#include <DivisionBiasTrackingModifier.hpp>

Inheritance diagram for DivisionBiasTrackingModifier< DIM >:

Collaboration diagram for DivisionBiasTrackingModifier< DIM >:

Public Member Functions
	DivisionBiasTrackingModifier (c_vector< double, DIM > divisionBiasVector)

virtual	~DivisionBiasTrackingModifier ()

const c_vector< double, DIM > &	rGetDivisionBiasVector () const

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)

void	UpdateCellData (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

void	OutputSimulationModifierParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM >
	AbstractCellBasedSimulationModifier ()

virtual	~AbstractCellBasedSimulationModifier ()

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0

virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0

virtual void	UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

void	OutputSimulationModifierInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Private Attributes
c_vector< double, DIM >	mDivisionBiasVector

Friends
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class DivisionBiasTrackingModifier< DIM >

A modifier class which at each simulation time step calculates a real number between zero and 1 for each cell, which represents the normalised distance of the cell along a given axis of the cell population through its centroid, and stores this number in the CellData property as "bias". To be used in conjunction with the BiasedBernoulliTrialCellCycleModel class.

Definition at line 52 of file DivisionBiasTrackingModifier.hpp.

Constructor & Destructor Documentation

◆ DivisionBiasTrackingModifier()

template<unsigned DIM>

DivisionBiasTrackingModifier< DIM >::DivisionBiasTrackingModifier ( c_vector< double, DIM > divisionBiasVector )

Constructor.

Parameters

divisionBiasVector the specified axis along which division probability is biased

Definition at line 40 of file DivisionBiasTrackingModifier.cpp.

References DivisionBiasTrackingModifier< DIM >::mDivisionBiasVector.

◆ ~DivisionBiasTrackingModifier()

template<unsigned DIM>

DivisionBiasTrackingModifier< DIM >::~DivisionBiasTrackingModifier ( )

virtual

Destructor.

Definition at line 49 of file DivisionBiasTrackingModifier.cpp.

Member Function Documentation

◆ OutputSimulationModifierParameters()

template<unsigned DIM>

void DivisionBiasTrackingModifier< DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile )

virtual

Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellBasedSimulationModifier< DIM, DIM >.

Definition at line 133 of file DivisionBiasTrackingModifier.cpp.

References AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters().

◆ rGetDivisionBiasVector()

template<unsigned DIM>

const c_vector< double, DIM > & DivisionBiasTrackingModifier< DIM >::rGetDivisionBiasVector ( ) const

Returns: mDivisionBiasVector.

Definition at line 54 of file DivisionBiasTrackingModifier.cpp.

◆ serialize()

template<unsigned DIM>

template<class Archive >

void DivisionBiasTrackingModifier< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 72 of file DivisionBiasTrackingModifier.hpp.

◆ SetupSolve()

template<unsigned DIM>

void DivisionBiasTrackingModifier< DIM >::SetupSolve	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		std::string	outputDirectory
	)

virtual

Overridden SetupSolve() method.

Specify what to do in the simulation before the start of the time loop.

Parameters

rCellPopulation	reference to the cell population
outputDirectory	the output directory, relative to where Chaste output is stored

Definition at line 66 of file DivisionBiasTrackingModifier.cpp.

◆ UpdateAtEndOfTimeStep()

template<unsigned DIM>

void DivisionBiasTrackingModifier< DIM >::UpdateAtEndOfTimeStep ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

virtual

Overridden UpdateAtEndOfTimeStep() method.

Specify what to do in the simulation at the end of each time step.

Parameters

rCellPopulation reference to the cell population

Definition at line 60 of file DivisionBiasTrackingModifier.cpp.

◆ UpdateCellData()

template<unsigned DIM>

void DivisionBiasTrackingModifier< DIM >::UpdateCellData ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

Helper method to calculate the normalised distance of each cell in the population along the division bias axis and store these in the CellData.

Parameters

rCellPopulation reference to the cell population

This hack is needed because in the case of a MeshBasedCellPopulation in which multiple cell divisions have occurred over one time step, the Voronoi tessellation (while existing) is out-of-date. Thus, if we did not regenerate the Voronoi tessellation here, an assertion may trip as we try to access a Voronoi element whose index exceeds the number of elements in the out-of-date tessellation.

Todo:: work out how to properly fix this (#1986)

Iterate over cell population and store each cell's signed distance along mDivisionBiasVector through the centroid of the cell population, where zero corresponds to a cell located at the centroid of the cell population.

Definition at line 76 of file DivisionBiasTrackingModifier.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 63 of file DivisionBiasTrackingModifier.hpp.

Member Data Documentation

◆ mDivisionBiasVector

template<unsigned DIM>

c_vector<double, DIM> DivisionBiasTrackingModifier< DIM >::mDivisionBiasVector

private

The specified axis along which division probability is biased. Initialized in the constructor.

Definition at line 60 of file DivisionBiasTrackingModifier.hpp.

Referenced by DivisionBiasTrackingModifier< DIM >::DivisionBiasTrackingModifier().

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

cell_based/src/simulation/modifiers/DivisionBiasTrackingModifier.hpp
cell_based/src/simulation/modifiers/DivisionBiasTrackingModifier.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ DivisionBiasTrackingModifier()

◆ ~DivisionBiasTrackingModifier()

Member Function Documentation

◆ OutputSimulationModifierParameters()

◆ rGetDivisionBiasVector()

◆ serialize()

◆ SetupSolve()

◆ UpdateAtEndOfTimeStep()

◆ UpdateCellData()

Friends And Related Symbol Documentation

◆ boost::serialization::access

Member Data Documentation

◆ mDivisionBiasVector