Allow tracking on `Instance`s (by adding `Instance.tracking_score`) #1302

roomrys · 2023-05-05T00:40:51Z

Description

Prior to Allow Retracking, we did not allow any tracking on user instances. Since re-tracking enables users to run tracking on user instances, we now need to either add a tracking_score attribute to user-instances, or refrain from assigning the tracking score if the matched instance is a user instance (see #1301). This PR adds an Instance.tracking_score attribute and updates spots where the tracking_score is written (including a FORMAT_ID bump in LabelsV1Adaptor).

Types of changes

Bugfix (Should have done this in Allow retracking #867)
New feature (Allow tracking on instances)
Refactor / Code style update (no logical changes)
Build / CI changes
Documentation Update
Other (explain)

Does this address any currently open issues?

Allow Tracking-Only Pipeline (GUI & CLI) #1296

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Summary by CodeRabbit

New Features
- Enhanced tracking capabilities with consistent recording, display, and persistence of tracking scores across the app.
- Improved instance tracking logic now prioritizes user-defined instances over automated predictions for greater accuracy.
Tests
- Added automated tests to verify the accurate preservation and functionality of tracking scores during data saving and loading.

codecov · 2023-05-05T01:11:31Z

Codecov Report

Attention: Patch coverage is 78.57143% with 3 lines in your changes missing coverage. Please review.

Project coverage is 76.16%. Comparing base (7991f14) to head (5ebf04a).
Report is 97 commits behind head on develop.

Files with missing lines	Patch %	Lines
sleap/nn/tracking.py	62.50%	3 Missing ⚠️

❌ Your patch check has failed because the patch coverage (78.57%) is below the target coverage (100.00%). You can increase the patch coverage or adjust the target coverage.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1302      +/-   ##
===========================================
+ Coverage    75.43%   76.16%   +0.73%     
===========================================
  Files          134      134              
  Lines        24749    24812      +63     
===========================================
+ Hits         18670    18899     +229     
+ Misses        6079     5913     -166

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

talmo · 2023-05-05T19:30:17Z

Quick question: what happens when there is a user Instance that was created from a PredictedInstance on a frame? Will the user Instance be used preferentially and the PredictedInstance ignored? If not, this may lead to issues where extraneous tracks are generated right?

roomrys · 2023-05-25T00:29:52Z

All instances in the labeled frame were being considered individually. I've added the following to prefer user labeled instances in the frame if any:

sleap/sleap/nn/tracking.py

Lines 1192 to 1213 in 1ea047d

    
           # Prefer user instances over predicted instances 
        
           instances = [] 
        
           if lf.has_user_instances: 
        
               instances_to_track = lf.user_instances 
        
               if lf.has_predicted_instances: 
        
                   instances = lf.predicted_instances 
        
           else: 
        
               instances_to_track = lf.predicted_instances 
        
           track_args = {"untracked_instances": instances_to_track} 
        
           if tracker.uses_image: 
        
               track_args["img"] = lf.video[lf.frame_idx] 
        
           else: 
        
               track_args["img"] = None 
        
           instances.extend(tracker.track(**track_args)) 
        
           new_lf = LabeledFrame( 
        
               frame_idx=lf.frame_idx, 
        
               video=lf.video, 
        
               instances=instances, 
        
           )

roomrys · 2023-05-25T21:20:27Z

Holding off on this PR since it would require a file format update... best to be worn in on the develop branch for a bit before tacking onto the release. This mean that retracking can only be done on prediction-only projects until this PR is merged (i.e. users need to remove their user-labeled instances before retracking to avoid error).

coderabbitai · 2025-02-04T22:44:24Z

Walkthrough

This pull request introduces explicit handling of tracking scores across multiple modules. A new tracking_score attribute is added to the Instance class, and associated functions are updated to assign and propagate this value. The changes modify tracking score assignment in occupancy matrix generation, file I/O adaptors (HDF5 and Nix), and the logic used by the tracker to prioritize user-defined instances. A new test function has also been added to verify that tracking scores persist correctly when labels are saved and reloaded.

Changes

File(s)	Change Summary
`sleap/info/write_tracking_h5.py`	Updated `get_occupancy_and_points_matrices` function by adding a line to assign the instance’s `tracking_score` to the tracking scores array.
`sleap/instance.py`	Added `tracking_score: float` attribute to `Instance` and updated `__repr__`; removed `tracking_score` from `PredictedInstance` and modified `from_instance` and `__getitem__` to pass and handle tracking scores properly.
`sleap/io/format/hdf5.py`, `sleap/io/format/nix.py`	Upgraded HDF5 adaptor’s `FORMAT_ID` to 1.3 and modified read/write methods (in HDF5) and chunked write (in Nix) to include explicit handling of `tracking_score`.
`sleap/nn/tracking.py`	Modified the `run_tracker` function to prioritize user instances over predicted ones and updated the `track_args` accordingly.
`tests/io/test_dataset.py`	Added a new test function `test_instance_cattr` to validate that tracking scores are properly saved and loaded within labels.

Sequence Diagram(s)

sequenceDiagram
    participant LF as LabeledFrame
    participant run as run_tracker
    participant Tracker as Tracker
    LF->>run: Provide instances (user & predicted)
    alt User instances present
       run->>run: Select user instances for tracking
       run->>Tracker: Call tracker.track(user instances)
    else No user instances
       run->>Tracker: Call tracker.track(predicted instances)
    end
    Tracker-->>run: Return tracked instances
    run->>LF: Update LabeledFrame with tracked instances

Possibly related PRs

Add tracking score as seekbar header options #2047: Introduced changes to add tracking_score as a constructor parameter for PredictedInstance and update occupancy matrix handling, which closely relates to these modifications.

Suggested labels

2024-hackathon

Suggested reviewers

talmo
gitttt-1234
eberrigan

Poem

I’m a rabbit in a code-filled glen,
Hopping through changes again and again.
Tracking scores now dance in the light,
With steps so nimble and logic so bright.
I nibble on bugs and skip past the fray,
Celebrating new code in my bunny way!
🐰💻

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📥 Commits

Reviewing files that changed from the base of the PR and between 59e1f70 and 5ebf04a.

📒 Files selected for processing (6)

sleap/info/write_tracking_h5.py (1 hunks)
sleap/instance.py (4 hunks)
sleap/io/format/hdf5.py (3 hunks)
sleap/io/format/nix.py (1 hunks)
sleap/nn/tracking.py (1 hunks)
tests/io/test_dataset.py (1 hunks)

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🔇 Additional comments (11)

sleap/info/write_tracking_h5.py (1)

180-180: LGTM! Tracking score assignment is now consistent for all instances.

The change ensures that tracking scores are correctly recorded for both user and predicted instances.

sleap/io/format/nix.py (1)

242-242: LGTM! Tracking score is now consistently written to NIX format.

The change ensures that tracking scores are correctly written to NIX format files for both user and predicted instances.

sleap/io/format/hdf5.py (2)

31-36: LGTM! Format version and documentation updated correctly.

The format version bump and documentation update properly track the addition of tracking scores for Instance objects.

226-228: LGTM! Backward compatibility is maintained for tracking scores.

The conditional assignment ensures backward compatibility by defaulting to 0.0 for older format versions while supporting tracking scores in version 1.3+.

tests/io/test_dataset.py (1)

750-778: LGTM! Comprehensive test coverage for tracking scores.

The test thoroughly verifies:

Default tracking score initialization

Tracking score modification

Persistence through save/load operations

Handling for both user and predicted instances

sleap/nn/tracking.py (2)

1566-1584: LGTM! The user instance prioritization logic is well implemented.

The changes correctly implement the prioritization of user instances over predicted instances during tracking, which aligns with the PR objectives. The logic handles both cases appropriately:

When user instances exist: They are assigned to instances_to_track while predicted instances go to instances.

When no user instances exist: Predicted instances are used for tracking.

775-787: LGTM! The tracking score assignment is correctly implemented.

The method properly assigns tracking scores to instances using attr.evolve, which is the recommended way to update attrs objects. The tracking score is correctly propagated from the match score.

sleap/instance.py (4)

373-374: LGTM! The tracking_score attribute is properly defined.

The tracking_score attribute is correctly added to the Instance class with appropriate type conversion and default value.

668-669: LGTM! The tracking score is properly included in the string representation.

The tracking score is correctly added to the __repr__ method with appropriate formatting (2 decimal places).

1458-1458: LGTM! The return type annotation is more accurate.

The return type annotation is correctly updated to Union[Instance, PredictedInstance], which better reflects the actual types that can be returned by this method.

1031-1032: LGTM! The tracking score is properly included in the predicted instance representation.

The tracking score is correctly added to the PredictedInstance.__repr__ method with consistent formatting, matching the base Instance class implementation.

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roomrys added 4 commits May 4, 2023 15:53

Add tracking_score attribute to Instances

2711269

Update adaptors to write tracking scores for Instances

91466b6

Set default Instance.tracking_score = 0.0

e4fc1b0

Bump FORMAT_ID and read/write Instance.tracking_score

eb8fda4

roomrys mentioned this pull request May 5, 2023

Allow tracking on Instances (by not assigning a tracking_score) #1301

Closed

11 tasks

roomrys added the Re-tracking Spread This PR is part of the re-tracking spread of PRs label May 5, 2023

roomrys marked this pull request as ready for review May 5, 2023 18:08

roomrys added 2 commits May 24, 2023 15:46

Prefer user instances when tracking

d882640

Add back instances that were not tracked

1ea047d

roomrys self-assigned this Jan 5, 2024

gitttt-1234 self-requested a review December 16, 2024 22:39

gitttt-1234 approved these changes Dec 16, 2024

View reviewed changes

Merge branch 'develop' into liezl/add-tracking-score-to-inst

5ebf04a

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Allow tracking on `Instance`s (by adding `Instance.tracking_score`) #1302

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roomrys commented May 5, 2023 • edited by coderabbitai bot Loading

Description

Types of changes

Does this address any currently open issues?

Outside contributors checklist

Thank you for contributing to SLEAP!

Summary by CodeRabbit

codecov bot commented May 5, 2023 • edited Loading

Codecov Report

talmo commented May 5, 2023

roomrys commented May 25, 2023

roomrys commented May 25, 2023 • edited Loading

coderabbitai bot commented Feb 4, 2025 • edited Loading

Walkthrough

Changes

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Allow tracking on `Instance`s (by adding `Instance.tracking_score`) #1302

Allow tracking on `Instance`s (by adding `Instance.tracking_score`) #1302

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