#include <AbstractPurkinjeCellFactory.hpp>

Inheritance diagram for AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
void	SetMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

AbstractCardiacCellInterface *	CreatePurkinjeCellForNode (Node< SPACE_DIM > pNode, AbstractCardiacCellInterface pCardiacCell)

virtual void	FinalisePurkinjeCellCreation (std::vector< AbstractCardiacCellInterface * > *pPurkinjeCellsDistributed, unsigned lo, unsigned hi)

MixedDimensionMesh < ELEMENT_DIM, SPACE_DIM > *	GetMixedDimensionMesh ()

Public Member Functions inherited from AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >
virtual AbstractCardiacCellInterface *	CreateCardiacCellForNode (Node< SPACE_DIM > *pNode)

virtual AbstractCardiacCellInterface *	CreateCardiacCellForTissueNode (Node< SPACE_DIM > *pNode)=0

virtual void	FinaliseCellCreation (std::vector< AbstractCardiacCellInterface * > *pCellsDistributed, unsigned lo, unsigned hi)

virtual void	FillInCellularTransmuralAreas ()

virtual unsigned	GetNumberOfCells ()

	AbstractCardiacCellFactory (boost::shared_ptr< AbstractIvpOdeSolver > pSolver=boost::shared_ptr< AbstractIvpOdeSolver >(new EulerIvpOdeSolver))

virtual	~AbstractCardiacCellFactory ()

AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > *	GetMesh ()

void	SetHeartGeometryInformation (HeartGeometryInformation< SPACE_DIM > *pHeartGeometryInformation)

HeartGeometryInformation < SPACE_DIM > *	GetHeartGeometryInformation ()

Protected Member Functions
virtual AbstractCardiacCellInterface *	CreatePurkinjeCellForTissueNode (Node< SPACE_DIM > pNode, AbstractCardiacCellInterface pCardiacCell)=0

void	CreateJunction (const Node< SPACE_DIM > pNode, AbstractCardiacCellInterface pPurkinjeCell, AbstractCardiacCellInterface *pCardiacCell, double resistance)

void	CreateJunctionFromFile (const Node< SPACE_DIM > pNode, AbstractCardiacCellInterface pPurkinjeCell, AbstractCardiacCellInterface *pCardiacCell)

Protected Attributes
MixedDimensionMesh < ELEMENT_DIM, SPACE_DIM > *	mpMixedDimensionMesh

std::set< unsigned >	mLocalPurkinjeNodes

std::map< unsigned, double >	mJunctionMap

Protected Attributes inherited from AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >
boost::shared_ptr< ZeroStimulus >	mpZeroStimulus

boost::shared_ptr < AbstractIvpOdeSolver >	mpSolver

Private Member Functions
void	ReadJunctionsFile ()

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >

Subclass for also creating cell models for Purkinje cells. The user has to implement the CreatePurkinjeCellForTissueNode() method.

The dimensions should be 2 or 3.

Definition at line 49 of file AbstractPurkinjeCellFactory.hpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateJunction	(	const Node< SPACE_DIM > *	pNode,
		AbstractCardiacCellInterface *	pPurkinjeCell,
		AbstractCardiacCellInterface *	pCardiacCell,
		double	resistance
	)

protected

Returns: a newly created purkinje-ventricular junction between the two cells provided.

Parameters

pNode	the node in the mesh at which this junction is located
pPurkinjeCell	the Purkinje cell
pCardiacCell	the ventricular cell
resistance	the junction resistance, in kilo-Ohms

Definition at line 121 of file AbstractPurkinjeCellFactory.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetAttribute(), HeartConfig::GetPurkinjeSurfaceAreaToVolumeRatio(), AbstractCardiacCellInterface::GetStimulusFunction(), HeartConfig::Instance(), and AbstractCardiacCellInterface::SetStimulusFunction().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateJunctionFromFile	(	const Node< SPACE_DIM > *	pNode,
		AbstractCardiacCellInterface *	pPurkinjeCell,
		AbstractCardiacCellInterface *	pCardiacCell
	)

protected

Returns: a newly created purkinje-ventricular junction between the two cells provided if the junction is defined in the corresponding .pvj file.

ReadJunctionsFile() must be called before calling this method

Parameters

pNode	the node in the mesh at which this junction is located
pPurkinjeCell	the Purkinje cell
pCardiacCell	the ventricular cell

Definition at line 215 of file AbstractPurkinjeCellFactory.cpp.

References Node< SPACE_DIM >::GetIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacCellInterface * AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreatePurkinjeCellForNode	(	Node< SPACE_DIM > *	pNode,
		AbstractCardiacCellInterface *	pCardiacCell
	)

Returns: a newly created cell object for the given node.

The default implementation checks whether the node is in a Purkinje node, in which case it calls CreatePurkinjeCellForTissueNode (which must be defined by subclasses), otherwise it returns a pointer to a (unique) fake cell

Parameters

pNode	pointer to node
pCardiacCell	the cardiac cell that has already been created at this node

Definition at line 188 of file AbstractPurkinjeCellFactory.cpp.

References Node< SPACE_DIM >::GetIndex().

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual AbstractCardiacCellInterface* AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreatePurkinjeCellForTissueNode	(	Node< SPACE_DIM > *	pNode,
		AbstractCardiacCellInterface *	pCardiacCell
	)

protectedpure virtual

Returns: a newly created purkinje cells for the given node. Must be overridden by subclasses to return a Purkinje cell object for the given node.

Parameters

pNode	pointer to node object
pCardiacCell	the cardiac cell that has already been created at this node

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::FinalisePurkinjeCellCreation	(	std::vector< AbstractCardiacCellInterface * > *	pPurkinjeCellsDistributed,
		unsigned	lo,
		unsigned	hi
	)

inlinevirtual

May be overridden by subclasses to perform any necessary work after all Purkinje cells have been created.

Parameters

pPurkinjeCellsDistributed	Pointer to a vector of Purkinje cell pointers.
lo	Lowest index owned by this process.
hi	Highest index owned by this process.

Definition at line 139 of file AbstractPurkinjeCellFactory.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > * AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMixedDimensionMesh ( )

Returns: the mixed dimension mesh (for possible use in CreatePurkinjeCellForTissueNode()). Note: GetMesh() just returns a pointer to an AbstractTetrahedralMesh.

Definition at line 205 of file AbstractPurkinjeCellFactory.cpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::ReadJunctionsFile ( )

private

Reads in node id and resistance values of junction nodes

The .pvj file path is specified by HeartConfig::Instance()->GetMeshFileName() + ".pvj"

Note, this is called by SetMesh

Definition at line 53 of file AbstractPurkinjeCellFactory.cpp.

References RelativeTo::AbsoluteOrCwd, EXCEPTION, FileFinder::Exists(), FileFinder::GetAbsolutePath(), HeartConfig::GetMeshName(), and HeartConfig::Instance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::SetMesh ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * pMesh )

virtual

Overridden set mesh which must take a MixedDimensionMesh

Parameters

pMesh Pointer to the mesh.

Reimplemented from AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >.

Definition at line 166 of file AbstractPurkinjeCellFactory.cpp.

References EXCEPTION, and AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::SetMesh().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::map<unsigned, double> AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::mJunctionMap

protected

A map between junction node ids and resistances

Definition at line 69 of file AbstractPurkinjeCellFactory.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::set<unsigned> AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::mLocalPurkinjeNodes

protected

A set of local purkinje node indices

Definition at line 66 of file AbstractPurkinjeCellFactory.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>* AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::mpMixedDimensionMesh

protected

Saved pointer to the mixed dimension mesh

Definition at line 63 of file AbstractPurkinjeCellFactory.hpp.

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

heart/src/problem/cell_factories/AbstractPurkinjeCellFactory.hpp
heart/src/problem/cell_factories/AbstractPurkinjeCellFactory.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM> class AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >