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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <CellPopulationAdjacencyMatrixWriter.hpp>
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) |
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 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.
CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::CellPopulationAdjacencyMatrixWriter | ( | ) |
Default constructor.
Definition at line 49 of file CellPopulationAdjacencyMatrixWriter.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 62 of file CellPopulationAdjacencyMatrixWriter.hpp.
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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.
pCellPopulation | a pointer to the CaBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 223 of file CellPopulationAdjacencyMatrixWriter.cpp.
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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 not 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.
pCellPopulation | a pointer to the ImmersedBoundaryCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 246 of file CellPopulationAdjacencyMatrixWriter.cpp.
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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.
pCellPopulation | a pointer to the MeshBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 139 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().
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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.
pCellPopulation | a pointer to the NodeBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 228 of file CellPopulationAdjacencyMatrixWriter.cpp.
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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.
pCellPopulation | a pointer to the PottsBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 234 of file CellPopulationAdjacencyMatrixWriter.cpp.
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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 not 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.
pCellPopulation | a pointer to the VertexBasedCellPopulation to visit. |
Implements AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 240 of file CellPopulationAdjacencyMatrixWriter.cpp.
void CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation | ( | AbstractCellPopulation< SPACE_DIM, SPACE_DIM > * | pCellPopulation | ) |
Visit the population and write the data.
pCellPopulation | a pointer to the population to visit. |
Definition at line 55 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().
Needed for serialization.
Definition at line 54 of file CellPopulationAdjacencyMatrixWriter.hpp.