#include <VesselNetwork.hpp>

Inheritance diagram for VesselNetwork< DIM >:

Collaboration diagram for VesselNetwork< DIM >:

Public Member Functions
	VesselNetwork ()

virtual	~VesselNetwork ()

void	AddVessel (boost::shared_ptr< Vessel< DIM > > pVessel)

void	AddVessels (std::vector< boost::shared_ptr< Vessel< DIM > > > vessels)

void	CopySegmentFlowProperties (unsigned index=0)

std::vector< boost::shared_ptr< Vessel< DIM > > >	CopyVessels ()

std::vector< boost::shared_ptr< Vessel< DIM > > >	CopyVessels (std::vector< boost::shared_ptr< Vessel< DIM > > > vessels)

virtual boost::shared_ptr< VesselNode< DIM > >	DivideVessel (boost::shared_ptr< Vessel< DIM > > pVessel, const DimensionalChastePoint< DIM > &rLocation)

virtual void	ExtendVessel (boost::shared_ptr< Vessel< DIM > > pVessel, boost::shared_ptr< VesselNode< DIM > > pEndNode, boost::shared_ptr< VesselNode< DIM > > pNewNode)

virtual boost::shared_ptr< Vessel< DIM > >	FormSprout (const DimensionalChastePoint< DIM > &sproutBaseLocation, const DimensionalChastePoint< DIM > &sproutTipLocation)

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

boost::shared_ptr< VesselNode< DIM > >	GetNearestNode (const DimensionalChastePoint< DIM > &rLocation)

boost::shared_ptr< VesselNode< DIM > >	GetNearestNode (boost::shared_ptr< VesselNode< DIM > > pInputNode)

std::pair< boost::shared_ptr< VesselSegment< DIM > >, units::quantity< unit::length > >	GetNearestSegment (boost::shared_ptr< VesselSegment< DIM > > pSegment)

std::pair< boost::shared_ptr< VesselSegment< DIM > >, units::quantity< unit::length > >	GetNearestSegment (boost::shared_ptr< VesselNode< DIM > > pNode, bool sameVessel=true)

std::pair< boost::shared_ptr< VesselSegment< DIM > >, units::quantity< unit::length > >	GetNearestSegment (const DimensionalChastePoint< DIM > &rLocation)

boost::shared_ptr< Vessel< DIM > >	GetNearestVessel (const DimensionalChastePoint< DIM > &rLocation)

unsigned	GetNodeIndex (boost::shared_ptr< VesselNode< DIM > > pNode)

unsigned	NumberOfNodesNearLocation (const DimensionalChastePoint< DIM > &rLocation, double tolerance=0.0)

std::pair< DimensionalChastePoint< DIM >, DimensionalChastePoint< DIM > >	GetExtents (bool useRadii=false)

boost::shared_ptr< VesselNode< DIM > >	GetNode (unsigned index)

std::vector< boost::shared_ptr< VesselNode< DIM > > >	GetNodes ()

unsigned	GetNumberOfNodes ()

unsigned	GetNumberOfVesselNodes ()

unsigned	GetNumberOfVessels ()

unsigned	GetMaxBranchesOnNode ()

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

std::vector< boost::shared_ptr< VesselNode< DIM > > >	GetVesselEndNodes ()

unsigned	GetVesselIndex (boost::shared_ptr< Vessel< DIM > > pVessel)

unsigned	GetVesselSegmentIndex (boost::shared_ptr< VesselSegment< DIM > > pVesselSegment)

std::vector< boost::shared_ptr< VesselSegment< DIM > > >	GetVesselSegments ()

boost::shared_ptr< Vessel< DIM > >	GetVessel (unsigned index)

std::vector< boost::shared_ptr< Vessel< DIM > > >	GetVessels ()

bool	NodeIsInNetwork (boost::shared_ptr< VesselNode< DIM > > pSourceNode)

void	MergeShortVessels (units::quantity< unit::length > cutoff=10.0 1.e-6 unit::metres)

void	MergeCoincidentNodes (double tolerance=0.0)

void	MergeCoincidentNodes (std::vector< boost::shared_ptr< Vessel< DIM > > > pVessels, double tolerance=0.0)

void	MergeCoincidentNodes (std::vector< boost::shared_ptr< VesselNode< DIM > > > nodes, double tolerance=0.0)

void	RemoveVessel (boost::shared_ptr< Vessel< DIM > > pVessel, bool deleteVessel=false)

void	RemoveShortVessels (units::quantity< unit::length > cutoff=10.0 1.e-6 unit::metres, bool endsOnly=true)

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

void	SetNodeRadiiFromSegments ()

void	SetSegmentProperties (boost::shared_ptr< VesselSegment< DIM > > prototype)

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

void	SetSegmentViscosity (units::quantity< unit::dynamic_viscosity > viscosity)

void	Translate (DimensionalChastePoint< DIM > rTranslationVector)

void	Translate (DimensionalChastePoint< DIM > rTranslationVector, std::vector< boost::shared_ptr< Vessel< DIM > > > vessels)

void	UpdateNodes ()

void	UpdateSegments ()

void	UpdateVesselNodes ()

void	UpdateVesselIds ()

void	UpdateAll (bool merge=false)

bool	VesselCrossesLineSegment (const DimensionalChastePoint< DIM > &rCoord1, const DimensionalChastePoint< DIM > &rCoord2, double tolerance=1e-6)

void	Write (const std::string &rFileName)

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< VesselNetwork< DIM > >	Create ()

Private Attributes
std::vector< boost::shared_ptr< Vessel< DIM > > >	mVessels

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

bool	mSegmentsUpToDate

std::vector< boost::shared_ptr< VesselNode< DIM > > >	mNodes

bool	mNodesUpToDate

std::vector< boost::shared_ptr< VesselNode< DIM > > >	mVesselNodes

bool	mVesselNodesUpToDate

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 VesselNetwork< DIM >

A vessel network is a collection of vessels.

Definition at line 53 of file VesselNetwork.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

VesselNetwork< DIM >::VesselNetwork ( )

Constructor.

Definition at line 45 of file VesselNetwork.cpp.

template<unsigned DIM>

VesselNetwork< DIM >::~VesselNetwork ( )

virtual

Destructor

Definition at line 58 of file VesselNetwork.cpp.

Member Function Documentation

template<unsigned DIM>

void VesselNetwork< DIM >::AddVessel ( boost::shared_ptr< Vessel< DIM > > pVessel )

Adds a vessel to the VesselNetwork.

Parameters

pVessel the vessel

Definition at line 71 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mNodesUpToDate, VesselNetwork< DIM >::mSegmentsUpToDate, VesselNetwork< DIM >::mVesselNodesUpToDate, and VesselNetwork< DIM >::mVessels.

Referenced by VesselNetwork< DIM >::DivideVessel(), and VesselNetwork< DIM >::FormSprout().

template<unsigned DIM>

void VesselNetwork< DIM >::AddVessels ( std::vector< boost::shared_ptr< Vessel< DIM > > > vessels )

Adds a collection of vessels to the VesselNetwork

Parameters

vessels the vessels

Definition at line 80 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mNodesUpToDate, VesselNetwork< DIM >::mSegmentsUpToDate, VesselNetwork< DIM >::mVesselNodesUpToDate, and VesselNetwork< DIM >::mVessels.

Referenced by VesselNetwork< DIM >::CopyVessels().

template<unsigned DIM>

void VesselNetwork< DIM >::CopySegmentFlowProperties ( unsigned index = 0 )

Copy flow properties from the specified segment to all other segments

Parameters

index the segment index to be copied

Definition at line 89 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVesselSegments().

template<unsigned DIM>

std::vector< boost::shared_ptr< Vessel< DIM > > > VesselNetwork< DIM >::CopyVessels ( )

Make a copy of all vessels, but with new nodes and segments in each copy. Return the new vessels.

Returns: the new vessels

Definition at line 101 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVessels.

template<unsigned DIM>

std::vector< boost::shared_ptr< Vessel< DIM > > > VesselNetwork< DIM >::CopyVessels ( std::vector< boost::shared_ptr< Vessel< DIM > > > vessels )

Make a copy of the selected vessels, but with new nodes and segments in each copy. Return the new vessels.

Parameters

vessels the vessels to be copied

Returns: the new vessels

Definition at line 107 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::AddVessels(), and VesselNetwork< DIM >::MergeCoincidentNodes().

template<unsigned DIM>

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

static

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

Returns: share pointer to the network

Definition at line 64 of file VesselNetwork.cpp.

Referenced by CsvVesselNetworkReader< DIM >::Create(), VesselNetworkReader< DIM >::Read(), and VesselNetworkGenerator< DIM >::SetReferenceLengthScale().

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNetwork< DIM >::DivideVessel	(	boost::shared_ptr< Vessel< DIM > >	pVessel,
		const DimensionalChastePoint< DIM > &	rLocation
	)

virtual

Divides a vessel into two at the specified location.

Parameters

pVessel	the vessel to be divided
rLocation	the division location

Returns: the node at the division location

Definition at line 130 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::AddVessel(), Vessel< DIM >::Create(), VesselNetwork< DIM >::GetNode(), VesselNetwork< DIM >::mNodesUpToDate, VesselNetwork< DIM >::mSegmentsUpToDate, VesselNetwork< DIM >::mVesselNodesUpToDate, and VesselNetwork< DIM >::RemoveVessel().

Referenced by VesselNetwork< DIM >::FormSprout().

template<unsigned DIM>

void VesselNetwork< DIM >::ExtendVessel	(	boost::shared_ptr< Vessel< DIM > >	pVessel,
		boost::shared_ptr< VesselNode< DIM > >	pEndNode,
		boost::shared_ptr< VesselNode< DIM > >	pNewNode
	)

virtual

Add a new node to the end of the vessel

Parameters

pVessel	the vessel to be extended
pEndNode	the node that the new segment will start on, should already be on the end of the vessel
pNewNode	the new node to be added to the end of the vessel

Definition at line 211 of file VesselNetwork.cpp.

References VesselSegment< DIM >::Create(), VesselNetwork< DIM >::mNodesUpToDate, VesselNetwork< DIM >::mSegmentsUpToDate, and VesselNetwork< DIM >::mVesselNodesUpToDate.

template<unsigned DIM>

boost::shared_ptr< Vessel< DIM > > VesselNetwork< DIM >::FormSprout	(	const DimensionalChastePoint< DIM > &	sproutBaseLocation,
		const DimensionalChastePoint< DIM > &	sproutTipLocation
	)

virtual

Forms a sprout at the specified locations.

Parameters

sproutBaseLocation	the sprout base
sproutTipLocation	the sprout tip

Returns: the new sprout

Definition at line 235 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::AddVessel(), VesselSegment< DIM >::Create(), Vessel< DIM >::Create(), VesselNode< DIM >::Create(), VesselNetwork< DIM >::DivideVessel(), and VesselNetwork< DIM >::GetNearestSegment().

template<unsigned DIM>

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

Get distance to nearest node

Parameters

rLocation the probe point

Returns: the distance to the node

Definition at line 376 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

template<unsigned DIM>

std::pair< DimensionalChastePoint< DIM >, DimensionalChastePoint< DIM > > VesselNetwork< DIM >::GetExtents ( bool useRadii = false )

Return the extents of the vessel network in the form ((xmin, xmax), (ymin, ymax), (zmin, zmax))

Parameters

useRadii use the vessel radii in calculations

Returns: the extents of the vessel network in the form ((xmin, xmax), (ymin, ymax), (zmin, zmax))

Definition at line 285 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes(), BaseUnits::GetReferenceLengthScale(), and BaseUnits::Instance().

template<unsigned DIM>

unsigned VesselNetwork< DIM >::GetMaxBranchesOnNode ( )

Return the number of branches on the most highly connected node

Returns: the number of branches on the most highly connected node

Definition at line 786 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVesselEndNodes().

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNetwork< DIM >::GetNearestNode ( const DimensionalChastePoint< DIM > & rLocation )

Get the node nearest to the specified location

Parameters

rLocation the probe point

Returns: the nearest node

Definition at line 419 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNetwork< DIM >::GetNearestNode ( boost::shared_ptr< VesselNode< DIM > > pInputNode )

Get the node nearest to the specified node

Parameters

pInputNode the probe point

Returns: the nearest node

Definition at line 396 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

template<unsigned DIM>

std::pair< boost::shared_ptr< VesselSegment< DIM > >, units::quantity< unit::length > > VesselNetwork< DIM >::GetNearestSegment ( boost::shared_ptr< VesselSegment< DIM > > pSegment )

Get the segment nearest to the specified segment and the distance to it

Parameters

pSegment the probe segment

Returns: the segment nearest to the specified segment and the distance to it

Definition at line 440 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVesselSegments().

Referenced by VesselNetwork< DIM >::FormSprout(), VesselNetwork< DIM >::GetNearestVessel(), and VesselNetwork< DIM >::VesselCrossesLineSegment().

template<unsigned DIM>

std::pair< boost::shared_ptr< VesselSegment< DIM > >, units::quantity< unit::length > > VesselNetwork< DIM >::GetNearestSegment	(	boost::shared_ptr< VesselNode< DIM > >	pNode,
		bool	sameVessel = `true`
	)

Get the segment nearest to the specified node and the distance to it

Parameters

pNode	the probe node
sameVessel	can it be on the same vessel

Returns: the segment nearest to the specified segment and the distance to it

Definition at line 549 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVessel(), and VesselNetwork< DIM >::GetVesselSegments().

template<unsigned DIM>

std::pair< boost::shared_ptr< VesselSegment< DIM > >, units::quantity< unit::length > > VesselNetwork< DIM >::GetNearestSegment ( const DimensionalChastePoint< DIM > & rLocation )

Get the segment nearest to the specified location and the distance to it

Parameters

rLocation the probe location

Returns: the segment nearest to the specified segment and the distance to it

Definition at line 593 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVesselSegments().

template<unsigned DIM>

boost::shared_ptr< Vessel< DIM > > VesselNetwork< DIM >::GetNearestVessel ( const DimensionalChastePoint< DIM > & rLocation )

Get the vessel nearest to the specified location

Parameters

rLocation the probe location

Returns: the vessel nearest to the specified segment and the distance to it

Definition at line 615 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNearestSegment().

template<unsigned DIM>

boost::shared_ptr< VesselNode< DIM > > VesselNetwork< DIM >::GetNode ( unsigned index )

Return the indexed node in the network This is dangerous as the node member array can be updated and this index will be out of date, use GetNodes instead.

Parameters

index the node index

Returns: the node

Definition at line 699 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mNodes, VesselNetwork< DIM >::mNodesUpToDate, and VesselNetwork< DIM >::UpdateNodes().

Referenced by VesselNetwork< DIM >::DivideVessel().

template<unsigned DIM>

unsigned VesselNetwork< DIM >::GetNodeIndex ( boost::shared_ptr< VesselNode< DIM > > pNode )

Get index of the node

Parameters

pNode the probe node

Returns: index of the node

Definition at line 732 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

template<unsigned DIM>

std::vector< boost::shared_ptr< VesselNode< DIM > > > VesselNetwork< DIM >::GetNodes ( )

Return the nodes in the network

Returns: all the network nodes

Definition at line 688 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mNodes, VesselNetwork< DIM >::mNodesUpToDate, and VesselNetwork< DIM >::UpdateNodes().

Referenced by VesselNetwork< DIM >::GetDistanceToNearestNode(), VesselNetwork< DIM >::GetExtents(), VesselNetwork< DIM >::GetNearestNode(), VesselNetwork< DIM >::GetNodeIndex(), VesselNetwork< DIM >::MergeCoincidentNodes(), VesselNetwork< DIM >::NodeIsInNetwork(), VesselNetwork< DIM >::NumberOfNodesNearLocation(), VesselNetwork< DIM >::SetNodeRadii(), and VesselNetwork< DIM >::SetNodeRadiiFromSegments().

template<unsigned DIM>

unsigned VesselNetwork< DIM >::GetNumberOfNodes ( )

Return the number of nodes in the network.

Returns: the number of nodes in the network.

Definition at line 710 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mNodes, VesselNetwork< DIM >::mNodesUpToDate, and VesselNetwork< DIM >::UpdateNodes().

template<unsigned DIM>

unsigned VesselNetwork< DIM >::GetNumberOfVesselNodes ( )

Return the number of vessel nodes in the network.

Returns: the number of vessel nodes in the network.

Definition at line 721 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVesselNodes, VesselNetwork< DIM >::mVesselNodesUpToDate, and VesselNetwork< DIM >::UpdateVesselNodes().

template<unsigned DIM>

unsigned VesselNetwork< DIM >::GetNumberOfVessels ( )

Return the number of vessels in the network.

Returns: the number of vessels in the network.

Definition at line 752 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVessels.

template<unsigned DIM>

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

virtual

Return a map of vessel network data for use by the vtk writer

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

Implements AbstractVesselNetworkComponent< DIM >.

Definition at line 369 of file VesselNetwork.cpp.

References AbstractVesselNetworkComponent< DIM >::mOutputData.

template<unsigned DIM>

boost::shared_ptr< Vessel< DIM > > VesselNetwork< DIM >::GetVessel ( unsigned index )

Return the indexed vessel

Parameters

index the query index

Returns: the indexed vessel

Definition at line 768 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVessels.

Referenced by VesselNetwork< DIM >::GetNearestSegment().

template<unsigned DIM>

std::vector< boost::shared_ptr< VesselNode< DIM > > > VesselNetwork< DIM >::GetVesselEndNodes ( )

Return the only the nodes at the ends of vessels in the network

Returns: the nodes at the ends of vessels in the network

Definition at line 758 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVesselNodes, VesselNetwork< DIM >::mVesselNodesUpToDate, and VesselNetwork< DIM >::UpdateVesselNodes().

Referenced by VesselNetwork< DIM >::GetMaxBranchesOnNode().

template<unsigned DIM>

unsigned VesselNetwork< DIM >::GetVesselIndex ( boost::shared_ptr< Vessel< DIM > > pVessel )

Return the Index of the specified vessel

Parameters

pVessel the query vessel

Returns: the Index of the specified vessel

Definition at line 807 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVessels.

template<unsigned DIM>

std::vector< boost::shared_ptr< Vessel< DIM > > > VesselNetwork< DIM >::GetVessels ( )

Return the vessels in the network

Returns: the vessels in the network

Definition at line 779 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVessels.

template<unsigned DIM>

unsigned VesselNetwork< DIM >::GetVesselSegmentIndex ( boost::shared_ptr< VesselSegment< DIM > > pVesselSegment )

Return the Index of the specified vessel segment

Parameters

pVesselSegment the query segment

Returns: the Index of the specified vessel segment

Definition at line 823 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVesselSegments().

template<unsigned DIM>

std::vector< boost::shared_ptr< VesselSegment< DIM > > > VesselNetwork< DIM >::GetVesselSegments ( )

Return the vessel segments in the network

Returns: the vessel segments in the network

Definition at line 840 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mSegments, VesselNetwork< DIM >::mSegmentsUpToDate, and VesselNetwork< DIM >::UpdateSegments().

Referenced by VesselNetwork< DIM >::CopySegmentFlowProperties(), VesselNetwork< DIM >::GetNearestSegment(), VesselNetwork< DIM >::GetVesselSegmentIndex(), VesselNetwork< DIM >::SetSegmentProperties(), VesselNetwork< DIM >::SetSegmentRadii(), and VesselNetwork< DIM >::SetSegmentViscosity().

template<unsigned DIM>

void VesselNetwork< DIM >::MergeCoincidentNodes ( double tolerance = 0.0 )

Merge nodes with the same spatial location. Useful for tidying up networks read from file.

Parameters

tolerance how close together are nodes for them to be coincident

Definition at line 858 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

Referenced by VesselNetwork< DIM >::CopyVessels(), VesselNetwork< DIM >::MergeCoincidentNodes(), VesselNetwork< DIM >::MergeShortVessels(), and VesselNetwork< DIM >::UpdateAll().

template<unsigned DIM>

void VesselNetwork< DIM >::MergeCoincidentNodes	(	std::vector< boost::shared_ptr< Vessel< DIM > > >	pVessels,
		double	tolerance = `0.0`
	)

Merge nodes with the same spatial location. Useful for tidying up networks read from file.

Parameters

pVessels	the vessels for merging
tolerance	how close together are nodes for them to be coincident

Definition at line 864 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::MergeCoincidentNodes().

template<unsigned DIM>

void VesselNetwork< DIM >::MergeCoincidentNodes	(	std::vector< boost::shared_ptr< VesselNode< DIM > > >	nodes,
		double	tolerance = `0.0`
	)

Merge nodes with the same spatial location. Useful for tidying up networks read from file.

Parameters

nodes	the nodes to merge
tolerance	how close together are nodes for them to be coincident

Definition at line 876 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mNodesUpToDate, VesselNetwork< DIM >::mSegmentsUpToDate, and VesselNetwork< DIM >::mVesselNodesUpToDate.

template<unsigned DIM>

void VesselNetwork< DIM >::MergeShortVessels ( units::quantity< unit::length > cutoff = 10.0 * 1.e-6 * unit::metres )

Merge short vessels in the network

Parameters

cutoff how short is short

Definition at line 647 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::MergeCoincidentNodes(), VesselNetwork< DIM >::mNodesUpToDate, VesselNetwork< DIM >::mSegmentsUpToDate, VesselNetwork< DIM >::mVesselNodesUpToDate, VesselNetwork< DIM >::mVessels, and VesselNetwork< DIM >::RemoveVessel().

template<unsigned DIM>

bool VesselNetwork< DIM >::NodeIsInNetwork ( boost::shared_ptr< VesselNode< DIM > > pSourceNode )

Return whether node is in network.

Parameters

pSourceNode the node

Returns: is the node in the network

Definition at line 851 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

template<unsigned DIM>

unsigned VesselNetwork< DIM >::NumberOfNodesNearLocation	(	const DimensionalChastePoint< DIM > &	rLocation,
		double	tolerance = `0.0`
	)

Get the number of nodes near to a specified point

Parameters

rLocation	the probe point
tolerance	the tolerance for proximty calculation

Returns: the number of nodes

Definition at line 672 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

template<unsigned DIM>

void VesselNetwork< DIM >::RemoveShortVessels	(	units::quantity< unit::length >	cutoff = `10.0* 1.e-6 * unit::metres`,
		bool	endsOnly = `true`
	)

Remove short vessels from the network

Parameters

cutoff	the minumum vessel length
endsOnly	just remove vessels with connectivity 1

Definition at line 621 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVessels, and VesselNetwork< DIM >::RemoveVessel().

template<unsigned DIM>

void VesselNetwork< DIM >::RemoveVessel	(	boost::shared_ptr< Vessel< DIM > >	pVessel,
		bool	deleteVessel = `false`
	)

Removes a vessel from the network

Parameters

pVessel	the vessel to remove
deleteVessel	also remove the vessel from its child segments and nodes if true.

Definition at line 967 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mNodesUpToDate, VesselNetwork< DIM >::mSegmentsUpToDate, VesselNetwork< DIM >::mVesselNodesUpToDate, and VesselNetwork< DIM >::mVessels.

Referenced by VesselNetwork< DIM >::DivideVessel(), VesselNetwork< DIM >::MergeShortVessels(), and VesselNetwork< DIM >::RemoveShortVessels().

template<unsigned DIM>

void VesselNetwork< DIM >::SetNodeRadii ( units::quantity< unit::length > radius )

Set the nodal radii to the same value

Parameters

radius the node radius value

Definition at line 990 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

template<unsigned DIM>

void VesselNetwork< DIM >::SetNodeRadiiFromSegments ( )

Get the node radius by averaging its segments

Definition at line 269 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetNodes().

template<unsigned DIM>

void VesselNetwork< DIM >::SetSegmentProperties ( boost::shared_ptr< VesselSegment< DIM > > prototype )

Set the properties of the segments in the network based on those of the prototype

Parameters

prototype a prototype segment from which to copy properties

Definition at line 926 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVesselSegments().

template<unsigned DIM>

void VesselNetwork< DIM >::SetSegmentRadii ( units::quantity< unit::length > radius )

Set the segment radii to the same value

Parameters

radius the segment radius

Definition at line 1002 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVesselSegments().

template<unsigned DIM>

void VesselNetwork< DIM >::SetSegmentViscosity ( units::quantity< unit::dynamic_viscosity > viscosity )

Set the segment viscosity to the same value

Parameters

viscosity the segment viscosity

Definition at line 1013 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::GetVesselSegments().

template<unsigned DIM>

void VesselNetwork< DIM >::Translate ( DimensionalChastePoint< DIM > rTranslationVector )

Translate the network along the provided vector

Parameters

rTranslationVector the translation vector

Definition at line 942 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVessels.

template<unsigned DIM>

void VesselNetwork< DIM >::Translate	(	DimensionalChastePoint< DIM >	rTranslationVector,
		std::vector< boost::shared_ptr< Vessel< DIM > > >	vessels
	)

Translate specific vessels along the provided vector

Parameters

rTranslationVector	the translation vector
vessels	the vessels to translate

Definition at line 948 of file VesselNetwork.cpp.

References DimensionalChastePoint< DIM >::Translate().

template<unsigned DIM>

void VesselNetwork< DIM >::UpdateAll ( bool merge = false )

Update all dynamic storage in the vessel network, optionally merge coincident nodes

Parameters

merge whether to merge co-incident nodes

Definition at line 1023 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::MergeCoincidentNodes(), VesselNetwork< DIM >::UpdateNodes(), VesselNetwork< DIM >::UpdateSegments(), VesselNetwork< DIM >::UpdateVesselIds(), and VesselNetwork< DIM >::UpdateVesselNodes().

template<unsigned DIM>

void VesselNetwork< DIM >::UpdateNodes ( )

Update the network node collection

Definition at line 1036 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mNodes, VesselNetwork< DIM >::mNodesUpToDate, and VesselNetwork< DIM >::mVessels.

Referenced by VesselNetwork< DIM >::GetNode(), VesselNetwork< DIM >::GetNodes(), VesselNetwork< DIM >::GetNumberOfNodes(), and VesselNetwork< DIM >::UpdateAll().

template<unsigned DIM>

void VesselNetwork< DIM >::UpdateSegments ( )

Update the network segment collection

Definition at line 1062 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mSegments, VesselNetwork< DIM >::mSegmentsUpToDate, and VesselNetwork< DIM >::mVessels.

Referenced by VesselNetwork< DIM >::GetVesselSegments(), and VesselNetwork< DIM >::UpdateAll().

template<unsigned DIM>

void VesselNetwork< DIM >::UpdateVesselIds ( )

Update the vessel id tags

Definition at line 1102 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVessels.

Referenced by VesselNetwork< DIM >::UpdateAll().

template<unsigned DIM>

void VesselNetwork< DIM >::UpdateVesselNodes ( )

Update the network vessel collection

Definition at line 1075 of file VesselNetwork.cpp.

References VesselNetwork< DIM >::mVesselNodes, VesselNetwork< DIM >::mVesselNodesUpToDate, and VesselNetwork< DIM >::mVessels.

Referenced by VesselNetwork< DIM >::GetNumberOfVesselNodes(), VesselNetwork< DIM >::GetVesselEndNodes(), and VesselNetwork< DIM >::UpdateAll().

template<unsigned DIM>

bool VesselNetwork< DIM >::VesselCrossesLineSegment	(	const DimensionalChastePoint< DIM > &	rCoord1,
		const DimensionalChastePoint< DIM > &	rCoord2,
		double	tolerance = `1e-6`
	)

Returns whether a vessel crosses a line segment.

Parameters

rCoord1	the start of the line segment
rCoord2	the end of the line segment
tolerance	how close to crossing is considered crossing

Returns: whether a vessel crosses a line segment.

Definition at line 1111 of file VesselNetwork.cpp.

References VesselSegment< DIM >::Create(), and VesselNetwork< DIM >::GetNearestSegment().

template<unsigned DIM>

void VesselNetwork< DIM >::Write ( const std::string & rFileName )

Write the network to file

Parameters

rFileName the filename

Definition at line 1129 of file VesselNetwork.cpp.

References VesselNetworkWriter< DIM >::Create().

Member Data Documentation

template<unsigned DIM>

std::vector<boost::shared_ptr<VesselNode<DIM> > > VesselNetwork< DIM >::mNodes

private

Container for nodes in the VesselNetwork.

Definition at line 76 of file VesselNetwork.hpp.

Referenced by VesselNetwork< DIM >::GetNode(), VesselNetwork< DIM >::GetNodes(), VesselNetwork< DIM >::GetNumberOfNodes(), and VesselNetwork< DIM >::UpdateNodes().

template<unsigned DIM>

bool VesselNetwork< DIM >::mNodesUpToDate

private

Is the data in mNodes up to date.

Definition at line 81 of file VesselNetwork.hpp.

Referenced by VesselNetwork< DIM >::AddVessel(), VesselNetwork< DIM >::AddVessels(), VesselNetwork< DIM >::DivideVessel(), VesselNetwork< DIM >::ExtendVessel(), VesselNetwork< DIM >::GetNode(), VesselNetwork< DIM >::GetNodes(), VesselNetwork< DIM >::GetNumberOfNodes(), VesselNetwork< DIM >::MergeCoincidentNodes(), VesselNetwork< DIM >::MergeShortVessels(), VesselNetwork< DIM >::RemoveVessel(), and VesselNetwork< DIM >::UpdateNodes().

template<unsigned DIM>

std::vector<boost::shared_ptr<VesselSegment<DIM> > > VesselNetwork< DIM >::mSegments

private

Container for vessel segments in the VesselNetwork.

Definition at line 66 of file VesselNetwork.hpp.

Referenced by VesselNetwork< DIM >::GetVesselSegments(), and VesselNetwork< DIM >::UpdateSegments().

template<unsigned DIM>

bool VesselNetwork< DIM >::mSegmentsUpToDate

private

Is the data in mSegments up to date.

Definition at line 71 of file VesselNetwork.hpp.

Referenced by VesselNetwork< DIM >::AddVessel(), VesselNetwork< DIM >::AddVessels(), VesselNetwork< DIM >::DivideVessel(), VesselNetwork< DIM >::ExtendVessel(), VesselNetwork< DIM >::GetVesselSegments(), VesselNetwork< DIM >::MergeCoincidentNodes(), VesselNetwork< DIM >::MergeShortVessels(), VesselNetwork< DIM >::RemoveVessel(), and VesselNetwork< DIM >::UpdateSegments().

template<unsigned DIM>

std::vector<boost::shared_ptr<VesselNode<DIM> > > VesselNetwork< DIM >::mVesselNodes

private

Container for vessel nodes in the VesselNetwork.

Definition at line 86 of file VesselNetwork.hpp.

Referenced by VesselNetwork< DIM >::GetNumberOfVesselNodes(), VesselNetwork< DIM >::GetVesselEndNodes(), and VesselNetwork< DIM >::UpdateVesselNodes().

template<unsigned DIM>

bool VesselNetwork< DIM >::mVesselNodesUpToDate

private

Is the data in mVesselNodes up to date.

Definition at line 91 of file VesselNetwork.hpp.

Referenced by VesselNetwork< DIM >::AddVessel(), VesselNetwork< DIM >::AddVessels(), VesselNetwork< DIM >::DivideVessel(), VesselNetwork< DIM >::ExtendVessel(), VesselNetwork< DIM >::GetNumberOfVesselNodes(), VesselNetwork< DIM >::GetVesselEndNodes(), VesselNetwork< DIM >::MergeCoincidentNodes(), VesselNetwork< DIM >::MergeShortVessels(), VesselNetwork< DIM >::RemoveVessel(), and VesselNetwork< DIM >::UpdateVesselNodes().

template<unsigned DIM>

std::vector<boost::shared_ptr<Vessel<DIM> > > VesselNetwork< DIM >::mVessels

private

Container for Vessels in the VesselNetwork.

Definition at line 61 of file VesselNetwork.hpp.

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<unsigned DIM> class VesselNetwork< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class VesselNetwork< DIM >