🔖 Release 1.5.0 by shaneahmed · Pull Request #757 · TissueImageAnalytics/tiatoolbox

shaneahmed · 2023-12-15T14:16:17Z

1.5.0 (2023-12-15)

Major Updates and Feature Improvements

Adds the bokeh visualization tool. ✨ Add bokeh Visualization #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 ✨ Extend Annotation to Support Init from WKB #639
Adds IOConfig for NuClick in pretrained_model.yaml 🐛 Add IOConfig for NuClick in pretrained_model.yaml #709
Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. ❇️ Add Function to Save Engines Output in the zarr Format #724
Adds Support for QuPath Annotation Imports ✨ Add 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. ♻️ Update model_to() and load_torch_model() methods in ModelABC #733
Replaces pretrained with weights to make the engines compatible with the new PyTorch API. ♻️ Replace deprecated input pretrained with weights #621
Adds support for high-level imports for various utility functions and classes such as WSIReader, PatchPredictor and imread ♻️ High Level misc functions Import #606, ♻️ High Level engines Import #607,
Adds tiatoolbox.typing for type hints. ✨ Add tiatoolbox.typing for TypeHints #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. 🐛 Return masks Instead of [mask] in Tissue Masker #748
- Fixes Tissue masker on multiple images #732

Bug Fixes and Other Changes

Fixes pixman incompability error on Colab [skip ci] 🐛 Fix pixman Incompatibility Error on Google Colab #601
Removes shapely.speedups. The module no longer has any affect in Shapely >=2.0. 🗑️ Remove shapely.speedups #622
Fixes errors in the slidegraph example notebook 🐛 Fix Errors in the slidegraph Example Notebook #608
Fixes bugs in WSI Registration Add check for Phase correlation transform #645, 🐛 Fix AffineWSITransformer.read_rect() #670, 🐛 Fix prealignment Function #693
Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. 🐛 Fix patch_coords #712
- Fixes Patch extractor can go (fully) out of bounds #710
Fixes Meet "RuntimeError: dictionary changed size during iteration " in extract_composition_features() function #738 raised by @xiachenrui

Development related changes

Replaces flake8 and isort with ruff ✨ Use ruff for Linting #625, ➖ Remove isort and Use ruff for sorting imports #666
Adds mypy checks to root and utils package. This will be rolled out in phases to other modules. 🚧 Add type checking using mypy #723
Adds a module to detect file types using magic number/signatures ✨ File Magic Detection & NGFF SQLite3 Support #616
Uses poetry for version updates instead of bump2version. 🧑‍💻 Use poetry for Version Updates #638
Removes setup.cfg and uses pyproject.toml for project configurations.
Reduces runtime for some unit tests e.g., ✅ Reduce run time for Mapde test #627, 🧪 Improve micronet Tests #630, ✅ Improve Tests for save_tiles to Reduce Runtime #631, 🧑‍💻 Reduce Test runtime for JP2 #629
Reuses models and datasets in tests on GitHub actions by utilising cache ✅ Reuse models and datasets in tests #641, 💚 Add CI Cache #644
Set up parallel tests locally 💚 Parallel tests #671

Full Changelog: v1.4.0...v1.5.0

updates: - [github.com/executablebooks/mdformat: 0.7.14 → 0.7.16](hukkin/mdformat@0.7.14...0.7.16) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

- Use app.add_css_file.

- Update requirements. - Sphinx 4.5.0 does not resolve on python 3.7 now. The requirement has been downgraded to 4.3.2 and checked html build locally. It passes the build and the output html looks fine. - Changed the base requirements to a single file `requirements.txt`. `requirements_dev.txt` installs any additional dependencies on top of base requirements. conda environment is also based on `requirements.txt` and `requirements_dev.txt` now. - This removes the need for pre-commit check. However, we should modify the pre-commit check according to this update. Co-authored-by: mostafajahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

- DOC: Edit metadata to make all cells visible to rtd. - MAINT: edit raw source of list for jnb-rtd consistency. - MAINT: Remove redundant initial ">" and incorrect double quotes. Then edit for clarity. - MAINT: change "temp" to "tmp" - MAINT: change "tail --lines 1" to "tail -n 1". Change wording around ON_GPU. - MAINT: correct typo - BUG: Remove pretence that ON_GPU=False is viable/meaningful with current software packages. - MAINT: Run Colab with GPU and make requisite changes. - MAINT: Change number of WORKERS to 4. Add comment that the notebook crashes if run without Cuda-enabled GPU. Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Add SCCNN architecture. Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: Dang Vu <24943262+vqdang@users.noreply.github.com>

- Add MapDe architecture. Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com>

- Corrects a single typo in a python module.

updates: - [github.com/psf/black: 22.6.0 → 22.8.0](psf/black@22.6.0...22.8.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

- Adds a GitHub workflow which installs openslide and openjpeg binaries and then runs pip install from the GitHub repo which will install the latest develop version. It then checks that `import tiatoolbox` runs without error. Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

Change md cells only 1. Insert empty line after each heading 2. Replace html format for links. html is a subset of md, but is not understood by rtd. 2. Replace unmatched left parenthesis in url by html tag 3. Change "tail --lines 1" to "tail -n 1" 4. Remove initial ">". JNB-RTD-Compatible indentation is not possible. 5. Change combination of backtick and asterisk to asterisk only. 6. Change ON_GPU from False to True in preparation for bug fix. 7. Cut code cell into three pieces to make it easier to find the bug Obtain the correct legend from overlay-prediction-mask. Save this version with ON_GPU = False with all output. Run under Macos without GPU (ON_GPU == False) and save with outpu Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

- Remove flake8-sql checks as this is not being maintained. - pgjones/flake8-sql#21 Co-authored-by: Shan Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

- DOC: Edit metadata to remove hidden cells. Fix one heading - MAINT: Remove incorrect initial ?>?. Delete incorect double quotes. - MAINT: Remove incooect double quotes. Improve text. Improve code comment. - MAINT: Remove incorrect initial ">" - MAINT: insert empty line before list several times - MAINT: Insert spaces round backticked words and phrases, where appropriate Note: The develop version of visualization.py is necessary for correct legends. Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

@John-P

- Use ABC for PatchExtractor - For SQLExpression, couldn't find an easy way to define it using ABC. Probably ABC is not necessary here? @John-P Please can you check? - Fix DeepSource error Module imports itself PYL-W0406 - Refactored tiatoolbox/models/abc to tiatoolbox/models/models_abc - Fix typos - Add typehints for PatchExtractor Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

- Adds the functionality described in[ #446 ](#446 ). - Adds a `min_mask_ratio` parameter to the patchextractor class so that one can define it as a percentage of the patch area that needs to include mask. Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com>

- Change name of notebook to avoid rtd search ambiguity and insert empty line below - Implement jnb-rtd consistency rules - Implement rules for JNB-RTD consistency and fix a few typos. - Insert missing "the" Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Implement rules for JNB-RTD consistency (see Wiki) - Change working slightly Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Change html theme to furo (https://pradyunsg.me/furo/quickstart/) for better visibility of links. Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

- Fix docstring rendering and typos. - Use `code-block` directive for json. - Exclude `requirements.txt` from sphinx build. - Fix hyperlinks. - Fix indentation for bullet points. - Fix underline for headings. - Fix GitHub links - Fix interpreted text or phrase reference start-string without end-string. Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix spacing around backticked words. - Unhide hidden cells. Change "tail --line 1" to "tail -n 1" Incorporate changes implemented by pre-commit hooks. - Change "tail --line 1" to "tail -n 1". Correct spacing around backticked word. - Rewrite text cell on restarting runtime, and replace non-ascii right-arrow by ampersand encoding. Apply pre-commit hooks.

- Edit notebooks.rst to remove nbgallery - Fix indent - Remove nbgallery from full pipeline and inference pipeline - Update README.md

- Adds feature matching functions for deep feature based registration. Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Add `docs/requirements.txt` to `requirements_dev.txt` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix spacing around backticked words. - Unhide hidden cells. Change "tail --line 1" to "tail -n 1" Incroporate changes implrmented by pre-commit hooks. - Change "tail --line 1" to "tail -n 1". Correct spacing around backticked word. - Rewrite text cell on restarting runtime, and replace non-ascii right-arrow by ampersand encoding. Apply pre-commit hooks. - Unhide hidden cells - Rewrite text cell about restarting runtime under Colab. Replace non-ascii em-dash by " —". Pre-commit hooks. - Redo previous commit more carefully.

- Fixes the colorbar bug cropping in `test_visualization.py`

- Use `requirements.txt` in `setup.py` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

- Adds PR adds macOS pip install test cases to the GitHub workflow. Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Setup workflow on push as GitHub variables for pull request do not work on push.

- Update citation in README.md and CITATION.cff Co-authored-by: John Pocock <John-P@users.noreply.github.com>

- Run pip install workflow only on requirements file - Update numpy requirements

- Improve TIAToolbox import using lazy imports. - Improves importing `import tiatoolbox` by 10 times. - This will improve execution of cli. Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

Add `mypy` checks to - `tiatoolbox/utils/exceptions.py` - `tiatoolbox/utils/magic.py` - `tiatoolbox/utils/metrics.py` - `tiatoolbox/utils/transforms.py` - `tiatoolbox/tiatoolbox.py` --------- Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

Add `utils/misc.py` to mypy --------- Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Update Dependency Link for `pytorch cuda` Version

- Fixes #732. - masks should be returned instead of [mask].

updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.6 → v0.1.7](astral-sh/ruff-pre-commit@v0.1.6...v0.1.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

- Add `mypy` checks to `image.py`

Adds the bokeh visualization. The main features this PR adds: Visualization interface with following features: 1. Viewing of slides 2. Viewing of annotation-store overlays 3. Viewing of graph overlays 4. Viewing of low-res image overlays 5. Dual linked window functionality 6. Various options to control how annotations are displayed/which annotations are displayed 7. Run hovernet on a selected region 8. Inspect annotation properties with double-click 9. 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. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk>

- Fix issue #722

- Add `mypy` checks to `visualization.py`

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@@            Coverage Diff             @@
##           master     #757      +/-   ##
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  Lines        6782     8518    +1736     
  Branches     1352     1637     +285     
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Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix Error in `06-semantic-segmentation` related to `overlay_prediction_mask`

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix example notebook 09

- Fix `idars` example notebook

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

pre-commit-ci bot and others added 30 commits August 30, 2022 10:27

[pre-commit.ci] pre-commit autoupdate (#453)

4d8288b

updates: - [github.com/executablebooks/mdformat: 0.7.14 → 0.7.16](hukkin/mdformat@0.7.14...0.7.16) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

[skip ci] DEV: Use app.add_css_file.

fd957af

- Use app.add_css_file.

MAINT: fix typo (#458)

11b1e10

- Corrects a single typo in a python module.

[pre-commit.ci] pre-commit autoupdate (#460)

fcfcfc2

updates: - [github.com/psf/black: 22.6.0 → 22.8.0](psf/black@22.6.0...22.8.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

DEP: Remove flake8-sql (#459)

966a608

- Remove flake8-sql checks as this is not being maintained. - pgjones/flake8-sql#21 Co-authored-by: Shan Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

DOC: JNB-RTD consistency for 01-wsi-reading.ipynb (#429)

09eff6c

- Implement rules for JNB-RTD consistency (see Wiki) - Change working slightly Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

[skip ci] DOC: Remove nbgallery (#469)

3d5a375

- Edit notebooks.rst to remove nbgallery - Fix indent - Remove nbgallery from full pipeline and inference pipeline - Update README.md

DEV: Add docs/requirements.txt to requirements_dev.txt (#470)

8b7855d

- Add `docs/requirements.txt` to `requirements_dev.txt` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

BUG: Fix the colorbar Bug with plt (#473)

419d7bb

- Fixes the colorbar bug cropping in `test_visualization.py`

DEV: Use requirements.txt in setup.py (#467)

1757f84

- Use `requirements.txt` in `setup.py` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com>

DEV: Add macOS To pip Install Workflow (#464)

3babb4a

- Adds PR adds macOS pip install test cases to the GitHub workflow. Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

DEV: Fix PIP Install Workflow (#477)

fafa65e

- Setup workflow on push as GitHub variables for pull request do not work on push.

[skip ci] DOC: Update citation in README.md and CITATION.cff (#480)

06e8a4f

- Update citation in README.md and CITATION.cff Co-authored-by: John Pocock <John-P@users.noreply.github.com>

DEV: Run PIP Workflow requirements files Only (#481)

bb0a09a

- Run pip install workflow only on requirements file - Update numpy requirements

Jiaqi-Lv and others added 12 commits November 22, 2023 12:28

🔨 Add utils/misc.py to mypy (#744)

df6e947

Add `utils/misc.py` to mypy --------- Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

📌 Update dependency link for pytorch cuda version (#746)

30fa13f

- Update Dependency Link for `pytorch cuda` Version

🐛 Return masks instead of [mask] (#748)

a4463ee

- Fixes #732. - masks should be returned instead of [mask].

[pre-commit.ci] pre-commit autoupdate (#754)

e0b5f5e

updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.6 → v0.1.7](astral-sh/ruff-pre-commit@v0.1.6...v0.1.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

✅ Add mypy checks to image.py (#753)

3afb52a

- Add `mypy` checks to `image.py`

🩹 Fix save_tiles (#752)

4edd779

- Fix issue #722

✅ Add mypy checks to visualization.py (#755)

445c19d

- Add `mypy` checks to `visualization.py`

📝 Update release notes for version 1.5.0

23fefcd

📝 Update version number to 1.5.0

05ad6ff

📝 Update links to master and pip install

16d8aef

shaneahmed added 11 commits December 15, 2023 15:49

Merge branch 'master' into pre-release

81ad7b5

📌 Pin dependencies

dc56927

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

[skip ci] 🐛 Fix error related to overlay_predictions (#758)

07fde55

- Fix Error in `06-semantic-segmentation` related to `overlay_prediction_mask`

Merge branch 'develop' into pre-release

73af404

🐛 Fix deepsource errors

2778454

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

[skip ci] 🐛 Fix example notebook 09 (#759)

6e0ee54

- Fix example notebook 09

[skip ci] 🐛 Fix idars example notebook (#760)

01eb4a2

- Fix `idars` example notebook

Merge branch 'develop' into pre-release

77b462b

📌 Fix pin on dependencies

9a207d4

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

[skip ci] 📝 Update HISTORY.md

6954fe7

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

[skip ci] 📝 Update AUTHORS.md

e7eac32

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

shaneahmed merged commit bba59ba into master Dec 15, 2023

shaneahmed deleted the pre-release branch December 15, 2023 22:28

shaneahmed added the release label Dec 15, 2023

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🔖 Release 1.5.0#757

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1.5.0 (2023-12-15)

Major Updates and Feature Improvements

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