Replace create_empty_hcs_zarr with iohub's create_empty_plate #540

Summary

create_empty_hcs_zarr in waveorder/cli/utils.py can be replaced by create_empty_plate from iohub.ngff.utils. The core logic is identical.

Details

Both functions:

1. Call open_ome_zarr(..., layout="hcs", mode="a") to create/open a plate
2. Loop over position_keys, check if each exists in output_plate.zgroup
3. If missing: create_position() → create_zeros() with a TransformationMeta scale transform
4. If existing: append any missing channel names via append_channel()

create_empty_plate in iohub additionally supports:

• Auto-calculated chunk sizes (via _limit_zyx_chunk_size)
• Sharding (v0.5)
• max_chunk_size_bytes parameter

Migration note

The one feature in create_empty_hcs_zarr not present in create_empty_plate is the plate_metadata parameter, which is used in apply_inverse_transfer_function.py to copy non-OME plate-level metadata. This needs to be handled separately after the call:

create_empty_plate(
    store_path, position_keys, channel_names, shape,
    chunks=chunks, scale=scale, dtype=dtype
)
if plate_metadata:
    with open_ome_zarr(str(store_path), mode="a") as plate:
        plate.zattrs.update(plate_metadata)

Alternatively, plate_metadata support could be added to create_empty_plate in iohub to make the replacement fully seamless.

Related

• biahub PR: Replace create_empty_hcs_zarr with iohub's create_empty_plate biahub#215