Add IZeroClampSeries and RoiResponseSeries to the neurodata type map; fix OptogeneticStimulusSite typo - #1946
Open
bendichter wants to merge 1 commit into
Open
bendichter wants to merge 1 commit into
bendichter wants to merge 1 commit into
Conversation
…OptogeneticStimulusSite typo
process_ndtypes drops any neurodata type not in neurodata_typemap, so
files whose only intracellular data is IZeroClampSeries, or whose ophys
data is only RoiResponseSeries, got no variableMeasured, technique or
approach for it. The OptogeneticStimulusSite entry was misspelled
("SIte") and so never matched the real type.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #1946 +/- ##
=======================================
Coverage 78.34% 78.34%
=======================================
Files 92 92
Lines 14109 14109
=======================================
Hits 11053 11053
Misses 3056 3056
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
yarikoptic
reviewed
Oct 1, 2026
| "module": "ogen", | ||
| "neurodata_type": "OptogeneticStimulusSIte", | ||
| "neurodata_type": "OptogeneticStimulusSite", | ||
| "technique": None, |
Member
There was a problem hiding this comment.
in
@rly proposed
Suggested change
| "technique": None, | |
| "technique": "surgical technique", |
I wonder if we should include this here, or just keep as is to the typo fix?
yarikoptic
approved these changes
Oct 1, 2026
yarikoptic
left a comment
Member
There was a problem hiding this comment.
could go in without further refine per comment to not make perfect be enemy of the good.
Just FTR: would cause conflicts with
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
process_ndtypesdrops any neurodata type that isn't a key inneurodata_typemap, so types missing from the map contribute nothing to an asset'svariableMeasured,measurementTechniqueorapproach. This fills two gaps and fixes a typo:IZeroClampSeries(icephys): current clamp with no injected current, socurrent clamp technique/electrophysiological approach, the same asCurrentClampSeries. Before this, a file whose only intracellular data wasIZeroClampSeriesgot no icephys metadata.RoiResponseSeries(ophys): no technique, since ROI traces can come from one- or two-photon imaging, andmicroscopy approach; cell population imaging, matchingImagingPlaneandPlaneSegmentation.OptogeneticStimulusSite: the key andneurodata_typewere spelledOptogeneticStimulusSIte, so the entry never matched the real type. The existing test case used the same typo, so I fixed it there too.Added
test_ndtypescases for the two new types.dandi/tests/test_metadata.pypasses locally, and so do the pre-commit hooks.Context: dandi/dandi-archive#2907 / dandi/dandi-archive#2946, which make archive search match NWB subtypes and rely on this map. The bigger gap, extension types that subclass a core type (e.g. an
ElectricalSeriessubclass), is also dropped here. Fixing that means resolving unknown types through the schemas cached in the file, which I'll leave for a separate change (see the TODO inget_neurodata_types_to_modalities_map).🤖 Generated with Claude Code