🆕 Add Reading Slide-level info & Simple Plugins for Visualization Tool #789
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…ics/tiatoolbox into add-slide-data
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #789 +/- ##
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- Coverage 99.89% 97.90% -1.99%
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Files 69 72 +3
Lines 8588 8802 +214
Branches 1645 1677 +32
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+ Hits 8579 8618 +39
- Misses 1 173 +172
- Partials 8 11 +3 ☔ View full report in Codecov by Sentry. |
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shaneahmed
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measty
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…ics/tiatoolbox into add-slide-data
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…ics/tiatoolbox into add-slide-data
shaneahmed
reviewed
Mar 15, 2024
| @@ -2102,6 +2170,7 @@ def setup_doc(self: DocConfig, base_doc: Document) -> tuple[Row, Tabs]: | |||
| base_doc.add_root(control_tabs) | |||
| base_doc.add_root(popup_table) | |||
| base_doc.add_root(slide_info) | |||
| base_doc.add_root(extra_layout) | |||
| base_doc.title = "Tiatoolbox Visualization Tool" | |||
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| base_doc.title = "Tiatoolbox Visualization Tool" | |
| base_doc.title = "TIAToolbox Visualization Tool" |
shaneahmed
reviewed
Mar 15, 2024
| @@ -0,0 +1 @@ | |||
| """plugins and templates for bokeh visualization app.""" | |||
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| """plugins and templates for bokeh visualization app.""" | |
| """Plugins and templates for bokeh visualization app.""" |
shaneahmed
reviewed
Mar 15, 2024
|
|
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| Returns: | ||
| list: A list containing the new children of the extra layout | ||
| """ |
shaneahmed
reviewed
Mar 15, 2024
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| Returns: | ||
| list: A list containing the new children of the extra layout | ||
| """ |
shaneahmed
reviewed
Mar 15, 2024
| file found within a folder for each slide. | ||
| - StatsPlot: Displays a histogram of the distributions of properties of annotations | ||
| contained within the selected box-shaped region of the slide. | ||
| """ |
shaneahmed
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…toolbox into add-slide-data
…ics/tiatoolbox into add-slide-data
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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.