Preserve zarr version in register command#198
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Add version parameter to create_empty_hcs_zarr() and detect input zarr version in register_cli() to ensure output version matches input (v2→v2, v3→v3). This maintains compatibility with both OME-NGFF v0.4 (zarr v2) and v0.5 (zarr v3) datasets. Changes follow the pattern from waveOrder PR#519: - Add optional version parameter to create_empty_hcs_zarr (default "0.4") - Pass version to open_ome_zarr when creating output plate - Detect input version from source plate in register_cli - Backward compatible: existing calls use default "0.4" Pair-coded-with: Soorya Pradeep <@Soorya19Pradeep> Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Convert shape, scale, and chunks to native Python types for zarr v3 compatibility (zarr v3 requires native Python ints/floats, not numpy types) - Fix position existence checking by using try/except instead of unreliable zgroup membership check - Fix channel appending to apply to all positions, not just the last one Fixes KeyError when accessing positions and TypeError when creating arrays with numpy int64 values in zarr v3 format. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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I have tested the PR on a Hummingbird dataset with the following conditions: |
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I have added the changes to concatenate to the same PR, as this is a very small number of lines of code as well. It was tested on zarr version 3 dataset with multiple positions. |
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Add version parameter to create_empty_hcs_zarr() and detect input zarr version in register_cli() to ensure output version matches input (v2→v2, v3→v3). This maintains compatibility with both OME-NGFF v0.4 (zarr v2) and v0.5 (zarr v3) datasets.
Changes follow the pattern from waveOrder PR#519:
Pair-coded-with: Soorya Pradeep <@Soorya19Pradeep>