🔖 Release 1.5.0

[shaneahmed]

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

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@@            Coverage Diff             @@
##           master     #757      +/-   ##
==========================================
+ Coverage   99.77%   99.91%   +0.13%     
==========================================
  Files          63       69       +6     
  Lines        6782     8518    +1736     
  Branches     1352     1637     +285     
==========================================
+ Hits         6767     8511    +1744     
+ Misses          7        0       -7     
+ Partials        8        7       -1     

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