#include <NeuroMesh.h>

Inheritance diagram for NeuroMesh:

Collaboration diagram for NeuroMesh:

Public Member Functions
void	buildNodeTree (const map< Id, unsigned int > &comptMap)

void	buildStencil ()
	Utility function to set up Stencil for diffusion in NeuroMesh. More...

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

bool	filterSpines (Id compt)

double	getAdx (unsigned int curr, unsigned int &parentFid) const

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

vector< unsigned int >	getDendVoxelsOnCompartment (ObjId compt) const

double	getDiffLength () const

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 >	getElecComptList () const

vector< Id >	getElecComptMap () const

vector< unsigned int >	getEndVoxelInCompt () const

string	getGeometryPolicy () const

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...

const vector< NeuroNode > &	getNodes () const

unsigned int	getNumDiffCompts () const

unsigned int	getNumSegments () const

vector< unsigned int >	getParentVoxel () const

bool	getSeparateSpines () const

vector< int >	getSpineVoxelOnDendVoxel () const

vector< unsigned int >	getSpineVoxelsOnCompartment (ObjId compt) const

vector< unsigned int >	getStartVoxelInCompt () const

vector< ObjId >	getSubTree (const Eref &e) const

string	getSubTreePath (const Eref &e) const

const vector< double > &	getVoxelArea () const

const vector< double > &	getVoxelLength () const

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

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

unsigned int	innerGetDimensions () const

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	insertDummyNodes ()

void	insertSingleDummy (unsigned int parent, unsigned int self, double x, double y, double z)

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

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

	NeuroMesh ()

	NeuroMesh (const NeuroMesh &other)

NeuroMesh &	operator= (const NeuroMesh &other)

Id	putSomaAtStart (Id origSoma, unsigned int maxDiaIndex)
	This shuffles the nodes_ vector to put soma node at the start. More...

void	setDiffLength (double v)

void	setGeometryPolicy (string v)

void	setSeparateSpines (bool v)

void	setSubTree (const Eref &e, vector< ObjId > compartments)

void	setSubTreePath (const Eref &e, string path)

void	transmitSpineInfo (const Eref &e)

void	updateCoords ()

void	updateShaftParents ()

double	vGetEntireVolume () const

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)

	~NeuroMesh ()

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)

virtual void	setMeshEntryVolume (unsigned int fid, double volume)

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_

double	diffLength_

string	geometryPolicy_

vector< Id >	head_
	Id of shaft compartment. More...

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

vector< unsigned int >	nodeIndex_

vector< NeuroNode >	nodes_

vector< unsigned int >	parent_
	Id of head compartment. More...

vector< unsigned int >	parentVoxel_
	Index of parent voxel of spines. More...

bool	separateSpines_
	Max permitted length constant for diffusion. More...

vector< Id >	shaft_

string	subTreePath_

double	surfaceGranularity_

vector< double >	vs_

Detailed Description

The NeuroMesh represents sections of a neuron whose spatial attributes are obtained from a neuronal model. Like the CylMesh, this is pseudo-1 dimension: Only the axial dimension is considered for diffusion and subdivisions. Branching is also handled.

Dendritic spines typically contain different reaction systems from the dendrite, but each spine has the same reactions. So they deserve their own mesh: SpineMesh. The idea is the the SpineMesh has just the spine head compartment, which duplicate the same reactions, but does not diffuse to other spine heads. Instead it has an effective diffusion constant to the parent dendrite compartment, obtained by treating the spine neck as a diffusion barrier with zero volume.

Definition at line 31 of file NeuroMesh.h.

Constructor & Destructor Documentation

NeuroMesh::NeuroMesh ( )

Definition at line 287 of file NeuroMesh.cpp.

References diffLength_, and nodes_.

Referenced by initCinfo().

     :
     nodes_(1),
     subTreePath_( "Undefined" ),
     nodeIndex_(1, 0 ),
     vs_( 1, NA * 1e-9 ),
     area_( 1, 1.0e-12 ),
     length_( 1, 1.0e-6 ),
     diffLength_( 1.0e-6 ),
     separateSpines_( false ),
     geometryPolicy_( "default" ),
     surfaceGranularity_( 0.1 ),
     parentVoxel_(1, -1)
 {
     nodes_[0].setLength( diffLength_ );
     nodes_[0].setDia( diffLength_ );
     nodes_[0].setNumDivs( 1 );
 }

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NeuroMesh::NeuroMesh ( const NeuroMesh & other )

Definition at line 306 of file NeuroMesh.cpp.

     :
     diffLength_( other.diffLength_ ),
     separateSpines_( other.separateSpines_ ),
     geometryPolicy_( other.geometryPolicy_ ),
     surfaceGranularity_( other.surfaceGranularity_ )
 {
     ;
 }

NeuroMesh::~NeuroMesh ( )

Definition at line 329 of file NeuroMesh.cpp.

 {
     ;
 }

Member Function Documentation

void NeuroMesh::buildNodeTree ( const map< Id, unsigned int > & comptMap )

buildNodeTree: This connects up parent and child nodes and if needed inserts dummy nodes to build up the model tree.

void NeuroMesh::buildStencil ( )

Utility function to set up Stencil for diffusion in NeuroMesh.

Definition at line 1166 of file NeuroMesh.cpp.

References MeshCompt::addRow(), getAdx(), MeshCompt::innerResetStencil(), nodeIndex_, parentVoxel_, and MeshCompt::setStencilSize().

Referenced by updateCoords().

 {
     parentVoxel_.clear();
     setStencilSize( nodeIndex_.size(), nodeIndex_.size() );
     SparseMatrix< double > sm( nodeIndex_.size(), nodeIndex_.size() );
     vector< vector< double > > paEntry( nodeIndex_.size() );
     vector< vector< unsigned int > > paColIndex( nodeIndex_.size() );
     // It is very easy to set up the matrix using the parent as there is
     // only one parent for every voxel.
     for ( unsigned int i = 0; i < nodeIndex_.size(); ++i )
     {
         unsigned int parentFid;
         double adx = getAdx( i, parentFid );
         parentVoxel_.push_back( parentFid );
         if ( adx < 0.0 ) // No diffusion, so don't put in any entry.
             continue;
         /*
         const NeuroNode &nn = nodes_[ nodeIndex_[i] ];
         const NeuroNode *pa = &nodes_[ nn.parent() ];
         double L1 = nn.getLength() / nn.getNumDivs();
         double L2 = L1;
         unsigned int parentFid = i - 1;
         if ( nn.startFid() == i ) {
             // We're at the start of the node, need to refer to parent for L
             const NeuroNode* realParent = pa;
             if ( pa->isDummyNode() ) {
                 realParent = &nodes_[ realParent->parent() ];
                 if ( realParent->isDummyNode() ) {
                     // Still dummy. So we're at a terminus. No diffusion
                     continue;
                 }
             }
             L2 = realParent->getLength() / realParent->getNumDivs();
             parentFid = realParent->startFid() +
                     realParent->getNumDivs() - 1;
         }
         assert( parentFid < nodeIndex_.size() );
         double length = 0.5 * (L1 + L2 );
         // Note that we use the parent node here even if it is a dummy.
         // It has the correct diameter.
         double adx = nn.getDiffusionArea( *pa, i - nn.startFid() ) / length;
         */
         paEntry[ i ].push_back( adx );
         paColIndex[ i ].push_back( parentFid );
         // Now put in the symmetric entries.
         paEntry[ parentFid ].push_back( adx );
         paColIndex[ parentFid ].push_back( i );
     }
 
     // Now go through the paEntry and paColIndex and build sparse matrix.
     // We have to do this separately because the sparse matrix has to be
     // build up in row order, and sorted, whereas the entries above
     // are random access.
     for ( unsigned int i = 0; i < nodeIndex_.size(); ++i )
     {
         unsigned int num = paColIndex[i].size();
         vector< Ecol > e( num );
         vector< double > entry( num );
         vector< unsigned int > colIndex( num );
         for ( unsigned int j = 0; j < num; ++j )
         {
             e[j] = Ecol( paEntry[i][j], paColIndex[i][j] );
         }
         sort( e.begin(), e.end() );
 
         for ( unsigned int j = 0; j < num; ++j )
         {
             entry[j] = e[j].e_;
             colIndex[j] = e[j].col_;
         }
         addRow( i, entry, colIndex );
     }
     innerResetStencil();
 }

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double NeuroMesh::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 971 of file NeuroMesh.cpp.

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

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

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bool NeuroMesh::filterSpines ( Id compt )

Returns true if it finds a compartment name that looks like it ought to be on a spine. It filters out the names "neck", "shaft", "spine" and "head". The latter two are classified into the head_ vector. The first two are classified into the shaft_ vector.

Definition at line 573 of file NeuroMesh.cpp.

References Id::element(), Element::getName(), head_, and shaft_.

 {
     if ( compt.element()->getName().find( "shaft" ) != string::npos ||
             compt.element()->getName().find( "neck" ) != string::npos )
     {
         shaft_.push_back( compt );
         return true;
     }
     if ( compt.element()->getName().find( "spine" ) != string::npos ||
             compt.element()->getName().find( "head" ) != string::npos )
     {
         head_.push_back( compt );
         return true;
     }
     return false;
 }

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double NeuroMesh::getAdx	(	unsigned int	curr,
		unsigned int &	parentFid
	)		const

Helper function for buildStencil, calculates diffusion term adx for rate between current compartment curr, and parent. By product: also passes back parent compartment index.

Definition at line 1126 of file NeuroMesh.cpp.

References CylBase::getDiffusionArea(), CylBase::getLength(), CylBase::getNumDivs(), NeuroNode::isDummyNode(), nodeIndex_, nodes_, NeuroNode::parent(), and NeuroNode::startFid().

Referenced by buildStencil().

 {
     const NeuroNode &nn = nodes_[ nodeIndex_[i] ];
     if ( nn.isDummyNode() || nn.parent() == ~0U )
         return -1; // No diffusion, bail out.
     const NeuroNode *pa = &nodes_[ nn.parent() ];
     double L1 = nn.getLength() / nn.getNumDivs();
     double L2 = L1;
     parentFid = i - 1;
     if ( nn.startFid() == i )
     {
         // We're at the start of the node, need to refer to parent for L
         const NeuroNode* realParent = pa;
         if ( pa->isDummyNode() )
         {
             if ( pa->parent() == ~0U )
             {
                 parentFid = -1;
                 return -1; // No diffusion, bail out.
             }
             assert( pa->parent() < nodes_.size() );
             realParent = &nodes_[ realParent->parent() ];
             if ( realParent->isDummyNode() )
             {
                 // Still dummy. So we're at a terminus. No diffusion
                 return -1;
             }
         }
         L2 = realParent->getLength() / realParent->getNumDivs();
         parentFid = realParent->startFid() +
                     realParent->getNumDivs() - 1;
     }
     assert( parentFid < nodeIndex_.size() );
     double length = 0.5 * (L1 + L2 );
     // Note that we use the parent node here even if it is a dummy.
     // It has the correct diameter.
     double adx = nn.getDiffusionArea( *pa, i - nn.startFid() ) / length;
     return adx;
 }

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

virtual

Virtual function to return coords of mesh Entry.

Virtual function to return coords of mesh Entry. For Cylindrical mesh, coords are x1y1z1 x2y2z2 r0 r1 phi0 phi1

Implements ChemCompt.

Definition at line 923 of file NeuroMesh.cpp.

References nodeIndex_, and nodes_.

 {
     assert( fid < nodeIndex_.size() );
     assert( nodeIndex_[fid] < nodes_.size() );
     const NeuroNode& node = nodes_[ nodeIndex_[fid] ];
     assert( fid >= node.startFid() );
     assert ( node.parent() < nodes_.size() );
     const NeuroNode& parent = nodes_[ node.parent() ];
 
     return node.getCoordinates( parent, fid - node.startFid() );
 }

vector< unsigned int > NeuroMesh::getDendVoxelsOnCompartment ( ObjId compt ) const

Definition at line 785 of file NeuroMesh.cpp.

References ObjId::id, and nodes_.

Referenced by initCinfo().

 {
     vector< unsigned int > ret;
     for ( vector< NeuroNode >::const_iterator
             i = nodes_.begin(); i != nodes_.end(); ++i )
     {
         if ( !i->isDummyNode() && i->elecCompt() == compt.id )
         {
             for ( unsigned int j = 0; j < i->getNumDivs(); ++j )
             {
                 ret.push_back( j + i->startFid() );
             }
         }
     }
     return ret;
 }

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double NeuroMesh::getDiffLength ( ) const

Definition at line 405 of file NeuroMesh.cpp.

References diffLength_.

Referenced by initCinfo().

 {
     return diffLength_;
 }

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vector< double > NeuroMesh::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 936 of file NeuroMesh.cpp.

References MeshCompt::getNeighbors(), nodeIndex_, and nodes_.

 {
     assert( fid < nodeIndex_.size() );
     assert( nodeIndex_[fid] < nodes_.size() );
     const NeuroNode& node = nodes_[ nodeIndex_[fid] ];
     assert( fid >= node.startFid() );
     assert ( node.parent() < nodes_.size() );
     const NeuroNode& parent = nodes_[ node.parent() ];
     vector< double > ret;
     vector< unsigned int > neighbors = getNeighbors( fid );
     for ( unsigned int i = 0; i < neighbors.size(); ++i )
     {
         ret.push_back( node.getDiffusionArea( parent, neighbors[ i ] ) );
     }
     return ret;
 }

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vector< double > NeuroMesh::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 956 of file NeuroMesh.cpp.

 {
     /*
     if ( nodeIndex_.size() <= 1 )
     return vector< double >( 0 );
 
     if ( !isToroid_ && ( fid == 0 || fid == (nodeIndex_.size() - 1) ) )
     return vector< double >( 1, 1.0 );
     */
 
     return vector< double >( 2, 1.0 );
 }

vector< Id > NeuroMesh::getElecComptList ( ) const

Definition at line 738 of file NeuroMesh.cpp.

References nodes_.

Referenced by getSubTree(), and initCinfo().

 {
     vector< Id > ret;
     for ( vector< NeuroNode >::const_iterator
             i = nodes_.begin(); i != nodes_.end(); ++i )
     {
         if ( !i->isDummyNode() )
             ret.push_back( i->elecCompt() );
     }
     return ret;
 }

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vector< Id > NeuroMesh::getElecComptMap ( ) const

Definition at line 726 of file NeuroMesh.cpp.

References nodeIndex_, and nodes_.

Referenced by initCinfo().

 {
     vector< Id > ret( nodeIndex_.size() );
     for ( unsigned int i = 0; i < nodeIndex_.size(); ++i )
     {
         ret[i] = nodes_[nodeIndex_[i]].elecCompt();
         // cout << i << "   " << nodeIndex_[i] << " " << ret[i] << endl;
 
     }
     return ret;
 }

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

Definition at line 762 of file NeuroMesh.cpp.

References nodes_.

Referenced by initCinfo().

 {
     vector< unsigned int > ret;
     for ( vector< NeuroNode >::const_iterator
             i = nodes_.begin(); i != nodes_.end(); ++i )
     {
         if ( !i->isDummyNode() )
             ret.push_back( i->startFid() + i->getNumDivs() );
     }
     return ret;
 }

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string NeuroMesh::getGeometryPolicy ( ) const

Definition at line 436 of file NeuroMesh.cpp.

References geometryPolicy_.

Referenced by initCinfo().

 {
     return geometryPolicy_;
 }

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

virtual

Virtual function to return dimensions of specified entry.

Implements ChemCompt.

Definition at line 900 of file NeuroMesh.cpp.

 {
     return 3;
 }

double NeuroMesh::getMeshEntryVolume ( unsigned int fid ) const

virtual

Virtual function to return volume of mesh Entry.

Implements ChemCompt.

Definition at line 906 of file NeuroMesh.cpp.

References nodeIndex_, and nodes_.

Referenced by extendedMeshEntryVolume(), and SpineMesh::matchNeuroMeshEntries().

 {
     if ( nodeIndex_.size() == 0 )
         return 1.0; // A default value to use before init
     assert( fid < nodeIndex_.size() );
     assert( nodeIndex_[fid] < nodes_.size() );
     const NeuroNode& node = nodes_[ nodeIndex_[fid] ];
     assert( fid >= node.startFid() );
     if ( node.parent() == ~0U )
         return node.voxelVolume( node, fid - node.startFid() );
     assert ( node.parent() < nodes_.size() );
     const NeuroNode& parent = nodes_[ node.parent() ];
     return node.voxelVolume( parent, fid - node.startFid() );
 }

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

virtual

Virtual function to return MeshType of specified entry.

Implements ChemCompt.

Definition at line 889 of file NeuroMesh.cpp.

References CYL, nodeIndex_, nodes_, and SPHERE_SHELL_SEG.

 {
     assert( fid < nodeIndex_.size() );
     assert( nodeIndex_[fid] < nodes_.size() );
     if ( nodes_[ nodeIndex_[fid] ].isSphere() )
         return SPHERE_SHELL_SEG;
 
     return CYL;
 }

const vector< NeuroNode > & NeuroMesh::getNodes ( ) const

Definition at line 1242 of file NeuroMesh.cpp.

References nodes_.

 {
     return nodes_;
 }

unsigned int NeuroMesh::getNumDiffCompts ( ) const

Definition at line 716 of file NeuroMesh.cpp.

References nodeIndex_.

Referenced by initCinfo().

 {
     return nodeIndex_.size();
 }

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unsigned int NeuroMesh::getNumSegments ( ) const

Definition at line 707 of file NeuroMesh.cpp.

References nodes_.

Referenced by initCinfo().

 {
     unsigned int ret = 0;
     for ( vector< NeuroNode >::const_iterator i = nodes_.begin();
             i != nodes_.end(); ++i )
         ret += !i->isDummyNode();
     return ret;
 }

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

virtual

Implements MeshCompt.

Definition at line 721 of file NeuroMesh.cpp.

References parentVoxel_.

Referenced by initCinfo().

 {
     return parentVoxel_;
 }

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bool NeuroMesh::getSeparateSpines ( ) const

Definition at line 702 of file NeuroMesh.cpp.

References separateSpines_.

Referenced by initCinfo().

 {
     return separateSpines_;
 }

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vector< int > NeuroMesh::getSpineVoxelOnDendVoxel ( ) const

Definition at line 774 of file NeuroMesh.cpp.

References nodeIndex_, and parent_.

Referenced by initCinfo().

 {
     vector< int > ret( nodeIndex_.size(), -1 ); //-1 means no spine present
     for ( unsigned int i = 0; i < parent_.size(); ++i )
     {
         assert( parent_[i] < ret.size() );
         ret[ parent_[i] ] = i;
     }
     return ret;
 }

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vector< unsigned int > NeuroMesh::getSpineVoxelsOnCompartment ( ObjId compt ) const

Definition at line 802 of file NeuroMesh.cpp.

References head_, ObjId::id, and shaft_.

Referenced by initCinfo().

 {
     vector< unsigned int > ret;
     assert( shaft_.size() == head_.size() );
     for ( unsigned int i = 0; i < shaft_.size(); ++i )
     {
         if ( shaft_[i] == compt.id || head_[i] == compt.id )
             ret.push_back(i);
     }
     return ret;
 }

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

Definition at line 750 of file NeuroMesh.cpp.

References nodes_.

Referenced by initCinfo().

 {
     vector< unsigned int > ret;
     for ( vector< NeuroNode >::const_iterator
             i = nodes_.begin(); i != nodes_.end(); ++i )
     {
         if ( !i->isDummyNode() )
             ret.push_back( i->startFid() );
     }
     return ret;
 }

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vector< ObjId > NeuroMesh::getSubTree ( const Eref & e ) const

Definition at line 670 of file NeuroMesh.cpp.

References getElecComptList().

Referenced by initCinfo().

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

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string NeuroMesh::getSubTreePath ( const Eref & e ) const

Definition at line 688 of file NeuroMesh.cpp.

References subTreePath_.

Referenced by initCinfo().

 {
     return subTreePath_;
 }

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

virtual

Implements MeshCompt.

Definition at line 845 of file NeuroMesh.cpp.

References area_.

 {
     return area_;
 }

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

virtual

Implements MeshCompt.

Definition at line 850 of file NeuroMesh.cpp.

References length_.

 {
     return length_;
 }

void NeuroMesh::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 1283 of file NeuroMesh.cpp.

References Vec::a0(), Vec::a1(), Vec::a2(), CylBase::getNumDivs(), CylBase::getX(), CylBase::getY(), CylBase::getZ(), innerGetNumEntries(), nodeIndex_, nodes_, NeuroNode::parent(), Vec::pointOnLine(), and NeuroNode::startFid().

 {
     if ( index >= innerGetNumEntries() )
         return;
     const NeuroNode& nn = nodes_[ nodeIndex_[ index ] ];
     const NeuroNode& pa = nodes_[ nn.parent() ];
     Vec a( pa.getX(), pa.getY(), pa.getZ() );
     Vec b( nn.getX(), nn.getY(), nn.getZ() );
     double frac = ( ( index - nn.startFid() ) + 0.5 ) / nn.getNumDivs();
     Vec pt = a.pointOnLine( b, frac );
     x = pt.a0();
     y = pt.a1();
     z = pt.a2();
 }

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const Cinfo * NeuroMesh::initCinfo ( )

static

Definition at line 66 of file NeuroMesh.cpp.

References getDendVoxelsOnCompartment(), getDiffLength(), getElecComptList(), getElecComptMap(), getEndVoxelInCompt(), getGeometryPolicy(), getNumDiffCompts(), getNumSegments(), getParentVoxel(), getSeparateSpines(), getSpineVoxelOnDendVoxel(), getSpineVoxelsOnCompartment(), getStartVoxelInCompt(), getSubTree(), getSubTreePath(), ChemCompt::initCinfo(), NeuroMesh(), neuroMeshCinfo, psdListOut(), setDiffLength(), setGeometryPolicy(), setSeparateSpines(), setSubTree(), setSubTreePath(), and spineListOut().

 {
     // Field Definitions
     static ElementValueFinfo< NeuroMesh, vector< ObjId > > subTree(
         "subTree",
         "Set of compartments in which to embed chemical reaction "
         "systems. If the compartments happen to be contiguous"
         "then also set up diffusion between them. Can also"
         "handle cases where the same cell is divided into multiple"
         "non-diffusively-coupled compartments",
         &NeuroMesh::setSubTree,
         &NeuroMesh::getSubTree
     );
     static ElementValueFinfo< NeuroMesh, string > subTreePath(
         "subTreePath",
         "Set of compartments to model, defined as a path string. "
         "If they happen to be contiguous "
         "then also set up diffusion between the compartments. Can also"
         "handle cases where the same cell is divided into multiple"
         "non-diffusively-coupled compartments",
         &NeuroMesh::setSubTreePath,
         &NeuroMesh::getSubTreePath
     );
     static ValueFinfo< NeuroMesh, bool > separateSpines(
         "separateSpines",
         "Flag: when separateSpines is true, the traversal separates "
         "any compartment with the strings "
         "'spine', 'head', 'shaft' or 'neck' in its name,"
         "Allows to set up separate mesh for spines, based on the "
         "same cell model. Requires for the spineListOut message to"
         "be sent to the target SpineMesh object.",
         &NeuroMesh::setSeparateSpines,
         &NeuroMesh::getSeparateSpines
     );
     static ReadOnlyValueFinfo< NeuroMesh, unsigned int > numSegments(
         "numSegments",
         "Number of cylindrical/spherical segments in model",
         &NeuroMesh::getNumSegments
     );
     static ReadOnlyValueFinfo< NeuroMesh, unsigned int > numDiffCompts(
         "numDiffCompts",
         "Number of diffusive compartments in model",
         &NeuroMesh::getNumDiffCompts
     );
     static ReadOnlyValueFinfo< NeuroMesh, vector< unsigned int > > parentVoxel(
         "parentVoxel",
         "Vector of indices of parents of each voxel.",
         &NeuroMesh::getParentVoxel
     );
     static ReadOnlyValueFinfo< NeuroMesh, 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. Additionally, there "
         "are typically many more voxels than there are electrical "
         "compartments. So many voxels point to the same elecCompt.",
         &NeuroMesh::getElecComptMap
     );
     static ReadOnlyValueFinfo< NeuroMesh, vector< Id > > elecComptList(
         "elecComptList",
         "Vector of Ids of all electrical compartments in this "
         "NeuroMesh. 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",
         &NeuroMesh::getElecComptList
     );
     static ReadOnlyValueFinfo< NeuroMesh, vector< unsigned int > > startVoxelInCompt(
         "startVoxelInCompt",
         "Index of first voxel that maps to each electrical "
         "compartment. Each elecCompt has one or more voxels. "
         "The voxels in a compartment are numbered sequentially.",
         &NeuroMesh::getStartVoxelInCompt
     );
     static ReadOnlyValueFinfo< NeuroMesh, vector< unsigned int > > endVoxelInCompt(
         "endVoxelInCompt",
         "Index of end voxel that maps to each electrical "
         "compartment. In keeping with C and Python convention, this "
         "is one more than the last voxel. "
         "Each elecCompt has one or more voxels. "
         "The voxels in a compartment are numbered sequentially.",
         &NeuroMesh::getEndVoxelInCompt
     );
 
     static ReadOnlyValueFinfo< NeuroMesh, vector< int > > spineVoxelOnDendVoxel(
         "spineVoxelOnDendVoxel",
         "Voxel index of spine voxel on each dend voxel. Assume that "
         "there is never more than one spine per dend voxel. If no "
         "spine present, the entry is -1. Note that the "
         "same index is used both for spine head and PSDs.",
         &NeuroMesh::getSpineVoxelOnDendVoxel
     );
 
     static ReadOnlyLookupValueFinfo< NeuroMesh, ObjId,
            vector< unsigned int > > dendVoxelsOnCompartment(
                "dendVoxelsOnCompartment",
                "Returns vector of all chem voxels on specified electrical "
                "compartment of the dendrite. Returns empty vec if none "
                "found, or if the compartment isn't on the dendrite.",
                &NeuroMesh::getDendVoxelsOnCompartment
            );
 
     static ReadOnlyLookupValueFinfo< NeuroMesh, ObjId,
            vector< unsigned int > > spineVoxelsOnCompartment(
                "spineVoxelsOnCompartment",
                "Returns vector of all chem voxels on specified electrical "
                "compartment, which should be a spine head or shaft . "
                "Returns empty vec if no chem voxels "
                "found, or if the compartment isn't on the dendrite. "
                "Note that spine and PSD voxel indices are the same for a "
                "given spine head.",
                &NeuroMesh::getSpineVoxelsOnCompartment
            );
 
     static ValueFinfo< NeuroMesh, double > diffLength(
         "diffLength",
         "Diffusive length constant to use for subdivisions. "
         "The system will"
         "attempt to subdivide cell using diffusive compartments of"
         "the specified diffusion lengths as a maximum."
         "In order to get integral numbers"
         "of compartments in each segment, it may subdivide more "
         "finely."
         "Uses default of 0.5 microns, that is, half typical lambda."
         "For default, consider a tau of about 1 second for most"
         "reactions, and a diffusion const of about 1e-12 um^2/sec."
         "This gives lambda of 1 micron",
         &NeuroMesh::setDiffLength,
         &NeuroMesh::getDiffLength
     );
 
     static ValueFinfo< NeuroMesh, string > geometryPolicy(
         "geometryPolicy",
         "Policy for how to interpret electrical model geometry (which "
         "is a branching 1-dimensional tree) in terms of 3-D constructs"
         "like spheres, cylinders, and cones."
         "There are three options, default, trousers, and cylinder:"
         "default mode:"
         " - Use frustrums of cones. Distal diameter is always from compt dia."
         " - For linear dendrites (no branching), proximal diameter is "
         " diameter of the parent compartment"
         " - For branching dendrites and dendrites emerging from soma,"
         " proximal diameter is from compt dia. Don't worry about overlap."
         " - Place somatic dendrites on surface of spherical soma, or at ends"
         " of cylindrical soma"
         " - Place dendritic spines on surface of cylindrical dendrites, not"
         " emerging from their middle."
         "trousers mode:"
         " - Use frustrums of cones. Distal diameter is always from compt dia."
         " - For linear dendrites (no branching), proximal diameter is "
         " diameter of the parent compartment"
         " - For branching dendrites, use a trouser function. Avoid overlap."
         " - For soma, use some variant of trousers. Here we must avoid overlap"
         " - For spines, use a way to smoothly merge into parent dend. Radius of"
         " curvature should be similar to that of the spine neck."
         " - Place somatic dendrites on surface of spherical soma, or at ends"
         " of cylindrical soma"
         " - Place dendritic spines on surface of cylindrical dendrites, not"
         " emerging from their middle."
         "cylinder mode:"
         " - Use cylinders. Diameter is just compartment dia."
         " - Place somatic dendrites on surface of spherical soma, or at ends"
         " of cylindrical soma"
         " - Place dendritic spines on surface of cylindrical dendrites, not"
         " emerging from their middle."
         " - Ignore spatial overlap.",
         &NeuroMesh::setGeometryPolicy,
         &NeuroMesh::getGeometryPolicy
     );
 
     // MsgDest Definitions
 
     // Field Elements
 
     static Finfo* neuroMeshFinfos[] =
     {
         &subTree,       // Value
         &subTreePath,       // Value
         &separateSpines,    // Value
         &numSegments,       // ReadOnlyValue
         &numDiffCompts,     // ReadOnlyValue
         &parentVoxel,           // ReadOnlyValue
         &elecComptList,         // ReadOnlyValue
         &elecComptMap,          // ReadOnlyValue
         &startVoxelInCompt,         // ReadOnlyValue
         &endVoxelInCompt,           // ReadOnlyValue
         &spineVoxelOnDendVoxel,     // ReadOnlyValue
         &dendVoxelsOnCompartment,   // ReadOnlyLookupValue
         &spineVoxelsOnCompartment,  // ReadOnlyLookupValue
         &diffLength,            // Value
         &geometryPolicy,        // Value
         spineListOut(),         // SrcFinfo
         psdListOut(),           // SrcFinfo
     };
 
     static Dinfo< NeuroMesh > dinfo;
     static Cinfo neuroMeshCinfo (
         "NeuroMesh",
         ChemCompt::initCinfo(),
         neuroMeshFinfos,
         sizeof( neuroMeshFinfos ) / sizeof ( Finfo* ),
         &dinfo
     );
 
     return &neuroMeshCinfo;
 }

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void NeuroMesh::innerBuildDefaultMesh	(	const Eref &	e,
		double	size,
		unsigned int	numEntries
	)

virtual

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

This is a bit odd, effectively asks to build an imaginary neuron and then subdivide it. I'll make do with a ball-and-stick model: Soma with a single apical dendrite with reasonable diameter. I will interpret size as total length of neuron, not as volume. Soma will have a diameter of up to 20 microns, anything bigger than this is treated as soma of 20 microns + dendrite of (specified length - 10 microns) for radius of soma. This means we avoid having miniscule dendrites protruding from soma, the shortest one will be 10 microns.

Implements ChemCompt.

Definition at line 1078 of file NeuroMesh.cpp.

References diffLength_, dummy, nodeIndex_, nodes_, numEntries, and updateCoords().

 {
 
     if ( size > 10e-3 )
     {
         cout << "Warning: attempt to build a neuron of dendritic length " <<
              size << " metres.\n Seems improbable.\n" <<
              "Using default of 0.001 m\n";
         size = 1e-3;
     }
 
     diffLength_ = size / numEntries;
 
     vector< unsigned int > noChildren( 0 );
     vector< unsigned int > oneChild( 1, 2 );
 
     if ( size < 20e-6 )
     {
         CylBase cb( 0, 0, 0, size, 0, numEntries );
         NeuroNode soma( cb, 0, noChildren, 0, Id(), true );
         nodes_.resize( 1, soma );
         nodeIndex_.resize( 1, 0 );
     }
     else
     {
         CylBase cb( 0, 0, 0, 20e-6, 0, 1 );
         NeuroNode soma( cb, 0, oneChild, 0, Id(), true );
         nodes_.resize( 1, soma );
         nodeIndex_.resize( 1, 0 );
 
         CylBase cbDummy( 0, 0, 10e-6, 4e-6, 0, 0 );
         NeuroNode dummy( cbDummy, 0, noChildren, 1, Id(), false );
         nodes_.push_back( dummy );
 
         CylBase cbDend( 0, 0, size, 2e-6, size - 10e-6, numEntries - 1);
         NeuroNode dend( cbDend, 1, noChildren, 2, Id(), false );
         nodes_.push_back( dend );
         for ( unsigned int i = 1; i < numEntries; ++i )
             nodeIndex_.push_back( 2 );
     }
     updateCoords();
 }

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unsigned int NeuroMesh::innerGetDimensions ( ) const

virtual

Implements ChemCompt.

Definition at line 441 of file NeuroMesh.cpp.

 {
     return 3;
 }

unsigned int NeuroMesh::innerGetNumEntries ( ) const

virtual

Inherited virtual func. Returns number of MeshEntry in array

Implements ChemCompt.

Definition at line 1030 of file NeuroMesh.cpp.

References nodeIndex_.

Referenced by indexToSpace().

 {
     return nodeIndex_.size();
 }

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

virtual

Implements ChemCompt.

Definition at line 1001 of file NeuroMesh.cpp.

 {
     /*
     unsigned int numEntries = nodeIndex_.size();
     vector< double > vols( numEntries, 0.0 );
     double oldVol = getMeshEntryVolume( 0 );
     for ( unsigned int i = 0; i < numEntries; ++i ) {
     assert( nodeIndex_[i] < nodes_.size() );
     NeuroNode& node = nodes_[ nodeIndex_[i] ];
     assert( nodes_.size() > node.parent() );
     NeuroNode& parent = nodes_[ node.parent() ];
     vols[i] = node.voxelVolume( parent, i );
     }
     vector< unsigned int > localEntries( numEntries );
     vector< vector< unsigned int > > outgoingEntries;
     vector< vector< unsigned int > > incomingEntries;
     meshSplit()->send( e,
     oldVol,
     vols, localEntries,
     outgoingEntries, incomingEntries );
     */
 }

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

void NeuroMesh::innerSetNumEntries ( unsigned int n )

virtual

Inherited virtual func.

Inherited virtual func. Assigns number of MeshEntries. This one doesn't set exact number, because each compartment has to fit integral numbers of voxels.

Implements ChemCompt.

Definition at line 1040 of file NeuroMesh.cpp.

References diffLength_, nodes_, and updateCoords().

 {
     static const unsigned int WayTooLarge = 1000000;
     if ( n == 0 || n > WayTooLarge )
     {
         cout << "Warning: NeuroMesh::innerSetNumEntries( " << n <<
              " ): out of range\n";
         return;
     }
     double totalLength = 0;
     for ( vector< NeuroNode >::iterator i = nodes_.begin();
             i != nodes_.end(); ++i )
     {
         if ( !i->isDummyNode() )
         {
             if ( i->isSphere() )
                 totalLength += i->getDia();
             else
                 totalLength += i->getLength();
         }
     }
     assert( totalLength > 0 );
     diffLength_ = totalLength / n;
     updateCoords();
 }

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void NeuroMesh::insertDummyNodes ( )

Puts in all the required dummy nodes for the tree.

Definition at line 530 of file NeuroMesh.cpp.

References Field< A >::get(), insertSingleDummy(), and nodes_.

Referenced by setSubTree().

 {
     // First deal with the soma, always positioned at node 0.
     unsigned int num = nodes_.size();
     for ( unsigned int i = 0; i < num; ++i )
     {
         if ( nodes_[i].parent() == ~0U )
         {
             Id elec = nodes_[i].elecCompt();
             double x = Field< double >::get( elec, "x0" );
             double y = Field< double >::get( elec, "y0" );
             double z = Field< double >::get( elec, "z0" );
             insertSingleDummy( ~0U, i, x, y, z );
         }
     }
 
     // Second pass: insert dummy nodes for children.
     // Need to know if parent has multiple children, because each of
     // them will need a dummyNode to connect to.
     // In all the policies so far, the dummy nodes take the same diameter
     // as the children that they host.
     for ( unsigned int i = 0; i < nodes_.size(); ++i )
     {
         vector< unsigned int > kids = nodes_[i].children();
         if ( (!nodes_[i].isDummyNode()) && kids.size() > 1 )
         {
             for( unsigned int j = 0; j < kids.size(); ++j )
             {
                 double x = nodes_[i].getX(); // use coords of parent.
                 double y = nodes_[i].getY();
                 double z = nodes_[i].getZ();
                 insertSingleDummy( i, kids[j], x, y, z );
                 // Replace the old kid entry with the dummy
                 kids[j] = nodes_.size() - 1;
             }
             // Connect up the parent to the dummy nodes.
             nodes_[i].clearChildren();
             for( unsigned int j = 0; j < kids.size(); ++j )
                 nodes_[i].addChild( kids[j] );
         }
     }
 }

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void NeuroMesh::insertSingleDummy	(	unsigned int	parent,
		unsigned int	self,
		double	x,
		double	y,
		double	z
	)

Puts in a dummy node between parent and self. Used to set up the correct size of proximal compartments.

Definition at line 503 of file NeuroMesh.cpp.

References NeuroNode::addChild(), NeuroNode::clearChildren(), doubleEq(), dummy, EPSILON, geometryPolicy_, nodes_, CylBase::setIsCylinder(), CylBase::setNumDivs(), NeuroNode::setParent(), CylBase::setX(), CylBase::setY(), and CylBase::setZ().

Referenced by insertDummyNodes().

 {
     static const double EPSILON = 1e-8;
     NeuroNode dummy( nodes_[ self ] );
     dummy.clearChildren();
     dummy.setNumDivs( 0 );
     bool isCylinder = (geometryPolicy_ == "cylinder" );
     dummy.setIsCylinder( isCylinder );
     dummy.setX( x );
     dummy.setY( y );
     dummy.setZ( z );
     // Now insert the dummy as a surrogate parent.
     dummy.setParent( parent );
     dummy.addChild( self );
     nodes_[ self ].setParent( nodes_.size() );
     // Idiot check for a bad dimensioned compartment.
     if ( nodes_[self].calculateLength( dummy ) < EPSILON )
     {
         double length = nodes_[self].getLength();
         dummy.setX( x - length );
         assert( doubleEq( nodes_[self].calculateLength( dummy ), length) );
     }
     nodes_.push_back( dummy );
 }

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

Definition at line 1329 of file NeuroMesh.cpp.

References NeuroNode::isDummyNode(), CylBase::matchCubeMeshEntries(), nodes_, NeuroNode::parent(), NeuroNode::startFid(), and surfaceGranularity_.

Referenced by matchMeshEntries().

 {
     for( unsigned int i = 0; i < nodes_.size(); ++i )
     {
         const NeuroNode& nn = nodes_[i];
         if ( !nn.isDummyNode() )
         {
             assert( nn.parent() < nodes_.size() );
             const NeuroNode& pa = nodes_[ nn.parent() ];
             nn.matchCubeMeshEntries( other, pa, nn.startFid(),
                                      surfaceGranularity_, ret, true, false );
         }
     }
 }

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void NeuroMesh::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 1251 of file NeuroMesh.cpp.

References ChemCompt::flipRet(), matchCubeMeshEntries(), EndoMesh::matchMeshEntries(), SpineMesh::matchNeuroMeshEntries(), and matchNeuroMeshEntries().

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

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

Definition at line 1345 of file NeuroMesh.cpp.

Referenced by matchMeshEntries().

1347 {

1348 }

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double NeuroMesh::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 1299 of file NeuroMesh.cpp.

References CylBase::getNumDivs(), NeuroNode::isDummyNode(), CylBase::nearest(), nodes_, NeuroNode::parent(), and NeuroNode::startFid().

 {
     double best = 1e12;
     index = 0;
     for( unsigned int i = 0; i < nodes_.size(); ++i )
     {
         const NeuroNode& nn = nodes_[i];
         if ( !nn.isDummyNode() )
         {
             assert( nn.parent() < nodes_.size() );
             const NeuroNode& pa = nodes_[ nn.parent() ];
             double linePos;
             double r;
             double near = nn.nearest( x, y, z, pa, linePos, r );
             if ( linePos >= 0 && linePos < 1.0 )
             {
                 if ( best > near )
                 {
                     best = near;
                     index = linePos * nn.getNumDivs() + nn.startFid();
                 }
             }
         }
     }
     if ( best == 1e12 )
         return -1;
     return best;
 }

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NeuroMesh & NeuroMesh::operator= ( const NeuroMesh & other )

Definition at line 316 of file NeuroMesh.cpp.

References area_, diffLength_, geometryPolicy_, length_, nodeIndex_, nodes_, separateSpines_, and vs_.

 {
     nodes_ = other.nodes_;
     nodeIndex_ = other.nodeIndex_;
     vs_ = other.vs_;
     area_ = other.area_;
     length_ = other.length_;
     diffLength_ = other.diffLength_;
     separateSpines_ = other.separateSpines_;
     geometryPolicy_ = other.geometryPolicy_;
     return *this;
 }

Id NeuroMesh::putSomaAtStart	(	Id	origSoma,
		unsigned int	maxDiaIndex
	)

This shuffles the nodes_ vector to put soma node at the start.

Definition at line 468 of file NeuroMesh.cpp.

References name, nodes_, and moose::strncasecmp().

 {
     Id soma = origSoma;
     if ( nodes_[maxDiaIndex].elecCompt() == soma )   // Happy, happy
     {
         ;
     }
     else if ( soma == Id() )
     {
         soma = nodes_[maxDiaIndex].elecCompt();
     }
     else     // Disagreement. Ugh.
     {
         string name = nodes_[ maxDiaIndex ].elecCompt().element()->getName();
         // OK, somehow this model has more than one soma compartment.
         if ( moose::strncasecmp( name.c_str(), "soma", 4 ) == 0 )
         {
             soma = nodes_[maxDiaIndex].elecCompt();
         }
         else
         {
             cout << "Warning: NeuroMesh::putSomaAtStart: named 'soma' compartment isn't biggest\n";
             soma = nodes_[maxDiaIndex].elecCompt();
         }
     }
     // Move soma to start of nodes_ vector.
     if ( maxDiaIndex != 0 )
     {
         NeuroNode temp = nodes_[0];
         nodes_[0] = nodes_[maxDiaIndex];
         nodes_[maxDiaIndex] = temp;
     }
     return soma;
 }

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void NeuroMesh::setDiffLength ( double v )

Definition at line 399 of file NeuroMesh.cpp.

References diffLength_, and updateCoords().

Referenced by initCinfo().

 {
     diffLength_ = v;
     updateCoords();
 }

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void NeuroMesh::setGeometryPolicy ( string v )

Definition at line 410 of file NeuroMesh.cpp.

References geometryPolicy_, and nodes_.

Referenced by initCinfo().

 {
     // STL magic! Converts the string v to lower case. Unfortunately
     // someone has overloaded tolower so it can have one or two args, so
     // this marvellous construct is useless.
     // std::transform( v.begin(), v.end(), v.begin(), std::tolower );
     for( string::iterator i = v.begin(); i != v.end(); ++i )
         *i = tolower( *i );
 
     if ( !( v == "cylinder" || v == "trousers" || v == "default" ) )
     {
         cout << "Warning: NeuroMesh::setGeometryPolicy( " << v <<
              " ):\n Mode must be one of cylinder, trousers, or default."
              "Using default\n";
         v = "default";
     }
 
     if ( v == geometryPolicy_ )
         return;
     geometryPolicy_ = v;
     bool isCylinder = ( v == "cylinder" );
     for ( vector< NeuroNode >::iterator
             i = nodes_.begin(); i != nodes_.end(); ++i )
         i->setIsCylinder( isCylinder );
 }

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void NeuroMesh::setSeparateSpines ( bool v )

Flag. True if NeuroMesh should configure a separate SpineMesh. The process is that both the NeuroMesh and SpineMesh should have been created, and a spineList message sent from the NeuroMesh to the SpineMesh. This may cascade down to PsdMesh.

Definition at line 693 of file NeuroMesh.cpp.

References separateSpines_, and updateCoords().

Referenced by initCinfo().

 {
     if ( v != separateSpines_ )
     {
         separateSpines_ = v;
         updateCoords();
     }
 }

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void NeuroMesh::setSubTree	(	const Eref &	e,
		vector< ObjId >	compartments
	)

The SubTree is a set of compartments to model. The first entry is the root of the tree, closest to the soma. The system does handle non-contiguous sets.

Definition at line 650 of file NeuroMesh.cpp.

References NeuroNode::buildSpinyTree(), NeuroNode::buildTree(), head_, insertDummyNodes(), nodes_, parent_, separateSpines_, shaft_, subTreePath_, transmitSpineInfo(), updateCoords(), and updateShaftParents().

Referenced by initCinfo(), and setSubTreePath().

 {
     sort( compts.begin(), compts.end() );
     if ( separateSpines_ )
     {
         NeuroNode::buildSpinyTree( compts, nodes_, shaft_, head_, parent_);
         insertDummyNodes();
         updateCoords();
         updateShaftParents();
         transmitSpineInfo( e );
     }
     else
     {
         NeuroNode::buildTree( nodes_, compts );
         insertDummyNodes();
         updateCoords();
     }
     subTreePath_ = "Undefined: subTree set as a compartment list";
 }

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void NeuroMesh::setSubTreePath	(	const Eref &	e,
		string	path
	)

This overloaded function sets up a presumed contiguous set of compartments, complains if they are not contiguous due to the check in NeuroNode::traverse.

The 'path' argument specifies a wildcard list of compartments, which can be also a comma-separated explicit list. Does not have to be in any particular order.

Definition at line 680 of file NeuroMesh.cpp.

References path, setSubTree(), subTreePath_, and wildcardFind().

Referenced by initCinfo().

 {
     vector< ObjId > compts;
     wildcardFind( path, compts );
     setSubTree( e, compts );
     subTreePath_ = path;
 }

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void NeuroMesh::transmitSpineInfo ( const Eref & e )

Transmits the information about spines to SpineMesh and PsdMesh.

Definition at line 591 of file NeuroMesh.cpp.

References Eref::element(), Element::hasMsgs(), head_, parent_, SpineEntry::psdCoords(), psdListOut(), shaft_, and spineListOut().

Referenced by setSubTree().

 {
     spineListOut()->send( e, shaft_, head_, parent_ );
 
     vector< double > ret;
     vector< double > psdCoords;
     vector< unsigned int > index( head_.size(), 0 );
     if ( e.element()->hasMsgs( psdListOut()->getBindIndex() ) )
     {
         // Later can refine to deal with spineless PSDs.
         for ( unsigned int i = 0; i < head_.size(); ++i )
         {
             SpineEntry se =
                 SpineEntry( shaft_[i], head_[i], parent_[i] );
             ret = se.psdCoords();
             assert( ret.size() == 8 );
             psdCoords.insert( psdCoords.end(), ret.begin(), ret.end() );
             index[i] = i;
         }
         // ids.clear();
         // e.element()->getNeighbors( ids, psdListOut() );
         psdListOut()->send( e, psdCoords, head_, index );
     }
 }

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void NeuroMesh::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 size, so does numEntries. Assumes that the soma node is at index 0.

Definition at line 343 of file NeuroMesh.cpp.

References area_, buildStencil(), diffLength_, CylBase::getMiddleArea(), CylBase::getNumDivs(), CylBase::getVoxelLength(), NeuroNode::isDummyNode(), length_, nodeIndex_, nodes_, NeuroNode::parent(), NeuroNode::startFid(), CylBase::voxelVolume(), and vs_.

Referenced by innerBuildDefaultMesh(), innerSetNumEntries(), setDiffLength(), setSeparateSpines(), and setSubTree().

 {
     unsigned int startFid = 0;
     if ( nodes_.size() <= 1 ) // One for soma and one for dummy pa of soma
     {
         buildStencil();
         return;
     }
     for ( vector< NeuroNode >::iterator i = nodes_.begin();
             i != nodes_.end(); ++i )
     {
         if ( !i->isDummyNode() )
         {
             double len = i->getLength();
             unsigned int numDivs = floor( 0.5 + len / diffLength_ );
             if ( numDivs < 1 )
                 numDivs = 1;
             i->setNumDivs( numDivs );
             i->setStartFid( startFid );
             startFid += numDivs;
         }
     }
     nodeIndex_.resize( startFid );
     for ( unsigned int i = 0; i < nodes_.size(); ++i )
     {
         if ( !nodes_[i].isDummyNode() )
         {
             unsigned int end = nodes_[i].startFid() +nodes_[i].getNumDivs();
             assert( end <= startFid );
             assert( nodes_[i].getNumDivs() > 0 );
             for ( unsigned int j = nodes_[i].startFid(); j < end; ++j )
                 nodeIndex_[j] = i;
         }
     }
     // Assign volumes and areas
     vs_.resize( startFid );
     area_.resize( startFid );
     length_.resize( startFid );
     for ( unsigned int i = 0; i < nodes_.size(); ++i )
     {
         const NeuroNode& nn = nodes_[i];
         if ( !nn.isDummyNode() )
         {
             assert( nn.parent() < nodes_.size() );
             const NeuroNode& parent = nodes_[ nn.parent() ];
             for ( unsigned int j = 0; j < nn.getNumDivs(); ++j )
             {
                 vs_[j + nn.startFid()] = nn.voxelVolume( parent, j );
                 area_[j + nn.startFid()] = nn.getMiddleArea( parent, j);
                 length_[j + nn.startFid()] = nn.getVoxelLength();
             }
         }
     }
     buildStencil();
 }

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void NeuroMesh::updateShaftParents ( )

converts the parents_ vector from identifying the parent NeuroNode to identifying the parent voxel, for each shaft entry.

Definition at line 620 of file NeuroMesh.cpp.

References Field< A >::get(), CylBase::getX(), CylBase::getY(), CylBase::getZ(), CylBase::nearest(), nodes_, NeuroNode::parent(), parent_, shaft_, and NeuroNode::startFid().

Referenced by setSubTree().

 {
     assert( shaft_.size() == parent_.size() );
     vector< unsigned int > pa = parent_;
     for ( unsigned int i = 0; i < shaft_.size(); ++i )
     {
         const NeuroNode& nn = nodes_[ pa[i] ];
         double x0 = Field< double >::get( shaft_[i], "x0" );
         double y0 = Field< double >::get( shaft_[i], "y0" );
         double z0 = Field< double >::get( shaft_[i], "z0" );
         const NeuroNode& pn = nodes_[ nn.parent() ];
         unsigned int index = 0;
         double r = nn.nearest( x0, y0, z0, pn, index );
         if ( r >= 0.0 )
         {
             parent_[i] = index + nn.startFid();
         }
         else
         {
             cout << "Warning: NeuroMesh::updateShaftParents: may be"
                  " misaligned on " << i << ", r=" << r <<
                  "\n pt=(" << x0 << "," << y0 << "," << z0 << ")" <<
                  "pa=(" << nn.getX() << "," << nn.getY() << "," << nn.getZ() << ")" <<
                  "\n";
             parent_[i] = index + nn.startFid();
         }
     }
 }

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double NeuroMesh::vGetEntireVolume ( ) const

virtual

Inherited virtual func. Returns volume of soma and whole dendritic tree of neuron, excluding spines. Any axonal compartments are also included.

Implements ChemCompt.

Definition at line 855 of file NeuroMesh.cpp.

References vs_.

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

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

virtual

Virtual func so that derived classes can return voxel midpoint.

Implements ChemCompt.

Definition at line 819 of file NeuroMesh.cpp.

References CylBase::getCoordinates(), CylBase::getNumDivs(), NeuroNode::isDummyNode(), nodes_, NeuroNode::parent(), and vs_.

 {
     static vector< double > midpoint;
     unsigned int num = vs_.size();
     midpoint.resize( num * 3 );
     vector< double >::iterator k = midpoint.begin();
     for ( unsigned int i = 0; i < nodes_.size(); ++i )
     {
         const NeuroNode& nn = nodes_[i];
         if ( !nn.isDummyNode() )
         {
             assert( nn.parent() < nodes_.size() );
             const NeuroNode& parent = nodes_[ nn.parent() ];
             for ( unsigned int j = 0; j < nn.getNumDivs(); ++j )
             {
                 vector< double > coords = nn.getCoordinates( parent, j );
                 *k = ( coords[0] + coords[3] ) / 2.0;
                 *(k + num ) = ( coords[1] + coords[4] ) / 2.0;
                 *(k + 2 * num ) = ( coords[2] + coords[5] ) / 2.0;
                 k++;
             }
         }
     }
     return midpoint;
 }

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

virtual

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

Implements ChemCompt.

Definition at line 814 of file NeuroMesh.cpp.

References vs_.

 {
     return vs_;
 }

bool NeuroMesh::vSetVolumeNotRates ( double volume )

virtual

Inherited virtual func. In the NeuroMesh this carries out a rescaling on all dimensions. The length and diameter of each compartment are scaled by the same factor = volscale^(1/3) The rescaling carries through to the spines and PSDs, which are also updated. They are not permitted to change their own volumes.

Implements ChemCompt.

Definition at line 864 of file NeuroMesh.cpp.

References area_, diffLength_, CylBase::getDia(), CylBase::getLength(), length_, nodeIndex_, nodes_, parentVoxel_, CylBase::setDia(), CylBase::setLength(), CylBase::volume(), and vs_.

 {
     assert( parentVoxel_.size() == nodeIndex_.size() );
     assert( parentVoxel_.size() == 1 );
     assert( vs_.size() == 1 );
     if ( parentVoxel_.size() > 1 ) // Can't handle multicompartments yet.
         return false;
     NeuroNode& n = nodes_[0];
     double oldvol = n.volume( nodes_[0] );
     double scale = pow( volume / oldvol, 1.0/3.0 );
     n.setLength( n.getLength() * scale );
     n.setDia( n.getDia() * scale );
     vs_[0] *= volume / oldvol;
     area_[0] *= scale * scale;
     length_[0] *= scale;
     diffLength_ = length_[0];
 
     return true;
 }

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Member Data Documentation

vector< double > NeuroMesh::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 300 of file NeuroMesh.h.

Referenced by getVoxelArea(), operator=(), updateCoords(), and vSetVolumeNotRates().

double NeuroMesh::diffLength_

private

Definition at line 306 of file NeuroMesh.h.

Referenced by getDiffLength(), innerBuildDefaultMesh(), innerSetNumEntries(), NeuroMesh(), operator=(), setDiffLength(), updateCoords(), and vSetVolumeNotRates().

string NeuroMesh::geometryPolicy_

private

Definition at line 316 of file NeuroMesh.h.

Referenced by getGeometryPolicy(), insertSingleDummy(), operator=(), and setGeometryPolicy().

vector< Id > NeuroMesh::head_

private

Id of shaft compartment.

Definition at line 330 of file NeuroMesh.h.

Referenced by filterSpines(), getSpineVoxelsOnCompartment(), setSubTree(), and transmitSpineInfo().

vector< double > NeuroMesh::length_

private

Pre-calculation of length of each MeshEntry.

Definition at line 303 of file NeuroMesh.h.

Referenced by getVoxelLength(), operator=(), updateCoords(), and vSetVolumeNotRates().

vector< unsigned int > NeuroMesh::nodeIndex_

private

nodeIndex_[fid_for_MeshEntry]. Looks up index of NeuroNode from the fid of each MeshEntry. In other words, node# = nodeIndex_[ voxel# ]. This is needed because there are typically many voxels in each electrical compartment of the neuron. The nodes_ map closely to the electrical compartments.

Definition at line 287 of file NeuroMesh.h.

Referenced by buildStencil(), extendedMeshEntryVolume(), getAdx(), getCoordinates(), getDiffusionArea(), getElecComptMap(), getMeshEntryVolume(), getMeshType(), getNumDiffCompts(), getSpineVoxelOnDendVoxel(), indexToSpace(), innerBuildDefaultMesh(), innerGetNumEntries(), operator=(), updateCoords(), and vSetVolumeNotRates().

vector< NeuroNode > NeuroMesh::nodes_

private

Array of geometry specifiers for each segment of the neuronal model. Includes information equivalent to the CylMesh, as well as information to tie the node back to the original 'compartment' from the neuronal model.

Definition at line 270 of file NeuroMesh.h.

Referenced by getAdx(), getCoordinates(), getDendVoxelsOnCompartment(), getDiffusionArea(), getElecComptList(), getElecComptMap(), getEndVoxelInCompt(), getMeshEntryVolume(), getMeshType(), getNodes(), getNumSegments(), getStartVoxelInCompt(), indexToSpace(), innerBuildDefaultMesh(), innerSetNumEntries(), insertDummyNodes(), insertSingleDummy(), matchCubeMeshEntries(), nearest(), NeuroMesh(), operator=(), putSomaAtStart(), setGeometryPolicy(), setSubTree(), updateCoords(), updateShaftParents(), vGetVoxelMidpoint(), and vSetVolumeNotRates().

vector< unsigned int > NeuroMesh::parent_

private

Id of head compartment.

Definition at line 331 of file NeuroMesh.h.

Referenced by getSpineVoxelOnDendVoxel(), setSubTree(), transmitSpineInfo(), and updateShaftParents().

vector< unsigned int > NeuroMesh::parentVoxel_

private

Index of parent voxel of spines.

Index of parent voxel of each voxel. The root voxel has a parent of -1.

Definition at line 336 of file NeuroMesh.h.

Referenced by buildStencil(), getParentVoxel(), and vSetVolumeNotRates().

bool NeuroMesh::separateSpines_

private

Max permitted length constant for diffusion.

Flag. True if NeuroMesh should configure a separate SpineMesh. The process is that both the NeuroMesh and SpineMesh should have been created, and a spineList message sent from the NeuroMesh to the SpineMesh.

Definition at line 314 of file NeuroMesh.h.

Referenced by getSeparateSpines(), operator=(), setSeparateSpines(), and setSubTree().

vector< Id > NeuroMesh::shaft_

private

The shaft vector and the matching head vector track the dendritic spines. The parent is the voxel to which the spine is attached.

Definition at line 329 of file NeuroMesh.h.

Referenced by filterSpines(), getSpineVoxelsOnCompartment(), setSubTree(), transmitSpineInfo(), and updateShaftParents().

string NeuroMesh::subTreePath_

private

Path of sub-tree used for the chemical model. This is undefined if the user assigns the subtree as a vector of objects, which is the case when using rdesigneur.

Definition at line 277 of file NeuroMesh.h.

Referenced by getSubTreePath(), setSubTree(), and setSubTreePath().

double NeuroMesh::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 323 of file NeuroMesh.h.

Referenced by matchCubeMeshEntries().

vector< double > NeuroMesh::vs_

private

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

Definition at line 294 of file NeuroMesh.h.

Referenced by operator=(), updateCoords(), vGetEntireVolume(), vGetVoxelMidpoint(), vGetVoxelVolume(), and vSetVolumeNotRates().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation