Adding support for more .nwb training data to SLEAP #101

keyaloding · 2024-06-28T19:12:24Z

Description

Right now, data from NWB (Neurodata without Borders) is partially supported in sleap-io. The PoseEstimation and PoseEstimationSeries data structures are supported, but the TrainingFrame, TrainingFrames, PoseTraining, and SourceVideos structures are not. These data structures correspond to data structures in SLEAP as shown in rly/ndx-pose#24. I will add support for these data types in sleap-io by allowing the user to save and load them.

My plan is to update the save_nwb and load_nwb functions in io/main.py to allow support for classes besides Labels. I will also update the read_nwb function in io/nwb.py so that it can read NWB data structures and return the corresponding SLEAP structures. So far, I have written a function convert_nwb that uses NWB objects to initialize corresponding SLEAP objects with the same attributes. https://github.com/keyaloding/io_fork/blob/70a34ede294d3c783d1758c55c1dd9752e29f1e7/sleap_io/io/nwb.py#L37-L72. I will write new tests that confirm that the attributes of the SLEAP data structures that are initialized have the same attributes as the NWB data structures used to create them.

I will also update the documentation to include information about how to use NWB data in SLEAP.

Types of changes

Does this address any currently open issues?

#100, #86, rly/ndx-pose#29

Outside contributors checklist

Review the guidelines for contributing to this repository
Read and sign the CLA and add yourself to the authors list
Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
Add tests that prove your fix is effective or that your feature works
Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

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coderabbitai · 2024-06-28T19:12:30Z

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tests/model/test_labeled_frame.py

codecov · 2024-06-29T16:58:43Z

Codecov Report

Attention: Patch coverage is 15.38462% with 11 lines in your changes missing coverage. Please review.

Project coverage is 95.42%. Comparing base (5a30110) to head (2bd6d91).

Files	Patch %	Lines
sleap_io/io/nwb.py	15.38%	11 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #101      +/-   ##
==========================================
- Coverage   96.04%   95.42%   -0.62%     
==========================================
  Files          17       17              
  Lines        2022     2034      +12     
==========================================
- Hits         1942     1941       -1     
- Misses         80       93      +13

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…res' into kloding/add_nwb_training_structures

sleap_io/io/nwb.py

tests/io/test_nwb.py

sleap_io/io/nwb.py

talmo · 2024-07-10T23:06:01Z

sleap_io/io/main.py

@@ -47,7 +47,7 @@ def save_slp(
    return slp.write_labels(filename, labels, embed=embed)


-def load_nwb(filename: str) -> Labels:
+def load_nwb(filename: str, format: str) -> Labels:


Suggestion: since we only have two "formats", it might be easier to just make this a boolean. For example:

def load_nwb(filename: str, as_training: bool | None = None): if as_training is None: as_training = ... # try to auto-detect based on whether there are tracks or user-labeled instances if as_training: return nwb.read_nwb_training(filename) else: return nwb.read_nwb(filename)

And maybe we want to rename nwb.read_nwb to nwb.read_nwb_predictions for clarity?

PS: We probably want to keep nwb.read_nwb and anything else that existed before as an alias for backwards compatibility.

sleap_io/io/main.py

sleap_io/io/nwb.py

talmo · 2024-07-10T23:09:44Z

tests/data/nwb/centered_pair_predictions.nwb

Definitely cannot commit a 16 MB test file!! Shoot for 1-2 MB max by reducing the contents of the file to the minimal subset that still allows for testing the functionality. If not possible, then maybe will need to generate the testing artifacts dynamically (e.g., converting from the base SLP file and saving to a temp dir).

talmo · 2024-07-10T23:10:32Z

tests/data/slp/minimal_instance.slp

Why is this getting changed? It's not a part of this PR's scope but is used in a lot of the rest of the package.

talmo · 2024-07-10T23:11:22Z

tests/data/slp/minimal_instance_w_prediction.slp

Is this new? Why can't we use one of the other SLP files in https://github.com/talmolab/sleap-io/tree/main/tests/data/slp?

sleap_io/io/nwb.py

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talmo reviewed Jun 28, 2024

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keyaloding and others added 17 commits July 1, 2024 13:58

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eberrigan requested changes Jul 8, 2024

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keyaloding added 6 commits July 8, 2024 15:43

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talmo requested changes Jul 10, 2024

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keyaloding added 7 commits July 10, 2024 17:08

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keyaloding closed this Jul 12, 2024

keyaloding deleted the kloding/add_nwb_training_structures branch July 12, 2024 16:18

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Adding support for more .nwb training data to SLEAP #101

Adding support for more .nwb training data to SLEAP #101

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Adding support for more .nwb training data to SLEAP #101

Adding support for more .nwb training data to SLEAP #101

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keyaloding commented Jun 28, 2024 • edited Loading

Description

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Does this address any currently open issues?

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