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]

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.