#include <AbstractCellPopulation.hpp>

Inheritance diagram for AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Classes
class	Iterator

Public Member Functions
	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_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, SPACE_DIM > &	rGetMesh ()

virtual TetrahedralMesh < ELEMENT_DIM, SPACE_DIM > *	GetTetrahedralMeshForPdeModifier ()=0

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

virtual double	GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)=0

std::list< CellPtr > &	rGetCells ()

virtual unsigned	GetNumNodes ()=0

virtual c_vector< double, SPACE_DIM >	GetLocationOfCellCentre (CellPtr pCell)=0

virtual Node< SPACE_DIM > *	GetNode (unsigned index)=0

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

virtual bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

virtual CellPtr	AddCell (CellPtr pNewCell, CellPtr pParentCell=CellPtr())=0

virtual double	GetDefaultTimeStep ()=0

virtual unsigned	RemoveDeadCells ()=0

virtual void	Update (bool hasHadBirthsOrDeaths=true)=0

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)

virtual void	AddCellUsingLocationIndex (unsigned index, CellPtr pCell)

virtual void	RemoveCellUsingLocationIndex (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 ()

virtual double	GetWidth (const unsigned &rDimension)=0

virtual double	GetVolumeOfCell (CellPtr pCell)=0

virtual std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)=0

virtual std::set< unsigned >	GetNeighbouringLocationIndices (CellPtr pCell)=0

c_vector< double, SPACE_DIM >	GetCentroidOfCellPopulation ()

virtual void	UpdateCellProcessLocation ()

virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

void	CloseWritersFiles ()

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

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

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

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

void	OutputCellPopulationInfo (out_stream &rParamsFile)

virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)=0

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

bool	GetOutputResultsForChasteVisualizer ()

template<template< unsigned, unsigned > class T>
void	AddPopulationWriter ()

template<template< unsigned, unsigned > class T>
void	AddCellWriter ()

template<template< unsigned, unsigned > class T>
void	AddCellPopulationCountWriter ()

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

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

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

template<template< unsigned, unsigned > class T>
bool	HasWriter () const

void	SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)

c_vector< double, SPACE_DIM >	GetSizeOfCellPopulation ()

virtual bool	IsRoomToDivide (CellPtr pCell)

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

Protected Member Functions
virtual void	Validate ()=0

virtual void	WriteVtkResultsToFile (const std::string &rDirectory)=0

	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

virtual void	AcceptCellWritersAcrossPopulation ()

Protected Attributes
std::map< unsigned, std::set < CellPtr > >	mLocationCellMap

std::map< Cell *, unsigned >	mCellLocationMap

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	mrMesh

std::list< CellPtr >	mCells

c_vector< double, SPACE_DIM >	mCentroid

out_stream	mpVtkMetaFile

boost::shared_ptr < CellPropertyRegistry >	mpCellPropertyRegistry

bool	mOutputResultsForChasteVisualizer

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

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

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

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

void	OpenRoundRobinWritersFilesForAppend (OutputFileHandler &rOutputFileHandler)

void	CloseRoundRobinWritersFiles ()

Friends
class	boost::serialization::access

Detailed Description

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

An abstract facade class encapsulating a cell population.

Contains a group of cells and associated methods.

Definition at line 75 of file AbstractCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation ( AbstractMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

protected

Constructor that just takes in a mesh.

Parameters

rMesh the mesh for the population.

Definition at line 106 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation	(	AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`
	)

AbstractCellPopulation Constructor.

Note: Warning: the passed-in vector of cells will be emptied, even if the constructor throws an exception!

Parameters

rMesh	a reference to the mesh underlying the cell population
rCells	a vector of cells. Copies of the cells will be stored in the cell population, and the passed-in vector cleared.
locationIndices	an optional vector of location indices that correspond to real cells

Definition at line 68 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPropertyRegistry.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Base class with virtual methods needs a virtual destructor.

Definition at line 112 of file AbstractCellPopulation.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

pure virtual

Accept a cell writer so it can write data from this object to file.

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

Parameters

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

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWritersAcrossPopulation ( )

protectedvirtual

Call AcceptCellWriter across the whole population.

By default the implementation here iterates over the cell population, but this is overridden in some classes that need to go over nodes.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 660 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationCountWriter ( boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationCountWriter )

pure virtual

Accept a cell population count writer so it can write data from this object to file.

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

Parameters

pPopulationCountWriter the population count writer.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationWriter ( boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter )

pure virtual

Accept a cell population writer so it can write data from this object to file.

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

Parameters

pPopulationWriter the population writer.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual CellPtr AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell	(	CellPtr	pNewCell,
		CellPtr	pParentCell = `CellPtr()`
	)

pure virtual

Add a new cell to the cell population.

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

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).

Implemented in NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< SPACE_DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<template< unsigned, unsigned > class T>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationCountWriter ( )

inline

Add a cell population count writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.

Returns: This method returns void

Definition at line 720 of file AbstractCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

inline

Add a cell population count writer through an input argument. This alternative to the templated AddCellPopulationCountWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.

Parameters

pCellPopulationCountWriter shared pointer to a cell population count writer

Returns: This method returns void

Definition at line 762 of file AbstractCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex	(	unsigned	index,
		CellPtr	pCell
	)

virtual

Adds a cell to a given location index.

Parameters

index	the location index
pCell	the cell.

Reimplemented in CaBasedCellPopulation< DIM >.

Definition at line 377 of file AbstractCellPopulation.cpp.

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation(), AbstractOnLatticeCellPopulation< DIM >::AbstractOnLatticeCellPopulation(), CaBasedCellPopulation< DIM >::AddCellUsingLocationIndex(), and VertexBasedCellPopulation< SPACE_DIM >::VertexBasedCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<template< unsigned, unsigned > class T>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellWriter ( )

inline

Add a cell writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.

Returns: This method returns void

Definition at line 708 of file AbstractCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

inline

Add a cell writer through an input argument. This alternative to the templated AddCellWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.

Parameters

pCellWriter shared pointer to a cell writer

Returns: This method returns void

Definition at line 748 of file AbstractCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<template< unsigned, unsigned > class T>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddPopulationWriter ( )

inline

Add a cell population writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.

Returns: This method returns void

Definition at line 696 of file AbstractCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

inline

Add a cell population writer through an input argument. This alternative to the templated AddPopulationWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.

Parameters

pPopulationWriter shared pointer to a cell population writer

Returns: This method returns void

Definition at line 734 of file AbstractCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin ( )

Returns: iterator pointing to the first cell in the cell population

Definition at line 989 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells.

Referenced by ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), IsolatedLabelledCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), ApoptoticCellKiller< SPACE_DIM >::CheckAndLabelCellsForApoptosisOrDeath(), RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath(), PlaneBasedCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), SloughingCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), EllipticBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), CryptProjectionStatistics::GetCryptSection(), CryptStatistics::GetCryptSection(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::ImposeBoundaryCondition(), AbstractBoxDomainPdeModifier< DIM >::InitialiseCellPdeElementMap(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), CellwiseDataGradient< DIM >::SetupGradients(), ParabolicBoxDomainPdeModifier< DIM >::SetupInitialSolutionVector(), VolumeDependentAveragedSourceEllipticPde< DIM >::SetupSourceTerms(), AveragedSourceEllipticPde< DIM >::SetupSourceTerms(), AveragedSourceParabolicPde< DIM >::SetupSourceTerms(), VolumeTrackingModifier< DIM >::UpdateCellData(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellData(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellPdeElementMap(), CryptProjectionForce::UpdateNode3dLocationMap(), CryptSimulationBoundaryCondition< DIM >::VerifyBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::VerifyBoundaryCondition(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), and RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseRoundRobinWritersFiles ( )

private

Close all files in mCellPopulationWriters and mCellWriters.

Files in mCellPopulationCountWriters are NOT closed in this call since they are not written in a round-robin fashion

Definition at line 466 of file AbstractCellPopulation.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::CloseFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseWritersFiles ( )

Close output files associated with any writers in the members mCellPopulationCountWriters, mCellPopulationWriters and mCellWriters.

The method also closes the .pvd output file if VTK is available.

Definition at line 482 of file AbstractCellPopulation.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::CloseFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns: a pair of indices ordered by node index. Used by the rest length routines.

Parameters

index1	a node index
index2	a node index

Definition at line 807 of file AbstractCellPopulation.cpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End ( )

Returns: iterator pointing to one past the last cell in the cell population

Definition at line 995 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells.

Referenced by ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath(), EllipticBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), CryptProjectionStatistics::GetCryptSection(), CryptStatistics::GetCryptSection(), AbstractBoxDomainPdeModifier< DIM >::InitialiseCellPdeElementMap(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), CellwiseDataGradient< DIM >::SetupGradients(), ParabolicBoxDomainPdeModifier< DIM >::SetupInitialSolutionVector(), VolumeTrackingModifier< DIM >::UpdateCellData(), AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellData(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellPdeElementMap(), CryptProjectionForce::UpdateNode3dLocationMap(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), and RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::set< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellAncestors ( )

Loops over cells and makes a list of the ancestors that are part of the cell population.

Returns: remaining_ancestors The size of this set tells you how many clonal populations remain.

Definition at line 181 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellCyclePhaseCount ( )

Find out how many cells in each cell cycle phase there are.

Returns: The number of cells of each phase (evaluated at each visualizer output) [0] = G_ZERO_PHASE [1] = G_ONE_PHASE [2] = S_PHASE [3] = G_TWO_PHASE [4] = M_PHASE

Definition at line 261 of file AbstractCellPopulation.cpp.

References EXCEPTION, PetscTools::GetWorld(), PetscTools::IsParallel(), and NEVER_REACHED.

Referenced by CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellDataItemAtPdeNode	(	unsigned	pdeNodeIndex,
		std::string &	rVariableName,
		bool	dirichletBoundaryConditionApplies = `false`,
		double	dirichletBoundaryValue = `0.0`
	)

pure virtual

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.

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

Implemented in VertexBasedCellPopulation< SPACE_DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractCentreBasedCellPopulation< DIM >.

Referenced by ParabolicGrowingDomainPdeModifier< DIM >::UpdateSolutionVector().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellMutationStateCount ( )

Find out how many cells of each mutation state there are

Returns: The number of cells of each mutation state (evaluated at each visualizer output), with default ordering [0] = healthy count [1] = APC one hit [2] = APC two hit [3] = beta catenin one hit

Definition at line 192 of file AbstractCellPopulation.cpp.

References PetscTools::GetWorld(), and PetscTools::IsParallel().

Referenced by CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellProliferativeTypeCount ( )

Find out how many cells of each type there are.

Returns: The number of cells of each type (evaluated at each visualizer output), with default ordering [0] = STEM [1] = TRANSIT [2] = DIFFERENTIATED [3] = DEFAULT

Definition at line 226 of file AbstractCellPopulation.cpp.

References PetscTools::GetWorld(), and PetscTools::IsParallel().

Referenced by CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

boost::shared_ptr< CellPropertyRegistry > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellPropertyRegistry ( )

Returns: registry of cell properties used in this cell population.

Definition at line 419 of file AbstractCellPopulation.cpp.

Referenced by AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), and CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::WriteHeader().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::set< CellPtr > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellsUsingLocationIndex ( unsigned index )

Get the set of cells corresponding to a given location index.

Note that the set may be empty.

Parameters

index the location index

Returns: the set of cells.

Definition at line 341 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

CellPtr AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex ( unsigned index )

virtual

Get the cell corresponding to a given location index.

This method assumes that there is at most one cell attached to a location index and an assertion fails if not.

Todo:: should be an exception?

Parameters

index the location index

Returns: the cell.

Reimplemented in NodeBasedCellPopulation< DIM >.

Definition at line 320 of file AbstractCellPopulation.cpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation ( )

Returns: the centroid of the cell population.

Definition at line 446 of file AbstractCellPopulation.cpp.

Referenced by RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDefaultTimeStep ( )

pure virtual

Returns: a default value for the time step to use when simulating the cell population.

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

Note that the time step can be reset by calling SetDt() on the simulation object used to simulate the cell population.

Implemented in VertexBasedCellPopulation< SPACE_DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, and AbstractOnLatticeCellPopulation< DIM >.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell ( CellPtr pCell )

Get the location index corresponding to a given cell.

Assumes there is one location index for each cell and an assertion fails if not.

Parameters

pCell the cell

Returns: the location index.

Definition at line 410 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual c_vector<double, SPACE_DIM> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre ( CellPtr pCell )

pure virtual

Find where a given cell is in space.

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

Parameters

pCell the cell

Returns: the location of the cell

Implemented in CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< SPACE_DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractCentreBasedCellPopulation< DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual std::set<unsigned> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices ( CellPtr pCell )

pure virtual

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

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

Parameters

pCell a cell

Returns: the set of neighbouring location indices.

Implemented in VertexBasedCellPopulation< SPACE_DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, and MeshBasedCellPopulationWithGhostNodes< DIM >.

Referenced by DeltaNotchTrackingModifier< DIM >::UpdateCellData(), and CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual std::set<unsigned> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices ( unsigned index )

pure virtual

Given a node index, returns the set of neighbouring node indices.

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

Parameters

index the node index

Returns: the set of neighbouring node indices.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< SPACE_DIM >, and AbstractOnLatticeCellPopulation< DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual Node<SPACE_DIM>* AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode ( unsigned index )

pure virtual

Get a pointer to the node with a given index.

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

Parameters

index global index of the specified node

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

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< SPACE_DIM >, PottsBasedCellPopulation< DIM >, and CaBasedCellPopulation< DIM >.

Referenced by ChemotacticForce< DIM >::AddForceContribution(), PopulationTestingForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), BuskeAdhesiveForce< DIM >::CalculateForceBetweenNodes(), BuskeElasticForce< DIM >::CalculateForceBetweenNodes(), CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >::GetVectorCellDataForVtkOutput(), and CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumAllCells ( )

This returns the number of cells that are present in the internal mCells vector. It also includes dead cells and cells that are associated with a deleted location in the mesh.

Returns: the number of real cells.

Definition at line 165 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( )

pure virtual

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

Returns: the number of nodes in the cell population.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, and VertexBasedCellPopulation< SPACE_DIM >.

Referenced by PopulationTestingForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution(), and AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells ( )

This counts the number of cells that the cell iterator covers. It does not include dead cells or cells that are associated with a deleted location in the mesh.

Returns: the number of real cells.

Definition at line 152 of file AbstractCellPopulation.cpp.

Referenced by CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputResultsForChasteVisualizer ( )

Returns: mOutputResultsForChasteVisualizer

Definition at line 759 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSizeOfCellPopulation ( )

Returns: The width (maximum distance to centroid) of the cell population in each dimension

Definition at line 777 of file AbstractCellPopulation.cpp.

Referenced by NodeBasedCellPopulation< DIM >::GetSizeOfCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetTetrahedralMeshForPdeModifier ( )

pure virtual

Returns: a shared to a tetrahedral mesh, for use with a PDE modifier. This method is called by AbstractGrowingDomainPdeModifier.

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

Implemented in VertexBasedCellPopulation< SPACE_DIM >, NodeBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and MeshBasedCellPopulationWithGhostNodes< DIM >.

Referenced by AbstractGrowingDomainPdeModifier< DIM >::GenerateFeMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell ( CellPtr pCell )

pure virtual

Returns: the volume (or area in 2D, or length in 1D) of a given cell.

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

Parameters

pCell boost shared pointer to a cell

Implemented in NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< SPACE_DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and PottsBasedCellPopulation< DIM >.

Referenced by CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), VolumeTrackingModifier< DIM >::UpdateCellData(), and CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWidth ( const unsigned & rDimension )

pure virtual

Calculate the 'width' of any dimension of the cell population.

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

Parameters

rDimension a dimension (0,1 or 2)

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

Implemented in VertexBasedCellPopulation< SPACE_DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, NodeBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<template< unsigned, unsigned > class T>

bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::HasWriter ( ) const

inline

Get whether the population has a writer of the specified type.

Returns: whether the population has this writer

Definition at line 773 of file AbstractCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::InitialiseCells ( )

Initialise each cell's cell-cycle model.

Definition at line 117 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell )

pure virtual

Helper method for establishing if a cell is real.

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

Parameters

pCell the cell

Returns: whether a given cell is associated with a deleted node (cell-centre models) or element (vertex models).

Implemented in CaBasedCellPopulation< DIM >, VertexBasedCellPopulation< SPACE_DIM >, PottsBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractCentreBasedCellPopulation< DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAttachedToLocationIndex ( unsigned index )

virtual

Returns whether or not a cell is associated with a location index

Parameters

index the location index

Returns: whether there is a cell attached.

Definition at line 348 of file AbstractCellPopulation.cpp.

Referenced by CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsPdeNodeAssociatedWithNonApoptoticCell ( unsigned pdeNodeIndex )

virtual

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.

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

Reimplemented in CaBasedCellPopulation< DIM >, and VertexBasedCellPopulation< SPACE_DIM >.

Definition at line 826 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsRoomToDivide ( CellPtr pCell )

virtual

Returns: whether there is room into which a given cell may divide. Returns true by default, but may be overridden in subclasses.

Parameters

pCell pointer to a cell

Reimplemented in CaBasedCellPopulation< DIM >.

Definition at line 771 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::MoveCellInLocationMap	(	CellPtr	pCell,
		unsigned	old_index,
		unsigned	new_index
	)

Change the location index of a cell in mLocationCellMap and mCellLocationMap

Parameters

pCell	the cell to move
old_index	the old location index
new_index	the new location index

Definition at line 400 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenRoundRobinWritersFilesForAppend ( OutputFileHandler & rOutputFileHandler )

private

Open all files in mCellPopulationWriters and mCellWriters in append mode for writing.

Files in mCellPopulationCountWriters are NOT opened in this call since they are not written in a round-robin fashion.

Parameters

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

Definition at line 554 of file AbstractCellPopulation.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFileForAppend().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles ( OutputFileHandler & rOutputFileHandler )

virtual

Open output files (and, if required, write headers) for any writers in the members mCellPopulationCountWriters, mCellPopulationWriters and mCellWriters.

The method also writes the header for the .pvd output file if VTK is available.

Before doing this, the method also creates appropriate writer objects if mOutputResultsForChasteVisualizer is set to true.

This method is public because it is called by the simulation class at the start of the Solve() call.

Parameters

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

Reimplemented in VertexBasedCellPopulation< SPACE_DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 504 of file AbstractCellPopulation.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFile(), and OutputFileHandler::OpenOutputFile().

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles(), PottsBasedCellPopulation< DIM >::OpenWritersFiles(), CaBasedCellPopulation< DIM >::OpenWritersFiles(), and VertexBasedCellPopulation< SPACE_DIM >::OpenWritersFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationInfo ( out_stream & rParamsFile )

Outputs CellPopulation used in the simulation to file and then calls OutputCellPopulationParameters to output all relevant parameters.

Parameters

rParamsFile the file stream to which the parameters are output

Loop over cells and generate a set of cell-cycle model classes that are present in the population.

Todo:: this currently ignores different parameter regimes (#1453)

Loop over cells and generate a set of SRN model classes that are present in the population.

Todo:: this currently ignores different parameter regimes (#1453)

Definition at line 676 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile )

pure 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

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, VertexBasedCellPopulation< SPACE_DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractOffLatticeCellPopulation< DIM >, AbstractOnLatticeCellPopulation< DIM >, NodeBasedCellPopulationWithParticles< DIM >, and NodeBasedCellPopulationWithBuskeUpdate< DIM >.

Definition at line 748 of file AbstractCellPopulation.cpp.

Referenced by AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters(), and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex	(	unsigned	index,
		CellPtr	pCell
	)

virtual

Removes a cell from a given location index.

Parameters

index	the location index
pCell	the cell.

Reimplemented in CaBasedCellPopulation< DIM >.

Definition at line 384 of file AbstractCellPopulation.cpp.

References EXCEPTION.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells ( )

pure virtual

Remove all cells labelled as dead.

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

Returns: number of cells removed

Implemented in NodeBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, VertexBasedCellPopulation< SPACE_DIM >, PottsBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::list< CellPtr > & AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetCells ( )

Returns: reference to mCells.

Definition at line 146 of file AbstractCellPopulation.cpp.

Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator::Iterator(), and AbstractTargetAreaModifier< DIM >::UpdateTargetAreas().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM > & AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh ( )

Returns: reference to the mesh, mrMesh.

Definition at line 140 of file AbstractCellPopulation.cpp.

Referenced by DiffusionForce< DIM >::AddForceContribution(), GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), and NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 89 of file AbstractCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellAncestorsToLocationIndices ( )

Sets the Ancestor index of all the cells at this time to be the same as their location index, can be used to trace clonal populations.

Definition at line 171 of file AbstractCellPopulation.cpp.

References MAKE_PTR_ARGS.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellUsingLocationIndex	(	unsigned	index,
		CellPtr	pCell
	)

Set the cell corresponding to a given location index.

Assumes there is one cell for each location index and replaces any existing cell attached to the location index. If you wish to attach an additional cell to a location index use AddCellUsingLocaitonIndex as SetCellUsingLocation Index will overwrite cells attached to this index.

Parameters

index	the location index
pCell	the cell.

Definition at line 363 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDataOnAllCells	(	const std::string &	rDataName,
		double	dataValue
	)

Add an item of cell data to every cell in the population

Parameters

rDataName	is the name associated with the data
dataValue	is the value of the data, initially the same for each cell

Definition at line 129 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDefaultCellMutationStateAndProliferativeTypeOrdering ( )

Set a default ordering on cell mutation states and cell proliferative types, so that existing tests don't need to specify the old ordering explicitly.

Definition at line 425 of file AbstractCellPopulation.cpp.

Referenced by CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::WriteHeader().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< SPACE_DIM > &	rNewLocation
	)

pure virtual

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

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

Parameters

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

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputResultsForChasteVisualizer ( bool outputResultsForChasteVisualizer )

Set mOutputResultsForChasteVisualizer.

Parameters

outputResultsForChasteVisualizer the new value of mOutputResultsForChasteVisualizer

Definition at line 765 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SimulationSetupHook ( AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM > * pSimulation )

virtual

Empty hook method to provide the ability to specify some additional property of a cell-based simulation object.

This method is called immediately prior to calling SetupSolve() within the Solve() method in AbstractCellBasedSimulation.

This method can be overridden, for example, to add a T2SwapCellKiller to the simulation object in the case of a VertexBasedCellPopulation. This functionality avoids the need for static or dynamic casts to specific cell population types within simulation methods.

Parameters

pSimulation pointer to a cell-based simulation object

Definition at line 754 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update ( bool hasHadBirthsOrDeaths = true )

pure virtual

Remove the Nodes (for cell-centre) or VertexElements (for cell-vertex) which have been marked as deleted and update the correspondence with Cells.

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

Parameters

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

Implemented in NodeBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, VertexBasedCellPopulation< SPACE_DIM >, and PottsBasedCellPopulation< DIM >.

Referenced by VolumeTrackingModifier< DIM >::UpdateCellData(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), and CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellProcessLocation ( )

virtual

Update the ownership of cell in a parallel cell-based simulation.

Reimplemented in NodeBasedCellPopulation< DIM >.

Definition at line 461 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate ( )

protectedpure virtual

Check consistency of our internal data structures.

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

Implemented in NodeBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, VertexBasedCellPopulation< SPACE_DIM >, PottsBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteDataToVisualizerSetupFile ( out_stream & pVizSetupFile )

virtual

Write any data necessary to a visualization setup file. Used by AbstractCellBasedSimulation::WriteVisualizerSetupFile().

Parameters

pVizSetupFile a visualization setup file

Reimplemented in VertexBasedCellPopulation< SPACE_DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 358 of file AbstractCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles ( const std::string & rDirectory )

virtual

Write results from the current cell population state to output files.

Parameters

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

Reimplemented in PottsBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 569 of file AbstractCellPopulation.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), PetscTools::BeginRoundRobin(), PetscTools::EndRoundRobin(), and AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFileForAppend().

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), and PottsBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile ( const std::string & rDirectory )

protectedpure virtual

Write the current results to mpVtkMetaFile.

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

Parameters

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

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithParticles< DIM >, PottsBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, VertexBasedCellPopulation< SPACE_DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractCentreBasedCellPopulation< DIM >.

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 80 of file AbstractCellPopulation.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::map<Cell*, unsigned> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap

protected

Map cells to location (node or VertexElement) indices.

Definition at line 126 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation(), and AbstractCellPopulation< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

protected

A list of cell population count writers.

Definition at line 153 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM, DIM >::AddCellPopulationCountWriter(), AbstractCellPopulation< DIM, DIM >::HasWriter(), and AbstractCellPopulation< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

protected

A list of cell population writers.

Definition at line 150 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM, DIM >::AddPopulationWriter(), AbstractCellPopulation< DIM, DIM >::HasWriter(), and AbstractCellPopulation< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::list<CellPtr> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells

protected

List of cells.

Definition at line 132 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and AbstractCellPopulation< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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