#include <NeuroNode.h>

Inheritance diagram for NeuroNode:

Collaboration diagram for NeuroNode:

Public Member Functions
void	addChild (unsigned int child)

double	calculateLength (const CylBase &parent)

const vector< unsigned int > &	children () const

void	clearChildren ()

Id	elecCompt () const

void	findConnectedCompartments (const map< Id, unsigned int > &nodeMap, const vector< NeuroNode > &nodes)

void	innerTraverse (vector< NeuroNode > &tree, const vector< NeuroNode > &nodes, vector< unsigned int > &seen) const

bool	isDummyNode () const

bool	isSphere () const

bool	isStartNode () const

	NeuroNode (const CylBase &cb, unsigned int parent, const vector< unsigned int > &children, unsigned int startFid_, Id elecCompt, bool isSphere)

	NeuroNode (Id elecCompt)

	NeuroNode ()

unsigned int	parent () const

void	setParent (unsigned int parent)

void	setParentAndChildren (unsigned int index, int dendParent, vector< NeuroNode > &nodes, const unordered_map< Id, unsigned int > &dendMap)

void	setStartFid (unsigned int f)

unsigned int	startFid () const

Public Member Functions inherited from CylBase
	CylBase (double x, double y, double z, double dia, double length, unsigned int numDivs)

	CylBase ()

vector< double >	getCoordinates (const CylBase &parent, unsigned int entry) const

double	getDia () const

double	getDiffusionArea (const CylBase &parent, unsigned int index) const

bool	getIsCylinder () const

double	getLength () const

double	getMiddleArea (const CylBase &parent, unsigned int index) const
	Return cross-section area of middle of specified voxel. More...

unsigned int	getNumDivs () const

double	getVoxelLength () const
	Return length of voxel. All are equal. More...

double	getX () const

double	getY () const

double	getZ () const

void	matchCubeMeshEntries (const ChemCompt *other, const CylBase &parent, unsigned int startIndex, double granularity, vector< VoxelJunction > &ret, bool useCylinderCurve, bool useCylinderCap) const

double	nearest (double x, double y, double z, const CylBase &parent, double &linePos, double &r) const

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

double	selectGridSize (double h, double dia1, double granularity) const

void	setDia (double v)

void	setIsCylinder (bool v)

void	setLength (double v)

void	setNumDivs (unsigned int v)

void	setX (double v)

void	setY (double v)

void	setZ (double v)

double	volume (const CylBase &parent) const
	Returns vol of current node. Usually needs to refer to parent. More...

double	voxelVolume (const CylBase &parent, unsigned int fid) const

Static Public Member Functions
static void	buildSpinyTree (vector< ObjId > &elist, vector< NeuroNode > &nodes, vector< Id > &shaftId, vector< Id > &headId, vector< unsigned int > &spineParent)

static void	buildTree (vector< NeuroNode > &nodes, vector< ObjId > elist)

static void	filterSpines (vector< NeuroNode > &nodes, vector< Id > &shaftId, vector< Id > &headId, vector< unsigned int > &parent)

static unsigned int	findStartNode (const vector< NeuroNode > &nodes)

static unsigned int	removeDisconnectedNodes (vector< NeuroNode > &nodes)

static void	traverse (vector< NeuroNode > &nodes, unsigned int start)

Private Attributes
vector< unsigned int >	children_

Id	elecCompt_
	Id of electrical compartment in which this diffusive compt lives. More...

bool	isSphere_

unsigned int	parent_

unsigned int	startFid_

Detailed Description

Helper class for the NeuroMesh. Defines the geometry of the branching neuron.

Definition at line 18 of file NeuroNode.h.

Constructor & Destructor Documentation

NeuroNode::NeuroNode	(	const CylBase &	cb,
		unsigned int	parent,
		const vector< unsigned int > &	children,
		unsigned int	startFid,
		Id	elecCompt,
		bool	isSphere
	)

This function explicitly fills in all fields of the NeuroNode

Helper class for the NeuroMesh. Defines the geometry of the branching neuron.

Definition at line 28 of file NeuroNode.cpp.

         :
                 CylBase( cb ),
                 parent_( parent ),
                 children_( children ),
                 startFid_( startFid ),
                 elecCompt_( elecCompt ),
                 isSphere_( isSphere )
 {;}

NeuroNode::NeuroNode ( Id elecCompt )

This builds the node using info from the compartment. But the parent and children have to be filled in later

Definition at line 41 of file NeuroNode.cpp.

References Field< A >::get(), CylBase::setDia(), CylBase::setLength(), CylBase::setX(), CylBase::setY(), and CylBase::setZ().

         :
                 parent_( ~0 ),
                 startFid_( 0 ),
                 elecCompt_( elecCompt ),
                 isSphere_( false )
 {
     double dia = Field< double >::get( elecCompt, "diameter" );
     setDia( dia );
     double length = Field< double >::get( elecCompt, "length" );
     setLength( length );
     double x = Field< double >::get( elecCompt, "x" );
     double y = Field< double >::get( elecCompt, "y" );
     double z = Field< double >::get( elecCompt, "z" );
     setX( x );
     setY( y );
     setZ( z );
 }

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NeuroNode::NeuroNode ( )

Empty constructor for vectors

Definition at line 61 of file NeuroNode.cpp.

         :
                 parent_( ~0 ),
                 startFid_( 0 ),
                 elecCompt_( Id() ),
                 isSphere_( false )
 {;}

Member Function Documentation

void NeuroNode::addChild ( unsigned int child )

Fills in child vector

Definition at line 101 of file NeuroNode.cpp.

References children_.

Referenced by NeuroMesh::insertSingleDummy().

 {
     children_.push_back( child );
 }

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void NeuroNode::buildSpinyTree	(	vector< ObjId > &	elist,
		vector< NeuroNode > &	nodes,
		vector< Id > &	shaftId,
		vector< Id > &	headId,
		vector< unsigned int > &	spineParent
	)

static

This function takes a list of elements and builds a tree. Info on any attached spines are placed in the shaft_, head_, and parent_ vectors. The list of elements can be discontiguous. This is meant to be insensitive to vagaries in how the user has set up the compartment messaging, provided that there is at least one recognized message between connected compartments.

static function.

Definition at line 491 of file NeuroNode.cpp.

References isPartOfDend(), setParentAndChildren(), sortByShaftIds(), and spinyTraverse().

Referenced by NeuroMesh::setSubTree().

 {
     nodes.clear();
     sort( elist.begin(), elist.end() );
     unordered_map< Id, unsigned int > dendMap;
     vector< Id > dend;
     for ( vector< ObjId >::iterator
         i = elist.begin(); i != elist.end(); ++i ) {
         if ( isPartOfDend( *i ) ) {
             dendMap[ *i ] = dend.size();
             //cout << "st: dendMap[" << *i << "] = " << dend.size() << endl;
             dend.push_back( *i );
         }
     }
     vector< int > seen( dend.size(), 0 );
     vector< int > dendParent( dend.size(), -1 );
     int numSeen = 0;
     for ( unsigned int i = 0; i < dend.size(); ++i ) {
         if ( !seen[i] )
             spinyTraverse( i, dend, dendMap, seen, ++numSeen,
             shaftId, headId,
             dendParent, spineParent );
     }
     // Here I sort by shaftIds. I have 4 parallel arrays, so I get the
     // Index order of the whole lot that will sort the shaftIds.
     sortByShaftIds( shaftId, headId, spineParent );
     if ( numSeen == 0 )
         return;
     for ( unsigned int i = 0; i < dend.size(); ++i )
         nodes.push_back( NeuroNode( dend[i] ) );
     for ( unsigned int i = 0; i < dend.size(); ++i )
         nodes[i].setParentAndChildren( i, dendParent[i], nodes, dendMap );
 
     if ( numSeen > 1 ) {
         cout << "Warning: NeuroNode::buildSpinyTree: There are " <<
             numSeen << " distinct subgroups on the given path\n";
     }
 }

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void NeuroNode::buildTree	(	vector< NeuroNode > &	nodes,
		vector< ObjId >	elist
	)

static

This function takes a list of elements that include connected compartments, and constructs a tree of nodes out of them. The generated nodes vector starts with the soma, and is a depth-first sequence of nodes. This is meant to be insensitive to vagaries in how the user has set up the compartment messaging, provided that there is at least one recognized message between connected compartments.

static function.

Definition at line 558 of file NeuroNode.cpp.

References findConnectedCompartments(), findStartNode(), removeDisconnectedNodes(), and traverse().

Referenced by NeuroMesh::setSubTree().

 {
     nodes.clear();
     map< Id, unsigned int > nodeMap;
     for ( vector< ObjId >::iterator
         i = elist.begin(); i != elist.end(); ++i ) {
         if ( i->element()->cinfo()->isA( "CompartmentBase" ) )
             nodes.push_back( NeuroNode( *i ) );
     }
     if ( nodes.size() <= 1 )
         return;
     for ( unsigned int i = 0; i < nodes.size(); ++i ) {
         if ( nodeMap.find( nodes[i].elecCompt() ) != nodeMap.end() ) {
             cout << "Warning: NeuroNode.buildTree(): Node[" << i <<
                 "] refers to existing compartment: " <<
                 nodes[i].elecCompt().path() << endl;
         }
         nodeMap[ nodes[i].elecCompt() ] = i;
     }
     assert( nodeMap.size() == nodes.size() );
     for ( unsigned int i = 0; i < nodes.size(); ++i )
         nodes[i].findConnectedCompartments( nodeMap, nodes );
     unsigned int numRemoved = removeDisconnectedNodes( nodes );
     if ( numRemoved > 0 ) {
         cout << "Warning: NeuroNode::buildTree: Removed " <<
                 numRemoved << " nodes because they were not connected\n";
     }
     unsigned int start = findStartNode( nodes );
     traverse( nodes, start );
 }

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double NeuroNode::calculateLength ( const CylBase & parent )

Calculates and returns compartment length, from parent xyz to self xyz. Assigns own length as a side-effect.

Definition at line 121 of file NeuroNode.cpp.

References CylBase::getLength(), CylBase::getX(), CylBase::getY(), CylBase::getZ(), and CylBase::setLength().

 {
     if ( &parent == this ) // Do nothing
             return getLength();
     double dx = parent.getX() - getX();
     double dy = parent.getY() - getY();
     double dz = parent.getZ() - getZ();
     double ret = sqrt( dx * dx + dy * dy + dz * dz );
     setLength( ret );
     return ret;
 }

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const vector< unsigned int > & NeuroNode::children ( ) const

Definition at line 96 of file NeuroNode.cpp.

References children_.

 {
         return children_;
 }

void NeuroNode::clearChildren ( )

Zeroes out the child vector

Definition at line 106 of file NeuroNode.cpp.

References children_.

Referenced by NeuroMesh::insertSingleDummy().

 {
     children_.resize( 0 );
 }

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Id NeuroNode::elecCompt ( ) const

Definition at line 79 of file NeuroNode.cpp.

References elecCompt_.

Referenced by filterSpines().

 {
         return elecCompt_;
 }

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void NeuroNode::filterSpines	(	vector< NeuroNode > &	nodes,
		vector< Id > &	shaftId,
		vector< Id > &	headId,
		vector< unsigned int > &	parent
	)

static

Trims off all spines from tree. Does so by identifying a set of reasonable names: shaft, head, spine, and variants in capitals. Having done this it builds two matching vectors of vector of shafts and heads, which is a hack that assumes that there are no sub-branches in spines. The returned nodes vector has non spine/shaft compartments only. The returned shaftId vector has all the shaft compartments. The returned headId vector has all the shaft compartments. The returned parent vector has the indices of the parent node for each shaft. There should be exactly the same number of entries in the shaftId, headId and parent vectors.

Trims off all spines from tree. Does so by identifying a set of reasonable names: shaft, head, spine, and variants in capitals. Having done this it builds two matching vectors of vector of shafts and heads, which is a hack that assumes that there are no sub-branches in spines. Then there is an index for parent NeuroNode entry. Static function

Definition at line 620 of file NeuroNode.cpp.

References elecCompt(), elecCompt_, Id::element(), Element::getName(), name, parent(), and reassignNodeIndices().

 {
     headId.clear();
     shaftId.clear();
     parent.clear();
     vector< NeuroNode > temp;
     temp.reserve( nodes.size() );
     vector< unsigned int > nodeToTempMap( nodes.size(), ~0U );
     vector< unsigned int > shaft;
     vector< unsigned int > reverseShaft( nodes.size(), ~0U );
     vector< unsigned int > head;
     for ( unsigned int i = 0; i < nodes.size(); ++i ) {
         const NeuroNode& n = nodes[i];
         string name = n.elecCompt_.element()->getName();
         for ( string::iterator j = name.begin(); j != name.end(); ++j )
             *j = tolower(*j);
 
         if ( name.find( "shaft" ) != string::npos ||
             name.find( "neck" ) != string::npos ) {
             reverseShaft[i] = shaft.size();
             shaft.push_back( i );
             // Remove from nodes vector by simply not copying.
         } else if ( name.find( "spine" ) != string::npos ||
             name.find( "head" ) != string::npos ) {
             head.push_back( i );
             // Remove from nodes vector by simply not copying.
         } else {
             nodeToTempMap[i] = temp.size();
             temp.push_back( n );
         }
 
         /*
         const char* name = n.elecCompt_.element()->getName().c_str();
         if ( strncasecmp( name, "shaft", 5 ) == 0 ||
             strncasecmp( name, "neck", 4 ) == 0 ||
             strncasecmp( name, "spine_neck", 10 ) == 0 ||
             strncasecmp( name, "spine_shaft", 11 ) == 0 ||
             strncasecmp( name, "stalk", 5 ) == 0 ) {
             reverseShaft[i] = shaft.size();
             shaft.push_back( i );
             // Remove from nodes vector by simply not copying.
         } else if ( strncasecmp( name, "spine", 5 ) == 0 ||
             strncasecmp( name, "head", 4 ) == 0 ) {
             head.push_back( i );
             // Remove from nodes vector by simply not copying.
         } else {
             nodeToTempMap[i] = temp.size();
             temp.push_back( n );
         }
         */
     }
     // Now go through finding spine shafts.
     for ( unsigned int i = 0; i < head.size(); ++i ) {
         const NeuroNode& n = nodes[ head[i] ];
         headId.push_back( n.elecCompt() );
         assert( reverseShaft[ n.parent() ] != ~0U );
         const NeuroNode& pa = nodes[ n.parent() ];
         shaftId.push_back( pa.elecCompt() );
         assert( nodeToTempMap[ pa.parent() ] != ~0U );
         parent.push_back( nodeToTempMap[ pa.parent() ] );
     }
     assert( shaftId.size() == headId.size() );
 
     reassignNodeIndices( temp, nodeToTempMap );
     nodes = temp;
 }

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void NeuroNode::findConnectedCompartments	(	const map< Id, unsigned int > &	nodeMap,
		const vector< NeuroNode > &	nodes
	)

Finds all the compartments connected to current node, put them all into the 'children' vector even if they may be 'parent' by the messaging. This is because this function has to be robust enough to sort this out

Definition at line 198 of file NeuroNode.cpp.

References children_, elecCompt_, and findAllConnectedCompartments().

Referenced by buildTree().

 {
     vector< Id > all = findAllConnectedCompartments( elecCompt_ );
     // Now we have a list of all compartments connected to the current one.
     // Convert to node indices.
     children_.resize( all.size() );
     // Note that the nodeMap only includes compts on list, which may be a
     // subset of compts in entire model. So we only want to explore those.
     for ( unsigned int i = 0; i < all.size(); ++i ) {
         map< Id, unsigned int >::const_iterator k = nodeMap.find( all[i] );
         if ( k != nodeMap.end() ) {
             children_[i] = k->second;
         } else {
             cout << "Warning: NeuroNode::findConnectedCompartments: could not find compartment " << all[i].path() << endl;
             // bruteForceFind( nodes, all[i] );
         }
     }
 }

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unsigned int NeuroNode::findStartNode ( const vector< NeuroNode > & nodes )

static

Find the start node, typically the soma, of a model. In terms of the solution, this should be the node at the root of the tree. Returns index in nodes vector. Technically the matrix solution could begin from any terminal branch, but it helps to keep the soma identical to the root of the tree.

Uses two heuristics to locate the start node: Looks for the node with the largest diameter, and also looks for node(s) with 'soma' in their name. If these disagree then it goes with the 'soma' node. If there are many of the soma nodes, it goes with the fattest.

Find the start node, typically the soma, of a model. In terms of the solution, this should be the node at the root of the tree. Returns index in nodes vector. Technically the matrix solution could begin from any terminal branch, but it helps to keep the soma identical to the root of the tree.

Uses two heuristics to locate the start node: Looks for the node with the largest diameter, and also looks for node(s) with 'soma' in their name. If these disagree then it goes with the 'soma' node. If there are many of the soma nodes, it goes with the fattest.

static func

Definition at line 270 of file NeuroNode.cpp.

References CylBase::getDia(), name, and moose::strncasecmp().

Referenced by buildTree().

 {
     double maxDia = 0.0;
     unsigned int somaIndex = ~0;
     for ( unsigned int i = 0; i < nodes.size(); ++i ) {
         const char* name = nodes[i].elecCompt_.element()->getName().c_str();
         if ( moose::strncasecmp( name, "soma", 4 ) == 0 ) {
             if ( maxDia < nodes[i].getDia() ) {
                 maxDia = nodes[i].getDia();
                 somaIndex = i;
             }
         }
     }
     if ( somaIndex == ~0U ) { // Didn't find any compartment called soma
         for ( unsigned int i =0; i < nodes.size(); ++i ) {
             if ( maxDia < nodes[i].getDia() ) {
                 maxDia = nodes[i].getDia();
                 somaIndex = i;
             }
         }
     }
     assert( somaIndex != ~0U );
     return somaIndex;
 }

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void NeuroNode::innerTraverse	(	vector< NeuroNode > &	tree,
		const vector< NeuroNode > &	nodes,
		vector< unsigned int > &	seen
	)		const

Helper recursive function for traversing nodes to build tree.

Definition at line 351 of file NeuroNode.cpp.

References children_.

 {
     unsigned int pa = tree.size() - 1;
     tree.back().children_.clear();
 
     for ( vector< unsigned int >::const_iterator i =
                     children_.begin(); i != children_.end(); ++i ) {
         assert( *i < nodes.size() );
 
         // Check that it is an unseen node, ie, not a parent.
         if ( seen[ *i ] == ~0U )  {
             seen[ *i ] = tree.size();
             tree[pa].children_.push_back( tree.size() );
             tree.push_back( nodes[ *i ] );
             tree.back().parent_ = pa;
             nodes[*i].innerTraverse( tree, nodes, seen );
         }
     }
     assert( tree.size() <= nodes.size() );
 }

bool NeuroNode::isDummyNode ( ) const

True when this is a dummy node to represent the coordinates of the start end of a compartment. For example, the start coords of a compartment sitting on a spherical soma, or the start coords of a spine neck along a longer dendritic compartment. In all other cases the start coordinates are just those of the end of the parent compartment.

When the isDummyNode is true, the elecCompt represents the Id of the compartment whose start it is.

Definition at line 83 of file NeuroNode.cpp.

References CylBase::getNumDivs().

Referenced by NeuroMesh::getAdx(), NeuroMesh::matchCubeMeshEntries(), NeuroMesh::nearest(), NeuroMesh::updateCoords(), and NeuroMesh::vGetVoxelMidpoint().

 {
         return ( getNumDivs() == 0 );
 }

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bool NeuroNode::isSphere ( ) const

Definition at line 87 of file NeuroNode.cpp.

References isSphere_.

 {
         return isSphere_;
 }

bool NeuroNode::isStartNode ( ) const

Definition at line 91 of file NeuroNode.cpp.

References startFid_.

 {
         return ( startFid_ == 0 );
 }

unsigned int NeuroNode::parent ( ) const

Definition at line 69 of file NeuroNode.cpp.

References parent_.

Referenced by filterSpines(), NeuroMesh::getAdx(), NeuroMesh::indexToSpace(), NeuroMesh::matchCubeMeshEntries(), NeuroMesh::nearest(), setParent(), NeuroMesh::updateCoords(), NeuroMesh::updateShaftParents(), and NeuroMesh::vGetVoxelMidpoint().

 {
         return parent_;
 }

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unsigned int NeuroNode::removeDisconnectedNodes ( vector< NeuroNode > & nodes )

static

Go through nodes vector and eliminate entries that have zero children, that is, are not connected to any others. Need to clean up 'children_' list after this is called.

Go through nodes vector and eliminate entries that have zero children, that is, are not connected to any others. Need to clean up 'children_' list.

static func

Definition at line 227 of file NeuroNode.cpp.

References children_.

Referenced by buildTree().

 {
     vector< NeuroNode > temp;
     vector< unsigned int > nodeMap( nodes.size() );
 
     unsigned int j = 0;
     for ( unsigned int i = 0; i < nodes.size(); ++i ) {
         if ( nodes[i].children_.size() > 0 ) {
             temp.push_back( nodes[i] );
             nodeMap[i] = j;
             ++j;
         } else {
             nodeMap[i] = ~0;
         }
     }
     for ( unsigned int i = 0; i < temp.size(); ++i ) {
         vector< unsigned int >& c = temp[i].children_;
         for ( vector< unsigned int >::iterator
                         j = c.begin(); j != c.end(); ++j ) {
             assert( nodeMap[ *j ] != ~0U );
             *j = nodeMap[ *j ];
         }
     }
     unsigned int numRemoved = nodes.size() - temp.size();
     nodes = temp;
     return numRemoved;
 }

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void NeuroNode::setParent ( unsigned int parent )

Assigns parent node info

Definition at line 111 of file NeuroNode.cpp.

References parent(), and parent_.

Referenced by NeuroMesh::insertSingleDummy().

 {
     parent_ = parent;
 }

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void NeuroNode::setParentAndChildren	(	unsigned int	index,
		int	dendParent,
		vector< NeuroNode > &	nodes,
		const unordered_map< Id, unsigned int > &	dendMap
	)

Definition at line 533 of file NeuroNode.cpp.

References elecCompt_, and parent_.

Referenced by buildSpinyTree().

 {
     if (dendParent < 0 || static_cast< unsigned int >(dendParent) >= nodes.size() )
         return; 
     parent_ = dendParent;
     const unordered_map< Id, unsigned int >::const_iterator dendLookup =
             dendMap.find( nodes[dendParent].elecCompt_ );
     if ( dendLookup != dendMap.end() ) {
         assert( dendLookup->second < nodes.size() );
         nodes[ dendLookup->second ].addChild( index );
     }
 }

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void NeuroNode::setStartFid ( unsigned int f )

Assignes startFid

Definition at line 116 of file NeuroNode.cpp.

References startFid_.

 {
     startFid_ = fid;
 }

unsigned int NeuroNode::startFid ( ) const

Definition at line 74 of file NeuroNode.cpp.

References startFid_.

Referenced by NeuroMesh::getAdx(), NeuroMesh::indexToSpace(), NeuroMesh::matchCubeMeshEntries(), NeuroMesh::nearest(), NeuroMesh::updateCoords(), and NeuroMesh::updateShaftParents().

 {
         return startFid_;
 }

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void NeuroNode::traverse	(	vector< NeuroNode > &	nodes,
		unsigned int	start
	)

static

Traverses the nodes list starting from the 'start' node, and sets up correct parent-child information. This involves removing the identified 'parent' node from the 'children_' vector and assigning it to the parent_ field. Then it redoes the entire nodes vector (with due care for indexing of children and parents) so that it is in the correct order for a depth-first traversal. This means that you can take any entry in the list, and the immediately following entries will be all the descendants, if any.

Static func

Definition at line 332 of file NeuroNode.cpp.

References diagnoseTree().

Referenced by buildTree().

 {
     vector< unsigned int > seen( nodes.size(), ~0 );
     vector< NeuroNode > tree;
     tree.reserve( nodes.size() );
     seen[ start ] = 0;
     tree.push_back( nodes[ start ] );
     tree.back().parent_ = ~0;
     nodes[start].innerTraverse( tree, nodes, seen );
 
     if ( tree.size() < nodes.size() ) {
         cout << "Warning: NeuroNode::traverse() unable to traverse all nodes:\n";
        cout << "Traversed= " << tree.size() << " < total numNodes = " << nodes.size() << endl;
        cout << "This situation may arise if the CellPortion has disjoint compartments\n";
         diagnoseTree( tree, nodes );
     }
     nodes = tree;
 }

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Member Data Documentation

vector< unsigned int > NeuroNode::children_

private

Index of children of this NeuroNode.

Definition at line 202 of file NeuroNode.h.

Referenced by addChild(), children(), clearChildren(), findConnectedCompartments(), innerTraverse(), and removeDisconnectedNodes().

Id NeuroNode::elecCompt_

private

Id of electrical compartment in which this diffusive compt lives.

Definition at line 212 of file NeuroNode.h.

Referenced by elecCompt(), filterSpines(), findConnectedCompartments(), and setParentAndChildren().

bool NeuroNode::isSphere_

private

Special case for soma, perhaps for spine heads. When true, xyz are centre, and dia is dia.

Definition at line 218 of file NeuroNode.h.

Referenced by isSphere().

unsigned int NeuroNode::parent_

private

Index of parent NeuroNode, typically a diffusive compartment. In the special case where the junction to the parent electrical compartment is NOT at the end of the parent compartment, this refers instead to a dummy NeuroNode which has the coordinates.

One of the nodes, typically the soma, will have no parent. This is indicated by the value ~0U.

Definition at line 197 of file NeuroNode.h.

Referenced by parent(), setParent(), and setParentAndChildren().

unsigned int NeuroNode::startFid_

private

Index of starting MeshEntry handled by this NeuroNode. Assumes a block of contiguous fids are handled by each NeuroNode.

Definition at line 208 of file NeuroNode.h.

Referenced by isStartNode(), setStartFid(), and startFid().

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

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

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