#include <PsdMesh.h>

Inheritance diagram for PsdMesh:

Collaboration diagram for PsdMesh:

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...

double	getThickness () const

const vector< double > &	getVoxelArea () const

const vector< double > &	getVoxelLength () const

void	handlePsdList (const Eref &e, vector< double > params, vector< Id > elecCompts, 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	innerHandleRequestMeshStats (const Eref &e, const SrcFinfo2< unsigned int, vector< double > > *meshStatsFinfo)

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

unsigned int	parent (unsigned int index) const

	PsdMesh ()

	PsdMesh (const PsdMesh &other)

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

void	setThickness (double v)

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...

	~PsdMesh ()

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_
	Vol. More...

vector< Id >	elecCompt_
	Parent voxel index. More...

vector< double >	length_
	area More...

vector< CylBase >	pa_
	Specified disk of psd. More...

vector< unsigned int >	parent_
	Specifies diff distance to PSD. More...

vector< double >	parentDist_
	Specifies direction of psd. Length ignored. More...

vector< CylBase >	psd_

double	surfaceGranularity_
	Ids of elec compts mapped to each voxel. More...

double	thickness_
	Thickness of PSD. More...

vector< double >	vs_

Detailed Description

The PsdMesh sets up the diffusion geometries for the PSD. It has to work in two contexts: first, as a PSD sitting on a spine head. Second, as a PSD sitting directly on the dendrite. In either case it is treated as a surface disc, not as a volume. On the dendrite this is a little strange conceptually (flat disc on round cylinder) but will do for now. Later can fine-tune the cap geometry.

In either case, the PsdMesh is filled by a message that contains information about the matching voxel index (either on spineMesh or NeuroMesh), the coordinates, the radial vector, and the diameter. The PsdMesh does not have any internal diffusion, and it expects to pass only N to the parent dendrite or spine.

Definition at line 27 of file PsdMesh.h.

Constructor & Destructor Documentation

PsdMesh::PsdMesh ( )

Definition at line 136 of file PsdMesh.cpp.

References psd_, and thickness_.

     :
         thickness_( 50.0e-9 ),
         psd_( 1 ),
         pa_( 1 ),
         parentDist_( 1, 1e-6 ),
         parent_( 1, 0 ),
         surfaceGranularity_( 0.1 ),
         vs_(1, 5.0e-21 ),
         area_(1, 1.0e-13 ),
         length_(1, 50.0e-9 )
 {
     const double defaultLength = 1e-6;
     psd_[0].setDia( defaultLength );
     psd_[0].setLength( thickness_ );
     psd_[0].setNumDivs( 1 );
     psd_[0].setIsCylinder( true );
 }

PsdMesh::PsdMesh ( const PsdMesh & other )

Definition at line 155 of file PsdMesh.cpp.

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

PsdMesh::~PsdMesh ( )

Definition at line 161 of file PsdMesh.cpp.

 {
     ;
 }

Member Function Documentation

void PsdMesh::buildStencil ( )

Definition at line 433 of file PsdMesh.cpp.

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

Referenced by updateCoords().

 {
     setStencilSize( psd_.size(), psd_.size() );
     innerResetStencil();
 }

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double PsdMesh::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 364 of file PsdMesh.cpp.

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

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

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vector< double > PsdMesh::getCoordinates ( unsigned int fid ) const

virtual

Virtual function to return coords of mesh Entry.

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

Implements ChemCompt.

Definition at line 331 of file PsdMesh.cpp.

References pa_, and psd_.

 {
     vector< double > ret;
     ret.push_back( psd_[fid].getX() );
     ret.push_back( psd_[fid].getY() );
     ret.push_back( psd_[fid].getZ() );
     ret.push_back( psd_[fid].getX() - pa_[fid].getX() );
     ret.push_back( psd_[fid].getY() - pa_[fid].getY() );
     ret.push_back( psd_[fid].getZ() - pa_[fid].getZ() );
     ret.push_back( psd_[fid].getDia() );
     return ret;
 }

vector< double > PsdMesh::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 345 of file PsdMesh.cpp.

References pa_, and psd_.

 {
     vector< double > ret;
     assert( fid < psd_.size() );
     ret.push_back( psd_[ fid ].getDiffusionArea( pa_[fid], 0 ) );
 
     return ret;
 }

vector< double > PsdMesh::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 357 of file PsdMesh.cpp.

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

vector< Id > PsdMesh::getElecComptMap ( ) const

Definition at line 190 of file PsdMesh.cpp.

References elecCompt_.

Referenced by initCinfo().

 {
     return elecCompt_;
 }

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

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

Definition at line 203 of file PsdMesh.cpp.

References elecCompt_.

Referenced by initCinfo().

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

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

virtual

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

Definition at line 303 of file PsdMesh.cpp.

 {
     return 2;
 }

double PsdMesh::getMeshEntryVolume ( unsigned int fid ) const

virtual

Virtual function to return volume of mesh Entry.

Implements ChemCompt.

Definition at line 309 of file PsdMesh.cpp.

References pa_, psd_, and thickness_.

Referenced by extendedMeshEntryVolume(), handlePsdList(), and matchSpineMeshEntries().

 {
     if ( psd_.size() == 0 ) // Default for meshes before init.
         return 1.0;
     assert( fid < psd_.size() );
     return thickness_ * psd_[ fid ].getDiffusionArea( pa_[fid], 0 );
 }

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

virtual

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

Definition at line 296 of file PsdMesh.cpp.

References DISK, and psd_.

 {
     assert( fid < psd_.size() );
     return DISK;
 }

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

Returns index of voxel on NeuroMesh to which this spine is connected. This isn't such a great function, as it only works if the spine is sitting directly on the NeuroMesh. Otherwise it returns the vector of voxels of parent spine heads, which isn't what the name indicates.

Definition at line 184 of file PsdMesh.cpp.

References parent_.

Referenced by initCinfo().

 {
     cout << "Warning: PsdMesh::getNeuronVoxel. Currently not working\n";
     return parent_;
 }

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vector< unsigned int > PsdMesh::getParentVoxel ( ) const

virtual

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

Implements MeshCompt.

Definition at line 542 of file PsdMesh.cpp.

References parent_.

 {
     vector< unsigned int > ret( parent_.size(), -1U );
     return ret;
     // return parent_;
 }

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

Returns index of first voxel mapping to elec compt.

Definition at line 195 of file PsdMesh.cpp.

References elecCompt_.

Referenced by initCinfo().

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

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double PsdMesh::getThickness ( ) const

An assumed thickness for PSD. The volume is computed as the PSD area passed in to each PSD, times this value. Defaults to 50 nanometres. For reference, membranes are 5 nm.

Definition at line 169 of file PsdMesh.cpp.

References thickness_.

Referenced by initCinfo().

 {
     return thickness_;
 }

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

virtual

Implements MeshCompt.

Definition at line 578 of file PsdMesh.cpp.

References area_.

 {
     return area_;
 }

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

virtual

Implements MeshCompt.

Definition at line 583 of file PsdMesh.cpp.

References length_.

 {
     return length_;
 }

void PsdMesh::handlePsdList	(	const Eref &	e,
		vector< double >	params,
		vector< Id >	elecCompts,
		vector< unsigned int >	parentVoxel
	)

Definition at line 227 of file PsdMesh.cpp.

References area_, elecCompt_, getMeshEntryVolume(), Eref::id(), length_, ChemCompt::lookupEntry(), pa_, parent_, parentDist_, psd_, thickness_, MeshEntry::triggerRemesh(), updateCoords(), Id::value(), and vs_.

Referenced by initCinfo().

 {
         double oldVol = getMeshEntryVolume( 0 );
         assert( diskCoords.size() == 8 * parentVoxel.size() );
         psd_.resize( parentVoxel.size() );
         pa_.resize( parentVoxel.size() );
         vs_.resize( parentVoxel.size() );
         area_.resize( parentVoxel.size() );
         length_.resize( parentVoxel.size() );
         elecCompt_ = elecCompt;
 
         psd_.clear();
         pa_.clear();
         parentDist_.clear();
         parent_.clear();
         vector< double >::const_iterator x = diskCoords.begin();
         for ( unsigned int i = 0; i < parentVoxel.size(); ++i ) {
             double p = *x;
             double q = *(x+1);
             double r = *(x+2);
 
             psd_.push_back( CylBase( p, q, r, 1, 0, 1 ));
             x += 3;
             pa_.push_back( CylBase( p - *x, q - *(x+1), r - *(x+2), 1, 0, 1 ));
             x += 3;
             psd_.back().setDia( *x++ );
             psd_.back().setIsCylinder( true );
                 // This is an entirely nominal
                 // length, so that the effective vol != 0.
             psd_.back().setLength( thickness_ );
 
             parentDist_.push_back( *x++ );
             vs_[i] = psd_.back().volume( psd_.back() );
             area_[i] = psd_.back().getDiffusionArea( psd_.back(), 0 );
             length_[i] = parentDist_.back();
         }
         parent_ = parentVoxel;
 
         updateCoords();
 
         Id meshEntry( e.id().value() + 1 );
 
         vector< unsigned int > localIndices( psd_.size() );
         vector< double > vols( psd_.size() );
         for ( unsigned int i = 0; i < psd_.size(); ++i ) {
             localIndices[i] = i;
             vols[i] = thickness_ * psd_[i].getDiffusionArea( pa_[i], 0 );
         }
         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 PsdMesh::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 464 of file PsdMesh.cpp.

References innerGetNumEntries(), and psd_.

 {
     if ( index >= innerGetNumEntries() )
         return;
     x = psd_[index].getX();
     y = psd_[index].getY();
     z = psd_[index].getZ();
 }

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const Cinfo * PsdMesh::initCinfo ( )

static

Definition at line 28 of file PsdMesh.cpp.

References getElecComptMap(), getEndVoxelInCompt(), getNeuronVoxel(), getStartVoxelInCompt(), getThickness(), handlePsdList(), ChemCompt::initCinfo(), psdMeshCinfo, and setThickness().

 {
         // Field Definitions
         static ValueFinfo< PsdMesh, double > thickness(
             "thickness",
             "An assumed thickness for PSD. The volume is computed as the"
             "PSD area passed in to each PSD, times this value."
             "defaults to 50 nanometres. For reference, membranes are 5 nm.",
             &PsdMesh::setThickness,
             &PsdMesh::getThickness
         );
 
         static ReadOnlyValueFinfo< PsdMesh, vector< unsigned int > >
             neuronVoxel
         (
             "neuronVoxel",
             "Vector of indices of voxels on parent NeuroMesh, from which "
             "the respective spines emerge.",
             &PsdMesh::getNeuronVoxel
         );
 
         static ReadOnlyValueFinfo< PsdMesh, 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 PSD. ",
             &PsdMesh::getElecComptMap
         );
         static ReadOnlyValueFinfo< PsdMesh, vector< Id > > elecComptList(
             "elecComptList",
             "Vector of Ids of all electrical compartments in this "
             "PsdMesh. 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",
             &PsdMesh::getElecComptMap
         );
         static ReadOnlyValueFinfo< PsdMesh, vector< unsigned int > > startVoxelInCompt(
             "startVoxelInCompt",
             "Index of first voxel that maps to each electrical "
             "compartment. This is a trivial function in the PsdMesh, as"
             "we have a single voxel per spine. So just a vector of "
             "its own indices.",
             &PsdMesh::getStartVoxelInCompt
         );
         static ReadOnlyValueFinfo< PsdMesh, 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",
             &PsdMesh::getEndVoxelInCompt
         );
 
         // MsgDest Definitions
 
         static DestFinfo psdList( "psdList",
             "Specifies the geometry of the spine,"
             "and the associated parent voxel"
             "Arguments: "
             "disk params vector with 8 entries per psd, "
             "vector of Ids of electrical compts mapped to voxels, "
             "parent voxel index ",
             new EpFunc3< PsdMesh,
                 vector< double >,
                 vector< Id >,
                 vector< unsigned int > >(
                 &PsdMesh::handlePsdList )
         );
 
         // Field Elements
 
     static Finfo* psdMeshFinfos[] = {
         &thickness,         // ValueFinfo
         &neuronVoxel,       // ReadOnlyValueFinfo
         &elecComptMap,      // ReadOnlyValueFinfo
         &elecComptList,     // ReadOnlyValueFinfo
         &startVoxelInCompt,     // ReadOnlyValueFinfo
         &endVoxelInCompt,       // ReadOnlyValueFinfo
         &psdList,           // DestFinfo
     };
 
     static Dinfo< PsdMesh > dinfo;
     static Cinfo psdMeshCinfo (
         "PsdMesh",
         ChemCompt::initCinfo(),
         psdMeshFinfos,
         sizeof( psdMeshFinfos ) / sizeof ( Finfo* ),
         &dinfo
     );
 
     return &psdMeshCinfo;
 }

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void PsdMesh::innerBuildDefaultMesh	(	const Eref &	e,
		double	volume,
		unsigned int	numEntries
	)

virtual

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

Not permitted

Implements ChemCompt.

Definition at line 424 of file PsdMesh.cpp.

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

unsigned int PsdMesh::innerGetDimensions ( ) const

virtual

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

Implements ChemCompt.

Definition at line 221 of file PsdMesh.cpp.

 {
     return 2;
 }

unsigned int PsdMesh::innerGetNumEntries ( ) const

virtual

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Definition at line 407 of file PsdMesh.cpp.

References psd_.

Referenced by indexToSpace().

 {
     return psd_.size();
 }

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

virtual

Implements ChemCompt.

Definition at line 388 of file PsdMesh.cpp.

391 {

392 }

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

More inherited virtual funcs: request comes in for mesh stats Not clear what this does.

Definition at line 381 of file PsdMesh.cpp.

 {
         ;
 }

void PsdMesh::innerSetNumEntries ( unsigned int n )

virtual

Inherited virtual func.

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

Implements ChemCompt.

Definition at line 416 of file PsdMesh.cpp.

417 {

418 }

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

Definition at line 520 of file PsdMesh.cpp.

References CylBase::matchCubeMeshEntries(), pa_, psd_, and surfaceGranularity_.

Referenced by matchMeshEntries().

 {
     for( unsigned int i = 0; i < psd_.size(); ++i ) {
         const CylBase& cb = psd_[i];
         cb.matchCubeMeshEntries( other, pa_[i],
         i, surfaceGranularity_, ret, false, true );
     }
 }

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void PsdMesh::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 443 of file PsdMesh.cpp.

References matchCubeMeshEntries(), matchNeuroMeshEntries(), and matchSpineMeshEntries().

 {
     const SpineMesh* sm = dynamic_cast< const SpineMesh* >( other );
     if ( sm ) {
         matchSpineMeshEntries( other, ret );
         return;
     }
     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;
     }
     cout << "Warning: PsdMesh::matchMeshEntries: unknown class\n";
 }

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

Definition at line 509 of file PsdMesh.cpp.

References pa_, parent_, parentDist_, and psd_.

Referenced by matchMeshEntries().

 {
     const NeuroMesh* nm = dynamic_cast< const NeuroMesh* >( other );
     assert( nm );
     for ( unsigned int i = 0; i < psd_.size(); ++i ) {
         double xda = psd_[i].getDiffusionArea( pa_[i], 0) / parentDist_[i];
         ret.push_back( VoxelJunction( i, parent_[i], xda ) );
     }
 }

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

Definition at line 493 of file PsdMesh.cpp.

References getMeshEntryVolume(), SpineMesh::getMeshEntryVolume(), pa_, parent_, parentDist_, and psd_.

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

 {
     const SpineMesh* sm = dynamic_cast< const SpineMesh* >( other );
     assert( sm );
     for ( unsigned int i = 0; i < psd_.size(); ++i ) {
         double xda = psd_[i].getDiffusionArea( pa_[i], 0 ) / parentDist_[i];
         ret.push_back( VoxelJunction( i, parent_[i], xda ) );
         ret.back().firstVol = getMeshEntryVolume( i );
         ret.back().secondVol = sm->getMeshEntryVolume( parent_[i] );
     }
 }

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double PsdMesh::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 474 of file PsdMesh.cpp.

References Vec::distance(), and psd_.

 {
     double best = 1e12;
     index = 0;
     for( unsigned int i = 0; i < psd_.size(); ++i ) {
         Vec a( psd_[i].getX(), psd_[i].getY(), psd_[i].getZ() );
         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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unsigned int PsdMesh::parent ( unsigned int index ) const

Return voxel# on parent compartment on spine or dendrite. For now PSD is always on spine, so it just returns the index.

Definition at line 395 of file PsdMesh.cpp.

References parent_.

 {
     if ( i < parent_.size() )
         return parent_[i];
     cout << "Error: PsdMesh::parent: Index " << i << " out of range: " <<
                 parent_.size() << "\n";
     return 0;
 }

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

virtual

Virtual function to set volume of mesh Entry.

Virtual function to assign volume of mesh Entry. Thickness not touched.

Reimplemented from ChemCompt.

Definition at line 318 of file PsdMesh.cpp.

References area_, PI, psd_, thickness_, and vs_.

 {
     if ( psd_.size() == 0 ) // Default for meshes before init.
         return;
     assert( fid < psd_.size() );
     vs_[fid] = volume;
     area_[fid] = volume / thickness_;
     double dia = 2.0 * sqrt( area_[fid] / PI );
     psd_[ fid ].setDia( dia );
 }

void PsdMesh::setThickness ( double v )

Definition at line 173 of file PsdMesh.cpp.

References thickness_.

Referenced by initCinfo().

 {
     thickness_ = v;
 }

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void PsdMesh::transmitChange ( const Eref & e )

void PsdMesh::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 216 of file PsdMesh.cpp.

References buildStencil().

Referenced by handlePsdList().

 {
     buildStencil();
 }

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double PsdMesh::vGetEntireVolume ( ) const

virtual

Inherited virtual func.

Implements ChemCompt.

Definition at line 588 of file PsdMesh.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 > & PsdMesh::vGetVoxelMidpoint ( ) const

virtual

Virtual func so that derived classes can return voxel midpoint.

Implements ChemCompt.

Definition at line 561 of file PsdMesh.cpp.

References pa_, and psd_.

 {
     static vector< double > midpoint;
     midpoint.resize( psd_.size() * 3 );
     vector< double >::iterator k = midpoint.begin();
     for ( unsigned int i = 0; i < psd_.size(); ++i ) {
         vector< double > coords =
                 psd_[i].getCoordinates( pa_[i], 0 );
         *k = ( coords[0] + coords[3] ) / 2.0;
         *(k + psd_.size() ) = ( coords[1] + coords[4] ) / 2.0;
         *(k + 2 * psd_.size() ) = ( coords[2] + coords[5] ) / 2.0;
         k++;
         // cout << i << " " << coords[0] << " " << coords[3]<< " " << coords[1]<< " " << coords[4]<< " " << coords[2]<< " " << coords[5] << " " << coords[6] << endl;
     }
     return midpoint;
 }

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

virtual

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

Implements ChemCompt.

Definition at line 549 of file PsdMesh.cpp.

References vs_.

 {
     return vs_;
 }

bool PsdMesh::vSetVolumeNotRates ( double volume )

virtual

Inherited virtual func.

Implements ChemCompt.

Definition at line 597 of file PsdMesh.cpp.

References area_, length_, psd_, thickness_, vGetEntireVolume(), and vs_.

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