Microstructure consisting of parallel cylinders. More...

#include <MicrostructureSingleFiber.h>

Inheritance diagram for MicrostructureSingleFiber:

Collaboration diagram for MicrostructureSingleFiber:

Public Member Functions
void	SetFiberOrientation (double dx, double dy, double dz)
	set cylinder orientation

void	SetCylinderDensity (double density)
	Set Cylinder Density;.

void	SetCylinderRadius (double inner, double outer=0)
	Set Cylinder Radius;.

void	SetRadiusDistribution (string filename)
	Set axon radius distribution, string: -> filename, three doubles: distribution from AxCaliber (Assaf 2008 MagResMed.); alpha, beta, cutoffradius.

void	SetRadiusDistribution (double alpha, double beta, double rmax)

void	SetSeed (int val)
	Set seed for random number generator.

void	SetD (double D, int index)
	Set Diffusion constants.

void	GenerateStructure ()
	builds Structure

virtual void	IndexObject (triple pos, int &LastId, int &shellid)

virtual double	GetD (int LastId, int shellid)

void	SetAxonToNeuronRadiusRatio (double ratio)
	sets ratio axon/(axion + myelin sheet). Needed if radius distribution of neurons is used

void	DumpStructure ()

Public Member Functions inherited from Microstructure
void	SetExternalDiffusionConstant (double d)

bool	isInsideBox (triple pos)

triple	PeriodicBoundary (triple trialpos)

void	SetBoxSize (double size)

double	GetBoxSize ()

Protected Member Functions
virtual bool	CylinderCollide (const neuron &test)

double	GetCylinderVolume (const neuron &test)

double	GetPointDistance (const triple pos, const neuron &tmp)
	Get distance between point pos and cylinder tmp.

double	GetCylinderDistance (const neuron &n1, const neuron &n2)
	Get distance between two cylinders.

virtual void	SetCylOrientation (neuron &tmp)
	sets orientation of cyl in GenerateStructure.

void	CalcPercentiles ()
	if radius distribution is used: calculate compartments (begin with largest radii, then fill up with smaller ones.)

void	GetRadius (neuron &tmp, const double complete_vol, const double used_vol)
	Get a trial axon radius.

Protected Attributes
double	m_fiber_orientation [3]
	orientation of cylinders

double	m_cyl_dens
	density of cylinders

double	m_cyl_radius_inner
	inner radius of cylinders

double	m_cyl_radius_outer
	outer radius of cylinders

double	m_D [2]
	diffusion constants per layer

vector< neuron >	m_axons
	container holding the neurons.

int	m_seed
	random number seed

bool	m_use_var_rad
	true for variable radius distribution

vector< int >	m_percentiles
	compartment indices (first place axons from large compartment)

vector< double >	m_radius_axis
	axis for radius distribution

vector< double >	m_radius_hist
	values for radius distribution

double	m_myelin_axon_ratio
	ratio axon to (axon+myelin). Between 0 and 1. Used for variable radii only; else myelin radius is set explicitly.

double	m_extracellular_spacing
	minimal space between neurons

Protected Attributes inherited from Microstructure
double	m_boxsize

double	m_D_external

RNG *	m_rng

Detailed Description

Microstructure consisting of parallel cylinders.

Member Function Documentation

◆ GetD()

double MicrostructureSingleFiber::GetD	(	int	LastId,
		int	shellid )

virtual

returns Diffusion constant. unit: mm^2/ms

Reimplemented from Microstructure.

◆ IndexObject()

void MicrostructureSingleFiber::IndexObject	(	triple	pos,
		int &	LastId,
		int &	shellid )

virtual

return index of Microstructure object; -1 -> outside. shellid: object may have multiple layer (myelinated axon). id of layer; shellid = -1 -> object has no layers. LastId: during tracking of spin: object where last position was in.

Reimplemented from Microstructure.

Here is the call graph for this function: