Major and Feature Improvements
- Adds `get_wsireader()` to return appropriate WSIReader.
- Adds new functions to allow reading of regions using WSIReader at different resolutions given in units of:
- microns per-pixel (mpp)
- objective lens power (power)
- pixels-per baseline (baseline)
- resolution level (level)
- Adds functions for reading regions are `read_bounds` and `read_rect`.
- `read_bounds` takes a tuple (left, top, right, bottom) of coordinates in baseline (level 0) reference frame and returns a region bounded by those.
- `read_rect` takes one coordinate in baseline reference frame and an output size in pixels.
- Adds `VirtualWSIReader` as a subclass of WSIReader which can be used to read visual fields (tiles).
- `VirtualWSIReader` accepts ndarray or image path as input.
- Adds MPP fall back to standard TIFF resolution tags with warning.
- If OpenSlide cannot determine microns per pixel (`mpp`) from the metadata, checks the TIFF resolution units (TIFF tags: `ResolutionUnit`, `XResolution` and `YResolution`) to calculate MPP. Additionally, add function to estimate missing objective power if MPP is known of derived from TIFF resolution tags.
- Estimates missing objective power from MPP with warning.
- Adds example notebooks for stain normalisation and WSI reader.
- Adds caching to slide info property. This is done by checking if a private `self._m_info` exists and returning it if so, otherwise `self._info` is called to create the info for the first time (or to force regenerating) and the result is assigned to `self._m_info`. This could in future be made much simpler with the `functools.cached_property` decorator in Python 3.8+.
- Adds pre processing step to stain normalisation where stain matrix encodes colour information from tissue region only.
Changes to API
- `read_region` refactored to be backwards compatible with openslide arguments.
- `slide_info` changed to `info`
- Updates WSIReader which only takes one input
- `WSIReader` `input_path` variable changed to `input_img`
- Adds `tile_read_size`, `tile_objective_value` and `output_dir` to WSIReader.save_tiles()
- Adds `tile_read_size` as a tuple
- `transforms.imresize` takes additional arguments `output_size` and interpolation method 'optimise' which selects `cv2.INTER_AREA` for `scale_factor<1` and `cv2.INTER_CUBIC` for `scale_factor>1`
Bug Fixes and Other Changes
- Refactors glymur code to use index slicing instead of deprecated read function.
- Refactors thumbnail code to use `read_bounds` and be a member of the WSIReader base class.
- Updates `README.md` to clarify installation instructions.
- Fixes slide_info.py for changes in WSIReader API.
- Fixes save_tiles.py for changes in WSIReader API.
- Updates `example_wsiread.ipynb` to reflect the changes in WSIReader.
- Adds Google Colab and Kaggle links to allow user to run notebooks directly on colab or kaggle.
- Fixes a bug in taking directory input for stainnorm operation for command line interface.
- Pins `numpy<=1.19.3` to avoid compatibility issues with opencv.
- Adds `scikit-image` or `jupyterlab` as a dependency.
Development related changes
- Moved `test_wsireader_jp2_save_tiles` to test_wsireader.py.
- Change recipe in Makefile for coverage to use pytest-cov instead of coverage.
- Runs travis only on PR.
- Adds [pre-commit](https://pre-commit.com/#install) for easy setup of client-side git [hooks](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) for [black code formatting](https://github.com/psf/black#version-control-integration) and flake8 linting.
- Adds [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to pre-commit for catching potential deepsource errors.
- Adds constants for test regions in `test_wsireader.py`.
- Rearranges `usage.rst` for better readability.
- Adds `pre-commit`, `flake8`, `flake8-bugbear`, `black`, `pytest-cov` and `recommonmark` as dependency.
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