Mesh data

A large part of Nanomesh deals with with generating and manipulating 2D and 3D meshes. To store the data, Nanomesh uses MeshContainer, which is a somewhat low-level, generic container for mesh data. It can store different types of cells and associated data. It is used to read/write data via meshio.

To deal with mesh data more directly, use a Mesh. Instantiating Mesh will create the appropriate subtype, LineMesh, TriangleMesh or TetraMesh. These contain dedicated methods for working with a specific type of mesh and plotting them.

In addition, each can be extracted from MeshContainer.

Classes

`nanomesh.MeshContainer`(points, cells[, ...])	Low-level container for storing mesh data.
`nanomesh.Mesh`(points, cells, args, *kwargs)	Generic mesh class.
`nanomesh.LineMesh`(points, cells, args, *kwargs)	Data class for line meshes.
`nanomesh.TriangleMesh`(points, cells, *args, ...)	Data class for triangle meshes.
`nanomesh.TetraMesh`(points, cells, *args, ...)	Data class for tetrahedral meshes.

Reference

class nanomesh.MeshContainer(points: ArrayLike, cells: dict[str, ArrayLike] | list[tuple[str, ArrayLike] | CellBlock], point_data: dict[str, ArrayLike] | None = None, cell_data: dict[str, list[ArrayLike]] | None = None, field_data=None, point_sets: dict[str, ArrayLike] | None = None, cell_sets: dict[str, list[ArrayLike]] | None = None, gmsh_periodic=None, info=None)[source]

Bases: Mesh, PruneZ0Mixin

Low-level container for storing mesh data.

Can contain multiple cell types sharing a set of points. It can store different types of cells and associated data. MeshContainer is based on meshio.Mesh (https://github.com/nschloe/meshio).

Parameters

points (numpy.ndarray) – Array storing the mesh points (e.g. vertices)
cells (list) – List of cell arrays
point_data (todo) –
cell_data (todo) –
field_data (dict) – Dictionary mapping field names to cell data values.
point_sets (todo) –
cell_sets (todo) –
gmsh_periodic (todo) –
info (todo) –

Attributes:

`cell_data_dict`
`cell_sets_dict`
`cell_types`	Return cell types in order.
`cells_dict`
`field_to_number`	Mapping from fields to numbers, proxy to `MeshContainer.field_data`.
`number_to_field`	Mapping from numbers to fields, proxy to `MeshContainer.field_data`.

Methods:

`cell_data_to_sets`(key)	Convert point_data to cell_sets.
`cell_sets_to_data`([data_name])
`copy`()
`from_mesh`(mesh)	Convert from `nanomesh.mesh.Mesh` to `MeshContainer`.
`from_triangle_dict`(triangle_dict)	Return instance of `MeshContainer` from triangle results dict.
`get`([cell_type])	Extract mesh with points/cells of cell_type.
`get_all_cell_data`([cell_type])	Get all cell data for given cell_type.
`get_cell_data`(name, cell_type)
`get_cells_type`(cell_type)
`get_default_type`()	Try to return highest dimension type.
`plot`([cell_type])	Plot data.
`plot_itk`([cell_type])	Plot data using `itk`.
`plot_mpl`([cell_type])	Plot data using `matplotlib`.
`plot_points`(**kwargs)	Plot points data using :mod:`matplotlib.
`plot_pyvista`([cell_type])	Plot data using `pyvista`.
`point_data_to_sets`(key)	Convert point_data to point_sets.
`point_sets_to_data`([join_char])
`prune_z_0`()	Drop third dimension (z) coordinates if present and all values are equal to 0 (within tolerance).
`read`(args, *kwargs)	Wrapper for `meshio.read()`.
`set_cell_data`(cell_type, key, value)	Set the cell data to the given value.
`set_field_data`(cell_type, field_data)	Update the values in `MeshContainer.field_data`.
`write`(filename[, file_format])	Thin wrapper of meshio.write to avoid altering class.

property cell_data_dict

cell_data_to_sets(key: str): Convert point_data to cell_sets.

property cell_sets_dict

cell_sets_to_data(data_name: str | None = None)

property cell_types: Return cell types in order.

property cells_dict

copy()

property field_to_number: Mapping from fields to numbers, proxy to MeshContainer.field_data.

classmethod from_mesh(mesh: Mesh)[source]

Convert from nanomesh.mesh.Mesh to MeshContainer.

Parameters: mesh (Mesh) – Input mesh, must be a subclass of nanomesh.mesh.Mesh.
Return type: MeshContainer

classmethod from_triangle_dict(triangle_dict: dict)[source]

Return instance of MeshContainer from triangle results dict.

Parameters: triangle_dict (dict) – Triangle triangulate output dictionary.
Returns: mesh
Return type: MeshContainer

get(cell_type: Optional[str] = None)[source]

Extract mesh with points/cells of cell_type.

Parameters: cell_type (str, optional) – Element type, such as line, triangle, tetra, etc.
Returns: Mesh of the given type
Return type: Mesh

get_all_cell_data(cell_type: Optional[str] = None) → dict[source]

Get all cell data for given cell_type.

Parameters: cell_type (str, optional) – Element type, such as line, triangle, tetra, etc.
Returns: data_dict – Dictionary with cell data
Return type: dict

get_cell_data(name: str, cell_type: str)

get_cells_type(cell_type: str)

get_default_type() → str[source]

Try to return highest dimension type.

Default to first type MeshContainer.cells_dict.

Returns: cell_type
Return type: str

property number_to_field: Mapping from numbers to fields, proxy to MeshContainer.field_data.

plot(cell_type: Optional[str] = None, **kwargs)[source]

Plot data.

Parameters

cell_type (str, optional) – Cell type to plot.
**kwargs – These parameters are passed to plotting method.

plot_itk(cell_type: Optional[str] = None, **kwargs)[source]

Plot data using itk.

Parameters

cell_type (str, optional) – Cell type to plot.
**kwargs – These parameters are passed to plotting method.

plot_mpl(cell_type: Optional[str] = None, **kwargs)[source]

Plot data using matplotlib.

Parameters

cell_type (str, optional) – Cell type to plot.
**kwargs – These parameters are passed to plotting method.

plot_points(**kwargs)[source]

Plot points data using :mod:`matplotlib.

Parameters: **kwargs – These parameters are passed to the plotting method.

plot_pyvista(cell_type: Optional[str] = None, **kwargs)[source]

Plot data using pyvista.

Parameters

cell_type (str, optional) – Cell type to plot.
**kwargs – These parameters are passed to plotting method.

point_data_to_sets(key: str): Convert point_data to point_sets.

point_sets_to_data(join_char: str = '-') → None

prune_z_0()

Drop third dimension (z) coordinates if present and all values are equal to 0 (within tolerance).

For compatibility, sometimes a column with zeroes is added, for example when exporting to gmsh2.2 format. This method drops that column.

classmethod read(*args, **kwargs) → MeshContainer[source]

Wrapper for meshio.read().

For gmsh:

remaps gmsh:physical -> physical
remaps gmsh:geometrical -> geometrical

Parameters

*args – These parameters passed to reader
**kwargs – These parameters are passed to the reader

Return type

MeshContainer

set_cell_data(cell_type: str, key: str, value: ndarray)[source]

Set the cell data to the given value.

Updates MeshContainer.cell_data.

Parameters

cell_type (str) – Cell type, must be in MeshContainer.cell_types
key (str) – The key of the value in MeshContainer.cell_data
value (numpy.ndarray) – Array of values to set

set_field_data(cell_type: str, field_data: Dict[int, str])[source]

Update the values in MeshContainer.field_data.

Parameters

cell_type (str) – Cell type to update the values for.
field_data (dict) – Dictionary with key-to-number mapping, i.e. field_data={0: ‘green’, 1: ‘blue’, 2: ‘red’} maps 0 to green, etc.

write(filename, file_format: Optional[str] = None, **kwargs)[source]

Thin wrapper of meshio.write to avoid altering class.

For gmsh: - remaps physical -> gmsh:physical - remaps geometrical -> gmsh:geometrical

Parameters

filename (str) – File to write to.
file_format (str, optional) – Specify file format. By default, this is guessed from the extension.
**kwargs – These parameters are passed to meshio.write().

class nanomesh.Mesh(points: ndarray, cells: ndarray, *args, **kwargs)[source]

Bases: object

Generic mesh class.

Depending on the number of dimensions of the cells, the appropriate subclass will be chosen if possible.

Parameters

points ((m, n) numpy.ndarray[float]) – Array with points.
cells ((i, j) numpy.ndarray[int]) – Index array describing the cells of the mesh.
fields (Dict[str, int]:) – Mapping from field names to labels
region_markers (RegionMarkerList, optional) – List of region markers used for assigning labels to regions. Defaults to an empty list.
**cell_data – Additional cell data. Argument must be a 1D numpy array matching the number of cells defined by i.

Attributes:

`cell_centers`	Return centers of cells (mean of corner points).
`cell_type`
`dimensions`	Return number of dimensions for point data.
`labels`	Shortcut for cell labels.
`number_to_field`	Mapping from numbers to fields, proxy to `{classname}.field_to_number`.
`zero_labels`	Return zero labels as fallback.

Methods:

`crop`([xmin, xmax, ymin, ymax, zmin, zmax, ...])	Crop mesh to given region.
`from_meshio`(mesh)	Return `{classname}` from meshio object.
`get_cell_data`(key[, default_value])	Get cell data with optional default value.
`plot`(**kwargs)
`plot_itk`(**kwargs)	Wrapper for `pyvista.plot_itk()`.
`plot_mpl`(**kwargs)
`plot_pyvista`(**kwargs)	Wrapper for `pyvista.plot()`.
`read`(filename, **kwargs)	Simple wrapper around `meshio.read()`.
`remove_cells`(*, label[, key])	Remove cells with cell data matching given label.
`remove_loose_points`()	Remove points that do not belong to any cells.
`reverse_cell_order`()	Reverse order of cells and cell data.
`to_meshio`()	Return instance of `meshio.Mesh()`.
`to_pyvista_unstructured_grid`()	Return instance of `pyvista.UnstructuredGrid`.
`write`(args, *kwargs)	Simple wrapper around `meshio.write()`.

property cell_centers: Return centers of cells (mean of corner points).

cell_type: str = 'generic'

crop(xmin: float = -inf, xmax: float = inf, ymin: float = -inf, ymax: float = inf, zmin: float = -inf, zmax: float = inf, include_partial: bool = False)[source]

Crop mesh to given region.

Parameters

xmin (float, optional) – Minimum x value.
xmax (float, optional) – Maximum x value.
ymin (float, optional) – Minimum y value.
ymax (float, optional) – Maximum y value.
zmin (float, optional) – Minimum z value (3D point data only).
zmax (float, optional) – Maximum z value (3D point data only).
include_partial (bool, optional) – If True, include cells that are partially inside the given crop region, i.e. one of its points is inside.

Returns

cropped_mesh – Cropped mesh

Return type

{classname}

property dimensions: int: Return number of dimensions for point data.

classmethod from_meshio(mesh: meshio.Mesh)[source]: Return {classname} from meshio object.

get_cell_data(key: str, default_value: float = 0) → ndarray[source]

Get cell data with optional default value.

Parameters

key (str) – Key of the cell data to retrieve.
default_value (float, optional) – Optional default value (if cell data does not exist)

Return type

numpy.ndarray

property labels: ndarray: Shortcut for cell labels.

property number_to_field: Mapping from numbers to fields, proxy to {classname}.field_to_number.

plot(**kwargs)[source]

plot_itk(**kwargs)[source]

Wrapper for pyvista.plot_itk().

Parameters: **kwargs – These parameters are passed to pyvista.plot_itk()

plot_mpl(**kwargs)[source]

plot_pyvista(**kwargs)[source]

Wrapper for pyvista.plot().

Parameters: **kwargs – These parameters are passed to pyvista.plot()

classmethod read(filename, **kwargs)[source]: Simple wrapper around meshio.read().

remove_cells(*, label: int, key: Optional[str] = None)[source]

Remove cells with cell data matching given label.

Parameters

label (int) – All cells with this label will be removed.
key (str, optional) – The key of the cell data to use. Uses Mesh.default_key if None.

remove_loose_points()[source]: Remove points that do not belong to any cells.

reverse_cell_order()[source]

Reverse order of cells and cell data.

Updates {classname}.cell_data.

to_meshio() → meshio.Mesh[source]: Return instance of meshio.Mesh().

to_pyvista_unstructured_grid() → pv.PolyData[source]

Return instance of pyvista.UnstructuredGrid.

References

https://docs.pyvista.org/core/point-grids.html#pv-unstructured-grid-class-methods

write(*args, **kwargs)[source]: Simple wrapper around meshio.write().

property zero_labels: ndarray: Return zero labels as fallback.

class nanomesh.LineMesh(points: ndarray, cells: ndarray, *args, **kwargs)[source]

Bases: Mesh

Data class for line meshes.

Depending on the number of dimensions of the cells, the appropriate subclass will be chosen if possible.

Parameters

points ((m, 2 or 3) numpy.ndarray[float]) – Array with points.
cells ((i, 2) numpy.ndarray[int]) – Index array describing the cells of the mesh.
fields (Dict[str, int]:) – Mapping from field names to labels
region_markers (RegionMarkerList, optional) – List of region markers used for assigning labels to regions. Defaults to an empty list.
**cell_data – Additional cell data. Argument must be a 1D numpy array matching the number of cells defined by i.

Attributes:

`cell_centers`	Return centers of cells (mean of corner points).
`cell_type`
`dimensions`	Return number of dimensions for point data.
`labels`	Shortcut for cell labels.
`number_to_field`	Mapping from numbers to fields, proxy to `LineMesh.field_to_number`.
`zero_labels`	Return zero labels as fallback.

Methods:

`crop`([xmin, xmax, ymin, ymax, zmin, zmax, ...])	Crop mesh to given region.
`from_meshio`()	Return `LineMesh` from meshio object.
`get_cell_data`(key[, default_value])	Get cell data with optional default value.
`label_boundaries`([left, right, top, bottom, key])	Labels the boundaries of the mesh with the given value.
`plot`(args, *kwargs)	Simple line mesh plot using `matplotlib`.
`plot_itk`(**kwargs)	Wrapper for `pyvista.plot_itk()`.
`plot_mpl`(args, *kwargs)	Simple line mesh plot using `matplotlib`.
`plot_pyvista`(**kwargs)	Wrapper for `pyvista.plot()`.
`read`(filename, **kwargs)	Simple wrapper around `meshio.read()`.
`remove_cells`(*, label[, key])	Remove cells with cell data matching given label.
`remove_loose_points`()	Remove points that do not belong to any cells.
`reverse_cell_order`()	Reverse order of cells and cell data.
`to_meshio`()	Return instance of `meshio.Mesh()`.
`to_pyvista_unstructured_grid`()	Return instance of `pyvista.UnstructuredGrid`.
`triangulate`([opts])
`write`(args, *kwargs)	Simple wrapper around `meshio.write()`.

property cell_centers: Return centers of cells (mean of corner points).

cell_type: str = 'line'

crop(xmin: float = -inf, xmax: float = inf, ymin: float = -inf, ymax: float = inf, zmin: float = -inf, zmax: float = inf, include_partial: bool = False)

Crop mesh to given region.

Parameters

xmin (float, optional) – Minimum x value.
xmax (float, optional) – Maximum x value.
ymin (float, optional) – Minimum y value.
ymax (float, optional) – Maximum y value.
zmin (float, optional) – Minimum z value (3D point data only).
zmax (float, optional) – Maximum z value (3D point data only).
include_partial (bool, optional) – If True, include cells that are partially inside the given crop region, i.e. one of its points is inside.

Returns

cropped_mesh – Cropped mesh

Return type

LineMesh

property dimensions: int: Return number of dimensions for point data.

classmethod from_meshio(): Return LineMesh from meshio object.

get_cell_data(key: str, default_value: float = 0) → ndarray

Get cell data with optional default value.

Parameters

key (str) – Key of the cell data to retrieve.
default_value (float, optional) – Optional default value (if cell data does not exist)

Return type

numpy.ndarray

label_boundaries(left: Optional[int | str] = None, right: Optional[int | str] = None, top: Optional[int | str] = None, bottom: Optional[int | str] = None, key: str = None)[source]

Labels the boundaries of the mesh with the given value.

Parameters

left (int | str, optional) – Labels left boundary segments with the given value. If a string is passed, the LineMesh.fields attribute is updated with the field / value pair.
right (int | str, optional) – Same as above.
top (int | str, optional) – Same as above.
bottom (int | str, optional) – Same as above.
key (str, optional) – Key of the LineMesh.cell_data dictionary to update. Defaults to LineMesh.default_key.

property labels: ndarray: Shortcut for cell labels.

property number_to_field: Mapping from numbers to fields, proxy to LineMesh.field_to_number.

plot(*args, **kwargs)[source]

Simple line mesh plot using matplotlib.

Shortcut for plotting.linemeshplot().

Parameters

*args – Arguments passed to plotting.linemeshplot()
**kwargs – Keyword arguments passed to plotting.linemeshplot()

Return type

plt.Axes

plot_itk(**kwargs)

Wrapper for pyvista.plot_itk().

Parameters: **kwargs – These parameters are passed to pyvista.plot_itk()

plot_mpl(*args, **kwargs) → Axes[source]

Simple line mesh plot using matplotlib.

Shortcut for plotting.linemeshplot().

Parameters

*args – Arguments passed to plotting.linemeshplot()
**kwargs – Keyword arguments passed to plotting.linemeshplot()

Return type

plt.Axes

plot_pyvista(**kwargs)

Wrapper for pyvista.plot().

Parameters: **kwargs – These parameters are passed to pyvista.plot()

classmethod read(filename, **kwargs): Simple wrapper around meshio.read().

remove_cells(*, label: int, key: Optional[str] = None)

Remove cells with cell data matching given label.

Parameters

label (int) – All cells with this label will be removed.
key (str, optional) – The key of the cell data to use. Uses Mesh.default_key if None.

remove_loose_points(): Remove points that do not belong to any cells.

reverse_cell_order()

Reverse order of cells and cell data.

Updates LineMesh.cell_data.

to_meshio() → meshio.Mesh: Return instance of meshio.Mesh().

to_pyvista_unstructured_grid() → pv.PolyData

Return instance of pyvista.UnstructuredGrid.

References

https://docs.pyvista.org/core/point-grids.html#pv-unstructured-grid-class-methods

triangulate(opts: str = 'pq30Aa100', **kwargs) → MeshContainer[source]

write(*args, **kwargs): Simple wrapper around meshio.write().

property zero_labels: ndarray: Return zero labels as fallback.

class nanomesh.TriangleMesh(points: ndarray, cells: ndarray, *args, **kwargs)[source]

Bases: Mesh, PruneZ0Mixin

Data class for triangle meshes.

Depending on the number of dimensions of the cells, the appropriate subclass will be chosen if possible.

Parameters

points ((m, 2 or 3) numpy.ndarray[float]) – Array with points.
cells ((i, 3) numpy.ndarray[int]) – Index array describing the cells of the mesh.
fields (Dict[str, int]:) – Mapping from field names to labels
region_markers (RegionMarkerList, optional) – List of region markers used for assigning labels to regions. Defaults to an empty list.
**cell_data – Additional cell data. Argument must be a 1D numpy array matching the number of cells defined by i.

Attributes:

`cell_centers`	Return centers of cells (mean of corner points).
`cell_type`
`dimensions`	Return number of dimensions for point data.
`labels`	Shortcut for cell labels.
`number_to_field`	Mapping from numbers to fields, proxy to `TriangleMesh.field_to_number`.
`zero_labels`	Return zero labels as fallback.

Methods:

`crop`([xmin, xmax, ymin, ymax, zmin, zmax, ...])	Crop mesh to given region.
`from_meshio`()	Return `TriangleMesh` from meshio object.
`from_open3d`(mesh)	Return instance of `TriangleMesh` from open3d.
`from_scipy`(mesh)	Return instance of `TriangleMesh` from `scipy.spatial.Delaunay` object.
`from_triangle_dict`(dct)	Return instance of `TriangleMesh` from triangle results dict.
`from_trimesh`(mesh)	Return instance of `TriangleMesh` from `trimesh`.
`get_cell_data`(key[, default_value])	Get cell data with optional default value.
`optimize`(*[, method, tol, max_num_steps])	Optimize mesh using `optimesh`.
`plot`(**kwargs)	Shortcut for `TriangleMesh.plot_mpl()` or `TriangleMesh.plot_itk()` depending on dimensions.
`plot_itk`(**kwargs)	Wrapper for `pyvista.plot_itk()`.
`plot_mpl`(args, *kwargs)	Simple triangle mesh plot using :mod:`matplotlib`.
`plot_pyvista`(**kwargs)	Wrapper for `pyvista.plot()`.
`prune_z_0`()	Drop third dimension (z) coordinates if present and all values are equal to 0 (within tolerance).
`read`(filename, **kwargs)	Simple wrapper around `meshio.read()`.
`remove_cells`(*, label[, key])	Remove cells with cell data matching given label.
`remove_loose_points`()	Remove points that do not belong to any cells.
`reverse_cell_order`()	Reverse order of cells and cell data.
`tetrahedralize`(**kwargs)	Tetrahedralize mesh using `tetrahedralize()`.
`to_meshio`()	Return instance of `meshio.Mesh()`.
`to_open3d`()	Return instance of `open3d.geometry.TriangleMesh`.
`to_polydata`()	Return instance of `pyvista.Polydata`.
`to_pyvista_unstructured_grid`()	Return instance of `pyvista.UnstructuredGrid`.
`to_trimesh`()	Return instance of `trimesh.Trimesh`.
`write`(args, *kwargs)	Simple wrapper around `meshio.write()`.

property cell_centers: Return centers of cells (mean of corner points).

cell_type: str = 'triangle'

crop(xmin: float = -inf, xmax: float = inf, ymin: float = -inf, ymax: float = inf, zmin: float = -inf, zmax: float = inf, include_partial: bool = False)

Crop mesh to given region.

Parameters

xmin (float, optional) – Minimum x value.
xmax (float, optional) – Maximum x value.
ymin (float, optional) – Minimum y value.
ymax (float, optional) – Maximum y value.
zmin (float, optional) – Minimum z value (3D point data only).
zmax (float, optional) – Maximum z value (3D point data only).
include_partial (bool, optional) – If True, include cells that are partially inside the given crop region, i.e. one of its points is inside.

Returns

cropped_mesh – Cropped mesh

Return type

TriangleMesh

property dimensions: int: Return number of dimensions for point data.

classmethod from_meshio(): Return TriangleMesh from meshio object.

classmethod from_open3d(mesh: open3d.geometry.TriangleMesh) → TriangleMesh[source]: Return instance of TriangleMesh from open3d.

classmethod from_scipy(mesh: scipy.spatial.qhull.Delaunay) → TriangleMesh[source]: Return instance of TriangleMesh from scipy.spatial.Delaunay object.

classmethod from_triangle_dict(dct: dict) → TriangleMesh[source]: Return instance of TriangleMesh from triangle results dict.

classmethod from_trimesh(mesh) → TriangleMesh[source]: Return instance of TriangleMesh from trimesh.

get_cell_data(key: str, default_value: float = 0) → ndarray

Get cell data with optional default value.

Parameters

key (str) – Key of the cell data to retrieve.
default_value (float, optional) – Optional default value (if cell data does not exist)

Return type

numpy.ndarray

property labels: ndarray: Shortcut for cell labels.

property number_to_field: Mapping from numbers to fields, proxy to TriangleMesh.field_to_number.

optimize(*, method='CVT (block-diagonal)', tol: float = 0.001, max_num_steps: int = 10, **kwargs) → TriangleMesh[source]

Optimize mesh using optimesh.

Parameters

method (str, optional) – Method name
tol (float, optional) – Tolerance
max_num_steps (int, optional) – Maximum number of optimization steps.
**kwargs – Arguments to pass to optimesh.optimize_points_cells()

Return type

TriangleMesh

plot(**kwargs)[source]: Shortcut for TriangleMesh.plot_mpl() or TriangleMesh.plot_itk() depending on dimensions.

plot_itk(**kwargs)

Wrapper for pyvista.plot_itk().

Parameters: **kwargs – These parameters are passed to pyvista.plot_itk()

plot_mpl(*args, **kwargs) → Axes[source]

Simple triangle mesh plot using :mod:matplotlib. See plotting.trianglemeshplot() for details.

Parameters

*args – Arguments passed to plotting.trianglemeshplot()
**kwargs – Keyword arguments passed to plotting.trianglemeshplot()

Return type

plt.Axes

plot_pyvista(**kwargs)

Wrapper for pyvista.plot().

Parameters: **kwargs – These parameters are passed to pyvista.plot()

prune_z_0()

Drop third dimension (z) coordinates if present and all values are equal to 0 (within tolerance).

For compatibility, sometimes a column with zeroes is added, for example when exporting to gmsh2.2 format. This method drops that column.

classmethod read(filename, **kwargs): Simple wrapper around meshio.read().

remove_cells(*, label: int, key: Optional[str] = None)

Remove cells with cell data matching given label.

Parameters

label (int) – All cells with this label will be removed.
key (str, optional) – The key of the cell data to use. Uses Mesh.default_key if None.

remove_loose_points(): Remove points that do not belong to any cells.

reverse_cell_order()

Reverse order of cells and cell data.

Updates TriangleMesh.cell_data.

tetrahedralize(**kwargs) → MeshContainer[source]

Tetrahedralize mesh using tetrahedralize().

Parameters

mesh (TriangleMesh) – Input contour mesh
opts (str, optional) –
Command-line options passed to tetgen.

More info: http://wias-berlin.de/software/tetgen/1.5/doc/manual/manual005.html

Some useful flags:
- -A: Assigns attributes to tetrahedra in different regions.
- -p: Tetrahedralizes a piecewise linear complex (PLC).
- -q: Refines mesh (to improve mesh quality).
- -a: Applies a maximum tetrahedron volume constraint.
Can be passed as a raw string, opts=’-pAq1.2’, or dict, `opts=dict(‘p’= True, ‘A’= True, ‘q’=1.2).
default_opts (dict, optional) – Dictionary with default options. These will be merged with opts.

Returns

Tetrahedralized mesh.

Return type

MeshContainer

to_meshio() → meshio.Mesh: Return instance of meshio.Mesh().

to_open3d() → open3d.geometry.TriangleMesh[source]: Return instance of open3d.geometry.TriangleMesh.

to_polydata() → pv.PolyData[source]: Return instance of pyvista.Polydata.

to_pyvista_unstructured_grid() → pv.PolyData

Return instance of pyvista.UnstructuredGrid.

References

https://docs.pyvista.org/core/point-grids.html#pv-unstructured-grid-class-methods

to_trimesh()[source]: Return instance of trimesh.Trimesh.

write(*args, **kwargs): Simple wrapper around meshio.write().

property zero_labels: ndarray: Return zero labels as fallback.

class nanomesh.TetraMesh(points: ndarray, cells: ndarray, *args, **kwargs)[source]

Bases: Mesh

Data class for tetrahedral meshes.

Depending on the number of dimensions of the cells, the appropriate subclass will be chosen if possible.

Parameters

points ((m, 3) numpy.ndarray[float]) – Array with points.
cells ((i, 4) numpy.ndarray[int]) – Index array describing the cells of the mesh.
fields (Dict[str, int]:) – Mapping from field names to labels
region_markers (RegionMarkerList, optional) – List of region markers used for assigning labels to regions. Defaults to an empty list.
**cell_data – Additional cell data. Argument must be a 1D numpy array matching the number of cells defined by i.

Attributes:

`cell_centers`	Return centers of cells (mean of corner points).
`cell_type`
`dimensions`	Return number of dimensions for point data.
`labels`	Shortcut for cell labels.
`number_to_field`	Mapping from numbers to fields, proxy to `TetraMesh.field_to_number`.
`zero_labels`	Return zero labels as fallback.

Methods:

`crop`([xmin, xmax, ymin, ymax, zmin, zmax, ...])	Crop mesh to given region.
`from_meshio`()	Return `TetraMesh` from meshio object.
`from_open3d`(mesh)	Return instance of `TetraMesh` from `open3d`.
`from_pyvista_unstructured_grid`(grid)	Return infance of `TetraMesh` from `pyvista.UnstructuredGrid`.
`get_cell_data`(key[, default_value])	Get cell data with optional default value.
`plot`(**kwargs)	Shortcut for `TetraMesh.plot_pyvista()`.
`plot_itk`(**kwargs)	Wrapper for `pyvista.plot_itk()`.
`plot_mpl`(**kwargs)
`plot_pyvista`(**kwargs)	Show grid using `pyvista`.
`plot_submesh`([index, along, invert, show, ...])	Show submesh using `pyvista`.
`read`(filename, **kwargs)	Simple wrapper around `meshio.read()`.
`remove_cells`(*, label[, key])	Remove cells with cell data matching given label.
`remove_loose_points`()	Remove points that do not belong to any cells.
`reverse_cell_order`()	Reverse order of cells and cell data.
`to_meshio`()	Return instance of `meshio.Mesh()`.
`to_open3d`()	Return instance of `open3d.geometry.TetraMesh`.
`to_pyvista_unstructured_grid`()	Return instance of `pyvista.UnstructuredGrid`.
`write`(args, *kwargs)	Simple wrapper around `meshio.write()`.

property cell_centers: Return centers of cells (mean of corner points).

cell_type: str = 'tetra'

crop(xmin: float = -inf, xmax: float = inf, ymin: float = -inf, ymax: float = inf, zmin: float = -inf, zmax: float = inf, include_partial: bool = False)

Crop mesh to given region.

Parameters

xmin (float, optional) – Minimum x value.
xmax (float, optional) – Maximum x value.
ymin (float, optional) – Minimum y value.
ymax (float, optional) – Maximum y value.
zmin (float, optional) – Minimum z value (3D point data only).
zmax (float, optional) – Maximum z value (3D point data only).
include_partial (bool, optional) – If True, include cells that are partially inside the given crop region, i.e. one of its points is inside.

Returns

cropped_mesh – Cropped mesh

Return type

TetraMesh

property dimensions: int: Return number of dimensions for point data.

classmethod from_meshio(): Return TetraMesh from meshio object.

classmethod from_open3d(mesh) → TetraMesh[source]: Return instance of TetraMesh from open3d.

classmethod from_pyvista_unstructured_grid(grid: pv.UnstructuredGrid)[source]: Return infance of TetraMesh from pyvista.UnstructuredGrid.

get_cell_data(key: str, default_value: float = 0) → ndarray

Get cell data with optional default value.

Parameters

key (str) – Key of the cell data to retrieve.
default_value (float, optional) – Optional default value (if cell data does not exist)

Return type

numpy.ndarray

property labels: ndarray: Shortcut for cell labels.

property number_to_field: Mapping from numbers to fields, proxy to TetraMesh.field_to_number.

plot(**kwargs)[source]: Shortcut for TetraMesh.plot_pyvista().

plot_itk(**kwargs)

Wrapper for pyvista.plot_itk().

Parameters: **kwargs – These parameters are passed to pyvista.plot_itk()

plot_mpl(**kwargs)

plot_pyvista(**kwargs)[source]

Show grid using pyvista.

Parameters: **kwargs – These parameters are first passed to pyvista.plot() and then to pyvista.Plotter().add_mesh().

plot_submesh(index: Optional[int] = None, along: str = 'x', invert: bool = False, show: bool = True, backend: Optional[str] = None, **kwargs)[source]

Show submesh using pyvista.

Parameters

index (int, optional) – Index of where to cut the mesh. Shows all tetrahedra with cell center < index. Picks the half-way point along the axis by default.
along (str, optional) – Direction along which to cut.
invert (bool, optional) – Invert the cutting operation, and show all tetrahedra with cell center > index.
show (bool, optional) – If true, show the plot
**kwargs – Keyword arguments passed to pyvista.Plotter.add_mesh().
plotter (pyvista.Plotter) – Return plotter instance.

classmethod read(filename, **kwargs): Simple wrapper around meshio.read().

remove_cells(*, label: int, key: Optional[str] = None)

Remove cells with cell data matching given label.

Parameters

label (int) – All cells with this label will be removed.
key (str, optional) – The key of the cell data to use. Uses Mesh.default_key if None.

remove_loose_points(): Remove points that do not belong to any cells.

reverse_cell_order()

Reverse order of cells and cell data.

Updates TetraMesh.cell_data.

to_meshio() → meshio.Mesh: Return instance of meshio.Mesh().

to_open3d()[source]: Return instance of open3d.geometry.TetraMesh.

to_pyvista_unstructured_grid() → pv.PolyData

Return instance of pyvista.UnstructuredGrid.

References

https://docs.pyvista.org/core/point-grids.html#pv-unstructured-grid-class-methods

write(*args, **kwargs): Simple wrapper around meshio.write().

property zero_labels: ndarray: Return zero labels as fallback.