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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <HeterotypicBoundaryLengthWriter.hpp>
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) |
virtual void | Visit (ImmersedBoundaryCellPopulation< SPACE_DIM > *pCellPopulation) |
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AbstractCellPopulationWriter (const std::string &rFileName) | |
virtual void | WriteHeader (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation) |
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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 () |
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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 | |
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std::string | mFileName |
out_stream | mpOutStream |
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.
The output file is called heterotypicboundary.dat by default.
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 57 of file HeterotypicBoundaryLengthWriter.hpp.
HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::HeterotypicBoundaryLengthWriter | ( | ) |
Default constructor.
Definition at line 53 of file HeterotypicBoundaryLengthWriter.cpp.
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inlineprivate |
Serialize the object and its member variables.
archive | the archive |
version | the current version of this class |
Definition at line 69 of file HeterotypicBoundaryLengthWriter.hpp.
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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.
pCellPopulation | a pointer to the CaBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 128 of file HeterotypicBoundaryLengthWriter.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 >::IsCellAttachedToLocationIndex(), and CaBasedCellPopulation< DIM >::rGetMesh().
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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]
This line is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.
pCellPopulation | a pointer to the ImmersedBoundaryCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 435 of file HeterotypicBoundaryLengthWriter.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), ImmersedBoundaryCellPopulation< DIM >::rGetMesh(), and ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::rGetNodeLocationsVoronoiDiagram().
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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.
pCellPopulation | a pointer to the MeshBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 59 of file HeterotypicBoundaryLengthWriter.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength(), and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsGhostNode().
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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.
pCellPopulation | a pointer to the NodeBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 193 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(), Node< SPACE_DIM >::GetRadius(), NodeBasedCellPopulation< DIM >::rGetMesh(), and NodeBasedCellPopulation< DIM >::Update().
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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.
pCellPopulation | a pointer to the PottsBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 276 of file HeterotypicBoundaryLengthWriter.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(), PottsBasedCellPopulation< DIM >::GetNeighbouringLocationIndices(), PottsBasedCellPopulation< DIM >::GetNode(), Node< SPACE_DIM >::rGetContainingElementIndices(), and PottsBasedCellPopulation< DIM >::rGetMesh().
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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.
pCellPopulation | a pointer to the VertexBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 373 of file HeterotypicBoundaryLengthWriter.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetEdgeLength(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), VertexBasedCellPopulation< DIM >::rGetMesh(), and VertexBasedCellPopulation< DIM >::Update().
Needed for serialization.
Definition at line 61 of file HeterotypicBoundaryLengthWriter.hpp.