siibra.features.tabular.cortical_profile

Module Contents

Classes

CorticalProfile

Represents a 1-dimensional profile of measurements along cortical depth,

class siibra.features.tabular.cortical_profile.CorticalProfile(description: str, modality: str, anchor: siibra.features.anchor.AnatomicalAnchor, depths: list | numpy.ndarray = None, values: list | numpy.ndarray = None, unit: str = None, boundary_positions: Dict[Tuple[int, int], float] = None, datasets: list = [], id: str = None)

Represents a 1-dimensional profile of measurements along cortical depth, measured at relative depths between 0 representing the pial surface, and 1 corresponding to the gray/white matter boundary.

Mandatory attributes are the list of depth coordinates and the list of corresponding measurement values, which have to be of equal length, as well as a unit and description of the measurements.

Optionally, the depth coordinates of layer boundaries can be specified.

Most attributes are modelled as properties, so dervide classes are able to implement lazy loading instead of direct initialiation.

property boundaries_mapped: bool

property boundary_positions: Dict[Tuple[int, int], float]

property data

Return a pandas Series representing the profile.

property name

Returns a short human-readable name of this feature.

property unit: str

Optionally overridden in derived classes.

BOUNDARIES

LAYERS

assign_layer(depth: float)

Compute the cortical layer for a given depth from the layer boundary positions. If no positions are available for this profile, return None.

plot(*args, backend='matplotlib', **kwargs)

Plot the profile.

Parameters:

• backend (str) – “matplotlib”, “plotly”, or others supported by pandas DataFrame plotting backend.

• **kwargs – Keyword arguments are passed on to the plot command. ‘layercolor’ can be used to specify a color for cortical layer shading.