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19 // * technical work of the GEANT4 collaboratio 19 // * technical work of the GEANT4 collaboration. *
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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 // SINGLETON 39 // SINGLETON
40 CellParameterisation * CellParameterisation::g 40 CellParameterisation * CellParameterisation::gInstance = 0;
41 41
42 CellParameterisation::CellParameterisation 42 CellParameterisation::CellParameterisation
43 (G4Material * nucleus1, G4Material * cytoplas 43 (G4Material * nucleus1, G4Material * cytoplasm1,
44 G4Material * nucleus2, G4Material * cytoplas 44 G4Material * nucleus2, G4Material * cytoplasm2,
45 G4Material * nucleus3, G4Material * cytoplas 45 G4Material * nucleus3, G4Material * cytoplasm3
46 ) 46 )
47 { 47 {
48 fNucleusMaterial1 = nucleus1; 48 fNucleusMaterial1 = nucleus1;
49 fCytoplasmMaterial1 = cytoplasm1; 49 fCytoplasmMaterial1 = cytoplasm1;
50 fNucleusMaterial2 = nucleus2; 50 fNucleusMaterial2 = nucleus2;
51 fCytoplasmMaterial2 = cytoplasm2; 51 fCytoplasmMaterial2 = cytoplasm2;
52 fNucleusMaterial3 = nucleus3; 52 fNucleusMaterial3 = nucleus3;
53 fCytoplasmMaterial3 = cytoplasm3; 53 fCytoplasmMaterial3 = cytoplasm3;
54 54
55 G4int ncols,nlines; 55 G4int ncols,nlines;
56 G4int shiftX, shiftY, shiftZ; 56 G4int shiftX, shiftY, shiftZ;
57 G4double x,y,z,mat,den,tmp,density; 57 G4double x,y,z,mat,den,tmp,density;
58 G4double denCyto1, denCyto2, denCyto3, denN 58 G4double denCyto1, denCyto2, denCyto3, denNucl1, denNucl2, denNucl3;
59 59
60 ncols = nlines = shiftX = shiftY = shiftZ = 60 ncols = nlines = shiftX = shiftY = shiftZ = 0;
61 x = y = z = mat = den = tmp = density = 61 x = y = z = mat = den = tmp = density =
62 denCyto1 = denCyto2 = denCyto3 = denNucl1 62 denCyto1 = denCyto2 = denCyto3 = denNucl1 = denNucl2 = denNucl3 = 0.0;
63 63
64 // READ PHANTOM 64 // READ PHANTOM
65 fNucleusMass = 0; 65 fNucleusMass = 0;
66 fCytoplasmMass = 0; 66 fCytoplasmMass = 0;
67 67
68 fDimCellBoxX = fDimCellBoxY = fDimCellBoxZ 68 fDimCellBoxX = fDimCellBoxY = fDimCellBoxZ = micrometer;
69 69
70 FILE *fMap; 70 FILE *fMap;
71 fMap = fopen("phantom.dat","r"); 71 fMap = fopen("phantom.dat","r");
72 72
73 while (1) 73 while (1)
74 { 74 {
75 if (nlines == 0) 75 if (nlines == 0)
76 { 76 {
77 ncols = fscanf(fMap,"%i %i %i",&fPhant 77 ncols = fscanf(fMap,"%i %i %i",&fPhantomTotalPixels,&fNucleusTotalPixels,&fCytoplasmTotalPixels);
78 fMapCell = new G4ThreeVector[fPhantomTota 78 fMapCell = new G4ThreeVector[fPhantomTotalPixels];
79 fMaterial = new G4double[fPhantomTot 79 fMaterial = new G4double[fPhantomTotalPixels];
80 fMass = new G4double[fPhantomTot 80 fMass = new G4double[fPhantomTotalPixels];
81 fTissueType = new G4int[fPhantomTotalP 81 fTissueType = new G4int[fPhantomTotalPixels];
82 } 82 }
83 83
84 if (nlines == 1) 84 if (nlines == 1)
85 { 85 {
86 ncols = fscanf(fMap,"%lf %lf %lf",&fDi 86 ncols = fscanf(fMap,"%lf %lf %lf",&fDimCellBoxX,&fDimCellBoxY,&fDimCellBoxZ);
87 fDimCellBoxX=fDimCellBoxX*micrometer; 87 fDimCellBoxX=fDimCellBoxX*micrometer;
88 fDimCellBoxY=fDimCellBoxY*micrometer; 88 fDimCellBoxY=fDimCellBoxY*micrometer;
89 fDimCellBoxZ=fDimCellBoxZ*micrometer; 89 fDimCellBoxZ=fDimCellBoxZ*micrometer;
90 } 90 }
91 91
92 // VOXEL SHIFT IN Z ASSUMED TO BE NEGATI 92 // VOXEL SHIFT IN Z ASSUMED TO BE NEGATIVE
93 if (nlines == 2) ncols = fscanf(fMap,"%i 93 if (nlines == 2) ncols = fscanf(fMap,"%i %i %i",&shiftX,&shiftY,&shiftZ);
94 94
95 if (nlines == 3) ncols = fscanf(fMap,"%l 95 if (nlines == 3) ncols = fscanf(fMap,"%lf %lf %lf",&denCyto1, &denCyto2, &denCyto3);
96 96
97 if (nlines == 4) ncols = fscanf(fMap,"%l 97 if (nlines == 4) ncols = fscanf(fMap,"%lf %lf %lf",&denNucl1, &denNucl2, &denNucl3);
98 98
99 if (nlines > 4) ncols = fscanf(fMap,"%l 99 if (nlines > 4) ncols = fscanf(fMap,"%lf %lf %lf %lf %lf %lf",&x,&y,&z,&mat,&den,&tmp);
100 100
101 if (ncols < 0) break; 101 if (ncols < 0) break;
102 102
103 // VOXEL SHIFT IN ORDER TO CENTER PHANTO 103 // VOXEL SHIFT IN ORDER TO CENTER PHANTOM
104 G4ThreeVector v(x+shiftX,y+shiftY,z-1500 104 G4ThreeVector v(x+shiftX,y+shiftY,z-1500/(fDimCellBoxZ/micrometer)-shiftZ);
105 if (nlines>4) 105 if (nlines>4)
106 { 106 {
107 107
108 fMapCell[nlines-5]=v; 108 fMapCell[nlines-5]=v;
109 fMaterial[nlines-5]=mat; 109 fMaterial[nlines-5]=mat;
110 fMass[nlines-5]=den; 110 fMass[nlines-5]=den;
111 111
112 // fTissueType: 1 is Cytoplasm - 2 is Nucl 112 // fTissueType: 1 is Cytoplasm - 2 is Nucleus
113 113
114 if( fMaterial[nlines-5] == 2 ) // fM 114 if( fMaterial[nlines-5] == 2 ) // fMaterial 2 is nucleus
115 { 115 {
116 if( fMass[nlines-5] == 1 ) 116 if( fMass[nlines-5] == 1 )
117 { 117 {
118 fTissueType[nlines-5]=2; 118 fTissueType[nlines-5]=2;
119 } 119 }
120 if( fMass[nlines-5] == 2 ) 120 if( fMass[nlines-5] == 2 )
121 { 121 {
122 fTissueType[nlines-5]=2; 122 fTissueType[nlines-5]=2;
123 } 123 }
124 if( fMass[nlines-5] == 3 ) 124 if( fMass[nlines-5] == 3 )
125 { 125 {
126 fTissueType[nlines-5]=2; 126 fTissueType[nlines-5]=2;
127 } 127 }
128 } 128 }
129 129
130 else if( fMaterial[nlines-5] == 1 ) 130 else if( fMaterial[nlines-5] == 1 ) // fMaterial 1 is cytoplasm
131 { 131 {
132 if( fMass[nlines-5] == 1 ) 132 if( fMass[nlines-5] == 1 )
133 { 133 {
134 fTissueType[nlines-5]=1; 134 fTissueType[nlines-5]=1;
135 } 135 }
136 if( fMass[nlines-5] == 2 ) 136 if( fMass[nlines-5] == 2 )
137 { 137 {
138 fTissueType[nlines-5]=2; 138 fTissueType[nlines-5]=2;
139 } 139 }
140 if( fMass[nlines-5] == 3 ) 140 if( fMass[nlines-5] == 3 )
141 { 141 {
142 fTissueType[nlines-5]=1; 142 fTissueType[nlines-5]=1;
143 } 143 }
144 } 144 }
145 145
146 // 146 //
147 147
148 if (std::abs(mat-2)<1.e-30) // NUCLEUS 148 if (std::abs(mat-2)<1.e-30) // NUCLEUS
149 { 149 {
150 if (std::abs(den-1)<1.e-30) density = de 150 if (std::abs(den-1)<1.e-30) density = denNucl1*(g/cm3);
151 if (std::abs(den-2)<1.e-30) density = de 151 if (std::abs(den-2)<1.e-30) density = denNucl2*(g/cm3);
152 if (std::abs(den-3)<1.e-30) density = de 152 if (std::abs(den-3)<1.e-30) density = denNucl3*(g/cm3);
153 fNucleusMass = fNucleusMass + densit 153 fNucleusMass = fNucleusMass + density * fDimCellBoxX * fDimCellBoxY * fDimCellBoxZ ;
154 } 154 }
155 155
156 if (std::abs(mat-1)<1.e-30) // CYTOP 156 if (std::abs(mat-1)<1.e-30) // CYTOPLASM
157 { 157 {
158 if (std::abs(den-1)<1e-30) density = den 158 if (std::abs(den-1)<1e-30) density = denCyto1*(g/cm3);
159 if (std::abs(den-2)<1e-30) density = den 159 if (std::abs(den-2)<1e-30) density = denCyto2*(g/cm3);
160 if (std::abs(den-3)<1e-30) density = den 160 if (std::abs(den-3)<1e-30) density = denCyto3*(g/cm3);
161 fCytoplasmMass = fCytoplasmMass + densit 161 fCytoplasmMass = fCytoplasmMass + density * fDimCellBoxX * fDimCellBoxY * fDimCellBoxZ ;
162 } 162 }
163 163
164 } 164 }
165 165
166 nlines++; 166 nlines++;
167 } 167 }
168 fclose(fMap); 168 fclose(fMap);
169 169
170 // NUCLEUS IN GREEN 170 // NUCLEUS IN GREEN
171 171
172 fNucleusAttributes1 = new G4VisAttributes; 172 fNucleusAttributes1 = new G4VisAttributes;
173 fNucleusAttributes1->SetColour(G4Colour(0,.8 173 fNucleusAttributes1->SetColour(G4Colour(0,.8,0));
174 fNucleusAttributes1->SetForceSolid(false); 174 fNucleusAttributes1->SetForceSolid(false);
175 175
176 fNucleusAttributes2 = new G4VisAttributes; 176 fNucleusAttributes2 = new G4VisAttributes;
177 fNucleusAttributes2->SetColour(G4Colour(0,.9 177 fNucleusAttributes2->SetColour(G4Colour(0,.9,0));
178 fNucleusAttributes2->SetForceSolid(false); 178 fNucleusAttributes2->SetForceSolid(false);
179 179
180 fNucleusAttributes3 = new G4VisAttributes; 180 fNucleusAttributes3 = new G4VisAttributes;
181 fNucleusAttributes3->SetColour(G4Colour(0,1, 181 fNucleusAttributes3->SetColour(G4Colour(0,1,0));
182 fNucleusAttributes3->SetForceSolid(false); 182 fNucleusAttributes3->SetForceSolid(false);
183 183
184 // CYTOPLASM IN RED 184 // CYTOPLASM IN RED
185 185
186 fCytoplasmAttributes1 = new G4VisAttributes; 186 fCytoplasmAttributes1 = new G4VisAttributes;
187 fCytoplasmAttributes1->SetColour(G4Colour(1, 187 fCytoplasmAttributes1->SetColour(G4Colour(1,0,0));
188 fCytoplasmAttributes1->SetForceSolid(false); 188 fCytoplasmAttributes1->SetForceSolid(false);
189 189
190 fCytoplasmAttributes2 = new G4VisAttributes; 190 fCytoplasmAttributes2 = new G4VisAttributes; // nucleoli in yellow
191 fCytoplasmAttributes2->SetColour(G4Colour(1. 191 fCytoplasmAttributes2->SetColour(G4Colour(1.,1.,0));
192 fCytoplasmAttributes2->SetForceSolid(false); 192 fCytoplasmAttributes2->SetForceSolid(false);
193 193
194 fCytoplasmAttributes3 = new G4VisAttributes; 194 fCytoplasmAttributes3 = new G4VisAttributes;
195 fCytoplasmAttributes3->SetColour(G4Colour(1, 195 fCytoplasmAttributes3->SetColour(G4Colour(1,0,0));
196 fCytoplasmAttributes3->SetForceSolid(false); 196 fCytoplasmAttributes3->SetForceSolid(false);
197 197
198 // 198 //
199 gInstance = this; 199 gInstance = this;
200 } 200 }
201 201
202 CellParameterisation::~CellParameterisation() 202 CellParameterisation::~CellParameterisation()
203 { 203 {
204 delete[] fMapCell; 204 delete[] fMapCell;
205 delete[] fMaterial; 205 delete[] fMaterial;
206 delete[] fMass; 206 delete[] fMass;
207 delete[] fTissueType; 207 delete[] fTissueType;
208 } 208 }
209 209
210 void CellParameterisation::ComputeTransformati 210 void CellParameterisation::ComputeTransformation
211 (const G4int copyNo, G4VPhysicalVolume* physVo 211 (const G4int copyNo, G4VPhysicalVolume* physVol) const
212 { 212 {
213 G4ThreeVector origin 213 G4ThreeVector origin
214 ( 214 (
215 fMapCell[copyNo].x()*fDimCellBoxX, 215 fMapCell[copyNo].x()*fDimCellBoxX,
216 fMapCell[copyNo].y()*fDimCellBoxY, 216 fMapCell[copyNo].y()*fDimCellBoxY,
217 fMapCell[copyNo].z()*fDimCellBoxZ 217 fMapCell[copyNo].z()*fDimCellBoxZ
218 ); 218 );
219 219
220 physVol->SetTranslation(origin); 220 physVol->SetTranslation(origin);
221 } 221 }
222 222
223 void CellParameterisation::ComputeDimensions 223 void CellParameterisation::ComputeDimensions
224 (G4Box&, const G4int, const G4VPhysicalVolume* 224 (G4Box&, const G4int, const G4VPhysicalVolume*) const
225 {} 225 {}
226 226
227 G4Material* 227 G4Material*
228 CellParameterisation::ComputeMaterial(const G4 228 CellParameterisation::ComputeMaterial(const G4int copyNo,
229 G4VPhysi 229 G4VPhysicalVolume* physVol,
230 const G4 230 const G4VTouchable*)
231 { 231 {
232 if( fMaterial[copyNo] == 2 ) // fMaterial 232 if( fMaterial[copyNo] == 2 ) // fMaterial 2 is nucleus
233 { 233 {
234 if( fMass[copyNo] == 1 ) 234 if( fMass[copyNo] == 1 )
235 { 235 {
236 physVol->GetLogicalVolume()->SetVisAttri 236 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes1 );
237 return fNucleusMaterial1; 237 return fNucleusMaterial1;
238 } 238 }
239 if( fMass[copyNo] == 2 ) 239 if( fMass[copyNo] == 2 )
240 { 240 {
241 physVol->GetLogicalVolume()->SetVisAttri 241 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes2 );
242 return fNucleusMaterial2; 242 return fNucleusMaterial2;
243 } 243 }
244 if( fMass[copyNo] == 3 ) 244 if( fMass[copyNo] == 3 )
245 { 245 {
246 physVol->GetLogicalVolume()->SetVisAttri 246 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes3 );
247 return fNucleusMaterial3; 247 return fNucleusMaterial3;
248 } 248 }
249 } 249 }
250 250
251 else if( fMaterial[copyNo] == 1 ) // fMate 251 else if( fMaterial[copyNo] == 1 ) // fMaterial 1 is cytoplasm
252 { 252 {
253 if( fMass[copyNo] == 1 ) 253 if( fMass[copyNo] == 1 )
254 { 254 {
255 physVol->GetLogicalVolume()->SetVisAttri 255 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes1 );
256 return fCytoplasmMaterial1; 256 return fCytoplasmMaterial1;
257 } 257 }
258 if( fMass[copyNo] == 2 ) 258 if( fMass[copyNo] == 2 )
259 { 259 {
260 // nucleoli so taken as nucleus ! 260 // nucleoli so taken as nucleus !
261 physVol->GetLogicalVolume()->SetVisAttri 261 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes2 );
262 return fCytoplasmMaterial2; 262 return fCytoplasmMaterial2;
263 } 263 }
264 if( fMass[copyNo] == 3 ) 264 if( fMass[copyNo] == 3 )
265 { 265 {
266 physVol->GetLogicalVolume()->SetVisAttri 266 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes3 );
267 return fCytoplasmMaterial3; 267 return fCytoplasmMaterial3;
268 } 268 }
269 } 269 }
270 270
271 return physVol->GetLogicalVolume()->GetMat 271 return physVol->GetLogicalVolume()->GetMaterial();
272 } 272 }
273 273