AbstractTissue< DIM > Class Template Reference

#include <AbstractTissue.hpp>

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List of all members.

Public Member Functions

 AbstractTissue (const std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
 AbstractTissue ()
virtual ~AbstractTissue ()
void InitialiseCells ()
std::list< TissueCell > & rGetCells ()
bool HasMesh ()
virtual unsigned GetNumNodes ()=0
virtual c_vector< double, DIM > GetLocationOfCellCentre (TissueCell *pCell)=0
virtual Node< DIM > * GetNode (unsigned index)=0
virtual unsigned AddNode (Node< DIM > *pNewNode)=0
virtual void SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)=0
virtual bool IsCellAssociatedWithADeletedNode (TissueCell &rCell)=0
virtual void UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)=0
virtual double GetDampingConstant (unsigned nodeIndex)=0
virtual TissueCell * AddCell (TissueCell &rNewCell, c_vector< double, DIM > newLocation, TissueCell *pParentCell=NULL)=0
virtual unsigned RemoveDeadCells ()=0
virtual void Update ()=0
c_vector< unsigned,
NUM_CELL_MUTATION_STATES > 		GetCellMutationStateCount ()
c_vector< unsigned,
NUM_CELL_TYPES > 		GetCellTypeCount ()
c_vector< unsigned, 5 > GetCellCyclePhaseCount ()
virtual bool IsGhostNode (unsigned index)
unsigned GetNumRealCells ()
void SetCellAncestorsToNodeIndices ()
std::set< unsigned > GetCellAncestors ()
TissueCell & rGetCellUsingLocationIndex (unsigned index)
unsigned GetLocationIndexUsingCell (TissueCell *pCell)
virtual void WriteMeshToFile (const std::string &rArchiveDirectory, const std::string &rMeshFileName)
virtual void CreateOutputFiles (const std::string &rDirectory, bool rCleanOutputDirectory, bool outputCellMutationStates, bool outputCellTypes, bool outputCellVariables, bool outputCellCyclePhases, bool outputCellAncestors)
virtual void WriteResultsToFiles (bool outputCellMutationStates, bool outputCellTypes, bool outputCellVariables, bool outputCellCyclePhases, bool outputCellAncestors)=0
void WriteTimeAndNodeResultsToFiles (bool outputCellMutationStates, bool outputCellTypes, bool outputCellVariables, bool outputCellCyclePhases, bool outputCellAncestors, std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
void GenerateCellResults (unsigned locationIndex, bool outputCellMutationStates, bool outputCellTypes, bool outputCellVariables, bool outputCellCyclePhases, bool outputCellAncestors, std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
void WriteCellResultsToFiles (bool outputCellMutationStates, bool outputCellTypes, bool outputCellVariables, bool outputCellCyclePhases, bool outputCellAncestors, std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
virtual void CloseOutputFiles (bool outputCellMutationStates, bool outputCellTypes, bool outputCellVariables, bool outputCellCyclePhases, bool outputCellAncestors)
Iterator Begin ()
Iterator End ()

Protected Member Functions

template<class Archive>
void serialize (Archive &archive, const unsigned int version)
virtual void Validate ()=0

Protected Attributes

std::list< TissueCell > mCells
std::map< unsigned, TissueCell * > mLocationCellMap
std::map< TissueCell *, unsigned > mCellLocationMap
c_vector< unsigned,
NUM_CELL_MUTATION_STATES > 		mCellMutationStateCount
c_vector< unsigned,
NUM_CELL_TYPES > 		mCellTypeCount
c_vector< unsigned, 5 > mCellCyclePhaseCount
out_stream mpVizNodesFile
out_stream mpVizCellTypesFile
out_stream mpCellMutationStatesFile
out_stream mpCellAncestorsFile
out_stream mpCellTypesFile
out_stream mpCellCyclePhasesFile
out_stream mpCellVariablesFile
bool mTissueContainsMesh

Friends

class boost::serialization::access

Classes

class  Iterator

Detailed Description

template<unsigned DIM>
class AbstractTissue< DIM >

An abstract facade class encapsulating a tissue.

Contains a group of cells and associated methods.

Definition at line 50 of file AbstractTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
AbstractTissue< DIM >::AbstractTissue ( const std::vector< TissueCell > &  rCells,
const std::vector< unsigned >  locationIndices = std::vector<unsigned>() 
) [inline]

Default constructor.

Parameters:
rCells a vector of cells
locationIndices an optional vector of location indices that correspond to real cells

Definition at line 33 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellCyclePhaseCount, AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCellMutationStateCount, AbstractTissue< DIM >::mCells, AbstractTissue< DIM >::mCellTypeCount, and AbstractTissue< DIM >::mLocationCellMap.

template<unsigned DIM>
AbstractTissue< DIM >::AbstractTissue (  )  [inline]

Constructor for use by archiving - doesn't take in cells, since these are dealt with by the serialize method.

Definition at line 133 of file AbstractTissue.hpp.

template<unsigned DIM>
virtual AbstractTissue< DIM >::~AbstractTissue (  )  [inline, virtual]

Base class with virtual methods needs a virtual destructor.

Definition at line 139 of file AbstractTissue.hpp.

Member Function Documentation

template<unsigned DIM>
template<class Archive>
void AbstractTissue< DIM >::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, protected]

Serialize the facade.

Parameters:
archive 
version 

Reimplemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 105 of file AbstractTissue.hpp.

template<unsigned DIM>
virtual void AbstractTissue< DIM >::Validate (  )  [protected, pure virtual]

Check consistency of our internal data structures.

Implemented in MeshBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

template<unsigned DIM>
void AbstractTissue< DIM >::InitialiseCells (  )  [inline]

Initialise each cell's cell cycle model.

Definition at line 82 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCells.

template<unsigned DIM>
std::list< TissueCell > & AbstractTissue< DIM >::rGetCells (  )  [inline]

Returns:
reference to mCells.

Definition at line 93 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCells.

Referenced by AbstractTissue< DIM >::Iterator::IsAtEnd(), and AbstractTissue< DIM >::Iterator::Iterator().

template<unsigned DIM>
bool AbstractTissue< DIM >::HasMesh (  )  [inline]

Returns:
whether the tissue contains a mesh.

Definition at line 99 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mTissueContainsMesh.

Referenced by GeneralisedLinearSpringForce< DIM >::AddForceContribution(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
virtual unsigned AbstractTissue< DIM >::GetNumNodes (  )  [pure virtual]

As this method is pure virtual, it must be overridden in subclasses.

Returns:
the number of nodes in the tissue.

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, and MeshBasedTissue< 2 >.

Referenced by AbstractCellCentreBasedTissue< DIM >::AddCell(), GeneralisedLinearSpringForce< DIM >::AddForceContribution(), AbstractCellCentreBasedTissue< DIM >::WriteResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
virtual c_vector<double, DIM> AbstractTissue< DIM >::GetLocationOfCellCentre ( TissueCell *  pCell  )  [pure virtual]

Find where a given cell is in space.

Parameters:
pCell pointer to the cell
Returns:
the location of the cell

Implemented in AbstractCellCentreBasedTissue< DIM >.

Referenced by WntConcentration::GetWntGradient(), WntConcentration::GetWntLevel(), and SloughingCellKiller::TestAndLabelCellsForApoptosisOrDeath().

template<unsigned DIM>
virtual Node<DIM>* AbstractTissue< DIM >::GetNode ( unsigned  index  )  [pure virtual]

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
index global index of the specified node
Returns:
a pointer to the node with a given index.

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, and MeshBasedTissue< 2 >.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), AbstractCellCentreBasedTissue< DIM >::IsCellAssociatedWithADeletedNode(), AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations(), AbstractCellCentreBasedTissue< DIM >::WriteResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
virtual unsigned AbstractTissue< DIM >::AddNode ( Node< DIM > *  pNewNode  )  [pure virtual]

Add a new node to the tissue.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
pNewNode pointer to the new node
Returns:
global index of new node in tissue.

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, and MeshBasedTissue< 2 >.

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

template<unsigned DIM>
virtual void AbstractTissue< DIM >::SetNode ( unsigned  nodeIndex,
ChastePoint< DIM > &  rNewLocation 
) [pure virtual]

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

As this method is pure virtual, it must be overridden in subclasses.

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

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, and MeshBasedTissue< 2 >.

Referenced by AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations().

template<unsigned DIM>
virtual bool AbstractTissue< DIM >::IsCellAssociatedWithADeletedNode ( TissueCell &  rCell  )  [pure virtual]

Helper method for establishing if a cell is real.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
rCell the cell
Returns:
whether a given cell is associated with a deleted node.

Implemented in AbstractCellCentreBasedTissue< DIM >.

Referenced by AbstractTissue< DIM >::Iterator::IsRealCell().

template<unsigned DIM>
virtual void AbstractTissue< DIM >::UpdateNodeLocations ( const std::vector< c_vector< double, DIM > > &  rNodeForces,
double  dt 
) [pure virtual]

Update the location of each node in the tissue given a vector of forces on nodes and a time step over which to integrate the equations of motion.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
rNodeForces forces on nodes
dt time step

Implemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

template<unsigned DIM>
virtual double AbstractTissue< DIM >::GetDampingConstant ( unsigned  nodeIndex  )  [pure virtual]

Get the damping constant for this node - ie d in drdt = F/d.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
nodeIndex the global index of this node
Returns:
the damping constant at the node.

Implemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissue< DIM >, and MeshBasedTissue< 2 >.

template<unsigned DIM>
virtual TissueCell* AbstractTissue< DIM >::AddCell ( TissueCell &  rNewCell,
c_vector< double, DIM >  newLocation,
TissueCell *  pParentCell = NULL 
) [pure virtual]

Add a new cell to the tissue.

As this method is pure virtual, it must be overridden in subclasses.

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).

Implemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, MeshBasedTissue< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

template<unsigned DIM>
virtual unsigned AbstractTissue< DIM >::RemoveDeadCells (  )  [pure virtual]

Remove all cells labelled as dead.

As this method is pure virtual, it must be overridden in subclasses.

Returns:
number of cells removed

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, and MeshBasedTissue< 2 >.

template<unsigned DIM>
virtual void AbstractTissue< DIM >::Update (  )  [pure virtual]

Remove the Nodes (for cell-centre) or VertexElements (for cell-vertex) which have been marked as deleted and update the correspondence with TissueCells.

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, and MeshBasedTissue< 2 >.

template<unsigned DIM>
c_vector< unsigned, NUM_CELL_MUTATION_STATES > AbstractTissue< DIM >::GetCellMutationStateCount (  )  [inline]

Find out how many cells of each mutation state there are

Returns:
The number of cells of each mutation state (evaluated at each visualizer output) [0] = healthy count [1] = labelled cells [2] = APC one hit [3] = APC two hit [4] = beta catenin one hit

Definition at line 136 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellMutationStateCount.

template<unsigned DIM>
c_vector< unsigned, NUM_CELL_TYPES > AbstractTissue< DIM >::GetCellTypeCount (  )  [inline]

Find out how many cells of each type there are

Returns:
The number of cells of each type (evaluated at each visualizer output) [0] = STEM [1] = TRANSIT [2] = DIFFERENTIATED [3] = APOPTOTIC

Definition at line 142 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellTypeCount.

template<unsigned DIM>
c_vector< unsigned, 5 > AbstractTissue< DIM >::GetCellCyclePhaseCount (  )  [inline]

Find out how many cells in each cell cycle phase there are

Returns:
The number of cells of each phase (evaluated at each visualizer output) [0] = G_ZERO_PHASE [1] = G_ONE_PHASE [2] = S_PHASE [3] = G_TWO_PHASE [4] = M_PHASE

Definition at line 148 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellCyclePhaseCount.

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

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

Parameters:
index the global index of a specified node
Returns:
whether the node is a ghost node

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

Definition at line 154 of file AbstractTissue.cpp.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), and AbstractTissue< DIM >::GenerateCellResults().

template<unsigned DIM>
unsigned AbstractTissue< DIM >::GetNumRealCells (  )  [inline]

Get the number of real cells.

Definition at line 105 of file AbstractTissue.cpp.

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

template<unsigned DIM>
void AbstractTissue< DIM >::SetCellAncestorsToNodeIndices (  )  [inline]

Sets the Ancestor index of all the cells at this time to be the same as their node index, can be used to trace clonal populations.

Definition at line 116 of file AbstractTissue.cpp.

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

template<unsigned DIM>
std::set< unsigned > AbstractTissue< DIM >::GetCellAncestors (  )  [inline]

Loops over cells and makes a list of the ancestors that are part of the tissue.

Returns:
remaining_ancestors The size of this set tells you how many clonal populations remain.

Definition at line 125 of file AbstractTissue.cpp.

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

template<unsigned DIM>
TissueCell & AbstractTissue< DIM >::rGetCellUsingLocationIndex ( unsigned  index  )  [inline]

Get the cell corresponding to a given location index.

Currently assumes there is one cell for each location index, and they are ordered identically in their vectors. An assertion fails if not.

Parameters:
index the location index
Returns:
the cell.

Definition at line 160 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mLocationCellMap.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), MeshBasedTissue< DIM >::CheckTissueCellPointers(), AbstractCellCentreBasedTissue< DIM >::GetDampingConstant(), MeshBasedTissue< DIM >::SpringIterator::rGetCellA(), MeshBasedTissue< DIM >::SpringIterator::rGetCellB(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
unsigned AbstractTissue< DIM >::GetLocationIndexUsingCell ( TissueCell *  pCell  )  [inline]

Get the location index corresponding to a given cell.

Currently assumes there is one cell for each location index, and they are ordered identically in their vectors. An assertion fails if not.

Parameters:
pCell the cell
Returns:
the location index.

Definition at line 173 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellLocationMap.

Referenced by CryptSimulation2d::ApplyTissueBoundaryConditions(), CryptSimulation2d::CalculateDividingCellCentreLocations(), MeshBasedTissue< DIM >::Validate(), and CryptSimulation2d::WriteBetaCatenin().

template<unsigned DIM>
void AbstractTissue< DIM >::WriteMeshToFile ( const std::string &  rArchiveDirectory,
const std::string &  rMeshFileName 
) [inline, virtual]

If the tissue contains a mesh, write this to file. For use by the TissueSimulationArchiver. Must be overridden in each subclass that contains a mesh.

Parameters:
rArchiveDirectory directory in which archive is stored
rMeshFileName base name for mesh files

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

Definition at line 184 of file AbstractTissue.cpp.

template<unsigned DIM>
void AbstractTissue< DIM >::CreateOutputFiles ( const std::string &  rDirectory,
bool  rCleanOutputDirectory,
bool  outputCellMutationStates,
bool  outputCellTypes,
bool  outputCellVariables,
bool  outputCellCyclePhases,
bool  outputCellAncestors 
) [inline, virtual]

Use an output file handler to create output files for visualizer and post-processing.

Parameters:
rDirectory pathname of the output directory, relative to where Chaste output is stored
rCleanOutputDirectory whether to delete the contents of the output directory prior to output file creation
outputCellMutationStates whether to create a cell mutation state results file
outputCellTypes whether to create a cell type results file
outputCellVariables whether to create a cell-cycle variable results file
outputCellCyclePhases whether to create a cell-cycle phase results file
outputCellAncestors whether to create a cell ancestor results file

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

Definition at line 189 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, AbstractTissue< DIM >::mpVizCellTypesFile, AbstractTissue< DIM >::mpVizNodesFile, and OutputFileHandler::OpenOutputFile().

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

template<unsigned DIM>
virtual void AbstractTissue< DIM >::WriteResultsToFiles ( bool  outputCellMutationStates,
bool  outputCellTypes,
bool  outputCellVariables,
bool  outputCellCyclePhases,
bool  outputCellAncestors 
) [pure virtual]

Write results from the current tissue state to output files.

Parameters:
outputCellMutationStates whether to output cell mutation state results
outputCellTypes whether to output cell type results
outputCellVariables whether to output cell-cycle variable results
outputCellCyclePhases whether to output cell-cycle phase results
outputCellAncestors whether to output cell ancestor results

Implemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissue< DIM >, and MeshBasedTissue< 2 >.

template<unsigned DIM>
void AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles ( bool  outputCellMutationStates,
bool  outputCellTypes,
bool  outputCellVariables,
bool  outputCellCyclePhases,
bool  outputCellAncestors,
std::vector< unsigned > &  rCellTypeCounter,
std::vector< unsigned > &  rCellMutationStateCounter,
std::vector< unsigned > &  rCellCyclePhaseCounter 
) [inline]

Write the current time and node results to output files.

Parameters:
outputCellMutationStates whether to output cell mutation state results
outputCellTypes whether to output cell type results
outputCellVariables whether to output cell-cycle variable results
outputCellCyclePhases whether to output cell-cycle phase results
outputCellAncestors whether to output cell ancestor results
rCellTypeCounter cell type counter
rCellMutationStateCounter cell mutation state counter
rCellCyclePhaseCounter cell cycle phase counter

Definition at line 478 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::GetNode(), AbstractTissue< DIM >::GetNumNodes(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractTissue< DIM >::mCellMutationStateCount, AbstractTissue< DIM >::mCellTypeCount, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, AbstractTissue< DIM >::mpVizCellTypesFile, and AbstractTissue< DIM >::mpVizNodesFile.

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

template<unsigned DIM>
void AbstractTissue< DIM >::GenerateCellResults ( unsigned  locationIndex,
bool  outputCellMutationStates,
bool  outputCellTypes,
bool  outputCellVariables,
bool  outputCellCyclePhases,
bool  outputCellAncestors,
std::vector< unsigned > &  rCellTypeCounter,
std::vector< unsigned > &  rCellMutationStateCounter,
std::vector< unsigned > &  rCellCyclePhaseCounter 
) [inline]

Generate results for a given cell in the current tissue state to output files.

Parameters:
locationIndex location index of the cell
outputCellMutationStates whether to output cell mutation state results
outputCellTypes whether to output cell type results
outputCellVariables whether to output cell-cycle variable results
outputCellCyclePhases whether to output cell-cycle phase results
outputCellAncestors whether to output cell ancestor results
rCellTypeCounter cell type counter
rCellMutationStateCounter cell mutation state counter
rCellCyclePhaseCounter cell cycle phase counter

Todo:
Note that the output format of mpCellVariablesFile has changed, it now

Definition at line 257 of file AbstractTissue.cpp.

References TissueCell::GetAncestor(), TissueCell::GetCellCycleModel(), TissueCell::GetCellType(), AbstractCellCycleModel::GetCurrentCellCyclePhase(), TissueCell::GetMutationState(), TissueCell::HasApoptosisBegun(), AbstractTissue< DIM >::IsGhostNode(), AbstractTissue< DIM >::mLocationCellMap, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellVariablesFile, and AbstractTissue< DIM >::mpVizCellTypesFile.

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

template<unsigned DIM>
void AbstractTissue< DIM >::WriteCellResultsToFiles ( bool  outputCellMutationStates,
bool  outputCellTypes,
bool  outputCellVariables,
bool  outputCellCyclePhases,
bool  outputCellAncestors,
std::vector< unsigned > &  rCellTypeCounter,
std::vector< unsigned > &  rCellMutationStateCounter,
std::vector< unsigned > &  rCellCyclePhaseCounter 
) [inline]

Write the current state of each cell to output files.

Parameters:
outputCellMutationStates whether to output cell mutation state results
outputCellTypes whether to output cell type results
outputCellVariables whether to output cell-cycle variable results
outputCellCyclePhases whether to output cell-cycle phase results
outputCellAncestors whether to output cell ancestor results
rCellTypeCounter cell type counter
rCellMutationStateCounter cell mutation state counter
rCellCyclePhaseCounter cell cycle phase counter

Definition at line 422 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellCyclePhaseCount, AbstractTissue< DIM >::mCellMutationStateCount, AbstractTissue< DIM >::mCellTypeCount, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, and AbstractTissue< DIM >::mpVizCellTypesFile.

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

template<unsigned DIM>
void AbstractTissue< DIM >::CloseOutputFiles ( bool  outputCellMutationStates,
bool  outputCellTypes,
bool  outputCellVariables,
bool  outputCellCyclePhases,
bool  outputCellAncestors 
) [inline, virtual]

Close any output files.

Parameters:
outputCellMutationStates whether a cell mutation state results file is open
outputCellTypes whether a cell type results file is open
outputCellVariables whether a cell-cycle variable results file is open
outputCellCyclePhases whether a cell-cycle phase results file is open
outputCellAncestors whether a cell ancestor results file is open

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

Definition at line 225 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, AbstractTissue< DIM >::mpVizCellTypesFile, and AbstractTissue< DIM >::mpVizNodesFile.

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

template<unsigned DIM>
AbstractTissue< DIM >::Iterator AbstractTissue< DIM >::Begin (  )  [inline]

Returns:
iterator pointing to the first cell in the tissue

Definition at line 665 of file AbstractTissue.hpp.

References AbstractTissue< DIM >::mCells.

Referenced by AbstractTissue< DIM >::GetCellAncestors(), CryptStatistics::GetCryptSection(), AbstractTissue< DIM >::GetNumRealCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), MeshBasedTissue< DIM >::SetBottomCellAncestors(), AbstractTissue< DIM >::SetCellAncestorsToNodeIndices(), SloughingCellKiller::TestAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< SPACE_DIM >::TestAndLabelCellsForApoptosisOrDeath(), AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations(), NodeBasedTissue< DIM >::Validate(), MeshBasedTissueWithGhostNodes< DIM >::Validate(), MeshBasedTissue< DIM >::Validate(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>
AbstractTissue< DIM >::Iterator AbstractTissue< DIM >::End (  )  [inline]

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

Definition at line 671 of file AbstractTissue.hpp.

References AbstractTissue< DIM >::mCells.

Referenced by AbstractTissue< DIM >::GetCellAncestors(), CryptStatistics::GetCryptSection(), AbstractTissue< DIM >::GetNumRealCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), MeshBasedTissue< DIM >::SetBottomCellAncestors(), AbstractTissue< DIM >::SetCellAncestorsToNodeIndices(), SloughingCellKiller::TestAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< SPACE_DIM >::TestAndLabelCellsForApoptosisOrDeath(), AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations(), NodeBasedTissue< DIM >::Validate(), MeshBasedTissueWithGhostNodes< DIM >::Validate(), MeshBasedTissue< DIM >::Validate(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 97 of file AbstractTissue.hpp.

Member Data Documentation

template<unsigned DIM>
std::list<TissueCell> AbstractTissue< DIM >::mCells [protected]

List of cells

Definition at line 55 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::AbstractTissue(), AbstractCellCentreBasedTissue< DIM >::AddCell(), AbstractTissue< DIM >::Begin(), MeshBasedTissue< DIM >::CheckTissueCellPointers(), AbstractTissue< DIM >::End(), AbstractTissue< DIM >::InitialiseCells(), MeshBasedTissue< DIM >::MeshBasedTissue(), NodeBasedTissue< DIM >::RemoveDeadCells(), MeshBasedTissue< DIM >::RemoveDeadCells(), AbstractTissue< DIM >::rGetCells(), AbstractTissue< SPACE_DIM >::serialize(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>
std::map<unsigned, TissueCell*> AbstractTissue< DIM >::mLocationCellMap [protected]

Map location (node or VertexElement) indices back to cells

Definition at line 58 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::AbstractTissue(), AbstractCellCentreBasedTissue< DIM >::AddCell(), AbstractTissue< DIM >::GenerateCellResults(), MeshBasedTissue< DIM >::RemoveDeadCells(), AbstractTissue< DIM >::rGetCellUsingLocationIndex(), AbstractTissue< SPACE_DIM >::serialize(), NodeBasedTissue< DIM >::Update(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>
std::map<TissueCell*, unsigned> AbstractTissue< DIM >::mCellLocationMap [protected]

Map cells to location (node or VertexElement) indices

Definition at line 61 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::AbstractTissue(), MeshBasedTissueWithGhostNodes< DIM >::AddCell(), AbstractCellCentreBasedTissue< DIM >::AddCell(), MeshBasedTissue< DIM >::CheckTissueCellPointers(), AbstractTissue< DIM >::GetLocationIndexUsingCell(), AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), AbstractCellCentreBasedTissue< DIM >::IsCellAssociatedWithADeletedNode(), NodeBasedTissue< DIM >::RemoveDeadCells(), MeshBasedTissue< DIM >::RemoveDeadCells(), AbstractTissue< SPACE_DIM >::serialize(), AbstractTissue< DIM >::SetCellAncestorsToNodeIndices(), NodeBasedTissue< DIM >::Update(), MeshBasedTissue< DIM >::Update(), AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations(), NodeBasedTissue< DIM >::Validate(), MeshBasedTissueWithGhostNodes< DIM >::Validate(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>
c_vector<unsigned, NUM_CELL_MUTATION_STATES> AbstractTissue< DIM >::mCellMutationStateCount [protected]

Current cell mutation state counts

Definition at line 64 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::AbstractTissue(), AbstractTissue< DIM >::GetCellMutationStateCount(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
c_vector<unsigned, NUM_CELL_TYPES> AbstractTissue< DIM >::mCellTypeCount [protected]

Current cell type counts

Definition at line 67 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::AbstractTissue(), AbstractTissue< DIM >::GetCellTypeCount(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
c_vector<unsigned, 5> AbstractTissue< DIM >::mCellCyclePhaseCount [protected]

Current cell cycle phase counts

Definition at line 70 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::AbstractTissue(), AbstractTissue< DIM >::GetCellCyclePhaseCount(), and AbstractTissue< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>
out_stream AbstractTissue< DIM >::mpVizNodesFile [protected]

Results file for node visualization

Definition at line 73 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
out_stream AbstractTissue< DIM >::mpVizCellTypesFile [protected]

Results file for cell visualization

Definition at line 76 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
out_stream AbstractTissue< DIM >::mpCellMutationStatesFile [protected]

Results file for cell mutation states

Definition at line 79 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
out_stream AbstractTissue< DIM >::mpCellAncestorsFile [protected]

Results file for cell ancestors

Definition at line 82 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
out_stream AbstractTissue< DIM >::mpCellTypesFile [protected]

Results file for cell types

Definition at line 85 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
out_stream AbstractTissue< DIM >::mpCellCyclePhasesFile [protected]

Results file for cell cycle phases

Definition at line 88 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
out_stream AbstractTissue< DIM >::mpCellVariablesFile [protected]

Results file for cell variables

Definition at line 91 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
bool AbstractTissue< DIM >::mTissueContainsMesh [protected]

Whether the tissue contains a mesh

Definition at line 94 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::HasMesh(), MeshBasedTissue< DIM >::MeshBasedTissue(), and AbstractTissue< SPACE_DIM >::serialize().

The documentation for this class was generated from the following files:
Generated on Wed Mar 18 12:52:13 2009 for Chaste by  doxygen 1.5.5