diff --git a/.github/release.yml b/.github/release.yml deleted file mode 100644 index 9745fc8..0000000 --- a/.github/release.yml +++ /dev/null @@ -1,16 +0,0 @@ -changelog: - exclude: - labels: - - ignore-for-release - categories: - - title: Breaking Changes 🛠 - labels: - - Semver-Major - - breaking-change - - title: New Features 🎉 - labels: - - Semver-Minor - - enhancement - - title: Other Changes - labels: - - '*' diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 3be9b46..66e4f97 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -4,15 +4,13 @@ on: push: branches: - main - tags: - - 'v*' pull_request: branches: - main workflow_dispatch: env: - POETRY_VERSION: 1.6.1 + UV_VERSION: '0.5.26' jobs: check: @@ -20,22 +18,28 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - - name: Install poetry - run: pipx install poetry==$POETRY_VERSION - - - name: Set up python - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + + # Note: We need to manually install uv because this action is not whitelisted. + # - name: Install uv + # uses: astral-sh/setup-uv@v5 + # with: + # version: ${{ env.UV_VERSION }} + # enable-cache: true + # cache-dependency-glob: 'uv.lock' + - name: Install uv + run: pipx install uv==$UV_VERSION + + - name: Set up Python + uses: actions/setup-python@v5 with: - python-version: '3.10' - cache: 'poetry' + python-version-file: '.python-version' - name: Install dependencies - run: poetry install + run: uv sync --all-extras --dev - name: Run checks - run: poetry run invoke check + run: uv run invoke check test: needs: [check] @@ -43,58 +47,24 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.10', '3.11'] + python-version: ['3.11', '3.12'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - name: Install poetry - run: pipx install poetry==$POETRY_VERSION + - name: Install uv + run: pipx install uv==$UV_VERSION - name: Set up python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - cache: 'poetry' - name: Install dependencies run: | sudo apt-get update sudo apt-get install qtbase5-dev xvfb - poetry install - poetry run pip install pyqt5 + uv sync --all-extras --dev - name: Run tests - run: poetry run xvfb-run invoke test - - release: - needs: [test] - name: Release - runs-on: ubuntu-latest - if: contains(github.ref, 'tags') - - steps: - - uses: actions/checkout@v3 - - - name: Install poetry - run: pipx install poetry==$POETRY_VERSION - - - name: Set up python - uses: actions/setup-python@v4 - with: - python-version: '3.10' - - - name: Build distribution - run: poetry build - - - name: Create release - run: | - VERSION="${GITHUB_REF/refs\/tags\/}" - if [[ "$VERSION" != *"rc"* ]]; then - gh release create $VERSION --verify-tag --generate-notes - else - gh release create $VERSION --verify-tag --generate-notes --prerelease - fi - gh release upload $VERSION dist/* - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: xvfb-run uv run invoke test diff --git a/.gitignore b/.gitignore index 73d56d3..442b617 100644 --- a/.gitignore +++ b/.gitignore @@ -1,84 +1,23 @@ -# Byte-compiled / optimized / DLL files +# Python __pycache__/ *.py[cod] -*$py.class -# C extensions -*.so - -# Distribution / packaging -.Python -env/ -build/ -develop-eggs/ +# Distribution / Packaging dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -*.egg-info/ -.installed.cfg -*.egg - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec -# Installer logs -pip-log.txt -pip-delete-this-directory.txt +# Caches +.mypy_cache/ +.pytest_cache/ +.ruff_cache/ -# Unit test / coverage reports -htmlcov/ -.tox/ +# Testing .coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*,cover -.hypothesis/ -.napari_cache - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py - -# Flask instance folder -instance/ - -# Sphinx documentation -docs/_build/ -# MkDocs documentation -/site/ - -# PyBuilder -target/ - -# Pycharm and VSCode +# IDEs +.conda/ .idea/ +.venv/ venv/ -.vscode/ - -# IPython Notebook -.ipynb_checkpoints - -# pyenv -.python-version # OS .DS_Store - -# written by setuptools_scm -**/_version.py diff --git a/.napari-hub/DESCRIPTION.md b/.napari-hub/DESCRIPTION.md index bbfaf35..e6124fe 100644 --- a/.napari-hub/DESCRIPTION.md +++ b/.napari-hub/DESCRIPTION.md @@ -1,36 +1,17 @@ # Description -This [napari] plugin provides a reader for various whole slide image formats. - -By default, any of the following formats is read using the [tifffile] library. -If the image file contains a tag `GDAL_METADATA`, the [rasterio] library is used -instead. - -- .bif -- .ndpi -- .qptiff -- .scn -- .svs -- .tif -- .tiff +This [napari] plugin provides a widget for reading various whole-slide image +formats using a common [zarr] store inteface, based on the libraries +[openslide], [rasterio], and [wsidicom]. # Quickstart -From the terminal: - -```bash -napari CMU-1.svs -``` - -From python: - -```python -import napari - -viewer = napari.Viewer() -viewer.open("CMU-1.svs") -``` +After installation, open the `Plugins` menu in the viewer and select +`WSI Reader` to open the widget. Then select a `Backend` to use, select a `Path` +to open, and click `Load`. [napari]: https://github.com/napari/napari +[openslide]: https://github.com/openslide/openslide-python [rasterio]: https://github.com/rasterio/rasterio -[tifffile]: https://github.com/cgohlke/tifffile +[wsidicom]: https://github.com/imi-bigpicture/wsidicom +[zarr]: https://github.com/zarr-developers/zarr-python diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..2c07333 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..9b38853 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,7 @@ +{ + "python.testing.pytestArgs": [ + "tests" + ], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true +} \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7bfc0ca..6d57b90 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -21,24 +21,19 @@ example. ## Setting up a development environment -This project uses [poetry] packaging and dependency management. +This project uses [uv] for packaging and dependency management. To install the +full set of dependencies needed for developement, run: ```bash -poetry install -poetry run pip install pyqt5 -poetry run napari +uv sync --all-extras --dev ``` -Note: `pyqt5` is not a direct dependency of this plugin, but is necessary to run -napari (see the [napari installation guide]). - -## Running checks and tests +To run a code formatter, a linter and all unit tests, run: ```bash -poetry run invoke check -poetry run invoke test +uv run invoke fix +uv run invoke check +uv run invoke test ``` -[napari installation guide]: - https://napari.org/stable/tutorials/fundamentals/installation.html#choosing-a-different-qt-backend -[poetry]: https://python-poetry.org/ +[uv]: https://github.com/astral-sh/uv diff --git a/README.md b/README.md index 93f913f..8ec10d4 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![Tests](https://github.com/AstraZeneca/napari-wsi/actions/workflows/main.yml/badge.svg)](https://github.com/AstraZeneca/napari-wsi/actions) ![Maturity Level-1](https://img.shields.io/badge/Maturity%20Level-ML--1-yellow) -A plugin to read whole slide images within [napari]. +A plugin to read whole-slide images within [napari]. --- @@ -14,48 +14,58 @@ A plugin to read whole slide images within [napari]. You can install `napari-wsi` via [pip]: ```bash -pip install napari-wsi +pip install napari-wsi[all] ``` -To install the latest development version, run: +This automatically installs all optional backends, as a shortcut for: + ```bash -pip install git+https://github.com/AstraZeneca/napari-wsi.git +pip install napari-wsi[openslide,rasterio,wsidicom] ``` +In addition, to be able to read images using the `openslide` backend, it is +required to install the OpenSlide library itself, for example by installing the +[openslide-bin] python package (also via [pip]). + # Description -This [napari] plugin provides a reader for various whole slide image formats. +This [napari] plugin provides a widget for reading various whole-slide image +formats using a common [zarr] store inteface, based on the libraries +[openslide], [rasterio], and [wsidicom]. + +# Quickstart -By default, any of the following formats is read using the [tifffile] library. -If the image file contains a tag `GDAL_METADATA`, the [rasterio] library is used -instead. +After installation, open the `Plugins` menu in the viewer and select +`WSI Reader` to open the widget. Then select a `Backend` to use, select a `Path` +to open, and click `Load`. -- .bif -- .ndpi -- .qptiff -- .scn -- .svs -- .tif -- .tiff +![The napari viewer displaying a sample image.](./resources/sample_data.jpg) -# Quickstart +If `sRGB` is selected in the `Color Space` menu and an ICC profile is attached +to the given image, a transformation to this color space will be applied when +the image data is read. Otherwise, the raw RGB image data will be displayed. -From the terminal: +This plugin can also be used to open image files via drag and drop into the +viewer window. The file suffixes '.bif', '.ndpi', '.scn', '.svs' are registered +with the `openslide` backend, while the suffixes '.tif' and '.tiff' are +registered with the `rasterio` backend. These files can also be opened directly +from the command line or from a python script: ```bash napari CMU-1.svs ``` -From python: - ```python -import napari +from napari.viewer import Viewer -viewer = napari.Viewer() -viewer.open("CMU-1.svs") +viewer = Viewer() +viewer.open("CMU-1.svs", plugin="napari-wsi") ``` [napari]: https://github.com/napari/napari -[pip]: https://pypi.org/project/pip/ +[openslide]: https://github.com/openslide/openslide-python +[openslide-bin]: https://pypi.org/project/openslide-bin/ +[pip]: https://github.com/pypa/pip [rasterio]: https://github.com/rasterio/rasterio -[tifffile]: https://github.com/cgohlke/tifffile +[wsidicom]: https://github.com/imi-bigpicture/wsidicom +[zarr]: https://github.com/zarr-developers/zarr-python diff --git a/napari_wsi/__init__.py b/napari_wsi/__init__.py index b1017b1..5f3c024 100644 --- a/napari_wsi/__init__.py +++ b/napari_wsi/__init__.py @@ -1,7 +1,3 @@ from importlib.metadata import version -from ._rasterio import read_rasterio -from ._tifffile import read_tifffile - -__all__ = ["read_rasterio", "read_tifffile"] __version__ = version(__package__) diff --git a/napari_wsi/_rasterio.py b/napari_wsi/_rasterio.py deleted file mode 100644 index 29633ae..0000000 --- a/napari_wsi/_rasterio.py +++ /dev/null @@ -1,128 +0,0 @@ -from pathlib import Path -from typing import Any - -import numpy as np -import rasterio -from napari.types import LayerDataTuple -from rasterio import DatasetReader -from rasterio.errors import NotGeoreferencedWarning -from rasterio.windows import Window - -from .multiscales import LevelInfo, MultiScalesStore, read_multiscales_data -from .util import Size, catch_warnings - - -class RasterioStore(MultiScalesStore): - def __init__(self, name: str, handle: DatasetReader): - if handle.count == 0: - raise ValueError("The image must have at least one channel.") - - factors = handle.overviews(1) - for band in range(2, handle.count + 1): - if handle.overviews(band) != factors: - raise ValueError("All channels must have the same number of overviews.") - - factors = [1] + factors # The base level has a factor of unity. - num_levels = len(factors) - - tile_size_per_channel = handle.block_shapes - if len(set(tile_size_per_channel)) != 1: - raise ValueError("All channels must have the same tile size.") - tile_size = tile_size_per_channel[0] - - dtype_per_channel = handle.dtypes - if len(set(dtype_per_channel)) != 1: - raise ValueError("All channels must have the same data type.") - dtype = dtype_per_channel[0] - - def _get_level_size(level) -> Size: - if level == 0: - return Size(height=handle.height, width=handle.width) - with rasterio.open(handle.name, overview_level=level - 1) as overview: - return Size(height=overview.height, width=overview.width) - - level_info = [ - LevelInfo(level=level, factor=factors[level], size=_get_level_size(level)) - for level in range(num_levels) - ] - - super().__init__( - name=name, - num_channels=handle.count, - tile_size=Size(height=tile_size[0], width=tile_size[1]), - scale=(1.0, 1.0), - dtype=np.dtype(dtype), - level_info=level_info, - ) - - self._handle = handle - - @property - def handle(self) -> DatasetReader: - return self._handle - - def __getitem__(self, key: str): - if key in self._store: - return self._store[key] - - try: - x, y, factor = self._parse_key(key) - tile = np.transpose( - self.handle.read( - indexes=list(range(1, self.num_channels + 1)), - window=Window( - int(x * factor * self.tile_size.width), - int(y * factor * self.tile_size.height), - int(factor * self.tile_size.width), - int(factor * self.tile_size.height), - ), - out_shape=( - self.num_channels, - self.tile_size.height, - self.tile_size.width, - ), - boundless=True, - fill_value=0, - ), - axes=[1, 2, 0], - ) - except Exception as err: - raise KeyError(key) from err - - return np.array(tile).tobytes() - - def close(self): - self.handle.close() - - -def _read_metadata(handle: DatasetReader) -> dict[str, Any]: - metadata: dict[str, Any] = {} - - # Set some basic image metadata. - metadata["file_path"] = handle.name - metadata["size"] = (handle.height, handle.width) - - return metadata - - -def read_rasterio(path: str | Path, *, split_rgb: bool = False) -> list[LayerDataTuple]: - """Read an image using rasterio. - - Args: - path: The path to the image file. - split_rgb: If True, a separate layer will be created for each RGB channel. - - Returns: - A list of layer data tuples. - """ - with catch_warnings(category=NotGeoreferencedWarning): - handle = rasterio.open(path) - - store = RasterioStore(name=Path(path).stem, handle=handle) - - return read_multiscales_data( - store=store, - name=store.name, - metadata=_read_metadata(handle), - split_rgb=split_rgb, - ) diff --git a/napari_wsi/_tifffile.py b/napari_wsi/_tifffile.py deleted file mode 100644 index c543621..0000000 --- a/napari_wsi/_tifffile.py +++ /dev/null @@ -1,65 +0,0 @@ -from pathlib import Path -from typing import Any - -import numpy as np -from napari.types import LayerDataTuple -from tifffile import TiffFile -from tifffile.tifffile import TiffPage, svs_description_metadata - -from .multiscales import read_multiscales_data -from .util import get_isotropic_resolution - - -def _read_metadata(handle: TiffFile, series: int) -> dict[str, Any]: - metadata: dict[str, Any] = {} - - page = handle.series[series].pages[0] - assert isinstance(page, TiffPage) - tags = page.tags - - # Set some basic image metadata. - metadata["file_path"] = handle.filehandle.path - metadata["size"] = (tags["ImageLength"].value, tags["ImageWidth"].value) - - # Collect additional metadata. - if handle.is_svs: - svs_metadata = svs_description_metadata(page.description) - if "MPP" in svs_metadata: - metadata["resolution"] = float(svs_metadata["MPP"]) * 1e-6 - else: - if all(key in tags for key in ["XResolution", "YResolution", "ResolutionUnit"]): - x_resolution = np.divide(*tags["XResolution"].value[::-1]) - y_resolution = np.divide(*tags["YResolution"].value[::-1]) - resolution = get_isotropic_resolution(x_resolution, y_resolution) - resolution_unit = tags["ResolutionUnit"].value - if resolution_unit.value == 2: - assert resolution_unit.name == "INCH" - metadata["resolution"] = resolution * 2.54e-2 - elif resolution_unit.value == 3: - assert resolution_unit.name == "CENTIMETER" - metadata["resolution"] = resolution * 1e-2 - - return metadata - - -def read_tifffile( - path: str | Path, *, series: int = 0, split_rgb: bool = False -) -> list[LayerDataTuple]: - """Read an image using tifffile. - - Args: - path: The path to the image file. - series: The image series to read. - split_rgb: If True, a separate layer will be created for each RGB channel. - - Returns: - A list of layer data tuples. - """ - handle = TiffFile(path) - - return read_multiscales_data( - store=handle.aszarr(series=series), - name=Path(handle.filename).stem, - metadata=_read_metadata(handle, series=series), - split_rgb=split_rgb, - ) diff --git a/napari_wsi/backends/__init__.py b/napari_wsi/backends/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/napari_wsi/backends/common.py b/napari_wsi/backends/common.py new file mode 100644 index 0000000..299d9c8 --- /dev/null +++ b/napari_wsi/backends/common.py @@ -0,0 +1,7 @@ +from enum import StrEnum + + +class WSIReaderBackend(StrEnum): + OPENSLIDE = "openslide" + RASTERIO = "rasterio" + WSIDICOM = "wsidicom" diff --git a/napari_wsi/backends/openslide.py b/napari_wsi/backends/openslide.py new file mode 100644 index 0000000..63304fc --- /dev/null +++ b/napari_wsi/backends/openslide.py @@ -0,0 +1,127 @@ +from contextlib import suppress +from functools import cached_property +from pathlib import Path + +import numpy as np +from upath import UPath +from zarr.abc.store import ByteRequest +from zarr.core.buffer import Buffer, BufferPrototype +from zarr.core.common import JSON + +try: + from openslide import ( + PROPERTY_NAME_MPP_X, + PROPERTY_NAME_MPP_Y, + OpenSlide, + ) +except ImportError as err: + raise ImportError("Please install the optional 'openslide' dependency.") from err + +from ..color_transform import ColorSpace, ColorTransform +from ..common import PyramidLevel, PyramidLevels, WSIStore + + +def _get_shape(handle: OpenSlide, level: int) -> tuple[int, int]: + width, height = handle.level_dimensions[level] + return height, width + + +def _get_chunks(handle: OpenSlide, level: int) -> tuple[int, int]: + with suppress(KeyError): + tile_width = int(handle.properties[f"openslide.level[{level}].tile-width"]) + tile_height = int(handle.properties[f"openslide.level[{level}].tile-height"]) + return tile_height, tile_width + return (512, 512) + + +def _get_resolution(handle: OpenSlide) -> tuple[float, float] | None: + with suppress(KeyError): + mpp_x = float(handle.properties[PROPERTY_NAME_MPP_X]) + mpp_y = float(handle.properties[PROPERTY_NAME_MPP_Y]) + return mpp_x, mpp_y + return None + + +class OpenSlideStore(WSIStore): + """A class for reading whole-slide images using the `openslide` backend.""" + + def __init__( + self, + path: str | Path | UPath, + color_space: ColorSpace = ColorSpace.RAW, + ) -> None: + """Initialize an `OpenSlideStore`. + + Args: + path: The path to the input image file. + color_space: The target color space. + """ + self._handle = OpenSlide(path) + + # We need to read some data to determine the number of channels and dtype. + sample_image = self._handle.read_region(location=(0, 0), level=0, size=(1, 1)) + + levels = PyramidLevels( + num_channels=len(sample_image.getbands()), + dtype=np.asarray(sample_image).dtype, + ) + for i in range(self._handle.level_count): + levels += PyramidLevel( + factor=round(self._handle.level_downsamples[i]), + shape=_get_shape(self._handle, level=i), + chunks=_get_chunks(self._handle, level=i), + ) + + super().__init__( + path=path, + levels=levels, + resolution=_get_resolution(self._handle), + color_transform=ColorTransform( + profile=self._handle.color_profile, + mode=sample_image.mode, + color_space=color_space, + ), + ) + + @cached_property + def metadata(self) -> dict[str, JSON]: + slide_metadata = dict(self._handle.properties) + return slide_metadata | super().metadata + + @cached_property + def label_image(self) -> np.ndarray | None: + if "label" in self._handle.associated_images: + return np.asarray(self._handle.associated_images["label"]) + return None + + async def get( + self, + key: str, + prototype: BufferPrototype, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + assert self._is_open + assert byte_range is None + if (match := self._parse_key(key)) is not None: + i, u, v = match + factor, data = self._pyramid[i] + tile_height, tile_width, _ = data.chunks + + tile = np.asarray( + self.color_transform( + self._handle.read_region( + location=(factor * v * tile_width, factor * u * tile_height), + level=i, + # We need to account for tiles that extend beyond the level + # dimensions, since openslide automatically returns zeros. + size=(tile_width, tile_height), + ) + ) + ) + + return prototype.buffer.from_bytes(tile.tobytes()) + return None + + def close(self) -> None: + self._handle.close() + return super().close() diff --git a/napari_wsi/backends/rasterio.py b/napari_wsi/backends/rasterio.py new file mode 100644 index 0000000..19b3ab8 --- /dev/null +++ b/napari_wsi/backends/rasterio.py @@ -0,0 +1,95 @@ +from pathlib import Path +from warnings import catch_warnings + +import numpy as np +from upath import UPath +from zarr.abc.store import ByteRequest +from zarr.core.buffer import Buffer, BufferPrototype + +try: + import rasterio + from rasterio.errors import NotGeoreferencedWarning + from rasterio.windows import Window +except ImportError as err: + raise ImportError("Please install the optional 'rasterio' dependency.") from err + +from ..common import PyramidLevel, PyramidLevels, WSIStore + + +class RasterioStore(WSIStore): + """A class for reading whole-slide images using the `rasterio` backend.""" + + def __init__(self, path: str | Path | UPath) -> None: + """Initialize a `RasterioStore`. + + Args: + path: The path to the input image file. + """ + with catch_warnings(category=NotGeoreferencedWarning, action="ignore"): + self._handle = rasterio.open(path) + num_channels = self._handle.count + + factors_per_channel = [ + (1, *self._handle.overviews(channel)) + for channel in range(1, num_channels + 1) + ] + if len(set(factors_per_channel)) != 1: + raise ValueError("Different number of overviews per channel.") + factors = factors_per_channel[0] + + chunks_per_channel = self._handle.block_shapes + if len(set(chunks_per_channel)) != 1: + raise ValueError("Different tile sizes per channel.") + chunks = chunks_per_channel[0] + + dtype_per_channel = self._handle.dtypes + if len(set(dtype_per_channel)) != 1: + raise ValueError("Different data types per channel.") + dtype = dtype_per_channel[0] + + levels = PyramidLevels(num_channels=num_channels, dtype=dtype) + for channel, factor in enumerate(factors): + if channel == 0: + shape = self._handle.height, self._handle.width + else: + with rasterio.open(path, overview_level=channel - 1) as overview: + shape = overview.height, overview.width + levels += PyramidLevel(factor=factor, shape=shape, chunks=chunks) + + super().__init__(path=path, levels=levels) + + async def get( + self, + key: str, + prototype: BufferPrototype, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + assert self._is_open + assert byte_range is None + if (match := self._parse_key(key)) is not None: + i, u, v = match + factor, data = self._pyramid[i] + _, _, num_channels = data.shape + tile_height, tile_width, _ = data.chunks + + tile = np.transpose( + self._handle.read( + window=Window( + factor * v * tile_width, + factor * u * tile_height, + factor * tile_width, + factor * tile_height, + ), + out_shape=(num_channels, tile_height, tile_width), + boundless=True, + fill_value=data.fill_value, + ), + axes=[1, 2, 0], + ) + + return prototype.buffer.from_bytes(tile.tobytes()) + return None + + def close(self) -> None: + self._handle.close() + return super().close() diff --git a/napari_wsi/backends/wsidicom.py b/napari_wsi/backends/wsidicom.py new file mode 100644 index 0000000..21d3374 --- /dev/null +++ b/napari_wsi/backends/wsidicom.py @@ -0,0 +1,161 @@ +import warnings +from contextlib import suppress +from functools import cached_property +from math import log2 +from pathlib import Path + +import numpy as np +from PIL.Image import Image +from upath import UPath +from zarr.abc.store import ByteRequest +from zarr.core.buffer import Buffer, BufferPrototype +from zarr.core.common import JSON + +try: + from wsidicom import WsiDicom + from wsidicom.errors import WsiDicomNotFoundError + from wsidicom.metadata import OpticalPath, WsiMetadata + from wsidicom.metadata.schema.json import WsiMetadataJsonSchema +except ImportError as err: + raise ImportError("Please install the optional 'wsidicom' dependency.") from err + +from ..color_transform import ColorSpace, ColorTransform +from ..common import PyramidLevel, PyramidLevels, WSIStore + + +def _get_optical_path( + metadata: WsiMetadata, identifier: str | None = None +) -> OpticalPath: + optical_paths = metadata.optical_paths + if len(optical_paths) == 0: + raise ValueError("No optical paths in metadata.") + + if identifier is not None: + for path in optical_paths: + if path.identifier == identifier: + return path + warnings.warn("No optical path with given identifier.") + + return optical_paths[0] + + +class WSIDicomStore(WSIStore): + """A class for reading whole-slide images using the `wsidicom` backend.""" + + def __init__( + self, + path: str | Path | UPath, + pyramid: int = 0, + optical_path: str | None = None, + color_space: ColorSpace = ColorSpace.RAW, + ) -> None: + """Initialize a `WSIDicomStore`. + + Args: + path: The path to the input image directory, or a URL. + pyramid: An index to select one of multiple image pyramids. + optical_path: An identifier to select one of multiple optical paths. + color_space: The target color space. + """ + self._handle = WsiDicom.open(path) + self._handle.set_selected_pyramid(pyramid) + + self._optical_path = _get_optical_path(self._handle.metadata, optical_path) + + # We need to read some data to determine the number of channels and dtype. + sample_image = self._read_region(location=(0, 0), level=0, size=(1, 1)) + + levels = PyramidLevels( + num_channels=len(sample_image.getbands()), + dtype=np.asarray(sample_image).dtype, + ) + for level in self._handle.pyramid.levels: + levels += PyramidLevel( + # The scale factor is always a power of two. + factor=2**level.level, + shape=(level.size.height, level.size.width), + chunks=(level.tile_size.height, level.tile_size.width), + ) + + super().__init__( + path=path, + levels=levels, + resolution=(self._handle.mpp.height, self._handle.mpp.width), + color_transform=ColorTransform( + profile=self._optical_path.icc_profile, + mode=sample_image.mode, + color_space=color_space, + ), + ) + + def _read_region( + self, location: tuple[int, int], level: int, size: tuple[int, int] + ) -> Image: + return self._handle.read_region( + location=location, + level=level, + size=size, + path=self._optical_path.identifier, + ) + + @cached_property + def typed_metadata(self) -> WsiMetadata: + return self._handle.metadata + + @cached_property + def metadata(self) -> dict[str, JSON]: + slide_metadata = WsiMetadataJsonSchema().dump(self.typed_metadata) + return slide_metadata | super().metadata + + @cached_property + def label_image(self) -> np.ndarray | None: + with suppress(WsiDicomNotFoundError): + return np.asarray(self._handle.read_label()) + return None + + @cached_property + def overview_image(self) -> np.ndarray | None: + with suppress(WsiDicomNotFoundError): + return np.asarray(self._handle.read_overview()) + return None + + async def get( + self, + key: str, + prototype: BufferPrototype, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + assert self._is_open + assert byte_range is None + if (match := self._parse_key(key)) is not None: + i, u, v = match + factor, data = self._pyramid[i] + height, width, num_channels = data.shape + tile_height, tile_width, _ = data.chunks + + # We need to account for tiles that extend beyond the level dimensions. + x0, y0 = v * tile_width, u * tile_height + x1, y1 = min(x0 + tile_width, width), min(y0 + tile_height, height) + clipped_tile_width, clipped_tile_height = x1 - x0, y1 - y0 + + tile = np.full( + (tile_height, tile_width, num_channels), + fill_value=data.fill_value, + dtype=data.dtype, + ) + tile[:clipped_tile_height, :clipped_tile_width] = np.asarray( + self.color_transform( + self._read_region( + location=(x0, y0), + level=int(log2(factor)), + size=(clipped_tile_width, clipped_tile_height), + ) + ) + ) + + return prototype.buffer.from_bytes(tile.tobytes()) + return None + + def close(self) -> None: + self._handle.close() + return super().close() diff --git a/napari_wsi/color_transform.py b/napari_wsi/color_transform.py new file mode 100644 index 0000000..003b005 --- /dev/null +++ b/napari_wsi/color_transform.py @@ -0,0 +1,65 @@ +from enum import StrEnum +from io import BytesIO + +from PIL.Image import Image +from PIL.ImageCms import ( + ImageCmsProfile, + ImageCmsTransform, + Intent, + applyTransform, + buildTransform, + createProfile, + getDefaultIntent, + getOpenProfile, +) + + +class ColorSpace(StrEnum): + RAW = "RAW" + sRGB = "sRGB" + + +class ColorTransform: + """A class for applying a color transform based on an ICC profile.""" + + def __init__( + self, + profile: ImageCmsProfile | bytes | None = None, + mode: str = "RGB", + color_space: ColorSpace = ColorSpace.RAW, + ) -> None: + """Initialize a `ColorTransform`. + + Args: + profile: The input ICC profile. + mode: The image mode, specifying the pixel format (usually 'RGB' or 'RGBA'). + color_space: The target color space. + """ + self._transform = None + self._color_space = color_space + if profile is not None and color_space != ColorSpace.RAW: + if not isinstance(profile, ImageCmsProfile): + profile = getOpenProfile(BytesIO(profile)) + self._transform = buildTransform( + profile, + createProfile(str(color_space)), # type: ignore + mode, + mode, + Intent(getDefaultIntent(profile)), + ) + + @property + def transform(self) -> ImageCmsTransform | None: + return self._transform + + @property + def color_space(self) -> ColorSpace: + return self._color_space + + def __call__(self, image: Image) -> Image: + if self.transform is not None: + transformed_image = applyTransform(image, self.transform) + # None is only returned if the transform is applied in-place. + assert transformed_image is not None + return transformed_image + return image diff --git a/napari_wsi/common.py b/napari_wsi/common.py new file mode 100644 index 0000000..1a7cd33 --- /dev/null +++ b/napari_wsi/common.py @@ -0,0 +1,198 @@ +import re +from abc import ABC +from collections.abc import Iterator +from dataclasses import dataclass +from functools import cached_property +from pathlib import Path +from typing import TYPE_CHECKING + +import dask.array as da +import numpy as np +import zarr +from numpy.typing import DTypeLike +from upath import UPath +from zarr.abc.metadata import Metadata +from zarr.core.array import Array +from zarr.core.common import JSON +from zarr.storage import MemoryStore + +from .backends.common import WSIReaderBackend + +if TYPE_CHECKING: + import napari + +from .color_transform import ColorSpace, ColorTransform + + +@dataclass(frozen=True) +class PyramidLevel(Metadata): + factor: int + shape: tuple[int, int] + chunks: tuple[int, int] + + +class PyramidLevels: + def __init__(self, num_channels: int, dtype: DTypeLike) -> None: + if num_channels <= 0: + raise ValueError("Invalid number of channels.") + self._num_channels = num_channels + self._dtype = np.dtype(dtype) + self._levels: list[PyramidLevel] = [] + + @property + def num_channels(self) -> int: + return self._num_channels + + @property + def dtype(self) -> DTypeLike: + return self._dtype + + def __iter__(self) -> Iterator[PyramidLevel]: + yield from self._levels + + def __iadd__(self, level: PyramidLevel) -> "PyramidLevels": + if len(self._levels) > 0: + top_level = self._levels[-1] + if level.factor <= top_level.factor: + raise ValueError("The downsample factor must increase.") + if np.any(np.array(level.shape) >= np.array(top_level.shape)): + raise ValueError("The shape must decrease.") + self._levels.append(level) + return self + + +class PyramidStore(MemoryStore, ABC): + def __init__(self, name: str, levels: PyramidLevels) -> None: + super().__init__() + self._name = name + self._pyramid: list[tuple[int, Array]] = [] + for i, level in enumerate(levels): + array = zarr.create_array( + self, + name=str(i), + shape=(*level.shape, levels.num_channels), + dtype=levels.dtype, + chunks=(*level.chunks, levels.num_channels), + shards=None, + filters=None, + compressors=None, + serializer="auto", + fill_value=0, + ) + self._pyramid.append((level.factor, array)) + self._read_only = True + + @property + def name(self) -> str: + return self._name + + @cached_property + def metadata(self) -> dict[str, JSON]: + return {} + + @staticmethod + def _parse_key(key: str) -> tuple[int, int, int] | None: + assert isinstance(key, str) + match = re.fullmatch(r"(\d*)\/c\/(\d*)\/(\d*)\/(\d*)", key) + if match is not None: + i, u, v, w = map(int, match.groups()) + # We expect the entire channel dimension to be one chunk. + assert w == 0 + return i, u, v + return None + + def to_layer_data_tuples( + self, rgb: bool = True, **kwargs + ) -> list["napari.types.LayerDataTuple"]: + """Convert to a napari layer data tuple. + + The multi-scale image data itself will be represented by a list of dask arrays. + + Args: + rgb: If `False`, the image data will be converted to channels-first format. + If `True`, 3- and 4-channel data will be left in channels-last format. + + Returns: + A one-element list containing a napari layer data tuple of type `image`. + """ + pyramid_data: list[da.Array] = [] + for _, array in self._pyramid: + level_data = da.from_zarr(array, chunks=array.chunks) + _, _, num_channels = level_data.shape + if (not rgb) or (num_channels not in [3, 4]): + # Move the channel dimension up, to enable the slider view in napari. + level_data = da.moveaxis(level_data, -1, 0) + pyramid_data.append(level_data) + + return [ + ( + pyramid_data, + { + "name": self.name, + "metadata": self.metadata, + "rgb": None, + **kwargs, + }, + "image", + ) + ] + + +class WSIStore(PyramidStore, ABC): + """A base class for reading multi-scale whole-slide images.""" + + def __init__( + self, + path: str | Path | UPath, + levels: PyramidLevels, + resolution: tuple[float, float] | None = None, + color_transform: ColorTransform | None = None, + ): + self._path = UPath(path) + self._resolution = resolution + self._color_transform = color_transform or ColorTransform() + super().__init__(name=self.path.stem, levels=levels) + + @property + def path(self) -> UPath: + return self._path + + @property + def resolution(self) -> tuple[float, float] | None: + return self._resolution + + @property + def color_transform(self) -> ColorTransform: + return self._color_transform + + @cached_property + def metadata(self) -> dict[str, JSON]: + return { + "path": str(self.path), + "resolution": self.resolution, + "color_space": str(self.color_transform.color_space), + } + + @cached_property + def label_image(self) -> np.ndarray | None: + return None + + +def open_store( + path: str | Path | UPath, + backend: WSIReaderBackend, + color_space: ColorSpace = ColorSpace.RAW, +) -> WSIStore: + if backend == WSIReaderBackend.OPENSLIDE: + from .backends.openslide import OpenSlideStore + + return OpenSlideStore(path, color_space=color_space) + if backend == WSIReaderBackend.RASTERIO: + from .backends.rasterio import RasterioStore + + return RasterioStore(path) + if backend == WSIReaderBackend.WSIDICOM: + from .backends.wsidicom import WSIDicomStore + + return WSIDicomStore(path, color_space=color_space) + raise ValueError(f"Invalid backend: {backend}") diff --git a/napari_wsi/multiscales.py b/napari_wsi/multiscales.py deleted file mode 100644 index 1e64267..0000000 --- a/napari_wsi/multiscales.py +++ /dev/null @@ -1,274 +0,0 @@ -from abc import ABC -from collections.abc import Iterator, Sequence -from dataclasses import dataclass -from typing import Any - -import dask.array as da -import numpy as np -import zarr.storage -from napari.types import LayerDataTuple -from numpy.typing import DTypeLike - -from .util import DEFAULT_COLORMAP, Size, as_layer_data_tuple, create_colormaps - - -@dataclass(frozen=True) -class LevelInfo: - level: int - factor: int | float - size: Size - - -class BaseStore(zarr.storage.BaseStore, ABC): - def __init__( - self, - name: str, - num_channels: int, - tile_size: Size, - scale: tuple[float, float], - dtype: DTypeLike, - store: zarr.storage.StoreLike, - ): - if not name: - raise ValueError("Invalid name for store.") - if num_channels <= 0: - raise ValueError("Invalid number of channels for store.") - if tile_size.width <= 0 or tile_size.height <= 0: - raise ValueError("Invalid tile size for store.") - if len(scale) != 2 or scale[0] <= 0 or scale[1] <= 0: - raise ValueError("Invalid scale for store.") - - self._name = name - self._num_channels = num_channels - self._tile_size = tile_size - self._scale = scale - self._dtype = dtype - - self._store = store - - @property - def name(self) -> str: - return self._name - - @property - def num_channels(self) -> int: - return self._num_channels - - @property - def tile_size(self) -> Size: - return self._tile_size - - @property - def scale(self) -> tuple[float, float]: - return self._scale - - @property - def dtype(self) -> DTypeLike: - return self._dtype - - def __iter__(self) -> Iterator[str]: - return iter(self._store) - - def __len__(self) -> int: - return len(self._store) - - def __contains__(self, key: str) -> bool: - if key in self._store: - return True - return self._contains(key) - - def __eq__(self, other): - raise NotImplementedError - - def __setitem__(self, key, val): - raise NotImplementedError - - def __delitem__(self, key): - raise NotImplementedError - - def _contains(self, key: str) -> bool: - raise NotImplementedError - - -class MultiScalesStore(BaseStore, ABC): - def __init__( - self, - name: str, - num_channels: int, - tile_size: Size, - scale: tuple[float, float], - dtype: DTypeLike, - level_info: Sequence[LevelInfo], - ): - if len(level_info) == 0: - raise ValueError("Invalid level information for store.") - - store: zarr.storage.StoreLike = {} - zarr.storage.init_group(store) - store[zarr.storage.attrs_key] = zarr.util.json_dumps( - { - "multiscales": [ - { - "name": name, - "datasets": [{"path": str(item.level)} for item in level_info], - "version": "0.1", - } - ] - } - ) - - channels = (num_channels,) if num_channels > 1 else () - for item in level_info: - zarr.storage.init_array( - store=store, - path=str(item.level), - shape=((item.size.height, item.size.width) + channels), - chunks=((tile_size.height, tile_size.width) + channels), - dtype=dtype, - compressor=None, - ) - - super().__init__( - name=name, - num_channels=num_channels, - tile_size=tile_size, - scale=scale, - dtype=dtype, - store=store, - ) - - self._level_info = level_info - - @property - def level_info(self) -> Sequence[LevelInfo]: - return self._level_info - - def _parse_key(self, key: str) -> tuple[int, int, int | float]: - level_str, chunk_key = key.split("/") - chunk_pos = chunk_key.split(".") - x, y = int(chunk_pos[1]), int(chunk_pos[0]) - level = int(level_str) - factor = self.level_info[level].factor - return x, y, factor - - def _contains(self, key: str) -> bool: - try: - self._parse_key(key) - except (ValueError, IndexError): - return False - return True - - -def read_pyramid(store: zarr.storage.StoreLike) -> list[da.Array]: - """Read an image pyramid from a zarr store. - - Args: - store: The zarr store to read from. - - Returns: - An image pyramid as a list of dask arrays. - """ - # Load the image data from the zarr store, either from a group or an array. - group = zarr.open(store, "r") - if isinstance(group, zarr.hierarchy.Group): - try: - pyramid = [ - da.from_zarr(store, component=dataset["path"]) - for dataset in group.attrs["multiscales"][0]["datasets"] - ] - except KeyError as err: - raise RuntimeError("Failed to read multiscales from zarr store.") from err - elif isinstance(group, zarr.hierarchy.Array): - pyramid = [da.from_zarr(group)] - else: - raise RuntimeError("Failed to read from zarr store.") - - if len(pyramid) == 0: - raise RuntimeError("Failed to read image pyramid.") - - return pyramid - - -def read_multiscales_data( - store: zarr.storage.StoreLike, - *, - name: str, - metadata: dict[str, Any], - split_rgb: bool = False, -) -> list[LayerDataTuple]: - """Read (multiscale) image data from a zarr store. - - If the image data has three channels, it is assumed to be an RGB image and a single layer data - tuple is returned, unless split_rgb is True. If the image data has any other number of - channels, one layer data tuple per channel is returned. - - Args: - store: The zarr store to read from. - name: The base name of the created layer(s). - metadata: The metadata of the created layer(s). - split_rgb: If True, a separate layer will be created for each RGB channel. - - Returns: - A list of layer data tuples. - """ - # Read the store data. - pyramid = read_pyramid(store) - assert len(pyramid) > 0 - - # Ensure that the data is three-dimensional. - pyramid = [da.atleast_3d(pyr_level) for pyr_level in pyramid] - - # Check that the data is valid image data. - shape_per_lev = [pyr_level.shape for pyr_level in pyramid] - if any(len(shape) != 3 for shape in shape_per_lev): - raise RuntimeError("Expected only 3D data in pyramid.") - - # Convert to channels-last format. - channel_axes = {np.argmin(shape) for shape in shape_per_lev} - if len(channel_axes) != 1: - raise RuntimeError("Different channel axes in pyramid.") - channel_axis = channel_axes.pop() - if len({shape[channel_axis] for shape in shape_per_lev}) != 1: - raise RuntimeError("Different number of channels in pyramid.") - if channel_axis != 2: - pyramid = [da.moveaxis(pyr_level, channel_axis, -1) for pyr_level in pyramid] - _, _, num_channels = pyramid[0].shape - - # Remove the channel axis for a one-channel image. - pyramid = [da.squeeze(pyr_level) for pyr_level in pyramid] - - # Create the layer data for display. - multiscale = len(pyramid) > 1 - # pylint: disable-next=consider-using-ternary - multichannel = (num_channels == 3 and split_rgb) or (num_channels not in [1, 3]) - layer_data, layer_names = [], [] - if multichannel: - for i in range(num_channels): - layer_data.append([pyr_level[:, :, i] for pyr_level in pyramid]) - layer_names.append(f"{name}_{i}") - else: - layer_data.append(pyramid) - layer_names.append(name) - if not multiscale: - layer_data = [pyramid[0] for pyramid in layer_data] - - # Set the layer display properties. - if multichannel: - colormaps, blending = list(create_colormaps(layer_names)), "additive" - else: - colormaps, blending = [DEFAULT_COLORMAP] * len(layer_data), "translucent" - - return [ - as_layer_data_tuple( - layer_data=data, - layer_params=dict( - name=name, - multiscale=multiscale, - metadata=metadata, - colormap=colormap, - blending=blending, - ), - layer_type="image", - ) - for data, name, colormap in zip(layer_data, layer_names, colormaps) - ] diff --git a/napari_wsi/napari.yaml b/napari_wsi/napari.yaml index 81f0a6c..1c8745e 100644 --- a/napari_wsi/napari.yaml +++ b/napari_wsi/napari.yaml @@ -2,16 +2,22 @@ name: napari-wsi display_name: WSI Reader contributions: commands: - - id: napari-wsi.get_wsi_reader - python_name: napari_wsi.reader:get_wsi_reader - title: A reader for whole slide image data. - - id: napari-wsi.get_wsi_reader_widget - python_name: napari_wsi.widget:get_wsi_reader_widget - title: A widget for reading whole slide image data. + - id: napari-wsi.wsi_reader_openslide + python_name: napari_wsi.reader:wsi_reader_openslide + title: A reader for whole-slide image data based on openslide. + - id: napari-wsi.wsi_reader_rasterio + python_name: napari_wsi.reader:wsi_reader_rasterio + title: A reader for whole-slide image data based on rasterio. + - id: napari-wsi.wsi_reader_widget + python_name: napari_wsi.widget:WSIReaderWidget + title: A widget for reading whole-slide image data. readers: - - command: napari-wsi.get_wsi_reader + - command: napari-wsi.wsi_reader_openslide accepts_directories: false - filename_patterns: ["*.bif", "*.ndpi", "*.qptiff", "*.scn", "*.svs", "*.tif", "*.tiff"] + filename_patterns: ["*.bif", "*.ndpi", "*.scn", "*.svs"] + - command: napari-wsi.wsi_reader_rasterio + accepts_directories: false + filename_patterns: ["*.tif", "*.tiff"] widgets: - - command: napari-wsi.get_wsi_reader_widget + - command: napari-wsi.wsi_reader_widget display_name: WSI Reader diff --git a/napari_wsi/py.typed b/napari_wsi/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/napari_wsi/reader.py b/napari_wsi/reader.py index 02788ba..5a5407a 100644 --- a/napari_wsi/reader.py +++ b/napari_wsi/reader.py @@ -1,20 +1,24 @@ from collections.abc import Callable, Sequence -from tifffile import TiffFile -from tifffile.tifffile import TiffPage +from napari_wsi.backends.common import WSIReaderBackend -from . import read_rasterio, read_tifffile +from .color_transform import ColorSpace +from .common import open_store -def get_wsi_reader(path: str | Sequence[str]) -> Callable | None: +def _wsi_reader( + path: str | Sequence[str], backend: WSIReaderBackend +) -> Callable | None: if not isinstance(path, str): return None - handle = TiffFile(path) + store = open_store(path=path, backend=backend, color_space=ColorSpace.sRGB) + return store.to_layer_data_tuples - page = handle.series[0].pages[0] - assert isinstance(page, TiffPage) - if "GDAL_METADATA" in page.tags: - return read_rasterio - return read_tifffile +def wsi_reader_openslide(path: str | Sequence[str]) -> Callable | None: + return _wsi_reader(path, backend=WSIReaderBackend.OPENSLIDE) + + +def wsi_reader_rasterio(path: str | Sequence[str]) -> Callable | None: + return _wsi_reader(path, backend=WSIReaderBackend.RASTERIO) diff --git a/napari_wsi/util.py b/napari_wsi/util.py deleted file mode 100644 index ac9a50f..0000000 --- a/napari_wsi/util.py +++ /dev/null @@ -1,117 +0,0 @@ -import re -import warnings -from collections.abc import Iterator, Sequence -from contextlib import contextmanager -from dataclasses import dataclass -from itertools import cycle -from typing import Any, cast - -import matplotlib -import matplotlib.colors -import numpy as np -from napari.types import LayerDataTuple -from napari.utils import Colormap -from napari.utils.colormaps import AVAILABLE_COLORMAPS - -DEFAULT_COLORMAP = AVAILABLE_COLORMAPS["gray"] - -ColorType = tuple[int, int, int, int] - - -@dataclass(frozen=True) -class Size: - height: int - width: int - - -def as_layer_data_tuple( - layer_data: Any, layer_params: dict[str, Any] | None, layer_type: str -) -> LayerDataTuple: - """Create a napari layer data tuple from the given arguments.""" - - return cast(LayerDataTuple, (layer_data, layer_params or {}, layer_type)) - - -@contextmanager -def catch_warnings(category: type[Warning]): - with warnings.catch_warnings(record=True) as caught_warnings: - try: - yield - finally: - for warning in caught_warnings: - if warning.category == category: - continue - warnings.warn(message=warning.message, category=warning.category) - - -def create_colormap(color: str | int | Sequence[int], name: str) -> Colormap: - """Create a napari alpha-blending color map for the given color.""" - - color_end = np.array(parse_color(color)) / 255 - color_start = color_end.copy() - color_start[-1] = 0 - return Colormap([color_start, color_end], name=name) - - -def create_colormaps( - layer_names: Sequence[str], cmap: str = "tab10" -) -> Iterator[Colormap]: - """Create napari color maps for the given layers.""" - - if not len(layer_names) == len(set(layer_names)): - raise RuntimeError("The layer names are not unique.") - - colormap = matplotlib.colormaps[cmap] - if not isinstance(colormap, matplotlib.colors.ListedColormap): - raise ValueError("The requested colormap must be a ListedColormap.") - - colors = (255 * np.array(colormap.colors)).astype(np.uint8) - iter_colors = cycle(colors) - for layer_name in layer_names: - # pylint: disable-next=stop-iteration-return - yield create_colormap(next(iter_colors), layer_name) - - -def get_isotropic_resolution(resolution_x: float, resolution_y: float) -> float: - """Compute the geometric mean of the given resolution values.""" - - if np.isclose(resolution_x, resolution_y): - return resolution_x - - warnings.warn("The resolution of the slide is different along the X and Y axes.") - - return np.sqrt(np.abs(resolution_x * resolution_y)) - - -def parse_color(color: str | int | Sequence[int]) -> ColorType: - """Parse the given input as a color, returning an RGBA tuple.""" - - if isinstance(color, int): - return _parse_int_color(color) - - if isinstance(color, str) and re.match(r"^0x[0-9a-fA-F]{6}$", color): - return _parse_hex_color(color) - - if isinstance(color, str): - return _parse_str_color(color) - - if len(color) == 3: - return tuple(color) + (255,) # type: ignore - - assert len(color) == 4 - return tuple(color) # type: ignore - - -def _parse_int_color(color: int) -> ColorType: - rgba_color = np.array([color], dtype=np.uint32).view(np.uint8) - assert rgba_color.shape == (4,) - return tuple(rgba_color) # type: ignore - - -def _parse_hex_color(color: str) -> ColorType: - return _parse_int_color(int(color, 16) + 0xFF000000) - - -def _parse_str_color(color: str) -> ColorType: - mpl_color = matplotlib.colors.to_rgba(color) - return tuple(int(255 * value) for value in mpl_color) # type: ignore diff --git a/napari_wsi/widget.py b/napari_wsi/widget.py index 43fbec8..37ef0cd 100644 --- a/napari_wsi/widget.py +++ b/napari_wsi/widget.py @@ -1,39 +1,138 @@ -from enum import Enum +from enum import StrEnum from pathlib import Path +from typing import TYPE_CHECKING -from magicgui import magic_factory -from napari.types import LayerDataTuple +from magicgui.types import FileDialogMode +from magicgui.widgets import ( + ComboBox, + Container, + FileEdit, + Image, + LineEdit, + PushButton, + RadioButtons, +) -from . import read_rasterio, read_tifffile +from .backends.common import WSIReaderBackend +from .color_transform import ColorSpace +from .common import WSIStore, open_store +if TYPE_CHECKING: + import napari -class WSIReaderBackend(Enum): - tifffile = "tifffile" - rasterio = "rasterio" +class PathChoice(StrEnum): + PATH = "Path" + URL = "URL" -DEFAULT_BACKEND = WSIReaderBackend.tifffile +class WSIReaderWidget(Container): + def __init__(self, viewer: "napari.viewer.Viewer") -> None: + super().__init__() + self._viewer = viewer + self._store: WSIStore | None = None -@magic_factory( - call_button="Load", - path={"label": "Path", "tooltip": "The file path."}, - backend={"label": "Backend", "tooltip": "The backend for reading WSI data."}, - series={"label": "Series", "tooltip": "The image series to read."}, - split_rgb={"label": "Split RGB", "tooltip": "If set, split 3-channel images."}, -) -def get_wsi_reader_widget( - path: Path, - backend: WSIReaderBackend = DEFAULT_BACKEND, - series: int = 0, - split_rgb: bool = False, -) -> list[LayerDataTuple]: - if not path.is_file(): - raise FileNotFoundError(path) - - if backend == WSIReaderBackend.tifffile: - return read_tifffile(path, series=series, split_rgb=split_rgb) - if backend == WSIReaderBackend.rasterio: - return read_rasterio(path, split_rgb=split_rgb) - - raise ValueError(f"Invalid backend {backend}.") + # Define the interactive widget elements. + self._backend_edit = ComboBox(label="Backend", choices=WSIReaderBackend) + self._color_space_edit = ComboBox(label="Color Space", choices=ColorSpace) + self._choice_edit = RadioButtons(choices=PathChoice, orientation="horizontal") + self._path_edit = FileEdit(label="Path") + self._url_edit = LineEdit(label="URL") + self._load_button = PushButton(name="Load") + + # Define the non-editable widget elements. + self._slide_field = LineEdit(label="Slide ID", enabled=False, visible=False) + self._patient_field = LineEdit(label="Patient ID", enabled=False, visible=False) + self._label_image_field = Image(visible=False) + + # Set up custom event handlers. + self._backend_edit.changed.connect(self._on_backend_changed) + self._choice_edit.changed.connect(self._on_choice_changed) + self._load_button.clicked.connect(self._on_load_button_clicked) + + # Set the initial values, triggering the changed events. + self._choice_edit.value = PathChoice.PATH + self._color_space_edit.value = ColorSpace.RAW + self._backend_edit.value = WSIReaderBackend.WSIDICOM + + self.extend( + [ + self._backend_edit, + self._choice_edit, + self._path_edit, + self._url_edit, + self._color_space_edit, + self._load_button, + self._slide_field, + self._patient_field, + # We don't add the label image to the container, so that it will + # be opened in a separate window, for better visibility. + ] + ) + + @property + def path(self) -> str | Path: + if self._choice_edit.value == PathChoice.PATH: + assert isinstance(self._path_edit.value, Path) + return self._path_edit.value + if self._choice_edit.value == PathChoice.URL: + return self._url_edit.value + raise ValueError(f"Invalid choice: {self._choice_edit.value}") + + @property + def backend(self) -> WSIReaderBackend: + return self._backend_edit.value + + @property + def color_space(self) -> ColorSpace: + return self._color_space_edit.value + + def _on_backend_changed(self, value: WSIReaderBackend) -> None: + if value == WSIReaderBackend.WSIDICOM: + self._path_edit.mode = FileDialogMode.EXISTING_DIRECTORY + self._choice_edit.visible = True + else: + self._path_edit.mode = FileDialogMode.EXISTING_FILE + self._choice_edit.visible = False + self._choice_edit.value = PathChoice.PATH + + def _on_choice_changed(self, value: str) -> None: + self._path_edit.visible = value == PathChoice.PATH + self._url_edit.visible = value == PathChoice.URL + + def _on_load_button_clicked(self) -> None: + self._store = open_store( + path=self.path, backend=self.backend, color_space=self.color_space + ) + + # Add the image layer(s) to the viewer. + for item in self._store.to_layer_data_tuples(): + layer_data, layer_params, layer_type = item + add_layer = getattr(self._viewer, f"add_{layer_type}") + add_layer(layer_data, **layer_params) + + # Display the label image, if available. + self._label_image_field.visible = False + if self._store.label_image is not None: + # Let's set the image width to the widget width, which should be reasonable. + self._label_image_field.set_data(self._store.label_image, width=self.width) + self._label_image_field.visible = True + + # Display additional metadata, if available. + self._slide_field.visible = False + self._patient_field.visible = False + if self.backend == WSIReaderBackend.WSIDICOM: + # The backend must be installed, or we could not have opened the store. + from .backends.wsidicom import WSIDicomStore + + assert isinstance(self._store, WSIDicomStore) + metadata = self._store.typed_metadata + self._slide_field.value = metadata.slide.identifier or "" + self._patient_field.value = metadata.patient.identifier or "" + self._slide_field.visible = True + self._patient_field.visible = True + + def close(self) -> None: + if self._store is not None: + self._store.close() + super().close() diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 80cb192..0000000 --- a/poetry.lock +++ /dev/null @@ -1,3728 +0,0 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. - 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(>=0.9.1)", "pytest-ruff"] - -[metadata] -lock-version = "2.0" -python-versions = ">=3.10,<3.12" -content-hash = "dd5cbb86443bf2599e6c81a3c5c35283d6c75c064fbc29bf9fb3d2a34e3874a6" diff --git a/pyproject.toml b/pyproject.toml index 5e27f5d..40c9071 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,74 +1,102 @@ [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling"] +build-backend = "hatchling.build" -[tool.poetry] +[project] name = "napari-wsi" -version = "0.1.4" -description = "A plugin to read whole slide images within napari." -license="Apache-2.0" +version = "1.0.0" +description = "A plugin to read whole-slide images within napari." +readme = "README.md" +requires-python = ">=3.11" +license = "Apache-2.0" +license-files = [ + "LICENSE", +] authors = [ - "Philipp Plewa ", + { name = "Philipp Plewa", email = "philipp.plewa@astrazeneca.com" }, ] maintainers = [ - "Philipp Plewa ", - "Robert Schweizer ", + { name = "Philipp Plewa", email = "philipp.plewa@astrazeneca.com" }, + { name = "Robert Schweizer", email = "robert.schweizer@astrazeneca.com" }, ] -readme = "README.md" -repository = "https://github.com/AstraZeneca/napari-wsi" classifiers = [ "Framework :: napari", "Intended Audience :: Developers", "Operating System :: OS Independent", "Topic :: Scientific/Engineering :: Image Processing", ] +dependencies = [ + "dask>=2025.1", + "magicgui>=0.10", + "numpy>=1.26", + "pillow>=11.1", + "universal-pathlib>=0.2", + "zarr>=3.0", +] -[tool.poetry.dependencies] -python = ">=3.10,<3.12" -dask = {version = ">=2023", extras = ["array"]} -imagecodecs = ">=2023.9.18" -magicgui = ">=0.7.3" -matplotlib = ">=3.8" -napari = ">=0.4.18" -numpy = ">=1.26" -rasterio = ">=1.3" -tifffile = ">=2023" -zarr = ">=2.16" +[project.optional-dependencies] +openslide = [ + "openslide-python>=1.4", +] +rasterio = [ + "rasterio>=1.4", +] +wsidicom = [ + "wsidicom>=0.22", +] +all = [ + "napari-wsi[openslide,rasterio,wsidicom]" +] -[tool.poetry.group.dev.dependencies] -black = "23.9.*" -invoke = "2.2.*" -isort = "5.12.*" -mypy= "1.6.*" -pylint = "3.0.*" -pytest = "7.4.*" -pytest-cov = "4.1.*" -pytest-qt = "4.2.*" -scikit-image = "0.22.*" +[dependency-groups] +dev = [ + "invoke>=2.2.0", + "mypy>=1.14", + "napari>=0.5", + "openslide-bin>=4.0", + "pyqt5>=5.15", + "pytest>=8.3", + "pytest-cov>=6.0", + "pytest-qt>=4.4", + "ruff>=0.9", + "scikit-image>=0.25", +] -[tool.poetry.plugins."napari.manifest"] -napari-wsi = "napari_wsi:napari.yaml" +[project.urls] +Repository = "https://github.com/AstraZeneca/napari-wsi" -[tool.isort] -profile = "black" +[project.entry-points."napari.manifest"] +napari-wsi = "napari_wsi:napari.yaml" [tool.mypy] -exclude = ["venv"] +check_untyped_defs = true +warn_unused_ignores = true [[tool.mypy.overrides]] +ignore_missing_imports = true module = [ "napari.*", "rasterio.*", - "zarr.*", + "wsidicom.*", ] -ignore_missing_imports = true -[tool.pylint."MESSAGES CONTROL"] -disable = """ -duplicate-code, -invalid-name, -missing-docstring, -too-many-arguments, -too-many-locals, -use-dict-literal, -""" +[tool.ruff] +target-version = "py310" +line-length = 88 +lint.select = [ + "E", "F", "W", #flake8 + "UP", # pyupgrade + "I", # isort + "BLE", # flake8-blind-exception + "B", # flake8-bugbear + "A", # flake8-builtins + "C4", # flake8-comprehensions + "ISC", # flake8-implicit-str-concat + "G", # flake8-logging-format + "PIE", # flake8-pie + "SIM", # flake8-simplify +] +lint.ignore = [ + "B028", # for warnings + "ISC001", # for ruff +] diff --git a/resources/sample_data.jpg b/resources/sample_data.jpg new file mode 100644 index 0000000..acee245 Binary files /dev/null and b/resources/sample_data.jpg differ diff --git a/tasks.py b/tasks.py index 22f56e3..c4128e0 100644 --- a/tasks.py +++ b/tasks.py @@ -1,28 +1,19 @@ -import invoke +from invoke import task -@invoke.task -def format(ctx): - print("## Run black") - ctx.run("black .") - print("## Run isort") - ctx.run("isort .") +@task +def fix(ctx): + ctx.run("ruff format .") + ctx.run("ruff check . --fix") -@invoke.task +@task def check(ctx): - print("## Check formatting") - ctx.run("black --check .") - print("## Check imports") - ctx.run("isort . --check-only") - print("## Check static typing") - ctx.run("mypy . --check-untyped-defs") - print("## Linting code") - ctx.run("pylint napari_wsi") - ctx.run("pylint tests") + ctx.run("ruff format . --check") + ctx.run("ruff check .") + ctx.run("mypy .") -@invoke.task +@task def test(ctx): - print("## Run tests") ctx.run("pytest --verbose --cov=napari_wsi tests") diff --git a/tests/conftest.py b/tests/conftest.py index f8ac0ea..f25b5eb 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,25 +1,20 @@ -from collections.abc import Callable from pathlib import Path +from warnings import catch_warnings -import numpy as np import pytest import rasterio import skimage.data import skimage.transform import skimage.util -import tifffile from attr import dataclass -from napari.layers import Image, Labels, Layer, Points, Shapes -from napari.types import LayerDataTuple -from napari.viewer import Viewer from pytest import FixtureRequest, TempPathFactory from rasterio.enums import Resampling -from tifffile import COMPRESSION +from rasterio.errors import NotGeoreferencedWarning -from napari_wsi import read_rasterio, read_tifffile -from napari_wsi.widget import DEFAULT_BACKEND, WSIReaderBackend +from napari_wsi.color_transform import ColorSpace +from napari_wsi.widget import WSIReaderBackend -TEST_DATA_PATH = Path("tests") / "data" +TEST_DATA_PATH = Path(__file__).parent.resolve() / "data" # https://github.com/rasterio/rasterio/blob/72bdbc05b4670043fb81413e6ee718f06617b86c/tests/data/RGB.byte.tif # https://creativecommons.org/publicdomain/zero/1.0/ @@ -29,184 +24,88 @@ # https://creativecommons.org/publicdomain/zero/1.0/ TEST_DATA_SVS = TEST_DATA_PATH / "CMU-1-Small-Region.svs" +# This is the SVS test image, converted to DICOM via wsidicomizer: +# https://github.com/imi-bigpicture/wsidicomizer +TEST_DATA_DCM = TEST_DATA_PATH / "CMU-1-Small-Region" + @dataclass(frozen=True) -# pylint: disable-next=too-many-instance-attributes -class TestCase: +class Case: id: str - expected_reader: Callable - expected_num_layers: int - expected_multiscale: bool - expected_rgb: bool + backend: WSIReaderBackend + multiscale: bool + rgb: bool + resolution: tuple[float, float] | None + color_space: ColorSpace file_path: Path | None = None file_fixture: str | None = None - split_rgb: bool = False - def get_path(self, request: FixtureRequest) -> Path: - path = self.file_path or request.getfixturevalue(self.file_fixture) # type: ignore - assert isinstance(path, Path) and path.is_file() - return path + def path(self, request: FixtureRequest) -> Path: + if self.file_path is not None: + path = self.file_path + elif self.file_fixture is not None: + path = request.getfixturevalue(self.file_fixture) + else: + raise ValueError("Need either 'file_path' or 'file_fixture'.") + assert isinstance(path, Path) and path.exists() + return path.resolve() DEFAULT_TEST_CASES = [ - TestCase( + Case( id="svs-default", file_path=TEST_DATA_SVS, - expected_reader=read_tifffile, - expected_num_layers=1, - expected_multiscale=False, - expected_rgb=True, + backend=WSIReaderBackend.OPENSLIDE, + resolution=(0.499, 0.499), + color_space=ColorSpace.RAW, + multiscale=False, + rgb=True, ), - TestCase( - id="gtiff-default", - file_path=TEST_DATA_GTIF, - expected_reader=read_rasterio, - expected_num_layers=1, - expected_multiscale=False, - expected_rgb=True, - ), - TestCase( - id="svs-split-rgb", + Case( + id="svs-icc", file_path=TEST_DATA_SVS, - split_rgb=True, - expected_reader=read_tifffile, - expected_num_layers=3, - expected_multiscale=False, - expected_rgb=False, + backend=WSIReaderBackend.OPENSLIDE, + resolution=(0.499, 0.499), + color_space=ColorSpace.sRGB, + multiscale=False, + rgb=True, ), - TestCase( - id="gtiff-split-rgb", + Case( + id="gtiff-default", file_path=TEST_DATA_GTIF, - split_rgb=True, - expected_reader=read_rasterio, - expected_num_layers=3, - expected_multiscale=False, - expected_rgb=False, + backend=WSIReaderBackend.RASTERIO, + resolution=None, + color_space=ColorSpace.RAW, + multiscale=False, + rgb=True, ), - TestCase( - id="ome-pyramid", - file_fixture="tmp_data_ome", - expected_reader=read_tifffile, - expected_num_layers=1, - expected_multiscale=True, - expected_rgb=False, - ), - TestCase( + Case( id="gtiff-pyramid", - file_fixture="tmp_data_gtiff", - expected_reader=read_rasterio, - expected_num_layers=1, - expected_multiscale=True, - expected_rgb=False, + file_fixture="dummy_gtiff", + backend=WSIReaderBackend.RASTERIO, + resolution=None, + color_space=ColorSpace.RAW, + multiscale=True, + rgb=False, + ), + Case( + id="dcm-default", + file_path=TEST_DATA_DCM, + backend=WSIReaderBackend.WSIDICOM, + resolution=(0.499, 0.499), + color_space=ColorSpace.RAW, + multiscale=False, + rgb=True, ), ] -def check_image_layers( - layers: list[Layer], - base_name: str | None = None, - viewer: Viewer | None = None, - **kwargs, -) -> bool: - if len(layers) == 1: - layer = layers[0] - if viewer is not None: - layer = viewer.add_layer(layer) - return check_image_layer(layer, name=base_name, **kwargs) - - for i, layer in enumerate(layers): - if viewer is not None: - layer = viewer.add_layer(layer) - if not check_image_layer(layer, name=f"{base_name}_{i}", **kwargs): - return False - - return True - - -# pylint: disable-next=too-many-return-statements -def check_image_layer( - layer: Layer, - name: str | None = None, - multiscale: bool | None = None, - rgb: bool | None = None, -) -> bool: - if not isinstance(layer, Image): - return False - if layer.ndim != 2: - return False - if not np.allclose(layer.scale, 1): - return False - - if name is not None and layer.name != name: - return False - if multiscale is not None and layer.multiscale != multiscale: - return False - if rgb is not None and layer.rgb != rgb: - return False - - return True - - -def from_layer_data_tuple(data: LayerDataTuple) -> Image | Labels | Shapes | Points: - layer_data, layer_params, layer_type = data - - if layer_type == "image": - return Image(layer_data, **layer_params) - if layer_type == "labels": - return Labels(layer_data, **layer_params) - if layer_type == "shapes": - return Shapes(layer_data, **layer_params) - if layer_type == "points": - return Points(layer_data, **layer_params) - - raise RuntimeError("Unexpected layer type.") - - -def get_backend(reader: Callable) -> WSIReaderBackend: - if reader is read_tifffile: - return WSIReaderBackend.tifffile - if reader is read_rasterio: - return WSIReaderBackend.rasterio - return DEFAULT_BACKEND - - @pytest.fixture(scope="session") -def pyramid() -> list[np.ndarray]: - return list( - map( - skimage.util.img_as_ubyte, - skimage.transform.pyramid_gaussian( - image=skimage.data.binary_blobs(2048), - max_layer=2, - ), - ) - ) +def dummy_gtiff(tmp_path_factory: TempPathFactory) -> Path: + path = tmp_path_factory.mktemp("data") / "image.tiff" - -@pytest.fixture(scope="session") -def tmp_data_ome( - tmp_path_factory: TempPathFactory, - pyramid: list[np.ndarray], # pylint: disable=redefined-outer-name -) -> Path: - path = tmp_path_factory.mktemp("data") / "image.ome.tif" - - with tifffile.TiffWriter(path, bigtiff=True) as handle: - options = dict(tile=(256, 256), dtype=np.uint8, compression=COMPRESSION.JPEG) - - assert len(pyramid) > 1 - handle.write(pyramid[0], subifds=len(pyramid) - 1, **options) # type: ignore - for pyr_level in pyramid[1:]: - handle.write(pyr_level, **options) # type: ignore - - return path - - -@pytest.fixture(scope="session") -def tmp_data_gtiff( - tmp_path_factory: TempPathFactory, - pyramid: list[np.ndarray], # pylint: disable=redefined-outer-name -) -> Path: - path = tmp_path_factory.mktemp("data") / "image.tif" + data = skimage.util.img_as_ubyte(skimage.data.binary_blobs(2048)) + height, width = data.shape profile = { "dtype": "uint8", @@ -218,13 +117,16 @@ def tmp_data_gtiff( "tiled": "yes", "blockxsize": 256, "blockysize": 256, - "width": pyramid[0].shape[1], - "height": pyramid[0].shape[0], + "width": width, + "height": height, "count": 1, } - with rasterio.open(path, "w", **profile) as handle: - handle.write(pyramid[0], 1) + with ( + catch_warnings(category=NotGeoreferencedWarning, action="ignore"), + rasterio.open(path, mode="w", **profile) as handle, + ): + handle.write(data, 1) handle.build_overviews([8, 16], Resampling.average) handle.update_tags(ns="rio_overview", resampling="average") diff --git a/tests/data/CMU-1-Small-Region/1.2.826.0.1.3680043.8.498.46702941076792458794464453066648511350.dcm b/tests/data/CMU-1-Small-Region/1.2.826.0.1.3680043.8.498.46702941076792458794464453066648511350.dcm new file mode 100644 index 0000000..dc014fd Binary files /dev/null and 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PyramidLevel(factor=1, shape=(256, 256), chunks=chunks) + with pytest.raises(ValueError, match="factor"): + levels += PyramidLevel(factor=1, shape=(128, 128), chunks=chunks) + with pytest.raises(ValueError, match="shape"): + levels += PyramidLevel(factor=2, shape=(256, 256), chunks=chunks) diff --git a/tests/test_reader.py b/tests/test_reader.py index ce269e5..470b3e1 100644 --- a/tests/test_reader.py +++ b/tests/test_reader.py @@ -1,48 +1,52 @@ from collections.abc import Callable import pytest +from napari.layers import Image from pytest import FixtureRequest -from napari_wsi.reader import get_wsi_reader +from napari_wsi.backends.common import WSIReaderBackend +from napari_wsi.reader import wsi_reader_openslide, wsi_reader_rasterio from .conftest import ( DEFAULT_TEST_CASES, TEST_DATA_GTIF, TEST_DATA_SVS, - TestCase, - check_image_layers, - from_layer_data_tuple, + Case, ) @pytest.mark.parametrize("case", DEFAULT_TEST_CASES, ids=lambda case: case.id) -def test_wsi_reader( - case: TestCase, request: FixtureRequest, make_napari_viewer: Callable -): +def test_wsi_reader(case: Case, request: FixtureRequest, make_napari_viewer: Callable): """Test that the napari reader works for the given sample data.""" - path = case.get_path(request) + if case.backend == WSIReaderBackend.OPENSLIDE: + get_wsi_reader = wsi_reader_openslide + elif case.backend == WSIReaderBackend.RASTERIO: + get_wsi_reader = wsi_reader_rasterio + else: + return + + viewer = make_napari_viewer() + path = case.path(request) reader = get_wsi_reader(str(path)) assert callable(reader) - assert reader == case.expected_reader - - result = reader(str(path), split_rgb=case.split_rgb) - layers = list(map(from_layer_data_tuple, result)) - assert len(layers) == case.expected_num_layers + items = reader(str(path)) + assert len(items) == 1 + layer_data, layer_params, layer_type = items[0] + add_layer = getattr(viewer, f"add_{layer_type}") + layer = add_layer(layer_data, **layer_params) + assert isinstance(layer, Image) - assert check_image_layers( - layers=layers, - base_name=path.stem, - multiscale=case.expected_multiscale, - rgb=case.expected_rgb, - viewer=make_napari_viewer(), - ) - -def test_wsi_reader_pass(): - """Test that the napari reader only accepts single file paths.""" +@pytest.mark.parametrize( + "get_wsi_reader", + [wsi_reader_openslide, wsi_reader_rasterio], + ids=["openslide", "rasterio"], +) +def test_wsi_reader_pass(get_wsi_reader: Callable): + """Test that the napari readers only accept single file paths.""" reader = get_wsi_reader([str(TEST_DATA_SVS), str(TEST_DATA_GTIF)]) assert reader is None diff --git a/tests/test_util.py b/tests/test_util.py deleted file mode 100644 index e4740a5..0000000 --- a/tests/test_util.py +++ /dev/null @@ -1,27 +0,0 @@ -from contextlib import nullcontext -from typing import Any - -import numpy as np -import pytest - -from napari_wsi.util import get_isotropic_resolution, parse_color - - -@pytest.mark.parametrize( - "x, y", - [(1.0, 1.0), (1.0, 2.0)], - ids=["isotropic", "anisotropic"], -) -def test_get_isotropic_resolution(x: float, y: float): - with nullcontext() if x == y else pytest.warns(UserWarning): # type: ignore - assert np.isclose(get_isotropic_resolution(x, y), np.sqrt(np.abs(x * y))) - - -@pytest.mark.parametrize( - "value", - ["0x0000FF", 4278190335, "red", (255, 0, 0), (255, 0, 0, 255)], - ids=["hex", "int", "str", "rgb", "rgba"], -) -def test_parse_color(value: Any): - color = parse_color(value) - assert color == (255, 0, 0, 255) diff --git a/tests/test_widget.py b/tests/test_widget.py index 19cfc17..50990f2 100644 --- a/tests/test_widget.py +++ b/tests/test_widget.py @@ -1,44 +1,47 @@ from collections.abc import Callable +import numpy as np import pytest +from napari.layers import Image from pytest import FixtureRequest -from napari_wsi.widget import get_wsi_reader_widget +from napari_wsi.widget import WSIReaderWidget from .conftest import ( DEFAULT_TEST_CASES, - TestCase, - check_image_layers, - from_layer_data_tuple, - get_backend, + Case, ) @pytest.mark.parametrize("case", DEFAULT_TEST_CASES, ids=lambda case: case.id) def test_wsi_reader_widget( - case: TestCase, request: FixtureRequest, make_napari_viewer: Callable + case: Case, request: FixtureRequest, make_napari_viewer: Callable ): """Test that the reader widget works for the given sample data.""" - path = case.get_path(request) + viewer = make_napari_viewer() + path = case.path(request) - # pylint: disable-next=no-value-for-parameter - widget = get_wsi_reader_widget() + widget = WSIReaderWidget(viewer) + widget._backend_edit.value = case.backend + widget._path_edit.value = path + widget._color_space_edit.value = case.color_space - result = widget( - path=path, - backend=get_backend(case.expected_reader), - split_rgb=case.split_rgb, - ) - assert result is not None + assert len(viewer.layers) == 0 + widget._on_load_button_clicked() + assert len(viewer.layers) == 1 + layer = viewer.layers[0] + assert isinstance(layer, 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