Edit timeline widget user guide

[anna-teruel]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?

The napari plugin now supports manually correcting tracked data and saving it back to movement native format. This widget includes: moving and removing keypoints, flagging edited points, navigating edits with a timeline, and saving the corrected dataset. But, none of this is documented in the user guide yet.

What does this PR do?

Adds a new "Edit tracked data" section to the GUI user guide (docs/source/user_guide/gui.md), placed between "Load the tracked dataset" and "Define regions of interest" to match the order of the widget's collapsible menus.

It covers:

• Move and remove keypoints: step-by-step instructions using the points layer controls, and a note that editing is disabled when the frame axis is not sliced (rolled/transposed dimensions or 3D view).
• What happens after an edit: tracks layer kept in sync, moved points shown as rings, confidence of moved points set to NaN.
• Find edited frames with the timeline: when the edited frames dock appears, it shows a bar for every edited frame. You can use the mouse to interact with the timeline: click on one bar to jump, scroll to zoom, double-click to reset. When there are multiple individuals, you can click on Display individuals and you will get an independent bar for every individual.
• Save the edited data: saving to netCDF via the Save tracked data menu, and what the saved dataset contains (including the new boolean edited variable, and which keypoints/individuals get dropped).
• Resume an editing session: reloading a saved file restores the rings and the timeline, and new edits accumulate on top of previous ones.
• A dropdown showing how to use the edited variable in Python.

It also adds five short GIFs (docs/source/_static/napari_edit_*.gif, napari_edited_points_rings.gif, napari_tracks_update.gif) illustrating each step, and mentions the editing functionality in the page introduction.

References

Documents the functionality added in #1011, #1024, #1025, #1041, #1044, #1053, #1054, #1057 and #1063. Relates to #993.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (1f04ca9) to head (dd6a759).
⚠️ Report is 9 commits behind head on main.

Additional details and impacted files

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[lochhh]

Thanks @anna-teruel for the comprehensive guide! It reads very well for now but I'm thinking we should make the structure easier to extend for when we have newer edit types and my suggestions are here. The GIFs are great 😍! and would be nicer if they could exclude the "loading dataset" part and just begin from whichever point is immediately relevant to the section it illustrates, e.g. a GIF in the select keypoint(s) section would start with keypoints already loaded in the viewer, and show how one keypoint is selected, multiple keypoints can be selected with shift-click , and drag. An even better version would be one that's annotated so the reader knows where to look at and what's going on, e.g. shift-click is unclear from the gif alone, having a text overlay that says "Hold shift + click" on it would be very helpful.

Another thing we would need to update is all the other screenshots that are still missing the new widgets you developed. This doesn't necessarily need to be in this PR, but we could track it as an issue.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[anna-teruel]

Thank you @lochhh for your comments and improving the text of the user guide! 🚀 🎉
I have accepted your PR on my forked repository, so the text is updated.

On my last commit, I updated the videos (changed gifs to mp4) with the notes that you made. Let me know what you think about it! 💃