Gabriele Cosmo
232 lines
9.2 KiB
C++
232 lines
9.2 KiB
C++
//
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// ********************************************************************
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// * License and Disclaimer *
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// * *
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// * The Geant4 software is copyright of the Copyright Holders of *
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// * the Geant4 Collaboration. It is provided under the terms and *
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// * conditions of the Geant4 Software License, included in the file *
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// * LICENSE and available at http://cern.ch/geant4/license . These *
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// * include a list of copyright holders. *
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// * *
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// * Neither the authors of this software system, nor their employing *
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// * institutes,nor the agencies providing financial support for this *
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// * work make any representation or warranty, express or implied, *
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// * regarding this software system or assume any liability for its *
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// * use. Please see the license in the file LICENSE and URL above *
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// * for the full disclaimer and the limitation of liability. *
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// * *
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// * This code implementation is the result of the scientific and *
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// * technical work of the GEANT4 collaboration. *
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// * By using, copying, modifying or distributing the software (or *
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// * any work based on the software) you agree to acknowledge its *
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// * use in resulting scientific publications, and indicate your *
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// * acceptance of all terms of the Geant4 Software license. *
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// ********************************************************************
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//
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// This example is provided by the Geant4-DNA collaboration
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// Any report or published results obtained using the Geant4-DNA software
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// shall cite the following Geant4-DNA collaboration publication:
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// Med. Phys. 37 (2010) 4692-4708
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// and papers
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// M. Batmunkh et al. J Radiat Res Appl Sci 8 (2015) 498-507
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// O. Belov et al. Physica Medica 32 (2016) 1510-1520
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// The Geant4-DNA web site is available at http://geant4-dna.org
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//
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// -------------------------------------------------------------------
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// November 2016
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// -------------------------------------------------------------------
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//
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//
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/// \file NeuronLoadDataFile.hh
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/// \brief Implementation of the NeuronLoadDataFile class
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#ifndef NeuronLoadDataFile_H
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#define NeuronLoadDataFile_H 1
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#include <vector>
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#include "G4ThreeVector.hh"
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#include "G4RotationMatrix.hh"
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#include "G4VSolid.hh"
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#include "G4Material.hh"
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#include "G4VisAttributes.hh"
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#include "G4Colour.hh"
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#include "G4SystemOfUnits.hh"
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// Geant4 Constructive Solid Geometry (CSG)
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#include "G4VPVParameterisation.hh"
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#include "G4Box.hh" // bounding volume
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#include "G4Tubs.hh" // axon, dendrite compartments
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#include "G4Sphere.hh" // soma compartments
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#include "G4Ellipsoid.hh" // soma compartments
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#include "G4Trd.hh"
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#include "G4Trap.hh"
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#include "G4Cons.hh" // stubby spine, filopodia
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#include "G4EllipticalTube.hh"
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#include "G4EllipticalCone.hh"
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#include "G4Orb.hh" // mushroom spine
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#include "G4Torus.hh"
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#include "G4Para.hh"
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#include "G4Polycone.hh"
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#include "G4Polyhedra.hh"
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#include "G4Hype.hh" // thin spine neck
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#include "G4Tet.hh"
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#include "G4TwistedBox.hh"
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#include "G4TwistedTrap.hh"
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#include "G4TwistedTrd.hh"
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#include "G4TwistedTubs.hh"
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//class NeuronLoadMessenger;
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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class NeuronLoadDataFile
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// default - G4PVPlacement volume
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// if use G4PVParameterised volume,
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// please enable following G4VPVParameterisation class!
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//: public G4VPVParameterisation
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{
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public:
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NeuronLoadDataFile();
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~NeuronLoadDataFile() = default;
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void SingleNeuronSWCfile(const G4String& filename);
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void NeuralNetworkDATAfile(const G4String& filename);
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// position, rotation of solids
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void ComputeTransformation (const G4int copyNo,
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G4VPhysicalVolume* physVol) const;
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void ComputeDimensions(G4Tubs& cylinderComp, const G4int copyNo,
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const G4VPhysicalVolume*) const;
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G4double GetwidthB() const { return fwidthB; }
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G4double GetheightB() const { return fheightB; }
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G4double GetdepthB() const { return fdepthB; }
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G4double GetdiagnlLength() const { return fdiagnlLength;}
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G4double GetshiftX() const { return fshiftX; }
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G4double GetshiftY() const { return fshiftY; }
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G4double GetshiftZ() const { return fshiftZ; }
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G4double GetTypeN(G4int i) { return fTypeN[i]; }
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G4int GetnbSomacomp() const { return fnbSomacomp; }
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G4double GetMassSomacomp(G4int i) const { return fMassSomacomp[i]; }
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G4double GetMassSomaTot() { return fMassSomaTot; }
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G4ThreeVector GetPosSomacomp(G4int i) const { return fPosSomacomp[i]; }
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G4double GetRadSomacomp(G4int i) const { return fRadSomacomp[i]; }
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G4int GetnbDendritecomp() const { return fnbDendritecomp; }
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G4double GetMassDendcomp(G4int i) const { return fMassDendcomp[i]; }
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G4double GetMassDendTot() { return fMassDendTot; }
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G4ThreeVector GetPosDendcomp(G4int i) const { return fPosDendcomp[i]; }
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G4double GetRadDendcomp(G4int i) const { return fRadDendcomp[i]; }
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G4double GetHeightDendcomp(G4int i) const { return fHeightDendcomp[i]; }
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G4double GetDistADendSoma(G4int i) const { return fDistADendSoma[i]; }
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G4double GetDistBDendSoma(G4int i) const { return fDistBDendSoma[i]; }
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G4RotationMatrix GetRotDendcomp(G4int i) const { return fRotDendcomp[i]; }
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G4int GetnbAxoncomp() const { return fnbAxoncomp; }
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G4double GetMassAxoncomp (G4int i) const { return fMassAxoncomp[i]; }
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G4double GetMassAxonTot() const { return fMassAxonTot; }
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G4ThreeVector GetPosAxoncomp(G4int i) const { return fPosAxoncomp[i]; }
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G4double GetRadAxoncomp(G4int i) const { return fRadAxoncomp[i]; }
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G4double GetHeightAxoncomp(G4int i) const { return fHeightAxoncomp[i]; }
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G4double GetDistAxonsoma(G4int i) const { return fDistAxonsoma[i]; }
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G4RotationMatrix GetRotAxoncomp(G4int i) const { return fRotAxoncomp[i]; }
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G4int GetnbSpinecomp() const { return fnbSpinecomp; }
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G4double GetMassSpinecomp (G4int i) const { return fMassSpinecomp[i]; }
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G4double GetMassSpineTot() const { return fMassSpineTot; }
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G4ThreeVector GetPosSpinecomp(G4int i) const { return fPosSpinecomp[i]; }
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G4double GetRadSpinecomp(G4int i) const { return fRadSpinecomp[i]; }
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G4double GetHeightSpinecomp(G4int i) const { return fHeightSpinecomp[i]; }
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G4double GetDistSpinesoma (G4int i) {return fDistSpinesoma[i];}
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G4RotationMatrix GetRotSpinecomp(G4int i) const { return fRotSpinecomp[i]; }
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G4int GetnbNeuroncomp() const { return fnbNeuroncomp; }
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G4double GetTotVolNeuron() const { return fTotVolNeuron; }
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G4double GetTotSurfNeuron() const { return fTotSurfNeuron; }
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G4double GetTotMassNeuron() const { return fTotMassNeuron; }
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G4double GetTotVolSlice() const { return fTotVolSlice; }
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G4double GetTotSurfSlice() const { return fTotSurfSlice; }
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G4double GetTotMassSlice() const { return fTotMassSlice; }
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G4double GetTotVolMedium() const { return fTotVolMedium; }
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G4double GetTotSurfMedium() const { return fTotSurfMedium; }
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G4double GetTotMassMedium() const { return fTotMassMedium; }
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private:
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//! NEURON filename
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G4String fNeuronFileNameSWC;
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G4String fNeuronFileNameDATA;
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G4int fnbSomacomp{0};
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G4int fnbDendritecomp{0};
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G4int fnbAxoncomp{0};
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G4int fnbSpinecomp{0};
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G4int fnbNeuroncomp{0};
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std::vector<G4int> fTypeN;
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// shift in oder to center VOLUME!
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G4double fshiftX{0.0};
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G4double fshiftY{0.0};
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G4double fshiftZ{0.0};
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G4double fwidthB{0.0};
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G4double fheightB{0.0};
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G4double fdepthB{0.0};
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G4double fdiagnlLength{0.0}; // diagonal and diameter
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G4double fMassSomaTot{0.0};
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G4double fMassDendTot{0.0};
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G4double fMassAxonTot{0.0};
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G4double fMassSpineTot{0.0};
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G4double fTotVolNeuron{0.0};
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G4double fTotSurfNeuron{0.0};
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G4double fTotMassNeuron{0.0};
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G4double fTotVolSlice{0.0};
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G4double fTotSurfSlice{0.0};
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G4double fTotMassSlice{0.0};
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G4double fTotVolMedium{0.0};
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G4double fTotSurfMedium{0.0};
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G4double fTotMassMedium{0.0};
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std::vector<G4ThreeVector> fPosSomacomp;
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std::vector<G4double> fRadSomacomp;
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std::vector<G4double> fMassSomacomp;
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std::vector<G4double> fRadDendcomp;
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std::vector<G4double> fDistADendSoma;
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std::vector<G4double> fDistBDendSoma;
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std::vector<G4double> fHeightDendcomp;
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std::vector<G4double> fMassDendcomp;
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std::vector<G4ThreeVector> fPosDendcomp; // VOXEL COORDINATES OF DENDRITES
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std::vector<G4RotationMatrix> fRotDendcomp; // RotationMatrix with Inverse
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std::vector<G4double> fRadAxoncomp;
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std::vector<G4double> fHeightAxoncomp;
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std::vector<G4double> fDistAxonsoma;
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std::vector<G4double> fMassAxoncomp;
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std::vector<G4ThreeVector> fPosAxoncomp; // VOXEL COORDINATES OF AXON
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std::vector<G4RotationMatrix> fRotAxoncomp;
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std::vector<G4double> fRadSpinecomp;
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std::vector<G4double> fHeightSpinecomp;
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std::vector<G4double> fDistSpinesoma;
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std::vector<G4double> fMassSpinecomp;
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std::vector<G4ThreeVector> fPosSpinecomp; // VOXEL COORDINATES OF SPINE
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std::vector<G4RotationMatrix> fRotSpinecomp;
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std::vector<G4double> fRadNeuroncomp;
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std::vector<G4double> fHeightNeuroncomp;
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std::vector<G4double> fDistNeuronsoma;
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std::vector<G4double> fMassNeuroncomp;
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std::vector<G4ThreeVector> fPosNeuroncomp; // VOXEL COORDINATES OF Neuron
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std::vector<G4RotationMatrix> fRotNeuroncomp;
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};
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#endif
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