Show progress bar in plugin when running tracking

[p-j-smith]

Fixes #271

• Use napari.utils.progress to provide updates during tracking
• Shows updates for the following steps:
  • Initialising the tracker
  • Convert segmentation to trackable objects
  • Run tracking
  • Run optimisation
  • Convert to napari tracks layer
• The activity dock is displayed during the tracking and hidden again afterwards (if it was hidden before)
• Once tracking has finished, a notification is shown to the user to say it has finished successfully

https://github.com/quantumjot/btrack/assets/29753790/574ff4af-5adb-4062-b383-6f2ab5391094

[codecov-commenter]

Codecov Report

Patch coverage: 33.33% and project coverage change: -0.45% :warning:

Comparison is base (392fbb8) 86.11% compared to head (6ea7da8) 85.67%.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #358 +/- ## ========================================== - Coverage 86.11% 85.67% -0.45% ========================================== Files 30 30 Lines 2125 2143 +18 Branches 394 394 ========================================== + Hits 1830 1836 +6 - Misses 214 226 +12 Partials 81 81 ``` | [Files Changed](https://app.codecov.io/gh/quantumjot/btrack/pull/358?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Alan+R+Lowe) | Coverage Δ | | |---|---|---| | [btrack/napari/main.py](https://app.codecov.io/gh/quantumjot/btrack/pull/358?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Alan+R+Lowe#diff-YnRyYWNrL25hcGFyaS9tYWluLnB5) | `66.15% <29.41%> (-4.29%)` | :arrow_down: | | [btrack/io/\_localization.py](https://app.codecov.io/gh/quantumjot/btrack/pull/358?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Alan+R+Lowe#diff-YnRyYWNrL2lvL19sb2NhbGl6YXRpb24ucHk=) | `90.43% <50.00%> (-1.53%)` | :arrow_down: |

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[deprecated-napari-hub-preview-bot[bot]]

Preview page for your plugin is ready here: https://preview.napari-hub.org/quantumjot/btrack/358 Updated: 2023-08-03T14:04:25.337908

[quantumjot]

This is so simple and so awesome!

[p-j-smith]

This is so simple and so awesome!

Yeah it's surprisingly straightforward!

Do you want to see nested progress bars when running segmentation_to_objects:

https://github.com/quantumjot/btrack/assets/29753790/c465e529-5977-41d1-a300-547cf968ec06

As far as I can tell, you're not using tqdm for the tracking BayesianTracker.track? But if you were we could show more fine-grained progress for that step too

[quantumjot]

Do you want to see nested progress bars

Yes - I think any feedback to the user that something is happening is very useful.

As far as I can tell, you're not using tqdm for the tracking

This would be a pretty simple change and probably be quite beneficial.

[p-j-smith]

Yes - I think any feedback to the user that something is happening is very useful.

Okay cool, I've added that now.

This would be a pretty simple change and probably be quite beneficial.

To get the progess bar to show in napari, all you would need to do is change the tqdm import to be like this:

https://github.com/quantumjot/btrack/blob/a60435083d01078d17fdf2f0876ede45ee99c3cb/btrack/io/_localization.py#L13-L16

napari.utils.progress inherits from tqdm.tqdm and it will display the progress bar in the activity dock if napari is open or in the terminal if not