#include <SpineMesh.h>

Inheritance diagram for SpineMesh:

Collaboration diagram for SpineMesh:

Public Member Functions
void	buildStencil ()

double	extendedMeshEntryVolume (unsigned int fid) const
	Vol of all mesh Entries including abutting diff-coupled voxels. More...

vector< double >	getCoordinates (unsigned int fid) const
	Virtual function to return coords of mesh Entry. More...

vector< double >	getDiffusionArea (unsigned int fid) const
	Virtual function to return diffusion X-section area. More...

vector< double >	getDiffusionScaling (unsigned int fid) const
	Virtual function to return scale factor for diffusion. 1 here. More...

vector< Id >	getElecComptMap () const

vector< unsigned int >	getEndVoxelInCompt () const
	Returns index of end voxel mapping to elec compt, just first+1. More...

unsigned int	getMeshDimensions (unsigned int fid) const
	Virtual function to return dimensions of specified entry. More...

double	getMeshEntryVolume (unsigned int fid) const
	Virtual function to return volume of mesh Entry. More...

unsigned int	getMeshType (unsigned int fid) const
	Virtual function to return MeshType of specified entry. More...

vector< unsigned int >	getNeuronVoxel () const

vector< unsigned int >	getParentVoxel () const

vector< unsigned int >	getStartVoxelInCompt () const
	Returns index of first voxel mapping to elec compt. More...

const vector< double > &	getVoxelArea () const

const vector< double > &	getVoxelLength () const

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

void	indexToSpace (unsigned int index, double &x, double &y, double &z) const

void	innerBuildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)
	Virtual func to make a mesh with specified Volume and numEntries. More...

unsigned int	innerGetDimensions () const
	Returns # of dimensions, always 3 here. Inherited pure virt func. More...

unsigned int	innerGetNumEntries () const

void	innerHandleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)

void	innerSetNumEntries (unsigned int n)
	Inherited virtual func. More...

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

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

void	matchNeuroMeshEntries (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	setMeshEntryVolume (unsigned int fid, double volume)
	Virtual function to assign volume of mesh Entry. More...

	SpineMesh ()

	SpineMesh (const SpineMesh &other)

const vector< SpineEntry > &	spines () const

void	transmitChange (const Eref &e)

void	updateCoords ()

double	vGetEntireVolume () const
	Inherited virtual func. More...

const vector< double > &	vGetVoxelMidpoint () const
	Virtual func so that derived classes can return voxel midpoint. More...

const vector< double > &	vGetVoxelVolume () const
	Virtual func so that derived classes can pass voxel volume back. More...

bool	vSetVolumeNotRates (double volume)
	Inherited virtual func. More...

	~SpineMesh ()

Public Member Functions inherited from MeshCompt
void	addRow (unsigned int index, const vector< double > &entry, const vector< unsigned int > &colIndex)

void	clearExtendedMeshEntryVolume ()
	Inherited virtual function to clear the vector of MeshEntryVolume. More...

void	extendStencil (const ChemCompt *other, const vector< VoxelJunction > &vj)
	Add boundary voxels to stencil for cross-solver junctions. More...

vector< unsigned int >	getNeighbors (unsigned int fid) const
	Looks up stencil to return vector of indices of coupled voxels. More...

const SparseMatrix< double > &	getStencil () const
	Returns entire sparse matrix of mesh. Used by diffusion solver. More...

unsigned int	getStencilRow (unsigned int meshIndex, const double entry, const unsigned int colIndex) const

vector< double >	innerGetStencilRate (unsigned int row) const

void	innerResetStencil ()
	virtual func implemented here. More...

	MeshCompt ()

void	setStencilSize (unsigned int numRows, unsigned int numCols)

	~MeshCompt ()

Public Member Functions inherited from ChemCompt
void	buildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)

void	buildJunction (ChemCompt *other, vector< VoxelJunction > &ret)

	ChemCompt ()

void	flipRet (vector< VoxelJunction > &ret) const
	Utility function for swapping first and second in VoxelJunctions. More...

void	getChildConcs (const Eref &e, vector< double > &childConcs) const

unsigned int	getDimensions () const

double	getEntireVolume (const Eref &e) const

bool	getIsMembraneBound () const

string	getMethod () const

unsigned int	getNumEntries () const

double	getOneVoxelVolume (const Eref &e, unsigned int voxel) const

vector< unsigned int >	getStencilIndex (unsigned int row) const

vector< double >	getStencilRate (unsigned int row) const

vector< double >	getVoxelMidpoint () const
	Returns vector of all voxel midpoints in compartment. More...

vector< double >	getVoxelVolume () const
	Returns vector of all voxel volumes in compartment. More...

void	handleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)

MeshEntry *	lookupEntry (unsigned int index)

void	resetStencil ()

unsigned int	setChildConcs (const Eref &e, const vector< double > &childConcs, unsigned int start) const

void	setEntireVolume (const Eref &e, double volume)

void	setIsMembraneBound (bool v)

void	setMethod (string method)

void	setNumEntries (unsigned int num)

void	setOneVoxelVolume (const Eref &e, unsigned int voxel, double volume)

void	setVolumeNotRates (double volume)

virtual	~ChemCompt ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from ChemCompt
static double	distance (double x, double y, double z)

static const Cinfo *	initCinfo ()

static SrcFinfo1< vector < double > > *	voxelVolOut ()

Private Attributes
vector< double >	area_

vector< double >	length_
	Pre-calculation of length of each MeshEntry. More...

vector< SpineEntry >	spines_

double	surfaceGranularity_

vector< double >	vs_

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.

Definition at line 26 of file SpineMesh.h.

Constructor & Destructor Documentation

SpineMesh::SpineMesh ( )

Definition at line 154 of file SpineMesh.cpp.

     :
         spines_( 1 ),
         surfaceGranularity_( 0.1 ),
         vs_( 1, 1.0e-18 ),
         area_( 1, 1.0e-12 ),
         length_( 1, 1.0e-6 )
 {;}

SpineMesh::SpineMesh ( const SpineMesh & other )

Definition at line 163 of file SpineMesh.cpp.

     :
         spines_( other.spines_ ),
         surfaceGranularity_( other.surfaceGranularity_ )
 {;}

SpineMesh::~SpineMesh ( )

Definition at line 169 of file SpineMesh.cpp.

 {
     ;
 }

Member Function Documentation

void SpineMesh::buildStencil ( )

Definition at line 475 of file SpineMesh.cpp.

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

Referenced by updateCoords().

 {
 // stencil_[0] = new NeuroStencil( nodes_, nodeIndex_, vs_, area_);
     setStencilSize( spines_.size(), spines_.size() );
     innerResetStencil();
 }

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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.

Definition at line 348 of file SpineMesh.cpp.

References MeshCompt::extendedMeshEntryVolume(), getMeshEntryVolume(), and spines_.

 {
     if ( fid < spines_.size() ) {
         return getMeshEntryVolume( fid );
     } else {
         return MeshCompt::extendedMeshEntryVolume( fid - spines_.size() );
     }
 }

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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.

Definition at line 325 of file SpineMesh.cpp.

 {
     vector< double > ret;
     return ret;
 }

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.

Definition at line 332 of file SpineMesh.cpp.

 {
     vector< double > ret;
     return ret;
 }

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.

Definition at line 341 of file SpineMesh.cpp.

 {
     return vector< double >( 2, 1.0 );
 }

vector< Id > SpineMesh::getElecComptMap ( ) const

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

Definition at line 204 of file SpineMesh.cpp.

References spines_.

Referenced by initCinfo().

 {
     vector< Id > ret( spines_.size() );
     for ( unsigned int i = 0; i < spines_.size(); ++i )
         ret[i] = spines_[i].headId();
     return ret;
 }

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

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

Definition at line 220 of file SpineMesh.cpp.

References spines_.

Referenced by initCinfo().

 {
     vector< unsigned int > ret( spines_.size() );
     for ( unsigned int i = 0; i < ret.size(); ++i )
         ret[i] = i+1;
     return ret;
 }

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unsigned int SpineMesh::getMeshDimensions ( unsigned int fid ) const

virtual

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

Definition at line 301 of file SpineMesh.cpp.

 {
     return 3;
 }

double SpineMesh::getMeshEntryVolume ( unsigned int fid ) const

virtual

Virtual function to return volume of mesh Entry.

Implements ChemCompt.

Definition at line 307 of file SpineMesh.cpp.

References spines_.

Referenced by extendedMeshEntryVolume(), handleSpineList(), and PsdMesh::matchSpineMeshEntries().

 {
     if ( spines_.size() == 0 )
         return 1.0;
     assert( fid < spines_.size() );
     return spines_[ fid % spines_.size() ].volume();
 }

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unsigned int SpineMesh::getMeshType ( unsigned int fid ) const

virtual

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

Definition at line 294 of file SpineMesh.cpp.

References CYL, and spines_.

 {
     assert( fid < spines_.size() );
     return CYL;
 }

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

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

Definition at line 196 of file SpineMesh.cpp.

References spines_.

Referenced by initCinfo().

 {
     vector< unsigned int > ret( spines_.size(), -1U );
     for ( unsigned int i = 0; i < spines_.size(); ++i )
         ret[i] = spines_[i].parent();
     return ret;
 }

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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.

Definition at line 185 of file SpineMesh.cpp.

References spines_.

Referenced by initCinfo().

 {
     vector< unsigned int > ret( spines_.size(), -1U );
     // for ( unsigned int i = 0; i < spines_.size(); ++i )
     //  ret[i] = spines_[i].parent(); // Wrong, returns voxel on NeuroMesh
     return ret;
 }

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

Returns index of first voxel mapping to elec compt.

Definition at line 212 of file SpineMesh.cpp.

References spines_.

Referenced by initCinfo().

 {
     vector< unsigned int > ret( spines_.size() );
     for ( unsigned int i = 0; i < ret.size(); ++i )
         ret[i] = i;
     return ret;
 }

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const vector< double > & SpineMesh::getVoxelArea ( ) const

virtual

Implements MeshCompt.

Definition at line 403 of file SpineMesh.cpp.

References area_.

 {
     return area_;
 }

const vector< double > & SpineMesh::getVoxelLength ( ) const

virtual

Implements MeshCompt.

Definition at line 408 of file SpineMesh.cpp.

References length_.

 {
     return length_;
 }

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

Definition at line 246 of file SpineMesh.cpp.

References area_, getMeshEntryVolume(), Eref::id(), length_, ChemCompt::lookupEntry(), spines_, MeshEntry::triggerRemesh(), updateCoords(), Id::value(), and vs_.

Referenced by initCinfo().

 {
         double oldVol = getMeshEntryVolume( 0 );
         assert( head.size() == parentVoxel.size() );
         assert( head.size() == shaft.size() );
         spines_.resize( head.size() );
         vs_.resize( head.size() );
         area_.resize( head.size() );
         length_.resize( head.size() );
 
         vector< double > ret;
         vector< double > psdCoords;
         vector< unsigned int > index( head.size(), 0 );
         for ( unsigned int i = 0; i < head.size(); ++i ) {
             spines_[i] = SpineEntry( shaft[i], head[i], parentVoxel[i] );
             // cout << i << "   " << head[i] << ", pa = " << parentVoxel[i] << endl;
             // ret = spines_[i].psdCoords();
             // assert( ret.size() == 8 );
             // psdCoords.insert( psdCoords.end(), ret.begin(), ret.end() );
             // index[i] = i;
             vs_[i] = spines_[i].volume();
             area_[i] = spines_[i].rootArea();
             length_[i] = spines_[i].diffusionLength();
         }
 
         updateCoords();
         Id meshEntry( e.id().value() + 1 );
 
         vector< unsigned int > localIndices( head.size() );
         vector< double > vols( head.size() );
         for ( unsigned int i = 0; i < head.size(); ++i ) {
             localIndices[i] = i;
             vols[i] = spines_[i].volume();
         }
         vector< vector< unsigned int > > outgoingEntries;
         vector< vector< unsigned int > > incomingEntries;
         // meshSplit()->send( e, oldVol, vols, localIndices, outgoingEntries, incomingEntries );
         lookupEntry( 0 )->triggerRemesh( meshEntry.eref(),
                         oldVol, 0, localIndices, vols );
 }

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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.

Definition at line 508 of file SpineMesh.cpp.

References innerGetNumEntries(), and spines_.

 {
     if ( index >= innerGetNumEntries() )
         return;
     spines_[ index ].mid( x, y, z );
 }

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const Cinfo * SpineMesh::initCinfo ( )

static

Definition at line 48 of file SpineMesh.cpp.

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

 {
         // Field Definitions
         static ReadOnlyValueFinfo< SpineMesh, vector< unsigned int > >
             parentVoxel
         (
             "parentVoxel",
             "Vector of indices of proximal voxels within this mesh."
             "Spines are at present modeled with just one compartment,"
             "so each entry in this vector is always set to EMPTY == -1U",
             &SpineMesh::getParentVoxel
         );
 
         static ReadOnlyValueFinfo< SpineMesh, vector< unsigned int > >
             neuronVoxel
         (
             "neuronVoxel",
             "Vector of indices of voxels on parent NeuroMesh, from which "
             "the respective spines emerge.",
             &SpineMesh::getNeuronVoxel
         );
 
         static ReadOnlyValueFinfo< SpineMesh, vector< Id > > elecComptMap(
             "elecComptMap",
             "Vector of Ids of electrical compartments that map to each "
             "voxel. This is necessary because the order of the IDs may "
             "differ from the ordering of the voxels. Note that there "
             "is always just one voxel per spine head. ",
             &SpineMesh::getElecComptMap
         );
         static ReadOnlyValueFinfo< SpineMesh, vector< Id > > elecComptList(
             "elecComptList",
             "Vector of Ids of all electrical compartments in this "
             "SpineMesh. Ordering is as per the tree structure built in "
             "the NeuroMesh, and may differ from Id order. Ordering "
             "matches that used for startVoxelInCompt and endVoxelInCompt",
             &SpineMesh::getElecComptMap
         );
         static ReadOnlyValueFinfo< SpineMesh, vector< unsigned int > > startVoxelInCompt(
             "startVoxelInCompt",
             "Index of first voxel that maps to each electrical "
             "compartment. This is a trivial function in the SpineMesh, as"
             "we have a single voxel per spine. So just a vector of "
             "its own indices.",
             &SpineMesh::getStartVoxelInCompt
         );
         static ReadOnlyValueFinfo< SpineMesh, vector< unsigned int > > endVoxelInCompt(
             "endVoxelInCompt",
             "Index of end voxel that maps to each electrical "
             "compartment. Since there is just one voxel per electrical "
             "compartment in the spine, this is just a vector of index+1",
             &SpineMesh::getEndVoxelInCompt
         );
 
         // MsgDest Definitions
 
         static DestFinfo spineList( "spineList",
             "Specifies the list of electrical compartments for the spine,"
             "and the associated parent voxel"
             "Arguments: shaft compartments, "
             "head compartments, parent voxel index ",
             new EpFunc3< SpineMesh, vector< Id >, vector< Id >,
             vector< unsigned int > >(
                 &SpineMesh::handleSpineList )
         );
 
         // Field Elements
 
     static Finfo* spineMeshFinfos[] = {
         &parentVoxel,       // ReadOnlyValueFinfo
         &neuronVoxel,       // ReadOnlyValueFinfo
         &elecComptMap,      // ReadOnlyValueFinfo
         &elecComptList,     // ReadOnlyValueFinfo
         &startVoxelInCompt,     // ReadOnlyValueFinfo
         &endVoxelInCompt,       // ReadOnlyValueFinfo
         &spineList,         // DestFinfo
         // psdListOut(),        // SrcFinfo
     };
 
     static Dinfo< SpineMesh > dinfo;
     static Cinfo spineMeshCinfo (
         "SpineMesh",
         ChemCompt::initCinfo(),
         spineMeshFinfos,
         sizeof( spineMeshFinfos ) / sizeof ( Finfo* ),
         &dinfo
     );
 
     return &spineMeshCinfo;
 }

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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.

Definition at line 460 of file SpineMesh.cpp.

 {
     cout << "Warning: SpineMesh::innerBuildDefaultMesh: attempt to build a default spine: not permitted\n";
 }

unsigned int SpineMesh::innerGetDimensions ( ) const

virtual

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

Implements ChemCompt.

Definition at line 240 of file SpineMesh.cpp.

 {
     return 3;
 }

unsigned int SpineMesh::innerGetNumEntries ( ) const

virtual

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Definition at line 443 of file SpineMesh.cpp.

References spines_.

Referenced by indexToSpace().

 {
     return spines_.size();
 }

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void SpineMesh::innerHandleNodeInfo	(	const Eref &	e,
		unsigned int	numNodes,
		unsigned int	numThreads
	)

virtual

Implements ChemCompt.

Definition at line 374 of file SpineMesh.cpp.

 {
 
 }

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.

Definition at line 452 of file SpineMesh.cpp.

453 {

454 }

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

Definition at line 557 of file SpineMesh.cpp.

References SpineEntry::matchCubeMeshEntriesToHead(), spines_, and surfaceGranularity_.

Referenced by matchMeshEntries().

 {
     for( unsigned int i = 0; i < spines_.size(); ++i ) {
         const SpineEntry& se = spines_[i];
         se.matchCubeMeshEntriesToHead( other, i, surfaceGranularity_, ret );
     }
 }

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

virtual

Returns the meshIndices (NOT spatial indices) of all adjacent mesh entry pairs on ether side of the (self, other) junction. meshIndices are the indices that look up entries in the vector of pools. spatialIndices are (iz * ny + iy) * nx + ix, that is, a linear conversion of cartesian spatial indices. So, for two touching cubes, the return vector is the paired meshIndices on either side of the plane of contact. If one mesh has a finer mesh than the other, or if there are more than one contact points from self to other (for example, at a corner), then we just have multiple pairs using the same meshIndex of the repeated voxel.

Implements ChemCompt.

Definition at line 486 of file SpineMesh.cpp.

References ChemCompt::flipRet(), matchCubeMeshEntries(), matchNeuroMeshEntries(), and PsdMesh::matchSpineMeshEntries().

 {
     const CubeMesh* cm = dynamic_cast< const CubeMesh* >( other );
     if ( cm ) {
         matchCubeMeshEntries( other, ret );
         return;
     }
     const NeuroMesh* nm = dynamic_cast< const NeuroMesh* >( other );
     if ( nm ) {
         matchNeuroMeshEntries( other, ret );
         return;
     }
     const PsdMesh* pm = dynamic_cast< const PsdMesh* >( other );
     if ( pm ) {
         pm->matchSpineMeshEntries( this, ret );
         flipRet( ret );
         return;
     }
     cout << "Warning: SpineMesh::matchMeshEntries: unknown class\n";
 }

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

Definition at line 543 of file SpineMesh.cpp.

References NeuroMesh::getMeshEntryVolume(), and spines_.

Referenced by matchMeshEntries(), and NeuroMesh::matchMeshEntries().

 {
     const NeuroMesh* nm = dynamic_cast< const NeuroMesh* >( other );
     assert( nm );
     for ( unsigned int i = 0; i < spines_.size(); ++i ) {
         double xda = spines_[i].rootArea() / spines_[i].diffusionLength();
         ret.push_back( VoxelJunction( i, spines_[i].parent(), xda ) );
         ret.back().firstVol = spines_[i].volume();
         ret.back().secondVol =
                 nm->getMeshEntryVolume( spines_[i].parent() );
     }
 }

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

Definition at line 538 of file SpineMesh.cpp.

540 {

541 }

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.

Definition at line 516 of file SpineMesh.cpp.

References Vec::distance(), SpineEntry::mid(), and spines_.

 {
     double best = 1e12;
     index = 0;
     for( unsigned int i = 0; i < spines_.size(); ++i ) {
         const SpineEntry& se = spines_[i];
         double a0, a1, a2;
         se.mid( a0, a1, a2 );
         Vec a( a0, a1, a2 );
         Vec b( x, y, z );
         double d = a.distance( b );
         if ( best > d ) {
             best = d;
             index = i;
         }
     }
     if ( best == 1e12 )
         return -1;
     return best;
 }

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void SpineMesh::setMeshEntryVolume	(	unsigned int	fid,
		double	volume
	)

virtual

Virtual function to assign volume of mesh Entry.

Reimplemented from ChemCompt.

Definition at line 315 of file SpineMesh.cpp.

References spines_.

 {
     if ( spines_.size() == 0 )
         return;
     assert( fid < spines_.size() );
     spines_[ fid % spines_.size() ].setVolume( volume );
 }

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

Definition at line 467 of file SpineMesh.cpp.

References spines_.

 {
         return spines_;
 }

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.

Definition at line 235 of file SpineMesh.cpp.

References buildStencil().

Referenced by handleSpineList().

 {
     buildStencil();
 }

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double SpineMesh::vGetEntireVolume ( ) const

virtual

Inherited virtual func.

Implements ChemCompt.

Definition at line 413 of file SpineMesh.cpp.

References vs_.

Referenced by vSetVolumeNotRates().

 {
     double ret = 0.0;
     for ( vector< double >::const_iterator i =
                     vs_.begin(); i != vs_.end(); ++i )
         ret += *i;
     return ret;
 }

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const vector< double > & SpineMesh::vGetVoxelMidpoint ( ) const

virtual

Virtual func so that derived classes can return voxel midpoint.

Implements ChemCompt.

Definition at line 390 of file SpineMesh.cpp.

References spines_.

 {
     static vector< double > midpoint;
     midpoint.resize( spines_.size() * 3 );
     for ( unsigned int i = 0; i < spines_.size(); ++i ) {
         spines_[i].mid( midpoint[i],
                         midpoint[i + spines_.size() ],
                         midpoint[i + 2 * spines_.size() ]
         );
     }
     return midpoint;
 }

const vector< double > & SpineMesh::vGetVoxelVolume ( ) const

virtual

Virtual func so that derived classes can pass voxel volume back.

Implements ChemCompt.

Definition at line 385 of file SpineMesh.cpp.

References vs_.

 {
     return vs_;
 }

bool SpineMesh::vSetVolumeNotRates ( double volume )

virtual

Inherited virtual func.

Implements ChemCompt.

Definition at line 422 of file SpineMesh.cpp.

References area_, length_, spines_, vGetEntireVolume(), and vs_.

 {
     double volscale = volume / vGetEntireVolume();
     double linscale = pow( volscale, 1.0/3.0 );
     assert( vs_.size() == spines_.size() );
     assert( area_.size() == spines_.size() );
     assert( length_.size() == spines_.size() );
     for ( unsigned int i = 0; i < spines_.size(); ++i ) {
         spines_[i].setVolume( volume );
         vs_[i] *= volscale;
         area_[i] *= linscale * linscale;
         length_[i] *= linscale;
     }
     return true;
 }

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Member Data Documentation

vector< double > SpineMesh::area_

private

Mesh junction area pre-calculations for each MeshEntry. This is the cross-section area of the middle of each voxel.

Definition at line 203 of file SpineMesh.h.

Referenced by getVoxelArea(), handleSpineList(), and vSetVolumeNotRates().

vector< double > SpineMesh::length_

private

Pre-calculation of length of each MeshEntry.

Definition at line 206 of file SpineMesh.h.

Referenced by getVoxelLength(), handleSpineList(), and vSetVolumeNotRates().

vector< SpineEntry > SpineMesh::spines_

private

These do the actual work.

Definition at line 183 of file SpineMesh.h.

Referenced by buildStencil(), extendedMeshEntryVolume(), getElecComptMap(), getEndVoxelInCompt(), getMeshEntryVolume(), getMeshType(), getNeuronVoxel(), getParentVoxel(), getStartVoxelInCompt(), handleSpineList(), indexToSpace(), innerGetNumEntries(), matchCubeMeshEntries(), matchNeuroMeshEntries(), nearest(), setMeshEntryVolume(), spines(), vGetVoxelMidpoint(), and vSetVolumeNotRates().

double SpineMesh::surfaceGranularity_

private

Decides how finely to subdivide diffLength_ or radius or cubic mesh side when computing surfacearea of intersections with CubeMesh. Defaults to 0.1.

Definition at line 190 of file SpineMesh.h.

Referenced by matchCubeMeshEntries().

vector< double > SpineMesh::vs_

private

Volscale pre-calculations for each MeshEntry. vs = #molecules / vol where vol is expressed in m^3.

Definition at line 197 of file SpineMesh.h.

Referenced by handleSpineList(), vGetEntireVolume(), vGetVoxelVolume(), and vSetVolumeNotRates().

The documentation for this class was generated from the following files:

moose-core/mesh/SpineMesh.h
moose-core/mesh/SpineMesh.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation