✨ Add `bokeh` Visualization #684

measty · 2023-08-04T08:47:00Z

This PR adds the bokeh visualization.

The main features this PR adds:

Visualization interface with following features:

Viewing of slides
Viewing of annotation-store overlays
Viewing of graph overlays
Viewing of low-res image overlays
Dual linked window functionality
Various options to control how annotations are displayed/which annotations are displayed
Run hovernet on a selected region
Inspect annotation properties with double-click
Slide info is shown below main view window

Adds cli command tiatoolbox visualize to launch UI. The usage has been changed to either:

tiatoolbox visualize --base-path path\to\parent\of\slides_and_overlays

or

tiatoolbox visualize --slides path\to\slides --overlays path\to\overlays

Adds a documentation page on how to use the UI, and providing some examples of how to create/modify an annotation store for visualization in some common scenarios.

Documentation available at this link https://tia-toolbox.readthedocs.io/en/add-bokeh-app/

…toolbox into add-bokeh-app

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requirements/requirements.txt

tests/test_bokeh_app.py

tiatoolbox/cli/visualize.py

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measty · 2023-11-30T21:45:18Z

I tried to load the output of Cerberus (.dat files) directly, but the annotations weren't scaled correctly, so I ended up having to manually calculate the scale factor then converting them into annotation store. This is not a big problem, but it would be good if this can be done automatically? (The output of Cerberus has information about base resolution of the WSI and process resolution)

I've added a check in store_from_dat that looks to see if resolution information is available in the .dat file, and will use it to calculate a scale_factor if it is there.

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Jiaqi-Lv · 2023-12-01T12:56:37Z

I have just noticed a bug, If I dis-select all types of annotations, all the annotations would still appear on the slide.

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measty · 2023-12-04T15:11:22Z

I have just noticed a bug, If I dis-select all types of annotations, all the annotations would still appear on the slide.

Those buttons aren't really meant to be used to turn everything off (just use the overlay toggle for that) but i've fixed it so that if someone does do this it will act as expected and turn all types off.

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shaneahmed

Thanks @measty

This is a great addition to the toolbox.

shaneahmed · 2023-12-08T14:11:37Z

@John-P Please can you confirm if you are happy with this PR? We are waiting for this PR to make the next release before Christmas.

shaneahmed · 2023-12-15T11:26:41Z

Thanks @measty for adding this feature to the toolbox.

@TomastpPereira

## 1.5.0 (2023-12-15) ### Major Updates and Feature Improvements - Adds the bokeh visualization tool. #684 - The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines. - This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/. - Extends Annotation to Support Init from WKB #639 - Adds `IOConfig` for NuClick in `pretrained_model.yaml` #709 - Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724 - Adds Support for QuPath Annotation Imports #721 ### Changes to API - Adds `model.to(device)` and `model.load_model_from_file()` functionality to make it compatible with PyTorch API. #733 - Replaces `pretrained` with `weights` to make the engines compatible with the new PyTorch API. #621 - Adds support for high-level imports for various utility functions and classes such as `WSIReader`, `PatchPredictor` and `imread` #606, #607, - Adds `tiatoolbox.typing` for type hints. #619 - Fixes incorrect file size saved by `save_tiles`, issue with certain WSIs raised by @TomastpPereira - TissueMasker transform now returns mask instead of a list. #748 - Fixes #732 ### Bug Fixes and Other Changes - Fixes `pixman` incompability error on Colab #601 - Removes `shapely.speedups`. The module no longer has any affect in Shapely >=2.0. #622 - Fixes errors in the slidegraph example notebook #608 - Fixes bugs in WSI Registration #645, #670, #693 - Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712 - Fixes #710 - Fixes #738 raised by @xiachenrui ### Development related changes - Replaces `flake8` and `isort` with `ruff` #625, #666 - Adds `mypy` checks to `root` and `utils` package. This will be rolled out in phases to other modules. #723 - Adds a module to detect file types using magic number/signatures #616 - Uses `poetry` for version updates instead of `bump2version`. #638 - Removes `setup.cfg` and uses `pyproject.toml` for project configurations. - Reduces runtime for some unit tests e.g., #627, #630, #631, #629 - Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644 - Set up parallel tests locally #671 **Full Changelog:** v1.4.0...v1.5.0 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mostafajahanifar <[email protected]> Co-authored-by: John Pocock <[email protected]> Co-authored-by: DavidBAEpstein <[email protected]> Co-authored-by: David Epstein <[email protected]> Co-authored-by: Ruqayya Awan <[email protected]> Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: Abdol <[email protected]> Co-authored-by: Jiaqi-Lv <[email protected]> Co-authored-by: Abishek <[email protected]> Co-authored-by: Dmitrii Blaginin <[email protected]>

@TomastpPereira

## 1.5.0 (2023-12-15) ### Major Updates and Feature Improvements - Adds the bokeh visualization tool. #684 - The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines. - This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/. - Extends Annotation to Support Init from WKB #639 - Adds `IOConfig` for NuClick in `pretrained_model.yaml` #709 - Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724 - Adds Support for QuPath Annotation Imports #721 ### Changes to API - Adds `model.to(device)` and `model.load_model_from_file()` functionality to make it compatible with PyTorch API. #733 - Replaces `pretrained` with `weights` to make the engines compatible with the new PyTorch API. #621 - Adds support for high-level imports for various utility functions and classes such as `WSIReader`, `PatchPredictor` and `imread` #606, #607, - Adds `tiatoolbox.typing` for type hints. #619 - Fixes incorrect file size saved by `save_tiles`, issue with certain WSIs raised by @TomastpPereira - TissueMasker transform now returns mask instead of a list. #748 - Fixes #732 ### Bug Fixes and Other Changes - Fixes `pixman` incompability error on Colab #601 - Removes `shapely.speedups`. The module no longer has any affect in Shapely >=2.0. #622 - Fixes errors in the slidegraph example notebook #608 - Fixes bugs in WSI Registration #645, #670, #693 - Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712 - Fixes #710 - Fixes #738 raised by @xiachenrui ### Development related changes - Replaces `flake8` and `isort` with `ruff` #625, #666 - Adds `mypy` checks to `root` and `utils` package. This will be rolled out in phases to other modules. #723 - Adds a module to detect file types using magic number/signatures #616 - Uses `poetry` for version updates instead of `bump2version`. #638 - Removes `setup.cfg` and uses `pyproject.toml` for project configurations. - Reduces runtime for some unit tests e.g., #627, #630, #631, #629 - Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644 - Set up parallel tests locally #671 **Full Changelog:** v1.4.0...v1.5.0

measty and others added 12 commits July 13, 2023 05:00

initial bokeh app commit

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shaneahmed assigned measty Aug 4, 2023

shaneahmed changed the title ~~ENH: Add bokeh visualization~~ ENH: Add bokeh Visualization Aug 4, 2023

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shaneahmed added this to the Release v1.5.0 milestone Aug 4, 2023

shaneahmed added the enhancement New feature or request label Aug 4, 2023

shaneahmed and others added 11 commits August 4, 2023 13:22

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shaneahmed added 3 commits December 8, 2023 14:22

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🔖 Release 1.5.0 #757

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🔖 Release 1.5.0 #761

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