CubeMesh Class Reference

#include <CubeMesh.h>

Inheritance diagram for CubeMesh:

Collaboration diagram for CubeMesh:

Public Member Functions
	CubeMesh ()
	~CubeMesh ()
void	setX0 (double v)
double	getX0 () const
void	setY0 (double v)
double	getY0 () const
void	setZ0 (double v)
double	getZ0 () const
void	setX1 (double v)
double	getX1 () const
void	setY1 (double v)
double	getY1 () const
void	setZ1 (double v)
double	getZ1 () const
void	setDx (double v)
double	getDx () const
void	setDy (double v)
double	getDy () const
void	setDz (double v)
double	getDz () const
void	setNx (unsigned int v)
unsigned int	getNx () const
void	setNy (unsigned int v)
unsigned int	getNy () const
void	setNz (unsigned int v)
unsigned int	getNz () const
void	innerSetCoords (const vector< double > &v)
void	setCoords (const Eref &e, vector< double > v)
vector< double >	getCoords (const Eref &e) const
void	setMeshToSpace (vector< unsigned int > v)
vector< unsigned int >	getMeshToSpace () const
void	setSpaceToMesh (vector< unsigned int > v)
vector< unsigned int >	getSpaceToMesh () const
void	setSurface (vector< unsigned int > v)
vector< unsigned int >	getSurface () const
unsigned int	innerGetDimensions () const
void	setIsToroid (bool v)
bool	getIsToroid () const
void	setPreserveNumEntries (bool v)
bool	getPreserveNumEntries () const
void	setAlwaysDiffuse (bool v)
bool	getAlwaysDiffuse () const
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.
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
	Virtual function to return volume of mesh Entry, including.
unsigned int	innerGetNumEntries () const
void	innerSetNumEntries (unsigned int n)
	Inherited virtual func.
void	innerHandleRequestMeshStats (const Eref &e, const SrcFinfo2< unsigned int, vector< double > > *meshStatsFinfo)
void	innerHandleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)
double	vGetEntireVolume () const
	Virtual func to get volume of entire compartment.
void	buildMesh (Id geom, double x, double y, double z)
void	addStoich (Id stoich)
void	innerBuildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)
	Virtual func to make a mesh with specified Volume and numEntries.
bool	vSetVolumeNotRates (double volume)
	Virtual func, assigns volume, usually to single voxel.
void	updateCoords ()
unsigned int	neighbor (unsigned int spaceIndex, int dx, int dy, int dz) const
void	transmitChange (const Eref &e, double oldvol)
bool	isInsideCuboid (double x, double y, double z) const
bool	isInsideSpheroid (double x, double y, double z) const
void	matchMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const
void	matchCubeMeshEntries (const CubeMesh *other, vector< VoxelJunction > &ret) const
void	matchCylMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const
void	matchAllEntries (const CubeMesh *other, vector< VoxelJunction > &ret) const
unsigned int	numDims () const
	Utility function for returning # of dimensions in mesh.
void	indexToSpace (unsigned int index, double &x, double &y, double &z) const
	Converts the integer meshIndex to spatial coords.
unsigned int	spaceToIndex (double x, double y, double z) const
	Converts the 3-D coords to an index. EMPTY if out of range.
double	nearest (double x, double y, double z, unsigned int &index) const
int	compareMeshSpacing (const CubeMesh *other) const
	Return 0 if spacing same, -1 if self smaller, +1 if self bigger.
void	defineIntersection (const CubeMesh *other, double &xmin, double &xmax, double &ymin, double &ymax, double &zmin, double &zmax) const
	Defines a cuboid volume of intersection between self and other.
void	fillTwoDimSurface ()
	Fills surface_ vector with spatial meshIndices for a rectangle.
void	fillThreeDimSurface ()
const vector< unsigned int > &	surface () const
	Utility and test function to read surface.
vector< unsigned int >	getParentVoxel () const
	Inherited virtual, do nothing for now.
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
void	buildStencil ()
void	fillSpaceToMeshLookup ()
void	deriveM2sFromS2m ()
void	deriveS2mFromM2s ()
void	assignVoxels (vector< pair< unsigned int, unsigned int > > &intersect, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax) const
void	setDiffScale (const CubeMesh *other, vector< VoxelJunction > &ret) const
	Assigns diffusion scaling info for the voxel junctions.
void	setJunctionVol (const CubeMesh *other, vector< VoxelJunction > &ret) const
	Assigns volume info for the voxel junctions.
void	updateM2s ()
void	updateS2m ()
Static Public Member Functions
static const Cinfo *	initCinfo ()
Static Public Attributes
static const unsigned int	EMPTY = ~0
static const unsigned int	SURFACE = ~1
static const unsigned int	ABUTX = ~2
static const unsigned int	ABUTY = ~3
static const unsigned int	ABUTZ = ~4
static const unsigned int	MULTI = ~5

Detailed Description

The CubeMesh represents a chemically identified compartment shaped like a cuboid. This is not really an effective geometry for most neurons because it would have to be rather finely subdivided to fit a typical dendrite or soma volume, but it is general.

Constructor & Destructor Documentation

CubeMesh::CubeMesh ( )

References updateCoords().

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CubeMesh::~CubeMesh ( )

Member Function Documentation

void CubeMesh::addStoich ( Id stoich )

void CubeMesh::assignVoxels	(	vector< pair< unsigned int, unsigned int > > &	intersect,
		double	xmin,
		double	xmax,
		double	ymin,
		double	ymax,
		double	zmin,
		double	zmax
	)			const

void CubeMesh::buildMesh	(	Id	geom,
		double	x,
		double	y,
		double	z
	)

Referenced by initCinfo().

void CubeMesh::buildStencil ( )

Sets up the stencil that defines how to combine neighboring mesh elements to set up the diffusion du/dt term, using the method of lines. This is a very general function. It uses the information in the m2s_ and s2m_ vectors to work out the adjacency matrix. So we could use an arbitrary 3-D image to define the diffusive volume and boundaries using m2s_ and s2m_. We could also use geometric shapes through the fillSpaceToMeshLookup() function, which is currently a dummy and just does a cuboid.

References MeshCompt::addRow(), EMPTY, MeshCompt::innerResetStencil(), q, and MeshCompt::setStencilSize().

Referenced by deriveM2sFromS2m(), deriveS2mFromM2s(), and updateCoords().

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int CubeMesh::compareMeshSpacing ( const CubeMesh * other ) const

Return 0 if spacing same, -1 if self smaller, +1 if self bigger.

References doubleApprox().

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void CubeMesh::defineIntersection	(	const CubeMesh *	other,
		double &	xmin,
		double &	xmax,
		double &	ymin,
		double &	ymax,
		double &	zmin,
		double &	zmax
	)			const

Defines a cuboid volume of intersection between self and other.

References swapIfBackward().

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void CubeMesh::deriveM2sFromS2m ( )

Updates the m2s_ vector after s2m_ has been changed, and rebuilds the Stencil too. Any earlier junction information is lost.

References buildStencil(), and EMPTY.

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void CubeMesh::deriveS2mFromM2s ( )

Updates the s2m_ vector after m2s_ has been changed, and rebuilds the Stencil too. Any earlier junction information is lost.

References buildStencil(), and EMPTY.

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

Virtual function to return volume of mesh Entry, including.

Utility function to return volume of any voxel including those diffusively coupled and aubtting the present volume.

Reimplemented from MeshCompt.

void CubeMesh::fillSpaceToMeshLookup ( )

References EMPTY, isInsideCuboid(), q, and y.

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void CubeMesh::fillThreeDimSurface ( )

Fills surface_ vector with spatial meshIndices for a cuboid, that is, puts the surfaces of the cuboid in the vector.

Referenced by updateCoords().

void CubeMesh::fillTwoDimSurface ( )

Fills surface_ vector with spatial meshIndices for a rectangle.

bool CubeMesh::getAlwaysDiffuse ( ) const

Referenced by initCinfo().

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

Virtual function to return coords of mesh Entry.

Virtual function to return coords of mesh Entry. For Cuboid mesh, coords are x1y1z1 x2y2z2

Implements ChemCompt.

vector< double > CubeMesh::getCoords ( const Eref & e ) const

Referenced by initCinfo(), and testCubeMesh().

vector< double > CubeMesh::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.

References EMPTY, and neighbor().

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

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

Implements ChemCompt.

double CubeMesh::getDx ( ) const

Referenced by initCinfo(), and testCubeMesh().

double CubeMesh::getDy ( ) const

Referenced by initCinfo(), and testCubeMesh().

double CubeMesh::getDz ( ) const

Referenced by initCinfo(), and testCubeMesh().

bool CubeMesh::getIsToroid ( ) const

Referenced by initCinfo().

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

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

Referenced by testCubeMesh(), and testCubeMeshExtendStencil().

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

Virtual function to return volume of mesh Entry.

Implements ChemCompt.

vector< unsigned int > CubeMesh::getMeshToSpace ( ) const

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

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

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

References CUBOID.

Referenced by testCubeMesh(), and testCubeMeshExtendStencil().

unsigned int CubeMesh::getNx ( ) const

Referenced by initCinfo(), and testCubeMesh().

unsigned int CubeMesh::getNy ( ) const

Referenced by initCinfo(), and testCubeMesh().

unsigned int CubeMesh::getNz ( ) const

Referenced by initCinfo(), and testCubeMesh().

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

Inherited virtual, do nothing for now.

Implements MeshCompt.

bool CubeMesh::getPreserveNumEntries ( ) const

Referenced by initCinfo().

vector< unsigned int > CubeMesh::getSpaceToMesh ( ) const

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

vector< unsigned int > CubeMesh::getSurface ( ) const

Referenced by initCinfo().

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

Implements MeshCompt.

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

Implements MeshCompt.

double CubeMesh::getX0 ( ) const

Referenced by initCinfo(), and testCubeMesh().

double CubeMesh::getX1 ( ) const

Referenced by initCinfo(), and testCubeMesh().

double CubeMesh::getY0 ( ) const

Referenced by initCinfo(), and testCubeMesh().

double CubeMesh::getY1 ( ) const

Referenced by initCinfo(), and testCubeMesh().

double CubeMesh::getZ0 ( ) const

Referenced by initCinfo(), and testCubeMesh().

double CubeMesh::getZ1 ( ) const

Referenced by initCinfo(), and testCubeMesh().

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

Converts the integer meshIndex to spatial coords.

Implements ChemCompt.

Referenced by nearest().

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

Reimplemented from ChemCompt.

References buildMesh(), getAlwaysDiffuse(), getCoords(), getDx(), getDy(), getDz(), getIsToroid(), getMeshToSpace(), getNx(), getNy(), getNz(), getPreserveNumEntries(), getSpaceToMesh(), getSurface(), getX0(), getX1(), getY0(), getY1(), getZ0(), getZ1(), ChemCompt::initCinfo(), setAlwaysDiffuse(), setCoords(), setDx(), setDy(), setDz(), setIsToroid(), setMeshToSpace(), setNx(), setNy(), setNz(), setPreserveNumEntries(), setSpaceToMesh(), setSurface(), setX0(), setX1(), setY0(), setY1(), setZ0(), setZ1(), and surface().

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

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

Builds something as close to a cube as can get. This needs a smarter boundary handling code than I have here. For now, goes for the nearest cube

Implements ChemCompt.

References setCoords().

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

Implements ChemCompt.

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

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Referenced by testCubeMesh().

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

Generate node decomposition of mesh, send it out along meshSplitFinfo msg

Implements ChemCompt.

void CubeMesh::innerHandleRequestMeshStats	(	const Eref &	e,
		const SrcFinfo2< unsigned int, vector< double > > *	meshStatsFinfo
	)

void CubeMesh::innerSetCoords ( const vector< double > & v )

Referenced by testCubeMesh(), testCubeMeshExtendStencil(), testCubeMeshFillTwoDimSurface(), testCubeMeshJunctionDiffSizeMesh(), testCubeMeshJunctionTwoDimSurface(), and testCubeMeshMultiJunctionTwoD().

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

Inherited virtual func.

Inherited virtual func. Assigns number of MeshEntries.

Implements ChemCompt.

bool CubeMesh::isInsideCuboid	(	double	x,
		double	y,
		double	z
	)			const

Referenced by fillSpaceToMeshLookup().

bool CubeMesh::isInsideSpheroid	(	double	x,
		double	y,
		double	z
	)			const

void CubeMesh::matchAllEntries	(	const CubeMesh *	other,
		vector< VoxelJunction > &	ret
	)			const

Dumbed-down version that does mesh matching based only on index. Useful for non-spatial matching and single-voxel systems.

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

Specialization for cube-to-cube mesh matching. Return vector is of pairs of meshIndices (not spatialIndices).

Referenced by testCubeMeshJunctionDiffSizeMesh(), and testCubeMeshJunctionTwoDimSurface().

void CubeMesh::matchCylMeshEntries	(	const ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)			const

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

Key virtual function for generating a map between facing surfaces on a CubeMesh and another ChemCompt

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

Virtual function to return the distance and index of nearest meshEntry. Places entry at centre of voxel.

Implements ChemCompt.

References ChemCompt::distance(), EMPTY, and indexToSpace().

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unsigned int CubeMesh::neighbor	(	unsigned int	spaceIndex,
		int	dx,
		int	dy,
		int	dz
	)			const

References EMPTY.

Referenced by getDiffusionArea().

unsigned int CubeMesh::numDims ( ) const

Utility function for returning # of dimensions in mesh.

Referenced by testCubeMeshFillTwoDimSurface().

void CubeMesh::setAlwaysDiffuse ( bool v )

Referenced by initCinfo().

void CubeMesh::setCoords	(	const Eref &	e,
		vector< double >	v
	)

Referenced by initCinfo(), and innerBuildDefaultMesh().

void CubeMesh::setDiffScale	(	const CubeMesh *	other,
		vector< VoxelJunction > &	ret
	)			const

Assigns diffusion scaling info for the voxel junctions.

void CubeMesh::setDx ( double v )

References updateCoords().

Referenced by initCinfo().

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void CubeMesh::setDy ( double v )

References updateCoords().

Referenced by initCinfo().

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void CubeMesh::setDz ( double v )

References updateCoords().

Referenced by initCinfo().

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void CubeMesh::setIsToroid ( bool v )

Referenced by initCinfo().

void CubeMesh::setJunctionVol	(	const CubeMesh *	other,
		vector< VoxelJunction > &	ret
	)			const

Assigns volume info for the voxel junctions.

void CubeMesh::setMeshToSpace ( vector< unsigned int > v )

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

void CubeMesh::setNx ( unsigned int v )

References updateCoords().

Referenced by initCinfo().

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void CubeMesh::setNy ( unsigned int v )

References updateCoords().

Referenced by initCinfo().

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void CubeMesh::setNz ( unsigned int v )

References updateCoords().

Referenced by initCinfo().

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void CubeMesh::setPreserveNumEntries ( bool v )

Referenced by initCinfo(), testCubeMesh(), testCubeMeshExtendStencil(), testCubeMeshFillTwoDimSurface(), testCubeMeshJunctionDiffSizeMesh(), testCubeMeshJunctionTwoDimSurface(), and testCubeMeshMultiJunctionTwoD().

void CubeMesh::setSpaceToMesh ( vector< unsigned int > v )

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

void CubeMesh::setSurface ( vector< unsigned int > v )

Referenced by initCinfo(), and testCubeMeshJunctionTwoDimSurface().

void CubeMesh::setX0 ( double v )

References updateCoords().

Referenced by initCinfo(), and testCubeMesh().

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void CubeMesh::setX1 ( double v )

References updateCoords().

Referenced by initCinfo(), and testCubeMesh().

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void CubeMesh::setY0 ( double v )

References updateCoords().

Referenced by initCinfo(), and testCubeMesh().

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void CubeMesh::setY1 ( double v )

References updateCoords().

Referenced by initCinfo(), and testCubeMesh().

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void CubeMesh::setZ0 ( double v )

References updateCoords().

Referenced by initCinfo(), and testCubeMesh().

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void CubeMesh::setZ1 ( double v )

References updateCoords().

Referenced by initCinfo(), and testCubeMesh().

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unsigned int CubeMesh::spaceToIndex	(	double	x,
		double	y,
		double	z
	)			const

Converts the 3-D coords to an index. EMPTY if out of range.

References EMPTY.

Referenced by fillPointsOnCircle().

const vector< unsigned int > & CubeMesh::surface ( ) const

Utility and test function to read surface.

Referenced by initCinfo(), testCubeMeshFillTwoDimSurface(), testCubeMeshJunctionDiffSizeMesh(), testCubeMeshJunctionTwoDimSurface(), and testCubeMeshMultiJunctionTwoD().

void CubeMesh::transmitChange	(	const Eref &	e,
		double	oldvol
	)

void CubeMesh::updateCoords ( )

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

This assumes that dx, dy, dz are the quantities to preserve, over numEntries. So when the compartment changes volume, so does numEntries. dx, dy, dz do not change, some of the sub-cuboids will partially be outside.

Temporarily fill out the whole cube for m2s and s2m. These

References buildStencil(), fillThreeDimSurface(), and swapIfBackward().

Referenced by CubeMesh(), setDx(), setDy(), setDz(), setNx(), setNy(), setNz(), setX0(), setX1(), setY0(), setY1(), setZ0(), and setZ1().