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db49709b532cdbe4a21775b0b28ce7fdf435e735
geant4/examples/extended/medical/dna/neuron/include/NeuronLoadDataFile.hh
T
Gabriele Cosmo db49709b53 Import Geant4 10.5.0 source tree
2018-12-07 15:15:39 +01:00

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//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// This example is provided by the Geant4-DNA collaboration
// Any report or published results obtained using the Geant4-DNA software
// shall cite the following Geant4-DNA collaboration publication:
// Med. Phys. 37 (2010) 4692-4708
// and papers
// M. Batmunkh et al. J Radiat Res Appl Sci 8 (2015) 498-507
// O. Belov et al. Physica Medica 32 (2016) 1510-1520
// The Geant4-DNA web site is available at http://geant4-dna.org
//
// -------------------------------------------------------------------
// November 2016
// -------------------------------------------------------------------
//
//
/// \file NeuronLoadDataFile.hh
/// \brief Implementation of the NeuronLoadDataFile class
#ifndef NeuronLoadDataFile_H
#define NeuronLoadDataFile_H 1
#include "G4ThreeVector.hh"
#include "G4RotationMatrix.hh"
#include "G4VSolid.hh"
#include "G4Material.hh"
#include "G4VisAttributes.hh"
#include "G4Colour.hh"
#include "G4SystemOfUnits.hh"
// Geant4 Constructive Solid Geometry (CSG)
#include "G4VPVParameterisation.hh"
#include "G4Box.hh" // bounding volume
#include "G4Tubs.hh" // axon, dendrite compartments
#include "G4Sphere.hh" // soma compartments
#include "G4Ellipsoid.hh" // soma compartments
#include "G4Trd.hh"
#include "G4Trap.hh"
#include "G4Cons.hh" // stubby spine, filopodia
#include "G4EllipticalTube.hh"
#include "G4EllipticalCone.hh"
#include "G4Orb.hh" // mushroom spine
#include "G4Torus.hh"
#include "G4Para.hh"
#include "G4Polycone.hh"
#include "G4Polyhedra.hh"
#include "G4Hype.hh" // thin spine neck
#include "G4Tet.hh"
#include "G4TwistedBox.hh"
#include "G4TwistedTrap.hh"
#include "G4TwistedTrd.hh"
#include "G4TwistedTubs.hh"
//class NeuronLoadMessenger;
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
class NeuronLoadDataFile
// default - G4PVPlacement volume
// if use G4PVParameterised volume,
// please enable following G4VPVParameterisation class!
//: public G4VPVParameterisation
{
public:
NeuronLoadDataFile();
virtual
~NeuronLoadDataFile();
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;}
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;}
G4VisAttributes GetSomaColour() {return fSomaColour;}
G4VisAttributes GetDendColour() {return fDendColour;}
G4VisAttributes GetAxonColour() {return fAxonColour;}
G4VisAttributes GetSpineColour() {return fSpineColour;}
G4VisAttributes GetNeuronColour() {return fNeuronColour;}
private:
//! NEURON filename
G4String fNeuronFileNameSWC;
G4String fNeuronFileNameDATA;
G4int fnbSomacomp;
G4int fnbDendritecomp;
G4int fnbAxoncomp;
G4int fnbSpinecomp;
G4int fnbNeuroncomp;
G4int * fnNn ;
G4int * fpNn ;
//G4int * ftypeC;
G4int * fnNd ;
G4int * fpNd ;
G4int * fnNa ;
G4int * fpNa ;
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
G4double * fRadAxoncomp ;
G4double * fHeightAxoncomp ;
G4double * fDistAxonsoma ;
G4double * fMassAxoncomp ;
G4double fMassAxonTot ;
G4ThreeVector * fPosAxoncomp ; // VOXEL COORDINATES OF AXON
G4RotationMatrix * fRotAxoncomp ;
G4double * fRadSpinecomp ;
G4double * fHeightSpinecomp ;
G4double * fDistSpinesoma ;
G4double * fMassSpinecomp ;
G4double fMassSpineTot ;
G4ThreeVector * fPosSpinecomp ; // VOXEL COORDINATES OF SPINE
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;
};
#endif
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