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🔖 Release 1.4.0 - #600
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🔖 Release 1.4.0#600
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### Major Updates and Feature Improvements - Adds an AnnotationTileGenerator and AnnotationRenderer which allows serving of tiles rendered directly from an annotation store. - Adds [DFBR](https://arxiv.org/abs/2202.09971) registration model and jupyter notebook example - Adds DICE metric - Adds [SCCNN](https://doi.org/10.1109/tmi.2016.2525803) architecture. \[[read the docs](https://tia-toolbox.readthedocs.io/en/develop/_autosummary/tiatoolbox.models.architecture.sccnn.SCCNN.html)\] - Adds [MapDe](https://arxiv.org/abs/1806.06970) architecture. \[[read the docs](https://tia-toolbox.readthedocs.io/en/develop/_autosummary/tiatoolbox.models.architecture.mapde.MapDe.html)\] - Adds support for reading MPP metadata from NGFF v0.4 - Adds enhancements to tiatoolbox.annotation.storage that are useful when using an AnnotationStore for visualization purposes. ### Changes to API - None ### Bug Fixes and Other Changes - Fixes colorbar_params #410 - Fixes Jupyter notebooks for better read the docs rendering - Fixes typos, metadata and links - Fixes nucleus_segmentor_engine for boundary artefacts - Fixes the colorbar cropping in tests - Adds citation in README.md and CITATION.cff to Nature Communications Medicine paper - Fixes a bug #452 raised by @rogertrullo where only the numerator of the TIFF resolution tags was being read. - Fixes HoVer-Net+ post-processing to be inline with original work. - Fixes a bug where an exception would be raised if the OME XML is missing objective power. ### Development related changes - Uses Furo theme for readthedocs - Replaces nbgallery and nbsphinx with myst-nb for jupyter notebook rendering - Uses myst for markdown parsing - Uses requirements.txt to define dependencies for requirements consistency - Adds notebook AST pre-commit hook - Adds check to validate python examples in the code - Adds check to resolve imports - Fixes an error in a docstring which triggered the failing test. - Adds pre-commit hooks to format markdown and notebook markdown - Adds pip install workflow to resolve dependencies when requirements file is updated - Improves TIAToolbox import using LazyLoader Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
# 1.3.1 (2022-12-20) ### Major Updates and Feature Improvements - Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449 - Adds Annotation Store Reader #476 - Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510 ### Changes to API - Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517 ### Bug Fixes and Other Changes - Simplifies example notebook for image reading for better readability - Restricts Shapely version to \<2.0.0 for compatibility ### Development related changes - Adds GitHub workflow for automatic generation of docker image - Updates dependencies - Updates bump2version config - Enables flake8 E800 checks for commented codes. - Fixes several errors generated by DeepSource. - Prevent test dumping file to root - Removes duplicate functions to generate parameterized test scenarios Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Roger Trullo <rogertrullo@hotmail.com>
- Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449 - Adds Annotation Store Reader #476 - Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510 - Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517 - Simplifies example notebook for image reading for better readability - Restricts Shapely version to \<2.0.0 for compatibility - Adds GitHub workflow for automatic generation of docker image - Updates dependencies - Updates bump2version config - Enables flake8 E800 checks for commented codes. - Fixes several errors generated by DeepSource. - Prevent test dumping file to root - Removes duplicate functions to generate parameterized test scenarios Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Roger Trullo <rogertrullo@hotmail.com>
- 🚑 Hotfix - Restricts wsidicom version to \<0.7.0 for compatibility - Fix bug related to reading DICOM files
## 1.3.3 (2023-03-02) ### Major Updates and Feature Improvements - Restricts dependency versions for long term stability of the current version ### Changes to API None ### Bug Fixes and Other Changes - Fix bug related to reading scikit-image ### Development related changes - Restricts dependency versions for compatibility
- Update HISTORY.md with release notes
- Update HISTORY.md with release notes
- Update Jupyter notebook links
- Pin dependencies for long term stable release
# Conflicts: # requirements/requirements.txt
- Update `numpy` pin
# Conflicts: # requirements/requirements.txt
- Update HISTORY.md
- Pin dependecies
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## develop #600 +/- ##
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Coverage 99.77% 99.77%
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- Revert updates to notebooks
- Revert changes to requirements.txt for master and tag release
- Revert changes to requirements.txt for master and tag release
- Revert changes to notebooks
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1.4.0 (2023-04-24)
Major Updates and Feature Improvements
pytorchSupport Python 3.11 pytorch/pytorch#86566 andopenslideworkflows: build wheels for all OS; python 3.11 support openslide/openslide-python#188AnnotationStore#540MultiTaskSegmentorengine ✨ Feature Engine for Multi-Task Segmenter #424WSIReadercan now be imported asfrom tiatoolbox.wsicore import WSIReaderWSIMetacan now be imported asfrom tiatoolbox.wsicore import WSIMetaHoVerNet,HoVerNetPlus,IDaRS,MapDe,MicroNet,NuClick,SCCNNcan now be imported as `from tiatoolbox.models import HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNNPatchExtractorperformance. UpdatesWSIPatchDatasetto be consistent. ⚡ Faster Filtering in Patch Dataset #571Licensefor clarity on source code and model weights license.Changes to API
Bug Fixes and Other Changes
read_region#564slide_thumbnailmethod does not work properly with DICOM WSIs #529scipy,matplotlib,scikit-imagedeprecated codeDICOMWSIReaderto make it compatible with latestwsidicomversion. 🚑 BUG: Fix DICOMWSIReader Metadata Reading #539, 🐛 Fix for RecentwsidicomUpdate #580shapelydependency to version >=2.0.0 and fixes any breaking changes.DictionaryStore.bqueryandgeometry=None, i.e. only a where predicate given.flake8,deepsourceerrors.loggerinstead ofwarningsandprintstatements to properly log runs.Development related changes
requirements*.txtfiles torequirementsfoldertoxpyproject.tomlforbdist_wheel,pytestandisortjoblibandnumbaas dependencies.