
#include "G4HadronInelasticQBBC.hh"
#include "G4IonBinaryCascadePhysics.hh"
#include "G4Decay.hh"
#include "G4DecayPhysics.hh"
#include "G4NeutronTrackingCut.hh"
#include "G4LossTableManager.hh"
#include "G4UnitsTable.hh"
#include "G4ProcessManager.hh"
#include "G4HadronPhysicsQGSP_BIC.hh"
#include "G4IonFluctuations.hh"
#include "G4IonParametrisedLossModel.hh"
#include "G4EmProcessOptions.hh"
#include "G4ParticleDefinition.hh"
#include "G4ProductionCutsTable.hh"
#include "G4ProcessManager.hh"
#include "globals.hh"
#include "G4Electron.hh"
#include "G4Gamma.hh"
#include "G4Positron.hh"
#include "G4UnitsTable.hh"
#include "G4DecayPhysics.hh"
#include "G4RadioactiveDecayPhysics.hh"
/////////////////////////////////////////////////////////////////////////////
IORTPhysicsList::IORTPhysicsList() : G4VModularPhysicsList()
{
G4LossTableManager::Instance();
defaultCutValue = 0.01 *mm; //1.*mm;
defaultCutValue = 0.1 *mm;
cutForGamma = defaultCutValue;
cutForElectron = defaultCutValue;
cutForPositron = defaultCutValue;
helIsRegistered = false;
bicIsRegistered = false;
biciIsRegistered = false;
locIonIonInelasticIsRegistered = false;
radioactiveDecayIsRegistered = false;
stepMaxProcess = 0;
pMessenger = new IORTPhysicsListMessenger(this);
@@ -128,29 +79,23 @@ IORTPhysicsList::IORTPhysicsList() : G4VModularPhysicsList()
SetVerboseLevel(1);
// EM physics
emPhysicsList = new G4EmStandardPhysics_option3(1);
emName = G4String("emstandard_opt3");
// Decay physics and all particles
emPhysicsList = new G4EmStandardPhysics_option4(1);
emName = G4String("emstandard_opt4");
decPhysicsList = new G4DecayPhysics();
}
/////////////////////////////////////////////////////////////////////////////
IORTPhysicsList::~IORTPhysicsList()
{
delete pMessenger;
delete emPhysicsList;
delete decPhysicsList;
for(size_t i=0; i<hadronPhys.size(); i++) {delete hadronPhys[i];}
}
/////////////////////////////////////////////////////////////////////////////
void IORTPhysicsList::ConstructParticle()
{
decPhysicsList->ConstructParticle();
}
/////////////////////////////////////////////////////////////////////////////
void IORTPhysicsList::ConstructProcess()
{
// transportation
@@ -160,20 +105,11 @@ void IORTPhysicsList::ConstructProcess()
emPhysicsList->ConstructProcess();
em_config.AddModels();
// decay physics list
decPhysicsList->ConstructProcess();
// hadronic physics lists
for(size_t i=0; i<hadronPhys.size(); i++) {
hadronPhys[i] -> ConstructProcess();
}
// step limitation (as a full process)
//
AddStepMax();
}
/////////////////////////////////////////////////////////////////////////////
void IORTPhysicsList::AddPhysicsList(const G4String& name)
{
@@ -182,10 +118,7 @@ void IORTPhysicsList::AddPhysicsList(const G4String& name)
}
if (name == emName) return;
/////////////////////////////////////////////////////////////////////////////
// ELECTROMAGNETIC MODELS
/////////////////////////////////////////////////////////////////////////////
if (name == "standard_opt3") {
if (name == "standard_opt3") {
emName = name;
delete emPhysicsList;
emPhysicsList = new G4EmStandardPhysics_option3();
@@ -193,127 +126,28 @@ void IORTPhysicsList::AddPhysicsList(const G4String& name)
G4cout << "THE FOLLOWING ELECTROMAGNETIC PHYSICS LIST HAS BEEN ACTIVATED: G4EmStandardPhysics_option3" << G4endl;
} else if (name == "LowE_Livermore") {
} else if (name == "livermore") {
emName = name;
delete emPhysicsList;
emPhysicsList = new G4EmLivermorePhysics();
G4RunManager::GetRunManager()-> PhysicsHasBeenModified();
G4cout << "THE FOLLOWING ELECTROMAGNETIC PHYSICS LIST HAS BEEN ACTIVATED: G4EmLivermorePhysics" << G4endl;
} else if (name == "LowE_Penelope") {
} else if (name == "penelope") {
emName = name;
delete emPhysicsList;
emPhysicsList = new G4EmPenelopePhysics();
G4RunManager::GetRunManager()-> PhysicsHasBeenModified();
G4cout << "THE FOLLOWING ELECTROMAGNETIC PHYSICS LIST HAS BEEN ACTIVATED: G4EmPenelopePhysics" << G4endl;
G4cout << "THE FOLLOWING ELECTROMAGNETIC PHYSICS LIST HAS BEEN ACTIVATED: G4EmPenelopePhysics" << G4endl;}
/////////////////////////////////////////////////////////////////////////////
// HADRONIC MODELS
/////////////////////////////////////////////////////////////////////////////
} else if (name == "Elastic")
{
if(!helIsRegistered)
{
G4cout << "THE FOLLOWING HADRONIC ELASTIC PHYSICS LIST HAS BEEN ACTIVATED: G4HadronElasticPhysics()" << G4endl;
hadronPhys.push_back( new G4HadronElasticPhysics());
helIsRegistered = true;
}
else G4cout << "AN ELASTIC PHYSICS HAS BEEN ALREADY ACTIVATED!" << G4endl;
}
else if (name == "DElastic")
{
if(!helIsRegistered)
{
hadronPhys.push_back( new G4HadronDElasticPhysics());
helIsRegistered = true;
}
else G4cout << "AN ELASTIC PHYSICS HAS BEEN ALREADY ACTIVATED!" << G4endl;
else if (name == "standard_opt4") {
emName = name;
delete emPhysicsList;
emPhysicsList = new G4EmStandardPhysics_option4();
G4RunManager::GetRunManager() -> PhysicsHasBeenModified();
G4cout << "THE FOLLOWING ELECTROMAGNETIC PHYSICS LIST HAS BEEN ACTIVATED: G4EmStandardPhysics_option4" << G4endl;
}
}
else if (name == "HElastic")
{
if(!helIsRegistered)
{
hadronPhys.push_back( new G4HadronHElasticPhysics());
helIsRegistered = true;
}
else G4cout << "AN ELASTIC PHYSICS HAS BEEN ALREADY ACTIVATED!" << G4endl;
}
else if (name == "Em_extra_physics")
{
hadronPhys.push_back( new G4EmExtraPhysics());
}
else if (name == "Stopping_physics")
{
hadronPhys.push_back( new G4StoppingPhysics());
}
else if (name == "Neutron_tracking_cut")
{
hadronPhys.push_back( new G4NeutronTrackingCut());
}
else if (name == "Hadron_QGSP_BIC")
{
hadronPhys.push_back( new G4HadronPhysicsQGSP_BIC());
// helIsRegistered = true;
}
else if (name == "Hadron_QBBC")
{
hadronPhys.push_back(new G4HadronInelasticQBBC());
//bicIsRegistered = true;
G4cout << "THE FOLLOWING HADRONIC INELASTIC PHYSICS LIST HAS BEEN ACTIVATED: G4HadronInelasticQBBC()" << G4endl;
}
else if (name == "binary")
{
hadronPhys.push_back(new G4HadronInelasticQBBC());
//bicIsRegisted = true;
G4cout << "THE FOLLOWING HADRONIC INELASTIC PHYSICS LIST HAS BEEN ACTIVATED: G4HadronInelasticQBBC()" << G4endl;
}
else if (name == "binary_ion")
{
hadronPhys.push_back(new G4IonBinaryCascadePhysics());
//biciIsRegistered = true;
}
/*
else if (name == "local_ion_ion_inelastic")
{
hadronPhys.push_back(new LocalIonIonInelasticPhysic());
locIonIonInelasticIsRegistered = true;
}
else if (name == "local_incl_ion_ion_inelastic")
{
hadronPhys.push_back(new LocalINCLIonIonInelasticPhysic());
locIonIonInelasticIsRegistered = true;
}
*/
else if (name == "decay")
{
hadronPhys.push_back(new G4DecayPhysics());
//radioactiveDecayIsRegistered = true;
}
else if (name == "radioactive_decay" && !radioactiveDecayIsRegistered )
{
hadronPhys.push_back(new G4RadioactiveDecayPhysics());
radioactiveDecayIsRegistered = true;
// The following is the construction of the QGSP_BIC_EMY Reference physics list
// reconstructed here like a builder: it should be identical to the
// one contained inside the $G4INSTALL/physics_lists/lists folder
}
else if (name == "QGSP_BIC_EMY")
{
AddPhysicsList("emstandard_opt3");
hadronPhys.push_back( new G4EmExtraPhysics());
hadronPhys.push_back( new G4HadronElasticPhysics());
hadronPhys.push_back( new G4StoppingPhysics());
hadronPhys.push_back( new G4IonBinaryCascadePhysics());
hadronPhys.push_back( new G4NeutronTrackingCut());
hadronPhys.push_back( new G4HadronPhysicsQGSP_BIC());
hadronPhys.push_back( new G4DecayPhysics());
}
else {
G4cout << "PhysicsList::AddPhysicsList: <" << name << ">"
@@ -322,7 +156,6 @@ void IORTPhysicsList::AddPhysicsList(const G4String& name)
}
}
/////////////////////////////////////////////////////////////////////////////
void IORTPhysicsList::AddStepMax()
{
// Step limitation seen as a process
@@ -341,7 +174,6 @@ void IORTPhysicsList::AddStepMax()
}
}
/////////////////////////////////////////////////////////////////////////////
void IORTPhysicsList::SetCuts()
{
@@ -361,21 +193,18 @@ void IORTPhysicsList::SetCuts()
if (verboseLevel>0) DumpCutValuesTable();
}
/////////////////////////////////////////////////////////////////////////////
void IORTPhysicsList::SetCutForGamma(G4double cut)
{
cutForGamma = cut;
SetParticleCuts(cutForGamma, G4Gamma::Gamma());
}
/////////////////////////////////////////////////////////////////////////////
void IORTPhysicsList::SetCutForElectron(G4double cut)
{
cutForElectron = cut;
SetParticleCuts(cutForElectron, G4Electron::Electron());
}
/////////////////////////////////////////////////////////////////////////////
void IORTPhysicsList::SetCutForPositron(G4double cut)
{
cutForPositron = cut;
examples/advanced/iort_therapy/src/IORTPhysicsListMessenger.cc
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/IORTPrimaryGeneratorAction.cc
+11 -28
View File
@@ -33,13 +33,12 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include <CLHEP/Units/SystemOfUnits.h>
#include "G4SystemOfUnits.hh"
#include "IORTPrimaryGeneratorAction.hh"
#include "IORTPrimaryGeneratorMessenger.hh"
@@ -49,9 +48,7 @@
#include "G4ParticleTable.hh"
#include "G4ParticleDefinition.hh"
#include "Randomize.hh"
#include "IORTAnalysisManager.hh"
IORTPrimaryGeneratorAction::IORTPrimaryGeneratorAction()
{
// Define the messenger
@@ -88,15 +85,9 @@ void IORTPrimaryGeneratorAction::SetDefaultPrimaryParticle()
G4double defaultsigmaEnergy = 100.0 *CLHEP::keV;
sigmaEnergy = defaultsigmaEnergy;
// Write these values into the analysis if needed. Have to be written separately on change.
IORTAnalysisManager::GetInstance()->
setBeamMetaData(meanKineticEnergy, sigmaEnergy);
// Define the parameters of the initial position:
// the y, z coordinates have a gaussian distribution
// the y, z coordinates have a gaussian distribution
G4double defaultX0 = -862.817 *CLHEP::mm;
X0 = defaultX0;
@@ -131,9 +122,6 @@ void IORTPrimaryGeneratorAction::SetDefaultPrimaryParticle()
void IORTPrimaryGeneratorAction::GeneratePrimaries(G4Event* anEvent)
{
// Increment the event counter
IORTAnalysisManager::GetInstance()->startNewEvent();
// ****************************************
// Set the beam angular apread
// and spot size
@@ -226,21 +214,16 @@ while (true) {
void IORTPrimaryGeneratorAction::SetmeanKineticEnergy (G4double val )
{
meanKineticEnergy = val;
// Update the beam-data in the analysis manager
IORTAnalysisManager::GetInstance()->
setBeamMetaData(meanKineticEnergy, sigmaEnergy);
meanKineticEnergy = val;
G4cout << "The mean Kinetic energy of the incident beam has been changed to (MeV):"
<< meanKineticEnergy/MeV << G4endl;
}
void IORTPrimaryGeneratorAction::SetsigmaEnergy (G4double val )
{
sigmaEnergy = val;
// Update the sigmaenergy in the metadata.
IORTAnalysisManager::GetInstance()->
setBeamMetaData(meanKineticEnergy, sigmaEnergy);
sigmaEnergy = val;
G4cout << "The sigma of the kinetic energy of the incident beam has been changed to (MeV):"
<< sigmaEnergy/MeV << G4endl;
}
void IORTPrimaryGeneratorAction::SetXposition (G4double val )
examples/advanced/iort_therapy/src/IORTPrimaryGeneratorMessenger.cc
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/IORTRunAction.cc
+5 -29
View File
@@ -33,57 +33,33 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include "IORTRunAction.hh"
#include "IORTEventAction.hh"
#include "G4Run.hh"
#include "G4RunManager.hh"
#include "G4UImanager.hh"
#include "G4ios.hh"
#include "IORTDetectorConstruction.hh"
#include "G4SDManager.hh"
#include "G4Timer.hh"
#include "IORTRunAction.hh"
#include "IORTAnalysisManager.hh"
#include "IORTMatrix.hh"
#include "G4SystemOfUnits.hh"
IORTRunAction::IORTRunAction()
{
}
{}
IORTRunAction::~IORTRunAction()
{
}
{ }
void IORTRunAction::BeginOfRunAction(const G4Run* aRun)
{
G4RunManager::GetRunManager()-> SetRandomNumberStore(true);
G4cout << "Run " << aRun -> GetRunID() << " starts ..." << G4endl;
electromagnetic = 0;
hadronic = 0;
}
void IORTRunAction::EndOfRunAction(const G4Run*)
{
//G4cout << " Summary of Run " << aRun -> GetRunID() <<" :"<< G4endl;
//G4cout << "Number of electromagnetic processes of primary particles in the phantom:"
// << electromagnetic << G4endl;
//G4cout << "Number of hadronic processes of primary particles in the phantom:"
// << hadronic << G4endl;
}
void IORTRunAction::AddEMProcess()
{
electromagnetic += 1;
}
void IORTRunAction::AddHadronicProcess()
{
hadronic += 1;
}
{}
examples/advanced/iort_therapy/src/IORTStepMax.cc
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/IORTStepMaxMessenger.cc
+1 -1
View File
@@ -33,7 +33,7 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
examples/advanced/iort_therapy/src/IORTSteppingAction.cc
+8 -154
View File
@@ -33,13 +33,12 @@
// (b) IBFM-CNR , Segrate (Milano), Italy
// (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
// (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
// (e) University of Wallongong, Australia
// (e) University of Wollongong, Australia
//
// *Corresponding author, email to carlo.casarino@polooncologicocefalu.it
//////////////////////////////////////////////////////////////////////////////////////////////
#include <CLHEP/Units/SystemOfUnits.h>
#include "G4SystemOfUnits.hh"
#include "G4SteppingManager.hh"
#include "G4TrackVector.hh"
#include "IORTSteppingAction.hh"
@@ -52,162 +51,17 @@
#include "G4TrackVector.hh"
#include "G4ParticleDefinition.hh"
#include "G4ParticleTypes.hh"
#include "G4UserEventAction.hh" // NOT INCLUDED IN geant4.9.3p01_version
#include "IORTAnalysisManager.hh"
#include "G4UserEventAction.hh"
#include "IORTRunAction.hh"
#include "G4SystemOfUnits.hh"
/////////////////////////////////////////////////////////////////////////////
IORTSteppingAction::IORTSteppingAction( IORTRunAction *run)
{
runAction = run;
}
IORTSteppingAction::IORTSteppingAction( IORTRunAction *)
{}
/////////////////////////////////////////////////////////////////////////////
IORTSteppingAction::~IORTSteppingAction()
{
}
{}
/////////////////////////////////////////////////////////////////////////////
void IORTSteppingAction::UserSteppingAction(const G4Step* aStep)
void IORTSteppingAction::UserSteppingAction(const G4Step*)
{
/*
// USEFULL METHODS TO RETRIEVE INFORMATION DURING THE STEPS
if( (aStep->GetTrack()->GetVolume()->GetName() == "DetectorPhys")
&& aStep->GetTrack()->GetDefinition()->GetParticleName() == "proton")
//G4int evtNb = G4RunManager::GetRunManager()->GetCurrentEvent() -> GetEventID();
{
G4cout << "ENERGIA: " << aStep->GetTrack()->GetKineticEnergy()
<< " VOLUME " << aStep->GetTrack()->GetVolume()->GetName()
<< " MATERIALE " << aStep -> GetTrack() -> GetMaterial() -> GetName()
<< " EVENTO " << G4RunManager::GetRunManager()->GetCurrentEvent() -> GetEventID()
<< " POS " << aStep->GetTrack()->GetPosition().x()
<< G4endl;
}
*/
if( aStep->GetTrack()->GetVolume()->GetName() == "NewDetectorPhys"){
G4ParticleDefinition *def = aStep->GetTrack()->GetDefinition();
G4double secondaryParticleKineticEnergy = aStep->GetTrack()->
GetKineticEnergy();
G4String particleType = def->GetParticleType(); // particle type = nucleus for d, t, He3, alpha, and heavier nuclei
G4String particleName = def->GetParticleName(); // e.g. for alpha: the name = "alpha" and type = "nucleus"
if(particleType == "nucleus") {
G4int A = def->GetBaryonNumber();
G4double Z = def->GetPDGCharge();
G4double posX = aStep->GetTrack()->GetPosition().x() /cm;
G4double posY = aStep->GetTrack()->GetPosition().y() /cm;
G4double posZ = aStep->GetTrack()->GetPosition().z() /cm;
G4double energy = secondaryParticleKineticEnergy / A /MeV;
IORTAnalysisManager* analysisMgr = IORTAnalysisManager::GetInstance();
analysisMgr->FillFragmentTuple(A, Z, energy, posX, posY, posZ);
} else if(particleName == "proton") { // proton (hydrogen-1) is a special case
G4double posX = aStep->GetTrack()->GetPosition().x() /cm ;
G4double posY = aStep->GetTrack()->GetPosition().y() /cm ;
G4double posZ = aStep->GetTrack()->GetPosition().z() / cm ;
G4double energy = secondaryParticleKineticEnergy / MeV; // Hydrogen-1: A = 1, Z = 1
IORTAnalysisManager::GetInstance()->FillFragmentTuple(1, 1.0, energy, posX, posY, posZ);
}
G4String secondaryParticleName = def -> GetParticleName();
//G4cout <<"Particle: " << secondaryParticleName << G4endl;
//G4cout <<"Energy: " << secondaryParticleKineticEnergy << G4endl;
IORTAnalysisManager* analysis = IORTAnalysisManager::GetInstance();
//There is a bunch of stuff recorded with the energy 0, something should perhaps be done about this.
if(secondaryParticleName == "proton") {
analysis->hydrogenEnergy(secondaryParticleKineticEnergy /MeV);
}
if(secondaryParticleName == "deuteron") {
analysis->hydrogenEnergy((secondaryParticleKineticEnergy/2) / MeV);
}
if(secondaryParticleName == "triton") {
analysis->hydrogenEnergy((secondaryParticleKineticEnergy/3) / MeV);
}
if(secondaryParticleName == "alpha") {
analysis->heliumEnergy((secondaryParticleKineticEnergy/4) / MeV);
}
if(secondaryParticleName == "He3"){
analysis->heliumEnergy((secondaryParticleKineticEnergy/3) / MeV);
}
aStep->GetTrack()->SetTrackStatus(fKillTrackAndSecondaries);
}
// Electromagnetic and hadronic processes of primary particles in the phantom
//setting phantomPhys correctly will break something here fixme
if ((aStep -> GetTrack() -> GetTrackID() == 1) &&
(aStep -> GetTrack() -> GetVolume() -> GetName() == "PhantomPhys") &&
(aStep -> GetPostStepPoint() -> GetProcessDefinedStep() != NULL))
{
G4String process = aStep -> GetPostStepPoint() ->
GetProcessDefinedStep() -> GetProcessName();
if ((process == "Transportation") || (process == "StepLimiter")) {;}
else
{
if ((process == "msc") || (process == "hLowEIoni") || (process == "hIoni"))
{
runAction -> AddEMProcess();
}
else
{
runAction -> AddHadronicProcess();
if ( (process != "LElastic") && (process != "ProtonInelastic") && (process != "hElastic") )
G4cout << "Warning! Unknown proton process: "<< process << G4endl;
}
}
}
// Retrieve information about the secondary particles originated in the phantom
G4SteppingManager* steppingManager = fpSteppingManager;
// check if it is alive
//if(theTrack-> GetTrackStatus() == fAlive) { return; }
// Retrieve the secondary particles
G4TrackVector* fSecondary = steppingManager -> GetfSecondary();
for(size_t lp1=0;lp1<(*fSecondary).size(); lp1++)
{
G4String volumeName = (*fSecondary)[lp1] -> GetVolume() -> GetName();
if (volumeName == "phantomPhys")
{
G4String secondaryParticleName = (*fSecondary)[lp1]->GetDefinition() -> GetParticleName();
G4double secondaryParticleKineticEnergy = (*fSecondary)[lp1] -> GetKineticEnergy();
IORTAnalysisManager* analysis = IORTAnalysisManager::GetInstance();
if (secondaryParticleName == "e-")
analysis -> electronEnergyDistribution(secondaryParticleKineticEnergy/MeV);
if (secondaryParticleName == "gamma")
analysis -> gammaEnergyDistribution(secondaryParticleKineticEnergy/MeV);
if (secondaryParticleName == "deuteron")
analysis -> deuteronEnergyDistribution(secondaryParticleKineticEnergy/MeV);
if (secondaryParticleName == "triton")
analysis -> tritonEnergyDistribution(secondaryParticleKineticEnergy/MeV);
if (secondaryParticleName == "alpha")
analysis -> alphaEnergyDistribution(secondaryParticleKineticEnergy/MeV);
G4double z = (*fSecondary)[lp1]-> GetDynamicParticle() -> GetDefinition() -> GetPDGCharge();
if (z > 0.)
{
G4int a = (*fSecondary)[lp1]-> GetDynamicParticle() -> GetDefinition() -> GetBaryonNumber();
G4int electronOccupancy = (*fSecondary)[lp1] -> GetDynamicParticle() -> GetTotalOccupancy();
// If a generic ion is originated in the detector, its baryonic number, PDG charge,
// total number of electrons in the orbitals are stored in a ntuple
analysis -> genericIonInformation(a, z, electronOccupancy, secondaryParticleKineticEnergy/MeV);
}
}
}
}