Import Geant4 11.2.1 source tree
This commit is contained in:
Gabriele Cosmo
@@ -43,6 +43,7 @@
|
||||
#ifndef NeuronLoadDataFile_H
|
||||
#define NeuronLoadDataFile_H 1
|
||||
|
||||
#include <vector>
|
||||
#include "G4ThreeVector.hh"
|
||||
#include "G4RotationMatrix.hh"
|
||||
#include "G4VSolid.hh"
|
||||
@@ -50,6 +51,7 @@
|
||||
#include "G4VisAttributes.hh"
|
||||
#include "G4Colour.hh"
|
||||
#include "G4SystemOfUnits.hh"
|
||||
|
||||
// Geant4 Constructive Solid Geometry (CSG)
|
||||
#include "G4VPVParameterisation.hh"
|
||||
#include "G4Box.hh" // bounding volume
|
||||
@@ -84,203 +86,144 @@ class NeuronLoadDataFile
|
||||
//: public G4VPVParameterisation
|
||||
|
||||
{
|
||||
public:
|
||||
NeuronLoadDataFile();
|
||||
virtual
|
||||
~NeuronLoadDataFile();
|
||||
public:
|
||||
NeuronLoadDataFile();
|
||||
~NeuronLoadDataFile() = default;
|
||||
|
||||
void SingleNeuronSWCfile(const G4String& filename);
|
||||
void NeuralNetworkDATAfile(const G4String& filename);
|
||||
|
||||
// position, rotation of solids
|
||||
void ComputeTransformation (const G4int copyNo,
|
||||
G4VPhysicalVolume* physVol) const;
|
||||
// Solid options: sphere or cylinder ...
|
||||
//G4VSolid* ComputeSolid (const G4int copyNo,
|
||||
// G4VPhysicalVolume* physiVol);
|
||||
// and ... for solids!
|
||||
void ComputeDimensions(G4Tubs& cylinderComp, const G4int copyNo,
|
||||
const G4VPhysicalVolume*) const ;
|
||||
void ComputeDimensions(G4Sphere& , const G4int ,
|
||||
const G4VPhysicalVolume*) const {}
|
||||
void ComputeDimensions(G4Ellipsoid& , const G4int ,
|
||||
const G4VPhysicalVolume*) const {}
|
||||
void ComputeDimensions(G4Box&, const G4int,
|
||||
const G4VPhysicalVolume*) const {}
|
||||
void ComputeDimensions(G4Cons&,const G4int,
|
||||
const G4VPhysicalVolume*) const {}
|
||||
void ComputeDimensions(G4Hype &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const {}
|
||||
void ComputeDimensions(G4Trd &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const {}
|
||||
void ComputeDimensions(G4Trap &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const {}
|
||||
void ComputeDimensions(G4Orb &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const {}
|
||||
void ComputeDimensions(G4Torus &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const {}
|
||||
void ComputeDimensions(G4Para &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const {}
|
||||
void ComputeDimensions(G4Polycone &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const {}
|
||||
void ComputeDimensions(G4Polyhedra &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const {}
|
||||
|
||||
G4double GetwidthB () {return fwidthB;}
|
||||
G4double GetheightB () {return fheightB;}
|
||||
G4double GetdepthB () {return fdepthB;}
|
||||
G4double GetdiagnlLength () {return fdiagnlLength;}
|
||||
G4double GetshiftX () {return fshiftX;}
|
||||
G4double GetshiftY () {return fshiftY;}
|
||||
G4double GetshiftZ () {return fshiftZ;}
|
||||
G4double GetTypeN (G4int i) {return fTypeN[i];}
|
||||
|
||||
G4int GetnbSomacomp() {return fnbSomacomp;}
|
||||
G4double GetMassSomacomp (G4int i) {return fMassSomacomp[i];}
|
||||
G4double GetMassSomaTot () {return fMassSomaTot;}
|
||||
G4ThreeVector GetPosSomacomp(G4int i) {return fPosSomacomp[i];}
|
||||
G4double GetRadSomacomp(G4int i) {return fRadSomacomp[i];}
|
||||
|
||||
G4int GetnbDendritecomp() {return fnbDendritecomp;}
|
||||
G4double GetMassDendcomp (G4int i) {return fMassDendcomp[i];}
|
||||
G4double GetMassDendTot () {return fMassDendTot;}
|
||||
G4ThreeVector GetPosDendcomp(G4int i) {return fPosDendcomp[i];}
|
||||
G4double GetRadDendcomp(G4int i) {return fRadDendcomp[i];}
|
||||
G4double GetHeightDendcomp(G4int i) {return fHeightDendcomp[i];}
|
||||
G4double GetDistADendSoma (G4int i) {return fDistADendSoma[i];}
|
||||
G4double GetDistBDendSoma (G4int i) {return fDistBDendSoma[i];}
|
||||
G4RotationMatrix GetRotDendcomp(G4int i) {return fRotDendcomp[i];}
|
||||
|
||||
G4int GetnbAxoncomp() {return fnbAxoncomp;}
|
||||
G4double GetMassAxoncomp (G4int i) {return fMassAxoncomp[i];}
|
||||
G4double GetMassAxonTot () {return fMassAxonTot;}
|
||||
G4ThreeVector GetPosAxoncomp(G4int i) {return fPosAxoncomp[i];}
|
||||
G4double GetRadAxoncomp(G4int i) {return fRadAxoncomp[i];}
|
||||
G4double GetHeightAxoncomp(G4int i) {return fHeightAxoncomp[i];}
|
||||
G4double GetDistAxonsoma (G4int i) {return fDistAxonsoma[i];}
|
||||
G4RotationMatrix GetRotAxoncomp(G4int i) {return fRotAxoncomp[i];}
|
||||
|
||||
G4int GetnbSpinecomp() {return fnbSpinecomp;}
|
||||
G4double GetMassSpinecomp (G4int i) {return fMassSpinecomp[i];}
|
||||
G4double GetMassSpineTot () {return fMassSpineTot;}
|
||||
G4ThreeVector GetPosSpinecomp(G4int i) {return fPosSpinecomp[i];}
|
||||
G4double GetRadSpinecomp(G4int i) {return fRadSpinecomp[i];}
|
||||
G4double GetHeightSpinecomp(G4int i) {return fHeightSpinecomp[i];}
|
||||
G4double GetDistSpinesoma (G4int i) {return fDistSpinesoma[i];}
|
||||
G4RotationMatrix GetRotSpinecomp(G4int i) {return fRotSpinecomp[i];}
|
||||
|
||||
G4int GetnbNeuroncomp() {return fnbNeuroncomp;}
|
||||
// position, rotation of solids
|
||||
void ComputeTransformation (const G4int copyNo,
|
||||
G4VPhysicalVolume* physVol) const;
|
||||
|
||||
G4double GetTotVolNeuron() {return fTotVolNeuron;}
|
||||
G4double GetTotSurfNeuron () {return fTotSurfNeuron;}
|
||||
G4double GetTotMassNeuron () {return fTotMassNeuron;}
|
||||
G4double GetTotVolSlice() {return fTotVolSlice;}
|
||||
G4double GetTotSurfSlice () {return fTotSurfSlice;}
|
||||
G4double GetTotMassSlice() {return fTotMassSlice;}
|
||||
G4double GetTotVolMedium() {return fTotVolMedium;}
|
||||
G4double GetTotSurfMedium() {return fTotSurfMedium;}
|
||||
G4double GetTotMassMedium() {return fTotMassMedium;}
|
||||
void ComputeDimensions(G4Tubs& cylinderComp, const G4int copyNo,
|
||||
const G4VPhysicalVolume*) const;
|
||||
G4double GetwidthB() const { return fwidthB; }
|
||||
G4double GetheightB() const { return fheightB; }
|
||||
G4double GetdepthB() const { return fdepthB; }
|
||||
G4double GetdiagnlLength() const { return fdiagnlLength;}
|
||||
G4double GetshiftX() const { return fshiftX; }
|
||||
G4double GetshiftY() const { return fshiftY; }
|
||||
G4double GetshiftZ() const { return fshiftZ; }
|
||||
G4double GetTypeN(G4int i) { return fTypeN[i]; }
|
||||
|
||||
G4int GetnbSomacomp() const { return fnbSomacomp; }
|
||||
G4double GetMassSomacomp(G4int i) const { return fMassSomacomp[i]; }
|
||||
G4double GetMassSomaTot() { return fMassSomaTot; }
|
||||
G4ThreeVector GetPosSomacomp(G4int i) const { return fPosSomacomp[i]; }
|
||||
G4double GetRadSomacomp(G4int i) const { return fRadSomacomp[i]; }
|
||||
|
||||
G4int GetnbDendritecomp() const { return fnbDendritecomp; }
|
||||
G4double GetMassDendcomp(G4int i) const { return fMassDendcomp[i]; }
|
||||
G4double GetMassDendTot() { return fMassDendTot; }
|
||||
G4ThreeVector GetPosDendcomp(G4int i) const { return fPosDendcomp[i]; }
|
||||
G4double GetRadDendcomp(G4int i) const { return fRadDendcomp[i]; }
|
||||
G4double GetHeightDendcomp(G4int i) const { return fHeightDendcomp[i]; }
|
||||
G4double GetDistADendSoma(G4int i) const { return fDistADendSoma[i]; }
|
||||
G4double GetDistBDendSoma(G4int i) const { return fDistBDendSoma[i]; }
|
||||
G4RotationMatrix GetRotDendcomp(G4int i) const { return fRotDendcomp[i]; }
|
||||
|
||||
G4int GetnbAxoncomp() const { return fnbAxoncomp; }
|
||||
G4double GetMassAxoncomp (G4int i) const { return fMassAxoncomp[i]; }
|
||||
G4double GetMassAxonTot() const { return fMassAxonTot; }
|
||||
G4ThreeVector GetPosAxoncomp(G4int i) const { return fPosAxoncomp[i]; }
|
||||
G4double GetRadAxoncomp(G4int i) const { return fRadAxoncomp[i]; }
|
||||
G4double GetHeightAxoncomp(G4int i) const { return fHeightAxoncomp[i]; }
|
||||
G4double GetDistAxonsoma(G4int i) const { return fDistAxonsoma[i]; }
|
||||
G4RotationMatrix GetRotAxoncomp(G4int i) const { return fRotAxoncomp[i]; }
|
||||
|
||||
G4VisAttributes GetSomaColour() {return fSomaColour;}
|
||||
G4VisAttributes GetDendColour() {return fDendColour;}
|
||||
G4VisAttributes GetAxonColour() {return fAxonColour;}
|
||||
G4VisAttributes GetSpineColour() {return fSpineColour;}
|
||||
G4VisAttributes GetNeuronColour() {return fNeuronColour;}
|
||||
G4int GetnbSpinecomp() const { return fnbSpinecomp; }
|
||||
G4double GetMassSpinecomp (G4int i) const { return fMassSpinecomp[i]; }
|
||||
G4double GetMassSpineTot() const { return fMassSpineTot; }
|
||||
G4ThreeVector GetPosSpinecomp(G4int i) const { return fPosSpinecomp[i]; }
|
||||
G4double GetRadSpinecomp(G4int i) const { return fRadSpinecomp[i]; }
|
||||
G4double GetHeightSpinecomp(G4int i) const { return fHeightSpinecomp[i]; }
|
||||
G4double GetDistSpinesoma (G4int i) {return fDistSpinesoma[i];}
|
||||
G4RotationMatrix GetRotSpinecomp(G4int i) const { return fRotSpinecomp[i]; }
|
||||
|
||||
G4int GetnbNeuroncomp() const { return fnbNeuroncomp; }
|
||||
|
||||
private:
|
||||
G4double GetTotVolNeuron() const { return fTotVolNeuron; }
|
||||
G4double GetTotSurfNeuron() const { return fTotSurfNeuron; }
|
||||
G4double GetTotMassNeuron() const { return fTotMassNeuron; }
|
||||
G4double GetTotVolSlice() const { return fTotVolSlice; }
|
||||
G4double GetTotSurfSlice() const { return fTotSurfSlice; }
|
||||
G4double GetTotMassSlice() const { return fTotMassSlice; }
|
||||
G4double GetTotVolMedium() const { return fTotVolMedium; }
|
||||
G4double GetTotSurfMedium() const { return fTotSurfMedium; }
|
||||
G4double GetTotMassMedium() const { return fTotMassMedium; }
|
||||
|
||||
private:
|
||||
|
||||
//! NEURON filename
|
||||
G4String fNeuronFileNameSWC;
|
||||
G4String fNeuronFileNameDATA;
|
||||
|
||||
G4int fnbSomacomp;
|
||||
G4int fnbDendritecomp;
|
||||
G4int fnbAxoncomp;
|
||||
G4int fnbSpinecomp;
|
||||
G4int fnbNeuroncomp;
|
||||
G4int fnbSomacomp{0};
|
||||
G4int fnbDendritecomp{0};
|
||||
G4int fnbAxoncomp{0};
|
||||
G4int fnbSpinecomp{0};
|
||||
G4int fnbNeuroncomp{0};
|
||||
|
||||
G4int * fnNn ;
|
||||
G4int * fpNn ;
|
||||
//G4int * ftypeC;
|
||||
G4int * fnNd ;
|
||||
G4int * fpNd ;
|
||||
G4int * fnNa ;
|
||||
G4int * fpNa ;
|
||||
G4int * fTypeN ;
|
||||
std::vector<G4int> fTypeN;
|
||||
|
||||
G4double fshiftX, fshiftY, fshiftZ; // shift in oder to center VOLUME!
|
||||
G4double fwidthB;
|
||||
G4double fheightB;
|
||||
G4double fdepthB;
|
||||
G4double fdiagnlLength; // diagonal and diameter
|
||||
|
||||
G4ThreeVector * fPosSomacomp ;
|
||||
G4double * fRadSomacomp ;
|
||||
G4double * fMassSomacomp ;
|
||||
G4double fMassSomaTot ;
|
||||
|
||||
G4double * fRadDendcomp ;
|
||||
G4double * fDistADendSoma ;
|
||||
G4double * fDistBDendSoma ;
|
||||
G4double * fHeightDendcomp ;
|
||||
G4double * fMassDendcomp ;
|
||||
G4double fMassDendTot ;
|
||||
G4ThreeVector * fPosDendcomp ; // VOXEL COORDINATES OF DENDRITES
|
||||
G4RotationMatrix * fRotDendcomp ; // RotationMatrix with Inverse
|
||||
// shift in oder to center VOLUME!
|
||||
G4double fshiftX{0.0};
|
||||
G4double fshiftY{0.0};
|
||||
G4double fshiftZ{0.0};
|
||||
G4double fwidthB{0.0};
|
||||
G4double fheightB{0.0};
|
||||
G4double fdepthB{0.0};
|
||||
G4double fdiagnlLength{0.0}; // diagonal and diameter
|
||||
|
||||
G4double * fRadAxoncomp ;
|
||||
G4double * fHeightAxoncomp ;
|
||||
G4double * fDistAxonsoma ;
|
||||
G4double * fMassAxoncomp ;
|
||||
G4double fMassAxonTot ;
|
||||
G4ThreeVector * fPosAxoncomp ; // VOXEL COORDINATES OF AXON
|
||||
G4RotationMatrix * fRotAxoncomp ;
|
||||
G4double fMassSomaTot{0.0};
|
||||
G4double fMassDendTot{0.0};
|
||||
G4double fMassAxonTot{0.0};
|
||||
G4double fMassSpineTot{0.0};
|
||||
|
||||
G4double * fRadSpinecomp ;
|
||||
G4double * fHeightSpinecomp ;
|
||||
G4double * fDistSpinesoma ;
|
||||
G4double * fMassSpinecomp ;
|
||||
G4double fMassSpineTot ;
|
||||
G4ThreeVector * fPosSpinecomp ; // VOXEL COORDINATES OF SPINE
|
||||
G4RotationMatrix * fRotSpinecomp ;
|
||||
G4double fTotVolNeuron{0.0};
|
||||
G4double fTotSurfNeuron{0.0};
|
||||
G4double fTotMassNeuron{0.0};
|
||||
G4double fTotVolSlice{0.0};
|
||||
G4double fTotSurfSlice{0.0};
|
||||
G4double fTotMassSlice{0.0};
|
||||
G4double fTotVolMedium{0.0};
|
||||
G4double fTotSurfMedium{0.0};
|
||||
G4double fTotMassMedium{0.0};
|
||||
|
||||
std::vector<G4ThreeVector> fPosSomacomp;
|
||||
std::vector<G4double> fRadSomacomp;
|
||||
std::vector<G4double> fMassSomacomp;
|
||||
|
||||
std::vector<G4double> fRadDendcomp;
|
||||
std::vector<G4double> fDistADendSoma;
|
||||
std::vector<G4double> fDistBDendSoma;
|
||||
std::vector<G4double> fHeightDendcomp;
|
||||
std::vector<G4double> fMassDendcomp;
|
||||
std::vector<G4ThreeVector> fPosDendcomp; // VOXEL COORDINATES OF DENDRITES
|
||||
std::vector<G4RotationMatrix> fRotDendcomp; // RotationMatrix with Inverse
|
||||
|
||||
std::vector<G4double> fRadAxoncomp;
|
||||
std::vector<G4double> fHeightAxoncomp;
|
||||
std::vector<G4double> fDistAxonsoma;
|
||||
std::vector<G4double> fMassAxoncomp;
|
||||
std::vector<G4ThreeVector> fPosAxoncomp; // VOXEL COORDINATES OF AXON
|
||||
std::vector<G4RotationMatrix> fRotAxoncomp;
|
||||
|
||||
std::vector<G4double> fRadSpinecomp;
|
||||
std::vector<G4double> fHeightSpinecomp;
|
||||
std::vector<G4double> fDistSpinesoma;
|
||||
std::vector<G4double> fMassSpinecomp;
|
||||
std::vector<G4ThreeVector> fPosSpinecomp; // VOXEL COORDINATES OF SPINE
|
||||
std::vector<G4RotationMatrix> fRotSpinecomp;
|
||||
|
||||
G4double * fRadNeuroncomp ;
|
||||
G4double * fHeightNeuroncomp ;
|
||||
G4double * fDistNeuronsoma ;
|
||||
G4double * fMassNeuroncomp ;
|
||||
//G4double fMassNeuronTot ;
|
||||
G4ThreeVector * fPosNeuroncomp ; // VOXEL COORDINATES OF Neuron
|
||||
G4RotationMatrix * fRotNeuroncomp ;
|
||||
|
||||
G4double fTotVolNeuron ;
|
||||
G4double fTotSurfNeuron ;
|
||||
G4double fTotMassNeuron ;
|
||||
G4double fTotVolSlice;
|
||||
G4double fTotSurfSlice ;
|
||||
G4double fTotMassSlice;
|
||||
G4double fTotVolMedium ;
|
||||
G4double fTotSurfMedium ;
|
||||
G4double fTotMassMedium ;
|
||||
|
||||
G4VisAttributes * fSomaColour;
|
||||
G4VisAttributes * fDendColour;
|
||||
G4VisAttributes * fAxonColour;
|
||||
G4VisAttributes * fSpineColour;
|
||||
G4VisAttributes * fNeuronColour;
|
||||
|
||||
//G4Sphere* fsphereComp;
|
||||
//G4Tubs* fcylinderConp;
|
||||
|
||||
//NeuronLoadMessenger * fpNeuronMessenger;
|
||||
|
||||
std::vector<G4double> fRadNeuroncomp;
|
||||
std::vector<G4double> fHeightNeuroncomp;
|
||||
std::vector<G4double> fDistNeuronsoma;
|
||||
std::vector<G4double> fMassNeuroncomp;
|
||||
std::vector<G4ThreeVector> fPosNeuroncomp; // VOXEL COORDINATES OF Neuron
|
||||
std::vector<G4RotationMatrix> fRotNeuroncomp;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
Reference in New Issue
Block a user