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NeuronLoadDataFile.hh
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29 // Med. Phys. 37 (2010) 4692-4708
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35 // -------------------------------------------------------------------
36 // November 2016
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39 //
42 
43 #ifndef NeuronLoadDataFile_H
44 #define NeuronLoadDataFile_H 1
45 
46 #include "G4ThreeVector.hh"
47 #include "G4RotationMatrix.hh"
48 #include "G4VSolid.hh"
49 #include "G4Material.hh"
50 #include "G4VisAttributes.hh"
51 #include "G4Colour.hh"
52 #include "G4SystemOfUnits.hh"
53 // Geant4 Constructive Solid Geometry (CSG)
54 #include "G4VPVParameterisation.hh"
55 #include "G4Box.hh" // bounding volume
56 #include "G4Tubs.hh" // axon, dendrite compartments
57 #include "G4Sphere.hh" // soma compartments
58 #include "G4Ellipsoid.hh" // soma compartments
59 #include "G4Trd.hh"
60 #include "G4Trap.hh"
61 #include "G4Cons.hh" // stubby spine, filopodia
62 #include "G4EllipticalTube.hh"
63 #include "G4EllipticalCone.hh"
64 #include "G4Orb.hh" // mushroom spine
65 #include "G4Torus.hh"
66 #include "G4Para.hh"
67 #include "G4Polycone.hh"
68 #include "G4Polyhedra.hh"
69 #include "G4Hype.hh" // thin spine neck
70 #include "G4Tet.hh"
71 #include "G4TwistedBox.hh"
72 #include "G4TwistedTrap.hh"
73 #include "G4TwistedTrd.hh"
74 #include "G4TwistedTubs.hh"
75 
76 //class NeuronLoadMessenger;
77 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
78 
79 class NeuronLoadDataFile
80 
81 // default - G4PVPlacement volume
82 // if use G4PVParameterised volume,
83 // please enable following G4VPVParameterisation class!
84 //: public G4VPVParameterisation
85 
86 {
87  public:
88  NeuronLoadDataFile();
89  virtual
90  ~NeuronLoadDataFile();
91 
92  void SingleNeuronSWCfile(const G4String& filename);
93  void NeuralNetworkDATAfile(const G4String& filename);
94 
95 // position, rotation of solids
96  void ComputeTransformation (const G4int copyNo,
97  G4VPhysicalVolume* physVol) const;
98 // Solid options: sphere or cylinder ...
99  //G4VSolid* ComputeSolid (const G4int copyNo,
100  // G4VPhysicalVolume* physiVol);
101 // and ... for solids!
102  void ComputeDimensions(G4Tubs& cylinderComp, const G4int copyNo,
103  const G4VPhysicalVolume*) const ;
104  void ComputeDimensions(G4Sphere& , const G4int ,
105  const G4VPhysicalVolume*) const {}
106  void ComputeDimensions(G4Ellipsoid& , const G4int ,
107  const G4VPhysicalVolume*) const {}
108  void ComputeDimensions(G4Box&, const G4int,
109  const G4VPhysicalVolume*) const {}
110  void ComputeDimensions(G4Cons&,const G4int,
111  const G4VPhysicalVolume*) const {}
112  void ComputeDimensions(G4Hype &,
113  const G4int,
114  const G4VPhysicalVolume *) const {}
115  void ComputeDimensions(G4Trd &,
116  const G4int,
117  const G4VPhysicalVolume *) const {}
118  void ComputeDimensions(G4Trap &,
119  const G4int,
120  const G4VPhysicalVolume *) const {}
121  void ComputeDimensions(G4Orb &,
122  const G4int,
123  const G4VPhysicalVolume *) const {}
124  void ComputeDimensions(G4Torus &,
125  const G4int,
126  const G4VPhysicalVolume *) const {}
127  void ComputeDimensions(G4Para &,
128  const G4int,
129  const G4VPhysicalVolume *) const {}
130  void ComputeDimensions(G4Polycone &,
131  const G4int,
132  const G4VPhysicalVolume *) const {}
133  void ComputeDimensions(G4Polyhedra &,
134  const G4int,
135  const G4VPhysicalVolume *) const {}
136 
137  G4double GetwidthB () {return fwidthB;}
138  G4double GetheightB () {return fheightB;}
139  G4double GetdepthB () {return fdepthB;}
140  G4double GetdiagnlLength () {return fdiagnlLength;}
141  G4double GetshiftX () {return fshiftX;}
142  G4double GetshiftY () {return fshiftY;}
143  G4double GetshiftZ () {return fshiftZ;}
144  G4double GetTypeN (G4int i) {return fTypeN[i];}
145 
146  G4int GetnbSomacomp() {return fnbSomacomp;}
147  G4double GetMassSomacomp (G4int i) {return fMassSomacomp[i];}
148  G4double GetMassSomaTot () {return fMassSomaTot;}
149  G4ThreeVector GetPosSomacomp(G4int i) {return fPosSomacomp[i];}
150  G4double GetRadSomacomp(G4int i) {return fRadSomacomp[i];}
151 
152  G4int GetnbDendritecomp() {return fnbDendritecomp;}
153  G4double GetMassDendcomp (G4int i) {return fMassDendcomp[i];}
154  G4double GetMassDendTot () {return fMassDendTot;}
155  G4ThreeVector GetPosDendcomp(G4int i) {return fPosDendcomp[i];}
156  G4double GetRadDendcomp(G4int i) {return fRadDendcomp[i];}
157  G4double GetHeightDendcomp(G4int i) {return fHeightDendcomp[i];}
158  G4double GetDistADendSoma (G4int i) {return fDistADendSoma[i];}
159  G4double GetDistBDendSoma (G4int i) {return fDistBDendSoma[i];}
160  G4RotationMatrix GetRotDendcomp(G4int i) {return fRotDendcomp[i];}
161 
162  G4int GetnbAxoncomp() {return fnbAxoncomp;}
163  G4double GetMassAxoncomp (G4int i) {return fMassAxoncomp[i];}
164  G4double GetMassAxonTot () {return fMassAxonTot;}
165  G4ThreeVector GetPosAxoncomp(G4int i) {return fPosAxoncomp[i];}
166  G4double GetRadAxoncomp(G4int i) {return fRadAxoncomp[i];}
167  G4double GetHeightAxoncomp(G4int i) {return fHeightAxoncomp[i];}
168  G4double GetDistAxonsoma (G4int i) {return fDistAxonsoma[i];}
169  G4RotationMatrix GetRotAxoncomp(G4int i) {return fRotAxoncomp[i];}
170 
171  G4int GetnbSpinecomp() {return fnbSpinecomp;}
172  G4double GetMassSpinecomp (G4int i) {return fMassSpinecomp[i];}
173  G4double GetMassSpineTot () {return fMassSpineTot;}
174  G4ThreeVector GetPosSpinecomp(G4int i) {return fPosSpinecomp[i];}
175  G4double GetRadSpinecomp(G4int i) {return fRadSpinecomp[i];}
176  G4double GetHeightSpinecomp(G4int i) {return fHeightSpinecomp[i];}
177  G4double GetDistSpinesoma (G4int i) {return fDistSpinesoma[i];}
178  G4RotationMatrix GetRotSpinecomp(G4int i) {return fRotSpinecomp[i];}
179 
180  G4int GetnbNeuroncomp() {return fnbNeuroncomp;}
181 
182  G4double GetTotVolNeuron() {return fTotVolNeuron;}
183  G4double GetTotSurfNeuron () {return fTotSurfNeuron;}
184  G4double GetTotMassNeuron () {return fTotMassNeuron;}
185  G4double GetTotVolSlice() {return fTotVolSlice;}
186  G4double GetTotSurfSlice () {return fTotSurfSlice;}
187  G4double GetTotMassSlice() {return fTotMassSlice;}
188  G4double GetTotVolMedium() {return fTotVolMedium;}
189  G4double GetTotSurfMedium() {return fTotSurfMedium;}
190  G4double GetTotMassMedium() {return fTotMassMedium;}
191 
192  G4VisAttributes GetSomaColour() {return fSomaColour;}
193  G4VisAttributes GetDendColour() {return fDendColour;}
194  G4VisAttributes GetAxonColour() {return fAxonColour;}
195  G4VisAttributes GetSpineColour() {return fSpineColour;}
196  G4VisAttributes GetNeuronColour() {return fNeuronColour;}
197 
198  private:
199 
201  G4String fNeuronFileNameSWC;
202  G4String fNeuronFileNameDATA;
203 
204  G4int fnbSomacomp;
205  G4int fnbDendritecomp;
206  G4int fnbAxoncomp;
207  G4int fnbSpinecomp;
208  G4int fnbNeuroncomp;
209 
210  G4int * fnNn ;
211  G4int * fpNn ;
212  //G4int * ftypeC;
213  G4int * fnNd ;
214  G4int * fpNd ;
215  G4int * fnNa ;
216  G4int * fpNa ;
217  G4int * fTypeN ;
218 
219  G4double fshiftX, fshiftY, fshiftZ; // shift in oder to center VOLUME!
220  G4double fwidthB;
221  G4double fheightB;
222  G4double fdepthB;
223  G4double fdiagnlLength; // diagonal and diameter
224 
225  G4ThreeVector * fPosSomacomp ;
226  G4double * fRadSomacomp ;
227  G4double * fMassSomacomp ;
228  G4double fMassSomaTot ;
229 
230  G4double * fRadDendcomp ;
231  G4double * fDistADendSoma ;
232  G4double * fDistBDendSoma ;
233  G4double * fHeightDendcomp ;
234  G4double * fMassDendcomp ;
235  G4double fMassDendTot ;
236  G4ThreeVector * fPosDendcomp ; // VOXEL COORDINATES OF DENDRITES
237  G4RotationMatrix * fRotDendcomp ; // RotationMatrix with Inverse
238 
239  G4double * fRadAxoncomp ;
240  G4double * fHeightAxoncomp ;
241  G4double * fDistAxonsoma ;
242  G4double * fMassAxoncomp ;
243  G4double fMassAxonTot ;
244  G4ThreeVector * fPosAxoncomp ; // VOXEL COORDINATES OF AXON
245  G4RotationMatrix * fRotAxoncomp ;
246 
247  G4double * fRadSpinecomp ;
248  G4double * fHeightSpinecomp ;
249  G4double * fDistSpinesoma ;
250  G4double * fMassSpinecomp ;
251  G4double fMassSpineTot ;
252  G4ThreeVector * fPosSpinecomp ; // VOXEL COORDINATES OF SPINE
253  G4RotationMatrix * fRotSpinecomp ;
254 
255  G4double * fRadNeuroncomp ;
256  G4double * fHeightNeuroncomp ;
257  G4double * fDistNeuronsoma ;
258  G4double * fMassNeuroncomp ;
259  //G4double fMassNeuronTot ;
260  G4ThreeVector * fPosNeuroncomp ; // VOXEL COORDINATES OF Neuron
261  G4RotationMatrix * fRotNeuroncomp ;
262 
263  G4double fTotVolNeuron ;
264  G4double fTotSurfNeuron ;
265  G4double fTotMassNeuron ;
266  G4double fTotVolSlice;
267  G4double fTotSurfSlice ;
268  G4double fTotMassSlice;
269  G4double fTotVolMedium ;
270  G4double fTotSurfMedium ;
271  G4double fTotMassMedium ;
272 
273  G4VisAttributes * fSomaColour;
274  G4VisAttributes * fDendColour;
275  G4VisAttributes * fAxonColour;
276  G4VisAttributes * fSpineColour;
277  G4VisAttributes * fNeuronColour;
278 
279  //G4Sphere* fsphereComp;
280  //G4Tubs* fcylinderConp;
281 
282  //NeuronLoadMessenger * fpNeuronMessenger;
283 
284 };
285 
286 #endif
287 
288