#include <VesselNode.hpp>

Inheritance diagram for VesselNode< DIM >:

Collaboration diagram for VesselNode< DIM >:

Public Member Functions
	VesselNode (double v1, double v2, double v3, units::quantity< unit::length > referenceLength)

	VesselNode (double v1=0.0, double v2=0.0, double v3=0.0)

	VesselNode (const DimensionalChastePoint< DIM > &location)

	VesselNode (const VesselNode< DIM > &rExistingNode)

	~VesselNode ()

unsigned	GetComparisonId ()

units::quantity< unit::length >	GetDistance (const DimensionalChastePoint< DIM > &rLocation) const

boost::shared_ptr< NodeFlowProperties< DIM > >	GetFlowProperties () const

const DimensionalChastePoint< DIM > &	rGetLocation () const

unsigned	GetNumberOfSegments () const

std::map< std::string, double >	GetOutputData ()

units::quantity< unit::length >	GetReferenceLengthScale () const

boost::shared_ptr< VesselSegment< DIM > >	GetSegment (unsigned index) const

std::vector< boost::shared_ptr< VesselSegment< DIM > > >	GetSegments () const

bool	IsAttachedTo (const boost::shared_ptr< VesselSegment< DIM > > pSegment) const

bool	IsCoincident (const DimensionalChastePoint< DIM > &rLocation) const

bool	IsMigrating () const

void	SetComparisonId (unsigned id)

void	SetFlowProperties (const NodeFlowProperties< DIM > &rFlowProperties)

void	SetIsMigrating (bool isMigrating)

void	SetLocation (const DimensionalChastePoint< DIM > &rLocation)

void	SetLocation (double x, double y, double z=0.0, units::quantity< unit::length > referenceLength=1.e-6 *unit::metres)

void	SetReferenceLengthScale (units::quantity< unit::length > lenthScale)

Public Member Functions inherited from AbstractVesselNetworkComponent< DIM >
	AbstractVesselNetworkComponent ()

virtual	~AbstractVesselNetworkComponent ()

virtual unsigned	GetId () const

virtual double	GetOutputDataValue (const std::string &rKey)

virtual std::vector< std::string >	GetOutputDataKeys ()

virtual units::quantity< unit::length >	GetRadius () const

virtual void	SetId (unsigned id)

virtual void	SetOutputData (const std::string &rKey, double value)

virtual void	SetRadius (units::quantity< unit::length > radius)

Static Public Member Functions
static boost::shared_ptr< VesselNode< DIM > >	Create (double v1=0.0, double v2=0.0, double v3=0.0)

static boost::shared_ptr< VesselNode< DIM > >	Create (double v1, double v2, double v3, units::quantity< unit::length > referenceLength)

static boost::shared_ptr< VesselNode< DIM > >	Create (const DimensionalChastePoint< DIM > &location)

static boost::shared_ptr< VesselNode< DIM > >	Create (const VesselNode< DIM > &rExistingNode)

static boost::shared_ptr< VesselNode< DIM > >	Create (boost::shared_ptr< VesselNode< DIM > > pExistingNode)

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

void	AddSegment (boost::shared_ptr< VesselSegment< DIM > > pVesselSegment)

void	RemoveSegment (boost::shared_ptr< VesselSegment< DIM > > pVesselSegment)

Private Attributes
DimensionalChastePoint< DIM >	mLocation

std::vector< boost::weak_ptr< VesselSegment< DIM > > >	mSegments

bool	mIsMigrating

boost::shared_ptr< NodeFlowProperties< DIM > >	mpFlowProperties

unsigned	mPtrComparisonId

Friends
class	boost::serialization::access

class	VesselSegment< DIM >

Additional Inherited Members
Protected Attributes inherited from AbstractVesselNetworkComponent< DIM >
std::map< std::string, double >	mOutputData

unsigned	mId

units::quantity< unit::length >	mRadius

Detailed Description

template<unsigned DIM>
class VesselNode< DIM >

This is a class for vessel nodes, which are vessel network components.

Nodes are point locations along a vessel. They are used for describing the end positions of straight line vessel segments.

Definition at line 65 of file VesselNode.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

VesselNode< DIM >::VesselNode	(	double	v1,
		double	v2,
		double	v3,
		units::quantity< unit::length >	referenceLength
	)

Constructor. Create a node using xyz coordinates

Parameters

v1	the node's x-coordinate
v2	the node's y-coordinate
v3	the node's z-coordinate
referenceLength	the reference length scale, defaults to micron

Definition at line 41 of file VesselNode.cpp.

References VesselNode< DIM >::mpFlowProperties.

template<unsigned DIM>

VesselNode< DIM >::VesselNode	(	double	v1 = `0.0`,
		double	v2 = `0.0`,
		double	v3 = `0.0`
	)

Constructor. Create a node using xyz coordinates

Parameters

v1	the node's x-coordinate (defaults to 0)
v2	the node's y-coordinate (defaults to 0)
v3	the node's z-coordinate (defaults to 0)

Definition at line 52 of file VesselNode.cpp.

References VesselNode< DIM >::mpFlowProperties.

template<unsigned DIM>

VesselNode< DIM >::VesselNode ( const DimensionalChastePoint< DIM > & location )

Constructor. Create a node using ublas c_vector

Parameters

location the node's location (defaults to 0.0)

Definition at line 63 of file VesselNode.cpp.

References VesselNode< DIM >::mpFlowProperties.

template<unsigned DIM>

VesselNode< DIM >::VesselNode ( const VesselNode< DIM > & rExistingNode )

Copy constructor.

Parameters

rExistingNode the node to copy from

Definition at line 74 of file VesselNode.cpp.

References VesselNode< DIM >::GetFlowProperties(), VesselNode< DIM >::IsMigrating(), VesselNode< DIM >::mIsMigrating, and VesselNode< DIM >::SetFlowProperties().

template<unsigned DIM>

VesselNode< DIM >::~VesselNode ( )

Destructor

Definition at line 88 of file VesselNode.cpp.

Member Function Documentation

template<unsigned DIM>

void VesselNode< DIM >::AddSegment ( boost::shared_ptr< VesselSegment< DIM > > pVesselSegment )

private

Add a vessel segment the node. Private because node-segment connectivity needs to be managed.

Parameters

pVesselSegment the segment to be added

Definition at line 132 of file VesselNode.cpp.

References VesselNode< DIM >::mSegments.

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNode< DIM >::Create	(	double	v1 = `0.0`,
		double	v2 = `0.0`,
		double	v3 = `0.0`
	)

static

Construct a new instance of the class and return a shared pointer to it.

Parameters

v1	the node's x-coordinate (defaults to 0 micron)
v2	the node's y-coordinate (defaults to 0 micron)
v3	the node's z-coordinate (defaults to 0 micron)

Returns: a pointer to the newly created node

Definition at line 100 of file VesselNode.cpp.

Referenced by Vessel< DIM >::DivideSegment(), AngiogenesisSolver< DIM >::DoAnastamosis(), VesselNetwork< DIM >::FormSprout(), and AngiogenesisSolver< DIM >::UpdateNodalPositions().

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNode< DIM >::Create	(	double	v1,
		double	v2,
		double	v3,
		units::quantity< unit::length >	referenceLength
	)

static

Construct a new instance of the class and return a shared pointer to it.

Parameters

v1	the node's x-coordinate (defaults to 0 micron)
v2	the node's y-coordinate (defaults to 0 micron)
v3	the node's z-coordinate (defaults to 0 micron)
referenceLength	the reference length scale

Returns: a pointer to the newly created node

Definition at line 93 of file VesselNode.cpp.

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNode< DIM >::Create ( const DimensionalChastePoint< DIM > & location )

static

Construct a new instance of the class and return a shared pointer to it.

Parameters

location the node's location (defaults to 0.0 micron)

Returns: a pointer to the newly created node

Definition at line 107 of file VesselNode.cpp.

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNode< DIM >::Create ( const VesselNode< DIM > & rExistingNode )

static

Construct a new instance of the class and return a shared pointer to it.

Parameters

rExistingNode the node to copy from

Returns: a pointer to the newly created node

Definition at line 114 of file VesselNode.cpp.

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNode< DIM >::Create ( boost::shared_ptr< VesselNode< DIM > > pExistingNode )

static

Construct a new instance of the class and return a shared pointer to it.

Parameters

pExistingNode the node to copy from

Returns: a pointer to the newly created node

Definition at line 121 of file VesselNode.cpp.

template<unsigned DIM>

unsigned VesselNode< DIM >::GetComparisonId ( )

Return the Id for comparing pointer contents

Returns: the node id

Definition at line 147 of file VesselNode.cpp.

References VesselNode< DIM >::mPtrComparisonId.

template<unsigned DIM>

units::quantity< unit::length > VesselNode< DIM >::GetDistance ( const DimensionalChastePoint< DIM > & rLocation ) const

Return the distance between the input location and the node

Parameters

rLocation the location to calculate the distance to

Returns: the distance to the location

Definition at line 153 of file VesselNode.cpp.

References VesselNode< DIM >::mLocation.

template<unsigned DIM>

boost::shared_ptr< NodeFlowProperties< DIM > > VesselNode< DIM >::GetFlowProperties ( ) const

Return the flow properties of the component

Returns: the flow properties of the component

Definition at line 159 of file VesselNode.cpp.

References VesselNode< DIM >::mpFlowProperties.

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

template<unsigned DIM>

unsigned VesselNode< DIM >::GetNumberOfSegments ( ) const

Return the number of attached segments

Returns: the number of segments attached to the node

Definition at line 171 of file VesselNode.cpp.

References VesselNode< DIM >::mSegments.

template<unsigned DIM>

std::map< std::string, double > VesselNode< DIM >::GetOutputData ( )

virtual

Return a map of output data for writers

Returns: a map of component data for use by the vtk writer

Implements AbstractVesselNetworkComponent< DIM >.

Definition at line 177 of file VesselNode.cpp.

References AbstractVesselNetworkComponent< DIM >::GetId(), AbstractVesselNetworkComponent< DIM >::GetRadius(), VesselNode< DIM >::IsMigrating(), AbstractVesselNetworkComponent< DIM >::mOutputData, and VesselNode< DIM >::mpFlowProperties.

template<unsigned DIM>

units::quantity< unit::length > VesselNode< DIM >::GetReferenceLengthScale ( ) const

Return the reference length scale for the node, default is micron

Returns: a ublas c_vector at the location of the node

Definition at line 189 of file VesselNode.cpp.

References VesselNode< DIM >::mLocation.

template<unsigned DIM>

boost::shared_ptr< VesselSegment< DIM > > VesselNode< DIM >::GetSegment ( unsigned index ) const

Return a pointer to the indexed vessel segment

Parameters

index the segment index

Returns: a vector of pointers to the attached vessel segments

Definition at line 195 of file VesselNode.cpp.

References VesselNode< DIM >::mSegments.

template<unsigned DIM>

std::vector< boost::shared_ptr< VesselSegment< DIM > > > VesselNode< DIM >::GetSegments ( ) const

Return a vector of pointers to the attached vessel segments.

Returns: a vector of pointers to the attached vessel segments

Definition at line 209 of file VesselNode.cpp.

References VesselNode< DIM >::mSegments.

template<unsigned DIM>

bool VesselNode< DIM >::IsAttachedTo ( const boost::shared_ptr< VesselSegment< DIM > > pSegment ) const

Return true if the input segment is attached to the node

Parameters

pSegment a pointer to the segment to query

Returns: whether the input segment is attached to the node

Definition at line 221 of file VesselNode.cpp.

template<unsigned DIM>

bool VesselNode< DIM >::IsCoincident ( const DimensionalChastePoint< DIM > & rLocation ) const

Return true if the node is coincident with the input location

Parameters

rLocation the query location

Returns: whether then node is coincident with the input location

Definition at line 228 of file VesselNode.cpp.

References VesselNode< DIM >::mLocation.

template<unsigned DIM>

bool VesselNode< DIM >::IsMigrating ( ) const

Has the node been designated as migrating. This is useful for keeping track of nodes in angiogenesis simulations.

Returns: whether the node is marked as migrating.

Definition at line 234 of file VesselNode.cpp.

References VesselNode< DIM >::mIsMigrating.

Referenced by VesselNode< DIM >::GetOutputData(), and VesselNode< DIM >::VesselNode().

template<unsigned DIM>

void VesselNode< DIM >::RemoveSegment ( boost::shared_ptr< VesselSegment< DIM > > pVesselSegment )

private

Remove a vessel segment from the node. Private because node-segment connectivity needs to be managed.

Parameters

pVesselSegment the segment to be removed

Definition at line 240 of file VesselNode.cpp.

References VesselNode< DIM >::mSegments.

template<unsigned DIM>

const DimensionalChastePoint< DIM > & VesselNode< DIM >::rGetLocation ( ) const

Return a reference to the location of the node, default is micron

Returns: a ublas c_vector at the location of the node

Definition at line 165 of file VesselNode.cpp.

References VesselNode< DIM >::mLocation.

template<unsigned DIM>

template<class Archive >

void VesselNode< DIM >::serialize	(	Archive &	ar,
		const unsigned int	version
	)

inlineprivate

Do the serialize

Parameters

ar	the archive
version	the archive version number

Definition at line 81 of file VesselNode.hpp.

References VesselNode< DIM >::mIsMigrating, VesselNode< DIM >::mLocation, VesselNode< DIM >::mpFlowProperties, and VesselNode< DIM >::mPtrComparisonId.

template<unsigned DIM>

void VesselNode< DIM >::SetComparisonId ( unsigned id )

Set the id used for comparing the contents of pointers. This is only used by certain methods in the VesselNetwork class. Use SetId for generic node labelling.

Parameters

id	for node comparison

Definition at line 254 of file VesselNode.cpp.

References VesselNode< DIM >::mPtrComparisonId.

template<unsigned DIM>

void VesselNode< DIM >::SetFlowProperties ( const NodeFlowProperties< DIM > & rFlowProperties )

Set the flow properties of the node

Parameters

rFlowProperties the flow properties to be set

Definition at line 260 of file VesselNode.cpp.

References VesselNode< DIM >::mpFlowProperties.

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

template<unsigned DIM>

void VesselNode< DIM >::SetIsMigrating ( bool isMigrating )

Set that the node is migrating

Parameters

isMigrating whether the node is migrating

Definition at line 278 of file VesselNode.cpp.

References VesselNode< DIM >::mIsMigrating.

template<unsigned DIM>

void VesselNode< DIM >::SetLocation ( const DimensionalChastePoint< DIM > & rLocation )

Set the location of the node. It is assumed that this location is consistent with the nodes reference length scale, default is micron.

Parameters

rLocation a ublas c_vector specifying the location

Definition at line 266 of file VesselNode.cpp.

References VesselNode< DIM >::mLocation.

template<unsigned DIM>

void VesselNode< DIM >::SetLocation	(	double	x,
		double	y,
		double	z = `0.0`,
		units::quantity< unit::length >	referenceLength = `1.e-6*unit::metres`
	)

Set the location of the node. It is assumed that this location is consistent with the nodes reference length scale, default is micron.

Parameters

x	the x location
y	the y location
z	the z location
referenceLength	the reference length scale

Definition at line 272 of file VesselNode.cpp.

References VesselNode< DIM >::mLocation.

template<unsigned DIM>

void VesselNode< DIM >::SetReferenceLengthScale ( units::quantity< unit::length > lenthScale )

Set the length scale used to dimensionalize the node location as stored in mLocation. If you want locations to be in metres, for example, set it to unit::metres. The node location values are changed accordingly when this value is changed.

Parameters

lenthScale the reference length scale for node locations

Definition at line 284 of file VesselNode.cpp.

References VesselNode< DIM >::mLocation.

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Archiving. Note that mSegments is not serialized here. Segments should add or remove themselves from nodes when serializing/de-serializing. It is not managed by nodes.

Definition at line 73 of file VesselNode.hpp.

template<unsigned DIM>

friend class VesselSegment< DIM >

friend

Allow segments to manage adding and removing themselves from nodes.

Definition at line 93 of file VesselNode.hpp.

Member Data Documentation

template<unsigned DIM>

bool VesselNode< DIM >::mIsMigrating

private

Is the vessel allowed to extend at this node

Definition at line 108 of file VesselNode.hpp.

Referenced by VesselNode< DIM >::IsMigrating(), VesselNode< DIM >::serialize(), VesselNode< DIM >::SetIsMigrating(), and VesselNode< DIM >::VesselNode().

template<unsigned DIM>

DimensionalChastePoint<DIM> VesselNode< DIM >::mLocation

private

Location of a node in space.

Definition at line 98 of file VesselNode.hpp.

Referenced by VesselNode< DIM >::GetDistance(), VesselNode< DIM >::GetReferenceLengthScale(), VesselNode< DIM >::IsCoincident(), VesselNode< DIM >::rGetLocation(), VesselNode< DIM >::serialize(), VesselNode< DIM >::SetLocation(), and VesselNode< DIM >::SetReferenceLengthScale().

template<unsigned DIM>

boost::shared_ptr<NodeFlowProperties<DIM> > VesselNode< DIM >::mpFlowProperties

private

A flow property collection for the node

Definition at line 113 of file VesselNode.hpp.

Referenced by VesselNode< DIM >::GetFlowProperties(), VesselNode< DIM >::GetOutputData(), VesselNode< DIM >::serialize(), VesselNode< DIM >::SetFlowProperties(), and VesselNode< DIM >::VesselNode().

template<unsigned DIM>

unsigned VesselNode< DIM >::mPtrComparisonId

private

This is used for comparing nodes in some VesselNetwork methods. It should not be used otherwise.

Definition at line 119 of file VesselNode.hpp.

Referenced by VesselNode< DIM >::GetComparisonId(), VesselNode< DIM >::serialize(), and VesselNode< DIM >::SetComparisonId().

template<unsigned DIM>

std::vector<boost::weak_ptr<VesselSegment<DIM> > > VesselNode< DIM >::mSegments

private

Collection of pointers to Vessel Segments connected to this node.

Definition at line 103 of file VesselNode.hpp.

Referenced by VesselNode< DIM >::AddSegment(), VesselNode< DIM >::GetNumberOfSegments(), VesselNode< DIM >::GetSegment(), VesselNode< DIM >::GetSegments(), and VesselNode< DIM >::RemoveSegment().

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

projects/MicrovesselChaste/src/population/vessel/VesselNode.hpp
projects/MicrovesselChaste/src/population/vessel/VesselNode.cpp

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned DIM> class VesselNode< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class VesselNode< DIM >