Moseq Pipeline

[samuelbray32]

Description

• Implementation of moseq withing spyglass pipelines.

  • Keypoint data sourced from PositionOutput
    • Added PositionOutput.get_pose_dataframe to allow fetching of full pose rather than centroid for appropriate pipelines.
  • PoseGroup used to combine multiple epochs of pose data into a training set (analagous to PositionGroup in decoding pipeline)
  • Model parameters and training arguments stored in MoseqModelParams
    • Can define initial model as an existing entry in MoseqModel for reuse and extended training
  • MoseqModelSelection combines PoseGroup andmodel parameters
  • MoseqModel trains model and stores in external project file
  • MoseqSyllable (and it's selction table) apply a trained model to an entry from PositionOutput
    • stores syllables and latent variables as a dataframe in an AnalysisNwbfile entry

• Added utility function get_position_interval_epoch

My To-dos

• improve the tutorial with more explanations of the steps
• update notebook image to use PositionOutput
• change the model stored directories to the spyglass config
• make a better standard version for getting epoch from the position interval name (as mentioned by Chris before)
• update changelog

Checklist:

• N This PR should be accompanied by a release: (yes/no/unsure)
• NA If release, I have updated the CITATION.cff
• N This PR makes edits to table definitions: (yes/no)
• NA If table edits, I have included an alter snippet for release notes.
• NA If this PR makes changes to position, I ran the relevant tests locally.
• I have updated the CHANGELOG.md with PR number and description.
• I have added/edited docs/notebooks to reflect the changes

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[CBroz1]

Took a first pass on the behavior subpackage - Can continue review tomorrow

[CBroz1]

Looking good so far!

[CBroz1]

I think I would migrate these to a separate method to clean up the indenting, something like declare_pos_analysis_file

[samuelbray32]

@CBroz1, reorganized this make function. Let me know if it looks cleaner to you

[samuelbray32]

I've now merged in the main branch and have tested it working with a dependency on PositionOutput rather than the introduced PoseOutput table proposed before.

[CBroz1]

Yeah. Do we want them in the default dependencies or should they be their own version similar to how we do the DLC ones?

A user will need a DLC project in place to use MoSeq, right? I think I might rename our 'dlc' optional dependency to 'position' and moseq dependencies in there - not sure which I prefer across the following:

pip install .[dlc,moseq] # separate categories in pyproject
pip install .[position] 
pip install .[pos_deps]

[samuelbray32]

Yeah. Do we want them in the default dependencies or should they be their own version similar to how we do the DLC ones?

A user will need a DLC project in place to use MoSeq, right? I think I might rename our 'dlc' optional dependency to 'position' and moseq dependencies in there - not sure which I prefer across the following:

pip install .[dlc,moseq] # separate categories in pyproject
pip install .[position] 
pip install .[pos_deps]

I may lean towards keeping them separate. You don't strictly need DLC in your environment to run the moseq pipeline.
Examples:

• User 2 is pulling pose data from a pre-existing DLC entry made by a different User 1
• I think it would be reasonable future enhancement to have some version of a ImportedPose table to allow new users to bring pre-existing DLC annotated data into spyglass (analogous to ImportedSpikeSorting)

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edeno commented on 2025-01-20T20:30:33Z
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Line #1.    from spyglass.behavior.core import PoseGroup

Should be:

from spyglass.behavior.v1.core import PoseGroup

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edeno commented on 2025-01-20T20:30:33Z
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Line #1.    from spyglass.behavior.moseq import (

should be:

from spyglass.behavior.v1.moseq import (

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edeno commented on 2025-01-20T20:30:34Z
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Line #5.    MoseqModel().populate(model_key)

This didn't work for me on testing but it also didn't give an informative error message as to why. Any thoughts?

samuelbray32 commented on 2025-01-27T23:02:28Z
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When I deleted and ran this again I had an issue related due to the project path. I changed the code to make it unique prior to creation of the moseq model

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edeno commented on 2025-01-20T20:30:35Z
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Line #2.    table.analyze_pca()

This failed for me as well:

TypeError: MoseqModel.analyze_pca() missing 1 required positional argument: 'key'

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edeno commented on 2025-01-20T20:30:36Z
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Line #3.    from spyglass.behavior.moseq import MoseqSyllableSelection, MoseqSyllable

from spyglass.behavior.v1.moseq import MoseqSyllableSelection, MoseqSyllable

[edeno]

I ran through the notebook and ran into a couple of problems. I was unable to run the moseq algorithm I think but it was unclear to me why.

[edeno]

Update the omit section because this module is currently untested.

[samuelbray32]

When I deleted and ran this again I had an issue related due to the project path. I changed the code to make it unique prior to creation of the moseq model

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