Data (ome_zarr.data)

Functions for generating synthetic data.

ome_zarr.data.astronaut() → tuple[list, list]

Sample data from skimage.

Returns:

• pyramids – List of pyramid arrays.

• labels – List of labels.

ome_zarr.data.coins() → tuple[list, list]

Sample data from skimage.

Returns:

• pyramids – List of pyramid arrays.

• labels – List of labels.

ome_zarr.data.create_zarr(zarr_directory: str, method: ~collections.abc.Callable[[...], tuple[list, list]] = <function coins>, label_name: str = 'coins', fmt: ~ome_zarr.format.Format = FormatV05, chunks: tuple | list | None = None) → Group

Generate a synthetic image pyramid with labels.

ome_zarr.data.make_circle(h: int, w: int, value: int, target: ndarray) → None

Apply a 2D circular mask to the given array.

>>> import numpy as np
>>> example = np.zeros((8, 8))
>>> make_circle(8, 8, 1, example)
>>> print(example)
[[0. 0. 0. 0. 0. 0. 0. 0.]
 [0. 0. 1. 1. 1. 1. 1. 0.]
 [0. 1. 1. 1. 1. 1. 1. 1.]
 [0. 1. 1. 1. 1. 1. 1. 1.]
 [0. 1. 1. 1. 1. 1. 1. 1.]
 [0. 1. 1. 1. 1. 1. 1. 1.]
 [0. 1. 1. 1. 1. 1. 1. 1.]
 [0. 0. 1. 1. 1. 1. 1. 0.]]

ome_zarr.data.rgb_to_5d(pixels: ndarray) → list

Convert an RGB image into 5D image (t, c, z, y, x).