Tiatoolbox

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:** https://github.com/TissueImageAnalytics/tiatoolbox/compare/v1.4.0...v1.5.0

Bug Fixes and Other Changes

- Fix dictionary changed size Error 626 (605)

Major Updates and Feature Improvements

- Adds Python 3.11 support \[experimental\] 500
- Python 3.11 is not fully supported by `pytorch` https://github.com/pytorch/pytorch/issues/86566 and `openslide` https://github.com/openslide/openslide-python/pull/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.

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

Major Updates and Feature Improvements

None

Changes to API

None

Bug Fixes and Other Changes

- Fix bug related to reading DICOM files

Development related changes

- Restricts wsidicom version to \<0.7.0 for compatibility

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