MeshBasedTissue< DIM > Class Template Reference

#include <MeshBasedTissue.hpp>

Inheritance diagram for MeshBasedTissue< DIM >:

Collaboration diagram for MeshBasedTissue< DIM >:

List of all members.

Public Member Functions

MeshBasedTissue (MutableMesh< DIM, DIM > &rMesh, const std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)

MeshBasedTissue (MutableMesh< DIM, DIM > &rMesh)

~MeshBasedTissue ()

MutableMesh< DIM, DIM > & rGetMesh ()

const MutableMesh< DIM, DIM > & rGetMesh () const

bool GetWriteVoronoiData ()

bool GetWriteTissueAreas ()

bool UseAreaBasedDampingConstant ()

void SetOutputVoronoiData (bool writeVoronoiData)

unsigned AddNode (Node< DIM > *pNewNode)

void SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)

virtual bool IsGhostNode (unsigned index)

double GetDampingConstant (unsigned nodeIndex)

void SetOutputTissueAreas (bool writeTissueAreas)

void SetAreaBasedDampingConstant (bool useAreaBasedDampingConstant)

virtual unsigned RemoveDeadCells ()

virtual TissueCell * AddCell (TissueCell &rNewCell, c_vector< double, DIM > newLocation, TissueCell *pParentCell=NULL)

void CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)

void CloseOutputFiles ()

void WriteResultsToFiles ()

virtual void Update (bool hasHadBirthsOrDeaths=true)

Node< DIM > * GetNode (unsigned index)

unsigned GetNumNodes ()

void SetBottomCellAncestors ()

void WriteVoronoiResultsToFile ()

void WriteTissueAreaResultsToFile ()

void WriteCellAreaResultsToFile ()

void CreateVoronoiTessellation ()

VoronoiTessellation< DIM > & rGetVoronoiTessellation ()

SpringIterator SpringsBegin ()

SpringIterator SpringsEnd ()

void CheckTissueCellPointers ()

bool IsMarkedSpring (TissueCell &, TissueCell &)

void MarkSpring (TissueCell &, TissueCell &)

void UnmarkSpring (TissueCell &, TissueCell &)

template<>

void CreateVoronoiTessellation ()

Protected Member Functions

std::set< TissueCell * > CreateCellPair (TissueCell &, TissueCell &)

virtual void UpdateGhostNodesAfterReMesh (NodeMap &rMap)

virtual void Validate ()

Protected Attributes

MutableMesh< DIM, DIM > & mrMesh

VoronoiTessellation< DIM > * mpVoronoiTessellation

bool mDeleteMesh

std::set< std::set< TissueCell * > > mMarkedSprings

out_stream mpElementFile

out_stream mpVoronoiFile

out_stream mpTissueAreasFile

out_stream mpCellAreasFile

bool mUseAreaBasedDampingConstant

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

Friends

class TestMeshBasedTissue

class boost::serialization::access

Classes

class SpringIterator

Detailed Description

template<unsigned DIM>
class MeshBasedTissue< DIM >

A facade class encapsulating a mesh-based 'tissue'

Contains a group of cells and maintains the associations between cells and nodes in the mesh.

Definition at line 52 of file MeshBasedTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

MeshBasedTissue< DIM >::MeshBasedTissue	(	MutableMesh< DIM, DIM > &	rMesh,
		const std::vector< TissueCell > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteMesh = `false`,
		bool	validate = `true`
	)			`[inline]`

Create a new tissue facade from a mesh and collection of cells.

There must be precisely 1 cell for each node of the mesh.

Parameters:

	rMesh	a mutable tetrahedral mesh
	rCells	TissueCells corresponding to the nodes of the mesh
	locationIndices	an optional vector of location indices that correspond to real cells
	deleteMesh	set to true if you want the tissue to free the mesh memory on destruction
	validate	whether to validate the tissue

Definition at line 33 of file MeshBasedTissue.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractTissue< DIM >::mCells, MeshBasedTissue< DIM >::mrMesh, AbstractTissue< DIM >::mTissueContainsMesh, and MeshBasedTissue< DIM >::Validate().

template<unsigned DIM>

MeshBasedTissue< DIM >::MeshBasedTissue ( MutableMesh< DIM, DIM > & rMesh ) [inline]

Constructor for use by the de-serializer.

Parameters:

rMesh

a mutable tetrahedral mesh.

Definition at line 56 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mDeleteMesh, MeshBasedTissue< DIM >::mpVoronoiTessellation, and AbstractTissue< DIM >::mTissueContainsMesh.

template<unsigned DIM>

MeshBasedTissue< DIM >::~MeshBasedTissue ( ) [inline]

Destructor.

Definition at line 65 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mDeleteMesh, MeshBasedTissue< DIM >::mpVoronoiTessellation, and MeshBasedTissue< DIM >::mrMesh.

Member Function Documentation

template<unsigned DIM>

template<class Archive>

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

Serialize the object and its member variables.

Note that serialization of the mesh and cells is handled by load/save_construct_data.

Note also that member data related to writers is not saved - output must be set up again by the caller after a restart.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 70 of file MeshBasedTissue.hpp.

template<unsigned DIM>

std::set< TissueCell * > MeshBasedTissue< DIM >::CreateCellPair	(	TissueCell &	rCell1,
		TissueCell &	rCell2
	)			`[inline, protected]`

Helper method used by the spring marking routines

Definition at line 754 of file MeshBasedTissue.cpp.

Referenced by MeshBasedTissue< DIM >::IsMarkedSpring(), MeshBasedTissue< DIM >::MarkSpring(), and MeshBasedTissue< DIM >::UnmarkSpring().

template<unsigned DIM>

void MeshBasedTissue< DIM >::UpdateGhostNodesAfterReMesh ( NodeMap & rMap ) [inline, protected, virtual]

Update mIsGhostNode if required by a remesh.

Parameters:

rMap

A map between node indices before and after remesh

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 361 of file MeshBasedTissue.cpp.

Referenced by MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

void MeshBasedTissue< DIM >::Validate ( ) [inline, protected, virtual]

Check consistency of our internal data structures. Each node must have a cell associated with it.

Implements AbstractTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 153 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), AbstractTissue< DIM >::GetLocationIndexUsingCell(), and MeshBasedTissue< DIM >::GetNumNodes().

Referenced by MeshBasedTissue< DIM >::MeshBasedTissue(), MeshBasedTissue< 2 >::serialize(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

MutableMesh< DIM, DIM > & MeshBasedTissue< DIM >::rGetMesh ( ) [inline]

Returns:: reference to mrMesh.

Definition at line 175 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mrMesh.

Referenced by CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), and CryptSimulation2d::WriteVisualizerSetupFile().

template<unsigned DIM>

const MutableMesh< DIM, DIM > & MeshBasedTissue< DIM >::rGetMesh ( ) const [inline]

Returns:: const reference to mrMesh (used in archiving).

Definition at line 181 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mrMesh.

template<unsigned DIM>

bool MeshBasedTissue< DIM >::GetWriteVoronoiData ( )

Returns:: mWriteVoronoiData.

template<unsigned DIM>

bool MeshBasedTissue< DIM >::GetWriteTissueAreas ( )

Returns:: mWriteTissueAreas.

template<unsigned DIM>

bool MeshBasedTissue< DIM >::UseAreaBasedDampingConstant ( ) [inline]

Returns:: mUseAreaBasedDampingConstant.

Definition at line 75 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mUseAreaBasedDampingConstant.

Referenced by MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

void MeshBasedTissue< DIM >::SetOutputVoronoiData ( bool writeVoronoiData )

Set method for mWriteVoronoiData.

Parameters:

writeVoronoiData

whether to output cell area and perimeter information

template<unsigned DIM>

unsigned MeshBasedTissue< DIM >::AddNode ( Node< DIM > * pNewNode ) [inline, virtual]

Overridden AddNode() method.

Add a new node to the tissue.

Parameters:

pNewNode

pointer to the new node

Returns:: global index of new node in tissue

Implements AbstractTissue< DIM >.

Definition at line 88 of file MeshBasedTissue.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), and MeshBasedTissue< DIM >::mrMesh.

template<unsigned DIM>

void MeshBasedTissue< DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< DIM > &	rNewLocation
	)			`[inline, virtual]`

Overridden SetNode() method.

Move the node with a given index to a new point in space.

Parameters:

	nodeIndex	the index of the node to be moved
	rNewLocation	the new target location of the node

Implements AbstractTissue< DIM >.

Definition at line 94 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mrMesh, and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

template<unsigned DIM>

bool MeshBasedTissue< DIM >::IsGhostNode ( unsigned index ) [inline, virtual]

Find if a given node is a ghost node. The method always returns false but is overridden in MeshBasedTissueWithGhostNodes.

Parameters:

index

the global index of a specified node

Returns:: whether the node is a ghost node

Reimplemented from AbstractTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 100 of file MeshBasedTissue.cpp.

template<unsigned DIM>

double MeshBasedTissue< DIM >::GetDampingConstant ( unsigned nodeIndex ) [inline, virtual]

Overridden GetDampingConstant() method that includes the case of a cell-area-based damping constant.

Parameters:

nodeIndex

the global index of this node

Returns:: the damping constant for the given TissueCell.

We use a linear dependence of the form

new_damping_const = old_damping_const * (d0+d1*A)

where d0, d1 are parameters, A is the cell's area, and old_damping_const is the damping constant if not using mUseAreaBasedDampingConstant

Compute the parameter d1 such that d0+A*d1=1, where A is the equilibrium area of a cell (this is equal to sqrt(3)/4, which is a third of the area of a regular hexagon of edge length 1)

The cell area should not be too large - the next assertion is to avoid getting an infinite cell area, which may occur if area-based viscosity is chosen in the absence of ghost nodes.

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Definition at line 106 of file MeshBasedTissue.cpp.

References TissueConfig::GetAreaBasedDampingConstantParameter(), AbstractCellCentreBasedTissue< DIM >::GetDampingConstant(), VoronoiTessellation< DIM >::GetFaceArea(), TissueConfig::Instance(), MeshBasedTissue< DIM >::mUseAreaBasedDampingConstant, and MeshBasedTissue< DIM >::rGetVoronoiTessellation().

template<unsigned DIM>

void MeshBasedTissue< DIM >::SetOutputTissueAreas ( bool writeTissueAreas )

Set method for mWriteTissueAreas.

Todo:: Extend this to 3D (possibly rename to SetOutputTissueVolumes?) - see also #738

Parameters:

writeTissueAreas

whether to output tissue area data

template<unsigned DIM>

void MeshBasedTissue< DIM >::SetAreaBasedDampingConstant ( bool useAreaBasedDampingConstant ) [inline]

Set method for mUseAreaBasedDampingConstant.

Parameters:

useAreaBasedDampingConstant

whether to use a viscosity that is linear in the cell area, rather than constant

Definition at line 81 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mUseAreaBasedDampingConstant.

template<unsigned DIM>

unsigned MeshBasedTissue< DIM >::RemoveDeadCells ( ) [inline, virtual]

Remove all cells that are labelled as dead.

Note that this now calls MutableMesh::DeleteNodePriorToReMesh() and therefore a ReMesh(map) must be called before any element information is used.

Note also that after calling this method the tissue will be in an inconsistent state until Update() is called! So don't try iterating over cells or anything like that.

Returns:: number of cells removed.

Implements AbstractTissue< DIM >.

Definition at line 187 of file MeshBasedTissue.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCells, AbstractTissue< DIM >::mLocationCellMap, MeshBasedTissue< DIM >::mMarkedSprings, and MeshBasedTissue< DIM >::mrMesh.

template<unsigned DIM>

TissueCell * MeshBasedTissue< DIM >::AddCell	(	TissueCell &	rNewCell,
		c_vector< double, DIM >	newLocation,
		TissueCell *	pParentCell = `NULL`
	)			`[inline, virtual]`

Overridden AddCell() method.

Add a new cell to the tissue and update mIsGhostNode.

Parameters:

	rNewCell	the cell to add
	newLocation	the position in space at which to put it
	pParentCell	pointer to a parent cell (if required)

Returns:: address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way)

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 366 of file MeshBasedTissue.cpp.

References AbstractCellCentreBasedTissue< DIM >::AddCell(), and MeshBasedTissue< DIM >::MarkSpring().

Referenced by MeshBasedTissueWithGhostNodes< DIM >::AddCell().

template<unsigned DIM>

void MeshBasedTissue< DIM >::CreateOutputFiles	(	const std::string &	rDirectory,
		bool	cleanOutputDirectory
	)			`[inline, virtual]`

Overridden CreateOutputFiles() method.

Parameters:

	rDirectory	pathname of the output directory, relative to where Chaste output is stored
	cleanOutputDirectory	whether to delete the contents of the output directory prior to output file creation

Reimplemented from AbstractTissue< DIM >.

Definition at line 384 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::CreateOutputFiles(), TissueConfig::Instance(), MeshBasedTissue< DIM >::mpCellAreasFile, MeshBasedTissue< DIM >::mpElementFile, MeshBasedTissue< DIM >::mpTissueAreasFile, MeshBasedTissue< DIM >::mpVoronoiFile, and OutputFileHandler::OpenOutputFile().

template<unsigned DIM>

void MeshBasedTissue< DIM >::CloseOutputFiles ( ) [inline, virtual]

Overridden CloseOutputFiles() method.

Reimplemented from AbstractTissue< DIM >.

Definition at line 406 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::CloseOutputFiles(), TissueConfig::Instance(), MeshBasedTissue< DIM >::mpCellAreasFile, MeshBasedTissue< DIM >::mpElementFile, MeshBasedTissue< DIM >::mpTissueAreasFile, and MeshBasedTissue< DIM >::mpVoronoiFile.

template<unsigned DIM>

void MeshBasedTissue< DIM >::WriteResultsToFiles ( ) [inline, virtual]

Overridden WriteResultsToFiles() method.

Reimplemented from AbstractTissue< DIM >.

Definition at line 427 of file MeshBasedTissue.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), SimulationTime::GetTime(), TissueConfig::Instance(), SimulationTime::Instance(), MeshBasedTissue< DIM >::mpElementFile, MeshBasedTissue< DIM >::mpVoronoiTessellation, MeshBasedTissue< DIM >::mrMesh, MeshBasedTissue< DIM >::WriteCellAreaResultsToFile(), AbstractTissue< DIM >::WriteResultsToFiles(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

void MeshBasedTissue< DIM >::Update ( bool hasHadBirthsOrDeaths = true ) [inline, virtual]

Overridden Update(bool hasHadBirthsOrDeaths) method. Fixes up the mappings between cells and nodes.

Parameters:

hasHadBirthsOrDeaths

- a bool saying whether tissue has had Births Or Deaths not needed in this tissue class

Implements AbstractTissue< DIM >.

Definition at line 245 of file MeshBasedTissue.cpp.

References GenericEventHandler< 9, CancerEventHandler >::BeginEvent(), Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), MeshBasedTissue< DIM >::CreateVoronoiTessellation(), GenericEventHandler< 9, CancerEventHandler >::EndEvent(), AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), TissueConfig::Instance(), AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCells, AbstractTissue< DIM >::mLocationCellMap, MeshBasedTissue< DIM >::mMarkedSprings, MeshBasedTissue< DIM >::mrMesh, MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Node< SPACE_DIM >::rGetContainingElementIndices(), MeshBasedTissue< DIM >::UpdateGhostNodesAfterReMesh(), MeshBasedTissue< DIM >::UseAreaBasedDampingConstant(), and MeshBasedTissue< DIM >::Validate().

template<unsigned DIM>

Node< DIM > * MeshBasedTissue< DIM >::GetNode ( unsigned index ) [inline, virtual]

Overridden GetNode() method.

Parameters:

index

global index of the specified Node

Returns:: pointer to the Node with given index.

Implements AbstractTissue< DIM >.

Definition at line 336 of file MeshBasedTissue.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), and MeshBasedTissue< DIM >::mrMesh.

Referenced by MeshBasedTissueWithGhostNodes< DIM >::CalculateForceBetweenNodes(), and MeshBasedTissueWithGhostNodes< DIM >::MeshBasedTissueWithGhostNodes().

template<unsigned DIM>

unsigned MeshBasedTissue< DIM >::GetNumNodes ( ) [inline, virtual]

Overridden GetNumNodes() method.

Returns:: the number of nodes in the tissue.

Implements AbstractTissue< DIM >.

Definition at line 342 of file MeshBasedTissue.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), and MeshBasedTissue< DIM >::mrMesh.

Referenced by MeshBasedTissueWithGhostNodes< DIM >::AddCell(), MeshBasedTissueWithGhostNodes< DIM >::MeshBasedTissueWithGhostNodes(), MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostNodesAfterReMesh(), MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions(), MeshBasedTissueWithGhostNodes< DIM >::Validate(), and MeshBasedTissue< DIM >::Validate().

template<unsigned DIM>

void MeshBasedTissue< DIM >::SetBottomCellAncestors ( ) [inline]

Sets the Ancestor index of all the cells at the bottom in order, can be used to trace clonal populations.

Definition at line 348 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), and AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell().

template<unsigned DIM>

void MeshBasedTissue< DIM >::WriteVoronoiResultsToFile ( ) [inline]

Write current results to mpVoronoiFile.

Definition at line 475 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), AbstractCellCentreBasedTissue< DIM >::GetLocationOfCellCentre(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractTissue< DIM >::mCellLocationMap, MeshBasedTissue< DIM >::mpVoronoiFile, and MeshBasedTissue< DIM >::rGetVoronoiTessellation().

Referenced by MeshBasedTissue< DIM >::WriteResultsToFiles().

template<unsigned DIM>

void MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile ( ) [inline]

Write current results to mpTissueAreasFile if in 2D.

The data is written in the form:

time total_area apoptotic_area

Definition at line 498 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), SimulationTime::GetTime(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), SimulationTime::Instance(), AbstractTissue< DIM >::mCellLocationMap, MeshBasedTissue< DIM >::mpTissueAreasFile, MeshBasedTissue< DIM >::mrMesh, and MeshBasedTissue< DIM >::rGetVoronoiTessellation().

Referenced by MeshBasedTissue< DIM >::WriteResultsToFiles().

template<unsigned DIM>

void MeshBasedTissue< DIM >::WriteCellAreaResultsToFile ( ) [inline]

Write current results to mpCellAreasFile.

In 2D, the data is written in the form:

time cell0_id cell0_x cell0_y cell0_area cell1_id cell1_x cell1_y cell1_area ...

and similarly in 3D.

Definition at line 528 of file MeshBasedTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), AbstractCellCentreBasedTissue< DIM >::GetLocationOfCellCentre(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractTissue< DIM >::mCellLocationMap, MeshBasedTissue< DIM >::mpCellAreasFile, and MeshBasedTissue< DIM >::rGetVoronoiTessellation().

Referenced by MeshBasedTissue< DIM >::WriteResultsToFiles().

template<unsigned DIM>

void MeshBasedTissue< DIM >::CreateVoronoiTessellation ( ) [inline]

Get a reference to a Voronoi tessellation of the mesh.

Definition at line 649 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mpVoronoiTessellation, and MeshBasedTissue< DIM >::mrMesh.

Referenced by MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

VoronoiTessellation< DIM > & MeshBasedTissue< DIM >::rGetVoronoiTessellation ( ) [inline]

Returns:: mpVoronoiTessellation.

Definition at line 667 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::mpVoronoiTessellation.

Referenced by MeshBasedTissue< DIM >::GetDampingConstant(), MeshBasedTissue< DIM >::WriteCellAreaResultsToFile(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

MeshBasedTissue< DIM >::SpringIterator MeshBasedTissue< DIM >::SpringsBegin ( ) [inline]

Returns:: iterator pointing to the first spring in the tissue

Definition at line 637 of file MeshBasedTissue.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin(), and MeshBasedTissue< DIM >::mrMesh.

template<unsigned DIM>

MeshBasedTissue< DIM >::SpringIterator MeshBasedTissue< DIM >::SpringsEnd ( ) [inline]

Returns:: iterator pointing to one past the last spring in the tissue

Definition at line 643 of file MeshBasedTissue.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesEnd(), and MeshBasedTissue< DIM >::mrMesh.

template<unsigned DIM>

void MeshBasedTissue< DIM >::CheckTissueCellPointers ( ) [inline]

Helper method for use in debugging.

Definition at line 674 of file MeshBasedTissue.cpp.

References AbstractCellCycleModel::GetCell(), TissueCell::GetCellCycleModel(), TissueCell::IsDead(), AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCells, MeshBasedTissue< DIM >::mMarkedSprings, and AbstractTissue< DIM >::rGetCellUsingLocationIndex().

template<unsigned DIM>

bool MeshBasedTissue< DIM >::IsMarkedSpring	(	TissueCell &	rCell1,
		TissueCell &	rCell2
	)			`[inline]`

Returns:: whether the spring between two given cells is marked.

Definition at line 763 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::CreateCellPair(), and MeshBasedTissue< DIM >::mMarkedSprings.

template<unsigned DIM>

void MeshBasedTissue< DIM >::MarkSpring	(	TissueCell &	rCell1,
		TissueCell &	rCell2
	)			`[inline]`

Mark the spring between the given cells.

Definition at line 770 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::CreateCellPair(), and MeshBasedTissue< DIM >::mMarkedSprings.

Referenced by MeshBasedTissue< DIM >::AddCell().

template<unsigned DIM>

void MeshBasedTissue< DIM >::UnmarkSpring	(	TissueCell &	rCell1,
		TissueCell &	rCell2
	)			`[inline]`

Stop marking the spring between the given cells.

Definition at line 777 of file MeshBasedTissue.cpp.

References MeshBasedTissue< DIM >::CreateCellPair(), and MeshBasedTissue< DIM >::mMarkedSprings.

template<>

void MeshBasedTissue< 1 >::CreateVoronoiTessellation ( ) [inline]

The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).

Definition at line 660 of file MeshBasedTissue.cpp.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCellCentreBasedTissue< DIM >.

Reimplemented in MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 57 of file MeshBasedTissue.hpp.

Member Data Documentation

template<unsigned DIM>

MutableMesh<DIM, DIM>& MeshBasedTissue< DIM >::mrMesh [protected]

Reference to the mesh.

Definition at line 93 of file MeshBasedTissue.hpp.

template<unsigned DIM>

VoronoiTessellation<DIM>* MeshBasedTissue< DIM >::mpVoronoiTessellation [protected]

Pointer to a Voronoi tessellation object. Used to calculate cell area and perimeter information if required.

Definition at line 99 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::CreateVoronoiTessellation(), MeshBasedTissue< DIM >::MeshBasedTissue(), MeshBasedTissue< DIM >::rGetVoronoiTessellation(), MeshBasedTissue< 2 >::serialize(), MeshBasedTissue< DIM >::WriteResultsToFiles(), and MeshBasedTissue< DIM >::~MeshBasedTissue().

template<unsigned DIM>

bool MeshBasedTissue< DIM >::mDeleteMesh [protected]

Whether to delete the mesh when we are destroyed. Needed if this tissue has been de-serialized.

Definition at line 105 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::MeshBasedTissue(), and MeshBasedTissue< DIM >::~MeshBasedTissue().

template<unsigned DIM>

std::set<std::set<TissueCell*> > MeshBasedTissue< DIM >::mMarkedSprings [protected]

Special springs that we want to keep track of for some reason. Currently used to track cells in the process of dividing (which are represented as two cells joined by a shorter spring).

Definition at line 112 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::CheckTissueCellPointers(), MeshBasedTissue< DIM >::IsMarkedSpring(), MeshBasedTissue< DIM >::MarkSpring(), MeshBasedTissue< DIM >::RemoveDeadCells(), MeshBasedTissue< 2 >::serialize(), MeshBasedTissue< DIM >::UnmarkSpring(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

out_stream MeshBasedTissue< DIM >::mpElementFile [protected]

Results file for elements.

Definition at line 115 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::CloseOutputFiles(), MeshBasedTissue< DIM >::CreateOutputFiles(), and MeshBasedTissue< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream MeshBasedTissue< DIM >::mpVoronoiFile [protected]

Results file for Voronoi data.

Definition at line 118 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::CloseOutputFiles(), MeshBasedTissue< DIM >::CreateOutputFiles(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

out_stream MeshBasedTissue< DIM >::mpTissueAreasFile [protected]

Results file for tissue area data.

Definition at line 121 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::CloseOutputFiles(), MeshBasedTissue< DIM >::CreateOutputFiles(), and MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile().

template<unsigned DIM>

out_stream MeshBasedTissue< DIM >::mpCellAreasFile [protected]

Results file for cell area data.

Definition at line 124 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::CloseOutputFiles(), MeshBasedTissue< DIM >::CreateOutputFiles(), and MeshBasedTissue< DIM >::WriteCellAreaResultsToFile().

template<unsigned DIM>

bool MeshBasedTissue< DIM >::mUseAreaBasedDampingConstant [protected]

Whether to use a viscosity that is linear in the cell area, rather than constant.

Definition at line 130 of file MeshBasedTissue.hpp.

Referenced by MeshBasedTissue< DIM >::GetDampingConstant(), MeshBasedTissue< 2 >::serialize(), MeshBasedTissue< DIM >::SetAreaBasedDampingConstant(), and MeshBasedTissue< DIM >::UseAreaBasedDampingConstant().

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

/tmp/release_1.1/cancer/src/tissue/MeshBasedTissue.hpp
/tmp/release_1.1/cancer/src/tissue/MeshBasedTissue.cpp


Public Member Functions
	MeshBasedTissue (MutableMesh< DIM, DIM > &rMesh, const std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)
	MeshBasedTissue (MutableMesh< DIM, DIM > &rMesh)
	~MeshBasedTissue ()
MutableMesh< DIM, DIM > &	rGetMesh ()
const MutableMesh< DIM, DIM > &	rGetMesh () const
bool	GetWriteVoronoiData ()
bool	GetWriteTissueAreas ()
bool	UseAreaBasedDampingConstant ()
void	SetOutputVoronoiData (bool writeVoronoiData)
unsigned	AddNode (Node< DIM > *pNewNode)
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)
virtual bool	IsGhostNode (unsigned index)
double	GetDampingConstant (unsigned nodeIndex)
void	SetOutputTissueAreas (bool writeTissueAreas)
void	SetAreaBasedDampingConstant (bool useAreaBasedDampingConstant)
virtual unsigned	RemoveDeadCells ()
virtual TissueCell *	AddCell (TissueCell &rNewCell, c_vector< double, DIM > newLocation, TissueCell *pParentCell=NULL)
void	CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
void	CloseOutputFiles ()
void	WriteResultsToFiles ()
virtual void	Update (bool hasHadBirthsOrDeaths=true)
Node< DIM > *	GetNode (unsigned index)
unsigned	GetNumNodes ()
void	SetBottomCellAncestors ()
void	WriteVoronoiResultsToFile ()
void	WriteTissueAreaResultsToFile ()
void	WriteCellAreaResultsToFile ()
void	CreateVoronoiTessellation ()
VoronoiTessellation< DIM > &	rGetVoronoiTessellation ()
SpringIterator	SpringsBegin ()
SpringIterator	SpringsEnd ()
void	CheckTissueCellPointers ()
bool	IsMarkedSpring (TissueCell &, TissueCell &)
void	MarkSpring (TissueCell &, TissueCell &)
void	UnmarkSpring (TissueCell &, TissueCell &)
template<>
void	CreateVoronoiTessellation ()
Protected Member Functions
std::set< TissueCell * >	CreateCellPair (TissueCell &, TissueCell &)
virtual void	UpdateGhostNodesAfterReMesh (NodeMap &rMap)
virtual void	Validate ()
Protected Attributes
MutableMesh< DIM, DIM > &	mrMesh
VoronoiTessellation< DIM > *	mpVoronoiTessellation
bool	mDeleteMesh
std::set< std::set< TissueCell * > >	mMarkedSprings
out_stream	mpElementFile
out_stream	mpVoronoiFile
out_stream	mpTissueAreasFile
out_stream	mpCellAreasFile
bool	mUseAreaBasedDampingConstant
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	TestMeshBasedTissue
class	boost::serialization::access
Classes
class	SpringIterator

MeshBasedTissue< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Classes

Detailed Description

template<unsigned DIM> class MeshBasedTissue< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class MeshBasedTissue< DIM >