feat: extract brain area anatomy from NWB location fields#1807
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bendichter wants to merge 2 commits intomasterfrom
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feat: extract brain area anatomy from NWB location fields#1807bendichter wants to merge 2 commits intomasterfrom
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Extract brain location values from NWB files (ImagingPlane.location, electrodes.location, IntracellularElectrode.location), match them against bundled Allen Mouse Brain Atlas CCF structures, and populate BioSample.anatomy within wasDerivedFrom. Closes #1806 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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- Cast json.load() return to explicit type - Use str() for AnyHttpUrl identifier comparisons - Add None-checks before indexing wasDerivedFrom in tests - Add explanatory comments to bare except clauses Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Additional details and impacted files@@ Coverage Diff @@
## master #1807 +/- ##
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+ Coverage 75.12% 75.39% +0.26%
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Files 84 87 +3
Lines 11925 12282 +357
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+ Hits 8959 9260 +301
- Misses 2966 3022 +56
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sister PR: NeurodataWithoutBorders/nwbinspector#671 |
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Summary
Closes #1806
ImagingPlane.location,electrodes.location,IntracellularElectrode.location)BioSample.anatomywithin thewasDerivedFromfield using MBAO identifiersNCBITaxon_10090); non-mouse species are skippedNew files
dandi/data/allen_ccf_structures.json— bundled Allen CCF structuresdandi/data/generate_allen_structures.py— regeneration script (python -m dandi.data.generate_allen_structures)dandi/metadata/brain_areas.py— parsing and matching moduledandi/tests/test_brain_areas.py— 29 unit testsModified files
dandi/pynwb_utils.py—_get_brain_locations()extracts location strings from NWBdandi/metadata/util.py—extract_wasDerivedFrom()now adds anatomy to deepest BioSampledandi/tests/test_metadata.py— 3 integration tests for anatomy in wasDerivedFromTest plan
python -m pytest dandi/tests/test_brain_areas.py -v— 29 unit tests passpython -m pytest dandi/tests/test_metadata.py -v -k anatomy— 3 integration tests passpre-commit run --files <all changed files>— all hooks pass🤖 Generated with Claude Code