ngff_zarr.to_ngff_zarr¶

Module Contents¶

Functions¶

_pop_metadata_optionals

_prep_for_to_zarr

to_ngff_zarr

Write an image pixel array and metadata to a Zarr store with the OME-NGFF standard data model.

API¶

ngff_zarr.to_ngff_zarr._pop_metadata_optionals(metadata_dict)¶
ngff_zarr.to_ngff_zarr._prep_for_to_zarr(store: Union[collections.abc.MutableMapping, str, pathlib.Path, zarr.storage.BaseStore], arr: dask.array.Array) → dask.array.Array¶
ngff_zarr.to_ngff_zarr.to_ngff_zarr(store: Union[collections.abc.MutableMapping, str, pathlib.Path, zarr.storage.BaseStore], multiscales: ngff_zarr.multiscales.Multiscales, overwrite: bool = True, chunk_store: Optional[Union[collections.abc.MutableMapping, str, pathlib.Path, zarr.storage.BaseStore]] = None, progress: Optional[Union[ngff_zarr.rich_dask_progress.NgffProgress, ngff_zarr.rich_dask_progress.NgffProgressCallback]] = None, **kwargs) → None¶

Write an image pixel array and metadata to a Zarr store with the OME-NGFF standard data model.

Parameters:

  • store (MutableMapping, str or Path, zarr.storage.BaseStore) – Store or path to directory in file system.

  • multiscales (Multiscales) – Multiscales OME-NGFF image pixel data and metadata. Can be generated with ngff_zarr.to_multiscales.

  • overwrite (bool, optional) – If True, delete any pre-existing data in store before creating groups.

  • chunk_store (MutableMapping, str or Path, zarr.storage.BaseStore, optional) – Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.

  • progress (RichDaskProgress) – Optional progress logger

  • **kwargs – Passed to the zarr.creation.create() function, e.g., compression options.