Add dict-based metadata pipeline for imaging #1677
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h-mayorquin merged 13 commits intomainfrom Mar 4, 2026
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A couple nits, otherwise looks good.
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1677 +/- ##
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+ Coverage 81.01% 81.08% +0.06%
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Files 160 160
Lines 12471 12574 +103
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+ Hits 10104 10195 +91
- Misses 2367 2379 +12
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Related to #269
Implements the dict-based metadata pipeline for imaging extractors as discussed in #1653.
add_imaging_to_nwbfilenow accepts the new dict-based metadata format keyed bymetadata_key. When old metadata is passed, the data goes through an alternative path, effectively segregating new and old formats. This keeps the functions backwards compatible and the diff simpler. New helper functions (_add_imaging_plane_to_nwbfile,_add_photon_series_to_nwbfile,_add_device_to_nwbfile) handle the dict-based format, while old list-based functions are renamed with an_old_list_formatsuffix to handle the old one.We introduce
get_full_ophys_metadata()which provides a user-facing example template (moving forward with #1557). When users provide metadata with missing required fields, a clearValueErroris raised listing the missing fields and their placeholders. See also NeurodataWithoutBorders/nwb-schema#672 for some of the design rationale.Closes #1653. Related: #1511, nwb-schema#672.