Geometry

Functions for parsing geometry data

yass.geometry.find_channel_neighbors(geom, radius)

Compute a neighbors matrix by using a radius

Parameters:

geom: np.array

Array with the cartesian coordinates for the channels

radius: float

Maximum radius for the channels to be considered neighbors

Returns:

numpy.ndarray (n_channels, n_channels)

Symmetric boolean matrix with the i, j as True if the ith and jth channels are considered neighbors

yass.geometry.make_channel_groups(n_channels, neighbors, geom)

[DESCRIPTION]

Parameters:

n_channels: int

Number of channels

neighbors: numpy.ndarray

Neighbors matrix

geom: numpy.ndarray

geometry matrix

Returns:

list

List of channel groups based on [?]

yass.geometry.make_channel_index(neighbors, channel_geometry, steps=1)

Compute an array whose whose ith row contains the ordered (by distance) neighbors for the ith channel

yass.geometry.n_steps_neigh_channels(neighbors_matrix, steps)

Compute a neighbors matrix by considering neighbors of neighbors

Parameters:

neighbors_matrix: numpy.ndarray

Neighbors matrix

steps: int

Number of steps to still consider channels as neighbors

Returns:

numpy.ndarray (n_channels, n_channels)

Symmetric boolean matrix with the i, j as True if the ith and jth channels are considered neighbors

yass.geometry.order_channels_by_distance(reference, channels, geom)

Order channels by distance using certain channel as reference

Parameters:

reference: int

Reference channel

channels: np.ndarray

Channels to order

geom

Geometry matrix

Returns:

numpy.ndarray

1D array with the channels ordered by distance using the reference channels

numpy.ndarray

1D array with the indexes for the ordered channels

yass.geometry.parse(path, n_channels)

Parse a geometry txt (one x, y pair per line, separated by spaces) or a npy file with shape (n_channels, 2), where every row contains a x, y pair

path: str

Path to geometry file

n_channels: int

Number of channels

Returns:

numpy.ndarray

2-dimensional numpy array where each row contains the x, y coordinates for a channel

Examples

from yass import geometry

geom = geometry.parse(‘path/to/geom.npy’, n_channels=500) geom = geometry.parse(‘path/to/geom.txt’, n_channels=500)