♻️ Refactor / Split wsireader into Multiple Modules#1075
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- Splits wsireader into multiple modules.
### 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
## 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 <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: DavidBAEpstein <David.Epstein@warwick.ac.uk> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: adamshephard <adam.shephard@warwick.ac.uk> Co-authored-by: Abdol <a@fkrtech.com> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: Abishek <abishekraj6797@gmail.com> Co-authored-by: Dmitrii Blaginin <blaginin@mbp.lan>
## 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 <John-P@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Adam Shephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: Dmitrii Blaginin <blaginin@mbp.lan> Co-authored-by: behnazelhaminia <30952176+behnazelhaminia@users.noreply.github.com> Co-authored-by: George Batchkala <46561186+GeorgeBatch@users.noreply.github.com> Co-authored-by: vqdang <24943262+vqdang@users.noreply.github.com> Co-authored-by: Jiaqi Lv <lvjiaqi9@gmail.com> Co-authored-by: Alon Alexander <alon008@gmail.com>
## TIAToolbox v2.0.0 (2026-03-11) ### ✨ Major Updates and Feature Improvements #### ⚙️ Engine Redesign (PR #578) TIAToolbox 2.0.0 introduces a completely re-engineered inference engine designed for significant performance, scalability, and memory-efficiency improvements. #### Key Enhancements - A modern processing stack built on **Dask** (parallel/distributed execution) and **Zarr** (chunked, out-of-core storage) - **Standardised output formats** across all engines: - Python `dict` - **Zarr** - **AnnotationStore** (SQLite-backed) - **QuPath JSON** - Cleaner runtime behavior with reduced warning noise and a unified progress bar - More predictable memory usage through chunked streaming - Broader test coverage across engine components ### 🗺️ Improved QuPath Support Enhancements include: - Better handling of **GeoJSON** - Support for **multipoint geometries** (#841) - Improved semantic output helpers: - `dict_to_store_semantic_segmentor` (#926) - OME-TIFF probability overlays (#929) ### 🔬 New Nucleus Detection Engine A dedicated nucleus detection pipeline has been added, built on the redesigned engine for improved accuracy and efficient large-scale processing. #### 🧠 KongNet Model Family TIAToolbox 2.0.0 introduces **KongNet**, a high-performance architecture that achieved top results across multiple international challenges: - 🥇 **1st place: MONKEY Challenge (overall detection)** - 🥇 **1st place: MIDOG (mitosis detection)** - ⭐ Top-tier performance on **PUMA** Multiple pretrained variants are available (CoNIC, PanNuke, MONKEY, PUMA, MIDOG), each with standardised IO configurations. ### 🧬 Expanded Foundation Model Support Additional foundation models are now supported (#906), broadening the range of high-capacity architectures available for feature extraction and downstream tasks. ### 🖼️ SAM Segmentation in TIAViz TIAViz now integrates Meta’s Segment Anything Model (SAM), enabling: - Interactive segmentation - Rapid region extraction - Exploratory annotation workflows Simplified SAM usage (#968) streamlines its integration into analysis pipelines. ### 🧩 Enhanced WSIReader & Metadata Handling Major improvements include: - More robust cross-vendor **metadata extraction** (#1001) - **Multichannel image support** (PR #825) for immunofluorescence and non-RGB modalities - Simplified Windows installation using `openslide-bin` (no manual DLL steps) - macOS Tileserver fix (#976) - Improved DICOM reading (#934) ### ☁️ New Cloud-Native Reader: FsspecJSONWSIReader (PR #897) A new reader supporting **fsspec-compatible filesystems**, enabling seamless access to WSIs stored on: - S3 - GCS - Azure - HPC clusters - Any fsspec-supported backend This enables cloud-native and distributed data workflows. Contributed by @aacic ### 🤗 Pretrained Models Migrated to Hugging Face All pretrained models and sample assets have been migrated (#945, #983), improving: - Download reliability - Versioning and reproducibility - Caching and CI integration - Licensing clarity per model family ### 🛡️ Security, Compatibility & Tooling #### 🔐 Security & Dependency Updates - Dependency upgrades - Internal security improvements - Explicit workflow permissions added (#1021, #1023) #### 🐍 Python Version Support - **Dropped:** Python **3.9** - **Added:** Python **3.13** - **Supported:** Python 3.10–3.13 - Updated CUDA wheel source to **cu126** #### 🛠️ Developer Tooling & CI/CD - Expanded **mypy** type-checking coverage (#912, #931, #935, #951) - Updated pre-commit hooks and general formatting - CI uses **CPU-only PyTorch** for faster, more reliable builds (#974, #979) - Updated pip install workflow (#1013) - Added new **Python 3.13 Docker images** (#1014, #1019) ### 🧹 Bug Fixes & Stability Improvements - Fixed multi-GPU behaviour with `torch.compile` (#923) - Fixed DICOM reading issue (#934) - Fixed annotation contour handling with holes (#956) - Fixed consecutive annotation load bug (#927) - Fixed SCCNN model issues (#970) - Fixed MapDe `dist_filter` shape issue (#914) - Improved notebook reliability on Colab (#1026–#1030) - macOS TileServer issues resolved (#976) ### 🧭 Migration Guide for Users #### 🔄 Updating from 1.x to 2.0.0 #### Update calls: replace `.predict()` with `.run()` ```python # Old results = segmentor.predict(imgs=[...], ioconfig=config) # New results = segmentor.run(images=[...], ioconfig=config) ``` #### Use `patch_mode`: replace `mode="patch"` with `patch_mode=True` and `mode="tile"` or "wsi" with `patch_mode=False` ```python # Old results = segmentor.predict(imgs=[...], mode="patch", ioconfig=config) # New results = segmentor.run(images=[...], patch_mode=True, ioconfig=config) ``` ```python # Old results = segmentor.predict(imgs=[...], mode="wsi", ioconfig=config) # New results = segmentor.run(images=[...], patch_mode=False, ioconfig=config) ``` #### Use the new I/O configs ```python from tiatoolbox.models.engine.io_config import IOSegmentorConfig config = IOSegmentorConfig( patch_input_shape=(256, 256), stride_shape=(240, 240), input_resolutions=[{"resolution": 0.25, "units": "mpp"}], save_resolution={"units": "baseline", "resolution": 1.0} ) ``` #### Specify the output format ```python results = segmentor.run( images=[...], ioconfig=ioconfig, output_type="zarr", # or "dict", "annotationstore", "qupath" save_dir="outputs/" ) ``` #### Update imports - `tiatoolbox.typing` → `tiatoolbox.type_hints` #### Install requirements - Python **3.10+** required - On Windows: install OpenSlide via `pip install openslide-bin` **Full Changelog:** v1.6.0...v2.0.0 --------- Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: measty <20169086+measty@users.noreply.github.com> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yijie Zhu <120978607+YijieZhu15@users.noreply.github.com> Co-authored-by: Aleksandar Acic <32873451+aacic@users.noreply.github.com> Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk> Co-authored-by: Abishek <abishekraj6797@gmail.com> Co-authored-by: behnazelhaminia <30952176+behnazelhaminia@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Adam Shephard <adam.shephard@warwick.ac.uk> Co-authored-by: gozdeg <gozdegunesli@gmail.com> Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com> Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Co-authored-by: mbasheer04 <78800844+mbasheer04@users.noreply.github.com> Co-authored-by: vqdang <24943262+vqdang@users.noreply.github.com>
## TIAToolbox v2.0.1 (2026-03-16) ### Bug Fixes and Other Changes - Fixes filtering of tiles for post-processing within masked region (#1037). - Fixes Calculation of `max_inst_value` for Instances where overlap is empty (#1038) **Full Changelog:** v2.0.0...v2.0.1
## TIAToolbox v2.1.0 (2026-05-19) ### ✨ Major Updates and Feature Improvements - Python ≥3.11 required - Supports up to 3.14 (#1035) - Drops support for 3.10 (#1034) - Zarr v3 Support (#904) - New storage APIs (zarr.Array, LocalStore, FsspecStore) - Removal of object arrays → rectangular storage via pad_contours - Update `FsspecJsonWSIReader` to support Zarr v3 (#1049), thanks to @aacic ###⚠️ API Changes - Python requirement updated → >=3.11, \<3.15 ### 🐞 Bug Fixes and Other Changes - Fixed - Contour serialization and padding issues (Zarr compatibility) (#904) - Invalid Geometry in JSON Outputs (#1057) - Fix typographical errors in `pre-trained` documentation (#1043, #1062) ### 🛠️ Development-Related Changes - Use `uv` to set up CI environments, reduces installation time - Update instructions for `uv` install - Use `max_image` for `remove_small_objects` in `scikit-image` usage (#1048) - Improve `mypy` workflow and typing errors (#1045) --------- Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: measty <20169086+measty@users.noreply.github.com> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: Aleksandar Acic <32873451+aacic@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Aakash Madhav Rao <axr1154@student.bham.ac.uk> Co-authored-by: Yijie Zhu <120978607+YijieZhu15@users.noreply.github.com> Co-authored-by: gozdeg <gozdegunesli@gmail.com> Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
This commit restructures the 7,678-line wsireader.py into a well-organized wsireader/ package with 11 modular files: - base.py: Base reader class and interfaces - tiled_readers/: Tiled format readers (SVS, OME-TIFF, CZI) - single_readers/: Single-image readers (Pillow-based) - generic_readers/: Generic/fallback readers - ndpi_reader.py: NDPI format support - vips_reader.py: libvips-based reader Benefits: - Improved code organization and maintainability - Easier to locate and modify specific reader implementations - Clearer separation of concerns - Backward compatible via wsireader.py wrapper All public APIs remain unchanged. Module structure enables future enhancements to individual readers without affecting the monolith.
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