Connectathon Pre-Testing

napari_wsi/backends/openslide.py

@@ -48,6 +48,7 @@ def __init__(
         Args:
             path: The path to the input image file.
             color_space: The target color space.
+
         """
         if not isinstance(color_space, ColorSpace):
             color_space = ColorSpace(color_space)

napari_wsi/backends/rasterio.py

@@ -26,6 +26,7 @@ def __init__(self, path: str | Path | UPath) -> None:
 
         Args:
             path: The path to the input image file.
+
         """
         with catch_warnings(category=NotGeoreferencedWarning, action="ignore"):
             path = UPath(path)
@@ -66,13 +67,14 @@ def __repr__(self) -> str:
 
     @property
     def spatial_transform(self) -> np.ndarray:
-        matrix = np.identity(3)
-        if self._handle.transform is None:
-            return matrix
         transform = self._handle.transform
-        matrix[0] = (transform.e, transform.d, transform.f)
-        matrix[1] = (transform.b, transform.a, transform.c)
-        return matrix
+        return np.array(
+            [
+                [transform.e, transform.d, transform.f],
+                [transform.b, transform.a, transform.c],
+                [0.0, 0.0, 1.0],
+            ]
+        )
 
     @cached_property
     def metadata(self) -> dict[str, JSON]:

napari_wsi/backends/wsidicom.py

@@ -19,7 +19,6 @@
     import pandas as pd
     from colorspacious import cspace_converter
     from shapely import LineString as ShapelyPolyline
-    from shapely import Point as ShapelyPoint
     from shapely import Polygon as ShapelyPolygon
     from wsidicom import WsiDicom, WsiDicomWebClient
     from wsidicom.errors import WsiDicomNotFoundError
@@ -41,6 +40,7 @@
 
 if TYPE_CHECKING:
     import napari
+    from shapely.geometry.base import BaseGeometry as ShapelyGeometry
 
 
 @dataclass(frozen=True)
@@ -79,26 +79,26 @@ def _validate_annotation(
 ) -> AnnotationData | None:
     coords = np.array(annotation.geometry.to_coords())[:, ::-1]
 
-    # We need check for invalid geometries to avoid errors on layer creation.
+    # We expect DICOM annotations to be valid geometries without
+    # holes, but let's check to avoid errors on layer creation.
+    if isinstance(annotation.geometry, Point):
+        assert len(coords) == 1
+        return AnnotationData(coords[0], shape_type="point")
     if isinstance(annotation.geometry, Polygon):
-        shape = ShapelyPolygon(coords)
+        shape: ShapelyGeometry = ShapelyPolygon(coords)
+        shape_type: Literal["polygon", "path"] = "polygon"
     elif isinstance(annotation.geometry, Polyline):
         shape = ShapelyPolyline(coords)
-    elif isinstance(annotation.geometry, Point):
-        shape = ShapelyPoint(coords)
+        shape_type = "path"
     else:
-        raise ValueError("Unsupported geometry type.")
+        raise TypeError("Unsupported geometry type.")
     if not shape.is_valid:
         return None
+    if len(getattr(shape, "interiors", [])) > 0:
+        return None
     if tol > 0:
         shape = shape.simplify(tol)
-
-    if isinstance(shape, ShapelyPolygon):
-        return AnnotationData(np.array(shape.exterior.coords), shape_type="polygon")
-    elif isinstance(shape, ShapelyPolyline):
-        return AnnotationData(np.array(shape.coords), shape_type="path")
-    assert isinstance(shape, ShapelyPoint)
-    return AnnotationData(np.array(shape.coords[0]), shape_type="point")
+    return AnnotationData(coords, shape_type=shape_type)
 
 
 def _get_shape_annotations(
@@ -200,7 +200,6 @@ def __init__(
         path: str | Path | UPath | None = None,
         *,
         client: WsiDicomWebClient | None = None,
-        name: str | None = None,
         pyramid: int = 0,
         optical_path: str | None = None,
         color_space: str | ColorSpace = ColorSpace.RAW,
@@ -215,10 +214,12 @@ def __init__(
             path: A path to the input image directory, or a URL.
             client: A previously initialized DICOMWeb client. A `study_uid` and
                 `series_uids` must be provided as additional keyword arguments.
-            name: A name to identify the image.
             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.
+            kwargs: All additional keyword arguments are passed to the `WsiDicom.open`
+                or `WsiDicom.open_web` method.
+
         """
         if not isinstance(color_space, ColorSpace):
             color_space = ColorSpace(color_space)
@@ -286,7 +287,7 @@ def spatial_transform(self) -> np.ndarray:
             return matrix
         scale_y, scale_x = self.resolution  # mu/px
         offset_y, offset_x = ics.origin.y * 1000, ics.origin.x * 1000  # mu
-        orientation = ics.orientation.values
+        orientation = ics.orientation.values  # noqa: PD011
         matrix[0] = (orientation[1] * scale_y, orientation[4] * scale_x, offset_y)
         matrix[1] = (orientation[0] * scale_y, orientation[3] * scale_x, offset_x)
         return matrix
@@ -370,9 +371,12 @@ def to_layer_data_tuples(
                 any subset of ("image", "shapes", "points").
             tol: A tolerance value used to simplify all shape annotations. If this is
                 not greater zero, no simplification is performed.
+            kwargs: All additional keword arguments are passed to the
+                `to_layer_data_tuples` method of the base class.
 
         Returns:
             A list containing a napari layer data tuple of the given types.
+
         """
         if isinstance(layer_type, str):
             layer_type = (layer_type,)

napari_wsi/color_transform.py

@@ -16,7 +16,7 @@
 
 class ColorSpace(StrEnum):
     RAW = "RAW"
-    sRGB = "sRGB"
+    sRGB = "sRGB"  # noqa: N815
 
 
 class ColorTransform:
@@ -34,6 +34,7 @@ def __init__(
             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
@@ -42,7 +43,7 @@ def __init__(
                 profile = getOpenProfile(BytesIO(profile))
             self._transform = buildTransform(
                 profile,
-                createProfile(str(color_space)),  # type: ignore
+                createProfile(str(color_space)),  # type: ignore[arg-type]
                 mode,
                 mode,
                 Intent(getDefaultIntent(profile)),

napari_wsi/common.py

@@ -10,9 +10,9 @@
 import numpy as np
 import zarr
 from numpy.typing import DTypeLike
+from typing_extensions import Self
 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
 
@@ -21,6 +21,7 @@
 
 if TYPE_CHECKING:
     import napari
+    from zarr.core.array import Array
 
 
 @dataclass(frozen=True)
@@ -49,7 +50,7 @@ def dtype(self) -> DTypeLike:
     def __iter__(self) -> Iterator[PyramidLevel]:
         yield from self._levels
 
-    def __iadd__(self, level: PyramidLevel) -> "PyramidLevels":
+    def __iadd__(self, level: PyramidLevel) -> Self:
         if len(self._levels) > 0:
             top_level = self._levels[-1]
             if level.factor <= top_level.factor:
@@ -110,9 +111,11 @@ def to_layer_data_tuples(
         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.
+            kwargs: All additional keyword arguments are used as layer parameters.
 
         Returns:
             A one-element list containing a napari layer data tuple of type `image`.
+
         """
         pyramid_data: list[da.Array] = []
         for _, array in self._pyramid:
@@ -133,14 +136,14 @@ def to_layer_data_tuples(
                     **kwargs,
                 },
                 "image",
-            )
+            ),
         ]
 
 
 class WSIStore(PyramidStore, ABC):
     """A base class for reading multi-scale whole-slide images."""
 
-    def __init__(self, path: UPath | None, levels: PyramidLevels):
+    def __init__(self, path: UPath | None, levels: PyramidLevels) -> None:
         self._path = path
         super().__init__(name=path.stem if path is not None else "Image", levels=levels)
 
@@ -191,19 +194,24 @@ def to_transformed_layer_data_tuples(
         return items
 
     def to_viewer(
-        self, viewer: "napari.viewer.Viewer", spatial_transform: bool = False, **kwargs
+        self,
+        viewer: "napari.viewer.Viewer",
+        *,
+        spatial_transform: bool = False,
+        **kwargs,
     ) -> list["napari.layers.Layer"]:
         """Add all available layer data to the napari viewer.
 
-        All additional keword arguments are passed to the `to_layer_data_tuples` method.
-
         Args:
             viewer: The napari viewer.
             spatial_transform: If `True` and a spatial transform is available, all
                 layers are display in the corresponding transfored coordinate system.
+            kwargs: All additional keword arguments are passed to the
+                `to_layer_data_tuples` method.
 
         Returns:
             A list of layers added to the viewer.
+
         """
         layers = []
         for item in (

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "napari-wsi"
-version = "1.2.0"
+version = "1.2.1"
 description = "A plugin to read whole-slide images within napari."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -30,6 +30,7 @@ dependencies = [
     "magicgui>=0.10",
     "numpy>=1.26",
     "pillow>=11.1",
+    "typing-extensions>=4.6.1",
     "universal-pathlib>=0.2",
     "zarr>=3.0",
 ]
@@ -64,6 +65,7 @@ dev = [
     "pytest-qt>=4.4",
     "ruff>=0.9",
     "scikit-image>=0.25",
+    "types-shapely>=2.0.0",
 ]
 
 [project.urls]
@@ -82,27 +84,38 @@ module = [
     "colorspacious.*",
     "napari.*",
     "rasterio.*",
-    "shapely.*",
     "wsidicom.*",
 ]
 
 [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
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "ANN003", # Missing type annotation for `**kwargs`
+    "B028", # No explicit `stacklevel` keyword argument found
+    "COM812", # May cause conflicts when used with the formatter
+    "D100", # Missing docstring in public module
+    "D101", # Missing docstring in public class
+    "D102", # Missing docstring in public method
+    "D103", # Missing docstring in public function
+    "D104", # Missing docstring in public package
+    "D105", # Missing docstring in magic method
+    "D107", # Missing docstring in `__init__`
+    "D203", # D203 and D211 are incompatible
+    "D213", # D213 and D212 are incompatible
+    "EM101", # Exception must not use a string literal
+    "EM102", # Exception must not use an f-string literal
+    "FBT001", # Boolean-typed positional argument in function definition
+    "S101", # Use of `assert`
+    "TID252", # Prefer absolute imports over relative imports from parent modules
+    "TRY003", # Avoid specifying long messages outside the exception class
 ]
-lint.ignore = [
-    "B028", # for warnings
-    "ISC001", # for ruff
+
+[tool.ruff.lint.per-file-ignores]
+"tests/test_*.py" = [
+    "PLR2004", # Magic value used in comparison
+    "SLF001", # Private member accessed
 ]

tasks.py

@@ -1,19 +1,20 @@
 from invoke import task
+from invoke.context import Context
 
 
 @task
-def fix(ctx):
+def fix(ctx: Context) -> None:
     ctx.run("ruff format .")
     ctx.run("ruff check . --fix")
 
 
 @task
-def check(ctx):
+def check(ctx: Context) -> None:
     ctx.run("ruff format . --check")
     ctx.run("ruff check .")
     ctx.run("mypy .")
 
 
 @task
-def test(ctx):
+def test(ctx: Context) -> None:
     ctx.run("pytest --verbose --cov=napari_wsi tests")

tests/conftest.py

@@ -7,7 +7,6 @@
 import skimage.transform
 import skimage.util
 from attr import dataclass
-from pytest import FixtureRequest, TempPathFactory
 from rasterio.enums import Resampling
 from rasterio.errors import NotGeoreferencedWarning
 
@@ -41,14 +40,15 @@ class Case:
     file_path: Path | None = None
     file_fixture: str | None = None
 
-    def path(self, request: FixtureRequest) -> Path:
+    def path(self, request: pytest.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()
+        assert isinstance(path, Path)
+        assert path.exists()
         return path.resolve()
 
 
@@ -92,7 +92,7 @@ def path(self, request: FixtureRequest) -> Path:
 
 
 @pytest.fixture(scope="session")
-def dummy_gtiff(tmp_path_factory: TempPathFactory) -> Path:
+def dummy_gtiff(tmp_path_factory: pytest.TempPathFactory) -> Path:
     path = tmp_path_factory.mktemp("data") / "image.tiff"
 
     data = skimage.util.img_as_ubyte(skimage.data.binary_blobs(2048))