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25 //
26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained using the Geant4-DNA software
28 // shall cite the following Geant4-DNA collaboration publication:
29 // Med. Phys. 37 (2010) 4692-4708
30 // and papers
31 // M. Batmunkh et al. J Radiat Res Appl Sci 8 (2015) 498-507
32 // O. Belov et al. Physica Medica 32 (2016) 1510-1520
33 // The Geant4-DNA web site is available at http://geant4-dna.org
34 //
35 // -------------------------------------------------------------------
36 // November 2016
37 // -------------------------------------------------------------------
38 //
39 //
40 /// \file NeuronLoadDataFile.hh
41 /// \brief Implementation of the NeuronLoadDataFile class
42
43 #ifndef NeuronLoadDataFile_H
44 #define NeuronLoadDataFile_H 1
45
46 #include "G4Colour.hh"
47 #include "G4Material.hh"
48 #include "G4RotationMatrix.hh"
49 #include "G4SystemOfUnits.hh"
50 #include "G4ThreeVector.hh"
51 #include "G4VSolid.hh"
52 #include "G4VisAttributes.hh"
53
54 #include <vector>
55
56 // Geant4 Constructive Solid Geometry (CSG)
57 #include "G4Box.hh" // bounding volume
58 #include "G4Cons.hh" // stubby spine, filopodia
59 #include "G4Ellipsoid.hh" // soma compartments
60 #include "G4EllipticalCone.hh"
61 #include "G4EllipticalTube.hh"
62 #include "G4Hype.hh" // thin spine neck
63 #include "G4Orb.hh" // mushroom spine
64 #include "G4Para.hh"
65 #include "G4Polycone.hh"
66 #include "G4Polyhedra.hh"
67 #include "G4Sphere.hh" // soma compartments
68 #include "G4Tet.hh"
69 #include "G4Torus.hh"
70 #include "G4Trap.hh"
71 #include "G4Trd.hh"
72 #include "G4Tubs.hh" // axon, dendrite compartments
73 #include "G4TwistedBox.hh"
74 #include "G4TwistedTrap.hh"
75 #include "G4TwistedTrd.hh"
76 #include "G4TwistedTubs.hh"
77 #include "G4VPVParameterisation.hh"
78
79 // class NeuronLoadMessenger;
80 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
81
82 class NeuronLoadDataFile
83
84 // default - G4PVPlacement volume
85 // if use G4PVParameterised volume,
86 // please enable following G4VPVParameterisation class!
87 //: public G4VPVParameterisation
88
89 {
90 public:
91 NeuronLoadDataFile();
92 ~NeuronLoadDataFile() = default;
93
94 void SingleNeuronSWCfile(const G4String& filename);
95 void NeuralNetworkDATAfile(const G4String& filename);
96
97 // position, rotation of solids
98 void ComputeTransformation(const G4int copyNo, G4VPhysicalVolume* physVol) const;
99
100 void ComputeDimensions(G4Tubs& cylinderComp, const G4int copyNo,
101 const G4VPhysicalVolume*) const;
102 G4double GetwidthB() const { return fwidthB; }
103 G4double GetheightB() const { return fheightB; }
104 G4double GetdepthB() const { return fdepthB; }
105 G4double GetdiagnlLength() const { return fdiagnlLength; }
106 G4double GetshiftX() const { return fshiftX; }
107 G4double GetshiftY() const { return fshiftY; }
108 G4double GetshiftZ() const { return fshiftZ; }
109 G4double GetTypeN(G4int i) { return fTypeN[i]; }
110
111 G4int GetnbSomacomp() const { return fnbSomacomp; }
112 G4double GetMassSomacomp(G4int i) const { return fMassSomacomp[i]; }
113 G4double GetMassSomaTot() { return fMassSomaTot; }
114 G4ThreeVector GetPosSomacomp(G4int i) const { return fPosSomacomp[i]; }
115 G4double GetRadSomacomp(G4int i) const { return fRadSomacomp[i]; }
116
117 G4int GetnbDendritecomp() const { return fnbDendritecomp; }
118 G4double GetMassDendcomp(G4int i) const { return fMassDendcomp[i]; }
119 G4double GetMassDendTot() { return fMassDendTot; }
120 G4ThreeVector GetPosDendcomp(G4int i) const { return fPosDendcomp[i]; }
121 G4double GetRadDendcomp(G4int i) const { return fRadDendcomp[i]; }
122 G4double GetHeightDendcomp(G4int i) const { return fHeightDendcomp[i]; }
123 G4double GetDistADendSoma(G4int i) const { return fDistADendSoma[i]; }
124 G4double GetDistBDendSoma(G4int i) const { return fDistBDendSoma[i]; }
125 G4RotationMatrix GetRotDendcomp(G4int i) const { return fRotDendcomp[i]; }
126
127 G4int GetnbAxoncomp() const { return fnbAxoncomp; }
128 G4double GetMassAxoncomp(G4int i) const { return fMassAxoncomp[i]; }
129 G4double GetMassAxonTot() const { return fMassAxonTot; }
130 G4ThreeVector GetPosAxoncomp(G4int i) const { return fPosAxoncomp[i]; }
131 G4double GetRadAxoncomp(G4int i) const { return fRadAxoncomp[i]; }
132 G4double GetHeightAxoncomp(G4int i) const { return fHeightAxoncomp[i]; }
133 G4double GetDistAxonsoma(G4int i) const { return fDistAxonsoma[i]; }
134 G4RotationMatrix GetRotAxoncomp(G4int i) const { return fRotAxoncomp[i]; }
135
136 G4int GetnbSpinecomp() const { return fnbSpinecomp; }
137 G4double GetMassSpinecomp(G4int i) const { return fMassSpinecomp[i]; }
138 G4double GetMassSpineTot() const { return fMassSpineTot; }
139 G4ThreeVector GetPosSpinecomp(G4int i) const { return fPosSpinecomp[i]; }
140 G4double GetRadSpinecomp(G4int i) const { return fRadSpinecomp[i]; }
141 G4double GetHeightSpinecomp(G4int i) const { return fHeightSpinecomp[i]; }
142 G4double GetDistSpinesoma(G4int i) { return fDistSpinesoma[i]; }
143 G4RotationMatrix GetRotSpinecomp(G4int i) const { return fRotSpinecomp[i]; }
144
145 G4int GetnbNeuroncomp() const { return fnbNeuroncomp; }
146
147 G4double GetTotVolNeuron() const { return fTotVolNeuron; }
148 G4double GetTotSurfNeuron() const { return fTotSurfNeuron; }
149 G4double GetTotMassNeuron() const { return fTotMassNeuron; }
150 G4double GetTotVolSlice() const { return fTotVolSlice; }
151 G4double GetTotSurfSlice() const { return fTotSurfSlice; }
152 G4double GetTotMassSlice() const { return fTotMassSlice; }
153 G4double GetTotVolMedium() const { return fTotVolMedium; }
154 G4double GetTotSurfMedium() const { return fTotSurfMedium; }
155 G4double GetTotMassMedium() const { return fTotMassMedium; }
156
157 private:
158 //! NEURON filename
159 G4String fNeuronFileNameSWC;
160 G4String fNeuronFileNameDATA;
161
162 G4int fnbSomacomp{0};
163 G4int fnbDendritecomp{0};
164 G4int fnbAxoncomp{0};
165 G4int fnbSpinecomp{0};
166 G4int fnbNeuroncomp{0};
167
168 std::vector<G4int> fTypeN;
169
170 // shift in oder to center VOLUME!
171 G4double fshiftX{0.0};
172 G4double fshiftY{0.0};
173 G4double fshiftZ{0.0};
174 G4double fwidthB{0.0};
175 G4double fheightB{0.0};
176 G4double fdepthB{0.0};
177 G4double fdiagnlLength{0.0}; // diagonal and diameter
178
179 G4double fMassSomaTot{0.0};
180 G4double fMassDendTot{0.0};
181 G4double fMassAxonTot{0.0};
182 G4double fMassSpineTot{0.0};
183
184 G4double fTotVolNeuron{0.0};
185 G4double fTotSurfNeuron{0.0};
186 G4double fTotMassNeuron{0.0};
187 G4double fTotVolSlice{0.0};
188 G4double fTotSurfSlice{0.0};
189 G4double fTotMassSlice{0.0};
190 G4double fTotVolMedium{0.0};
191 G4double fTotSurfMedium{0.0};
192 G4double fTotMassMedium{0.0};
193
194 std::vector<G4ThreeVector> fPosSomacomp;
195 std::vector<G4double> fRadSomacomp;
196 std::vector<G4double> fMassSomacomp;
197
198 std::vector<G4double> fRadDendcomp;
199 std::vector<G4double> fDistADendSoma;
200 std::vector<G4double> fDistBDendSoma;
201 std::vector<G4double> fHeightDendcomp;
202 std::vector<G4double> fMassDendcomp;
203 std::vector<G4ThreeVector> fPosDendcomp; // VOXEL COORDINATES OF DENDRITES
204 std::vector<G4RotationMatrix> fRotDendcomp; // RotationMatrix with Inverse
205
206 std::vector<G4double> fRadAxoncomp;
207 std::vector<G4double> fHeightAxoncomp;
208 std::vector<G4double> fDistAxonsoma;
209 std::vector<G4double> fMassAxoncomp;
210 std::vector<G4ThreeVector> fPosAxoncomp; // VOXEL COORDINATES OF AXON
211 std::vector<G4RotationMatrix> fRotAxoncomp;
212
213 std::vector<G4double> fRadSpinecomp;
214 std::vector<G4double> fHeightSpinecomp;
215 std::vector<G4double> fDistSpinesoma;
216 std::vector<G4double> fMassSpinecomp;
217 std::vector<G4ThreeVector> fPosSpinecomp; // VOXEL COORDINATES OF SPINE
218 std::vector<G4RotationMatrix> fRotSpinecomp;
219
220 std::vector<G4double> fRadNeuroncomp;
221 std::vector<G4double> fHeightNeuroncomp;
222 std::vector<G4double> fDistNeuronsoma;
223 std::vector<G4double> fMassNeuroncomp;
224 std::vector<G4ThreeVector> fPosNeuroncomp; // VOXEL COORDINATES OF Neuron
225 std::vector<G4RotationMatrix> fRotNeuroncomp;
226 };
227
228 #endif
229