#include <CellPopulationAdjacencyMatrixWriter.hpp>

Inheritance diagram for CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	CellPopulationAdjacencyMatrixWriter ()

void	VisitAnyPopulation (AbstractCellPopulation< SPACE_DIM, SPACE_DIM > *pCellPopulation)

virtual void	Visit (MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)

virtual void	Visit (CaBasedCellPopulation< SPACE_DIM > *pCellPopulation)

virtual void	Visit (NodeBasedCellPopulation< SPACE_DIM > *pCellPopulation)

virtual void	Visit (PottsBasedCellPopulation< SPACE_DIM > *pCellPopulation)

virtual void	Visit (VertexBasedCellPopulation< SPACE_DIM > *pCellPopulation)

Public Member Functions inherited from AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractCellPopulationWriter (const std::string &rFileName)

virtual void	WriteHeader (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)

Public Member Functions inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractCellBasedWriter (const std::string &rFileName)

virtual	~AbstractCellBasedWriter ()

void	CloseFile ()

virtual void	OpenOutputFile (OutputFileHandler &rOutputFileHandler)

void	OpenOutputFileForAppend (OutputFileHandler &rOutputFileHandler)

virtual void	WriteTimeStamp ()

virtual void	WriteNewline ()

void	SetFileName (std::string fileName)

std::string	GetFileName ()

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

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

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >
std::string	mFileName

out_stream	mpOutStream

Detailed Description

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

A class written using the visitor pattern for writing the cell population adjacency (i.e. connectivity) matrix to file.

The output file is called cellpopulationadjacency.dat by default.

Definition at line 50 of file CellPopulationAdjacencyMatrixWriter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::CellPopulationAdjacencyMatrixWriter ( )

Default constructor.

Definition at line 48 of file CellPopulationAdjacencyMatrixWriter.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void CellPopulationAdjacencyMatrixWriter< 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 62 of file CellPopulationAdjacencyMatrixWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM > * pCellPopulation )

virtual

Visit the population and write the adjacency matrix (as a long vector).

Outputs a line of tab-separated values of the form: [number of cells] [adjacency 1 1] [adjacency 1 2] [adjacency 1 3]...

where, in the case of N cells, the (i,j)th entry of the adjacency matrix corresponds to the (1 + i + N*j)th entry in the line (the additional 1 is for the initial entry, which gives N).

This line is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.

If cells i and j are adjacent and neither are labelled (as determined by the CellLabel property), then we have [adjacency i j] = 1; if they are adjacent and both are labelled, then we have [adjacency i j] = 2; if they are adjacent and exactly one is labelled, then we have [adjacency i j] = 3; otherwise, if they are no adjacent, then we have [adjacency i i] = 0.

By default we have [adjacency i i] = 0, i.e. cells are not considered to be adjacent to themselves.

Parameters

pCellPopulation a pointer to the MeshBasedCellPopulation to visit.

Todo:: #2645 - if efficiency is an issue, check if this is really needed

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 138 of file CellPopulationAdjacencyMatrixWriter.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( CaBasedCellPopulation< SPACE_DIM > * pCellPopulation )

virtual

Visit the population and write the adjacency matrix (as a long vector).

Outputs a line of tab-separated values of the form: [number of cells] [adjacency 1 1] [adjacency 1 2] [adjacency 1 3]...

where, in the case of N cells, the (i,j)th entry of the adjacency matrix corresponds to the (1 + i + N*j)th entry in the line (the additional 1 is for the initial entry, which gives N).

This line is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.

If cells i and j are adjacent and neither are labelled (as determined by the CellLabel property), then we have [adjacency i j] = 1; if they are adjacent and both are labelled, then we have [adjacency i j] = 2; if they are adjacent and exactly one is labelled, then we have [adjacency i j] = 3; otherwise, if they are no adjacent, then we have [adjacency i i] = 0.

By default we have [adjacency i i] = 0, i.e. cells are not considered to be adjacent to themselves.

Parameters

pCellPopulation a pointer to the CaBasedCellPopulation to visit.

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 222 of file CellPopulationAdjacencyMatrixWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( NodeBasedCellPopulation< SPACE_DIM > * pCellPopulation )

virtual

Visit the population and write the adjacency matrix (as a long vector).

Outputs a line of tab-separated values of the form: [number of cells] [adjacency 1 1] [adjacency 1 2] [adjacency 1 3]...

where, in the case of N cells, the (i,j)th entry of the adjacency matrix corresponds to the (1 + i + N*j)th entry in the line (the additional 1 is for the initial entry, which gives N).

This line is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.

If cells i and j are adjacent and neither are labelled (as determined by the CellLabel property), then we have [adjacency i j] = 1; if they are adjacent and both are labelled, then we have [adjacency i j] = 2; if they are adjacent and exactly one is labelled, then we have [adjacency i j] = 3; otherwise, if they are no adjacent, then we have [adjacency i i] = 0.

By default we have [adjacency i i] = 0, i.e. cells are not considered to be adjacent to themselves.

Parameters

pCellPopulation a pointer to the NodeBasedCellPopulation to visit.

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 227 of file CellPopulationAdjacencyMatrixWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( PottsBasedCellPopulation< SPACE_DIM > * pCellPopulation )

virtual

Visit the population and write the adjacency matrix (as a long vector).

Outputs a line of tab-separated values of the form: [number of cells] [adjacency 1 1] [adjacency 1 2] [adjacency 1 3]...

where, in the case of N cells, the (i,j)th entry of the adjacency matrix corresponds to the (1 + i + N*j)th entry in the line (the additional 1 is for the initial entry, which gives N).

This line is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.

If cells i and j are adjacent and neither are labelled (as determined by the CellLabel property), then we have [adjacency i j] = 1; if they are adjacent and both are labelled, then we have [adjacency i j] = 2; if they are adjacent and exactly one is labelled, then we have [adjacency i j] = 3; otherwise, if they are no adjacent, then we have [adjacency i i] = 0.

By default we have [adjacency i i] = 0, i.e. cells are not considered to be adjacent to themselves.

Parameters

pCellPopulation a pointer to the PottsBasedCellPopulation to visit.

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 233 of file CellPopulationAdjacencyMatrixWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( VertexBasedCellPopulation< SPACE_DIM > * pCellPopulation )

virtual

Visit the population and write the adjacency matrix (as a long vector).

Outputs a line of tab-separated values of the form: [number of cells] [adjacency 1 1] [adjacency 1 2] [adjacency 1 3]...

where, in the case of N cells, the (i,j)th entry of the adjacency matrix corresponds to the (1 + i + N*j)th entry in the line (the additional 1 is for the initial entry, which gives N).

This line is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.

If cells i and j are adjacent and neither are labelled (as determined by the CellLabel property), then we have [adjacency i j] = 1; if they are adjacent and both are labelled, then we have [adjacency i j] = 2; if they are adjacent and exactly one is labelled, then we have [adjacency i j] = 3; otherwise, if they are no adjacent, then we have [adjacency i i] = 0.

By default we have [adjacency i i] = 0, i.e. cells are not considered to be adjacent to themselves.

Parameters

pCellPopulation a pointer to the VertexBasedCellPopulation to visit.

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 239 of file CellPopulationAdjacencyMatrixWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation ( AbstractCellPopulation< SPACE_DIM, SPACE_DIM > * pCellPopulation )

Visit the population and write the data.

Parameters

pCellPopulation a pointer to the population to visit.

Todo:: #2645 - if efficiency is an issue, check if this is really needed

Definition at line 54 of file CellPopulationAdjacencyMatrixWriter.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 54 of file CellPopulationAdjacencyMatrixWriter.hpp.

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

cell_based/src/writers/population_writers/CellPopulationAdjacencyMatrixWriter.hpp
cell_based/src/writers/population_writers/CellPopulationAdjacencyMatrixWriter.cpp

Public Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

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