#include <MultipleCaBasedCellPopulation.hpp>

Inheritance diagram for MultipleCaBasedCellPopulation< DIM >:

Collaboration diagram for MultipleCaBasedCellPopulation< DIM >:

Public Member Functions
	MultipleCaBasedCellPopulation (PottsMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), unsigned latticeCarryingCapacity=1u, bool deleteMesh=false, bool validate=false)
	MultipleCaBasedCellPopulation (PottsMesh< DIM > &rMesh)
virtual	~MultipleCaBasedCellPopulation ()
std::vector< unsigned > &	rGetAvailableSpaces ()
bool	IsSiteAvailable (unsigned index)
PottsMesh< DIM > &	rGetMesh ()
const PottsMesh< DIM > &	rGetMesh () const
Node< DIM > *	GetNode (unsigned index)
unsigned	GetNumNodes ()
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, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())
unsigned	RemoveDeadCells ()
void	UpdateCellLocations (double dt)
bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)
void	Update (bool hasHadBirthsOrDeaths=true)
void	CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
void	CloseOutputFiles ()
void	WriteResultsToFiles ()
void	WriteCellVolumeResultsToFile ()
double	GetVolumeOfCell (CellPtr pCell)
virtual void	GenerateCellResultsAndWriteToFiles ()
double	GetWidth (const unsigned &rDimension)
void	AddUpdateRule (boost::shared_ptr< AbstractMultipleCaUpdateRule< DIM > > pUpdateRule)
void	RemoveAllUpdateRules ()
const std::vector < boost::shared_ptr < AbstractMultipleCaUpdateRule < DIM > > > &	rGetUpdateRuleCollection () const
void	OutputCellPopulationParameters (out_stream &rParamsFile)
std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)
Private Member Functions
void	SetEmptySites (const std::set< unsigned > &rEmptySiteIndices)
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
void	Validate ()
void	WriteVtkResultsToFile ()
Private Attributes
unsigned	mLatticeCarryingCapacity
out_stream	mpVizLocationsFile
std::vector< boost::shared_ptr < AbstractMultipleCaUpdateRule < DIM > > >	mUpdateRuleCollection
std::vector< unsigned >	mAvailableSpaces
Friends
class	TestMultipleCaBasedCellPopulation
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class MultipleCaBasedCellPopulation< DIM >

Todo:: This description is pasted from Potts. Please change it.

A facade class encapsulating a cell population under the Cellular Potts Model framework.

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

The code currently requires the PottsMesh object to be fixed, in the sense that no new nodes or elements can be added.

Definition at line 69 of file MultipleCaBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

Create a new cell population facade from a mesh and collection of cells.

There must be precisely one CellPtr for each PottsElement in the mesh.

Parameters:

rMesh	reference to a PottsMesh
rCells	reference to a vector of CellPtrs
locationIndices	an optional 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 52 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

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

Constructor for use by the de-serializer.

Parameters:

rMesh a vertex mesh.

Definition at line 89 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

MultipleCaBasedCellPopulation< DIM >::~MultipleCaBasedCellPopulation ( ) [virtual]

Destructor, which frees any memory allocated by the constructor.

Definition at line 95 of file MultipleCaBasedCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

CellPtr MultipleCaBasedCellPopulation< DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		CellPtr	pParentCell = `CellPtr()`
	)

Overridden AddCell() method.

Add a new cell to the cell population.

Parameters:

pNewCell	the cell to add
rCellDivisionVector	this parameter is not yet used in this class (see #1737)
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)

Definition at line 176 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

void MultipleCaBasedCellPopulation< 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 155 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

void MultipleCaBasedCellPopulation< DIM >::AddUpdateRule ( boost::shared_ptr< AbstractMultipleCaUpdateRule< DIM > > pUpdateRule )

Add an update rule to be used in this simulation (use this to set up how cells move).

Parameters:

pUpdateRule pointer to an update rule

Definition at line 492 of file MultipleCaBasedCellPopulation.cpp.

Referenced by OnLatticeSimulation< DIM >::AddMultipleCaUpdateRule().

template<unsigned DIM>

void MultipleCaBasedCellPopulation< DIM >::CloseOutputFiles ( ) [virtual]

Overridden CloseOutputFiles() method.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 381 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

void MultipleCaBasedCellPopulation< DIM >::CreateOutputFiles	(	const std::string &	rDirectory,
		bool	cleanOutputDirectory
	)		`[virtual]`

Overridden CreateOutputFiles() method.

Parameters:

rDirectory	pathname of the output directory, relative to where Chaste output is stored
cleanOutputDirectory	whether to delete the contents of the output directory prior to output file creation

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 372 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

void MultipleCaBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles ( ) [virtual]

Overridden GenerateCellResultsAndWriteToFiles() method.

Implements AbstractCellPopulation< DIM >.

Definition at line 454 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

c_vector< double, DIM > MultipleCaBasedCellPopulation< 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 centre of mass of the element corresponding to this cell.

Implements AbstractCellPopulation< DIM >.

Definition at line 143 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

std::set< unsigned > MultipleCaBasedCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned index ) [virtual]

Overridden GetNeighbouringNodeIndices() method.

This method currently returns an exception as the two types of neighbourhood (Moore and Von Neumann) are defined in the PottsMesh.

Parameters:

index the node index

Returns:: the set of neighbouring node indices.

Implements AbstractCellPopulation< DIM >.

Definition at line 517 of file MultipleCaBasedCellPopulation.cpp.

References EXCEPTION.

template<unsigned DIM>

Node< DIM > * MultipleCaBasedCellPopulation< 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 131 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

Node< DIM > * MultipleCaBasedCellPopulation< 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 149 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

unsigned MultipleCaBasedCellPopulation< DIM >::GetNumNodes ( ) [virtual]

Overridden GetNumNodes() method.

Returns:: the number of nodes in the cell population.

Implements AbstractCellPopulation< DIM >.

Definition at line 137 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

double MultipleCaBasedCellPopulation< DIM >::GetVolumeOfCell ( CellPtr pCell ) [virtual]

Overridden GetVolumeOfCell() method.

Parameters:

pCell boost shared pointer to a cell

Implements AbstractCellPopulation< DIM >.

Definition at line 446 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

double MultipleCaBasedCellPopulation< 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 483 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

bool MultipleCaBasedCellPopulation< 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 361 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

bool MultipleCaBasedCellPopulation< DIM >::IsSiteAvailable ( unsigned index )

Find if a given node Has space available.

Parameters:

index the global index of a specified node

Returns:: whether the node is an empty site

Definition at line 113 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

void MultipleCaBasedCellPopulation< 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 510 of file MultipleCaBasedCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

void MultipleCaBasedCellPopulation< DIM >::RemoveAllUpdateRules ( )

Method to remove all the update rules

Definition at line 498 of file MultipleCaBasedCellPopulation.cpp.

Referenced by OnLatticeSimulation< DIM >::RemoveAllMultipleCaUpdateRules().

template<unsigned DIM>

void MultipleCaBasedCellPopulation< 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 166 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

unsigned MultipleCaBasedCellPopulation< 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 240 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

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

Returns:: mAvailableSpaces.

Definition at line 107 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

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

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

Definition at line 125 of file MultipleCaBasedCellPopulation.cpp.

template<unsigned DIM>

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

Returns:: reference to mrMesh.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 119 of file MultipleCaBasedCellPopulation.cpp.

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

template<unsigned DIM>

const std::vector< boost::shared_ptr< AbstractMultipleCaUpdateRule< DIM > > > & MultipleCaBasedCellPopulation< DIM >::rGetUpdateRuleCollection ( ) const

Get the collection of update rules to be used in this simulation.