Replace create_empty_hcs_zarr with iohub's create_empty_plate#554
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talonchandler merged 2 commits intomainfrom Apr 24, 2026
Merged
Replace create_empty_hcs_zarr with iohub's create_empty_plate#554talonchandler merged 2 commits intomainfrom
talonchandler merged 2 commits intomainfrom
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iohub's `create_empty_plate` does the same plate + channel create/append work. The only waveorder-specific behavior was writing a `plate_metadata` dict into the plate's zattrs; that's now done inline in apply_inverse_transfer_function.py after create_empty_plate returns. Tests: 347 passed, 1 skipped, 2 xfailed. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Apr 23, 2026
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Thanks @ieivanov!
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Summary
waveorder.cli.utils.create_empty_hcs_zarr. iohub'screate_empty_platedoes the same plate/channel creation work.plate_metadatadict into the plate's zattrs; that's done inline inapply_inverse_transfer_function.pyaftercreate_empty_platereturns, matching the pattern used in biahub (Replace create_empty_hcs_zarr with iohub's create_empty_plate czbiohub-sf/biahub#215, Preserve OME-Zarr version across pipelines, with override knob czbiohub-sf/biahub#241).tests/util_tests/test_create_empty.py,tests/cli_tests/test_zarr_v3_reconstruct.py) tocreate_empty_plate.Why not also replace
apply_inverse_to_zyx_and_save?iohub's
process_single_positionis numpy-native: it loadsndarrayslices viaoindexand writes them back the same way.apply_inverse_to_zyx_and_saveoperates onxr.DataArray— it selects channels by name, passes the xarray to the waveorder reconstruction functions (birefringence/phase/fluorescence.apply_inverse_transfer_function, all xarray-in/xarray-out), and writes viaoutput_position.write_xarray(...)so thetcoord and attributes are preserved. A drop-in swap would either require refactoring the reconstruction API to become numpy-native (loses xarray coord semantics and breaks public API) or adding a numpy↔xarray wrapper that duplicates logic iohub doesn't expose. Deferred.Test plan
uv run pytest— 347 passed, 1 skipped, 2 xfailed.🤖 Generated with Claude Code