AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractCardiacCellFactory.hpp>

Inheritance diagram for AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
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 ()
virtual void	SetMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	GetMesh ()
void	SetHeartGeometryInformation (HeartGeometryInformation< SPACE_DIM > *pHeartGeometryInformation)
HeartGeometryInformation< SPACE_DIM > *	GetHeartGeometryInformation ()

Protected Attributes
boost::shared_ptr< ZeroStimulus >	mpZeroStimulus
boost::shared_ptr< AbstractIvpOdeSolver >	mpSolver

Private Attributes
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh
HeartGeometryInformation< SPACE_DIM > *	mpHeartGeometryInformation

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >

A factory to ease creating cardiac cell objects for use in a mono/bidomain simulation.

The user should implement their own concrete class, in particular implementing CreateCardiacCellForTissueNode(Node*), which should return the cell corresponding to a given node. The user should also implement GetNumberOfCells() if this isn't equal to the number of nodes. FinaliseCellCreation() can be used to (eg) add stimuli to certain cells after they have been created.

This class saves the user having to create cells in parallel, that work is done by the pde instead.

Template Parameters

ELEMENT_DIM	Dimension of the elements.
SPACE_DIM	Dimension of the space. If not specified, it defaults to ELEMENT_DIM.

Definition at line 70 of file AbstractCardiacCellFactory.hpp.

Constructor & Destructor Documentation

AbstractCardiacCellFactory()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacCellFactory

(

boost::shared_ptr< AbstractIvpOdeSolver >

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

)

Default constructor.

Parameters

pSolver

the ODE solver to use to simulate this cell.

Definition at line 93 of file AbstractCardiacCellFactory.cpp.

~AbstractCardiacCellFactory()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::~AbstractCardiacCellFactory ( )

virtual

Destructor: free solver, zero stimulus and fake bath cell.

Definition at line 103 of file AbstractCardiacCellFactory.cpp.

Member Function Documentation

CreateCardiacCellForNode()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacCellInterface * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode ( Node< SPACE_DIM > *  pNode )

virtual

Returns

a newly created cell object for the given node.

The default implementation checks whether the node is in the bath (in which case a pointer to a (unique) fake cell is returned) and if not, calls CreateCardiacCellForTissueNode (which must be defined by subclasses).

Parameters

pNode

Pointer to node object.

Definition at line 42 of file AbstractCardiacCellFactory.cpp.

References HeartConfig::GetPdeTimeStep(), Node< SPACE_DIM >::GetRegion(), HeartConfig::Instance(), and HeartRegionCode::IsRegionBath().

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

CreateCardiacCellForTissueNode()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

virtual AbstractCardiacCellInterface * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode ( Node< SPACE_DIM > *  pNode )

pure virtual

Must be overridden by subclasses to return a cell object for the given node.

Parameters

pNode

Pointer to node object.

Returns

a newly created cell object for the given tissue node.

Implemented in HeartConfigRelatedCellFactory< SPACE_DIM >, PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >, and PlaneStimulusCellFactory< CELL, ELEMENT_DIM, ELEMENT_DIM >.

FillInCellularTransmuralAreas()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::FillInCellularTransmuralAreas ( )

virtual

Method that fills in the vector of heterogeneity areas with the NodesLists that correspond to a given layer (implemented in subclasses)

Reimplemented in HeartConfigRelatedCellFactory< SPACE_DIM >, and HeartConfigRelatedCellFactory< SPACE_DIM >.

Definition at line 78 of file AbstractCardiacCellFactory.cpp.

References EXCEPTION.

FinaliseCellCreation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

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

Parameters

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

Definition at line 70 of file AbstractCardiacCellFactory.cpp.

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

GetHeartGeometryInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeartGeometryInformation< SPACE_DIM > * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetHeartGeometryInformation

(

)

Returns

the HeartGeometryInformation object

Definition at line 130 of file AbstractCardiacCellFactory.cpp.

References EXCEPTION.

GetMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh

(

)

Returns

the mesh used to create the cells.

Definition at line 114 of file AbstractCardiacCellFactory.cpp.

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

GetNumberOfCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells ( )

virtual

Returns

The number of cells

Definition at line 86 of file AbstractCardiacCellFactory.cpp.

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

SetHeartGeometryInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::SetHeartGeometryInformation

(

HeartGeometryInformation< SPACE_DIM > *

pHeartGeometryInformation

)

Set the HeartGeometryInformation object

Parameters

pHeartGeometryInformation

the HeartGeometryInformation object that is to be set

Definition at line 124 of file AbstractCardiacCellFactory.cpp.

SetMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Parameters

pMesh

the mesh for which to create cardiac cells.

Reimplemented in AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >.

Definition at line 108 of file AbstractCardiacCellFactory.cpp.

Referenced by CardiacSimulation::CreateAndRun(), and AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::SetMesh().

Member Data Documentation

mpHeartGeometryInformation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeartGeometryInformation<SPACE_DIM>* AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpHeartGeometryInformation

private

A pointer to an HeartGeometryInformation information object Can be accessed via get and set methods in this class.

Definition at line 82 of file AbstractCardiacCellFactory.hpp.

mpMesh

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpMesh

private

The mesh is automatically set in MonodomainProblem and BidomainProblem. This member variable should be accessed through GetMesh(), which will check if it has been set before and throw an exception otherwise.

Definition at line 76 of file AbstractCardiacCellFactory.hpp.

mpSolver

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

boost::shared_ptr<AbstractIvpOdeSolver> AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpSolver

protected

The solver to give each of the cells

Definition at line 88 of file AbstractCardiacCellFactory.hpp.

Referenced by PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode().

mpZeroStimulus

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

boost::shared_ptr<ZeroStimulus> AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::mpZeroStimulus

protected

For use at un-stimulated cells.

Definition at line 86 of file AbstractCardiacCellFactory.hpp.

Referenced by PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode().

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

• heart/src/problem/cell_factories/AbstractCardiacCellFactory.hpp
• heart/src/problem/cell_factories/AbstractCardiacCellFactory.cpp