NodeBasedTissue< DIM > Class Template Reference

#include <NodeBasedTissue.hpp>

Inheritance diagram for NodeBasedTissue< DIM >:

Collaboration diagram for NodeBasedTissue< DIM >:

List of all members.

Public Member Functions

NodeBasedTissue (const std::vector< Node< DIM > * > nodes, const std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteNodes=true)

NodeBasedTissue (const std::vector< Node< DIM > * > nodes, bool deleteNodes=true)

NodeBasedTissue (const AbstractMesh< DIM, DIM > &rMesh, const std::vector< TissueCell > &rCells)

~NodeBasedTissue ()

unsigned GetNumNodes ()

Node< DIM > * GetNode (unsigned index)

unsigned RemoveDeadCells ()

void Clear ()

void Update (bool hasHadBirthsOrDeaths=true)

std::vector< Node< DIM > * > & rGetNodes ()

const std::vector< Node< DIM > * > & rGetNodes () const

NodeBoxCollection< DIM > * GetNodeBoxCollection ()

std::set< std::pair< Node< DIM >
*, Node< DIM > * > > & rGetNodePairs ()

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

unsigned AddNode (Node< DIM > *pNewNode)

void SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)

void Validate ()

void SplitUpIntoBoxes (double cutOffLength, c_vector< double, 2 *DIM > domainSize)

void FindMaxAndMin ()

Private Attributes

std::vector< Node< DIM > * > mNodes

std::vector< unsigned > mDeletedNodeIndices

bool mAddedNodes

NodeBoxCollection< DIM > * mpNodeBoxCollection

c_vector< double, DIM > mMinSpatialPositions

c_vector< double, DIM > mMaxSpatialPositions

std::set< std::pair< Node< DIM >
*, Node< DIM > * > > mNodePairs

bool mDeleteNodes

Friends

class TestNodeBasedTissue

class TestNodeBoxCollection

class boost::serialization::access

Detailed Description

template<unsigned DIM>
class NodeBasedTissue< DIM >

A NodeBasedTissue is a Tissue consisting of only nodes in space with associated cells. There are no elements and no mesh.

Definition at line 45 of file NodeBasedTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

NodeBasedTissue< DIM >::NodeBasedTissue	(	const std::vector< Node< DIM > * >	nodes,
		const std::vector< TissueCell > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteNodes = `true`
	)			`[inline]`

Default constructor.

Note that the tissue will take responsibility for freeing the memory used by the nodes.

Parameters:

	nodes	a vector of Nodes
	rCells	a vector of TissueCells
	locationIndices	an optional vector of location indices that correspond to real cells
	deleteNodes	whether to delete nodes in destructor

Definition at line 32 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::Validate().

template<unsigned DIM>

NodeBasedTissue< DIM >::NodeBasedTissue	(	const std::vector< Node< DIM > * >	nodes,
		bool	deleteNodes = `true`
	)			`[inline]`

Constructor for use by the archiving - doesn't take in cells, since these are dealt with by the serialize method of our base class.

Note that the tissue will take responsibility for freeing the memory used by the nodes.

Parameters:

	nodes	a vector of Nodes
	deleteNodes	whether to delete nodes in destructor

Definition at line 47 of file NodeBasedTissue.cpp.

template<unsigned DIM>

NodeBasedTissue< DIM >::NodeBasedTissue	(	const AbstractMesh< DIM, DIM > &	rMesh,
		const std::vector< TissueCell > &	rCells
	)			`[inline]`

Constructor which takes in a mesh and takes a copy of its nodes. The mesh is not changed and no references to any of its data are created.

This constructor is a helper constructor: it is generally easier for the user to create a mesh than a set of nodes.

Parameters:

	rMesh	any mesh.
	rCells	a vector of TissueCells.

Definition at line 58 of file NodeBasedTissue.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), NodeBasedTissue< DIM >::mAddedNodes, NodeBasedTissue< DIM >::mNodes, and NodeBasedTissue< DIM >::Validate().

template<unsigned DIM>

NodeBasedTissue< DIM >::~NodeBasedTissue ( ) [inline]

Destructor.

Frees all our node memory.

Definition at line 77 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::Clear(), NodeBasedTissue< DIM >::mDeleteNodes, and NodeBasedTissue< DIM >::mNodes.

Member Function Documentation

template<unsigned DIM>

template<class Archive>

void NodeBasedTissue< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Note that serialization of the nodes is handled by load/save_construct_data, so we don't actually have to do anything here except delegate to the base class.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Definition at line 89 of file NodeBasedTissue.hpp.

References NodeBasedTissue< DIM >::Validate().

template<unsigned DIM>

unsigned NodeBasedTissue< DIM >::AddNode ( Node< DIM > * pNewNode ) [inline, private, virtual]

Overridden AddNode() method.

Add a new node to the tissue.

Parameters:

pNewNode

pointer to the new node

Returns:: global index of new node in tissue

Implements AbstractTissue< DIM >.

Definition at line 317 of file NodeBasedTissue.cpp.

References Node< SPACE_DIM >::GetIndex(), NodeBasedTissue< DIM >::mAddedNodes, NodeBasedTissue< DIM >::mDeletedNodeIndices, NodeBasedTissue< DIM >::mNodes, and Node< SPACE_DIM >::SetIndex().

template<unsigned DIM>

void NodeBasedTissue< DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< DIM > &	rNewLocation
	)			`[inline, private, virtual]`

Move the node with a given index to a new point in space.

Parameters:

	nodeIndex	the index of the node to be moved
	rNewLocation	the new target location of the node

Implements AbstractTissue< DIM >.

Definition at line 202 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodes.

template<unsigned DIM>

void NodeBasedTissue< DIM >::Validate ( ) [inline, private, virtual]

Check consistency of our internal data structures.

Implements AbstractTissue< DIM >.

Definition at line 104 of file NodeBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), NodeBasedTissue< DIM >::GetNumNodes(), and AbstractTissue< DIM >::mCellLocationMap.

Referenced by NodeBasedTissue< DIM >::NodeBasedTissue(), NodeBasedTissue< DIM >::serialize(), and NodeBasedTissue< DIM >::Update().

template<unsigned DIM>

void NodeBasedTissue< DIM >::SplitUpIntoBoxes	(	double	cutOffLength,
		c_vector< double, 2 *DIM >	domainSize
	)			`[inline, private]`

Method for Initially Splitting up tissue into neighbouring boxes, to decrease runtime.

Parameters:

	cutOffLength	length of spring cut off between nodes
	domainSize	c_vector of size 2*dimension reads minX, maxX, minY, maxY, etc

Definition at line 145 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodes, and NodeBasedTissue< DIM >::mpNodeBoxCollection.

Referenced by NodeBasedTissue< DIM >::Update().

template<unsigned DIM>

void NodeBasedTissue< DIM >::FindMaxAndMin ( ) [inline, private]

Loops over nodes and sets mMinSpatialPositions and mMaxSpatialPositions

Definition at line 158 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::GetNode(), NodeBasedTissue< DIM >::mMaxSpatialPositions, NodeBasedTissue< DIM >::mMinSpatialPositions, and NodeBasedTissue< DIM >::mNodes.

Referenced by NodeBasedTissue< DIM >::Update().

template<unsigned DIM>

unsigned NodeBasedTissue< DIM >::GetNumNodes ( ) [inline, virtual]

Returns:: the number of nodes in the tissue.

Implements AbstractTissue< DIM >.

Definition at line 338 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mDeletedNodeIndices, and NodeBasedTissue< DIM >::mNodes.

Referenced by NodeBasedTissue< DIM >::Validate().

template<unsigned DIM>

Node< DIM > * NodeBasedTissue< DIM >::GetNode ( unsigned index ) [inline, virtual]

Overridden GetNode() method.

Parameters:

index

global index of the specified node

Returns:: a pointer to the node with a given index.

Implements AbstractTissue< DIM >.

Definition at line 195 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodes.

Referenced by NodeBasedTissue< DIM >::FindMaxAndMin().

template<unsigned DIM>

unsigned NodeBasedTissue< DIM >::RemoveDeadCells ( ) [inline, virtual]

Remove all cells labelled as dead.

Note that after calling this method the tissue will be in an inconsistent state until the equivalent of a 'remesh' is performed! So don't try iterating over cells or anything like that.

Returns:: number of cells removed

Implements AbstractTissue< DIM >.

Definition at line 294 of file NodeBasedTissue.cpp.

References AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCells, and NodeBasedTissue< DIM >::mDeletedNodeIndices.

template<unsigned DIM>

void NodeBasedTissue< DIM >::Clear ( ) [inline]

Reset the member variables mDeletedNodeIndices, mAddedNodes, mNodePairs, and mpNodeBoxCollection.

Definition at line 93 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mAddedNodes, NodeBasedTissue< DIM >::mDeletedNodeIndices, NodeBasedTissue< DIM >::mNodePairs, and NodeBasedTissue< DIM >::mpNodeBoxCollection.

Referenced by NodeBasedTissue< DIM >::Update(), and NodeBasedTissue< DIM >::~NodeBasedTissue().

template<unsigned DIM>

void NodeBasedTissue< DIM >::Update ( bool hasHadBirthsOrDeaths = true ) [inline, virtual]

Remove nodes that have been marked as deleted and update the node cell map.

Parameters:

hasHadBirthsOrDeaths

whether tissue has had Births Or Deaths

Implements AbstractTissue< DIM >.

Definition at line 209 of file NodeBasedTissue.cpp.

template<unsigned DIM>

std::vector< Node< DIM > * > & NodeBasedTissue< DIM >::rGetNodes ( ) [inline]

Method for getting all nodes in the tissue.

Returns:: vector of Nodes

Definition at line 131 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodes.

template<unsigned DIM>

const std::vector< Node< DIM > * > & NodeBasedTissue< DIM >::rGetNodes ( ) const [inline]

Method for getting all nodes in the tissue (for archiving).

Returns:: vector of Nodes

Definition at line 138 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodes.

template<unsigned DIM>

NodeBoxCollection< DIM > * NodeBasedTissue< DIM >::GetNodeBoxCollection ( ) [inline]

Returns:: pointer to a node box collection.

Definition at line 345 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mpNodeBoxCollection.

template<unsigned DIM>

std::set< std::pair< Node< DIM > *, Node< DIM > * > > & NodeBasedTissue< DIM >::rGetNodePairs ( ) [inline]

Returns:: Node pairs for force calculation.

Definition at line 352 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodePairs.

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Definition at line 78 of file NodeBasedTissue.hpp.

Member Data Documentation

template<unsigned DIM>

std::vector<Node<DIM>* > NodeBasedTissue< DIM >::mNodes [private]

List of nodes.

Definition at line 52 of file NodeBasedTissue.hpp.

Referenced by NodeBasedTissue< DIM >::AddNode(), NodeBasedTissue< DIM >::FindMaxAndMin(), NodeBasedTissue< DIM >::GetNode(), NodeBasedTissue< DIM >::GetNumNodes(), NodeBasedTissue< DIM >::NodeBasedTissue(), NodeBasedTissue< DIM >::rGetNodes(), NodeBasedTissue< DIM >::SetNode(), NodeBasedTissue< DIM >::SplitUpIntoBoxes(), NodeBasedTissue< DIM >::Update(), and NodeBasedTissue< DIM >::~NodeBasedTissue().

template<unsigned DIM>

std::vector<unsigned> NodeBasedTissue< DIM >::mDeletedNodeIndices [private]

Indices of nodes that have been deleted, to be reused when adding new nodes.

Definition at line 55 of file NodeBasedTissue.hpp.

Referenced by NodeBasedTissue< DIM >::AddNode(), NodeBasedTissue< DIM >::Clear(), NodeBasedTissue< DIM >::GetNumNodes(), and NodeBasedTissue< DIM >::RemoveDeadCells().

template<unsigned DIM>

bool NodeBasedTissue< DIM >::mAddedNodes [private]

Whether nodes have been added to the tissue.

Definition at line 58 of file NodeBasedTissue.hpp.

Referenced by NodeBasedTissue< DIM >::AddNode(), NodeBasedTissue< DIM >::Clear(), and NodeBasedTissue< DIM >::NodeBasedTissue().

template<unsigned DIM>

NodeBoxCollection<DIM>* NodeBasedTissue< DIM >::mpNodeBoxCollection [private]

Pointer to a Node box collection

Definition at line 61 of file NodeBasedTissue.hpp.

Referenced by NodeBasedTissue< DIM >::Clear(), NodeBasedTissue< DIM >::GetNodeBoxCollection(), NodeBasedTissue< DIM >::SplitUpIntoBoxes(), and NodeBasedTissue< DIM >::Update().

template<unsigned DIM>

c_vector<double, DIM> NodeBasedTissue< DIM >::mMinSpatialPositions [private]

Vector of minimal spatial positions in each dimension

Definition at line 64 of file NodeBasedTissue.hpp.

Referenced by NodeBasedTissue< DIM >::FindMaxAndMin(), and NodeBasedTissue< DIM >::Update().

template<unsigned DIM>

c_vector<double, DIM> NodeBasedTissue< DIM >::mMaxSpatialPositions [private]

Vector of maximal spatial positions in each dimension

Definition at line 67 of file NodeBasedTissue.hpp.

Referenced by NodeBasedTissue< DIM >::FindMaxAndMin(), and NodeBasedTissue< DIM >::Update().

template<unsigned DIM>

std::set< std::pair<Node<DIM>*, Node<DIM>* > > NodeBasedTissue< DIM >::mNodePairs [private]

Node pairs for force calculations

Definition at line 70 of file NodeBasedTissue.hpp.

Referenced by NodeBasedTissue< DIM >::Clear(), NodeBasedTissue< DIM >::rGetNodePairs(), and NodeBasedTissue< DIM >::Update().

template<unsigned DIM>

bool NodeBasedTissue< DIM >::mDeleteNodes [private]

Whether to delete the nodes (taken in one of the constructors, defaults to true)

Definition at line 75 of file NodeBasedTissue.hpp.

Referenced by NodeBasedTissue< DIM >::~NodeBasedTissue().

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

/tmp/release_1.1/cancer/src/tissue/NodeBasedTissue.hpp
/tmp/release_1.1/cancer/src/tissue/NodeBasedTissue.cpp


Public Member Functions
	NodeBasedTissue (const std::vector< Node< DIM > * > nodes, const std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteNodes=true)
	NodeBasedTissue (const std::vector< Node< DIM > * > nodes, bool deleteNodes=true)
	NodeBasedTissue (const AbstractMesh< DIM, DIM > &rMesh, const std::vector< TissueCell > &rCells)
	~NodeBasedTissue ()
unsigned	GetNumNodes ()
Node< DIM > *	GetNode (unsigned index)
unsigned	RemoveDeadCells ()
void	Clear ()
void	Update (bool hasHadBirthsOrDeaths=true)
std::vector< Node< DIM > * > &	rGetNodes ()
const std::vector< Node< DIM > * > &	rGetNodes () const
NodeBoxCollection< DIM > *	GetNodeBoxCollection ()
std::set< std::pair< Node< DIM > , Node< DIM > > > &	rGetNodePairs ()
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
unsigned	AddNode (Node< DIM > *pNewNode)
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)
void	Validate ()
void	SplitUpIntoBoxes (double cutOffLength, c_vector< double, 2 *DIM > domainSize)
void	FindMaxAndMin ()
Private Attributes
std::vector< Node< DIM > * >	mNodes
std::vector< unsigned >	mDeletedNodeIndices
bool	mAddedNodes
NodeBoxCollection< DIM > *	mpNodeBoxCollection
c_vector< double, DIM >	mMinSpatialPositions
c_vector< double, DIM >	mMaxSpatialPositions
std::set< std::pair< Node< DIM > , Node< DIM > > >	mNodePairs
bool	mDeleteNodes
Friends
class	TestNodeBasedTissue
class	TestNodeBoxCollection
class	boost::serialization::access

NodeBasedTissue< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class NodeBasedTissue< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class NodeBasedTissue< DIM >