🔖 Release 1.6.0 #898
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🔖 Release 1.6.0 #898
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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 <[email protected]>
# 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 <[email protected]> Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: Ruqayya Awan <[email protected]> Co-authored-by: Mostafa Jahanifar <[email protected]> Co-authored-by: kesixu <[email protected]> Co-authored-by: David Epstein <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: Simon Graham <[email protected]> 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 <[email protected]>
- 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 <[email protected]> Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: Ruqayya Awan <[email protected]> Co-authored-by: Mostafa Jahanifar <[email protected]> Co-authored-by: kesixu <[email protected]> Co-authored-by: David Epstein <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: Simon Graham <[email protected]> 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 <[email protected]>
- 🚑 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
## 1.4.0 (2023-04-24) ### Major Updates and Feature Improvements - Adds Python 3.11 support \[experimental\] #500 - Python 3.11 is not fully supported by `pytorch` pytorch/pytorch#86566 and `openslide` openslide/openslide-python#188 - Removes Python 3.7 support - This allows upgrading all the dependencies which were dependent on an older version of Python. - Adds Neighbourhood Querying Support To AnnotationStore #540 - This enables easy and efficient querying of annotations within a neighbourhood of other annotations. - Adds `MultiTaskSegmentor` engine #424 - Fixes an issue with stain augmentation to apply augmentation to only tissue regions. - #546 contributed by @navidstuv - Filters logger output to stdout instead of stderr. - Fixes #255 - Allows import of some modules at higher level for improved usability - `WSIReader` can now be imported as `from tiatoolbox.wsicore import WSIReader` - `WSIMeta` can now be imported as `from tiatoolbox.wsicore import WSIMeta` - `HoVerNet`, `HoVerNetPlus`, `IDaRS`, `MapDe`, `MicroNet`, `NuClick`, `SCCNN` can now be imported as \`from tiatoolbox.models import HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNN - Improves `PatchExtractor` performance. Updates `WSIPatchDataset` to be consistent. #571 - Updates documentation for `License` for clarity on source code and model weights license. ### Changes to API - Updates SCCNN architecture to make it consistent with other models. #544 ### Bug Fixes and Other Changes - Fixes Parsing Missing Omero Version NGFF Metadata #568 - Fixes #535 raised by @benkamphaus - Fixes reading of DICOM WSIs at the correct level #564 - Fixes #529 - Fixes `scipy`, `matplotlib`, `scikit-image` deprecated code - Fixes breaking changes in `DICOMWSIReader` to make it compatible with latest `wsidicom` version. #539, #580 - Updates `shapely` dependency to version >=2.0.0 and fixes any breaking changes. - Fixes bug with `DictionaryStore.bquery` and `geometry=None`, i.e. only a where predicate given. - Partly Fixes #532 raised by @blaginin - Fixes local tests for Windows/Linux - Fixes `flake8`, `deepsource` errors. - Uses `logger` instead of `warnings` and `print` statements to properly log runs. ### Development related changes - Upgrades dependencies which are dependent on Python 3.7 - Moves `requirements*.txt` files to `requirements` folder - Removes `tox` - Uses `pyproject.toml` for `bdist_wheel`, `pytest` and `isort` - Adds `joblib` and `numba` as dependencies.
## 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]>
## 1.5.1 (2023-12-16) ### Development related changes - Specifies compatible Python versions - Fixes `tiatoolbox-feedstock` build for conda-forge release #763 **Full Changelog:** v1.5.0...v1.5.1
## TIAToolbox v1.6.0 (2024-12-12) ### Major Updates and Feature Improvements - **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch) - Introduced `TimmBackbone` for running additional PyTorch Image Models. - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`. - Added an example notebook demonstrating feature extraction with foundation models. - `timm` added as a dependency. - **Performance Enhancements with `torch.compile`** (#716) - Improved performance on newer GPUs using `torch.compile`. - **Multichannel Input Support in `WSIReader`** (#742) - **AnnotationStore Filtering for Patch Extraction** (#822) - **Python 3.12 Support** - **Deprecation of Python 3.8 Support** - **CLI Response Time Improvements** (#795) ### API Changes - **Device Specification Update** (#882) - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality. - **Windows Compatibility Enhancement** (#769) - Replaced `POWER` with explicit multiplication. ### Bug Fixes and Other Changes - **TIFFWSIReader Bound Reading Adjustment** (#777) - Fixed `read_bound` to use adjusted bounds. - Reduced code complexity in `WSIReader` (#814). - **Annotation Rendering Fixes** (#813) - Corrected rendering of annotations with holes. - **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch) - **HoVer-Net Documentation Update** (#751) - Corrected class output information. - **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander) - **Bokeh Compatibility Updates** - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`. - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796). - **JSON Extraction Fixes** (#772) - Restructured SQL expression construction for JSON properties with dots in keys. - **VahadaneExtractor Warning** (#871) - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382). - **PatchExtractor Error Message Refinement** (#883) - **Immutable Output Fix in `WSIReader`** (#850) ### Development-Related Changes - **Mypy Checks Added** - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`. - **ReadTheDocs PDF Build Deprecation** - **Formatter Update** - Replaced `black` with `ruff-format`. - **Dependency Removal** - Removed `jinja2`. - **Test Environment Update** - Updated to `Ubuntu 24.04`. - **Conda Environment Workflow Update** - Implemented `micromamba` setup. - **Codecov Reporting Fix** (#811) **Full Changelog:** v1.5.1...v1.6.0 --------- Co-authored-by: John Pocock <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Adam Shephard <[email protected]> Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: Mostafa Jahanifar <[email protected]> Co-authored-by: Simon Graham <[email protected]> Co-authored-by: Abdol A <[email protected]> Co-authored-by: Jiaqi-Lv <[email protected]> Co-authored-by: Dmitrii Blaginin <[email protected]> Co-authored-by: behnazelhaminia <[email protected]> Co-authored-by: George Batchkala <[email protected]> Co-authored-by: vqdang <[email protected]> Co-authored-by: Jiaqi Lv <[email protected]> Co-authored-by: Alon Alexander <[email protected]>
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# Conflicts: # .github/workflows/conda-env-create.yml # .github/workflows/docker-publish.yml # .github/workflows/python-package.yml # .pre-commit-config.yaml # AUTHORS.md # CITATION.cff # HISTORY.md # docs/installation.rst # pyproject.toml # requirements/requirements_dev.txt # setup.py # tiatoolbox/__init__.py # tiatoolbox/wsicore/wsireader.py
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TIAToolbox v1.6.0 (2024-12-12)
Major Updates and Feature Improvements
timmAPI (🆕 Integrate Foundation Models Available VIAtimm:UNI,Prov-GigaPath,H-optimus-0#856, contributed by @GeorgeBatch)TimmBackbonefor running additional PyTorch Image Models.UNI,Prov-GigaPath, andH-optimus-0.timmadded as a dependency.torch.compile(⚡️Addtorch.compileFunctionality #716)torch.compile.WSIReader(🚸 Handle MultidimensionalFeaturesinWSIReader#742)cli.visualizeto ImprovecliResponse #795)API Changes
has_gpuwithdevicefor specifying GPU or CPU usage, aligning with PyTorch'sModel.to()functionality.POWERfrom sqlite-dist Calculations #769)POWERwith explicit multiplication.Bug Fixes and Other Changes
TIFFWSIReaderread_bound#777)read_boundto use adjusted bounds.WSIReader(🐛 Fix Code Complexity inwsireader#814).WSIReader(🚸 Add Support forignore_is_tiled_tiffinWSIReader.open()#807, contributed by @GeorgeBatch)HoVer-NetClass Output Information indocs#751)cffconvert(🐛 FixCITATION.cffto Make it Compatible withcffconvert#869, contributed by @Alon-Alexander)bokeh_appfor compatibility withbokeh>=3.5.0.sizetoradiusforbokeh>3.4.0compatibility (👽 Changesizetoradiusforbokeh 3.4Compatibility #796).json_extractConstruction #772)VahadaneExtractorAlgorithm Instability #871)scikit-learn>0.23.0dictionary learning (Vahadane stain-norm fails #382).PatchExtractorError Message #883)WSIReader(🐛 Fix Immutable Output fromWSIReader#850)Development-Related Changes
utils,tools,data,annotation, andcli/common.blackwithruff-format.jinja2.Ubuntu 24.04.micromambasetup.codecovReporting #811)Full Changelog: v1.5.1...v1.6.0