| 1 | // |
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| 2 | // ******************************************************************** |
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| 3 | // * License and Disclaimer * |
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| 4 | // * * |
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| 5 | // * The Geant4 software is copyright of the Copyright Holders of * |
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| 6 | // * the Geant4 Collaboration. It is provided under the terms and * |
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| 7 | // * conditions of the Geant4 Software License, included in the file* |
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| 8 | // * LICENSE and available at http://cern.ch/geant4/license . These * |
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| 9 | // * include a list of copyright holders. * |
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| 10 | // * * |
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| 11 | // * Neither the authors of this software system, nor their employing * |
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| 12 | // * institutes,nor the agencies providing financial support for this * |
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| 13 | // * work make any representation or warranty, express or implied, * |
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| 14 | // * regarding this software system or assume any liability for its * |
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| 15 | // * use. Please see the license in the file LICENSE and URL above * |
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| 16 | // * for the full disclaimer and the limitation of liability. * |
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| 17 | // * * |
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| 18 | // * This code implementation is the result of the scientific and * |
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| 19 | // * technical work of the GEANT4 collaboration. * |
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| 20 | // * By using, copying, modifying or distributing the software (or * |
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| 21 | // * any work based on the software) you agree to acknowledge its * |
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| 22 | // * use in resulting scientific publications, and indicate your * |
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| 23 | // * acceptance of all terms of the Geant4 Software license. * |
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| 24 | // ******************************************************************** |
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| 25 | // |
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| 26 | // $Id: HadrontherapyMatrix.cc; |
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| 27 | // See more at: http://g4advancedexamples.lngs.infn.it/Examples/hadrontherapy// |
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| 28 | |
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| 29 | #include "HadrontherapyMatrix.hh" |
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| 30 | #include "HadrontherapyAnalysisManager.hh" |
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| 31 | #include "G4RunManager.hh" |
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| 32 | #include "HadrontherapyPrimaryGeneratorAction.hh" |
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| 33 | #include "G4ParticleGun.hh" |
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| 34 | |
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| 35 | #include <fstream> |
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| 36 | #include <unistd.h> |
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| 37 | #include <iostream> |
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| 38 | #include <sstream> |
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| 39 | #include <iomanip> |
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| 40 | #include "globals.hh" |
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| 41 | |
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| 42 | // Units definition: CLHEP/Units/SystemOfUnits.h |
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| 43 | // |
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| 44 | HadrontherapyMatrix* HadrontherapyMatrix::instance = NULL; |
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| 45 | G4bool HadrontherapyMatrix::secondaries = false; |
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| 46 | // Only return a pointer to matrix |
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| 47 | HadrontherapyMatrix* HadrontherapyMatrix::GetInstance() |
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| 48 | { |
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| 49 | return instance; |
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| 50 | } |
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| 51 | // This STATIC method delete (!) the old matrix and rewrite a new object returning a pointer to it |
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| 52 | // TODO A check on the parameters is required! |
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| 53 | HadrontherapyMatrix* HadrontherapyMatrix::GetInstance(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass) |
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| 54 | { |
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| 55 | if (instance) delete instance; |
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| 56 | instance = new HadrontherapyMatrix(voxelX, voxelY, voxelZ, mass); |
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| 57 | instance -> Initialize();// XXX |
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| 58 | return instance; |
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| 59 | } |
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| 60 | HadrontherapyMatrix::HadrontherapyMatrix(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass): |
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| 61 | filename("Dose.out"), |
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| 62 | doseUnit(MeV/g) |
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| 63 | { |
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| 64 | // Number of the voxels of the phantom |
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| 65 | // For Y = Z = 1 the phantom is divided in slices (and not in voxels) |
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| 66 | // orthogonal to the beam axis |
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| 67 | numberOfVoxelAlongX = voxelX; |
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| 68 | numberOfVoxelAlongY = voxelY; |
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| 69 | numberOfVoxelAlongZ = voxelZ; |
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| 70 | massOfVoxel = mass; |
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| 71 | // Create the dose matrix |
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| 72 | matrix = new G4double[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ]; |
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| 73 | if (matrix) |
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| 74 | { |
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| 75 | G4cout << "HadrontherapyMatrix: Memory space to store physical dose into " << |
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| 76 | numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ << |
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| 77 | " voxels has been allocated " << G4endl; |
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| 78 | } |
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| 79 | else G4Exception(" HadrontherapyMatrix::HadrontherapyMatrix. Can't allocate memory to store physical dose!"); |
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| 80 | // Hit voxel (TrackID) marker |
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| 81 | // This array mark the status of voxel, if a hit occur, with the trackID of the particle |
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| 82 | // Must be initialized |
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| 83 | hitTrack = new G4int[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ]; |
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| 84 | ClearHitTrack(); |
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| 85 | } |
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| 86 | |
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| 87 | ///////////////////////////////////////////////////////////////////////////// |
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| 88 | HadrontherapyMatrix::~HadrontherapyMatrix() |
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| 89 | { |
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| 90 | delete[] matrix; |
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| 91 | delete[] hitTrack; |
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| 92 | // clear fluences/dose data |
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| 93 | Clear(); |
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| 94 | } |
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| 95 | |
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| 96 | ///////////////////////////////////////////////////////////////////////////// |
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| 97 | void HadrontherapyMatrix::Clear() |
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| 98 | { |
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| 99 | for (size_t i=0; i<ionStore.size(); i++) |
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| 100 | { |
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| 101 | delete[] ionStore[i].dose; |
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| 102 | delete[] ionStore[i].fluence; |
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| 103 | } |
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| 104 | ionStore.clear(); |
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| 105 | } |
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| 106 | |
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| 107 | ///////////////////////////////////////////////////////////////////////////// |
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| 108 | // Initialise the elements of the matrix to zero |
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| 109 | void HadrontherapyMatrix::Initialize() |
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| 110 | { |
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| 111 | Clear(); |
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| 112 | for(int i=0;i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;i++) |
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| 113 | { |
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| 114 | matrix[i] = 0; |
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| 115 | } |
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| 116 | } |
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| 117 | ///////////////////////////////////////////////////////////////////////////// |
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| 118 | ///////////////////////////////////////////////////////////////////////////// |
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| 119 | // Print generated nuclides list |
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| 120 | void HadrontherapyMatrix::PrintNuclides() |
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| 121 | { |
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| 122 | for (size_t i=0; i<ionStore.size(); i++) |
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| 123 | { |
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| 124 | G4cout << ionStore[i].name << G4endl; |
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| 125 | } |
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| 126 | } |
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| 127 | ///////////////////////////////////////////////////////////////////////////// |
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| 128 | // Clear Hit voxel (TrackID) markers |
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| 129 | void HadrontherapyMatrix::ClearHitTrack() |
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| 130 | { |
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| 131 | for(G4int i=0; i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; i++) hitTrack[i] = 0; |
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| 132 | } |
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| 133 | // Return Hit status |
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| 134 | G4int* HadrontherapyMatrix::GetHitTrack(G4int i, G4int j, G4int k) |
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| 135 | { |
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| 136 | return &(hitTrack[Index(i,j,k)]); |
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| 137 | } |
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| 138 | ///////////////////////////////////////////////////////////////////////////// |
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| 139 | // Dose methods... |
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| 140 | // Fill DOSE/fluence matrix for particle/ion: |
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| 141 | // If fluence parameter is true (default value is FALSE) then fluence at voxel (i, j, k) is increased. |
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| 142 | // The energyDeposit parameter fill the dose matrix for voxel (i,j,k) |
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| 143 | ///////////////////////////////////////////////////////////////////////////// |
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| 144 | |
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| 145 | G4bool HadrontherapyMatrix::Fill(G4int trackID, |
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| 146 | G4ParticleDefinition* particleDef, |
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| 147 | G4int i, G4int j, G4int k, |
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| 148 | G4double energyDeposit, |
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| 149 | G4bool fluence) |
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| 150 | { |
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| 151 | if (energyDeposit <=0. && !fluence || !secondaries) return false; |
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| 152 | // Get Particle Data Group particle ID |
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| 153 | G4int PDGencoding = particleDef -> GetPDGEncoding(); |
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| 154 | PDGencoding -= PDGencoding%10; |
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| 155 | |
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| 156 | // Search for already allocated data... |
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| 157 | for (size_t l=0; l < ionStore.size(); l++) |
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| 158 | { |
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| 159 | if (ionStore[l].PDGencoding == PDGencoding ) |
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| 160 | { // Is it a primary or a secondary particle? |
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| 161 | if ( trackID ==1 && ionStore[l].isPrimary || trackID !=1 && !ionStore[l].isPrimary) |
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| 162 | { |
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| 163 | if (energyDeposit > 0.) ionStore[l].dose[Index(i, j, k)] += energyDeposit/massOfVoxel; |
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| 164 | |
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| 165 | // Fill a matrix per each ion with the fluence |
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| 166 | if (fluence) ionStore[l].fluence[Index(i, j, k)]++; |
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| 167 | return true; |
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| 168 | } |
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| 169 | } |
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| 170 | } |
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| 171 | |
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| 172 | G4int Z = particleDef-> GetAtomicNumber(); |
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| 173 | G4int A = particleDef-> GetAtomicMass(); |
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| 174 | |
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| 175 | G4String fullName = particleDef -> GetParticleName(); |
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| 176 | G4String name = fullName.substr (0, fullName.find("[") ); // cut excitation energy |
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| 177 | // Let's put a new particle in our store... |
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| 178 | ion newIon = |
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| 179 | { |
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| 180 | (trackID == 1) ? true:false, |
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| 181 | PDGencoding, |
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| 182 | name, |
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| 183 | name.length(), |
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| 184 | Z, |
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| 185 | A, |
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| 186 | new G4double[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ], |
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| 187 | new unsigned int[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ] |
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| 188 | }; |
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| 189 | // Initialize data |
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| 190 | if (newIon.dose && newIon.fluence) |
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| 191 | { |
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| 192 | for(G4int m=0; m<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; m++) |
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| 193 | { |
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| 194 | newIon.dose[m] = 0.; |
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| 195 | newIon.fluence[m] = 0; |
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| 196 | } |
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| 197 | if (energyDeposit > 0.) newIon.dose[Index(i, j, k)] += energyDeposit/massOfVoxel; |
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| 198 | if (fluence) newIon.fluence[Index(i, j, k)]++; |
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| 199 | |
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| 200 | ionStore.push_back(newIon); |
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| 201 | |
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| 202 | // TODO Put some verbosity check |
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| 203 | /* |
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| 204 | G4cout << "Memory space to store the DOSE/FLUENCE into " << |
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| 205 | numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ << |
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| 206 | " voxels has been allocated for the nuclide " << newIon.name << |
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| 207 | " (Z = " << Z << ", A = " << A << ")" << G4endl ; |
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| 208 | */ |
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| 209 | return true; |
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| 210 | } |
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| 211 | else // XXX Out of memory! XXX |
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| 212 | { |
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| 213 | return false; |
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| 214 | } |
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| 215 | |
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| 216 | } |
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| 217 | |
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| 218 | ///////////////////////////////////////////////////////////////////////////// |
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| 219 | ///////////////////////////////////////////////////////////////////////////// |
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| 220 | // Methods to store data to filenames... |
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| 221 | //////////////////////////////////////////////////////////////////////////// |
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| 222 | //////////////////////////////////////////////////////////////////////////// |
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| 223 | // |
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| 224 | // General method to store matrix data to filename |
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| 225 | void HadrontherapyMatrix::StoreMatrix(G4String file, void* data, size_t psize) |
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| 226 | { |
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| 227 | if (data) |
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| 228 | { |
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| 229 | ofs.open(file, std::ios::out); |
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| 230 | if (ofs.is_open()) |
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| 231 | { |
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| 232 | for(G4int i = 0; i < numberOfVoxelAlongX; i++) |
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| 233 | for(G4int j = 0; j < numberOfVoxelAlongY; j++) |
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| 234 | for(G4int k = 0; k < numberOfVoxelAlongZ; k++) |
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| 235 | { |
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| 236 | G4int n = Index(i, j, k); |
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| 237 | // Check for data type: u_int, G4double, XXX |
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| 238 | if (psize == sizeof(unsigned int)) |
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| 239 | { |
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| 240 | unsigned int* pdata = (unsigned int*)data; |
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| 241 | if (pdata[n]) ofs << i << '\t' << j << '\t' << |
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| 242 | k << '\t' << pdata[n] << G4endl; |
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| 243 | } |
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| 244 | else if (psize == sizeof(G4double)) |
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| 245 | { |
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| 246 | G4double* pdata = (G4double*)data; |
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| 247 | if (pdata[n]) ofs << i << '\t' << j << '\t' << |
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| 248 | k << '\t' << pdata[n] << G4endl; |
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| 249 | } |
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| 250 | } |
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| 251 | ofs.close(); |
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| 252 | } |
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| 253 | } |
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| 254 | } |
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| 255 | |
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| 256 | // Store fluence per single ion in multiple files |
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| 257 | void HadrontherapyMatrix::StoreFluenceData() |
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| 258 | { |
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| 259 | for (size_t i=0; i < ionStore.size(); i++){ |
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| 260 | StoreMatrix(ionStore[i].name + "_Fluence.out", ionStore[i].fluence, sizeof(unsigned int)); |
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| 261 | } |
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| 262 | } |
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| 263 | // Store dose per single ion in multiple files |
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| 264 | void HadrontherapyMatrix::StoreDoseData() |
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| 265 | { |
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| 266 | |
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| 267 | for (size_t i=0; i < ionStore.size(); i++){ |
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| 268 | StoreMatrix(ionStore[i].name + "_Dose.out", ionStore[i].dose, sizeof(G4double)); |
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| 269 | } |
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| 270 | } |
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| 271 | ///////////////////////////////////////////////////////////////////////// |
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| 272 | // Store dose for all ions into a single file and into ntuples. |
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| 273 | // Please note that this function is called via messenger commands |
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| 274 | // defined in the HadrontherapyAnalysisFileMessenger.cc class file |
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| 275 | void HadrontherapyMatrix::StoreDoseFluenceAscii() |
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| 276 | { |
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| 277 | // Sort like periodic table |
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| 278 | std::sort(ionStore.begin(), ionStore.end()); |
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| 279 | #define width 15L |
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| 280 | ofs.open(filename, std::ios::out); |
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| 281 | if (ofs.is_open()) |
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| 282 | { |
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| 283 | |
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| 284 | // |
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| 285 | // Write the voxels index and the list of particles/ions |
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| 286 | ofs << std::setprecision(6) << std::left << |
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| 287 | "i\tj\tk\t"; |
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| 288 | /* |
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| 289 | G4RunManager *runManager = G4RunManager::GetRunManager(); |
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| 290 | HadrontherapyPrimaryGeneratorAction *pPGA = (HadrontherapyPrimaryGeneratorAction*)runManager -> GetUserPrimaryGeneratorAction(); |
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| 291 | G4String name = pPGA -> GetParticleGun() -> GetParticleDefinition() -> GetParticleName(); |
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| 292 | */ |
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| 293 | // Total dose |
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| 294 | ofs << std::setw(width) << "Dose"; |
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| 295 | |
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| 296 | for (size_t l=0; l < ionStore.size(); l++) |
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| 297 | { |
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| 298 | G4String a = (ionStore[l].isPrimary) ? "_1":""; // is it a primary? |
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| 299 | ofs << std::setw(width) << ionStore[l].name + a << |
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| 300 | std::setw(width) << ionStore[l].name + a; |
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| 301 | } |
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| 302 | ofs << G4endl; |
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| 303 | |
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| 304 | /* |
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| 305 | // PDGencoding |
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| 306 | ofs << std::setprecision(6) << std::left << |
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| 307 | "0\t0\t0\t"; |
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| 308 | |
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| 309 | // Total dose |
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| 310 | ofs << std::setw(width) << '0'; |
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| 311 | for (size_t l=0; l < ionStore.size(); l++) |
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| 312 | { |
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| 313 | ofs << std::setw(width) << ionStore[l].PDGencoding << |
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| 314 | std::setw(width) << ionStore[l].PDGencoding; |
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| 315 | } |
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| 316 | ofs << G4endl; |
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| 317 | */ |
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| 318 | // Write data |
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| 319 | for(G4int i = 0; i < numberOfVoxelAlongX; i++) |
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| 320 | for(G4int j = 0; j < numberOfVoxelAlongY; j++) |
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| 321 | for(G4int k = 0; k < numberOfVoxelAlongZ; k++) |
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| 322 | { |
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| 323 | G4int n = Index(i, j, k); |
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| 324 | // Write only not identically null data lines |
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| 325 | if (matrix[n]) |
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| 326 | { |
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| 327 | ofs << G4endl; |
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| 328 | ofs << i << '\t' << j << '\t' << k << '\t'; |
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| 329 | // Total dose |
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| 330 | ofs << std::setw(width) << matrix[n]/(doseUnit); |
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| 331 | { |
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| 332 | for (size_t l=0; l < ionStore.size(); l++) |
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| 333 | { |
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| 334 | // Fill ASCII file rows |
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| 335 | ofs << std::setw(width) << ionStore[l].dose[n]/(doseUnit) << |
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| 336 | std::setw(width) << ionStore[l].fluence[n]; |
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| 337 | } |
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| 338 | } |
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| 339 | } |
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| 340 | } |
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| 341 | ofs.close(); |
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| 342 | } |
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| 343 | } |
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| 344 | ///////////////////////////////////////////////////////////////////////////// |
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| 345 | |
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| 346 | #ifdef G4ANALYSIS_USE_ROOT |
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| 347 | void HadrontherapyMatrix::StoreDoseFluenceRoot() |
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| 348 | { |
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| 349 | HadrontherapyAnalysisManager* analysis = HadrontherapyAnalysisManager::GetInstance(); |
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| 350 | for(G4int i = 0; i < numberOfVoxelAlongX; i++) |
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| 351 | for(G4int j = 0; j < numberOfVoxelAlongY; j++) |
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| 352 | for(G4int k = 0; k < numberOfVoxelAlongZ; k++) |
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| 353 | { |
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| 354 | G4int n = Index(i, j, k); |
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| 355 | for (size_t l=0; l < ionStore.size(); l++) |
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| 356 | |
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| 357 | { |
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| 358 | // Do the same work for .root file: fill dose/fluence ntuple |
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| 359 | analysis -> FillVoxelFragmentTuple( i, j, k, |
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| 360 | ionStore[l].A, |
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| 361 | ionStore[l].Z, |
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| 362 | ionStore[l].dose[n]/(doseUnit), |
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| 363 | ionStore[l].fluence[n] ); |
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| 364 | |
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| 365 | |
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| 366 | } |
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| 367 | } |
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| 368 | } |
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| 369 | #endif |
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| 370 | |
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| 371 | void HadrontherapyMatrix::Fill(G4int i, G4int j, G4int k, |
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| 372 | G4double energyDeposit) |
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| 373 | { |
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| 374 | if (matrix) |
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| 375 | matrix[Index(i,j,k)] += energyDeposit; |
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| 376 | |
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| 377 | // Store the energy deposit in the matrix element corresponding |
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| 378 | // to the phantom voxel |
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| 379 | } |
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| 380 | void HadrontherapyMatrix::TotalEnergyDeposit() |
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| 381 | { |
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| 382 | // Convert energy deposited to dose. |
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| 383 | // Store the information of the matrix in a ntuple and in |
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| 384 | // a 1D Histogram |
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| 385 | |
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| 386 | #ifdef G4ANALYSIS_USE_ROOT |
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| 387 | HadrontherapyAnalysisManager* analysis = HadrontherapyAnalysisManager::GetInstance(); |
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| 388 | #endif |
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| 389 | if (matrix) |
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| 390 | { |
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| 391 | for(G4int i = 0; i < numberOfVoxelAlongX; i++) |
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| 392 | for(G4int j = 0; j < numberOfVoxelAlongY; j++) |
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| 393 | for(G4int k = 0; k < numberOfVoxelAlongZ; k++) |
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| 394 | { |
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| 395 | G4int n = Index(i,j,k); |
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| 396 | matrix[n] = matrix[n] / massOfVoxel; |
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| 397 | #ifdef G4ANALYSIS_USE_ROOT |
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| 398 | analysis -> FillEnergyDeposit(i, j, k, matrix[n]/doseUnit); |
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| 399 | analysis -> BraggPeak(i, matrix[n]/doseUnit); |
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| 400 | #endif |
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| 401 | } |
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| 402 | } |
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| 403 | } |
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| 404 | |
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