VertexMeshWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <VertexMeshWriter.hpp>

Inherits AbstractMeshWriter< 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	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 ()
Private Attributes
VertexMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh
MeshWriterIterators < ELEMENT_DIM, SPACE_DIM > *	mpIters
NodeMap *	mpNodeMap
unsigned	mNodeMapCurrentIndex
vtkUnstructuredGrid *	mpVtkUnstructedMesh

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 64 of file VertexMeshWriter.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`
	)			`[inline]`

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 49 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 ( ) [inline]

Destructor.

Definition at line 68 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
	)			`[inline]`

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 268 of file VertexMeshWriter.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 285 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 ( ) [inline, 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 170 of file VertexMeshWriter.cpp.

References 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, 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 ( ) [inline]

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 117 of file VertexMeshWriter.cpp.

References ElementData::AttributeValue, 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, 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 ( ) [inline, virtual]

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

Reimplemented from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 90 of file VertexMeshWriter.cpp.

References 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 >::WriteFiles ( ) [inline, 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 332 of file VertexMeshWriter.cpp.

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 ) [inline]

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 303 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().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

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

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 79 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 74 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 >::WriteFiles(), 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 71 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 77 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 84 of file VertexMeshWriter.hpp.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), 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/VertexMeshWriter.hpp
mesh/src/vertex/VertexMeshWriter.cpp

VertexMeshWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Public Member Functions

Private Attributes

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 >