Created
February 23, 2024 14:09
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| 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) |
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