🆕 Add Reading Slide-level info & Simple Plugins for Visualization Tool

[measty]

This PR adds in a feature from the most recent version of TIAViz to allow a .csv to be provided in the slides folder that can contain slide level predictions or ground truth labels/other slide level info.

When loading a slide in the UI, if the slide name (including suffix) appears in the "Image File" column of the .csv, any information in the corresponding row of the .csv will appear in the UI below the main window in a nicely formatted string.

Only the "Image File" column is required for this to work, the rest of the columns can be anything you need to have displayed.

Also adds entry in documentation describing feature.

In response to Mostafa's request for more flexibility in what sort of extra info you can add to the UI, i've also added some basic plugin functionality to this PR (and converted to draft for now as it has become much larger and needs tests/docs to be added over the coming weeks, and may be tweaked a bit).

Plugins are defined as a class following an ABC and can add a collection of bokeh UI elements and/or plots below the main view window (and can potentially also insert additional UI elements into the main controls section). This is pretty flexible and can add some quite complex extras in there as you have all the power of bokeh to work with.

I have added 3 pre-built plugins that will cover some use-cases, and provide examples which users can adapt or take inspiration from to make their own custom plugin.

The 3 provided are:
ImageGrid: if each slide has a folder of images associated with it, this plugin will show the images in a grid-like layout below the slide view window.
BarPLotGrid: makes a gridlike layout of bar charts from csv files associated with each slide
StatsPlot: adds some UI elements to show a histogram showing the distribution of a property over the annotations in the selected box on the slide window

To add plugins when launching the tool, you can add one or more --plugin arguments each with a path pointing to the file where the plugin class is.

[codecov]

Codecov Report

❌ Patch coverage is 22.60870% with 178 lines in your changes missing coverage. Please review.
✅ Project coverage is 97.49%. Comparing base (1b4f642) to head (a0de89f).

Files with missing lines	Patch %	Lines
...ox/visualization/bokeh_app/templates/stats_plot.py	0.00%	73 Missing ⚠️
...visualization/bokeh_app/templates/bar_plot_grid.py	0.00%	44 Missing ⚠️
...ox/visualization/bokeh_app/templates/image_grid.py	0.00%	30 Missing ⚠️
tiatoolbox/visualization/bokeh_app/main.py	54.23%	21 Missing and 6 partials ⚠️
tiatoolbox/visualization/ui_utils.py	81.81%	4 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #789      +/-   ##
===========================================
- Coverage    99.37%   97.49%   -1.89%     
===========================================
  Files           71       74       +3     
  Lines         9176     9389     +213     
  Branches      1197     1221      +24     
===========================================
+ Hits          9119     9154      +35     
- Misses          31      203     +172     
- Partials        26       32       +6     

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[shaneahmed]

Suggested change

	base_doc.title = "Tiatoolbox Visualization Tool"
	base_doc.title = "TIAToolbox Visualization Tool"

[shaneahmed]

Suggested change

	"""plugins and templates for bokeh visualization app."""
	"""Plugins and templates for bokeh visualization app."""

[JiwaniZakir]

In tests/test_app_bokeh.py around line 162, the fetch_sample_to_dir call for "test_meta" is missing its closing parenthesis and second argument (the destination directory), leaving the call syntactically broken — this will cause the fixture to fail at runtime. Compare it to every other fetch_sample_to_dir invocation in the same fixture, which all pass a destination path as the second positional argument.

The rename of UI_elements_1/UI_elements_2 to ui_elements_1/ui_elements_2 in docs/visualization.rst (lines 473 and 488) is a silently breaking change for anyone with an existing config file using the old key names. It would be worth either adding a deprecation path in the config-loading code that accepts both casings, or at minimum calling out the rename explicitly as a breaking change in the docs rather than quietly updating the example snippet.

The --plugin CLI help string in tiatoolbox/cli/visualize.py uses a Windows-style backslash path (tiatoolbox\visualization\templates) which will render as escape sequences or just look wrong on Linux/macOS — it should use forward slashes or os.path.join-style notation in documentation strings.