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This commit is contained in:
Gabriele Cosmo
2025-06-26 09:17:29 +02:00
parent 20a218bbe1
commit a499fb82e9
1941 changed files with 203285 additions and 95593 deletions
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examples/advanced/dna/cellularPhantom/include/ActionInitialization.hh
+5 -4
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@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,7 +38,7 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef ActionInitialization_h
#define ActionInitialization_h 1
examples/advanced/dna/cellularPhantom/include/CellParameterisation.hh
+7 -6
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@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,7 +38,7 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef CellParameterisation_H
#define CellParameterisation_H 1
@@ -82,8 +83,8 @@ class CellParameterisation : public G4VPVParameterisation
inline auto GetGreenMass() const { return fGreenMass; }
inline auto GetBlueMass() const { return fBlueMass; }
inline auto GetVoxelThreeVector(G4int i) const { return fMapCell[i]; }
inline auto GetVoxelThreeVectorPixel(G4int i) const { return fMapCellPxl[i]; }
//inline auto GetVoxelThreeVector(G4int i) const { return fMapCell[i]; }
//inline auto GetVoxelThreeVectorPixel(G4int i) const { return fMapCellPxl[i]; }
inline auto GetVoxelThreeVectorOriginal(G4int i) const { return fMapCellOriginal[i]; }
inline auto GetMaterial(G4int i) const { return fMaterial[i]; }
examples/advanced/dna/cellularPhantom/include/DetectorConstruction.hh
+5 -4
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@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,7 +38,7 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef DetectorConstruction_h
#define DetectorConstruction_h 1
examples/advanced/dna/cellularPhantom/include/DetectorMessenger.hh
+5 -4
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@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,7 +38,7 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef DetectorMessenger_h
#define DetectorMessenger_h 1
examples/advanced/dna/cellularPhantom/include/EventAction.hh
+5 -4
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@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,7 +38,7 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef EventAction_h
#define EventAction_h 1
examples/advanced/dna/cellularPhantom/include/PhysicsList.hh
+5 -6
View File
@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,7 +38,7 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef PhysicsList_h
#define PhysicsList_h 1
@@ -54,8 +55,6 @@ class PhysicsList: public G4VModularPhysicsList
~PhysicsList() override;
void SetCuts() override;
private:
};
#endif
examples/advanced/dna/cellularPhantom/include/PrimaryGeneratorAction.hh
+5 -4
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@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,7 +38,7 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef PrimaryGeneratorAction_h
#define PrimaryGeneratorAction_h 1
examples/advanced/dna/cellularPhantom/include/Run.hh
+71
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@@ -0,0 +1,71 @@
//
// ********************************************************************
// * 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. *
// ********************************************************************
//
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
// "Monte-Carlo dosimetry on a realistic cell monolayer
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// -----------------------------------------------------------------------------
#ifndef Run_h
#define Run_h 1
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
#include "DetectorConstruction.hh"
#include "G4Run.hh"
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
class Run : public G4Run
{
public:
Run();
~Run();
void AddVoxelEdeposit(G4int i, G4double e) { fVoxelEdeposit[i] += e; }
inline G4double GetVoxelEdeposit(G4int i) const { return fVoxelEdeposit[i]; }
void Merge(const G4Run*) override;
void EndOfRun();
private:
G4double * fVoxelEdeposit = nullptr;
const CellParameterisation * fMyPhantomParam = nullptr;
};
#endif
examples/advanced/dna/cellularPhantom/include/RunAction.hh
+8 -9
View File
@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,12 +38,12 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef RunAction_h
#define RunAction_h 1
#include "DetectorConstruction.hh"
#include "Run.hh"
#include "G4UserRunAction.hh"
#include "G4AnalysisManager.hh"
@@ -59,14 +60,12 @@ class RunAction : public G4UserRunAction
void BeginOfRunAction(const G4Run*) override;
void EndOfRunAction(const G4Run*) override;
void AddDoseBox(G4int i, G4double x) {fVoxelEnergy[i] +=x;}
G4double GetDoseBox(G4int i) {return fVoxelEnergy[i];}
G4Run* GenerateRun() override;
private:
const CellParameterisation * fMyPhantomParam = nullptr;
G4double * fVoxelEnergy = nullptr;
G4int fNbVoxels = 0;
Run* fRun;
};
#endif
examples/advanced/dna/cellularPhantom/include/SteppingAction.hh
+7 -7
View File
@@ -23,13 +23,14 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
// MONTE CARLO SIMULATION OF REALISTIC GEOMETRY FROM MICROSCOPES IMAGES
//
// Authors and contributors:
// P. Barberet, S. Incerti, N. H. Tran, L. Morelli
// P. Barberet (a), S. Incerti (a), N. H. Tran (a), L. Morelli (a,b)
//
// University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// a) University of Bordeaux, CNRS, LP2i, UMR5797, Gradignan, France
// b) Politecnico di Milano, Italy
//
// If you use this code, please cite the following publication:
// P. Barberet et al.,
@@ -37,12 +38,12 @@
// geometry exposed to alpha particles."
// Ph. Barberet et al 2012 Phys. Med. Biol. 57 2189
// doi: 110.1088/0031-9155/57/8/2189
// --------------------------------------------------------------------------------
// -----------------------------------------------------------------------------
#ifndef SteppingAction_h
#define SteppingAction_h 1
#include "RunAction.hh"
#include "CellParameterisation.hh"
#include "G4UserSteppingAction.hh"
@@ -51,13 +52,12 @@
class SteppingAction : public G4UserSteppingAction
{
public:
explicit SteppingAction(RunAction*);
explicit SteppingAction();
~SteppingAction() override = default;
void UserSteppingAction(const G4Step*) override;
private:
RunAction* fRunAction = nullptr;
const CellParameterisation * fMyPhantomParam = nullptr;
};