MicrostructureSingleFiber.h

/*
 * MicrostructureSingleFiber.h
 *
 *  Created on: Jan 22, 2010
 *      Author: dpflug
 */
 
 
/*
 *  JEMRIS Copyright (C) 
 *                        2006-2025  Tony Stoecker
 *                        2007-2018  Kaveh Vahedipour
 *                        2009-2019  Daniel Pflugfelder
 *                                  
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 */
 
#ifndef MICROSTRUCTURESINGLEFIBER_H_
#define MICROSTRUCTURESINGLEFIBER_H_
 
#include "Microstructure.h"
#include <vector>
 
class MicrostructureSingleFiber: public Microstructure {
public:
        MicrostructureSingleFiber();
        virtual ~MicrostructureSingleFiber();
 
        void SetFiberOrientation(double dx,double dy,double dz);
 
        void SetCylinderDensity(double density){if((density>0) && (density<1)) m_cyl_dens = density; else cout <<"density must be between 0 and 1!"<<endl;};
 
        void SetCylinderRadius(double inner, double outer=0) {m_cyl_radius_inner = inner; if (outer > inner) m_cyl_radius_outer=outer; else m_cyl_radius_outer=inner;};
 
        void SetRadiusDistribution(string filename);
        void SetRadiusDistribution(double alpha, double beta, double rmax);
 
        void SetSeed(int val) {m_seed = val;}
 
        void SetD(double D,int index) {m_D[index]=D;};
 
        void GenerateStructure();
 
        virtual void IndexObject(triple pos,  int &LastId ,int &shellid);
 
        virtual double GetD(int LastId,int shellid);
 
        void SetAxonToNeuronRadiusRatio(double ratio) {m_myelin_axon_ratio=ratio;};
 
        /*
         * @brief Dump microstructure to file
         */
        void DumpStructure();
 
protected:
 
        virtual bool    CylinderCollide(const neuron &test);            /* test if this neuron is overlapping with any other in structure. */
        double  GetCylinderVolume(const neuron &test);  /* calculate volume of cylinder in box.  */
        double GetPointDistance(const triple pos, const neuron &tmp);
 
        double GetCylinderDistance(const neuron&n1, const neuron&n2);
        virtual void SetCylOrientation(neuron &tmp) {tmp.dx = m_fiber_orientation[0];tmp.dy = m_fiber_orientation[1];tmp.dz = m_fiber_orientation[2];};
 
        void CalcPercentiles();
 
        void GetRadius(neuron &tmp,const double complete_vol, const double used_vol);
 
 
        double m_fiber_orientation[3];          
        double m_cyl_dens;                      
        double m_cyl_radius_inner;              
        double m_cyl_radius_outer;              
        double m_D[2];                          
        vector<neuron> m_axons;                 
        int m_seed;                             
        /* variables for axon radius distribution */
        bool m_use_var_rad;             
        vector<int> m_percentiles;      
        vector<double> m_radius_axis;   
        vector<double> m_radius_hist;   
        double m_myelin_axon_ratio;     
        double m_extracellular_spacing; 
};
 
#endif /* MICROSTRUCTURESINGLEFIBER_H_ */