Moseq Pipeline #1056

samuelbray32 · 2024-08-06T19:20:58Z

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

…t for Pose-dependent analysis

review-notebook-app · 2024-08-06T19:21:04Z

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CBroz1

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

src/spyglass/behavior/core.py

src/spyglass/behavior/moseq.py

CBroz1

Looking good so far!

CBroz1 · 2024-08-09T14:33:29Z

src/spyglass/position/v1/position_dlc_selection.py

-            comments=pos_obj.comments,
-            description=pos_obj.description,
-        )
+        if isinstance(pos_nwb["dlc_position"], pd.DataFrame):


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

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

src/spyglass/position/v1/position_dlc_pose_estimation.py

src/spyglass/position/v1/position_trodes_position.py

Co-authored-by: Chris Broz <[email protected]>

samuelbray32 · 2024-12-20T23:00:25Z

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.

edeno

Can you add the dependencies to the pyproject.toml and environment.yml?

samuelbray32 · 2025-01-02T15:43:27Z

Can you add the dependencies to the pyproject.toml and environment.yml?

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

CBroz1

I did another pass here with some comments. Are pytests in the scope of this PR, or do we want to hold off?

src/spyglass/behavior/core.py

src/spyglass/behavior/moseq.py

CBroz1 · 2025-01-02T16:34:08Z

src/spyglass/behavior/moseq.py

+        # increment param name
+        if new_name is None:
+            # increment the extension number
+            if model_key["model_params_name"][:-1].endswith("_extension"):


Could this be avoided by adding a pk field for extension that's an int with a default value of 0?

CBroz1 · 2025-01-02T17:55:26Z

src/spyglass/common/common_behav.py

@@ -686,6 +686,30 @@ def get_interval_list_name_from_epoch(nwb_file_name: str, epoch: int) -> str:
    return interval_names[0]


+def get_position_interval_epoch(
+    nwb_file_name: str, position_interval_name: str


Suggested change

nwb_file_name: str, position_interval_name: str

nwb_file_name: str, position_interval_name: str, limit=1

CBroz1 · 2025-01-02T17:56:35Z

src/spyglass/common/common_behav.py

+    query = PositionIntervalMap * TaskEpoch & key
+    if query:
+        return query.fetch1("epoch")
+    return None


Allows you to try N times, whatever you set the default value of limit to

Suggested change

query = PositionIntervalMap * TaskEpoch & key

if query:

return query.fetch1("epoch")

return None

return get_position_interval_epoch(limit=limit-1) if limit else None

Shouldn't need to try more than twice. The second attempt is just after ensuring that all epoch intervals have been mapped to a position interval. That wouldn't change with further attempts

CBroz1 · 2025-01-02T18:00:15Z

src/spyglass/position/v1/position_dlc_pose_estimation.py

@@ -409,6 +409,16 @@ def fetch_dataframe(self, *attrs, **kwargs) -> pd.DataFrame:
            axis=1,
        )

+    def fetch_video_path(self):
+        """Return the video path for pose estimate


Normally, we pass key as an arg for this kind of thing. It's not clear to me why you break the pattern here. If no arg, it could be a property, yeah? If kept, I'd add example use to the docstring

Suggested change

"""Return the video path for pose estimate

"""Return the video path for pose estimate

>>> (DLCPoseEstimation & key).fetch_video_path()

CBroz1 · 2025-01-02T18:01:23Z

src/spyglass/position/v1/position_dlc_selection.py

+
+    def fetch_video_path(self):
+        """Return the video path for pose estimate
+


See above note on break from key-as-arg convention

CBroz1 · 2025-01-02T18:01:43Z

src/spyglass/position/v1/position_dlc_selection.py

@@ -269,6 +294,27 @@ def evaluate_pose_estimation(cls, key):
        }
        return sub_thresh_percent_dict

+    def fetch_pose_dataframe(self):
+        """fetches the pose data from the pose estimation table
+


See above note on break from key-as-arg convention

This one I think is reasonable as-is. It matches the convention we use for fetch1_dataframe or fetch_nwb

CBroz1 · 2025-01-02T18:05:16Z

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]

Co-authored-by: Chris Broz <[email protected]>

samuelbray32 · 2025-01-03T18:20:21Z

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)

…o moseq

samuelbray32 and others added 10 commits June 10, 2024 15:50

Add organization tables for keypoint pose data

9d6d3e1

Add model training tables

28748f1

apply fit moseq model to data

7d5d66c

add ability to initialize model training from pre-existing model

09779a6

make model names unique

983f179

add initial tutorial

fdaff80

add moseq pipeline diagram

c2b4d4f

get rid of PoseOutput and fetch pose data from PositionOutput

2e9ea46

remove PoseOutput and corresponding references

62c8eef

allow passing of null entries from DLCPoseEstimation to PositionOutpu…

36ad016

…t for Pose-dependent analysis

edeno requested a review from CBroz1 August 8, 2024 18:37

CBroz1 reviewed Aug 8, 2024

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CBroz1 reviewed Aug 9, 2024

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edeno added enhancement New feature or request position labels Sep 25, 2024

samuelbray32 and others added 7 commits December 20, 2024 09:38

Apply suggestions from code review

fe3c6d4

Co-authored-by: Chris Broz <[email protected]>

Merge branch 'master' into moseq

ccf370f

lint

b8dfd42

implement changes from review

310abf7

rename fetch_video_name to fetch_video_path

69335a8

cleanup outdated usages of PoseOutput

fc46b37

Cleanup errors from removal of PoseOutput

c3c7b84

samuelbray32 added 6 commits December 20, 2024 15:56

add get_position_interval_epoch

e5b2c1b

Add method to get training results pdf

dc8435c

Add description and example of hyperparameter sweep

f92320b

move moseq dir definition to spyglass config

d663e0e

move moseq config function to method

3a1c079

Update changelog

589bdb2

samuelbray32 marked this pull request as ready for review December 27, 2024 19:58

edeno requested review from CBroz1 and edeno December 27, 2024 20:56

update pipeline diagram

7d30fc1

edeno requested changes Jan 1, 2025

View reviewed changes

CBroz1 reviewed Jan 2, 2025

View reviewed changes

samuelbray32 and others added 9 commits January 2, 2025 10:49

Apply suggestions from code review

81f3dfa

Co-authored-by: Chris Broz <[email protected]>

move moseq into v1 folder

3bfcb9f

add docstrings

8fd900b

make video symlink more robust

5a33090

cleanup setup_project call

bd29c76

cleanup config method

c7ea1f5

Implement suggestions from code review

5901edc

cleanup readability of DLCPosV1 make conditions

e5af455

allow key argument when fetching video path

04c2a37

samuelbray32 added 7 commits January 16, 2025 09:39

add moseq dependencies

8106929

Add moseq install instructions to tutorials

2bff705

accept key in all get video path functions

31014f9

Merge branch 'master' into moseq

3dacc40

fix spelling

f61f10c

Merge branch 'moseq' of https://github.com/LorenFrankLab/spyglass int…

719486b

…o moseq

fix spelling

24e1150

samuelbray32 requested a review from edeno January 16, 2025 18:26

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Moseq Pipeline #1056

Moseq Pipeline #1056

samuelbray32 commented Aug 6, 2024 •

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samuelbray32 commented Jan 3, 2025

	nwb_file_name: str, position_interval_name: str
	nwb_file_name: str, position_interval_name: str, limit=1


		def fetch_video_path(self):
		"""Return the video path for pose estimate

Moseq Pipeline #1056

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Moseq Pipeline #1056

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samuelbray32 commented Aug 6, 2024 • edited Loading

Description

My To-dos

Checklist:

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CBroz1 commented Jan 2, 2025

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