mne.viz.LayeredMesh

class mne.viz.LayeredMesh(renderer, vertices, triangles, normals)

A mesh with support for layered RGBA overlays and optional smoothing.

This class manages a single brain-surface mesh and composites multiple named overlays (e.g., curvature, data, labels) on top of each other using alpha blending. It is the object stored in Brain.layered_meshes.

Warning

This class is not meant to be instantiated directly, and the initialization API could change at any time! Use mne.viz.Brain.add_data() to create instances.

Parameters:

rendererinstance of _Renderer

The renderer used to create the underlying mesh polydata.

verticesarray, shape (n_vertices, 3)

Vertex coordinates in metres.

trianglesarray, shape (n_triangles, 3)

Triangle indices into vertices.

normalsarray, shape (n_vertices, 3)

Vertex normals.

Attributes:

smooth_matscipy.sparse.csr_array or None

Optional spatial smoother / upsampler applied to scalar data before rendering. When set (e.g., by set_data_smoothing()), every call to update_overlay() will multiply the incoming scalars by this matrix before storing them. Shape must be (n_surface_vertices, n_source_vertices).

Methods

add_overlay(scalars, colormap, rng, opacity, ...)	Add a named overlay to the mesh.
remove_overlay(names)	Remove one or more overlays by name.
update([colors])	Recompose all overlays and refresh the mesh texture.
update_geometry(vertices, normals[, triangles])	Update the mesh's vertex positions and normals in place.
update_overlay(name[, scalars, colormap, ...])	Update an existing overlay in-place.

Notes

New in v1.13.

add_overlay(scalars, colormap, rng, opacity, name, smooth=False)

Add a named overlay to the mesh.

Parameters:

scalarsarray, shape (n_vertices,)

Scalar values to display. If smooth=True and smooth_mat is set, shape must be (n_src_vertices,).

colormaparray, shape (n_colors, 4)

RGBA colormap table (values in [0, 255]).

rngarray_like, shape (2,)

[min, max] range for colormap mapping.

opacityfloat | None

Overlay opacity in [0, 1]. None keeps the existing value.

namestr

Unique key identifying this overlay.

smoothbool

If True and smooth_mat is set, multiply scalars by smooth_mat before rendering. Use True only for source-space data; surface-space overlays (curvature, labels, annotations) should use the default False.

remove_overlay(names)

Remove one or more overlays by name.

Parameters:

namesstr | list of str

Name(s) of the overlay(s) to remove.

update(colors=None)

Recompose all overlays and refresh the mesh texture.

Parameters:

colorsarray_like of shape (n_triangles, 4) | None

Pre-composited RGBA colors to blend over the cached layer stack. If None, all overlays are recomposed from scratch.

Examples using update:

Plotting with mne.viz.Brain

Plotting with mne.viz.Brain

update_geometry(vertices, normals, triangles=None)

Update the mesh’s vertex positions and normals in place.

Parameters:

verticesarray, shape (n_vertices, 3)

New vertex coordinates. Must match the existing vertex count.

normalsarray, shape (n_vertices, 3)

New vertex normals.

trianglesarray, shape (n_triangles, 3) | None

New triangulation. Only needed when the new geometry is not just a displacement of the old one, e.g. a flat patch of the cortex, whose triangles outside the patch are dropped. The vertex count must stay the same either way, so the overlays keep their scalars.

New in v1.13.

update_overlay(name, scalars=None, colormap=None, opacity=None, rng=None, update=True)

Update an existing overlay in-place.

Parameters:

namestr

Key of the overlay to update (must already exist).

scalarsarray, shape (n_vertices,) | None

New scalar values. If None, scalars are unchanged. If smooth_mat is set, smoothing is applied automatically (matching the behaviour of the original add_data() call that created the overlay).

colormaparray, shape (n_colors, 4) | None

New RGBA colormap table. If None, colormap is unchanged.

opacityfloat | None

New opacity in [0, 1]. If None, opacity is unchanged.

rngarray_like, shape (2,) | None

New [min, max] colormap range. If None, range is unchanged.

updatebool

If True (default), recompose overlays and refresh the mesh immediately. Pass False to stage the change without triggering a recompose; the caller is then responsible for calling update() once all overlays have been staged.

Examples using update_overlay:

Plotting with mne.viz.Brain

Plotting with mne.viz.Brain

Examples using mne.viz.LayeredMesh

Plotting with mne.viz.Brain

Plotting with mne.viz.Brain