Simple mesh class for storing and manipulating meshes consisting of 2 and 3D simplexes (triangles or tetrahedra) More...

#include <mesh.h>

Collaboration diagram for AtomProbe::Mesh:

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Public Member Functions
void	setNode (unsigned int index, Point3D node)
	Set the nodes value. More...

void	resizeNodes (unsigned int newSize)
	Resize the node vector. More...

Point3D	getNodes (unsigned int index)
	Retrieve an object. More...

unsigned int	loadGmshMesh (const char *meshfile, unsigned int &curLine, bool allowBadMeshes=true)

unsigned int	saveGmshMesh (const char *meshfile) const

size_t	elementCount () const

void	setTriangleMesh (const std::vector< float > &ptsA, const std::vector< float > &ptsB, const std::vector< float > &ptsC)

void	reassignGroups (unsigned int i)
	reassign the physical groups to a single number More...

void	removeDuplicateTris ()
	Remove exact duplicate triangles. More...

void	mergeDuplicateVertices (float tolerance)

bool	isSane (bool output=false, std::ostream &outStream=std::cerr) const
	Perform various sanity tests on mesh. Should return true if your mesh is sane. More...

void	getBounds (BoundCube &b) const
	Get the Axis aligned bounding box for this mesh. More...

unsigned int	countTriNodes () const
	Count the number of unique nodes shared by triangles. More...

void	translate ()
	Translate mesh around node centroid. More...

void	translate (const Point3D &origin)
	Translate mesh to specified position. More...

void	scale (const Point3D &origin, float scaleFactor)
	Scale the mesh around a specified origin. More...

void	scale (float scaleFactor)
	Scale the mesh around origin. More...

void	rotate (const Point3D &axis, const Point3D &origin, float angle)
	Rotate mesh. More...

float	getVolume () const
	Obtain the volume of the triangulated space. More...

void	clear ()
	Clear the mesh. More...

void	getContainedNodes (const BoundCube &b, std::vector< size_t > &nodes) const
	Return all the nodes that are contained within specified bounding box. More...

void	getIntersectingPrimitives (std::vector< size_t > &searchNodes, std::vector< size_t > &lines, std::vector< size_t > &triangles, std::vector< size_t > &tetrahedra) const
	Return all primitives that are WHOLLY contained withing bounding box. More...

unsigned int	divideMeshSurface (float divisionAngle, unsigned int newPhysGroupStart, const std::vector< size_t > &physGroupsToSplit)

void	getCurPhysGroups (std::vector< std::pair< unsigned int, size_t > > &curPhys) const

void	erasePhysGroup (unsigned int group, unsigned int typeMask)

unsigned int	numDupVertices (float tolerance) const
	obtain the number of duplicate vertices in the mesh More...

unsigned int	numDupTris () const
	Obtain the number of duplicate triangles in the mesh. More...

void	print (std::ostream &o) const
	Print some statistics about the mesh data. More...

bool	isOrientedCoherently () const
	Returns true if the mesh is coherently oriented. More...

void	killOrphanNodes ()
	Kill specified orphan nodes within this dataset. More...

void	pointsInside (const std::vector< Point3D > &p, std::vector< bool > &meshResults, unsigned int &prog) const
	Find the points that lie inside a this mesh. More...

void	pointsInside (const std::vector< Point3D > &p, std::vector< bool > &meshResults) const
	Convenience wraper for pointsInside. More...

size_t	getNearestTri (const Point3D &p, float &distance) const
	Find the nearest triangle to a particular point. More...

void	getTriNormal (size_t tri, Point3D &normal) const

Public Attributes
std::vector< Point3D >	nodes
	Point storage for 3D Data (nodes/coords/vertices..) More...

std::vector< std::string >	physGroupNames
	Physical group storage. More...

std::vector< TETRAHEDRON >	tetrahedra
	Storage for node connectivity in tetrahedral form. More...

std::vector< TRIANGLE >	triangles
	Storage for node connectivity in triangle form (take in groups of 3) More...

std::vector< LINE >	lines
	Storage for line segments. .size()%2 should always==0. More...

std::vector< unsigned long long >	points
	points More...

Detailed Description

Simple mesh class for storing and manipulating meshes consisting of 2 and 3D simplexes (triangles or tetrahedra)

Definition at line 78 of file mesh.h.

Member Function Documentation

◆ clear()

void AtomProbe::Mesh::clear ( )

Clear the mesh.

Definition at line 936 of file mesh.cpp.

References lines, nodes, physGroupNames, points, tetrahedra, and triangles.

Referenced by setTriangleMesh().

◆ countTriNodes()

unsigned int AtomProbe::Mesh::countTriNodes ( ) const

Count the number of unique nodes shared by triangles.

Definition at line 1350 of file mesh.cpp.

References triangles.

◆ divideMeshSurface()

unsigned int AtomProbe::Mesh::divideMeshSurface	(	float	divisionAngle,
		unsigned int	newPhysGroupStart,
		const std::vector< size_t > &	physGroupsToSplit
	)

Definition at line 1597 of file mesh.cpp.

References AtomProbe::Point3D::angle(), ASSERT, AtomProbe::BoundCube::expand(), getTriNormal(), nodes, AtomProbe::BoundCube::setBounds(), AtomProbe::BoundCube::setInverseLimits(), and triangles.

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◆ elementCount()

size_t AtomProbe::Mesh::elementCount ( ) const

Definition at line 1977 of file mesh.cpp.

References lines, points, tetrahedra, and triangles.

Referenced by loadGmshMesh().

◆ erasePhysGroup()

void AtomProbe::Mesh::erasePhysGroup	(	unsigned int	group,
		unsigned int	typeMask
	)

Definition at line 1880 of file mesh.cpp.

References AtomProbe::ELEMENT_LINE, AtomProbe::ELEMENT_TETRAHEDRON, AtomProbe::ELEMENT_TRIANGLE, tetrahedra, and triangles.

◆ getBounds()

void AtomProbe::Mesh::getBounds ( BoundCube & b ) const

Get the Axis aligned bounding box for this mesh.

Definition at line 1532 of file mesh.cpp.

References ASSERT, nodes, AtomProbe::BoundCube::setBounds(), and triangles.

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◆ getContainedNodes()

void AtomProbe::Mesh::getContainedNodes	(	const BoundCube &	b,
		std::vector< size_t > &	nodes
	)		const

Return all the nodes that are contained within specified bounding box.

Definition at line 1761 of file mesh.cpp.

References ASSERT, AtomProbe::BoundCube::containsPt(), and nodes.

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◆ getCurPhysGroups()

void AtomProbe::Mesh::getCurPhysGroups ( std::vector< std::pair< unsigned int, size_t > > & curPhys ) const

Definition at line 1829 of file mesh.cpp.

References tetrahedra, and triangles.

◆ getIntersectingPrimitives()

void AtomProbe::Mesh::getIntersectingPrimitives	(	std::vector< size_t > &	searchNodes,
		std::vector< size_t > &	lines,
		std::vector< size_t > &	triangles,
		std::vector< size_t > &	tetrahedra
	)		const

Return all primitives that are WHOLLY contained withing bounding box.

Definition at line 1772 of file mesh.cpp.

References ASSERT, lines, tetrahedra, and triangles.

◆ getNearestTri()

size_t AtomProbe::Mesh::getNearestTri	(	const Point3D &	p,
		float &	distance
	)		const

Find the nearest triangle to a particular point.

returns index of nearest triangle, and distance (reference)

Definition at line 2126 of file mesh.cpp.

References getTriNormal(), nodes, AtomProbe::signedDistanceToFacet(), and triangles.

Referenced by AtomProbe::TRIANGLE::edgesMismatch(), and main().

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◆ getNodes()

Point3D AtomProbe::Mesh::getNodes ( unsigned int index )

Retrieve an object.

Definition at line 863 of file mesh.cpp.

References nodes.

◆ getTriNormal()

void AtomProbe::Mesh::getTriNormal	(	size_t	tri,
		Point3D &	normal
	)		const

Definition at line 1753 of file mesh.cpp.

References ASSERT, AtomProbe::Point3D::crossProd(), nodes, AtomProbe::Point3D::normalise(), and triangles.

Referenced by divideMeshSurface(), and getNearestTri().

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◆ getVolume()

float AtomProbe::Mesh::getVolume ( ) const

Obtain the volume of the triangulated space.

Definition at line 1946 of file mesh.cpp.

References ASSERT, AtomProbe::Point3D::crossProd(), AtomProbe::Point3D::dotProd(), isOrientedCoherently(), isSane(), nodes, AtomProbe::TRIANGLE::p, and triangles.

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◆ isOrientedCoherently()

bool AtomProbe::Mesh::isOrientedCoherently ( ) const

Returns true if the mesh is coherently oriented.

Definition at line 2152 of file mesh.cpp.

References ASSERT, isSane(), and triangles.

Referenced by AtomProbe::TRIANGLE::edgesMismatch(), getVolume(), and pointsInside().

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◆ isSane()

bool AtomProbe::Mesh::isSane	(	bool	output = `false`,
		std::ostream &	outStream = `std::cerr`
	)		const

Perform various sanity tests on mesh. Should return true if your mesh is sane.

Definition at line 572 of file mesh.cpp.

References lines, nodes, tetrahedra, and triangles.

Referenced by AtomProbe::TRIANGLE::edgesMismatch(), getVolume(), isOrientedCoherently(), killOrphanNodes(), loadGmshMesh(), mergeDuplicateVertices(), numDupTris(), print(), removeDuplicateTris(), saveGmshMesh(), and setTriangleMesh().

◆ killOrphanNodes()

void AtomProbe::Mesh::killOrphanNodes ( )

Kill specified orphan nodes within this dataset.

Definition at line 820 of file mesh.cpp.

References ASSERT, isSane(), lines, nodes, points, tetrahedra, and triangles.

Referenced by mergeDuplicateVertices(), and print().

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◆ loadGmshMesh()

unsigned int AtomProbe::Mesh::loadGmshMesh	(	const char *	meshfile,
		unsigned int &	curLine,
		bool	allowBadMeshes = `true`
	)

◆ mergeDuplicateVertices()

void AtomProbe::Mesh::mergeDuplicateVertices ( float tolerance )

Definition at line 738 of file mesh.cpp.

References ASSERT, AtomProbe::findNearVerticies(), isSane(), killOrphanNodes(), lines, nodes, points, tetrahedra, and triangles.

Referenced by main().

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◆ numDupTris()

unsigned int AtomProbe::Mesh::numDupTris ( ) const

Obtain the number of duplicate triangles in the mesh.

Definition at line 868 of file mesh.cpp.

References ASSERT, isSane(), nodes, and triangles.

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◆ numDupVertices()

unsigned int AtomProbe::Mesh::numDupVertices ( float tolerance ) const

obtain the number of duplicate vertices in the mesh

Definition at line 911 of file mesh.cpp.

References nodes.

◆ pointsInside() [1/2]

void AtomProbe::Mesh::pointsInside	(	const std::vector< Point3D > &	p,
		std::vector< bool > &	meshResults,
		unsigned int &	prog
	)		const

Find the points that lie inside a this mesh.

Definition at line 1989 of file mesh.cpp.

References ASSERT, AtomProbe::BoundCube::containsPt(), AtomProbe::intersect_RayTriangle(), isOrientedCoherently(), nodes, AtomProbe::PROGRESS_REDUCE, AtomProbe::BoundCube::setBounds(), tetrahedra, and triangles.

Referenced by main(), and pointsInside().

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◆ pointsInside() [2/2]

void AtomProbe::Mesh::pointsInside	(	const std::vector< Point3D > &	p,
		std::vector< bool > &	meshResults
	)		const

Convenience wraper for pointsInside.

Definition at line 2119 of file mesh.cpp.

References pointsInside().

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◆ print()

void AtomProbe::Mesh::print ( std::ostream & o ) const

Print some statistics about the mesh data.

Definition at line 445 of file mesh.cpp.

References ASSERT, isSane(), killOrphanNodes(), lines, nodes, AtomProbe::TRIANGLE::p, points, AtomProbe::BoundCube::setBounds(), tetrahedra, and triangles.

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◆ reassignGroups()

void AtomProbe::Mesh::reassignGroups ( unsigned int i )

reassign the physical groups to a single number

Definition at line 1375 of file mesh.cpp.

References lines, tetrahedra, and triangles.

◆ removeDuplicateTris()

void AtomProbe::Mesh::removeDuplicateTris ( )

Remove exact duplicate triangles.

Definition at line 691 of file mesh.cpp.

References ASSERT, isSane(), nodes, and triangles.

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◆ resizeNodes()

void AtomProbe::Mesh::resizeNodes ( unsigned int newSize )

Resize the node vector.

Definition at line 858 of file mesh.cpp.

References nodes.

◆ rotate()

void AtomProbe::Mesh::rotate	(	const Point3D &	axis,
		const Point3D &	origin,
		float	angle
	)

Rotate mesh.

Definition at line 1453 of file mesh.cpp.

References AtomProbe::Point3f::fx, AtomProbe::Point3f::fy, AtomProbe::Point3f::fz, nodes, AtomProbe::quat_get_rot_quat(), and AtomProbe::quat_rot_apply_quat().

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◆ saveGmshMesh()

unsigned int AtomProbe::Mesh::saveGmshMesh ( const char * meshfile ) const

Definition at line 1390 of file mesh.cpp.

References ASSERT, AtomProbe::ELEM_FOUR_NODE_TETRAHEDRON, AtomProbe::ELEM_SINGLE_NODE_POINT, AtomProbe::ELEM_THREE_NODE_TRIANGLE, AtomProbe::ELEM_TWO_NODE_LINE, isSane(), lines, nodes, points, tetrahedra, and triangles.

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◆ scale() [1/2]

void AtomProbe::Mesh::scale	(	const Point3D &	origin,
		float	scaleFactor
	)

Scale the mesh around a specified origin.

Definition at line 1514 of file mesh.cpp.

References nodes.

◆ scale() [2/2]

void AtomProbe::Mesh::scale ( float scaleFactor )

Scale the mesh around origin.

Definition at line 1525 of file mesh.cpp.

References nodes.

◆ setNode()

void AtomProbe::Mesh::setNode	(	unsigned int	index,
		Point3D	node
	)

Set the nodes value.

Definition at line 853 of file mesh.cpp.

References nodes.

◆ setTriangleMesh()

void AtomProbe::Mesh::setTriangleMesh	(	const std::vector< float > &	ptsA,
		const std::vector< float > &	ptsB,
		const std::vector< float > &	ptsC
	)

Definition at line 946 of file mesh.cpp.

References ASSERT, clear(), AtomProbe::findNearVerticies(), isSane(), nodes, AtomProbe::TRIANGLE::p, and triangles.

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◆ translate() [1/2]

void AtomProbe::Mesh::translate ( )

Translate mesh around node centroid.

Definition at line 1496 of file mesh.cpp.

References nodes.

◆ translate() [2/2]

void AtomProbe::Mesh::translate ( const Point3D & origin )

Translate mesh to specified position.

Definition at line 1507 of file mesh.cpp.

References nodes.

Member Data Documentation

◆ lines

std::vector<LINE> AtomProbe::Mesh::lines

Storage for line segments. .size()%2 should always==0.

Definition at line 123 of file mesh.h.

Referenced by clear(), elementCount(), getIntersectingPrimitives(), isSane(), killOrphanNodes(), loadGmshMesh(), mergeDuplicateVertices(), print(), reassignGroups(), and saveGmshMesh().

◆ nodes

std::vector<Point3D> AtomProbe::Mesh::nodes

Point storage for 3D Data (nodes/coords/vertices..)

Definition at line 110 of file mesh.h.

Referenced by clear(), divideMeshSurface(), AtomProbe::TRIANGLE::edgesMismatch(), getBounds(), getContainedNodes(), getNearestTri(), getNodes(), getTriNormal(), getVolume(), isSane(), killOrphanNodes(), loadGmshMesh(), main(), mergeDuplicateVertices(), numDupTris(), numDupVertices(), pointsInside(), print(), removeDuplicateTris(), resizeNodes(), rotate(), saveGmshMesh(), scale(), setNode(), setTriangleMesh(), and translate().

◆ physGroupNames

std::vector<std::string> AtomProbe::Mesh::physGroupNames

Physical group storage.

Definition at line 113 of file mesh.h.

Referenced by clear().

◆ points

std::vector<unsigned long long> AtomProbe::Mesh::points

points

Definition at line 125 of file mesh.h.

Referenced by clear(), elementCount(), killOrphanNodes(), loadGmshMesh(), mergeDuplicateVertices(), print(), and saveGmshMesh().

◆ tetrahedra

std::vector<TETRAHEDRON> AtomProbe::Mesh::tetrahedra

Storage for node connectivity in tetrahedral form.

Definition at line 118 of file mesh.h.

Referenced by clear(), elementCount(), erasePhysGroup(), getCurPhysGroups(), getIntersectingPrimitives(), isSane(), killOrphanNodes(), loadGmshMesh(), mergeDuplicateVertices(), pointsInside(), print(), reassignGroups(), and saveGmshMesh().

◆ triangles

std::vector<TRIANGLE> AtomProbe::Mesh::triangles

Storage for node connectivity in triangle form (take in groups of 3)

Definition at line 121 of file mesh.h.

Referenced by clear(), countTriNodes(), divideMeshSurface(), AtomProbe::TRIANGLE::edgesMismatch(), elementCount(), erasePhysGroup(), getBounds(), getCurPhysGroups(), getIntersectingPrimitives(), getNearestTri(), getTriNormal(), getVolume(), isOrientedCoherently(), isSane(), killOrphanNodes(), loadGmshMesh(), main(), mergeDuplicateVertices(), numDupTris(), pointsInside(), print(), reassignGroups(), removeDuplicateTris(), saveGmshMesh(), and setTriangleMesh().

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

include/atomprobe/primitives/mesh.h
src/primitives/mesh.cpp

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

◆ clear()

◆ countTriNodes()

◆ divideMeshSurface()

◆ elementCount()

◆ erasePhysGroup()

◆ getBounds()

◆ getContainedNodes()

◆ getCurPhysGroups()

◆ getIntersectingPrimitives()

◆ getNearestTri()

◆ getNodes()

◆ getTriNormal()

◆ getVolume()

◆ isOrientedCoherently()

◆ isSane()

◆ killOrphanNodes()

◆ loadGmshMesh()

◆ mergeDuplicateVertices()

◆ numDupTris()

◆ numDupVertices()

◆ pointsInside() [1/2]

◆ pointsInside() [2/2]

◆ print()

◆ reassignGroups()

◆ removeDuplicateTris()

◆ resizeNodes()

◆ rotate()

◆ saveGmshMesh()

◆ scale() [1/2]

◆ scale() [2/2]

◆ setNode()

◆ setTriangleMesh()

◆ translate() [1/2]

◆ translate() [2/2]

Member Data Documentation

◆ lines

◆ nodes

◆ physGroupNames

◆ points

◆ tetrahedra

◆ triangles