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25 // 25 //
26 // This example is provided by the Geant4-DNA 26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained us 27 // Any report or published results obtained using the Geant4-DNA software
28 // shall cite the following Geant4-DNA collabo 28 // shall cite the following Geant4-DNA collaboration publication:
29 // Med. Phys. 37 (2010) 4692-4708 29 // Med. Phys. 37 (2010) 4692-4708
30 // The Geant4-DNA web site is available at htt 30 // The Geant4-DNA web site is available at http://geant4-dna.org
31 // 31 //
32 // If you use this example, please cite the fo 32 // If you use this example, please cite the following publication:
33 // Rad. Prot. Dos. 133 (2009) 2-11 33 // Rad. Prot. Dos. 133 (2009) 2-11
34 34
35 #include "CellParameterisation.hh" 35 #include "CellParameterisation.hh"
36 #include "G4LogicalVolume.hh" 36 #include "G4LogicalVolume.hh"
37 #include "G4SystemOfUnits.hh" 37 #include "G4SystemOfUnits.hh"
38 38
>> 39 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 40
39 // SINGLETON 41 // SINGLETON
40 CellParameterisation * CellParameterisation::g 42 CellParameterisation * CellParameterisation::gInstance = 0;
41 43
>> 44
42 CellParameterisation::CellParameterisation 45 CellParameterisation::CellParameterisation
43 (G4Material * nucleus1, G4Material * cytoplas 46 (G4Material * nucleus1, G4Material * cytoplasm1,
44 G4Material * nucleus2, G4Material * cytoplas 47 G4Material * nucleus2, G4Material * cytoplasm2,
45 G4Material * nucleus3, G4Material * cytoplas 48 G4Material * nucleus3, G4Material * cytoplasm3
46 ) 49 )
47 { 50 {
48 fNucleusMaterial1 = nucleus1; 51 fNucleusMaterial1 = nucleus1;
49 fCytoplasmMaterial1 = cytoplasm1; 52 fCytoplasmMaterial1 = cytoplasm1;
50 fNucleusMaterial2 = nucleus2; 53 fNucleusMaterial2 = nucleus2;
51 fCytoplasmMaterial2 = cytoplasm2; 54 fCytoplasmMaterial2 = cytoplasm2;
52 fNucleusMaterial3 = nucleus3; 55 fNucleusMaterial3 = nucleus3;
53 fCytoplasmMaterial3 = cytoplasm3; 56 fCytoplasmMaterial3 = cytoplasm3;
54 57
55 G4int ncols,nlines; 58 G4int ncols,nlines;
56 G4int shiftX, shiftY, shiftZ; 59 G4int shiftX, shiftY, shiftZ;
57 G4double x,y,z,mat,den,tmp,density; 60 G4double x,y,z,mat,den,tmp,density;
58 G4double denCyto1, denCyto2, denCyto3, denN 61 G4double denCyto1, denCyto2, denCyto3, denNucl1, denNucl2, denNucl3;
59 <<
60 ncols = nlines = shiftX = shiftY = shiftZ = <<
61 x = y = z = mat = den = tmp = density = <<
62 denCyto1 = denCyto2 = denCyto3 = denNucl1 <<
63 62
64 // READ PHANTOM << 63 density=0;
>> 64 denCyto1=0;
>> 65 denCyto2=0;
>> 66 denCyto3=0;
>> 67 denNucl1=0;
>> 68 denNucl2=0;
>> 69 denNucl3=0;
>> 70
>> 71 ncols=0; nlines=0;
>> 72
>> 73 // READ PHANTOM
>> 74
65 fNucleusMass = 0; 75 fNucleusMass = 0;
66 fCytoplasmMass = 0; 76 fCytoplasmMass = 0;
67 <<
68 fDimCellBoxX = fDimCellBoxY = fDimCellBoxZ <<
69 77
70 FILE *fMap; 78 FILE *fMap;
71 fMap = fopen("phantom.dat","r"); 79 fMap = fopen("phantom.dat","r");
72 80
73 while (1) 81 while (1)
74 { 82 {
75 if (nlines == 0) 83 if (nlines == 0)
76 { 84 {
77 ncols = fscanf(fMap,"%i %i %i",&fPhant 85 ncols = fscanf(fMap,"%i %i %i",&fPhantomTotalPixels,&fNucleusTotalPixels,&fCytoplasmTotalPixels);
78 fMapCell = new G4ThreeVector[fPhantomTota << 86 fMapCell = new G4ThreeVector[fPhantomTotalPixels];
79 fMaterial = new G4double[fPhantomTot << 87 fMaterial = new G4double[fPhantomTotalPixels];
80 fMass = new G4double[fPhantomTot << 88 fMass = new G4double[fPhantomTotalPixels];
81 fTissueType = new G4int[fPhantomTotalP 89 fTissueType = new G4int[fPhantomTotalPixels];
82 } 90 }
83 91
84 if (nlines == 1) 92 if (nlines == 1)
85 { 93 {
86 ncols = fscanf(fMap,"%lf %lf %lf",&fDi << 94 ncols = fscanf(fMap,"%lf %lf %lf",&fDimCellBoxX,&fDimCellBoxY,&fDimCellBoxZ);
>> 95
87 fDimCellBoxX=fDimCellBoxX*micrometer; 96 fDimCellBoxX=fDimCellBoxX*micrometer;
88 fDimCellBoxY=fDimCellBoxY*micrometer; 97 fDimCellBoxY=fDimCellBoxY*micrometer;
89 fDimCellBoxZ=fDimCellBoxZ*micrometer; 98 fDimCellBoxZ=fDimCellBoxZ*micrometer;
90 } 99 }
91 100
92 // VOXEL SHIFT IN Z ASSUMED TO BE NEGATI << 101 if (nlines == 2) ncols = fscanf(fMap,"%i %i %i",&shiftX,&shiftY,&shiftZ); // VOXEL SHIFT IN Z ASSUMED TO BE NEGATIVE
93 if (nlines == 2) ncols = fscanf(fMap,"%i <<
94 102
95 if (nlines == 3) ncols = fscanf(fMap,"%l 103 if (nlines == 3) ncols = fscanf(fMap,"%lf %lf %lf",&denCyto1, &denCyto2, &denCyto3);
96 104
97 if (nlines == 4) ncols = fscanf(fMap,"%l 105 if (nlines == 4) ncols = fscanf(fMap,"%lf %lf %lf",&denNucl1, &denNucl2, &denNucl3);
98 106
99 if (nlines > 4) ncols = fscanf(fMap,"%l 107 if (nlines > 4) ncols = fscanf(fMap,"%lf %lf %lf %lf %lf %lf",&x,&y,&z,&mat,&den,&tmp);
100 108
101 if (ncols < 0) break; 109 if (ncols < 0) break;
102 110
103 // VOXEL SHIFT IN ORDER TO CENTER PHANTO << 111 G4ThreeVector v(x+shiftX,y+shiftY,z-1500/(fDimCellBoxZ/micrometer)-shiftZ); // VOXEL SHIFT IN ORDER TO CENTER PHANTOM
104 G4ThreeVector v(x+shiftX,y+shiftY,z-1500 << 112
105 if (nlines>4) 113 if (nlines>4)
106 { 114 {
107 115
108 fMapCell[nlines-5]=v; 116 fMapCell[nlines-5]=v;
109 fMaterial[nlines-5]=mat; 117 fMaterial[nlines-5]=mat;
110 fMass[nlines-5]=den; 118 fMass[nlines-5]=den;
111 119
112 // fTissueType: 1 is Cytoplasm - 2 is Nucl 120 // fTissueType: 1 is Cytoplasm - 2 is Nucleus
113 121
114 if( fMaterial[nlines-5] == 2 ) // fM 122 if( fMaterial[nlines-5] == 2 ) // fMaterial 2 is nucleus
115 { 123 {
116 if( fMass[nlines-5] == 1 ) 124 if( fMass[nlines-5] == 1 )
117 { 125 {
118 fTissueType[nlines-5]=2; 126 fTissueType[nlines-5]=2;
119 } 127 }
120 if( fMass[nlines-5] == 2 ) 128 if( fMass[nlines-5] == 2 )
121 { 129 {
122 fTissueType[nlines-5]=2; 130 fTissueType[nlines-5]=2;
123 } 131 }
124 if( fMass[nlines-5] == 3 ) 132 if( fMass[nlines-5] == 3 )
125 { 133 {
126 fTissueType[nlines-5]=2; 134 fTissueType[nlines-5]=2;
127 } 135 }
128 } 136 }
129 137
130 else if( fMaterial[nlines-5] == 1 ) 138 else if( fMaterial[nlines-5] == 1 ) // fMaterial 1 is cytoplasm
131 { 139 {
132 if( fMass[nlines-5] == 1 ) 140 if( fMass[nlines-5] == 1 )
133 { 141 {
134 fTissueType[nlines-5]=1; 142 fTissueType[nlines-5]=1;
135 } 143 }
136 if( fMass[nlines-5] == 2 ) 144 if( fMass[nlines-5] == 2 )
137 { 145 {
138 fTissueType[nlines-5]=2; 146 fTissueType[nlines-5]=2;
139 } 147 }
140 if( fMass[nlines-5] == 3 ) 148 if( fMass[nlines-5] == 3 )
141 { 149 {
142 fTissueType[nlines-5]=1; 150 fTissueType[nlines-5]=1;
143 } 151 }
144 } 152 }
145 153
146 // << 154 //
>> 155
147 156
148 if (std::abs(mat-2)<1.e-30) // NUCLEUS 157 if (std::abs(mat-2)<1.e-30) // NUCLEUS
149 { 158 {
150 if (std::abs(den-1)<1.e-30) density = de 159 if (std::abs(den-1)<1.e-30) density = denNucl1*(g/cm3);
151 if (std::abs(den-2)<1.e-30) density = de 160 if (std::abs(den-2)<1.e-30) density = denNucl2*(g/cm3);
152 if (std::abs(den-3)<1.e-30) density = de 161 if (std::abs(den-3)<1.e-30) density = denNucl3*(g/cm3);
153 fNucleusMass = fNucleusMass + densit 162 fNucleusMass = fNucleusMass + density * fDimCellBoxX * fDimCellBoxY * fDimCellBoxZ ;
154 } 163 }
155 164
156 if (std::abs(mat-1)<1.e-30) // CYTOP 165 if (std::abs(mat-1)<1.e-30) // CYTOPLASM
157 { 166 {
158 if (std::abs(den-1)<1e-30) density = den 167 if (std::abs(den-1)<1e-30) density = denCyto1*(g/cm3);
159 if (std::abs(den-2)<1e-30) density = den 168 if (std::abs(den-2)<1e-30) density = denCyto2*(g/cm3);
160 if (std::abs(den-3)<1e-30) density = den 169 if (std::abs(den-3)<1e-30) density = denCyto3*(g/cm3);
161 fCytoplasmMass = fCytoplasmMass + densit 170 fCytoplasmMass = fCytoplasmMass + density * fDimCellBoxX * fDimCellBoxY * fDimCellBoxZ ;
162 } 171 }
163 172
164 } 173 }
165 174
166 nlines++; 175 nlines++;
167 } 176 }
168 fclose(fMap); 177 fclose(fMap);
169 178
170 // NUCLEUS IN GREEN 179 // NUCLEUS IN GREEN
171 180
172 fNucleusAttributes1 = new G4VisAttributes; 181 fNucleusAttributes1 = new G4VisAttributes;
173 fNucleusAttributes1->SetColour(G4Colour(0,.8 182 fNucleusAttributes1->SetColour(G4Colour(0,.8,0));
174 fNucleusAttributes1->SetForceSolid(false); 183 fNucleusAttributes1->SetForceSolid(false);
175 184
176 fNucleusAttributes2 = new G4VisAttributes; 185 fNucleusAttributes2 = new G4VisAttributes;
177 fNucleusAttributes2->SetColour(G4Colour(0,.9 186 fNucleusAttributes2->SetColour(G4Colour(0,.9,0));
178 fNucleusAttributes2->SetForceSolid(false); 187 fNucleusAttributes2->SetForceSolid(false);
179 188
180 fNucleusAttributes3 = new G4VisAttributes; 189 fNucleusAttributes3 = new G4VisAttributes;
181 fNucleusAttributes3->SetColour(G4Colour(0,1, 190 fNucleusAttributes3->SetColour(G4Colour(0,1,0));
182 fNucleusAttributes3->SetForceSolid(false); 191 fNucleusAttributes3->SetForceSolid(false);
183 192
184 // CYTOPLASM IN RED 193 // CYTOPLASM IN RED
185 194
186 fCytoplasmAttributes1 = new G4VisAttributes; 195 fCytoplasmAttributes1 = new G4VisAttributes;
187 fCytoplasmAttributes1->SetColour(G4Colour(1, 196 fCytoplasmAttributes1->SetColour(G4Colour(1,0,0));
188 fCytoplasmAttributes1->SetForceSolid(false); 197 fCytoplasmAttributes1->SetForceSolid(false);
189 198
190 fCytoplasmAttributes2 = new G4VisAttributes; 199 fCytoplasmAttributes2 = new G4VisAttributes; // nucleoli in yellow
191 fCytoplasmAttributes2->SetColour(G4Colour(1. 200 fCytoplasmAttributes2->SetColour(G4Colour(1.,1.,0));
192 fCytoplasmAttributes2->SetForceSolid(false); 201 fCytoplasmAttributes2->SetForceSolid(false);
193 202
194 fCytoplasmAttributes3 = new G4VisAttributes; 203 fCytoplasmAttributes3 = new G4VisAttributes;
195 fCytoplasmAttributes3->SetColour(G4Colour(1, 204 fCytoplasmAttributes3->SetColour(G4Colour(1,0,0));
196 fCytoplasmAttributes3->SetForceSolid(false); 205 fCytoplasmAttributes3->SetForceSolid(false);
197 206
198 // 207 //
>> 208
199 gInstance = this; 209 gInstance = this;
>> 210
200 } 211 }
201 212
>> 213 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 214
202 CellParameterisation::~CellParameterisation() 215 CellParameterisation::~CellParameterisation()
203 { 216 {
204 delete[] fMapCell; 217 delete[] fMapCell;
205 delete[] fMaterial; 218 delete[] fMaterial;
206 delete[] fMass; 219 delete[] fMass;
207 delete[] fTissueType; 220 delete[] fTissueType;
208 } 221 }
209 222
>> 223 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 224
210 void CellParameterisation::ComputeTransformati 225 void CellParameterisation::ComputeTransformation
211 (const G4int copyNo, G4VPhysicalVolume* physVo 226 (const G4int copyNo, G4VPhysicalVolume* physVol) const
212 { 227 {
213 G4ThreeVector origin << 228 G4ThreeVector
214 ( << 229 origin(
215 fMapCell[copyNo].x()*fDimCellBoxX, 230 fMapCell[copyNo].x()*fDimCellBoxX,
216 fMapCell[copyNo].y()*fDimCellBoxY, 231 fMapCell[copyNo].y()*fDimCellBoxY,
217 fMapCell[copyNo].z()*fDimCellBoxZ << 232 fMapCell[copyNo].z()*fDimCellBoxZ);
218 ); <<
219 233
220 physVol->SetTranslation(origin); << 234 physVol->SetTranslation(origin);
221 } 235 }
222 236
>> 237 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 238
223 void CellParameterisation::ComputeDimensions 239 void CellParameterisation::ComputeDimensions
224 (G4Box&, const G4int, const G4VPhysicalVolume* << 240 (G4Box& /*trackerChamber*/, const G4int /*copyNo*/, const G4VPhysicalVolume*) const
225 {} 241 {}
226 242
>> 243 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 244
227 G4Material* 245 G4Material*
228 CellParameterisation::ComputeMaterial(const G4 246 CellParameterisation::ComputeMaterial(const G4int copyNo,
229 G4VPhysi << 247 G4VPhysicalVolume* physVol,
230 const G4 << 248 const G4VTouchable*)
231 { 249 {
232 if( fMaterial[copyNo] == 2 ) // fMaterial 250 if( fMaterial[copyNo] == 2 ) // fMaterial 2 is nucleus
233 { 251 {
234 if( fMass[copyNo] == 1 ) 252 if( fMass[copyNo] == 1 )
235 { 253 {
236 physVol->GetLogicalVolume()->SetVisAttri 254 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes1 );
237 return fNucleusMaterial1; 255 return fNucleusMaterial1;
238 } 256 }
239 if( fMass[copyNo] == 2 ) 257 if( fMass[copyNo] == 2 )
240 { 258 {
241 physVol->GetLogicalVolume()->SetVisAttri 259 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes2 );
242 return fNucleusMaterial2; 260 return fNucleusMaterial2;
243 } 261 }
244 if( fMass[copyNo] == 3 ) 262 if( fMass[copyNo] == 3 )
245 { 263 {
246 physVol->GetLogicalVolume()->SetVisAttri 264 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes3 );
247 return fNucleusMaterial3; 265 return fNucleusMaterial3;
248 } 266 }
249 } 267 }
250 268
251 else if( fMaterial[copyNo] == 1 ) // fMate 269 else if( fMaterial[copyNo] == 1 ) // fMaterial 1 is cytoplasm
252 { 270 {
253 if( fMass[copyNo] == 1 ) 271 if( fMass[copyNo] == 1 )
254 { 272 {
255 physVol->GetLogicalVolume()->SetVisAttri 273 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes1 );
256 return fCytoplasmMaterial1; 274 return fCytoplasmMaterial1;
257 } 275 }
258 if( fMass[copyNo] == 2 ) 276 if( fMass[copyNo] == 2 )
259 { 277 {
260 // nucleoli so taken as nucleus ! 278 // nucleoli so taken as nucleus !
261 physVol->GetLogicalVolume()->SetVisAttri 279 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes2 );
262 return fCytoplasmMaterial2; 280 return fCytoplasmMaterial2;
263 } 281 }
264 if( fMass[copyNo] == 3 ) 282 if( fMass[copyNo] == 3 )
265 { 283 {
266 physVol->GetLogicalVolume()->SetVisAttri 284 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes3 );
267 return fCytoplasmMaterial3; 285 return fCytoplasmMaterial3;
268 } 286 }
269 } 287 }
270 288
271 return physVol->GetLogicalVolume()->GetMat 289 return physVol->GetLogicalVolume()->GetMaterial();
272 } 290 }
273 291