#include <VertexMeshWriter.hpp>

Inheritance diagram for VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	VertexMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)

	~VertexMeshWriter ()

void	WriteFilesUsingMesh (VertexMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

void	WriteVtkUsingMesh (VertexMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::string stamp="")

void	MakeVtkMesh (VertexMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

void	AddCellData (std::string dataName, std::vector< double > dataPayload)

void	AddPointData (std::string dataName, std::vector< double > dataPayload)

std::vector< double >	GetNextNode ()

ElementData	GetNextElement ()

VertexElementData	GetNextElementWithFaces ()

void	WriteFiles ()

template<>
void	WriteVtkUsingMesh (VertexMesh< 2, 2 > &rMesh, std::string stamp)

Public Member Functions inherited from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)

virtual	~AbstractMeshWriter ()

std::string	GetOutputDirectory ()

virtual unsigned	GetNumNodes ()

unsigned	GetNumElements ()

unsigned	GetNumBoundaryFaces ()

unsigned	GetNumCableElements ()

virtual ElementData	GetNextBoundaryElement ()

virtual ElementData	GetNextCableElement ()

void	WriteFilesUsingMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)

Private Attributes
VertexMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

MeshWriterIterators< ELEMENT_DIM, SPACE_DIM > *	mpIters

NodeMap *	mpNodeMap

unsigned	mNodeMapCurrentIndex

vtkUnstructuredGrid *	mpVtkUnstructedMesh

Additional Inherited Members
Protected Attributes inherited from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
OutputFileHandler *	mpOutputFileHandler

std::string	mBaseName

AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > *	mpMeshReader

unsigned	mNumNodes

unsigned	mNumElements

unsigned	mNumBoundaryElements

unsigned	mNumCableElements

Detailed Description

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

A mesh writer class for vertex-based meshes.

Definition at line 40 of file MutableVertexMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::VertexMeshWriter	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		const bool	clearOutputDir = `true`
	)

Constructor.

Parameters

rDirectory	reference to the output directory, relative to where Chaste output is stored
rBaseName	reference to the base name for results files
clearOutputDir	whether to clear the output directory prior to writing files

Definition at line 58 of file VertexMeshWriter.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters, and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::~VertexMeshWriter ( )

Destructor.

Definition at line 77 of file VertexMeshWriter.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpNodeMap, and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData	(	std::string	dataName,
		std::vector< double >	dataPayload
	)

Add data to a future VTK file.

Parameters

dataName	a tag to go into the VTK file
dataPayload	a pay-load of length (number of elements)

Definition at line 350 of file VertexMeshWriter.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

Referenced by VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData	(	std::string	dataName,
		std::vector< double >	dataPayload
	)

Add data to a future VTK file.

Parameters

dataName	a tag to go into the VTK file
dataPayload	a pay-load of length (number of nodes)

Definition at line 367 of file VertexMeshWriter.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ElementData VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement ( )

virtual

Returns: the data (indices/attributes) of the next element to be written to file

Todo:: Assert this method should only be called in 2D? (#1076/#1377)

Reimplemented from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 179 of file VertexMeshWriter.cpp.

References NodeMap::GetNewIndex(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumElements, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMesh, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpNodeMap, and ElementData::NodeIndices.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexElementData VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElementWithFaces ( )

Returns: the data (indices/attributes) of the next element to be written to file, including its faces. This method should only be called in 3D.

Todo:: Store face orientations? (#1076/#1377)

Definition at line 126 of file VertexMeshWriter.cpp.

References ElementData::AttributeValue, VertexElement< ELEMENT_DIM, SPACE_DIM >::GetFace(), NodeMap::GetNewIndex(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumElements, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMesh, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpNodeMap, VertexElementData::NodeIndices, and ElementData::NodeIndices.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< double > VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode ( )

virtual

Returns: the coordinates of the next node to be written to file

Reimplemented from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 99 of file VertexMeshWriter.cpp.

References AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumNodes, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters, and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMesh.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh ( VertexMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

Populate mpVtkUnstructedMesh using a vertex-based mesh. Called by WriteVtkUsingMesh().

Parameters

rMesh reference to the vertex-based mesh

Definition at line 303 of file VertexMeshWriter.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles ( )

virtual

Write mesh data to files. This method must be overridden in concrete classes.

Todo:: Store face orientations? (#1076/#1377)

Implements AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 413 of file VertexMeshWriter.cpp.

References VertexElementData::AttributeValue, ElementData::AttributeValue, VertexElementData::Faces, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElementWithFaces(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), ChasteBuildInfo::GetProvenanceString(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBaseName, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, VertexElementData::NodeIndices, ElementData::NodeIndices, and OutputFileHandler::OpenOutputFile().

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh ( VertexMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

Todo:: Mesh should be const (#1076)

Write files using a mesh.

Parameters

rMesh reference to the vertex-based mesh

Todo:: Mesh should be const (#1076)

Definition at line 385 of file VertexMeshWriter.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodeMapCurrentIndex, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumElements, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumNodes, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMesh, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMeshReader, VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpNodeMap, NodeMap::SetNewIndex(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles().

Referenced by VertexMesh< DIM, DIM >::save(), and PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh	(	VertexMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		std::string	stamp = `""`
	)

Write VTK file using a mesh.

Parameters

rMesh	reference to the vertex-based mesh
stamp	is an optional stamp (like a time-stamp) to put into the name of the file

Definition at line 208 of file VertexMeshWriter.cpp.

References OutputFileHandler::GetOutputDirectoryFullPath(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBaseName, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

Referenced by VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

template<>

void VertexMeshWriter< 2, 2 >::WriteVtkUsingMesh	(	VertexMesh< 2, 2 > &	rMesh,
		std::string	stamp
	)

Write VTK file using a mesh.

Parameters

rMesh	reference to the vertex-based mesh
stamp	is an optional stamp (like a time-stamp) to put into the name of the file

Definition at line 250 of file VertexMeshWriter.cpp.

References OutputFileHandler::GetOutputDirectoryFullPath(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBaseName, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodeMapCurrentIndex

private

What was the last index written to mpNodeMap ?

Definition at line 86 of file VertexMeshWriter.hpp.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MeshWriterIterators<ELEMENT_DIM,SPACE_DIM>* VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters

private

Iterators over the mesh

Definition at line 81 of file VertexMeshWriter.hpp.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElementWithFaces(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::VertexMeshWriter(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::~VertexMeshWriter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh<ELEMENT_DIM,SPACE_DIM>* VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMesh

private

If writing from a mesh object, the mesh to write to disk. Otherwise NULL.

Definition at line 78 of file VertexMeshWriter.hpp.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElementWithFaces(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

NodeMap* VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpNodeMap

private

Track deleted nodes so they don't get written

Definition at line 84 of file VertexMeshWriter.hpp.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElementWithFaces(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::~VertexMeshWriter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

vtkUnstructuredGrid* VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh

private

Todo:: Merge into VtkMeshWriter (#1076)

Definition at line 91 of file VertexMeshWriter.hpp.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::VertexMeshWriter(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::~VertexMeshWriter().

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

mesh/src/vertex/MutableVertexMesh.hpp
mesh/src/vertex/VertexMeshWriter.hpp
mesh/src/vertex/VertexMeshWriter.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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