#include <CaBasedCellPopulation.hpp>

Inheritance diagram for CaBasedCellPopulation< DIM >:

Collaboration diagram for CaBasedCellPopulation< DIM >:

Public Member Functions
	CaBasedCellPopulation (PottsMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices, unsigned latticeCarryingCapacity=1u, bool deleteMesh=false, bool validate=false)

	CaBasedCellPopulation (PottsMesh< DIM > &rMesh)

virtual	~CaBasedCellPopulation ()

std::vector< unsigned > &	rGetAvailableSpaces ()

virtual bool	IsSiteAvailable (unsigned index, CellPtr pCell)

PottsMesh< DIM > &	rGetMesh ()

const PottsMesh< DIM > &	rGetMesh () const

virtual TetrahedralMesh< DIM, DIM > *	GetTetrahedralMeshForPdeModifier ()

Node< DIM > *	GetNode (unsigned index)

unsigned	GetNumNodes ()

std::set< unsigned >	GetNeighbouringLocationIndices (CellPtr pCell)

c_vector< double, DIM >	GetLocationOfCellCentre (CellPtr pCell)

void	AddCellUsingLocationIndex (unsigned index, CellPtr pCell)

void	RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell)

Node< DIM > *	GetNodeCorrespondingToCell (CellPtr pCell)

CellPtr	AddCell (CellPtr pNewCell, CellPtr pParentCell=CellPtr())

virtual double	EvaluateDivisionPropensity (unsigned currentNodeIndex, unsigned targetNodeIndex, CellPtr pCell)

unsigned	RemoveDeadCells ()

virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

void	UpdateCellLocations (double dt)

bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)

void	Update (bool hasHadBirthsOrDeaths=true)

virtual void	AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< DIM, DIM > > pPopulationWriter)

virtual void	AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< DIM, DIM > > pPopulationCountWriter)

virtual void	AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< DIM, DIM > > pCellWriter, CellPtr pCell)

double	GetVolumeOfCell (CellPtr pCell)

double	GetWidth (const unsigned &rDimension)

void	RemoveAllUpdateRules ()

void	OutputCellPopulationParameters (out_stream &rParamsFile)

bool	IsRoomToDivide (CellPtr pCell)

boost::shared_ptr < AbstractCaBasedDivisionRule < DIM > >	GetCaBasedDivisionRule ()

void	SetCaBasedDivisionRule (boost::shared_ptr< AbstractCaBasedDivisionRule< DIM > > pCaBasedDivisionRule)

virtual void	AddUpdateRule (boost::shared_ptr< AbstractUpdateRule< DIM > > pUpdateRule)

virtual const std::vector < boost::shared_ptr < AbstractUpdateRule< DIM > > >	GetUpdateRuleCollection () const

virtual double	GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

Public Member Functions inherited from AbstractOnLatticeCellPopulation< DIM >
	AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)

virtual	~AbstractOnLatticeCellPopulation ()

bool	GetUpdateNodesInRandomOrder ()

void	SetUpdateNodesInRandomOrder (bool updateNodesInRandomOrder)

void	SetIterateRandomlyOverUpdateRuleCollection (bool iterateRandomly)

bool	GetIterateRandomlyOverUpdateRuleCollection ()

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

std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)

virtual double	GetDefaultTimeStep ()

Public Member Functions inherited from AbstractCellPopulation< DIM >
	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

virtual	~AbstractCellPopulation ()

void	InitialiseCells ()

void	SetDataOnAllCells (const std::string &rDataName, double dataValue)

AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &	rGetMesh ()

std::list< CellPtr > &	rGetCells ()

virtual void	SetNode (unsigned nodeIndex, ChastePoint< ELEMENT_DIM > &rNewLocation)=0

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

std::vector< unsigned >	GetCellMutationStateCount ()

std::vector< unsigned >	GetCellProliferativeTypeCount ()

std::vector< unsigned >	GetCellCyclePhaseCount ()

unsigned	GetNumRealCells ()

unsigned	GetNumAllCells ()

void	SetCellAncestorsToLocationIndices ()

std::set< unsigned >	GetCellAncestors ()

virtual CellPtr	GetCellUsingLocationIndex (unsigned index)

std::set< CellPtr >	GetCellsUsingLocationIndex (unsigned index)

virtual bool	IsCellAttachedToLocationIndex (unsigned index)

void	SetCellUsingLocationIndex (unsigned index, CellPtr pCell)

void	MoveCellInLocationMap (CellPtr pCell, unsigned old_index, unsigned new_index)

unsigned	GetLocationIndexUsingCell (CellPtr pCell)

boost::shared_ptr < CellPropertyRegistry >	GetCellPropertyRegistry ()

void	SetDefaultCellMutationStateAndProliferativeTypeOrdering ()

c_vector< double, ELEMENT_DIM >	GetCentroidOfCellPopulation ()

virtual void	UpdateCellProcessLocation ()

void	CloseWritersFiles ()

virtual void	WriteResultsToFiles (const std::string &rDirectory)

virtual void	AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, ELEMENT_DIM > > pPopulationWriter)=0

virtual void	AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, ELEMENT_DIM > > pPopulationCountWriter)=0

virtual void	AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, ELEMENT_DIM > > pCellWriter, CellPtr pCell)=0

void	OutputCellPopulationInfo (out_stream &rParamsFile)

virtual void	SimulationSetupHook (AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM > *pSimulation)

bool	GetOutputResultsForChasteVisualizer ()

void	AddPopulationWriter ()

void	AddPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, ELEMENT_DIM > > pPopulationWriter)

void	AddCellWriter ()

void	AddCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, ELEMENT_DIM > > pCellWriter)

void	AddCellPopulationCountWriter ()

void	AddCellPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, ELEMENT_DIM > > pCellPopulationCountWriter)

bool	HasWriter () const

void	SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)

c_vector< double, ELEMENT_DIM >	GetSizeOfCellPopulation ()

std::pair< unsigned, unsigned >	CreateOrderedPair (unsigned index1, unsigned index2)

Iterator	Begin ()

Iterator	End ()

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Private Member Functions
void	SetEmptySites (const std::set< unsigned > &rEmptySiteIndices)

template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

void	Validate ()

virtual void	WriteVtkResultsToFile (const std::string &rDirectory)

Private Attributes
unsigned	mLatticeCarryingCapacity

std::vector< boost::shared_ptr < AbstractUpdateRule< DIM > > >	mSwitchingUpdateRuleCollection

std::vector< unsigned >	mAvailableSpaces

boost::shared_ptr < AbstractCaBasedDivisionRule < DIM > >	mpCaBasedDivisionRule

Friends
class	TestCaBasedCellPopulation

class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractOnLatticeCellPopulation< DIM >
	AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh)

Protected Member Functions inherited from AbstractCellPopulation< DIM >
	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh)

virtual void	AcceptCellWritersAcrossPopulation ()

Protected Attributes inherited from AbstractOnLatticeCellPopulation< DIM >
std::vector< boost::shared_ptr < AbstractUpdateRule< DIM > > >	mUpdateRuleCollection

bool	mDeleteMesh

bool	mUpdateNodesInRandomOrder

bool	mIterateRandomlyOverUpdateRuleCollection

Protected Attributes inherited from AbstractCellPopulation< DIM >
std::map< unsigned, std::set < CellPtr > >	mLocationCellMap

std::map< Cell *, unsigned >	mCellLocationMap

AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &	mrMesh

std::list< CellPtr >	mCells

c_vector< double, ELEMENT_DIM >	mCentroid

out_stream	mpVtkMetaFile

boost::shared_ptr < CellPropertyRegistry >	mpCellPropertyRegistry

bool	mOutputResultsForChasteVisualizer

std::vector< boost::shared_ptr < AbstractCellWriter < ELEMENT_DIM, ELEMENT_DIM > > >	mCellWriters

std::vector< boost::shared_ptr < AbstractCellPopulationWriter < ELEMENT_DIM, ELEMENT_DIM > > >	mCellPopulationWriters

std::vector< boost::shared_ptr < AbstractCellPopulationCountWriter < ELEMENT_DIM, ELEMENT_DIM > > >	mCellPopulationCountWriters

Detailed Description

template<unsigned DIM>
class CaBasedCellPopulation< DIM >

A facade class encapsulating a cell population under the Cellular Automaton (CA) framework.

Contains a group of cells and maintains the associations between CellPtrs and nodes in a specialised PottsMesh class.

When used here the PottsMesh has no elements as Cells are associated with nodes. The PottsMesh is used to define node connectivity.

Multiple cells can be associated at a single node.

Definition at line 64 of file CaBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CaBasedCellPopulation< DIM >::CaBasedCellPopulation	(	PottsMesh< DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices,
		unsigned	latticeCarryingCapacity = `1u`,
		bool	deleteMesh = `false`,
		bool	validate = `false`
	)

Create a new cell population facade from a mesh, a vector of location indices and a collection of cells.

There must be precisely one CellPtr for each entry of the locationIndices vector.

Parameters

rMesh	reference to a PottsMesh
rCells	reference to a vector of CellPtrs
locationIndices	a vector of location indices that correspond to real cells
latticeCarryingCapacity	an optional parameter to allow more than one cell per site
deleteMesh	set to true if you want the cell population to free the mesh memory on destruction (defaults to false)
validate	whether to validate the cell population when it is created (defaults to false as not used in CA simulations)

Definition at line 60 of file CaBasedCellPopulation.cpp.

References EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), CaBasedCellPopulation< DIM >::GetNumNodes(), CaBasedCellPopulation< DIM >::IsSiteAvailable(), CaBasedCellPopulation< DIM >::mAvailableSpaces, AbstractCellPopulation< DIM >::mCells, CaBasedCellPopulation< DIM >::mpCaBasedDivisionRule, and AbstractCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

CaBasedCellPopulation< DIM >::CaBasedCellPopulation ( PottsMesh< DIM > & rMesh )

Constructor for use by the de-serializer.

Parameters

rMesh a Ca mesh.

Definition at line 101 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

CaBasedCellPopulation< DIM >::~CaBasedCellPopulation ( )

virtual

Destructor, which frees any memory allocated by the constructor.

Definition at line 107 of file CaBasedCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AcceptCellWriter	(	boost::shared_ptr< AbstractCellWriter< DIM, DIM > >	pCellWriter,
		CellPtr	pCell
	)

virtual

A virtual method to accept a cell writer so it can write data from this object to file.

Parameters

pCellWriter	the population writer.
pCell	the cell whose data are being written.

Definition at line 517 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AcceptPopulationCountWriter ( boost::shared_ptr< AbstractCellPopulationCountWriter< DIM, DIM > > pPopulationCountWriter )

virtual

A virtual method to accept a cell population count writer so it can write data from this object to file.

Parameters

pPopulationCountWriter the population count writer.

Definition at line 511 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AcceptPopulationWriter ( boost::shared_ptr< AbstractCellPopulationWriter< DIM, DIM > > pPopulationWriter )

virtual

A virtual method to accept a cell population writer so it can write data from this object to file.

Parameters

pPopulationWriter the population writer.

Definition at line 505 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

CellPtr CaBasedCellPopulation< DIM >::AddCell	(	CellPtr	pNewCell,
		CellPtr	pParentCell = `CellPtr()`
	)

virtual

Overridden AddCell() method.

Add a new cell to the cell population.

Parameters

pNewCell	the cell to add
pParentCell	pointer to a parent cell (if required)

Returns: address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way)

Implements AbstractCellPopulation< DIM >.

Definition at line 231 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AddCellUsingLocationIndex	(	unsigned	index,
		CellPtr	pCell
	)

virtual

Overridden AddCellUsingLocationIndex method to add a cell to a given location index. Also updates mAvailableSpaces

Parameters

index	the location index
pCell	the cell.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 203 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), and EXCEPTION.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AddUpdateRule ( boost::shared_ptr< AbstractUpdateRule< DIM > > pUpdateRule )

virtual

Overridden AddUpdateRule() method.

Parameters

pUpdateRule pointer to an update rule

Implements AbstractOnLatticeCellPopulation< DIM >.

Definition at line 551 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

double CaBasedCellPopulation< DIM >::EvaluateDivisionPropensity	(	unsigned	currentNodeIndex,
		unsigned	targetNodeIndex,
		CellPtr	pCell
	)

virtual

Calculate the propensity of a dividing into a given site. Overridden in child classes to define other division methods, e.g. directed division.

Todo:: This functionality should be moved into the CA-based division rule hierarchy

Parameters

currentNodeIndex	The index of the current node/lattice site
targetNodeIndex	The index of the target node/lattice site
pCell	a pointer to the cell (needed if more than one cell per lattice site

Returns: The probability of the cell dividing from the current node to the target node

Definition at line 246 of file CaBasedCellPopulation.cpp.

Referenced by ExclusionCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), and ShovingCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex().

template<unsigned DIM>

boost::shared_ptr< AbstractCaBasedDivisionRule< DIM > > CaBasedCellPopulation< DIM >::GetCaBasedDivisionRule ( )

Returns: The Ca division rule that is currently being used.

Definition at line 595 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

double CaBasedCellPopulation< DIM >::GetCellDataItemAtPdeNode	(	unsigned	pdeNodeIndex,
		std::string &	rVariableName,
		bool	dirichletBoundaryConditionApplies = `false`,
		double	dirichletBoundaryValue = `0.0`
	)

virtual

Overridden GetCellDataItemAtPdeNode() method.

Parameters

pdeNodeIndex	index of a node in a tetrahedral mesh for use with a PDE modifier
rVariableName	the name of the cell data item to get
dirichletBoundaryConditionApplies	where a Dirichlet boundary condition is used (optional; defaults to false)
dirichletBoundaryValue	the value of the Dirichlet boundary condition, if used (optional; defaults to 0.0)

Returns: the value of a CellData item (interpolated if necessary) at a node, specified by its index in a tetrahedral mesh for use with a PDE modifier. This method can be called by PDE modifier classes.

Implements AbstractCellPopulation< DIM >.

Definition at line 785 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

c_vector< double, DIM > CaBasedCellPopulation< DIM >::GetLocationOfCellCentre ( CellPtr pCell )

virtual

Overridden GetLocationOfCellCentre() method. Find where a given cell is in space.

Parameters

pCell the cell

Returns: the location of the node corresponding to this cell.

Implements AbstractCellPopulation< DIM >.

Definition at line 191 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

std::set< unsigned > CaBasedCellPopulation< DIM >::GetNeighbouringLocationIndices ( CellPtr pCell )

virtual

Overridden GetNeighbouringLocationIndices() method.

Given a cell, returns the set of location indices corresponding to neighbouring cells.

Note: In keeping with other parts of the code in this class, we assume a Moore neighbourhood. Also, at present this method assumes a unit carrying capacity at each lattice site.

Parameters

pCell a cell

Returns: the set of neighbouring location indices.

Implements AbstractCellPopulation< DIM >.

Definition at line 171 of file CaBasedCellPopulation.cpp.

References PottsMesh< DIM >::GetMooreNeighbouringNodeIndices().

template<unsigned DIM>

Node< DIM > * CaBasedCellPopulation< DIM >::GetNode ( unsigned index )

virtual

Overridden GetNode() method.

Parameters

index global index of the specified node

Returns: a pointer to the node.

Implements AbstractCellPopulation< DIM >.

Definition at line 159 of file CaBasedCellPopulation.cpp.

Referenced by DiffusionCaUpdateRule< DIM >::EvaluateProbability().

template<unsigned DIM>

Node< DIM > * CaBasedCellPopulation< DIM >::GetNodeCorrespondingToCell ( CellPtr pCell )

Get a pointer to the node corresponding to a given CellPtr.

Parameters

pCell the cell

Returns: pointer to the node.

Definition at line 197 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

unsigned CaBasedCellPopulation< DIM >::GetNumNodes ( )

virtual

Overridden GetNumNodes() method.

Returns: the number of nodes in the cell population.

Implements AbstractCellPopulation< DIM >.

Definition at line 165 of file CaBasedCellPopulation.cpp.

Referenced by CaBasedCellPopulation< DIM >::CaBasedCellPopulation().

template<unsigned DIM>

TetrahedralMesh< DIM, DIM > * CaBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier ( )

virtual

Overridden GetTetrahedralMeshForPdeModifier() method.

Returns: a pointer to a tetrahedral mesh, for use with a PDE modifier.

This method is called by AbstractGrowingDomainPdeModifier.

Implements AbstractCellPopulation< DIM >.

Definition at line 141 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

const std::vector< boost::shared_ptr< AbstractUpdateRule< DIM > > > CaBasedCellPopulation< DIM >::GetUpdateRuleCollection ( ) const

virtual

Overridden AddUpdateRule() method.

Get the collection of update rules to be used with this population. This vector is comprised of mUpdateRuleCollection and mSwitchingUpdateRuleCollection, one after the other.

Returns: the update rule collection

Reimplemented from AbstractOnLatticeCellPopulation< DIM >.

Definition at line 578 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

double CaBasedCellPopulation< DIM >::GetVolumeOfCell ( CellPtr pCell )

virtual

Overridden GetVolumeOfCell() method.

Parameters

pCell boost shared pointer to a cell

Returns: volume via associated mesh element

Implements AbstractCellPopulation< DIM >.

Definition at line 537 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

double CaBasedCellPopulation< DIM >::GetWidth ( const unsigned & rDimension )

virtual

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the cell population by calling GetWidth() on the mesh.

Note this returns the size of the underlying mesh not the population of cells so here it will be the same for all time.

Parameters

rDimension a dimension (0,1 or 2)

Returns: The maximum distance between any nodes in this dimension.

Implements AbstractCellPopulation< DIM >.

Definition at line 544 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

bool CaBasedCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell )

virtual

Overridden IsCellAssociatedWithADeletedLocation() method.

Parameters

pCell the cell

Returns: whether a given cell is associated with a deleted node.

Implements AbstractCellPopulation< DIM >.

Definition at line 494 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

bool CaBasedCellPopulation< DIM >::IsPdeNodeAssociatedWithNonApoptoticCell ( unsigned pdeNodeIndex )

virtual

Overridden IsPdeNodeAssociatedWithNonApoptoticCell() method.

Parameters

pdeNodeIndex index of a node in a tetrahedral mesh for use with a PDE modifier

Returns: if a node, specified by its index in a tetrahedral mesh for use with a PDE modifier, is associated with a non-apoptotic cell. This method can be called by PDE classes.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 805 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

bool CaBasedCellPopulation< DIM >::IsRoomToDivide ( CellPtr pCell )

virtual

Overridden IsRoomToDivide() method. Returns whether there are any available neighbouring sites to the one occupied by a given cell.

Parameters

pCell pointer to a cell

Returns: whether the cell has any free neighbouring sites

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 225 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

bool CaBasedCellPopulation< DIM >::IsSiteAvailable	(	unsigned	index,
		CellPtr	pCell
	)

virtual

Find if a given node has space available. Overridden in subclasses to implement different division regimes.

Todo:: Which subclasses? Why is the second input argument needed?

Parameters

index	The global index of a specified node.
pCell	The cell wanting to divide into the lattice site (defaults to NULL).

Returns: whether the node is an empty site

Todo:: this is where to deal with carrying capacity

Definition at line 122 of file CaBasedCellPopulation.cpp.

Referenced by CaBasedCellPopulation< DIM >::CaBasedCellPopulation(), ExclusionCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), ShovingCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), CryptShovingCaBasedDivisionRule::CalculateDaughterNodeIndex(), and ExclusionCaBasedDivisionRule< SPACE_DIM >::IsRoomToDivide().

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::OpenWritersFiles ( OutputFileHandler & rOutputFileHandler )

virtual

Overridden OpenWritersFiles() method.

Open all files in mCellPopulationWriters and mCellWriters for writing (not appending).

Parameters

rOutputFileHandler handler for the directory in which to open this file.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 523 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles().

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile )

virtual

Outputs CellPopulation parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOnLatticeCellPopulation< DIM >.

Definition at line 607 of file CaBasedCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::RemoveAllUpdateRules ( )

virtual

Overridden RemoveAllUpdateRules() method.

Remove any update rules previously passed to this population by clearing mUpdateRuleCollection and mSwitchingUpdateRuleCollection.

Reimplemented from AbstractOnLatticeCellPopulation< DIM >.

Definition at line 568 of file CaBasedCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::RemoveAllUpdateRules().

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::RemoveCellUsingLocationIndex	(	unsigned	index,
		CellPtr	pCell
	)

virtual

Overridden AddCellUsingLocationIndex method to remove a cell from a given location index. Also updates mAvailableSpaces

Parameters

index	the location index
pCell	the cell.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 215 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex().

template<unsigned DIM>

unsigned CaBasedCellPopulation< DIM >::RemoveDeadCells ( )

virtual

Remove all cells labelled as dead.

Note that after calling this method the cell population 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 AbstractCellPopulation< DIM >.

Definition at line 254 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

std::vector< unsigned > & CaBasedCellPopulation< DIM >::rGetAvailableSpaces ( )

Returns: mAvailableSpaces.

Definition at line 116 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

PottsMesh< DIM > & CaBasedCellPopulation< DIM >::rGetMesh ( )

Returns: reference to mrMesh.

Definition at line 129 of file CaBasedCellPopulation.cpp.

Referenced by ExclusionCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), ShovingCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), CryptShovingCaBasedDivisionRule::CalculateDaughterNodeIndex(), DiffusionCaUpdateRule< DIM >::EvaluateProbability(), ExclusionCaBasedDivisionRule< SPACE_DIM >::IsRoomToDivide(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>

const PottsMesh< DIM > & CaBasedCellPopulation< DIM >::rGetMesh ( ) const

Returns: const reference to mrMesh (used in archiving).

Definition at line 135 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

template<class Archive >

void CaBasedCellPopulation< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the object and its member variables.

Note that serialization of the mesh and cells is handled by load/save_construct_data.

Note also that member data related to writers is not saved - output must be set up again by the caller after a restart.

Parameters

archive	the archive
version	the current version of this class

Definition at line 106 of file CaBasedCellPopulation.hpp.

References CaBasedCellPopulation< DIM >::mAvailableSpaces, CaBasedCellPopulation< DIM >::mLatticeCarryingCapacity, CaBasedCellPopulation< DIM >::mpCaBasedDivisionRule, and CaBasedCellPopulation< DIM >::mSwitchingUpdateRuleCollection.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::SetCaBasedDivisionRule ( boost::shared_ptr< AbstractCaBasedDivisionRule< DIM > > pCaBasedDivisionRule )

Set the division rule for this population.

Parameters

pCaBasedDivisionRule pointer to the new division rule

Definition at line 601 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::SetEmptySites ( const std::set< unsigned > & rEmptySiteIndices )

private

Set the empty sites by taking in a set of which nodes indices are empty sites.

Parameters

rEmptySiteIndices set of node indices corresponding to empty sites

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::Update ( bool hasHadBirthsOrDeaths = true )

virtual

Overridden Update() method.

Checks association of nodes with CellPtrs.

Parameters

hasHadBirthsOrDeaths - a bool saying whether cell population has had Births Or Deaths

Implements AbstractCellPopulation< DIM >.

Definition at line 500 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::UpdateCellLocations ( double dt )

virtual

Overridden UpdateCellLocations() method.

Parameters

dt time step

Todo:: make this sweep random

Implements AbstractOnLatticeCellPopulation< DIM >.

Definition at line 283 of file CaBasedCellPopulation.cpp.

References EXCEPTION, PottsMesh< DIM >::GetMooreNeighbouringNodeIndices(), RandomNumberGenerator::Instance(), NEVER_REACHED, RandomNumberGenerator::randMod(), RandomNumberGenerator::ranf(), and RandomNumberGenerator::Shuffle().

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::Validate ( )

privatevirtual

Overridden Validate() method.

Not used in CA simulations so just contains NEVER_REACHED

Implements AbstractCellPopulation< DIM >.

Definition at line 53 of file CaBasedCellPopulation.cpp.

References NEVER_REACHED.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::WriteVtkResultsToFile ( const std::string & rDirectory )

privatevirtual

Overridden WriteVtkResultsToFile() method.

This method offsets cells so can visulaise multiple cells at a single site

Parameters

rDirectory pathname of the output directory, relative to where Chaste output is stored

Implements AbstractCellPopulation< DIM >.

Definition at line 619 of file CaBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), SimulationTime::GetTimeStepsElapsed(), NodesOnlyMesh< SPACE_DIM >::GetWidth(), SimulationTime::Instance(), RandomNumberGenerator::Instance(), and RandomNumberGenerator::ranf().

Member Data Documentation

template<unsigned DIM>

std::vector<unsigned> CaBasedCellPopulation< DIM >::mAvailableSpaces

private

Records for each node the node the number of spaces available.

Definition at line 80 of file CaBasedCellPopulation.hpp.

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

template<unsigned DIM>

unsigned CaBasedCellPopulation< DIM >::mLatticeCarryingCapacity

private

The carrying capacity (number of cells allowed per site).

Definition at line 71 of file CaBasedCellPopulation.hpp.

Referenced by CaBasedCellPopulation< DIM >::serialize().

template<unsigned DIM>

boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > CaBasedCellPopulation< DIM >::mpCaBasedDivisionRule

private

A pointer to a division rule that is used to specify how cells divide. I.e do they move other cells out of the way. This is a specialisation for CA models.

Definition at line 84 of file CaBasedCellPopulation.hpp.

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

template<unsigned DIM>

std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > > CaBasedCellPopulation< DIM >::mSwitchingUpdateRuleCollection

private

The update rules used to determine the new location of the cells. These rules specify is cells switch locations.

Definition at line 77 of file CaBasedCellPopulation.hpp.

Referenced by CaBasedCellPopulation< DIM >::serialize().

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

cell_based/src/population/CaBasedCellPopulation.hpp
cell_based/src/population/CaBasedCellPopulation.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned DIM> class CaBasedCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class CaBasedCellPopulation< DIM >