HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <HeterotypicBoundaryLengthWriter.hpp>

Inherits AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Collaboration diagram for HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	HeterotypicBoundaryLengthWriter ()
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)
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

Detailed Description

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

A class written using the visitor pattern for writing the length of the boundaries between labelled and unlabelled cells (as determined by the cell property CellLabel) in a cell population to file. This is a measure of how mixed the populations are.

For usage of this measure for cell sorting, see for example the heterotypic boundary length described in Zhang et al (2011). Computer simulations of cell sorting due to differential adhesion. PLOS ONE 6(10):e24999. doi:10.1371/journal.pone.0024999

Definition at line 55 of file HeterotypicBoundaryLengthWriter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::HeterotypicBoundaryLengthWriter ( ) [inline]

Default constructor.

Definition at line 45 of file HeterotypicBoundaryLengthWriter.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 67 of file HeterotypicBoundaryLengthWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( VertexBasedCellPopulation< SPACE_DIM > * pCellPopulation ) [inline, virtual]

Visit the population and write the labelled boundary length data.

Outputs a line of tab-separated values of the form: [fractional_length] [total_length] [fractional_neighbours] [total_neighbours]

Here the indexing of nodes is as given by the NodeIterator.

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

Parameters:

pCellPopulation

a pointer to the VertexBasedCellPopulation to visit.

Todo:: #2273 - check if this call to Update() is needed

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 288 of file HeterotypicBoundaryLengthWriter.cpp.

References AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetCellUsingLocationIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetEdgeLength(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetLocationIndexUsingCell(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream, VertexBasedCellPopulation< DIM >::rGetMesh(), and VertexBasedCellPopulation< DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( PottsBasedCellPopulation< SPACE_DIM > * pCellPopulation ) [inline, virtual]

Visit the population and write the labelled boundary length data.

Outputs a line of tab-separated values of the form: [fractional_length] [total_length] [fractional_neighbours] [total_neighbours]

Here the indexing of nodes is as given by the NodeIterator.

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

Parameters:

pCellPopulation

a pointer to the PottsBasedCellPopulation to visit.

Todo:: #2273 - investigate whether there is a hard-coded assumption that neighbouring nodes in Potts simulations are unit distance apart

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 208 of file HeterotypicBoundaryLengthWriter.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), PottsBasedCellPopulation< DIM >::GetNode(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream, and PottsBasedCellPopulation< DIM >::rGetMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( NodeBasedCellPopulation< SPACE_DIM > * pCellPopulation ) [inline, virtual]

Visit the population and write the labelled boundary length data.

Outputs a line of tab-separated values of the form: [fractional_length] [total_length] [fractional_neighbours] [total_neighbours]

Here the indexing of nodes is as given by the NodeIterator.

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

Parameters:

pCellPopulation

a pointer to the NodeBasedCellPopulation to visit.

Todo:: #2273 - check if this call to Update() is needed

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 125 of file HeterotypicBoundaryLengthWriter.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), NodeBasedCellPopulation< DIM >::GetCellUsingLocationIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), NodeBasedCellPopulation< DIM >::GetNode(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream, NodeBasedCellPopulation< DIM >::rGetMesh(), and NodeBasedCellPopulation< DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( CaBasedCellPopulation< SPACE_DIM > * pCellPopulation ) [inline, virtual]

Visit the population and write the data.

This is an empty dummy function, since this class is not defined for use with a CaBasedCellPopulation.

Parameters:

pCellPopulation

a pointer to the CaBasedCellPopulation to visit.

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 120 of file HeterotypicBoundaryLengthWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit ( MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM > * pCellPopulation ) [inline, virtual]

Visit the population and write the labelled boundary length data.

Outputs a line of tab-separated values of the form: [fractional_length] [total_length] [fractional_neighbours] [total_neighbours]

Here the indexing of nodes is as given by the NodeIterator.

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

Parameters:

pCellPopulation

a pointer to the MeshBasedCellPopulation to visit.

Todo:: #2273 - check if this call is needed

Todo:: #2273 - check we have correctly dealt with ghost nodes

Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 51 of file HeterotypicBoundaryLengthWriter.cpp.

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 59 of file HeterotypicBoundaryLengthWriter.hpp.

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

cell_based/src/population/writers/population_writers/HeterotypicBoundaryLengthWriter.hpp
cell_based/src/population/writers/population_writers/HeterotypicBoundaryLengthWriter.cpp

HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Public Member Functions

Private Member Functions

Friends

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

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