Implement addition of optogenetic metadata

[samuelbray32]

Fixes #110

Related PR's:

• yaml generator
• nwb extension
• spyglass import

To Do:

• FS gui spatial filters. Update extension for multiplefilters per epoch and polygonal filters
  • In progress. have nodes parsed and added just couple little entries left
• Source and add epoch-level metadata
• Load in "device" yamls for new objects. Propose generalizing "probe_metadata" to "device_metadata" and using it to passing around metadata for multiple device types (virus, excitation source, etc.)
• Add tests
• cameras defining spatial regions
  • Implemented in yaml generator but not yet in this package test yaml file

[codecov]

Codecov Report

Attention: Patch coverage is 90.41096% with 21 lines in your changes missing coverage. Please review.

Project coverage is 89.50%. Comparing base (73e14e6) to head (539095c).
Report is 8 commits behind head on main.

Files with missing lines	Patch %	Lines
src/trodes_to_nwb/convert_optogenetics.py	90.29%	20 Missing ⚠️
src/trodes_to_nwb/convert.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #118      +/-   ##
==========================================
+ Coverage   89.32%   89.50%   +0.17%     
==========================================
  Files          12       13       +1     
  Lines        1471     1686     +215     
==========================================
+ Hits         1314     1509     +195     
- Misses        157      177      +20     

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[Copilot]

Pull Request Overview

This PR adds support for ingesting and converting optogenetic metadata into the NWB export pipeline by generalizing “probe_metadata” to “device_metadata”, introducing a new convert_optogenetics module, and providing sample/test YAMLs and device metadata files.

• Renamed and extended metadata loading to handle multiple device types (probes, viruses, fibers, light sources).
• Added convert_optogenetics to parse and inject optogenetic devices, injections, fibers, and stimulation epochs.
• Introduced test fixtures (fsgui_*.yaml, geometry.trackgeometry), updated sample metadata, and new unit tests for optogenetics.

Reviewed Changes

Copilot reviewed 19 out of 28 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/trodes_to_nwb/convert.py	Swapped probe → device metadata paths, hooked in add_optogenetics
src/trodes_to_nwb/convert_optogenetics.py	New module: builds optogenetic devices, fibers, viruses, epochs
src/trodes_to_nwb/tests/test_convert_optogenetics.py	Unit tests validating optogenetic device and epoch creation
src/trodes_to_nwb/tests/test_data/fsgui_theta_trigger.yaml	FS GUI YAML for theta-triggered optogenetic epochs
src/trodes_to_nwb/tests/test_data/20230622_sample_metadata.yml	Added virus_injection, opto_excitation_source, optical_fiber, FS‐GUI YAML refs

Comments suppressed due to low confidence (2)

src/trodes_to_nwb/tests/test_data/fsgui_theta_trigger.yaml:1

• The list items under nodes: are not indented, which will produce invalid YAML. Prefix each item with two spaces before - (e.g., - type_id: ...).

nodes:

src/trodes_to_nwb/tests/test_data/20230622_sample_metadata.yml:656

• Inconsistent key casing: you have both volume_in_uL and volume_in_ul. Standardize to a single key (e.g., volume_in_uL) to avoid lookup errors.

    volume_in_ul: 100.0

[edeno]

Looks good to me.

I had a couple questions:

1. What happens if an old user has an old yaml and uses the new version of trodes_to_nwb.
2. Where does someone go to find documentation about the different opto objects and what they correspond to?

[edeno]

Err actually the docstrings are in the google format and not the numpy docstring style. Would be nice to be consistent.

[samuelbray32]

I think the new pynwb=3.1.0 release is breaking. I might pin the version and solve in a separate PR