BasicTools.Containers.UnstructuredMeshGraphTools module
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_ComputeElementToElementGraph(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_ComputeMeshLaplacianEigenmaps(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_ComputeNodalAveragedStretchMetric(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_ComputeNodeToNodeGraph(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_FloaterMesh3DParametrization(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_FloaterMesh3DParametrizationStarDomain(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_FloaterMeshParametrization(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_InitializeGraphPointsFromMeshElements(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_InitializeGraphPointsFromMeshPoints(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.CheckIntegrity_PartitionMesh_Metis(GUI=False)[source]
- BasicTools.Containers.UnstructuredMeshGraphTools.ComputeElementToElementGraph(inMesh: UnstructuredMesh, dimensionality: int | None = None, connectivityDimension: int | None = None)[source]
Creates a networkx graph from the element connectivity on an UnstructuredMesh in the following sense: an element is linked to another in the graph if they share:
a face if connectivityDimension = 2
an edge if connectivityDimension = 1
a vertex if connectivityDimension = 0
(if connectivityDimension is initialized to None, it will be set to dimensionality - 1)
- Parameters:
inMesh (UnstructuredMesh) – input mesh
dimensionality (int) – dimension of the elements considered to initialize the graph
connectivityDimension (int) – dimension of the connectivity
- Returns:
Element to element graph
- Return type:
networkx.Graph
- BasicTools.Containers.UnstructuredMeshGraphTools.ComputeMeshLaplacianEigenmaps(inMesh: UnstructuredMesh, dimensionality: int | None = None, nEigenmaps: int = 10, distFunc: Callable | None = None, normalizedLaplacian: bool = False)[source]
Computes the Laplacian engenmaps of a mesh
- Parameters:
mesh (UnstructuredMesh) – input mesh
dimensionality (int) – dimension of the elements considered to initalize the graph
nEigenmaps (int) – number of computed eigenmaps (less or equal to the number of nodes of mesh)
distFunc (func) – function applied to the length of the edges of the mesh, and attached of the corresponding edge of the graph of the mesh
normalizedLaplacian (bool) – if “True”, the normalized Laplacian matrix is taken
- Returns:
ndarray(nEigenmaps) – eigenvalues
ndarray(numberOfNodes, nEigenmaps) – Laplacian eigenmaps
- BasicTools.Containers.UnstructuredMeshGraphTools.ComputeNodalAveragedStretchMetric(originMesh: UnstructuredMesh, parametrizedMesh: UnstructuredMesh)[source]
Computes a nodal-averaged stretch metric between an inital triangle mesh and its parametrization, as defined in [1].
- Parameters:
originMesh (UnstructuredMesh) – Renumbered triangular mesh to parametrize
parametrizedMesh (int) – Parametrization of originMesh
- Returns:
texture stretch metric
- Return type:
np.ndarray, of size(nNodes)
Notes
mesh mush be a renumbered UnstructuredMesh of triangles (either in a 2D or 3D ambiant space), with a line boundary (no closed surface in 3D)
References
[1] S. Yoshizawa, A. Belyaev, H.-P. Seidel. A fast and simple stretch-minimizing mesh parameterization, 2004. URL, http://www2.riken.jp/brict/Yoshizawa/Papers/smi04ybs.pdf
- BasicTools.Containers.UnstructuredMeshGraphTools.ComputeNodeToNodeGraph(inMesh: UnstructuredMesh, dimensionality: int | None = None, distFunc: Callable | None = None)[source]
Creates a networkx graph from the node connectivity on an UnstructuredMesh through edges
- Parameters:
inMesh (UnstructuredMesh) – input mesh
dimensionality (int) – dimension of the elements considered to initialize the graph
distFunc (Callable) – function applied to the length of the edges of the mesh, and attached of the corresponding edge of the graph of the mesh
- Returns:
Element to element graph
- Return type:
networkx.Graph
- BasicTools.Containers.UnstructuredMeshGraphTools.ComputeStretchMetric(originMesh: UnstructuredMesh, parametrizedMesh: UnstructuredMesh)[source]
Computes the texture stretch metric between an inital triangle mesh and its parametrization, as defined in [1].
- Parameters:
originMesh (UnstructuredMesh) – Renumbered triangular mesh to parametrize
parametrizedMesh (int) – Parametrization of originMesh
- Returns:
np.ndarray, of size(nTriangles) – texture stretch metric
np.ndarray, of size(nTriangles) – areas of the triangles of the mesh
Notes
mesh mush be a renumbered UnstructuredMesh of triangles (either in a 2D or 3D ambiant space), with a line boundary (no closed surface in 3D)
References
[1] P.V. Sander, J. Snyder, S.J. Gortler, H. Hoppe. Texture mapping progressive meshes, 2001. URL: https://hhoppe.com/tmpm.pdf
- BasicTools.Containers.UnstructuredMeshGraphTools.FloaterMesh3DParametrization(inMesh: UnstructuredMesh, boundaryTag: str, inPlace: bool = True, fixedInteriorPoints=None, fixedBoundaryPoints=None)[source]
STILL LARGELY EXPERIMENTAL
Only for linear tetrahedral meshes
Computes a 3D mesh parametrization by cutting a 3D mesh using a plane and applying the 2D mesh parametrization to the boundaries of the half-meshes on disks, projecting the meshes on two half-spheres, and then morphing the interior points.
- Parameters:
inMesh (UnstructuredMesh) – Renumbered triangular mesh to parametrize
boundaryTag (str) – element tag for the surface triangles of half of the boundary of inMesh (whichever one)
inPlace (bool) – if “True”, inMesh is modified if “False”, inMesh is let unmodified, and a new mesh is produced
boundaryOrientation (str) – if “direct, the boundary of the parametrisation is constructed in the direct trigonometric order if “indirect”, the boundary of the parametrisation is constructed in the indirect trigonometric order
fixedInteriorPoints (dict) –
- with two keys: “skinIds1”, and “skinIds2”, and dict as value:
with one key, and corresponding value, a list: [ndarray(n), ndarray(n,2)], with n the number of interior points to be fixed; the first ndarray is the index of the considered interior point, the second ndarray is the corresponding prescribed positions if key is “mean”, the interior points are displaced by the mean of the prescribed positions if key is “value”, the interior points are displaced by the value of the prescribed positions
fixedBoundaryPoints (list) – list of lists: [ndarray(2), ndarray(2)], helping definining a point in inMesh; the first ndarray is the component of a point on the boundary, and the second array is the value of corresponding component. Tested for triangular meshes in the 3D space.
- Returns:
UnstructuredMesh – parametrization of the 3D mesh
ndarray(1) of ints – renumbering of the nodes of the returned parametrized mesh, with respect to inMesh
dict – containing 4 keys: “minEdge” and “maxEdge”, with values floats containing the minimal and maximal edged length of the parametrized mesh; and “paramMesh1” and “paramMesh2”, containing the 2D mesh parametrization (disks) of each half-boundary on inMesh
Notes
inMesh must have its skin partitionned in two, with boundaryTag being a element tag for surface triangles of one element of this partition
- BasicTools.Containers.UnstructuredMeshGraphTools.FloaterMesh3DParametrizationStarDomain(inMesh: UnstructuredMesh, boundaryTag: str, shape: Dict | None = None)[source]
Floater algorithm for 3D Mesh (Star Domain) Naive implementation only for linear tetrahedral meshes and 3D star domains
- Parameters:
inMesh (UnstructuredMesh) – input mesh of a 3D star domain
boundaryTag (str) – elementtag for the boundary of the mesh
shape (dict) – with key “type”:str, “center”:None or ndarray(3) of floats , “dimension”:ndarray(3) of floats if shape == “None”, the boundary of inMesh is mapped into a ball of radius 1, centered at the origin if “type”=”cuboid”, inMesh is mapped into a cuboid if “type”=”ellipsoid”, inMesh is mapped into a ellipsoid “center” defined the center of symmetry of the obtained parametrized mesh “dimension” defined the diameter of the obtained parametrized mesh along each direction
- Returns:
UnstructuredMesh – parametrization of mesh
ndarray(1) of ints – renumbering of the nodes of the returned parametrized mesh, with respect to inMesh
dict – containing two keys: “minEdge” and “maxEdge”, with values floats containing the minimal and maximal edged length of the parametrized mesh
Notes
mesh mush be a UnstructuredMesh of linear tetrahedrons, with an elementSet defining the boundary (the skin)
- BasicTools.Containers.UnstructuredMeshGraphTools.FloaterMeshParametrization(inMesh, nBoundary: int, outShape: str = 'circle', boundaryOrientation: str = 'direct', curvAbsBoundary: bool = True, fixedInteriorPoints: dict | None = None, fixedBoundaryPoints: list | None = None)[source]
STILL LARGELY EXPERIMENTAL
Only for linear triangular meshes
Computes the Mesh Parametrization algorithm [1] proposed by Floater, in the case of target parametrization fitted to the unit 2D circle (R=1) or square (L=1). Adapted for ML need: the outShape’s boundary is sampled following the curvilinear abscissa along the boundary on inMesh (only for outShape = “circle” for the moment)
- Parameters:
inMesh (UnstructuredMesh) – Renumbered triangular mesh to parametrize
nBoundary (int) – number nodes on the line boundary
outShape (str) – if “circle”, the boundary of inMesh is mapped into the unit circle if “square”, the boundary of inMesh is mapped into the unit square
boundaryOrientation (str) – if “direct, the boundary of the parametrisation is constructed in the direct trigonometric order if “indirect”, the boundary of the parametrisation is constructed in the indirect trigonometric order
curvAbsBoundary (bool) – only if fixedInteriorPoints = None if True, the point density on the boundary of outShape is the same as the point density on the boundary of inMesh if False, the point density on the boundary is uniform
fixedInteriorPoints (dict) – with one key, and corresponding value, a list: [ndarray(n), ndarray(n,2)], with n the number of interior points to be fixed; the first ndarray is the index of the considered interior point, the second ndarray is the corresponding prescribed positions if key is “mean”, the interior points are displaced by the mean of the prescribed positions if key is “value”, the interior points are displaced by the value of the prescribed positions
fixedBoundaryPoints (list) – list of lists: [ndarray(2), ndarray(2)], helping definining a point in inMesh; the first ndarray is the component of a point on the boundary, and the second array is the value of corresponding component. Tested for triangular meshes in the 3D space.
- Returns:
UnstructuredMesh – parametrization of mesh
dict – containing 3 keys: “minEdge”, “maxEdge” and “weights”, with values floats containing the minimal and maximal edged length of the parametrized mesh, and the weights (lambda) in the Floater algorithm
Notes
mesh mush be a renumbered UnstructuredMesh of triangles (either in a 2D or 3D ambiant space), with a line boundary (no closed surface in 3D). outShape = “circle” is more robust in the sense that is inMesh has a 2D square-like, for triangles may ended up flat with outShape = “square”
References
[1] M. S. Floater. Parametrization and smooth approximation of surface triangulations, 1997. URL: https://www.sciencedirect.com/science/article/abs/pii/S0167839696000313
- BasicTools.Containers.UnstructuredMeshGraphTools.InitializeGraphPointsFromMeshElements(inMesh: UnstructuredMesh, dimensionality=None)[source]
Initializes a networkx graph with nodes consistent with the number of elements of an UnstructuredMesh. This enables further edge addition compatible with a chosen global numbering of the elements of the UnstructuredMesh.
- Parameters:
inMesh (UnstructuredMesh) – input mesh
dimensionality (int) – dimension of the elements considered to initialize the graph
- Returns:
initialized graph
- Return type:
networkx.Graph
- BasicTools.Containers.UnstructuredMeshGraphTools.InitializeGraphPointsFromMeshPoints(inMesh: UnstructuredMesh)[source]
Initializes a networkx graph with nodes consistent with the number of nodes of an UnstructuredMesh. This enables further edge addition compatible with the connectivity of the elements of the UnstructuredMesh.
- Parameters:
inMesh (UnstructuredMesh) – input mesh
- Returns:
initialized graph
- Return type:
networkx.Graph
- BasicTools.Containers.UnstructuredMeshGraphTools.PartitionMesh(inmesh: UnstructuredMesh, nbSubdomains: int, driver: str = 'Metis')[source]
Generates a partition vector providing labels ordered for each element of the input mesh based on a third party graph partitioning solver. Current working options are: Metis
- Parameters:
inmesh (UnstructuredMesh) – the mesh to compute the partition on
nbSubdomains (int) – Number of subdomain, must be > 1
driver (str, optional) – library to use for the partition, for the moment only Metis is available, default “Metis”
- BasicTools.Containers.UnstructuredMeshGraphTools.RenumberMeshForParametrization(inMesh: UnstructuredMesh, inPlace=True, boundaryOrientation='direct', fixedBoundaryPoints=None, startingPointRankOnBoundary=None)[source]
Only for linear triangle meshes Renumber the node IDs, such that the points on the boundary are placed at the end of the numbering. Serves as a preliminary step for mesh parametrization.
- Parameters:
inMesh (UnstructuredMesh) – input triangular to be renumbered
inPlace (bool) – if “True”, inMesh is modified if “False”, inMesh is let unmodified, and a new mesh is produced
boundaryOrientation (str) – if “direct, the boundary of the parametrization is constructed in the direct trigonometric order if “indirect”, the boundary of the parametrization is constructed in the indirect trigonometric order
fixedBoundaryPoints (list) – list containing lists of two np.ndarray. Each 2-member list is used to identify one point on the boundary: the first array contains the specified components, and the second the
startingPointRankOnBoundary (int) – node id (in the complete mesh) of the point on the boundary where the mapping starts
- Returns:
UnstructuredMesh – renumbered mesh
ndarray(1) of ints – renumbering of the nodes of the returned renumbered mesh, with respect to inMesh
int – number of node of the boundary of inMesh