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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" <<
38 37
39 // SINGLETON << 38 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
40 CellParameterisation * CellParameterisation::g <<
41 39
42 CellParameterisation::CellParameterisation 40 CellParameterisation::CellParameterisation
43 (G4Material * nucleus1, G4Material * cytoplas << 41 (G4int NoBoxes, G4float DimBoxX, G4float DimBoxY, G4float DimBoxZ,
>> 42 G4Material * nucleus1, G4Material * cytoplasm1,
44 G4Material * nucleus2, G4Material * cytoplas 43 G4Material * nucleus2, G4Material * cytoplasm2,
45 G4Material * nucleus3, G4Material * cytoplas 44 G4Material * nucleus3, G4Material * cytoplasm3
46 ) 45 )
47 { 46 {
48 fNucleusMaterial1 = nucleus1; 47 fNucleusMaterial1 = nucleus1;
49 fCytoplasmMaterial1 = cytoplasm1; 48 fCytoplasmMaterial1 = cytoplasm1;
50 fNucleusMaterial2 = nucleus2; 49 fNucleusMaterial2 = nucleus2;
51 fCytoplasmMaterial2 = cytoplasm2; 50 fCytoplasmMaterial2 = cytoplasm2;
52 fNucleusMaterial3 = nucleus3; 51 fNucleusMaterial3 = nucleus3;
53 fCytoplasmMaterial3 = cytoplasm3; 52 fCytoplasmMaterial3 = cytoplasm3;
54 53
>> 54 fNoCellBoxes = NoBoxes;
>> 55 fDimCellBoxX = DimBoxX;
>> 56 fDimCellBoxY = DimBoxY;
>> 57 fDimCellBoxZ = DimBoxZ;
>> 58
>> 59 fMapCell = new G4ThreeVector[fNoCellBoxes];
>> 60 fMaterial = new G4float[fNoCellBoxes];
>> 61 fMass = new G4float[fNoCellBoxes];
>> 62
55 G4int ncols,nlines; 63 G4int ncols,nlines;
56 G4int shiftX, shiftY, shiftZ; 64 G4int shiftX, shiftY, shiftZ;
57 G4double x,y,z,mat,den,tmp,density; << 65 G4float x,y,z,mat,den,tmp,sizeZ;
58 G4double denCyto1, denCyto2, denCyto3, denN <<
59 <<
60 ncols = nlines = shiftX = shiftY = shiftZ = <<
61 x = y = z = mat = den = tmp = density = <<
62 denCyto1 = denCyto2 = denCyto3 = denNucl1 <<
63 66
64 // READ PHANTOM << 67 ncols=0; nlines=0;
65 fNucleusMass = 0; <<
66 fCytoplasmMass = 0; <<
67 <<
68 fDimCellBoxX = fDimCellBoxY = fDimCellBoxZ <<
69 68
>> 69 // READ PHANTOM
>> 70
70 FILE *fMap; 71 FILE *fMap;
71 fMap = fopen("phantom.dat","r"); 72 fMap = fopen("phantom.dat","r");
72 << 73
73 while (1) 74 while (1)
74 { 75 {
75 if (nlines == 0) << 76 if (nlines >= 0 && nlines <=1 ) ncols = fscanf(fMap,"%f %f %f",&tmp,&tmp,&sizeZ);
76 { << 77 if (nlines == 2) ncols = fscanf(fMap,"%i %i %i",&shiftX,&shiftY,&shiftZ); // VOXEL SHIFT IN Z ASSUMED TO BE NEGATIVE
77 ncols = fscanf(fMap,"%i %i %i",&fPhant << 78 if (nlines == 3) ncols = fscanf(fMap,"%f %f %f",&tmp,&tmp,&tmp);
78 fMapCell = new G4ThreeVector[fPhantomTota << 79 if (nlines == 4) ncols = fscanf(fMap,"%f %f %f",&tmp,&tmp,&tmp);
79 fMaterial = new G4double[fPhantomTot << 80 if (nlines > 4) ncols = fscanf(fMap,"%f %f %f %f %f %f",&x,&y,&z,&mat,&den,&tmp);
80 fMass = new G4double[fPhantomTot <<
81 fTissueType = new G4int[fPhantomTotalP <<
82 } <<
83 <<
84 if (nlines == 1) <<
85 { <<
86 ncols = fscanf(fMap,"%lf %lf %lf",&fDi <<
87 fDimCellBoxX=fDimCellBoxX*micrometer; <<
88 fDimCellBoxY=fDimCellBoxY*micrometer; <<
89 fDimCellBoxZ=fDimCellBoxZ*micrometer; <<
90 } <<
91 <<
92 // VOXEL SHIFT IN Z ASSUMED TO BE NEGATI <<
93 if (nlines == 2) ncols = fscanf(fMap,"%i <<
94 <<
95 if (nlines == 3) ncols = fscanf(fMap,"%l <<
96 <<
97 if (nlines == 4) ncols = fscanf(fMap,"%l <<
98 <<
99 if (nlines > 4) ncols = fscanf(fMap,"%l <<
100 <<
101 if (ncols < 0) break; 81 if (ncols < 0) break;
102 82
103 // VOXEL SHIFT IN ORDER TO CENTER PHANTO << 83 G4ThreeVector v(x+shiftX,y+shiftY,z-1500/sizeZ-shiftZ); // VOXEL SHIFT IN ORDER TO CENTER PHANTOM
104 G4ThreeVector v(x+shiftX,y+shiftY,z-1500 << 84
105 if (nlines>4) 85 if (nlines>4)
106 { 86 {
107 <<
108 fMapCell[nlines-5]=v; 87 fMapCell[nlines-5]=v;
109 fMaterial[nlines-5]=mat; 88 fMaterial[nlines-5]=mat;
110 fMass[nlines-5]=den; 89 fMass[nlines-5]=den;
111 <<
112 // fTissueType: 1 is Cytoplasm - 2 is Nucl <<
113 <<
114 if( fMaterial[nlines-5] == 2 ) // fM <<
115 { <<
116 if( fMass[nlines-5] == 1 ) <<
117 { <<
118 fTissueType[nlines-5]=2; <<
119 } <<
120 if( fMass[nlines-5] == 2 ) <<
121 { <<
122 fTissueType[nlines-5]=2; <<
123 } <<
124 if( fMass[nlines-5] == 3 ) <<
125 { <<
126 fTissueType[nlines-5]=2; <<
127 } <<
128 } <<
129 <<
130 else if( fMaterial[nlines-5] == 1 ) <<
131 { <<
132 if( fMass[nlines-5] == 1 ) <<
133 { <<
134 fTissueType[nlines-5]=1; <<
135 } <<
136 if( fMass[nlines-5] == 2 ) <<
137 { <<
138 fTissueType[nlines-5]=2; <<
139 } <<
140 if( fMass[nlines-5] == 3 ) <<
141 { <<
142 fTissueType[nlines-5]=1; <<
143 } <<
144 } <<
145 <<
146 // <<
147 <<
148 if (std::abs(mat-2)<1.e-30) // NUCLEUS <<
149 { <<
150 if (std::abs(den-1)<1.e-30) density = de <<
151 if (std::abs(den-2)<1.e-30) density = de <<
152 if (std::abs(den-3)<1.e-30) density = de <<
153 fNucleusMass = fNucleusMass + densit <<
154 } <<
155 <<
156 if (std::abs(mat-1)<1.e-30) // CYTOP <<
157 { <<
158 if (std::abs(den-1)<1e-30) density = den <<
159 if (std::abs(den-2)<1e-30) density = den <<
160 if (std::abs(den-3)<1e-30) density = den <<
161 fCytoplasmMass = fCytoplasmMass + densit <<
162 } <<
163 <<
164 } 90 }
165 91
166 nlines++; 92 nlines++;
167 } 93 }
168 fclose(fMap); 94 fclose(fMap);
169 << 95
170 // NUCLEUS IN GREEN 96 // NUCLEUS IN GREEN
171 97
172 fNucleusAttributes1 = new G4VisAttributes; 98 fNucleusAttributes1 = new G4VisAttributes;
173 fNucleusAttributes1->SetColour(G4Colour(0,.8 99 fNucleusAttributes1->SetColour(G4Colour(0,.8,0));
174 fNucleusAttributes1->SetForceSolid(false); 100 fNucleusAttributes1->SetForceSolid(false);
175 101
176 fNucleusAttributes2 = new G4VisAttributes; 102 fNucleusAttributes2 = new G4VisAttributes;
177 fNucleusAttributes2->SetColour(G4Colour(0,.9 103 fNucleusAttributes2->SetColour(G4Colour(0,.9,0));
178 fNucleusAttributes2->SetForceSolid(false); 104 fNucleusAttributes2->SetForceSolid(false);
179 105
180 fNucleusAttributes3 = new G4VisAttributes; 106 fNucleusAttributes3 = new G4VisAttributes;
181 fNucleusAttributes3->SetColour(G4Colour(0,1, 107 fNucleusAttributes3->SetColour(G4Colour(0,1,0));
182 fNucleusAttributes3->SetForceSolid(false); 108 fNucleusAttributes3->SetForceSolid(false);
183 109
184 // CYTOPLASM IN RED 110 // CYTOPLASM IN RED
185 111
186 fCytoplasmAttributes1 = new G4VisAttributes; 112 fCytoplasmAttributes1 = new G4VisAttributes;
187 fCytoplasmAttributes1->SetColour(G4Colour(1, 113 fCytoplasmAttributes1->SetColour(G4Colour(1,0,0));
188 fCytoplasmAttributes1->SetForceSolid(false); 114 fCytoplasmAttributes1->SetForceSolid(false);
189 115
190 fCytoplasmAttributes2 = new G4VisAttributes; 116 fCytoplasmAttributes2 = new G4VisAttributes; // nucleoli in yellow
191 fCytoplasmAttributes2->SetColour(G4Colour(1. 117 fCytoplasmAttributes2->SetColour(G4Colour(1.,1.,0));
192 fCytoplasmAttributes2->SetForceSolid(false); 118 fCytoplasmAttributes2->SetForceSolid(false);
193 119
194 fCytoplasmAttributes3 = new G4VisAttributes; 120 fCytoplasmAttributes3 = new G4VisAttributes;
195 fCytoplasmAttributes3->SetColour(G4Colour(1, 121 fCytoplasmAttributes3->SetColour(G4Colour(1,0,0));
196 fCytoplasmAttributes3->SetForceSolid(false); 122 fCytoplasmAttributes3->SetForceSolid(false);
>> 123 }
197 124
198 // << 125 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
199 gInstance = this; <<
200 } <<
201 126
202 CellParameterisation::~CellParameterisation() 127 CellParameterisation::~CellParameterisation()
203 { 128 {
204 delete[] fMapCell; 129 delete[] fMapCell;
205 delete[] fMaterial; 130 delete[] fMaterial;
206 delete[] fMass; 131 delete[] fMass;
207 delete[] fTissueType; <<
208 } 132 }
209 133
>> 134 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 135
210 void CellParameterisation::ComputeTransformati 136 void CellParameterisation::ComputeTransformation
211 (const G4int copyNo, G4VPhysicalVolume* physVo 137 (const G4int copyNo, G4VPhysicalVolume* physVol) const
212 { 138 {
213 G4ThreeVector origin << 139 G4ThreeVector
214 ( << 140 origin(
215 fMapCell[copyNo].x()*fDimCellBoxX, << 141 fMapCell[copyNo].x()*fDimCellBoxX*2,
216 fMapCell[copyNo].y()*fDimCellBoxY, << 142 fMapCell[copyNo].y()*fDimCellBoxY*2,
217 fMapCell[copyNo].z()*fDimCellBoxZ << 143 fMapCell[copyNo].z()*fDimCellBoxZ*2);
218 ); <<
219 144
220 physVol->SetTranslation(origin); 145 physVol->SetTranslation(origin);
221 } 146 }
222 147
>> 148 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 149
223 void CellParameterisation::ComputeDimensions 150 void CellParameterisation::ComputeDimensions
224 (G4Box&, const G4int, const G4VPhysicalVolume* << 151 (G4Box& /*trackerChamber*/, const G4int /*copyNo*/, const G4VPhysicalVolume*) const
225 {} 152 {}
226 153
>> 154 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 155
227 G4Material* 156 G4Material*
228 CellParameterisation::ComputeMaterial(const G4 157 CellParameterisation::ComputeMaterial(const G4int copyNo,
229 G4VPhysi << 158 G4VPhysicalVolume* physVol,
230 const G4 << 159 const G4VTouchable*)
231 { 160 {
232 if( fMaterial[copyNo] == 2 ) // fMaterial 161 if( fMaterial[copyNo] == 2 ) // fMaterial 2 is nucleus
233 { 162 {
234 if( fMass[copyNo] == 1 ) 163 if( fMass[copyNo] == 1 )
235 { 164 {
236 physVol->GetLogicalVolume()->SetVisAttri << 165 physVol->SetName("physicalNucleus");
237 return fNucleusMaterial1; << 166 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes1 );
>> 167 return fNucleusMaterial1;
238 } 168 }
239 if( fMass[copyNo] == 2 ) 169 if( fMass[copyNo] == 2 )
240 { 170 {
241 physVol->GetLogicalVolume()->SetVisAttri << 171 physVol->SetName("physicalNucleus");
242 return fNucleusMaterial2; << 172 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes2 );
>> 173 return fNucleusMaterial2;
243 } 174 }
244 if( fMass[copyNo] == 3 ) 175 if( fMass[copyNo] == 3 )
245 { 176 {
246 physVol->GetLogicalVolume()->SetVisAttri << 177 physVol->SetName("physicalNucleus");
247 return fNucleusMaterial3; << 178 physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes3 );
>> 179 return fNucleusMaterial3;
248 } 180 }
249 } 181 }
250 182
251 else if( fMaterial[copyNo] == 1 ) // fMate 183 else if( fMaterial[copyNo] == 1 ) // fMaterial 1 is cytoplasm
252 { 184 {
253 if( fMass[copyNo] == 1 ) 185 if( fMass[copyNo] == 1 )
254 { 186 {
255 physVol->GetLogicalVolume()->SetVisAttri << 187 physVol->SetName("physicalCytoplasm");
256 return fCytoplasmMaterial1; << 188 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes1 );
>> 189 return fCytoplasmMaterial1;
257 } 190 }
258 if( fMass[copyNo] == 2 ) 191 if( fMass[copyNo] == 2 )
259 { 192 {
260 // nucleoli so taken as nucleus ! << 193 physVol->SetName("physicalNucleus"); // nucleoli
261 physVol->GetLogicalVolume()->SetVisAttri << 194 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes2 );
262 return fCytoplasmMaterial2; << 195 return fCytoplasmMaterial2;
263 } 196 }
264 if( fMass[copyNo] == 3 ) 197 if( fMass[copyNo] == 3 )
265 { 198 {
266 physVol->GetLogicalVolume()->SetVisAttri << 199 physVol->SetName("physicalCytoplasm");
267 return fCytoplasmMaterial3; << 200 physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes3 );
>> 201 return fCytoplasmMaterial3;
268 } 202 }
269 } 203 }
270 204
271 return physVol->GetLogicalVolume()->GetMat 205 return physVol->GetLogicalVolume()->GetMaterial();
272 } 206 }
273 207