#include <Part.hpp>

Collaboration diagram for Part< DIM >:

Public Member Functions
	Part ()

	~Part ()

boost::shared_ptr< Polygon< DIM > >	AddCircle (units::quantity< unit::length > radius, DimensionalChastePoint< DIM > centre, unsigned numSegments=24)

void	AddCylinder (units::quantity< unit::length > radius, units::quantity< unit::length > depth, DimensionalChastePoint< DIM > centre, unsigned numSegments=24)

void	AddCuboid (units::quantity< unit::length > sizeX, units::quantity< unit::length > sizeY, units::quantity< unit::length > sizeZ, DimensionalChastePoint< DIM > origin)

void	AddHoleMarker (DimensionalChastePoint< DIM > location)

boost::shared_ptr< Polygon< DIM > >	AddPolygon (std::vector< boost::shared_ptr< DimensionalChastePoint< DIM > > > vertices, bool newFacet=false, boost::shared_ptr< Facet< DIM > > pFacet=boost::shared_ptr< Facet< DIM > >())

boost::shared_ptr< Polygon< DIM > >	AddPolygon (boost::shared_ptr< Polygon< DIM > > pPolygon, bool newFacet=false, boost::shared_ptr< Facet< DIM > > pFacet=boost::shared_ptr< Facet< DIM > >())

boost::shared_ptr< Polygon< DIM > >	AddRectangle (units::quantity< unit::length > sizeX, units::quantity< unit::length > sizeY, DimensionalChastePoint< DIM > origin)

void	AddVesselNetwork (boost::shared_ptr< VesselNetwork< DIM > > pVesselNetwork, bool surface=false)

void	BooleanWithNetwork (boost::shared_ptr< VesselNetwork< DIM > > pVesselNetwork)

void	Extrude (boost::shared_ptr< Polygon< DIM > > pPolygon, units::quantity< unit::length > distance)

std::vector< units::quantity< unit::length > >	GetBoundingBox ()

std::vector< unsigned >	GetContainingGridIndices (unsigned num_x, unsigned num_y, unsigned num_z, units::quantity< unit::length > spacing)

std::vector< DimensionalChastePoint< DIM > >	GetHoleMarkers ()

std::vector< boost::shared_ptr< Facet< DIM > > >	GetFacets ()

boost::shared_ptr< Facet< DIM > >	GetFacet (const DimensionalChastePoint< DIM > &rLocation)

std::vector< boost::shared_ptr< Polygon< DIM > > >	GetPolygons ()

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

std::vector< std::pair< unsigned, unsigned > >	GetSegmentIndices ()

std::vector< boost::shared_ptr< DimensionalChastePoint< DIM > > >	GetVertices ()

std::vector< DimensionalChastePoint< DIM > >	GetVertexLocations ()

vtkSmartPointer< vtkPolyData >	GetVtk ()

bool	IsPointInPart (DimensionalChastePoint< DIM > location)

std::vector< bool >	IsPointInPart (const std::vector< DimensionalChastePoint< DIM > > &location)

void	MergeCoincidentVertices ()

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

void	Translate (DimensionalChastePoint< DIM > vector)

void	Write (const std::string &rFilename, GeometryFormat::Value format=GeometryFormat::VTP)

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

Private Attributes
std::vector< boost::shared_ptr< Facet< DIM > > >	mFacets

vtkSmartPointer< vtkPolyData >	mVtkPart

std::vector< DimensionalChastePoint< DIM > >	mHoleMarkers

std::vector< DimensionalChastePoint< DIM > >	mRegionMarkers

units::quantity< unit::length >	mReferenceLength

bool	mVtkIsUpToDate

Detailed Description

template<unsigned DIM>
class Part< DIM >

A geometric feature described using a PLC (piecewise linear complex) description (see the tetgen manual for details:http://wias-berlin.de/software/tetgen/). These descriptions allow parts to be meshed using triangle or tetgen.

Definition at line 60 of file Part.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

Part< DIM >::Part ( )

Constructor

Definition at line 52 of file Part.cpp.

template<unsigned DIM>

Part< DIM >::~Part ( )

Destructor

Definition at line 70 of file Part.cpp.

Member Function Documentation

template<unsigned DIM>

boost::shared_ptr< Polygon< DIM > > Part< DIM >::AddCircle	(	units::quantity< unit::length >	radius,
		DimensionalChastePoint< DIM >	centre,
		unsigned	numSegments = `24`
	)

Add a circle to the part. If a target facet is not specified the default position is normal to the z-axis.

Parameters

radius	the circle radius
centre	the centre of the circle
numSegments	the number of linear segments the circle is described with

Returns: polygon corresponding to the circle, useful for further operations, such as extrusion.

Definition at line 76 of file Part.cpp.

References Part< DIM >::AddPolygon(), DimensionalChastePoint< DIM >::GetLocation(), DimensionalChastePoint< DIM >::GetReferenceLengthScale(), Part< DIM >::mReferenceLength, and Part< DIM >::mVtkIsUpToDate.

Referenced by Part< DIM >::AddCylinder().

template<unsigned DIM>

void Part< DIM >::AddCuboid	(	units::quantity< unit::length >	sizeX,
		units::quantity< unit::length >	sizeY,
		units::quantity< unit::length >	sizeZ,
		DimensionalChastePoint< DIM >	origin
	)

Add a cuboid to the part.

Parameters

sizeX	the dimension in x
sizeY	the dimension in y
sizeZ	the dimension in z
origin	the bottom, left, front corner

Definition at line 111 of file Part.cpp.

References Part< DIM >::AddRectangle(), Part< DIM >::Extrude(), and Part< DIM >::mVtkIsUpToDate.

template<unsigned DIM>

void Part< DIM >::AddCylinder	(	units::quantity< unit::length >	radius,
		units::quantity< unit::length >	depth,
		DimensionalChastePoint< DIM >	centre,
		unsigned	numSegments = `24`
	)

Add a cylinder to the part.

Parameters

radius	the radius
depth	the depth
centre	the centre of the base
numSegments	the number of line segments the base is described with

Definition at line 100 of file Part.cpp.

References Part< DIM >::AddCircle(), Part< DIM >::Extrude(), and Part< DIM >::mVtkIsUpToDate.

template<unsigned DIM>

void Part< DIM >::AddHoleMarker ( DimensionalChastePoint< DIM > location )

Add a hole marker to the part

Parameters

location the location of the hole

Definition at line 122 of file Part.cpp.

References Part< DIM >::mHoleMarkers.

Referenced by Part< DIM >::AddVesselNetwork().

template<unsigned DIM>

boost::shared_ptr< Polygon< DIM > > Part< DIM >::AddPolygon	(	std::vector< boost::shared_ptr< DimensionalChastePoint< DIM > > >	vertices,
		bool	newFacet = `false`,
		boost::shared_ptr< Facet< DIM > >	pFacet = `boost::shared_ptr<Facet<DIM> >()`
	)

Add a polygon described by a vector or vertices. The vertices should be planar. This is not checked.

Parameters

vertices	a vector of vertices making up the polygon
newFacet	whether to add a new facet
pFacet	an optional facet that the circle can be generated on

Returns: the new polygon, useful for further operations, such as extrusion.

Definition at line 128 of file Part.cpp.

References Polygon< DIM >::Create(), and Part< DIM >::mVtkIsUpToDate.

Referenced by Part< DIM >::AddCircle(), Part< DIM >::AddRectangle(), and VesselSurfaceGenerator< DIM >::GetVtkSurface().

template<unsigned DIM>

boost::shared_ptr< Polygon< DIM > > Part< DIM >::AddPolygon	(	boost::shared_ptr< Polygon< DIM > >	pPolygon,
		bool	newFacet = `false`,
		boost::shared_ptr< Facet< DIM > >	pFacet = `boost::shared_ptr<Facet<DIM> >()`
	)

Add a polygon

Parameters

pPolygon	a polygon to add to the part
newFacet	whether to add a new facet
pFacet	an optional facet that the polygon can be generated on

Returns: the new polygon, useful for further operations, such as extrusion.

Definition at line 138 of file Part.cpp.

References Part< DIM >::mFacets, and Part< DIM >::mVtkIsUpToDate.

template<unsigned DIM>

boost::shared_ptr< Polygon< DIM > > Part< DIM >::AddRectangle	(	units::quantity< unit::length >	sizeX,
		units::quantity< unit::length >	sizeY,
		DimensionalChastePoint< DIM >	origin
	)

Add a rectangle to the part, oriented by default with out of plane direction along the z-axis.

Parameters

sizeX	the dimension in the x direction
sizeY	the dimension in the y direction
origin	the bottom left corner

Returns: the new polygon, useful for further operations, such as extrusion.

Definition at line 161 of file Part.cpp.

References Part< DIM >::AddPolygon(), DimensionalChastePoint< DIM >::GetLocation(), Part< DIM >::mReferenceLength, and Part< DIM >::mVtkIsUpToDate.

Referenced by Part< DIM >::AddCuboid().

template<unsigned DIM>

void Part< DIM >::AddVesselNetwork	(	boost::shared_ptr< VesselNetwork< DIM > >	pVesselNetwork,
		bool	surface = `false`
	)

Add a vessel network to the part.

Parameters

pVesselNetwork	the vessel network to be added
surface	true if a surface representation of the network is required

Definition at line 189 of file Part.cpp.

References Part< DIM >::AddHoleMarker(), Polygon< DIM >::Create(), VesselSurfaceGenerator< DIM >::GetHoles(), VesselSurfaceGenerator< DIM >::GetSurfacePolygons(), Part< DIM >::mFacets, and Part< DIM >::mVtkIsUpToDate.

template<unsigned DIM>

void Part< DIM >::BooleanWithNetwork ( boost::shared_ptr< VesselNetwork< DIM > > pVesselNetwork )

Remove vessels outside the part

Parameters

pVesselNetwork the vessel network to be pruned

Definition at line 323 of file Part.cpp.

References Part< DIM >::IsPointInPart().

template<unsigned DIM>

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

static

Factory constructor method

Returns: a shared pointer to a new part

Definition at line 63 of file Part.cpp.

Referenced by VoronoiGenerator< DIM >::Generate(), MappableGridGenerator::GeneratePlane(), VesselNetworkGenerator< DIM >::SetReferenceLengthScale(), and Owen11CellPopulationGenerator< DIM >::Update().

template<unsigned DIM>

void Part< DIM >::Extrude	(	boost::shared_ptr< Polygon< DIM > >	pPolygon,
		units::quantity< unit::length >	distance
	)

Extrude the part along the z-axis, inserting planar faces in place of edges.

Parameters

pPolygon	the polygon to extrude
distance	the extrusion distance

Definition at line 274 of file Part.cpp.

References Polygon< DIM >::Create(), Part< DIM >::mFacets, Part< DIM >::mReferenceLength, and Part< DIM >::mVtkIsUpToDate.

Referenced by Part< DIM >::AddCuboid(), and Part< DIM >::AddCylinder().

template<unsigned DIM>

std::vector< units::quantity< unit::length > > Part< DIM >::GetBoundingBox ( )

Return the bounding box

Returns: the bounding box of the part (xmin, xmax, ymin, ymax, zmin, zmax)

Definition at line 433 of file Part.cpp.

References Part< DIM >::GetVertices(), and Part< DIM >::mReferenceLength.

template<unsigned DIM>

std::vector< unsigned > Part< DIM >::GetContainingGridIndices	(	unsigned	num_x,
		unsigned	num_y,
		unsigned	num_z,
		units::quantity< unit::length >	spacing
	)

Return the indices of the grid that are inside the part

Parameters

num_x	number of grid points in x
num_y	number of grid points in y
num_z	number of grid points in z
spacing	the grid spacing

Returns: a vector of grid indices

Definition at line 386 of file Part.cpp.

References Part< DIM >::IsPointInPart(), and Part< DIM >::mReferenceLength.

template<unsigned DIM>

boost::shared_ptr< Facet< DIM > > Part< DIM >::GetFacet ( const DimensionalChastePoint< DIM > & rLocation )

Return the FIRST facet found on the point. Strict method, returns exception if there is no facet at the point.

Parameters

rLocation the probe point

Returns: the FIRST found facet on the point.

Definition at line 351 of file Part.cpp.

References Part< DIM >::mFacets.

template<unsigned DIM>

std::vector< boost::shared_ptr< Facet< DIM > > > Part< DIM >::GetFacets ( )

Return the facets

Returns: the facets

Definition at line 472 of file Part.cpp.

References Part< DIM >::mFacets.

template<unsigned DIM>

std::vector< DimensionalChastePoint< DIM > > Part< DIM >::GetHoleMarkers ( )

Return the hole marker locations

Returns: the hole marker locations

Definition at line 339 of file Part.cpp.

References Part< DIM >::mHoleMarkers.

template<unsigned DIM>

std::vector< boost::shared_ptr< Polygon< DIM > > > Part< DIM >::GetPolygons ( )

Return the polygons

Returns: the polygons

Definition at line 421 of file Part.cpp.

References Part< DIM >::mFacets.

Referenced by Part< DIM >::GetVertices(), Part< DIM >::GetVtk(), and Part< DIM >::MergeCoincidentVertices().

template<unsigned DIM>

units::quantity< unit::length > Part< DIM >::GetReferenceLengthScale ( )

Return the reference length scale

Returns: the reference length scale

Definition at line 345 of file Part.cpp.

References Part< DIM >::mReferenceLength.

template<unsigned DIM>

std::vector< std::pair< unsigned, unsigned > > Part< DIM >::GetSegmentIndices ( )

Return the segment indexes, used for 2D meshing

Returns: the indices of vertices corresponding to segments (edges) in the part

Definition at line 478 of file Part.cpp.

References Part< DIM >::GetVertices(), and Part< DIM >::mFacets.

template<unsigned DIM>

std::vector< DimensionalChastePoint< DIM > > Part< DIM >::GetVertexLocations ( )

Return the vertex locations

Returns: the vertex locations

Definition at line 409 of file Part.cpp.

References Part< DIM >::GetVertices().

template<unsigned DIM>

std::vector< boost::shared_ptr< DimensionalChastePoint< DIM > > > Part< DIM >::GetVertices ( )

Return the unique vertices

Returns: the unique vertices

Definition at line 364 of file Part.cpp.

References Part< DIM >::GetPolygons().

Referenced by Part< DIM >::GetBoundingBox(), Part< DIM >::GetSegmentIndices(), Part< DIM >::GetVertexLocations(), and Part< DIM >::Translate().

template<unsigned DIM>

vtkSmartPointer< vtkPolyData > Part< DIM >::GetVtk ( )

Return the a vtk polydata representation of the part

Returns: a vtk representation of the part

Definition at line 511 of file Part.cpp.

References Part< DIM >::GetPolygons(), Part< DIM >::mReferenceLength, Part< DIM >::mVtkIsUpToDate, and Part< DIM >::mVtkPart.

Referenced by VesselSurfaceGenerator< DIM >::GetVtkSurface(), Part< DIM >::IsPointInPart(), and Part< DIM >::Write().

template<unsigned DIM>

bool Part< DIM >::IsPointInPart ( DimensionalChastePoint< DIM > location )

Is the point inside the part

Parameters

location the location of the point

Returns: bool true if the point is inside the part

Definition at line 564 of file Part.cpp.

References DimensionalChastePoint< DIM >::GetLocation(), Part< DIM >::GetVtk(), and Part< DIM >::mReferenceLength.

Referenced by Part< DIM >::BooleanWithNetwork(), and Part< DIM >::GetContainingGridIndices().

template<unsigned DIM>

std::vector< bool > Part< DIM >::IsPointInPart ( const std::vector< DimensionalChastePoint< DIM > > & location )

Is the point inside the part

Parameters

location the location of the point

Returns: bool true if the point is inside the part

Definition at line 599 of file Part.cpp.

References Part< DIM >::GetVtk(), and Part< DIM >::mReferenceLength.

template<unsigned DIM>

void Part< DIM >::MergeCoincidentVertices ( )

Merge vertices that overlap in polygons and facets

Definition at line 644 of file Part.cpp.

References Part< DIM >::GetPolygons(), Part< DIM >::mFacets, and Part< DIM >::mVtkIsUpToDate.

template<unsigned DIM>

void Part< DIM >::SetReferenceLengthScale ( units::quantity< unit::length > referenceLength )

Set the reference length scale

Parameters

referenceLength the reference length scale

Definition at line 678 of file Part.cpp.

References Part< DIM >::mReferenceLength, and Part< DIM >::mVtkIsUpToDate.

template<unsigned DIM>

void Part< DIM >::Translate ( DimensionalChastePoint< DIM > vector )

Move the part along the translation vector

Parameters

vector the vector to move the part along

Definition at line 685 of file Part.cpp.

References Part< DIM >::GetVertices(), and Part< DIM >::mVtkIsUpToDate.

template<unsigned DIM>

void Part< DIM >::Write	(	const std::string &	rFilename,
		GeometryFormat::Value	format = `GeometryFormat::VTP`
	)

Write the part to file in vtk format

Parameters

rFilename	the path to the file to be written, without extension
format	the output format

Definition at line 698 of file Part.cpp.

References Part< DIM >::GetVtk(), GeometryWriter::SetFileName(), GeometryWriter::SetInput(), GeometryWriter::SetOutputFormat(), and GeometryWriter::Write().

Member Data Documentation

template<unsigned DIM>

std::vector<boost::shared_ptr<Facet<DIM> > > Part< DIM >::mFacets

private

Planar collections of polygons

Definition at line 65 of file Part.hpp.

Referenced by Part< DIM >::AddPolygon(), Part< DIM >::AddVesselNetwork(), Part< DIM >::Extrude(), Part< DIM >::GetFacet(), Part< DIM >::GetFacets(), Part< DIM >::GetPolygons(), Part< DIM >::GetSegmentIndices(), and Part< DIM >::MergeCoincidentVertices().

template<unsigned DIM>

std::vector<DimensionalChastePoint<DIM> > Part< DIM >::mHoleMarkers

private

The locations of hole markers (see PLC definition)

Definition at line 75 of file Part.hpp.

Referenced by Part< DIM >::AddHoleMarker(), and Part< DIM >::GetHoleMarkers().

template<unsigned DIM>

units::quantity<unit::length> Part< DIM >::mReferenceLength

private

The reference length scale

Definition at line 85 of file Part.hpp.

Referenced by Part< DIM >::AddCircle(), Part< DIM >::AddRectangle(), Part< DIM >::Extrude(), Part< DIM >::GetBoundingBox(), Part< DIM >::GetContainingGridIndices(), Part< DIM >::GetReferenceLengthScale(), Part< DIM >::GetVtk(), Part< DIM >::IsPointInPart(), and Part< DIM >::SetReferenceLengthScale().

template<unsigned DIM>

std::vector<DimensionalChastePoint<DIM> > Part< DIM >::mRegionMarkers

private

The locations of region markers (see PLC definition)

Definition at line 80 of file Part.hpp.

template<unsigned DIM>

bool Part< DIM >::mVtkIsUpToDate

private

Is the vtk representation up-to-date

Definition at line 90 of file Part.hpp.

Referenced by Part< DIM >::AddCircle(), Part< DIM >::AddCuboid(), Part< DIM >::AddCylinder(), Part< DIM >::AddPolygon(), Part< DIM >::AddRectangle(), Part< DIM >::AddVesselNetwork(), Part< DIM >::Extrude(), Part< DIM >::GetVtk(), Part< DIM >::MergeCoincidentVertices(), Part< DIM >::SetReferenceLengthScale(), and Part< DIM >::Translate().

template<unsigned DIM>

vtkSmartPointer<vtkPolyData> Part< DIM >::mVtkPart

private

A vtk representation of the part

Definition at line 70 of file Part.hpp.

Referenced by Part< DIM >::GetVtk().

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

projects/MicrovesselChaste/src/geometry/Part.hpp
projects/MicrovesselChaste/src/geometry/Part.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

template<unsigned DIM> class Part< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class Part< DIM >