cedalion.vis.anatomy.brain_and_scalp

Functions

plot_brain_and_scalp(brain_mesh, scalp_mesh, ...)

Plots a 3D visualization of brain and scalp meshes.

plot_brain_in_axes(ts, geo3d, metric, ...[, ...])

Using pyvista render a brain, colored by a metric, and display it in MPL axes.
cedalion.vis.anatomy.brain_and_scalp.plot_brain_and_scalp(
brain_mesh,
scalp_mesh,
geo3d,
timeseries,
poly_lines=[],
brain_scalars=None,
plotter=None,
)[source]

Plots a 3D visualization of brain and scalp meshes.

Parameters:

  • brain_mesh (TrimeshSurface) – The brain mesh as a TrimeshSurface object.

  • scalp_mesh (TrimeshSurface) – The scalp mesh as a TrimeshSurface object.

  • geo3d (xarray.Dataset) – Dataset containing 3-dimentional point centers.

  • timeseries – Time series data array.

  • poly_lines – List of lists of points to be plotted as polylines.

  • brain_scalars – Scalars to be used for coloring the brain mesh.

  • plotter (pv.Plotter, optional) – An existing PyVista plotter instance to use for plotting. If None, a new PyVista plotter instance is created. Default: None.

Initial Contributors:
cedalion.vis.anatomy.brain_and_scalp.plot_brain_in_axes(
ts: Annotated[DataArray, DataArraySchema(dims='time', coords='time', 'time', 'samples')],
geo3d: Annotated[DataArray, DataArraySchema(dims='label', coords='label', 'label', 'type')],
metric: DataArray | _Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes],
brain_surface: TrimeshSurface,
ax: Axes,
title: str | None = None,
vmin: float | None = None,
vmax: float | None = None,
cmap: str | Colormap = 'RdBu_r',
bad_color: tuple[float, float, float] | str | tuple[float, float, float, float] | tuple[tuple[float, float, float] | str, float] | tuple[tuple[float, float, float, float], float] = [0.7, 0.7, 0.7],
cb_label: str = '',
camera_pos: _Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes] | None = None,
)[source]

Using pyvista render a brain, colored by a metric, and display it in MPL axes.