#include <HeartConfigRelatedCellFactory.hpp>

Inheritance diagram for HeartConfigRelatedCellFactory< SPACE_DIM >:

Collaboration diagram for HeartConfigRelatedCellFactory< SPACE_DIM >:

Public Member Functions
	HeartConfigRelatedCellFactory ()

	~HeartConfigRelatedCellFactory ()

AbstractCardiacCellInterface *	CreateCellWithIntracellularStimulus (boost::shared_ptr< AbstractStimulusFunction > intracellularStimulus, unsigned nodeIndex)

AbstractCardiacCellInterface *	CreateCardiacCellForTissueNode (Node< SPACE_DIM > *pNode)

void	FillInCellularTransmuralAreas ()

void	SetCellParameters (AbstractCardiacCellInterface *pCell, unsigned nodeIndex)

void	SetCellIntracellularStimulus (AbstractCardiacCellInterface *pCell, unsigned nodeIndex)

void	FillInCellularTransmuralAreas ()

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

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

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 ()

Private Member Functions
void	PreconvertCellmlFiles ()

DynamicCellModelLoaderPtr	LoadDynamicModel (const cp::ionic_model_selection_type &rModel, bool isCollective)

Private Attributes
cp::ionic_model_selection_type	mDefaultIonicModel

std::vector< boost::shared_ptr< AbstractChasteRegion< SPACE_DIM > > >	mIonicModelRegions

std::vector< cp::ionic_model_selection_type >	mIonicModelsDefined

std::vector< boost::shared_ptr< AbstractChasteRegion< SPACE_DIM > > >	mStimulatedAreas

std::vector< boost::shared_ptr< AbstractStimulusFunction > >	mStimuliApplied

std::vector< boost::shared_ptr< AbstractChasteRegion< SPACE_DIM > > >	mCellHeterogeneityAreas

std::vector< double >	mScaleFactorGks

std::vector< double >	mScaleFactorIto

std::vector< double >	mScaleFactorGkr

std::vector< std::map< std::string, double > >	mParameterSettings

Additional Inherited Members
Protected Attributes inherited from AbstractCardiacCellFactory< SPACE_DIM >
boost::shared_ptr< ZeroStimulus >	mpZeroStimulus

boost::shared_ptr< AbstractIvpOdeSolver >	mpSolver

Detailed Description

template<unsigned SPACE_DIM>
class HeartConfigRelatedCellFactory< SPACE_DIM >

This is a cardiac cell factory which uses the settings from HeartConfig to set up the cells.

It thus supports such features as heterogeneities (in both the type of cell, and for some cells, cell model parameters), and the ability to dynamically convert CellML files into C++ code, compile this, and load the resulting model.

Definition at line 96 of file HeartConfigRelatedCellFactory.hpp.

Constructor & Destructor Documentation

◆ HeartConfigRelatedCellFactory()

template<unsigned SPACE_DIM>

HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory ( )

Constructor reads settings from the configuration file.

Note: Must be called collectively.

Definition at line 50 of file HeartConfigRelatedCellFactory.cpp.

◆ ~HeartConfigRelatedCellFactory()

template<unsigned SPACE_DIM>

HeartConfigRelatedCellFactory< SPACE_DIM >::~HeartConfigRelatedCellFactory ( )

Destructor

Definition at line 106 of file HeartConfigRelatedCellFactory.cpp.

Member Function Documentation

◆ CreateCardiacCellForTissueNode()

template<unsigned SPACE_DIM>

AbstractCardiacCellInterface * HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCardiacCellForTissueNode ( Node< SPACE_DIM > * pNode )

virtual

Returns: a newly created correct stimulated tissue cell for a given region in the mesh The stimulus is determined in this method (using the list of stimulation regions). The cardiac cell type (and parameters) are determined in the CreateCellWithIntracellularStimulus method

Parameters

pNode pointer to the node.

Implements AbstractCardiacCellFactory< SPACE_DIM >.

Definition at line 334 of file HeartConfigRelatedCellFactory.cpp.

References Node< SPACE_DIM >::GetIndex(), and Node< SPACE_DIM >::GetPoint().

◆ CreateCellWithIntracellularStimulus()

template<unsigned SPACE_DIM>

AbstractCardiacCellInterface * HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCellWithIntracellularStimulus	(	boost::shared_ptr< AbstractStimulusFunction >	intracellularStimulus,
		unsigned	nodeIndex
	)

Returns: a newly created correct tissue cell for a given region in the mesh

Parameters

intracellularStimulus	is computed in CreateCardiacCellForTissueNode determined by the list of stimulation regions
nodeIndex	is the global index within the mesh

Definition at line 111 of file HeartConfigRelatedCellFactory.cpp.

References EXCEPTION, AbstractCardiacCellInterface::GetLookupTableCollection(), HeartConfig::Instance(), and NEVER_REACHED.

◆ FillInCellularTransmuralAreas() [1/2]

void HeartConfigRelatedCellFactory< 3u >::FillInCellularTransmuralAreas ( )

virtual

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

Reimplemented from AbstractCardiacCellFactory< SPACE_DIM >.

Definition at line 362 of file HeartConfigRelatedCellFactory.cpp.

References HeartConfig::GetEndoLayerFraction(), HeartConfig::GetEndoLayerIndex(), HeartConfig::GetEpiLayerFraction(), HeartConfig::GetEpiLayerIndex(), HeartConfig::GetMeshName(), HeartConfig::GetMidLayerIndex(), HeartConfig::Instance(), and NEVER_REACHED.

◆ FillInCellularTransmuralAreas() [2/2]

template<unsigned SPACE_DIM>

void HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas ( )

virtual

Helper method to calculate and fill in the heterogeneities areas (mCellHeterogeneityAreas)

Reimplemented from AbstractCardiacCellFactory< SPACE_DIM >.

Definition at line 355 of file HeartConfigRelatedCellFactory.cpp.

References NEVER_REACHED.

◆ LoadDynamicModel()

template<unsigned SPACE_DIM>

DynamicCellModelLoaderPtr HeartConfigRelatedCellFactory< SPACE_DIM >::LoadDynamicModel	(	const cp::ionic_model_selection_type &	rModel,
		bool	isCollective
	)

private

Returns: a loader for the given (dynamically loadable) cell model.

Parameters

rModel	model to load
isCollective	whether we are being called collectively

Definition at line 95 of file HeartConfigRelatedCellFactory.cpp.

References CellMLToSharedLibraryConverter::Convert().

◆ PreconvertCellmlFiles()

template<unsigned SPACE_DIM>

void HeartConfigRelatedCellFactory< SPACE_DIM >::PreconvertCellmlFiles ( )

private

Called by the constructor to convert any CellML files used as dynamically loaded cell models to shared libraries. This is necessary since the conversion process must be done collectively.

Note: Must be called collectively.

Definition at line 79 of file HeartConfigRelatedCellFactory.cpp.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().

◆ SetCellIntracellularStimulus()

template<unsigned SPACE_DIM>

void HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellIntracellularStimulus	(	AbstractCardiacCellInterface *	pCell,
		unsigned	nodeIndex
	)

Set the intracellular stimulus for a cell based on the definitions in HeartConfig.

Parameters

pCell	the cell to set stimulus of
nodeIndex	the index of the node corresponding to this cell in the mesh

Definition at line 316 of file HeartConfigRelatedCellFactory.cpp.

References AbstractCardiacCellInterface::SetIntracellularStimulusFunction().

Referenced by CardiacSimulation::CreateAndRun().

◆ SetCellParameters()

template<unsigned SPACE_DIM>

void HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters	(	AbstractCardiacCellInterface *	pCell,
		unsigned	nodeIndex
	)

Set parameters of a cell based on heterogeneity definitions in HeartConfig.

Parameters

pCell	the cell to set parameters of
nodeIndex	the index of the node corresponding to this cell in the mesh

#1166 applying Hill function for drug action

Definition at line 250 of file HeartConfigRelatedCellFactory.cpp.

References HeartConfig::GetDrugDose(), HeartConfig::GetIc50Values(), AbstractCardiacCellInterface::GetParameter(), AbstractUntemplatedParameterisedSystem::HasParameter(), HeartConfig::Instance(), and AbstractCardiacCellInterface::SetParameter().

Referenced by CardiacSimulation::CreateAndRun().

Member Data Documentation

◆ mCellHeterogeneityAreas

template<unsigned SPACE_DIM>

std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > HeartConfigRelatedCellFactory< SPACE_DIM >::mCellHeterogeneityAreas

private

List of regions which represent areas in which to give parametric heterogeneity (scaling gating parameters) This vector will be filled in by the HeartConfig::GetCellHeterogeneity method if the user requested to specify the heterogeneity areas by cuboids, or, alternatively, by the FillInCellularTransmuralAreas method in the cell factory called by the problem class AFTER setting the mesh (which is needed for the calculations of the distance maps for the calculations of heterogeneities).

When creating a cardiac cell for each node (CreateCardiacCellForTissueNode) the code will check whether that node is contained in the heterogeneity area or not.

Definition at line 122 of file HeartConfigRelatedCellFactory.hpp.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().