#include <AngiogenesisSolver.hpp>

Collaboration diagram for AngiogenesisSolver< DIM >:

Public Member Functions
	AngiogenesisSolver ()

virtual	~AngiogenesisSolver ()

virtual void	Increment ()

bool	IsSproutingRuleSet ()

void	Run (bool writeOutput=false)

void	SetAnastamosisRadius (units::quantity< unit::length > radius)

void	SetBoundingDomain (boost::shared_ptr< Part< DIM > > pDomain)

void	SetCellPopulation (boost::shared_ptr< AbstractCellPopulation< DIM > > pCellPopulation, units::quantity< unit::length > cellPopulationReferenceLength)

void	SetMigrationRule (boost::shared_ptr< AbstractMigrationRule< DIM > > pMigrationRule)

void	SetOutputFileHandler (boost::shared_ptr< OutputFileHandler > pHandler)

void	SetSproutingRule (boost::shared_ptr< AbstractSproutingRule< DIM > > pSproutingRule)

void	SetVesselGrid (boost::shared_ptr< RegularGrid< DIM > >pVesselGrid)

void	SetVesselNetwork (boost::shared_ptr< VesselNetwork< DIM > > pNetwork)

Static Public Member Functions
static boost::shared_ptr< AngiogenesisSolver< DIM > >	Create ()

Protected Member Functions
virtual void	DoSprouting ()

virtual void	DoAnastamosis ()

virtual void	UpdateNodalPositions (bool sprouting=false)

Private Attributes
boost::shared_ptr< VesselNetwork< DIM > >	mpNetwork

units::quantity< unit::length >	mNodeAnastamosisRadius

boost::shared_ptr< AbstractMigrationRule< DIM > >	mpMigrationRule

boost::shared_ptr< AbstractSproutingRule< DIM > >	mpSproutingRule

boost::shared_ptr< Part< DIM > >	mpBoundingDomain

boost::shared_ptr< OutputFileHandler >	mpFileHandler

boost::shared_ptr< RegularGrid< DIM > >	mpVesselGrid

boost::shared_ptr< AbstractCellPopulation< DIM > >	mpCellPopulation

units::quantity< unit::length >	mCellPopulationReferenceLength

std::vector< boost::shared_ptr< Cell > >	mTipCells

std::map< boost::shared_ptr< Cell >, boost::shared_ptr< VesselNode< DIM > > >	mCellNodeMap

Detailed Description

template<unsigned DIM>
class AngiogenesisSolver< DIM >

This class is for simulating modifications to the vessel network due to sprouting angiogenesis.

Definition at line 53 of file AngiogenesisSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AngiogenesisSolver< DIM >::AngiogenesisSolver ( )

Constructor.

Definition at line 48 of file AngiogenesisSolver.cpp.

template<unsigned DIM>

AngiogenesisSolver< DIM >::~AngiogenesisSolver ( )

virtual

Destructor.

Definition at line 65 of file AngiogenesisSolver.cpp.

Member Function Documentation

template<unsigned DIM>

boost::shared_ptr< AngiogenesisSolver< DIM > > AngiogenesisSolver< DIM >::Create ( )

static

Factory constructor method

Returns: a shared pointer to a new solver

Definition at line 71 of file AngiogenesisSolver.cpp.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::DoAnastamosis ( )

protectedvirtual

Do the anastamosis step

Definition at line 272 of file AngiogenesisSolver.cpp.

References VesselNode< DIM >::Create(), AngiogenesisSolver< DIM >::mNodeAnastamosisRadius, AngiogenesisSolver< DIM >::mpNetwork, and AngiogenesisSolver< DIM >::mpVesselGrid.

Referenced by AngiogenesisSolver< DIM >::Increment().

template<unsigned DIM>

void AngiogenesisSolver< DIM >::DoSprouting ( )

protectedvirtual

Identify and grow sprouts

Definition at line 133 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mpNetwork, AngiogenesisSolver< DIM >::mpSproutingRule, and AngiogenesisSolver< DIM >::UpdateNodalPositions().

Referenced by AngiogenesisSolver< DIM >::Increment().

template<unsigned DIM>

void AngiogenesisSolver< DIM >::Increment ( )

virtual

Increment the solver one step in time

Definition at line 359 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::DoAnastamosis(), AngiogenesisSolver< DIM >::DoSprouting(), AngiogenesisSolver< DIM >::mCellPopulationReferenceLength, AngiogenesisSolver< DIM >::mpCellPopulation, AngiogenesisSolver< DIM >::mpMigrationRule, AngiogenesisSolver< DIM >::mpNetwork, AngiogenesisSolver< DIM >::mpSproutingRule, AngiogenesisSolver< DIM >::mpVesselGrid, and AngiogenesisSolver< DIM >::UpdateNodalPositions().

Referenced by AngiogenesisSolver< DIM >::Run().

template<unsigned DIM>

bool AngiogenesisSolver< DIM >::IsSproutingRuleSet ( )

Has a sprouting rule been set

Returns: bool true if a sprouting rule has been set

Definition at line 78 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mpSproutingRule.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::Run ( bool writeOutput = false )

Run until the specified end time

Parameters

writeOutput whether to write output

Definition at line 460 of file AngiogenesisSolver.cpp.

References VesselNetworkWriter< DIM >::Create(), AngiogenesisSolver< DIM >::Increment(), AngiogenesisSolver< DIM >::mpCellPopulation, AngiogenesisSolver< DIM >::mpFileHandler, and AngiogenesisSolver< DIM >::mpNetwork.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::SetAnastamosisRadius ( units::quantity< unit::length > radius )

Set the radius within which anastamosis of vessels is allowed

Parameters

radius the radius within which anastamosis of vessels is allowed

Definition at line 84 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mNodeAnastamosisRadius.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::SetBoundingDomain ( boost::shared_ptr< Part< DIM > > pDomain )

A domain which vessels a not permitted to leave

Parameters

pDomain the domain which vessels a not permitted to leave

Definition at line 90 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mpBoundingDomain.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::SetCellPopulation	(	boost::shared_ptr< AbstractCellPopulation< DIM > >	pCellPopulation,
		units::quantity< unit::length >	cellPopulationReferenceLength
	)

Set a cell population for discrete cell solves

Parameters

pCellPopulation the cell population for discrete cell solves

Definition at line 96 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mCellPopulationReferenceLength, and AngiogenesisSolver< DIM >::mpCellPopulation.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::SetMigrationRule ( boost::shared_ptr< AbstractMigrationRule< DIM > > pMigrationRule )

Add a migration rule for tip cells

Parameters

pMigrationRule a migration rule for tip cells

Definition at line 103 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mpMigrationRule.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::SetOutputFileHandler ( boost::shared_ptr< OutputFileHandler > pHandler )

Set the output file handler

Parameters

pHandler the output file handler

Definition at line 109 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mpFileHandler.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::SetSproutingRule ( boost::shared_ptr< AbstractSproutingRule< DIM > > pSproutingRule )

Set the rule for managing sprouting

Parameters

pSproutingRule the rule for vessel sprouting

Definition at line 115 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mpSproutingRule.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::SetVesselGrid ( boost::shared_ptr< RegularGrid< DIM > > pVesselGrid )

Set a vessel grid, this means that on-lattice rules will be used

Parameters

pVesselGrid the grid for the vessel network

Definition at line 121 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mpVesselGrid.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::SetVesselNetwork ( boost::shared_ptr< VesselNetwork< DIM > > pNetwork )

Set the vessel network

Parameters

pNetwork the vessel network

Definition at line 127 of file AngiogenesisSolver.cpp.

References AngiogenesisSolver< DIM >::mpNetwork.

template<unsigned DIM>

void AngiogenesisSolver< DIM >::UpdateNodalPositions ( bool sprouting = false )

protectedvirtual

Update the position of all nodes

Parameters

sprouting whether to do sprouting during this call

Definition at line 146 of file AngiogenesisSolver.cpp.

References VesselNode< DIM >::Create(), AngiogenesisSolver< DIM >::mpBoundingDomain, AngiogenesisSolver< DIM >::mpMigrationRule, AngiogenesisSolver< DIM >::mpNetwork, and AngiogenesisSolver< DIM >::mpVesselGrid.

Referenced by AngiogenesisSolver< DIM >::DoSprouting(), and AngiogenesisSolver< DIM >::Increment().

Member Data Documentation

template<unsigned DIM>

std::map<boost::shared_ptr<Cell> , boost::shared_ptr<VesselNode<DIM> > > AngiogenesisSolver< DIM >::mCellNodeMap

private

Cell node map for discrete cell angiogenesis models

Definition at line 108 of file AngiogenesisSolver.hpp.

template<unsigned DIM>

units::quantity<unit::length> AngiogenesisSolver< DIM >::mCellPopulationReferenceLength

private

The reference length scale for the cellpopulation.

Definition at line 98 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::Increment(), and AngiogenesisSolver< DIM >::SetCellPopulation().

template<unsigned DIM>

units::quantity<unit::length> AngiogenesisSolver< DIM >::mNodeAnastamosisRadius

private

The radius in which anastamosis is allowed in angiogenesis simulations

Definition at line 63 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::DoAnastamosis(), and AngiogenesisSolver< DIM >::SetAnastamosisRadius().

template<unsigned DIM>

boost::shared_ptr<Part<DIM> > AngiogenesisSolver< DIM >::mpBoundingDomain

private

The bounding domain for the vessel network

Definition at line 78 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::SetBoundingDomain(), and AngiogenesisSolver< DIM >::UpdateNodalPositions().

template<unsigned DIM>

boost::shared_ptr<AbstractCellPopulation<DIM> > AngiogenesisSolver< DIM >::mpCellPopulation

private

The cell population for discrete cell angiogenesis models

Definition at line 93 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::Increment(), AngiogenesisSolver< DIM >::Run(), and AngiogenesisSolver< DIM >::SetCellPopulation().

template<unsigned DIM>

boost::shared_ptr<OutputFileHandler> AngiogenesisSolver< DIM >::mpFileHandler

private

File handler containing output directory information

Definition at line 83 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::Run(), and AngiogenesisSolver< DIM >::SetOutputFileHandler().

template<unsigned DIM>

boost::shared_ptr<AbstractMigrationRule<DIM> > AngiogenesisSolver< DIM >::mpMigrationRule

private

The migration rule for tip cells

Definition at line 68 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::Increment(), AngiogenesisSolver< DIM >::SetMigrationRule(), and AngiogenesisSolver< DIM >::UpdateNodalPositions().

template<unsigned DIM>

boost::shared_ptr<VesselNetwork<DIM> > AngiogenesisSolver< DIM >::mpNetwork

private

The vessel network

Definition at line 58 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::DoAnastamosis(), AngiogenesisSolver< DIM >::DoSprouting(), AngiogenesisSolver< DIM >::Increment(), AngiogenesisSolver< DIM >::Run(), AngiogenesisSolver< DIM >::SetVesselNetwork(), and AngiogenesisSolver< DIM >::UpdateNodalPositions().

template<unsigned DIM>

boost::shared_ptr<AbstractSproutingRule<DIM> > AngiogenesisSolver< DIM >::mpSproutingRule

private

The sprouting rule for angiogenesis

Definition at line 73 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::DoSprouting(), AngiogenesisSolver< DIM >::Increment(), AngiogenesisSolver< DIM >::IsSproutingRuleSet(), and AngiogenesisSolver< DIM >::SetSproutingRule().

template<unsigned DIM>

boost::shared_ptr<RegularGrid<DIM> > AngiogenesisSolver< DIM >::mpVesselGrid

private

The grid for lattice based angiogenesis simulations

Definition at line 88 of file AngiogenesisSolver.hpp.

Referenced by AngiogenesisSolver< DIM >::DoAnastamosis(), AngiogenesisSolver< DIM >::Increment(), AngiogenesisSolver< DIM >::SetVesselGrid(), and AngiogenesisSolver< DIM >::UpdateNodalPositions().

template<unsigned DIM>

std::vector<boost::shared_ptr<Cell> > AngiogenesisSolver< DIM >::mTipCells

private

Tip cell collection for discrete cell angiogenesis models

Definition at line 103 of file AngiogenesisSolver.hpp.

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

projects/MicrovesselChaste/src/simulation/angiogenesis/AngiogenesisSolver.hpp
projects/MicrovesselChaste/src/simulation/angiogenesis/AngiogenesisSolver.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

template<unsigned DIM> class AngiogenesisSolver< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class AngiogenesisSolver< DIM >