zarr3conv.py

import os
os.environ["ZARR_V3_EXPERIMENTAL_API"] = "1"

import zarr
import argparse


parser = argparse.ArgumentParser(description="Convert ome.zarr from zarr spec 2 to 3")
parser.add_argument("input", help="The input zarr")
parser.add_argument("output", nargs="?", help="Optional output zarr")
args = parser.parse_args()
if not args.output:
    args.output = f"{args.input}3"


def copy_visitor(k, v):
    if isinstance(v, zarr.hierarchy.Group):
        print(f"Copy Group {k} from {args.input} to {args.output}")
        out_group = out_store.create_group(k)
        out_group.attrs.update(v.attrs)
    elif isinstance(v, zarr.core.Array):
        print(f"Copy Array {k} from {args.input} to {args.output}")
        out_store.array(k, v)
    else:
        print(f"Can't handle {v}")


in_store = zarr.open(args.input, mode='r', zarr_version=2)
out_store = zarr.open(args.output, mode='w', zarr_version=3)
in_store.visititems(copy_visitor)