SpineMesh Class Reference

#include <SpineMesh.h>

Inheritance diagram for SpineMesh:

Collaboration diagram for SpineMesh:

Public Member Functions
	SpineMesh ()
	SpineMesh (const SpineMesh &other)
	~SpineMesh ()
void	updateCoords ()
vector< unsigned int >	getParentVoxel () const
vector< unsigned int >	getNeuronVoxel () const
vector< Id >	getElecComptMap () const
vector< unsigned int >	getStartVoxelInCompt () const
	Returns index of first voxel mapping to elec compt.
vector< unsigned int >	getEndVoxelInCompt () const
	Returns index of end voxel mapping to elec compt, just first+1.
unsigned int	getMeshType (unsigned int fid) const
	Virtual function to return MeshType of specified entry.
unsigned int	getMeshDimensions (unsigned int fid) const
	Virtual function to return dimensions of specified entry.
double	getMeshEntryVolume (unsigned int fid) const
	Virtual function to return volume of mesh Entry.
void	setMeshEntryVolume (unsigned int fid, double volume)
	Virtual function to assign volume of mesh Entry.
vector< double >	getCoordinates (unsigned int fid) const
	Virtual function to return coords of mesh Entry.
vector< double >	getDiffusionArea (unsigned int fid) const
	Virtual function to return diffusion X-section area.
vector< double >	getDiffusionScaling (unsigned int fid) const
	Virtual function to return scale factor for diffusion. 1 here.
double	extendedMeshEntryVolume (unsigned int fid) const
	Vol of all mesh Entries including abutting diff-coupled voxels.
unsigned int	innerGetNumEntries () const
void	innerSetNumEntries (unsigned int n)
	Inherited virtual func.
unsigned int	innerGetDimensions () const
	Returns # of dimensions, always 3 here. Inherited pure virt func.
double	vGetEntireVolume () const
	Inherited virtual func.
bool	vSetVolumeNotRates (double volume)
	Inherited virtual func.
void	innerBuildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)
	Virtual func to make a mesh with specified Volume and numEntries.
void	innerHandleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)
void	handleSpineList (const Eref &e, vector< Id > shaft, vector< Id > head, vector< unsigned int > parentVoxel)
void	transmitChange (const Eref &e)
void	buildStencil ()
void	matchMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const
void	matchNeuroMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const
void	matchCubeMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const
void	matchSpineMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const
double	nearest (double x, double y, double z, unsigned int &index) const
void	indexToSpace (unsigned int index, double &x, double &y, double &z) const
const vector< double > &	vGetVoxelVolume () const
	Virtual func so that derived classes can pass voxel volume back.
const vector< double > &	vGetVoxelMidpoint () const
	Virtual func so that derived classes can return voxel midpoint.
const vector< double > &	getVoxelArea () const
const vector< double > &	getVoxelLength () const
const vector< SpineEntry > &	spines () const
Static Public Member Functions
static const Cinfo *	initCinfo ()

Detailed Description

The SpineMesh sets up the diffusion geometries for dendritic spines. It is filled by a message from a NeuroMesh that contains information about the matching voxel on the NeuroMesh, and the compartment Ids for the spine shaft and head. The SpineMesh can further generate a PSD mesh with the info for the PSD geometries. This assumes that the each spine is a single voxel: single diffusive compartment, well-stirred. The shaft is treated as zero volume diffusion barrier to the dendrite. The PSD is a separate compt with its own diffusion coupling to the spine head.

Constructor & Destructor Documentation

SpineMesh::SpineMesh ( )

SpineMesh::SpineMesh ( const SpineMesh & other )

SpineMesh::~SpineMesh ( )

Member Function Documentation

void SpineMesh::buildStencil ( )

References MeshCompt::innerResetStencil(), and MeshCompt::setStencilSize().

Referenced by updateCoords().

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double SpineMesh::extendedMeshEntryVolume ( unsigned int fid ) const [virtual]

Vol of all mesh Entries including abutting diff-coupled voxels.

Virtual function to return volume of mesh Entry, including for diffusively coupled voxels from other solvers.

Reimplemented from MeshCompt.

References getMeshEntryVolume().

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vector< double > SpineMesh::getCoordinates ( unsigned int fid ) const [virtual]

Virtual function to return coords of mesh Entry.

Virtual function to return coords of mesh Entry. For SpineMesh, coords are x1y1z1 x2y2z2 x3y3z3 r0 r1

Implements ChemCompt.

vector< double > SpineMesh::getDiffusionArea ( unsigned int fid ) const [virtual]

Virtual function to return diffusion X-section area.

Virtual function to return diffusion X-section area for each neighbor.

Implements ChemCompt.

vector< double > SpineMesh::getDiffusionScaling ( unsigned int fid ) const [virtual]

Virtual function to return scale factor for diffusion. 1 here.

Virtual function to return scale factor for diffusion. I think all dendite tips need to return just one entry of 1.

Implements ChemCompt.

vector< Id > SpineMesh::getElecComptMap ( ) const

Returns vector of Ids of electrical compts that map to respective voxels in SpineMesh

Referenced by initCinfo().

vector< unsigned int > SpineMesh::getEndVoxelInCompt ( ) const

Returns index of end voxel mapping to elec compt, just first+1.

Referenced by initCinfo().

unsigned int SpineMesh::getMeshDimensions ( unsigned int fid ) const [virtual]

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

double SpineMesh::getMeshEntryVolume ( unsigned int fid ) const [virtual]

Virtual function to return volume of mesh Entry.

Implements ChemCompt.

Referenced by extendedMeshEntryVolume().

unsigned int SpineMesh::getMeshType ( unsigned int fid ) const [virtual]

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

References CYL.

vector< unsigned int > SpineMesh::getNeuronVoxel ( ) const

Returns index of voxel on NeuroMesh to which this spine is connected.

Referenced by initCinfo().

vector< unsigned int > SpineMesh::getParentVoxel ( ) const [virtual]

This function returns the diffusively connected parent voxel within the current (spine) mesh. Since each spine is treated as an independed voxel, there is no such voxel, so we return -1U for each spine. Note that there is a separate function that returns the parentVoxel referred to the NeuroMesh that this spine sits on.

Implements MeshCompt.

Referenced by initCinfo().

vector< unsigned int > SpineMesh::getStartVoxelInCompt ( ) const

Returns index of first voxel mapping to elec compt.

Referenced by initCinfo().

const vector< double > & SpineMesh::getVoxelArea ( ) const [virtual]

Implements MeshCompt.

const vector< double > & SpineMesh::getVoxelLength ( ) const [virtual]

Implements MeshCompt.

void SpineMesh::handleSpineList	(	const Eref &	e,
		vector< Id >	shaft,
		vector< Id >	head,
		vector< unsigned int >	parentVoxel
	)

Referenced by initCinfo().

void SpineMesh::indexToSpace	(	unsigned int	index,
		double &	x,
		double &	y,
		double &	z
	)			const `[virtual]`

Converts specified index to xyz coords of middle of voxel Values out of range return original xyz

Implements ChemCompt.

References innerGetNumEntries().

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const Cinfo * SpineMesh::initCinfo ( ) [static]

Reimplemented from ChemCompt.

References getElecComptMap(), getEndVoxelInCompt(), getNeuronVoxel(), getParentVoxel(), getStartVoxelInCompt(), handleSpineList(), and ChemCompt::initCinfo().

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void SpineMesh::innerBuildDefaultMesh	(	const Eref &	e,
		double	volume,
		unsigned int	numEntries
	)			`[virtual]`

Virtual func to make a mesh with specified Volume and numEntries.

Not allowed.

Implements ChemCompt.

unsigned int SpineMesh::innerGetDimensions ( ) const [virtual]

Returns # of dimensions, always 3 here. Inherited pure virt func.

Implements ChemCompt.

unsigned int SpineMesh::innerGetNumEntries ( ) const [virtual]

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Referenced by indexToSpace().

void SpineMesh::innerHandleNodeInfo	(	const Eref &	e,
		unsigned int	numNodes,
		unsigned int	numThreads
	)			`[virtual]`

Implements ChemCompt.

void SpineMesh::innerSetNumEntries ( unsigned int n ) [virtual]

Inherited virtual func.

Inherited virtual func. Assigns number of MeshEntries. Doesn't do anything, we have to set spine # from geometry.

Implements ChemCompt.

void SpineMesh::matchCubeMeshEntries	(	const ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)			const

void SpineMesh::matchMeshEntries	(	const ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)			const

void SpineMesh::matchNeuroMeshEntries	(	const ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)			const

void SpineMesh::matchSpineMeshEntries	(	const ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)			const

double SpineMesh::nearest	(	double	x,
		double	y,
		double	z,
		unsigned int &	index
	)			const `[virtual]`

This works a little different from other subclass versions of the function. It finds the index of the mesh entry whose centre is closest to the specified coords, and returns the distance to the centre. Doesn't worry about whether this distance is inside or outside cell.

Implements ChemCompt.

References a, d, Vec::distance(), and SpineEntry::mid().

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void SpineMesh::setMeshEntryVolume	(	unsigned int	fid,
		double	volume
	)			`[virtual]`

Virtual function to assign volume of mesh Entry.

Reimplemented from ChemCompt.

const vector< SpineEntry > & SpineMesh::spines ( ) const

void SpineMesh::transmitChange ( const Eref & e )

void SpineMesh::updateCoords ( )

Recomputes all local coordinate and meshing data following a change in any of the coord parameters

This assumes that lambda is the quantity to preserve, over numEntries. So when the compartment changes volume, numEntries changes too. Assumes that the soma node is at index 0.

References buildStencil().

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