nabu.io.ome_zarr

source module nabu.io.ome_zarr

Classes

• OmeZarrWriter

• Axis — See https://ngff.openmicroscopy.org/0.5/#axes-md

• BinnedArraysWriter

• CachedChunkWriter

Functions

• delete_group

• ome_attribute — See https://ngff.openmicroscopy.org/0.5/#metadata

source class OmeZarrWriter(location: str, group_name: str, shape: tuple[int, int, int], dtype: npt.DTypeLike, chunks_shape: tuple[int, int, int], shards_shape: tuple[int, int, int], translation: Sequence[float] | None = None, scale: Sequence[float] | None = None, metadata: dict[str, Any] | None = None, atleast_size: int = 256)

source property OmeZarrWriter.shape: tuple[int, int, int]

source delete_group(location: str, group_name: str)

source class Axis()

Bases : TypedDict

See https://ngff.openmicroscopy.org/0.5/#axes-md

source ome_attribute(axes: Sequence[Axis], nb_levels: int, name: str | None = None, translation: Sequence[float] | None = None, scale: Sequence[float] | None = None, downsampling_type: str | None = None, downsampling_metadata: dict | None = None) → dict[str, Any]

See https://ngff.openmicroscopy.org/0.5/#metadata

Raises

• ValueError

source class BinnedArraysWriter(arrays: Sequence, chunk_sizes: int | tuple[int, ...])

Methods

• append

• flush

source method BinnedArraysWriter.append(data: np.ndarray) → None

source method BinnedArraysWriter.flush() → None

source class CachedChunkWriter(array, chunk_size: int)

Methods

• append

• flush

source method CachedChunkWriter.append(data: np.ndarray, copy: bool = True) → Generator[np.ndarray, None, None]

Raises

• RuntimeError

source method CachedChunkWriter.flush() → np.ndarray | None