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Please see the license in the file LICENSE and URL above * 16 // * for the full disclaimer and the limitatio 16 // * for the full disclaimer and the limitation of liability. * 17 // * 17 // * * 18 // * This code implementation is the result 18 // * This code implementation is the result of the scientific and * 19 // * technical work of the GEANT4 collaboratio 19 // * technical work of the GEANT4 collaboration. * 20 // * By using, copying, modifying or distri 20 // * By using, copying, modifying or distributing the software (or * 21 // * any work based on the software) you ag 21 // * any work based on the software) you agree to acknowledge its * 22 // * use in resulting scientific publicati 22 // * use in resulting scientific publications, and indicate your * 23 // * acceptance of all terms of the Geant4 Sof 23 // * acceptance of all terms of the Geant4 Software license. * 24 // ******************************************* 24 // ******************************************************************** 25 // 25 // >> 26 // $Id: DicomDetectorConstruction.cc 101807 2016-11-30 13:42:28Z gunter $ 26 // 27 // 27 /// \file medical/DICOM/src/DicomDetectorCons 28 /// \file medical/DICOM/src/DicomDetectorConstruction.cc 28 /// \brief Implementation of the DicomDetector 29 /// \brief Implementation of the DicomDetectorConstruction class 29 // 30 // 30 31 31 #include "DicomDetectorConstruction.hh" << 32 #include "globals.hh" 32 << 33 #include "CLHEP/Units/SystemOfUnits.h" << 34 #include "DicomHandler.hh" << 35 #include "DicomPhantomZSliceHeader.hh" << 36 33 37 #include "G4Box.hh" 34 #include "G4Box.hh" 38 #include "G4Element.hh" << 39 #include "G4LogicalVolume.hh" 35 #include "G4LogicalVolume.hh" 40 #include "G4Material.hh" << 36 #include "G4VPhysicalVolume.hh" 41 #include "G4NistManager.hh" << 42 #include "G4PVPlacement.hh" 37 #include "G4PVPlacement.hh" 43 #include "G4PhysicalConstants.hh" << 38 #include "G4Material.hh" >> 39 #include "G4Element.hh" 44 #include "G4UIcommand.hh" 40 #include "G4UIcommand.hh" 45 #include "G4VPhysicalVolume.hh" << 41 #include "G4PhysicalConstants.hh" 46 #include "globals.hh" << 42 #include "G4NistManager.hh" >> 43 // #include "G4SystemOfUnits.hh" >> 44 #include "CLHEP/Units/SystemOfUnits.h" >> 45 >> 46 #include "DicomDetectorConstruction.hh" >> 47 #include "DicomPhantomZSliceHeader.hh" 47 48 >> 49 #include "DicomRunAction.hh" >> 50 #include "DicomRun.hh" 48 #ifdef G4_DCMTK 51 #ifdef G4_DCMTK 49 # include "DicomFileMgr.hh" << 52 #include "DicomFileMgr.hh" 50 #endif 53 #endif 51 #include "G4VisAttributes.hh" 54 #include "G4VisAttributes.hh" 52 55 >> 56 using CLHEP::m; 53 using CLHEP::cm3; 57 using CLHEP::cm3; >> 58 using CLHEP::mole; 54 using CLHEP::g; 59 using CLHEP::g; 55 using CLHEP::m; << 56 using CLHEP::mg; 60 using CLHEP::mg; 57 using CLHEP::mole; << 58 using CLHEP::perCent; << 59 61 60 //....oooOO0OOooo........oooOO0OOooo........oo << 62 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 61 DicomDetectorConstruction::DicomDetectorConstr 63 DicomDetectorConstruction::DicomDetectorConstruction() 62 : G4VUserDetectorConstruction(), << 64 : G4VUserDetectorConstruction(), 63 fAir(0), << 65 fAir(0), 64 66 65 fWorld_solid(0), << 67 fWorld_solid(0), 66 fWorld_logic(0), << 68 fWorld_logic(0), 67 fWorld_phys(0), << 69 fWorld_phys(0), >> 70 >> 71 fContainer_solid(0), >> 72 fContainer_logic(0), >> 73 fContainer_phys(0), >> 74 >> 75 fNoFiles(0), >> 76 fMateIDs(0), >> 77 >> 78 fZSliceHeaderMerged(0), >> 79 >> 80 fNVoxelX(0), >> 81 fNVoxelY(0), >> 82 fNVoxelZ(0), >> 83 fVoxelHalfDimX(0), >> 84 fVoxelHalfDimY(0), >> 85 fVoxelHalfDimZ(0), 68 86 69 fContainer_solid(0), << 87 fConstructed(false) 70 fContainer_logic(0), << 88 { 71 fContainer_phys(0), << 72 << 73 fNoFiles(0), << 74 fMateIDs(0), << 75 << 76 fZSliceHeaderMerged(0), << 77 << 78 fNoVoxelsX(0), << 79 fNoVoxelsY(0), << 80 fNoVoxelsZ(0), << 81 fVoxelHalfDimX(0), << 82 fVoxelHalfDimY(0), << 83 fVoxelHalfDimZ(0), << 84 89 85 fConstructed(false) << 90 } 86 {} << 87 91 88 //....oooOO0OOooo........oooOO0OOooo........oo << 92 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 89 DicomDetectorConstruction::~DicomDetectorConst << 93 DicomDetectorConstruction::~DicomDetectorConstruction() >> 94 { >> 95 } 90 96 91 //....oooOO0OOooo........oooOO0OOooo........oo << 97 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 92 G4VPhysicalVolume* DicomDetectorConstruction:: 98 G4VPhysicalVolume* DicomDetectorConstruction::Construct() 93 { 99 { 94 if (!fConstructed || fWorld_phys == 0) { << 100 if(!fConstructed || fWorld_phys == 0) { 95 fConstructed = true; 101 fConstructed = true; 96 InitialisationOfMaterials(); 102 InitialisationOfMaterials(); 97 103 98 //----- Build world 104 //----- Build world 99 G4double worldXDimension = 1. * m; << 105 G4double worldXDimension = 1.*m; 100 G4double worldYDimension = 1. * m; << 106 G4double worldYDimension = 1.*m; 101 G4double worldZDimension = 1. * m; << 107 G4double worldZDimension = 1.*m; 102 << 108 103 fWorld_solid = new G4Box("WorldSolid", wor << 109 fWorld_solid = new G4Box( "WorldSolid", 104 << 110 worldXDimension, 105 fWorld_logic = new G4LogicalVolume(fWorld_ << 111 worldYDimension, 106 << 112 worldZDimension ); 107 fWorld_phys = new G4PVPlacement(0, G4Three << 113 108 << 114 fWorld_logic = new G4LogicalVolume( fWorld_solid, 109 fWorld_logic->SetVisAttributes(G4VisAttrib << 115 fAir, >> 116 "WorldLogical", >> 117 0, 0, 0 ); >> 118 >> 119 fWorld_phys = new G4PVPlacement( 0, >> 120 G4ThreeVector(0,0,0), >> 121 "World", >> 122 fWorld_logic, >> 123 0, >> 124 false, >> 125 0 ); 110 126 111 #ifdef G4_DCMTK 127 #ifdef G4_DCMTK 112 ReadPhantomDataNew(); 128 ReadPhantomDataNew(); 113 ConstructPhantomContainerNew(); 129 ConstructPhantomContainerNew(); 114 #else 130 #else 115 ReadPhantomData(); 131 ReadPhantomData(); 116 ConstructPhantomContainer(); 132 ConstructPhantomContainer(); 117 #endif 133 #endif 118 << 134 119 ConstructPhantom(); 135 ConstructPhantom(); 120 } 136 } 121 return fWorld_phys; << 137 return fWorld_phys; 122 } 138 } 123 139 124 //....oooOO0OOooo........oooOO0OOooo........oo << 140 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 125 void DicomDetectorConstruction::Initialisation 141 void DicomDetectorConstruction::InitialisationOfMaterials() 126 { 142 { 127 // Creating elements : << 143 // Creating elements : 128 G4double z, a, density; << 144 G4double z, a, density; 129 G4String name, symbol; << 145 G4String name, symbol; 130 << 146 131 G4Element* elC = new G4Element(name = "Carbo << 147 G4Element* elC = new G4Element( name = "Carbon", 132 G4Element* elH = new G4Element(name = "Hydro << 148 symbol = "C", 133 G4Element* elN = new G4Element(name = "Nitro << 149 z = 6.0, a = 12.011 * g/mole ); 134 G4Element* elO = new G4Element(name = "Oxyge << 150 G4Element* elH = new G4Element( name = "Hydrogen", 135 G4Element* elNa = << 151 symbol = "H", 136 new G4Element(name = "Sodium", symbol = "N << 152 z = 1.0, a = 1.008 * g/mole ); 137 G4Element* elMg = << 153 G4Element* elN = new G4Element( name = "Nitrogen", 138 new G4Element(name = "Magnesium", symbol = << 154 symbol = "N", 139 G4Element* elP = << 155 z = 7.0, a = 14.007 * g/mole ); 140 new G4Element(name = "Phosphorus", symbol << 156 G4Element* elO = new G4Element( name = "Oxygen", 141 G4Element* elS = new G4Element(name = "Sulfu << 157 symbol = "O", 142 G4Element* elCl = << 158 z = 8.0, a = 16.00 * g/mole ); 143 new G4Element(name = "Chlorine", symbol = << 159 G4Element* elNa = new G4Element( name = "Sodium", 144 G4Element* elK = << 160 symbol = "Na", 145 new G4Element(name = "Potassium", symbol = << 161 z= 11.0, a = 22.98977* g/mole ); 146 << 162 G4Element* elS = new G4Element( name = "Sulfur", 147 G4Element* elFe = new G4Element(name = "Iron << 163 symbol = "S", 148 << 164 z = 16.0,a = 32.065* g/mole ); 149 G4Element* elCa = new G4Element(name = "Calc << 165 G4Element* elCl = new G4Element( name = "Chlorine", 150 << 166 symbol = "P", 151 G4Element* elZn = new G4Element(name = "Zinc << 167 z = 17.0, a = 35.453* g/mole ); 152 << 168 G4Element* elK = new G4Element( name = "Potassium", 153 // Creating Materials : << 169 symbol = "P", 154 G4int numberofElements; << 170 z = 19.0, a = 30.0983* g/mole ); 155 << 171 G4Element* elP = new G4Element( name = "Phosphorus", 156 // Air << 172 symbol = "P", 157 fAir = new G4Material("Air", 1.290 * mg / cm << 173 z = 30.0, a = 30.973976* g/mole ); 158 fAir->AddElement(elN, 0.7); << 174 G4Element* elFe = new G4Element( name = "Iron", 159 fAir->AddElement(elO, 0.3); << 175 symbol = "Fe", 160 << 176 z = 26, a = 56.845* g/mole ); 161 // Soft tissue (ICRP - NIST) << 177 G4Element* elMg = new G4Element( name = "Magnesium", 162 G4Material* softTissue = new G4Material("Sof << 178 symbol = "Mg", 163 softTissue->AddElement(elH, 10.4472 * perCen << 179 z = 12.0, a = 24.3050* g/mole ); 164 softTissue->AddElement(elC, 23.219 * perCent << 180 G4Element* elCa = new G4Element( name="Calcium", 165 softTissue->AddElement(elN, 2.488 * perCent) << 181 symbol = "Ca", 166 softTissue->AddElement(elO, 63.0238 * perCen << 182 z = 20.0, a = 40.078* g/mole ); 167 softTissue->AddElement(elNa, 0.113 * perCent << 183 168 softTissue->AddElement(elMg, 0.0113 * perCen << 184 // Creating Materials : 169 softTissue->AddElement(elP, 0.113 * perCent) << 185 G4int numberofElements; 170 softTissue->AddElement(elS, 0.199 * perCent) << 186 171 softTissue->AddElement(elCl, 0.134 * perCent << 187 // Air 172 softTissue->AddElement(elK, 0.199 * perCent) << 188 fAir = new G4Material( "Air", 173 softTissue->AddElement(elCa, 0.023 * perCent << 189 1.290*mg/cm3, 174 softTissue->AddElement(elFe, 0.005 * perCent << 190 numberofElements = 2 ); 175 softTissue->AddElement(elZn, 0.003 * perCent << 191 fAir->AddElement(elN, 0.7); 176 << 192 fAir->AddElement(elO, 0.3); 177 // Lung Inhale << 193 178 G4Material* lunginhale = << 194 // Lung Inhale 179 new G4Material("LungInhale", density = 0.2 << 195 G4Material* lunginhale = new G4Material( "LungInhale", 180 lunginhale->AddElement(elH, 0.103); << 196 density = 0.217*g/cm3, 181 lunginhale->AddElement(elC, 0.105); << 197 numberofElements = 9); 182 lunginhale->AddElement(elN, 0.031); << 198 lunginhale->AddElement(elH,0.103); 183 lunginhale->AddElement(elO, 0.749); << 199 lunginhale->AddElement(elC,0.105); 184 lunginhale->AddElement(elNa, 0.002); << 200 lunginhale->AddElement(elN,0.031); 185 lunginhale->AddElement(elP, 0.002); << 201 lunginhale->AddElement(elO,0.749); 186 lunginhale->AddElement(elS, 0.003); << 202 lunginhale->AddElement(elNa,0.002); 187 lunginhale->AddElement(elCl, 0.002); << 203 lunginhale->AddElement(elP,0.002); 188 lunginhale->AddElement(elK, 0.003); << 204 lunginhale->AddElement(elS,0.003); 189 << 205 lunginhale->AddElement(elCl,0.002); 190 // Lung exhale << 206 lunginhale->AddElement(elK,0.003); 191 G4Material* lungexhale = << 207 192 new G4Material("LungExhale", density = 0.5 << 208 // Lung exhale 193 lungexhale->AddElement(elH, 0.103); << 209 G4Material* lungexhale = new G4Material( "LungExhale", 194 lungexhale->AddElement(elC, 0.105); << 210 density = 0.508*g/cm3, 195 lungexhale->AddElement(elN, 0.031); << 211 numberofElements = 9 ); 196 lungexhale->AddElement(elO, 0.749); << 212 lungexhale->AddElement(elH,0.103); 197 lungexhale->AddElement(elNa, 0.002); << 213 lungexhale->AddElement(elC,0.105); 198 lungexhale->AddElement(elP, 0.002); << 214 lungexhale->AddElement(elN,0.031); 199 lungexhale->AddElement(elS, 0.003); << 215 lungexhale->AddElement(elO,0.749); 200 lungexhale->AddElement(elCl, 0.002); << 216 lungexhale->AddElement(elNa,0.002); 201 lungexhale->AddElement(elK, 0.003); << 217 lungexhale->AddElement(elP,0.002); 202 << 218 lungexhale->AddElement(elS,0.003); 203 // Adipose tissue << 219 lungexhale->AddElement(elCl,0.002); 204 G4Material* adiposeTissue = << 220 lungexhale->AddElement(elK,0.003); 205 new G4Material("AdiposeTissue", density = << 221 206 adiposeTissue->AddElement(elH, 0.114); << 222 // Adipose tissue 207 adiposeTissue->AddElement(elC, 0.598); << 223 G4Material* adiposeTissue = new G4Material( "AdiposeTissue", 208 adiposeTissue->AddElement(elN, 0.007); << 224 density = 0.967*g/cm3, 209 adiposeTissue->AddElement(elO, 0.278); << 225 numberofElements = 7); 210 adiposeTissue->AddElement(elNa, 0.001); << 226 adiposeTissue->AddElement(elH,0.114); 211 adiposeTissue->AddElement(elS, 0.001); << 227 adiposeTissue->AddElement(elC,0.598); 212 adiposeTissue->AddElement(elCl, 0.001); << 228 adiposeTissue->AddElement(elN,0.007); 213 << 229 adiposeTissue->AddElement(elO,0.278); 214 // Brain (ICRP - NIST) << 230 adiposeTissue->AddElement(elNa,0.001); 215 G4Material* brainTissue = new G4Material("Br << 231 adiposeTissue->AddElement(elS,0.001); 216 brainTissue->AddElement(elH, 11.0667 * perCe << 232 adiposeTissue->AddElement(elCl,0.001); 217 brainTissue->AddElement(elC, 12.542 * perCen << 233 218 brainTissue->AddElement(elN, 1.328 * perCent << 234 // Breast 219 brainTissue->AddElement(elO, 73.7723 * perCe << 235 G4Material* breast = new G4Material( "Breast", 220 brainTissue->AddElement(elNa, 0.1840 * perCe << 236 density = 0.990*g/cm3, 221 brainTissue->AddElement(elMg, 0.015 * perCen << 237 numberofElements = 8 ); 222 brainTissue->AddElement(elP, 0.356 * perCent << 238 breast->AddElement(elH,0.109); 223 brainTissue->AddElement(elS, 0.177 * perCent << 239 breast->AddElement(elC,0.506); 224 brainTissue->AddElement(elCl, 0.236 * perCen << 240 breast->AddElement(elN,0.023); 225 brainTissue->AddElement(elK, 0.31 * perCent) << 241 breast->AddElement(elO,0.358); 226 brainTissue->AddElement(elCa, 0.009 * perCen << 242 breast->AddElement(elNa,0.001); 227 brainTissue->AddElement(elFe, 0.005 * perCen << 243 breast->AddElement(elP,0.001); 228 brainTissue->AddElement(elZn, 0.001 * perCen << 244 breast->AddElement(elS,0.001); 229 << 245 breast->AddElement(elCl,0.001); 230 // Breast << 246 231 G4Material* breast = new G4Material("Breast" << 247 // Water 232 breast->AddElement(elH, 0.109); << 248 G4Material* water = new G4Material( "Water", 233 breast->AddElement(elC, 0.506); << 249 density = 1.0*g/cm3, 234 breast->AddElement(elN, 0.023); << 250 numberofElements = 2 ); 235 breast->AddElement(elO, 0.358); << 251 water->AddElement(elH,0.112); 236 breast->AddElement(elNa, 0.001); << 252 water->AddElement(elO,0.888); 237 breast->AddElement(elP, 0.001); << 253 238 breast->AddElement(elS, 0.001); << 254 // Muscle 239 breast->AddElement(elCl, 0.001); << 255 G4Material* muscle = new G4Material( "Muscle", 240 << 256 density = 1.061*g/cm3, 241 // Spinal Disc << 257 numberofElements = 9 ); 242 G4Material* spinalDisc = new G4Material("Spi << 258 muscle->AddElement(elH,0.102); 243 spinalDisc->AddElement(elH, 9.60 * perCent); << 259 muscle->AddElement(elC,0.143); 244 spinalDisc->AddElement(elC, 9.90 * perCent); << 260 muscle->AddElement(elN,0.034); 245 spinalDisc->AddElement(elN, 2.20 * perCent); << 261 muscle->AddElement(elO,0.710); 246 spinalDisc->AddElement(elO, 74.40 * perCent) << 262 muscle->AddElement(elNa,0.001); 247 spinalDisc->AddElement(elNa, 0.50 * perCent) << 263 muscle->AddElement(elP,0.002); 248 spinalDisc->AddElement(elP, 2.20 * perCent); << 264 muscle->AddElement(elS,0.003); 249 spinalDisc->AddElement(elS, 0.90 * perCent); << 265 muscle->AddElement(elCl,0.001); 250 spinalDisc->AddElement(elCl, 0.30 * perCent) << 266 muscle->AddElement(elK,0.004); 251 << 267 252 // Water << 268 // Liver 253 G4Material* water = new G4Material("Water", << 269 G4Material* liver = new G4Material( "Liver", 254 water->AddElement(elH, 0.112); << 270 density = 1.071*g/cm3, 255 water->AddElement(elO, 0.888); << 271 numberofElements = 9); 256 << 272 liver->AddElement(elH,0.102); 257 // Muscle << 273 liver->AddElement(elC,0.139); 258 G4Material* muscle = new G4Material("Muscle" << 274 liver->AddElement(elN,0.030); 259 muscle->AddElement(elH, 0.102); << 275 liver->AddElement(elO,0.716); 260 muscle->AddElement(elC, 0.143); << 276 liver->AddElement(elNa,0.002); 261 muscle->AddElement(elN, 0.034); << 277 liver->AddElement(elP,0.003); 262 muscle->AddElement(elO, 0.710); << 278 liver->AddElement(elS,0.003); 263 muscle->AddElement(elNa, 0.001); << 279 liver->AddElement(elCl,0.002); 264 muscle->AddElement(elP, 0.002); << 280 liver->AddElement(elK,0.003); 265 muscle->AddElement(elS, 0.003); << 281 266 muscle->AddElement(elCl, 0.001); << 282 // Trabecular Bone 267 muscle->AddElement(elK, 0.004); << 283 G4Material* trabecularBone = new G4Material( "TrabecularBone", 268 << 284 density = 1.159*g/cm3, 269 // Liver << 285 numberofElements = 12 ); 270 G4Material* liver = new G4Material("Liver", << 286 trabecularBone->AddElement(elH,0.085); 271 liver->AddElement(elH, 0.102); << 287 trabecularBone->AddElement(elC,0.404); 272 liver->AddElement(elC, 0.139); << 288 trabecularBone->AddElement(elN,0.058); 273 liver->AddElement(elN, 0.030); << 289 trabecularBone->AddElement(elO,0.367); 274 liver->AddElement(elO, 0.716); << 290 trabecularBone->AddElement(elNa,0.001); 275 liver->AddElement(elNa, 0.002); << 291 trabecularBone->AddElement(elMg,0.001); 276 liver->AddElement(elP, 0.003); << 292 trabecularBone->AddElement(elP,0.034); 277 liver->AddElement(elS, 0.003); << 293 trabecularBone->AddElement(elS,0.002); 278 liver->AddElement(elCl, 0.002); << 294 trabecularBone->AddElement(elCl,0.002); 279 liver->AddElement(elK, 0.003); << 295 trabecularBone->AddElement(elK,0.001); 280 << 296 trabecularBone->AddElement(elCa,0.044); 281 // Tooth Dentin << 297 trabecularBone->AddElement(elFe,0.001); 282 G4Material* toothDentin = new G4Material("To << 298 283 toothDentin->AddElement(elH, 2.67 * perCent) << 299 // Dense Bone 284 toothDentin->AddElement(elC, 12.77 * perCent << 300 G4Material* denseBone = new G4Material( "DenseBone", 285 toothDentin->AddElement(elN, 4.27 * perCent) << 301 density = 1.575*g/cm3, 286 toothDentin->AddElement(elO, 40.40 * perCent << 302 numberofElements = 11 ); 287 toothDentin->AddElement(elNa, 0.65 * perCent << 303 denseBone->AddElement(elH,0.056); 288 toothDentin->AddElement(elMg, 0.59 * perCent << 304 denseBone->AddElement(elC,0.235); 289 toothDentin->AddElement(elP, 11.86 * perCent << 305 denseBone->AddElement(elN,0.050); 290 toothDentin->AddElement(elCl, 0.04 * perCent << 306 denseBone->AddElement(elO,0.434); 291 toothDentin->AddElement(elCa, 26.74 * perCen << 307 denseBone->AddElement(elNa,0.001); 292 toothDentin->AddElement(elZn, 0.01 * perCent << 308 denseBone->AddElement(elMg,0.001); 293 << 309 denseBone->AddElement(elP,0.072); 294 // Trabecular Bone << 310 denseBone->AddElement(elS,0.003); 295 G4Material* trabecularBone = << 311 denseBone->AddElement(elCl,0.001); 296 new G4Material("TrabecularBone", density = << 312 denseBone->AddElement(elK,0.001); 297 trabecularBone->AddElement(elH, 0.085); << 313 denseBone->AddElement(elCa,0.146); 298 trabecularBone->AddElement(elC, 0.404); << 314 299 trabecularBone->AddElement(elN, 0.058); << 315 //----- Put the materials in a vector 300 trabecularBone->AddElement(elO, 0.367); << 316 fOriginalMaterials.push_back(fAir); // rho = 0.00129 301 trabecularBone->AddElement(elNa, 0.001); << 317 fOriginalMaterials.push_back(lunginhale); // rho = 0.217 302 trabecularBone->AddElement(elMg, 0.001); << 318 fOriginalMaterials.push_back(lungexhale); // rho = 0.508 303 trabecularBone->AddElement(elP, 0.034); << 319 fOriginalMaterials.push_back(adiposeTissue); // rho = 0.967 304 trabecularBone->AddElement(elS, 0.002); << 320 fOriginalMaterials.push_back(breast ); // rho = 0.990 305 trabecularBone->AddElement(elCl, 0.002); << 321 fOriginalMaterials.push_back(water); // rho = 1.018 306 trabecularBone->AddElement(elK, 0.001); << 322 fOriginalMaterials.push_back(muscle); // rho = 1.061 307 trabecularBone->AddElement(elCa, 0.044); << 323 fOriginalMaterials.push_back(liver); // rho = 1.071 308 trabecularBone->AddElement(elFe, 0.001); << 324 fOriginalMaterials.push_back(trabecularBone); // rho = 1.159 309 << 325 fOriginalMaterials.push_back(denseBone); // rho = 1.575 310 // Trabecular bone used in the DICOM Head << 326 311 << 312 G4Material* trabecularBone_head = << 313 new G4Material("TrabecularBone_HEAD", 1.18 << 314 trabecularBone_head->AddElement(elH, 8.50 * << 315 trabecularBone_head->AddElement(elC, 40.40 * << 316 trabecularBone_head->AddElement(elN, 2.80 * << 317 trabecularBone_head->AddElement(elO, 36.70 * << 318 trabecularBone_head->AddElement(elNa, 0.10 * << 319 trabecularBone_head->AddElement(elMg, 0.10 * << 320 trabecularBone_head->AddElement(elP, 3.40 * << 321 trabecularBone_head->AddElement(elS, 0.20 * << 322 trabecularBone_head->AddElement(elCl, 0.20 * << 323 trabecularBone_head->AddElement(elK, 0.10 * << 324 trabecularBone_head->AddElement(elCa, 7.40 * << 325 trabecularBone_head->AddElement(elFe, 0.10 * << 326 << 327 // Dense Bone << 328 G4Material* denseBone = << 329 new G4Material("DenseBone", density = 1.57 << 330 denseBone->AddElement(elH, 0.056); << 331 denseBone->AddElement(elC, 0.235); << 332 denseBone->AddElement(elN, 0.050); << 333 denseBone->AddElement(elO, 0.434); << 334 denseBone->AddElement(elNa, 0.001); << 335 denseBone->AddElement(elMg, 0.001); << 336 denseBone->AddElement(elP, 0.072); << 337 denseBone->AddElement(elS, 0.003); << 338 denseBone->AddElement(elCl, 0.001); << 339 denseBone->AddElement(elK, 0.001); << 340 denseBone->AddElement(elCa, 0.146); << 341 << 342 // Cortical Bone (ICRP - NIST) << 343 G4Material* corticalBone = new G4Material("C << 344 corticalBone->AddElement(elH, 4.7234 * perCe << 345 corticalBone->AddElement(elC, 14.4330 * perC << 346 corticalBone->AddElement(elN, 4.199 * perCen << 347 corticalBone->AddElement(elO, 44.6096 * perC << 348 corticalBone->AddElement(elMg, 0.22 * perCen << 349 corticalBone->AddElement(elP, 10.497 * perCe << 350 corticalBone->AddElement(elS, 0.315 * perCen << 351 corticalBone->AddElement(elCa, 20.993 * perC << 352 corticalBone->AddElement(elZn, 0.01 * perCen << 353 << 354 // Tooth enamel << 355 G4Material* toothEnamel = new G4Material("To << 356 toothEnamel->AddElement(elH, 0.95 * perCent) << 357 toothEnamel->AddElement(elC, 1.11 * perCent) << 358 toothEnamel->AddElement(elN, 0.23 * perCent) << 359 toothEnamel->AddElement(elO, 41.66 * perCent << 360 toothEnamel->AddElement(elNa, 0.79 * perCent << 361 toothEnamel->AddElement(elMg, 0.23 * perCent << 362 toothEnamel->AddElement(elP, 18.71 * perCent << 363 toothEnamel->AddElement(elCl, 0.34 * perCent << 364 toothEnamel->AddElement(elCa, 35.97 * perCen << 365 toothEnamel->AddElement(elZn, 0.02 * perCent << 366 << 367 #ifdef DICOM_USE_HEAD << 368 //----- Put the materials in a vector HEAD P << 369 fOriginalMaterials.push_back(fAir); // 0.00 << 370 fOriginalMaterials.push_back(softTissue); / << 371 fOriginalMaterials.push_back(brainTissue); << 372 fOriginalMaterials.push_back(spinalDisc); / << 373 fOriginalMaterials.push_back(trabecularBone_ << 374 fOriginalMaterials.push_back(toothDentin); << 375 fOriginalMaterials.push_back(corticalBone); << 376 fOriginalMaterials.push_back(toothEnamel); << 377 G4cout << "The materials of the DICOM Head h << 378 #else << 379 fOriginalMaterials.push_back(fAir); // rho << 380 fOriginalMaterials.push_back(lunginhale); / << 381 fOriginalMaterials.push_back(lungexhale); / << 382 fOriginalMaterials.push_back(adiposeTissue); << 383 fOriginalMaterials.push_back(breast); // rh << 384 fOriginalMaterials.push_back(water); // rho << 385 fOriginalMaterials.push_back(muscle); // rh << 386 fOriginalMaterials.push_back(liver); // rho << 387 fOriginalMaterials.push_back(trabecularBone) << 388 fOriginalMaterials.push_back(denseBone); // << 389 G4cout << "Default materials of the DICOM Ex << 390 #endif << 391 } 327 } 392 328 393 //....oooOO0OOooo........oooOO0OOooo........oo << 329 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 394 void DicomDetectorConstruction::ReadPhantomDat 330 void DicomDetectorConstruction::ReadPhantomDataNew() 395 { 331 { 396 #ifdef G4_DCMTK 332 #ifdef G4_DCMTK 397 G4String fileName = DicomFileMgr::GetInstanc 333 G4String fileName = DicomFileMgr::GetInstance()->GetFileOutName(); 398 << 334 399 std::ifstream fin(fileName); 335 std::ifstream fin(fileName); 400 std::vector<G4String> wl; 336 std::vector<G4String> wl; 401 G4int nMaterials; 337 G4int nMaterials; 402 fin >> nMaterials; 338 fin >> nMaterials; 403 G4String mateName; 339 G4String mateName; 404 G4int nmate; 340 G4int nmate; 405 for (G4int ii = 0; ii < nMaterials; ++ii) { << 341 for( G4int ii = 0; ii < nMaterials; ii++ ){ 406 fin >> nmate; 342 fin >> nmate; 407 fin >> mateName; 343 fin >> mateName; 408 if (mateName[0] == '"' && mateName[mateNam << 344 if( mateName[0] == '"' && mateName[mateName.length()-1] == '"' ) { 409 mateName = mateName.substr(1, mateName.l << 345 mateName = mateName.substr(1,mateName.length()-2); 410 } 346 } 411 G4cout << "GmReadPhantomG4Geometry::ReadPh << 347 G4cout << "GmReadPhantomG4Geometry::ReadPhantomData reading nmate " << ii << " = " << nmate 412 << " mate " << mateName << G4endl; 348 << " mate " << mateName << G4endl; 413 if (ii != nmate) << 349 if( ii != nmate ) G4Exception("GmReadPhantomG4Geometry::ReadPhantomData", 414 G4Exception("GmReadPhantomG4Geometry::Re << 350 "Wrong argument", 415 FatalErrorInArgument, << 351 FatalErrorInArgument, 416 "Material number should be i << 352 "Material number should be in increasing order: wrong material number "); 417 353 418 G4Material* mate = 0; 354 G4Material* mate = 0; 419 const G4MaterialTable* matTab = G4Material 355 const G4MaterialTable* matTab = G4Material::GetMaterialTable(); 420 for (auto matite = matTab->cbegin(); matit << 356 std::vector<G4Material*>::const_iterator matite; 421 if ((*matite)->GetName() == mateName) { << 357 for( matite = matTab->begin(); matite != matTab->end(); ++matite ) { >> 358 if( (*matite)->GetName() == mateName ) { 422 mate = *matite; 359 mate = *matite; 423 } 360 } 424 } 361 } 425 if (mate == 0) { << 362 if( mate == 0 ) { 426 mate = G4NistManager::Instance()->FindOr 363 mate = G4NistManager::Instance()->FindOrBuildMaterial(mateName); 427 } 364 } 428 if (!mate) << 365 if( !mate ) G4Exception("GmReadPhantomG4Geometry::ReadPhantomData", 429 G4Exception("GmReadPhantomG4Geometry::Re << 366 "Wrong argument", 430 FatalErrorInArgument, ("Mate << 367 FatalErrorInArgument, 431 fPhantomMaterialsOriginal[nmate] = mate; << 368 ("Material not found" + mateName).c_str()); >> 369 thePhantomMaterialsOriginal[nmate] = mate; 432 } 370 } 433 371 434 fin >> fNoVoxelsX >> fNoVoxelsY >> fNoVoxels << 372 fin >> fNVoxelX >> fNVoxelY >> fNVoxelZ; 435 G4cout << "GmReadPhantomG4Geometry::ReadPhan << 373 G4cout << "GmReadPhantomG4Geometry::ReadPhantomData fNVoxel X/Y/Z " << fNVoxelX << " " 436 << fNoVoxelsY << " " << fNoVoxelsZ << << 374 << fNVoxelY << " " << fNVoxelZ << G4endl; 437 fin >> fMinX >> fMaxX; 375 fin >> fMinX >> fMaxX; 438 fin >> fMinY >> fMaxY; 376 fin >> fMinY >> fMaxY; 439 fin >> fMinZ >> fMaxZ; 377 fin >> fMinZ >> fMaxZ; 440 fVoxelHalfDimX = (fMaxX - fMinX) / fNoVoxels << 378 fVoxelHalfDimX = (fMaxX-fMinX)/fNVoxelX/2.; 441 fVoxelHalfDimY = (fMaxY - fMinY) / fNoVoxels << 379 fVoxelHalfDimY = (fMaxY-fMinY)/fNVoxelY/2.; 442 fVoxelHalfDimZ = (fMaxZ - fMinZ) / fNoVoxels << 380 fVoxelHalfDimZ = (fMaxZ-fMinZ)/fNVoxelZ/2.; 443 # ifdef G4VERBOSE << 381 #ifdef G4VERBOSE 444 G4cout << " Extension in X " << fMinX << " " << 382 G4cout << " Extension in X " << fMinX << " " << fMaxX << G4endl 445 << " " << fMaxY << G4endl << " Extens << 383 << " Extension in Y " << fMinY << " " << fMaxY << G4endl 446 # endif << 384 << " Extension in Z " << fMinZ << " " << fMaxZ << G4endl; 447 << 385 #endif 448 fMateIDs = new size_t[fNoVoxelsX * fNoVoxels << 386 449 for (G4int iz = 0; iz < fNoVoxelsZ; ++iz) { << 387 fMateIDs = new size_t[fNVoxelX*fNVoxelY*fNVoxelZ]; 450 for (G4int iy = 0; iy < fNoVoxelsY; ++iy) << 388 for( G4int iz = 0; iz < fNVoxelZ; iz++ ) { 451 for (G4int ix = 0; ix < fNoVoxelsX; ++ix << 389 for( G4int iy = 0; iy < fNVoxelY; iy++ ) { >> 390 for( G4int ix = 0; ix < fNVoxelX; ix++ ) { 452 G4int mateID; 391 G4int mateID; 453 fin >> mateID; << 392 fin >> mateID; 454 G4int nnew = ix + (iy)*fNoVoxelsX + (i << 393 G4int nnew = ix + (iy)*fNVoxelX + (iz)*fNVoxelX*fNVoxelY; 455 if (mateID < 0 || mateID >= nMaterials << 394 if( mateID < 0 || mateID >= nMaterials ) { 456 G4Exception("GmReadPhantomG4Geometry << 395 G4Exception("GmReadPhantomG4Geometry::ReadPhantomData", >> 396 "Wrong index in phantom file", 457 FatalException, 397 FatalException, 458 G4String("It should be b 398 G4String("It should be between 0 and " 459 + G4UIcommand:: << 399 + G4UIcommand::ConvertToString(nMaterials-1) 460 + G4UIcommand:: << 400 + ", while it is " 461 .c_str()); << 401 + G4UIcommand::ConvertToString(mateID)).c_str()); 462 } 402 } 463 fMateIDs[nnew] = mateID; 403 fMateIDs[nnew] = mateID; 464 } 404 } 465 } 405 } 466 } 406 } 467 407 468 ReadVoxelDensities(fin); << 408 ReadVoxelDensities( fin ); 469 409 470 fin.close(); 410 fin.close(); 471 #endif 411 #endif >> 412 472 } 413 } 473 414 474 //....oooOO0OOooo........oooOO0OOooo........oo << 415 475 void DicomDetectorConstruction::ReadVoxelDensi << 416 void DicomDetectorConstruction::ReadVoxelDensities( std::ifstream& fin ) 476 { 417 { 477 G4String stemp; 418 G4String stemp; 478 std::map<G4int, std::pair<G4double, G4double << 419 std::map<G4int, std::pair<G4double,G4double> > densiMinMax; 479 std::map<G4int, std::pair<G4double, G4double << 420 std::map<G4int, std::pair<G4double,G4double> >::iterator mpite; 480 for (G4int ii = 0; ii < G4int(fPhantomMateri << 421 for( size_t ii = 0; ii < thePhantomMaterialsOriginal.size(); ii++ ){ 481 densiMinMax[ii] = std::pair<G4double, G4do << 422 densiMinMax[ii] = std::pair<G4double,G4double>(DBL_MAX,-DBL_MAX); 482 } 423 } 483 424 484 char* part = std::getenv("DICOM_CHANGE_MATER << 425 char* part = getenv( "DICOM_CHANGE_MATERIAL_DENSITY" ); 485 G4double densityDiff = -1.; 426 G4double densityDiff = -1.; 486 if (part) densityDiff = G4UIcommand::Convert << 427 if( part ) densityDiff = G4UIcommand::ConvertToDouble(part); 487 428 488 std::map<G4int, G4double> densityDiffs; << 429 std::map<G4int,G4double> densityDiffs; 489 for (G4int ii = 0; ii < G4int(fPhantomMateri << 430 for( size_t ii = 0; ii < thePhantomMaterialsOriginal.size(); ii++ ){ 490 densityDiffs[ii] = densityDiff; // curren << 431 densityDiffs[ii] = densityDiff; //currently all materials with same step 491 } 432 } 492 // densityDiffs[0] = 0.0001; //air 433 // densityDiffs[0] = 0.0001; //air 493 434 494 //--- Calculate the average material density 435 //--- Calculate the average material density for each material/density bin 495 std::map<std::pair<G4Material*, G4int>, matI << 436 std::map< std::pair<G4Material*,G4int>, matInfo* > newMateDens; 496 437 497 //---- Read the material densities 438 //---- Read the material densities 498 G4double dens; 439 G4double dens; 499 for (G4int iz = 0; iz < fNoVoxelsZ; ++iz) { << 440 for( G4int iz = 0; iz < fNVoxelZ; iz++ ) { 500 for (G4int iy = 0; iy < fNoVoxelsY; ++iy) << 441 for( G4int iy = 0; iy < fNVoxelY; iy++ ) { 501 for (G4int ix = 0; ix < fNoVoxelsX; ++ix << 442 for( G4int ix = 0; ix < fNVoxelX; ix++ ) { 502 fin >> dens; << 443 fin >> dens; 503 G4int copyNo = ix + (iy)*fNoVoxelsX + << 444 // G4cout << ix << " " << iy << " " << iz << " density " << dens << G4endl; 504 << 445 G4int copyNo = ix + (iy)*fNVoxelX + (iz)*fNVoxelX*fNVoxelY; 505 if (densityDiff != -1.) continue; << 446 506 << 447 if( densityDiff != -1. ) continue; 507 //--- store the minimum and maximum de << 448 508 mpite = densiMinMax.find(G4int(fMateID << 449 //--- store the minimum and maximum density for each material (just for printing) 509 if (dens < (*mpite).second.first) (*mp << 450 mpite = densiMinMax.find( fMateIDs[copyNo] ); 510 if (dens > (*mpite).second.second) (*m << 451 if( dens < (*mpite).second.first ) (*mpite).second.first = dens; >> 452 if( dens > (*mpite).second.second ) (*mpite).second.second = dens; 511 //--- Get material from original list 453 //--- Get material from original list of material in file 512 G4int mateID = G4int(fMateIDs[copyNo]) << 454 int mateID = fMateIDs[copyNo]; 513 std::map<G4int, G4Material*>::const_it << 455 std::map<G4int,G4Material*>::const_iterator imite = 514 << 456 thePhantomMaterialsOriginal.find(mateID); >> 457 // G4cout << copyNo << " mateID " << mateID << G4endl; 515 //--- Check if density is equal to the 458 //--- Check if density is equal to the original material density 516 if (std::fabs(dens - (*imite).second-> << 459 if( std::fabs(dens - (*imite).second->GetDensity()/CLHEP::g*CLHEP::cm3 ) < 1.e-9 ) continue; 517 continue; << 460 518 << 461 //--- Build material name with thePhantomMaterialsOriginal name + density 519 //--- Build material name with fPhanto << 462 // float densityBin = densityDiffs[mateID] * (G4int(dens/densityDiffs[mateID])+0.5); 520 G4int densityBin = (G4int(dens / densi << 463 G4int densityBin = (G4int(dens/densityDiffs[mateID])); 521 464 522 G4String mateName = (*imite).second->G << 465 G4String mateName = (*imite).second->GetName()+G4UIcommand::ConvertToString(densityBin); 523 //--- Look if it is the first voxel wi 466 //--- Look if it is the first voxel with this material/densityBin 524 std::pair<G4Material*, G4int> matdens( << 467 std::pair<G4Material*,G4int> matdens((*imite).second, densityBin ); 525 468 526 auto mppite = newMateDens.find(matdens << 469 std::map< std::pair<G4Material*,G4int>, matInfo* >::iterator mppite = 527 if (mppite != newMateDens.cend()) { << 470 newMateDens.find( matdens ); >> 471 if( mppite != newMateDens.end() ){ 528 matInfo* mi = (*mppite).second; 472 matInfo* mi = (*mppite).second; 529 mi->fSumdens += dens; 473 mi->fSumdens += dens; 530 mi->fNvoxels++; 474 mi->fNvoxels++; 531 fMateIDs[copyNo] = fPhantomMaterials << 475 fMateIDs[copyNo] = thePhantomMaterialsOriginal.size()-1 + mi->fId; 532 } << 476 } else { 533 else { << 534 matInfo* mi = new matInfo; 477 matInfo* mi = new matInfo; 535 mi->fSumdens = dens; 478 mi->fSumdens = dens; 536 mi->fNvoxels = 1; 479 mi->fNvoxels = 1; 537 mi->fId = G4int(newMateDens.size() + << 480 mi->fId = newMateDens.size()+1; 538 newMateDens[matdens] = mi; 481 newMateDens[matdens] = mi; 539 fMateIDs[copyNo] = fPhantomMaterials << 482 fMateIDs[copyNo] = thePhantomMaterialsOriginal.size()-1 + mi->fId; 540 } 483 } 541 } 484 } 542 } 485 } 543 } 486 } 544 487 545 if (densityDiff != -1.) { << 488 if( densityDiff != -1. ) { 546 for (mpite = densiMinMax.begin(); mpite != << 489 for( mpite = densiMinMax.begin(); mpite != densiMinMax.end(); mpite++ ){ 547 #ifdef G4VERBOSE 490 #ifdef G4VERBOSE 548 G4cout << "DicomDetectorConstruction::Re << 491 G4cout << "DicomDetectorConstruction::ReadVoxelDensities ORIG MATERIALS DENSITY " 549 << " ORIG MATERIALS DENSITY " << << 492 << (*mpite).first << " MIN " << (*mpite).second.first << " MAX " 550 << " MAX " << (*mpite).second.sec << 493 << (*mpite).second.second << G4endl; 551 #endif 494 #endif 552 } 495 } 553 } 496 } 554 497 555 //----- Build the list of phantom materials 498 //----- Build the list of phantom materials that go to Parameterisation 556 //--- Add original materials 499 //--- Add original materials 557 for (auto mimite = fPhantomMaterialsOriginal << 500 std::map<G4int,G4Material*>::const_iterator mimite; 558 ++mimite) << 501 for( mimite = thePhantomMaterialsOriginal.begin(); mimite != thePhantomMaterialsOriginal.end(); 559 { << 502 mimite++ ){ 560 fMaterials.push_back((*mimite).second); << 503 fMaterials.push_back( (*mimite).second ); 561 } 504 } 562 // << 505 // 563 //---- Build and add new materials 506 //---- Build and add new materials 564 for (auto mppite = newMateDens.cbegin(); mpp << 507 std::map< std::pair<G4Material*,G4int>, matInfo* >::iterator mppite; 565 G4double averdens = (*mppite).second->fSum << 508 for( mppite= newMateDens.begin(); mppite != newMateDens.end(); mppite++ ){ 566 G4double saverdens = G4int(1000.001 * aver << 509 G4double averdens = (*mppite).second->fSumdens/(*mppite).second->fNvoxels; >> 510 G4double saverdens = G4int(1000.001*averdens)/1000.; 567 #ifndef G4VERBOSE 511 #ifndef G4VERBOSE 568 G4cout << "DicomDetectorConstruction::Read << 512 G4cout << "DicomDetectorConstruction::ReadVoxelDensities AVER DENS " << averdens << " -> " 569 << saverdens << " -> " << G4int(100 << 513 << saverdens << " -> " << G4int(1000*averdens) << " " << G4int(1000*averdens)/1000 570 << " " << G4int(1000 * averdens) / << 514 << " " << G4int(1000*averdens)/1000. << G4endl; 571 #endif 515 #endif 572 516 573 G4String mateName = << 517 G4String mateName = ((*mppite).first).first->GetName() + "_" 574 ((*mppite).first).first->GetName() + "_" << 518 + G4UIcommand::ConvertToString(saverdens); 575 fMaterials.push_back( << 519 fMaterials.push_back( BuildMaterialWithChangingDensity( 576 BuildMaterialWithChangingDensity((*mppit << 520 (*mppite).first.first, averdens, mateName ) ); 577 } 521 } >> 522 578 } 523 } 579 524 580 //....oooOO0OOooo........oooOO0OOooo........oo << 525 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 581 void DicomDetectorConstruction::ReadPhantomDat 526 void DicomDetectorConstruction::ReadPhantomData() 582 { 527 { 583 G4String dataFile = DicomHandler::GetDicomDa << 584 std::ifstream finDF(dataFile.c_str()); << 585 G4String fname; << 586 528 587 if (finDF.good() != 1) { << 529 G4String dataFile = "Data.dat"; 588 G4String descript = "Problem reading data << 530 std::ifstream finDF(dataFile.c_str()); 589 G4Exception(" DicomDetectorConstruction::R << 531 G4String fname; 590 } << 532 if(finDF.good() != 1 ) { 591 << 533 G4String descript = "Problem reading data file: "+dataFile; 592 G4int compression; << 534 G4Exception(" DicomDetectorConstruction::ReadPhantomData", 593 finDF >> compression; // not used here << 535 "", 594 finDF >> fNoFiles; << 536 FatalException, 595 << 537 descript); 596 for (G4int i = 0; i < fNoFiles; ++i) { << 538 } 597 finDF >> fname; << 539 >> 540 G4int compression; >> 541 finDF >> compression; // not used here >> 542 >> 543 finDF >> fNoFiles; >> 544 for(G4int i = 0; i < fNoFiles; i++ ) { >> 545 finDF >> fname; >> 546 //--- Read one data file >> 547 fname += ".g4dcm"; >> 548 ReadPhantomDataFile(fname); >> 549 } 598 550 599 //--- Read one data file << 551 //----- Merge data headers 600 fname += ".g4dcm"; << 552 MergeZSliceHeaders(); 601 553 602 ReadPhantomDataFile(fname); << 554 finDF.close(); 603 } << 604 555 605 //----- Merge data headers << 606 MergeZSliceHeaders(); << 607 finDF.close(); << 608 } 556 } 609 557 610 //....oooOO0OOooo........oooOO0OOooo........oo << 558 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 611 void DicomDetectorConstruction::ReadPhantomDat 559 void DicomDetectorConstruction::ReadPhantomDataFile(const G4String& fname) 612 { 560 { 613 G4cout << " DicomDetectorConstruction::ReadP << 561 G4cout << " DicomDetectorConstruction::ReadPhantomDataFile opening file " 614 << G4endl; // GDEB << 562 << fname << G4endl; //GDEB 615 << 616 #ifdef G4VERBOSE 563 #ifdef G4VERBOSE 617 G4cout << " DicomDetectorConstruction::ReadP << 564 G4cout << " DicomDetectorConstruction::ReadPhantomDataFile opening file " >> 565 << fname << G4endl; 618 #endif 566 #endif 619 << 620 std::ifstream fin(fname.c_str(), std::ios_ba 567 std::ifstream fin(fname.c_str(), std::ios_base::in); 621 if (!fin.is_open()) { << 568 if( !fin.is_open() ) { 622 G4Exception("DicomDetectorConstruction::Re << 569 G4Exception("DicomDetectorConstruction::ReadPhantomDataFile", 623 G4String("File not found " + f << 570 "", >> 571 FatalErrorInArgument, >> 572 G4String("File not found " + fname ).c_str()); 624 } 573 } 625 //----- Define density differences (maximum 574 //----- Define density differences (maximum density difference to create 626 // a new material) 575 // a new material) 627 char* part = std::getenv("DICOM_CHANGE_MATER << 576 char* part = getenv( "DICOM_CHANGE_MATERIAL_DENSITY" ); 628 G4double densityDiff = -1.; 577 G4double densityDiff = -1.; 629 if (part) densityDiff = G4UIcommand::Convert << 578 if( part ) densityDiff = G4UIcommand::ConvertToDouble(part); 630 if (densityDiff != -1.) { << 579 if( densityDiff != -1. ) { 631 for (unsigned int ii = 0; ii < fOriginalMa << 580 for( unsigned int ii = 0; ii < fOriginalMaterials.size(); ii++ ){ 632 fDensityDiffs[ii] = densityDiff; // cur << 581 fDensityDiffs[ii] = densityDiff; //currently all materials with 633 // same difference 582 // same difference 634 } 583 } 635 } << 584 }else { 636 else { << 585 if( fMaterials.size() == 0 ) { // do it only for first slice 637 if (fMaterials.size() == 0) { // do it on << 586 for( unsigned int ii = 0; ii < fOriginalMaterials.size(); ii++ ){ 638 for (unsigned int ii = 0; ii < fOriginal << 587 fMaterials.push_back( fOriginalMaterials[ii] ); 639 fMaterials.push_back(fOriginalMaterial << 640 } 588 } 641 } 589 } 642 } 590 } 643 << 591 644 //----- Read data header 592 //----- Read data header 645 DicomPhantomZSliceHeader* sliceHeader = new << 593 DicomPhantomZSliceHeader* sliceHeader = new DicomPhantomZSliceHeader( fin ); 646 fZSliceHeaders.push_back(sliceHeader); << 594 fZSliceHeaders.push_back( sliceHeader ); 647 << 595 648 //----- Read material indices 596 //----- Read material indices 649 G4int nVoxels = sliceHeader->GetNoVoxels(); 597 G4int nVoxels = sliceHeader->GetNoVoxels(); 650 << 598 651 //--- If first slice, initiliaze fMateIDs 599 //--- If first slice, initiliaze fMateIDs 652 if (fZSliceHeaders.size() == 1) { << 600 if( fZSliceHeaders.size() == 1 ) { 653 // fMateIDs = new unsigned int[fNoFiles*nV << 601 //fMateIDs = new unsigned int[fNoFiles*nVoxels]; 654 fMateIDs = new size_t[fNoFiles * nVoxels]; << 602 fMateIDs = new size_t[fNoFiles*nVoxels]; >> 603 655 } 604 } 656 << 605 657 unsigned int mateID; 606 unsigned int mateID; 658 // number of voxels from previously read sli 607 // number of voxels from previously read slices 659 G4int voxelCopyNo = G4int((fZSliceHeaders.si << 608 G4int voxelCopyNo = (fZSliceHeaders.size()-1)*nVoxels; 660 for (G4int ii = 0; ii < nVoxels; ++ii, voxel << 609 for( G4int ii = 0; ii < nVoxels; ii++, voxelCopyNo++ ){ 661 fin >> mateID; 610 fin >> mateID; 662 fMateIDs[voxelCopyNo] = mateID; 611 fMateIDs[voxelCopyNo] = mateID; 663 } 612 } 664 << 613 665 //----- Read material densities and build ne 614 //----- Read material densities and build new materials if two voxels have 666 // same material but its density is in a di << 615 // same material but its density is in a different density interval 667 // (size of density intervals defined by den 616 // (size of density intervals defined by densityDiff) 668 G4double density; 617 G4double density; 669 // number of voxels from previously read sli 618 // number of voxels from previously read slices 670 voxelCopyNo = G4int((fZSliceHeaders.size() - << 619 voxelCopyNo = (fZSliceHeaders.size()-1)*nVoxels; 671 for (G4int ii = 0; ii < nVoxels; ++ii, voxel << 620 for( G4int ii = 0; ii < nVoxels; ii++, voxelCopyNo++ ){ 672 fin >> density; 621 fin >> density; 673 << 622 674 //-- Get material from list of original ma 623 //-- Get material from list of original materials 675 mateID = unsigned(fMateIDs[voxelCopyNo]); << 624 mateID = fMateIDs[voxelCopyNo]; 676 G4Material* mateOrig = fOriginalMaterials[ << 625 G4Material* mateOrig = fOriginalMaterials[mateID]; 677 << 626 678 //-- Get density bin: middle point of the 627 //-- Get density bin: middle point of the bin in which the current 679 // density is included 628 // density is included 680 G4String newMateName = mateOrig->GetName() 629 G4String newMateName = mateOrig->GetName(); 681 G4float densityBin = 0.; << 630 float densityBin = 0.; 682 if (densityDiff != -1.) { << 631 if( densityDiff != -1.) { 683 densityBin = G4float(fDensityDiffs[mateI << 632 densityBin = fDensityDiffs[mateID] * >> 633 (G4int(density/fDensityDiffs[mateID])+0.5); 684 //-- Build the new material name 634 //-- Build the new material name 685 newMateName += G4UIcommand::ConvertToStr 635 newMateName += G4UIcommand::ConvertToString(densityBin); 686 } 636 } 687 << 637 688 //-- Look if a material with this name is 638 //-- Look if a material with this name is already created 689 // (because a previous voxel was already 639 // (because a previous voxel was already in this density bin) 690 unsigned int im; 640 unsigned int im; 691 for (im = 0; im < fMaterials.size(); ++im) << 641 for( im = 0; im < fMaterials.size(); im++ ){ 692 if (fMaterials[im]->GetName() == newMate << 642 if( fMaterials[im]->GetName() == newMateName ) { 693 break; 643 break; 694 } 644 } 695 } 645 } 696 //-- If material is already created use in 646 //-- If material is already created use index of this material 697 if (im != fMaterials.size()) { << 647 if( im != fMaterials.size() ) { 698 fMateIDs[voxelCopyNo] = im; 648 fMateIDs[voxelCopyNo] = im; 699 //-- else, create the material 649 //-- else, create the material 700 } << 650 } else { 701 else { << 651 if( densityDiff != -1.) { 702 if (densityDiff != -1.) { << 652 fMaterials.push_back( BuildMaterialWithChangingDensity( mateOrig, 703 fMaterials.push_back(BuildMaterialWith << 653 densityBin, newMateName ) ); 704 fMateIDs[voxelCopyNo] = fMaterials.siz << 654 fMateIDs[voxelCopyNo] = fMaterials.size()-1; 705 } << 655 } else { 706 else { << 656 G4cerr << " im " << im << " < " << fMaterials.size() << " name " 707 G4cerr << " im " << im << " < " << fMa << 657 << newMateName << G4endl; 708 G4Exception("DicomDetectorConstruction << 658 G4Exception("DicomDetectorConstruction::ReadPhantomDataFile", 709 "Wrong index in material") << 659 "", >> 660 FatalErrorInArgument, >> 661 "Wrong index in material"); //it should never reach here 710 } 662 } 711 } 663 } 712 } 664 } >> 665 713 } 666 } 714 667 715 //....oooOO0OOooo........oooOO0OOooo........oo << 668 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 716 void DicomDetectorConstruction::MergeZSliceHea 669 void DicomDetectorConstruction::MergeZSliceHeaders() 717 { 670 { 718 //----- Images must have the same dimension 671 //----- Images must have the same dimension ... 719 fZSliceHeaderMerged = new DicomPhantomZSlice << 672 fZSliceHeaderMerged = new DicomPhantomZSliceHeader( *fZSliceHeaders[0] ); 720 for (unsigned int ii = 1; ii < fZSliceHeader << 673 for( unsigned int ii = 1; ii < fZSliceHeaders.size(); ii++ ) { 721 *fZSliceHeaderMerged += *fZSliceHeaders[ii 674 *fZSliceHeaderMerged += *fZSliceHeaders[ii]; 722 } << 675 }; >> 676 723 } 677 } 724 678 725 //....oooOO0OOooo........oooOO0OOooo........oo << 679 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 726 G4Material* DicomDetectorConstruction::BuildMa << 680 G4Material* DicomDetectorConstruction::BuildMaterialWithChangingDensity( 727 << 681 const G4Material* origMate, float density, G4String newMateName ) 728 << 729 { 682 { 730 //----- Copy original material, but with new 683 //----- Copy original material, but with new density 731 G4int nelem = G4int(origMate->GetNumberOfEle << 684 G4int nelem = origMate->GetNumberOfElements(); 732 G4Material* mate = << 685 G4Material* mate = new G4Material( newMateName, density*g/cm3, nelem, 733 new G4Material(newMateName, density * g / << 686 kStateUndefined, STP_Temperature ); 734 << 687 735 for (G4int ii = 0; ii < nelem; ++ii) { << 688 for( G4int ii = 0; ii < nelem; ii++ ){ 736 G4double frac = origMate->GetFractionVecto 689 G4double frac = origMate->GetFractionVector()[ii]; 737 G4Element* elem = const_cast<G4Element*>(o 690 G4Element* elem = const_cast<G4Element*>(origMate->GetElement(ii)); 738 mate->AddElement(elem, frac); << 691 mate->AddElement( elem, frac ); 739 } 692 } 740 << 693 741 return mate; 694 return mate; 742 } 695 } 743 696 744 //....oooOO0OOooo........oooOO0OOooo........oo << 697 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 745 void DicomDetectorConstruction::ConstructPhant 698 void DicomDetectorConstruction::ConstructPhantomContainer() 746 { 699 { 747 //---- Extract number of voxels and voxel di 700 //---- Extract number of voxels and voxel dimensions 748 fNoVoxelsX = fZSliceHeaderMerged->GetNoVoxel << 701 fNVoxelX = fZSliceHeaderMerged->GetNoVoxelX(); 749 fNoVoxelsY = fZSliceHeaderMerged->GetNoVoxel << 702 fNVoxelY = fZSliceHeaderMerged->GetNoVoxelY(); 750 fNoVoxelsZ = fZSliceHeaderMerged->GetNoVoxel << 703 fNVoxelZ = fZSliceHeaderMerged->GetNoVoxelZ(); 751 << 704 752 fVoxelHalfDimX = fZSliceHeaderMerged->GetVox 705 fVoxelHalfDimX = fZSliceHeaderMerged->GetVoxelHalfX(); 753 fVoxelHalfDimY = fZSliceHeaderMerged->GetVox 706 fVoxelHalfDimY = fZSliceHeaderMerged->GetVoxelHalfY(); 754 fVoxelHalfDimZ = fZSliceHeaderMerged->GetVox 707 fVoxelHalfDimZ = fZSliceHeaderMerged->GetVoxelHalfZ(); 755 #ifdef G4VERBOSE 708 #ifdef G4VERBOSE 756 G4cout << " fNoVoxelsX " << fNoVoxelsX << " << 709 G4cout << " fNVoxelX " << fNVoxelX << " fVoxelHalfDimX " << fVoxelHalfDimX 757 G4cout << " fNoVoxelsY " << fNoVoxelsY << " << 710 <<G4endl; 758 G4cout << " fNoVoxelsZ " << fNoVoxelsZ << " << 711 G4cout << " fNVoxelY " << fNVoxelY << " fVoxelHalfDimY " << fVoxelHalfDimY 759 G4cout << " totalPixels " << fNoVoxelsX * fN << 712 <<G4endl; >> 713 G4cout << " fNVoxelZ " << fNVoxelZ << " fVoxelHalfDimZ " << fVoxelHalfDimZ >> 714 <<G4endl; >> 715 G4cout << " totalPixels " << fNVoxelX*fNVoxelY*fNVoxelZ << G4endl; 760 #endif 716 #endif 761 << 717 762 //----- Define the volume that contains all 718 //----- Define the volume that contains all the voxels 763 fContainer_solid = new G4Box("phantomContain << 719 fContainer_solid = new G4Box("phantomContainer",fNVoxelX*fVoxelHalfDimX, 764 fNoVoxelsY * fV << 720 fNVoxelY*fVoxelHalfDimY, >> 721 fNVoxelZ*fVoxelHalfDimZ); 765 fContainer_logic = 722 fContainer_logic = 766 new G4LogicalVolume(fContainer_solid, << 723 new G4LogicalVolume( fContainer_solid, 767 // the material is not << 724 //the material is not important, it will be fully filled by the voxels 768 fMaterials[0], "phanto << 725 fMaterials[0], >> 726 "phantomContainer", >> 727 0, 0, 0 ); 769 //--- Place it on the world 728 //--- Place it on the world 770 G4double fOffsetX = (fZSliceHeaderMerged->Ge << 729 G4double fOffsetX = (fZSliceHeaderMerged->GetMaxX() + 771 G4double fOffsetY = (fZSliceHeaderMerged->Ge << 730 fZSliceHeaderMerged->GetMinX() ) /2.; 772 G4double fOffsetZ = (fZSliceHeaderMerged->Ge << 731 G4double fOffsetY = (fZSliceHeaderMerged->GetMaxY() + 773 G4ThreeVector posCentreVoxels(fOffsetX, fOff << 732 fZSliceHeaderMerged->GetMinY() ) /2.; >> 733 G4double fOffsetZ = (fZSliceHeaderMerged->GetMaxZ() + >> 734 fZSliceHeaderMerged->GetMinZ() ) /2.; >> 735 G4ThreeVector posCentreVoxels(fOffsetX,fOffsetY,fOffsetZ); 774 #ifdef G4VERBOSE 736 #ifdef G4VERBOSE 775 G4cout << " placing voxel container volume a 737 G4cout << " placing voxel container volume at " << posCentreVoxels << G4endl; 776 #endif 738 #endif 777 fContainer_phys = new G4PVPlacement(0, // r << 739 fContainer_phys = 778 posCentr << 740 new G4PVPlacement(0, // rotation 779 fContain << 741 posCentreVoxels, 780 "phantom << 742 fContainer_logic, // The logic volume 781 fWorld_l << 743 "phantomContainer", // Name 782 false, << 744 fWorld_logic, // Mother 783 1); // << 745 false, // No op. bool. >> 746 1); // Copy number >> 747 >> 748 //fContainer_logic->SetVisAttributes(new G4VisAttributes(G4Colour(1.,0.,0.))); 784 } 749 } 785 750 786 //....oooOO0OOooo........oooOO0OOooo........oo 751 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 787 void DicomDetectorConstruction::ConstructPhant 752 void DicomDetectorConstruction::ConstructPhantomContainerNew() 788 { 753 { 789 #ifdef G4_DCMTK 754 #ifdef G4_DCMTK 790 //---- Extract number of voxels and voxel di 755 //---- Extract number of voxels and voxel dimensions 791 # ifdef G4VERBOSE << 756 #ifdef G4VERBOSE 792 G4cout << " fNoVoxelsX " << fNoVoxelsX << " << 757 G4cout << " fNVoxelX " << fNVoxelX << " fVoxelHalfDimX " << fVoxelHalfDimX 793 G4cout << " fNoVoxelsY " << fNoVoxelsY << " << 758 <<G4endl; 794 G4cout << " fNoVoxelsZ " << fNoVoxelsZ << " << 759 G4cout << " fNVoxelY " << fNVoxelY << " fVoxelHalfDimY " << fVoxelHalfDimY 795 G4cout << " totalPixels " << fNoVoxelsX * fN << 760 <<G4endl; 796 # endif << 761 G4cout << " fNVoxelZ " << fNVoxelZ << " fVoxelHalfDimZ " << fVoxelHalfDimZ 797 << 762 <<G4endl; >> 763 G4cout << " totalPixels " << fNVoxelX*fNVoxelY*fNVoxelZ << G4endl; >> 764 #endif >> 765 798 //----- Define the volume that contains all 766 //----- Define the volume that contains all the voxels 799 fContainer_solid = new G4Box("phantomContain << 767 fContainer_solid = new G4Box("phantomContainer",fNVoxelX*fVoxelHalfDimX, 800 fNoVoxelsY * fV << 768 fNVoxelY*fVoxelHalfDimY, >> 769 fNVoxelZ*fVoxelHalfDimZ); 801 fContainer_logic = 770 fContainer_logic = 802 new G4LogicalVolume(fContainer_solid, << 771 new G4LogicalVolume( fContainer_solid, 803 // the material is not << 772 //the material is not important, it will be fully filled by the voxels 804 fMaterials[0], "phanto << 773 fMaterials[0], >> 774 "phantomContainer", >> 775 0, 0, 0 ); 805 776 806 G4ThreeVector posCentreVoxels((fMinX + fMaxX << 777 G4ThreeVector posCentreVoxels((fMinX+fMaxX)/2.,(fMinY+fMaxY)/2.,(fMinZ+fMaxZ)/2.); 807 # ifdef G4VERBOSE << 778 #ifdef G4VERBOSE 808 G4cout << " placing voxel container volume a 779 G4cout << " placing voxel container volume at " << posCentreVoxels << G4endl; 809 # endif << 780 #endif 810 fContainer_phys = new G4PVPlacement(0, // r << 781 fContainer_phys = 811 posCentr << 782 new G4PVPlacement(0, // rotation 812 fContain << 783 posCentreVoxels, 813 "phantom << 784 fContainer_logic, // The logic volume 814 fWorld_l << 785 "phantomContainer", // Name 815 false, << 786 fWorld_logic, // Mother 816 1); // << 787 false, // No op. bool. >> 788 1); // Copy number >> 789 >> 790 //fContainer_logic->SetVisAttributes(new G4VisAttributes(G4Colour(1.,0.,0.))); 817 #endif 791 #endif 818 } 792 } 819 793 >> 794 #include "G4SDManager.hh" 820 #include "G4MultiFunctionalDetector.hh" 795 #include "G4MultiFunctionalDetector.hh" 821 #include "G4PSDoseDeposit.hh" 796 #include "G4PSDoseDeposit.hh" 822 #include "G4PSDoseDeposit3D.hh" 797 #include "G4PSDoseDeposit3D.hh" 823 #include "G4SDManager.hh" << 824 798 825 //....oooOO0OOooo........oooOO0OOooo........oo << 799 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 826 void DicomDetectorConstruction::SetScorer(G4Lo 800 void DicomDetectorConstruction::SetScorer(G4LogicalVolume* voxel_logic) 827 { 801 { >> 802 828 #ifdef G4VERBOSE 803 #ifdef G4VERBOSE 829 G4cout << "\t SET SCORER : " << voxel_logic- 804 G4cout << "\t SET SCORER : " << voxel_logic->GetName() << G4endl; 830 #endif 805 #endif 831 << 806 832 fScorers.insert(voxel_logic); 807 fScorers.insert(voxel_logic); >> 808 833 } 809 } 834 810 835 //....oooOO0OOooo........oooOO0OOooo........oo << 811 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo...... 836 812 837 void DicomDetectorConstruction::ConstructSDand 813 void DicomDetectorConstruction::ConstructSDandField() 838 { 814 { >> 815 839 #ifdef G4VERBOSE 816 #ifdef G4VERBOSE 840 G4cout << "\t CONSTRUCT SD AND FIELD" << G4e 817 G4cout << "\t CONSTRUCT SD AND FIELD" << G4endl; 841 #endif 818 #endif 842 << 819 843 // G4SDManager* SDman = G4SDManager::GetSDMp << 820 //G4SDManager* SDman = G4SDManager::GetSDMpointer(); 844 << 821 845 // SDman->SetVerboseLevel(1); << 822 //SDman->SetVerboseLevel(1); 846 << 823 847 // 824 // 848 // Sensitive Detector Name 825 // Sensitive Detector Name 849 G4String concreteSDname = "phantomSD"; 826 G4String concreteSDname = "phantomSD"; 850 std::vector<G4String> scorer_names; 827 std::vector<G4String> scorer_names; 851 scorer_names.push_back(concreteSDname); 828 scorer_names.push_back(concreteSDname); 852 //------------------------ 829 //------------------------ 853 // MultiFunctionalDetector 830 // MultiFunctionalDetector 854 //------------------------ 831 //------------------------ 855 // 832 // 856 // Define MultiFunctionalDetector with name. 833 // Define MultiFunctionalDetector with name. 857 // declare MFDet as a MultiFunctionalDetecto 834 // declare MFDet as a MultiFunctionalDetector scorer 858 G4MultiFunctionalDetector* MFDet = new G4Mul << 835 G4MultiFunctionalDetector* MFDet = 859 G4SDManager::GetSDMpointer()->AddNewDetector << 836 new G4MultiFunctionalDetector(concreteSDname); 860 char* nest = std::getenv("DICOM_NESTED_PARAM << 837 G4SDManager::GetSDMpointer()->AddNewDetector( MFDet ); 861 if (nest && G4String(nest) == "1") { << 838 //G4VPrimitiveScorer* dosedep = new G4PSDoseDeposit("DoseDeposit"); 862 G4VPrimitiveScorer* dosedep = new G4PSDose << 839 G4VPrimitiveScorer* dosedep = 863 "DoseDeposit", fNoVoxelsZ, fNoVoxelsY, f << 840 new G4PSDoseDeposit3D("DoseDeposit", fNVoxelX, fNVoxelY, fNVoxelZ); 864 // - the last 3 arguments correspond to th << 841 MFDet->RegisterPrimitive(dosedep); 865 MFDet->RegisterPrimitive(dosedep); << 842 866 } << 843 for(std::set<G4LogicalVolume*>::iterator ite = fScorers.begin(); 867 else { << 844 ite != fScorers.end(); ++ite) { 868 G4VPrimitiveScorer* dosedep = new G4PSDose << 869 MFDet->RegisterPrimitive(dosedep); << 870 } << 871 << 872 for (auto ite = fScorers.cbegin(); ite != fS << 873 SetSensitiveDetector(*ite, MFDet); 845 SetSensitiveDetector(*ite, MFDet); 874 } 846 } >> 847 >> 848 /*if(DicomRunAction::Instance()->GetDicomRun()) { >> 849 DicomRunAction::Instance()->GetDicomRun()->ConstructMFD(scorer_names); >> 850 }*/ >> 851 875 } 852 } 876 853