pymif.microscope_manager.utils.to_zarr

Functions

_metadata_for_write(→ dict)
_build_multiscales(→ dict)
to_zarr(path, data_levels, metadata, *[, config])	Write a pyramid of dask arrays to an OME-Zarr root group.
write_multiscale_to_group(group, data_levels, metadata, *)	Write a pyramid of Dask arrays into an existing zarr group.

Module Contents

pymif.microscope_manager.utils.to_zarr._metadata_for_write(metadata: dict, axes: tuple[str, Ellipsis], *, config: pymif.microscope_manager.utils.ngff.ZarrWriteConfig, is_label: bool | None = None) → dict

pymif.microscope_manager.utils.to_zarr._build_multiscales(metadata: dict, axes: tuple[str, Ellipsis], *, name: str | None, n_levels: int) → dict

pymif.microscope_manager.utils.to_zarr.to_zarr(path: str | pathlib.Path, data_levels: Sequence[dask.array.Array], metadata: dict, *, config: pymif.microscope_manager.utils.ngff.ZarrWriteConfig | None = None)

Write a pyramid of dask arrays to an OME-Zarr root group.

Parameters

pathstr | Path

Destination zarr store.

data_levelssequence of dask.array.Array

Pyramid levels ordered from finest to coarsest resolution.

metadatadict

Normalized PyMIF metadata dictionary describing axes, scales, channel metadata and units.

configZarrWriteConfig | None

Output configuration controlling NGFF version, zarr format, overwrite behaviour and compression.

pymif.microscope_manager.utils.to_zarr.write_multiscale_to_group(group: zarr.Group, data_levels: Sequence[dask.array.Array], metadata: dict, *, config: pymif.microscope_manager.utils.ngff.ZarrWriteConfig | None = None, name: str | None = None, is_label: bool = False)

Write a pyramid of Dask arrays into an existing zarr group.

Used by pymif.microscope_manager.ZarrManager for raw data, image subgroups and label groups. The axes may be any subset of tczyx.