ngff_zarr.rfc9_zip

RFC-9: Zipped OME-Zarr (.ozx) support

This module provides utilities for reading and writing OME-Zarr hierarchies in ZIP archives according to RFC-9 specification.

Module Contents

Functions

is_ozx_path

Check if a path refers to a .ozx file.

write_store_to_zip

Write a zarr store to a ZIP archive following RFC-9 specification.

read_ozx_version

Read the OME-Zarr version from a .ozx file’s ZIP comment.

read_ozx_json_first

Read the jsonFirst flag from a .ozx file’s ZIP comment.

API

ngff_zarr.rfc9_zip.is_ozx_path(path: Union[str, pathlib.Path]) → bool

Check if a path refers to a .ozx file.

Parameters

path : str or Path Path to check

Returns

bool True if path ends with .ozx extension

ngff_zarr.rfc9_zip.write_store_to_zip(
source_store: Union[zarr.storage.StoreLike, str, pathlib.Path],
zip_path: Union[str, pathlib.Path],
version: str = '0.5',
compression: int = zipfile.ZIP_STORED,
) → None

Write a zarr store to a ZIP archive following RFC-9 specification.

According to RFC-9:

  • Root-level zarr.json must be the first entry

  • Other zarr.json files should follow in breadth-first order

  • ZIP-level compression should be disabled (ZIP_STORED)

  • ZIP64 format should be used

  • A comment with OME-Zarr version should be added

This function can be used to convert any existing zarr store (including HCS plates) to .ozx format after it has been written.

Parameters

source_store : zarr.storage.StoreLike, str, or Path Source zarr store to write from. Can be a store object (LocalStore, DirectoryStore) or a path string to a directory containing zarr data. zip_path : str or Path Path to output .ozx file version : str, optional OME-Zarr version string (e.g., “0.5”) compression : int, optional ZIP compression method (default: ZIP_STORED for no compression)

Examples

Convert an existing HCS plate to .ozx:

from ngff_zarr.rfc9_zip import write_store_to_zip

After writing plate with to_hcs_zarr or HCSPlateWriter

write_store_to_zip(“my_plate.ome.zarr”, “my_plate.ozx”, version=”0.5”)

ngff_zarr.rfc9_zip.read_ozx_version(
zip_path: Union[str, pathlib.Path],
) → Optional[str]

Read the OME-Zarr version from a .ozx file’s ZIP comment.

Parameters

zip_path : str or Path Path to the .ozx file

Returns

str or None OME-Zarr version string if found, None otherwise

ngff_zarr.rfc9_zip.read_ozx_json_first(zip_path: Union[str, pathlib.Path]) → bool

Read the jsonFirst flag from a .ozx file’s ZIP comment.

The jsonFirst flag indicates that zarr.json files are ordered breadth-first in the central directory and precede other content.

Parameters

zip_path : str or Path Path to the .ozx file

Returns

bool True if jsonFirst is set to true in the ZIP comment, False otherwise