dlup 0.3.26__tar.gz → 0.3.28__tar.gz

{dlup-0.3.26 → dlup-0.3.28}/MANIFEST.in

@@ -1,9 +1,10 @@
 include CONTRIBUTING.rst
 include LICENSE
 include README.md
+include dlup/py.typed
 
 recursive-include tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
-recursive-include docs *.rst *.md conf.py Makefile make.bat *.jpg *.png *.gif *.typed
+recursive-include docs *.rst *.md conf.py Makefile make.bat *.jpg *.png *.gif

{dlup-0.3.26/dlup.egg-info → dlup-0.3.28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dlup
-Version: 0.3.26
+Version: 0.3.28
 Home-page: https://github.com/NKI-AI/dlup
 Author: Jonas Teuwen
 Author-email: j.teuwen@nki.nl
@@ -15,8 +15,28 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: numpy>=1.21
+Requires-Dist: scikit-image>=0.19
+Requires-Dist: tifftools
+Requires-Dist: tifffile>=2023.8.12
+Requires-Dist: pyvips>=2.2.1
+Requires-Dist: tqdm
+Requires-Dist: pillow>=9.2.0
+Requires-Dist: openslide-python
+Requires-Dist: opencv-python>=4.8.1.78
+Requires-Dist: shapely>=2.0.0
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: mypy>=1.4.1; extra == "dev"
+Requires-Dist: pytest-mock; extra == "dev"
+Requires-Dist: sphinx_copybutton; extra == "dev"
+Requires-Dist: numpydoc; extra == "dev"
+Requires-Dist: myst_parser; extra == "dev"
+Requires-Dist: sphinx-book-theme; extra == "dev"
+Requires-Dist: pylint; extra == "dev"
+Requires-Dist: pydantic>=2.1.1; extra == "dev"
+Requires-Dist: types-requests; extra == "dev"
 
 # Deep Learning Utilities for Pathology
 [![pypi](https://img.shields.io/pypi/v/dlup.svg)](https://pypi.python.org/pypi/dlup)

{dlup-0.3.26 → dlup-0.3.28}/dlup/__init__.py

@@ -1,13 +1,11 @@
-# coding=utf-8
-# Copyright (c) dlup contributors
-"""Top-level package for dlup."""
+# Copyright (c) dlup contributors"""Top-level package for dlup."""
 
-from ._exceptions import DlupError, UnsupportedSlideError
+from ._exceptions import UnsupportedSlideError
 from ._image import SlideImage
 from ._region import BoundaryMode, RegionView
 
 __author__ = """dlup contributors"""
 __email__ = "j.teuwen@nki.nl"
-__version__ = "0.3.26"
+__version__ = "0.3.28"
 
 __all__ = ("SlideImage", "RegionView", "UnsupportedSlideError", "BoundaryMode")

{dlup-0.3.26 → dlup-0.3.28}/dlup/_image.py

@@ -1,4 +1,3 @@
-# coding=utf-8
 # Copyright (c) dlup contributors
 
 """Whole slide image access objects.
@@ -13,17 +12,19 @@ import errno
 import os
 import pathlib
 from enum import IntEnum
-from typing import Callable, Type, TypeVar, cast
+from types import TracebackType
+from typing import Any, Literal, Optional, Type, TypeVar, cast
 
-import numpy as np  # type: ignore
-import openslide  # type: ignore
+import numpy as np
+import numpy.typing as npt
 import PIL
-import PIL.Image  # type: ignore
+import PIL.Image
 
 from dlup import UnsupportedSlideError
 from dlup._region import BoundaryMode, RegionView
-from dlup.experimental_backends import AbstractSlideBackend, ImageBackend
-from dlup.types import GenericFloatArray, GenericIntArray, GenericNumber, PathLike
+from dlup.backends.common import AbstractSlideBackend
+from dlup.experimental_backends import ImageBackend  # type: ignore
+from dlup.types import GenericFloatArray, GenericIntArray, GenericNumber, GenericNumberArray, PathLike
 from dlup.utils.image import check_if_mpp_is_valid
 
 _Box = tuple[GenericNumber, GenericNumber, GenericNumber, GenericNumber]
@@ -42,7 +43,12 @@ class Resampling(IntEnum):
 class _SlideImageRegionView(RegionView):
     """Represents an image view tied to a slide image."""
 
-    def __init__(self, wsi: _TSlideImage, scaling: GenericNumber, boundary_mode: BoundaryMode | None = None):
+    def __init__(
+        self,
+        wsi: _TSlideImage,
+        scaling: GenericNumber,
+        boundary_mode: BoundaryMode | None = None,
+    ):
         """Initialize with a slide image object and the scaling level."""
         # Always call the parent init
         super().__init__(boundary_mode=boundary_mode)
@@ -66,7 +72,9 @@ class _SlideImageRegionView(RegionView):
         return self._wsi.read_region((x, y), self._scaling, (w, h))
 
 
-def _clip2size(a: np.ndarray, size: tuple[GenericNumber, GenericNumber]) -> np.ndarray:
+def _clip2size(
+    a: npt.NDArray[np.int_ | np.float_], size: tuple[GenericNumber, GenericNumber]
+) -> npt.NDArray[np.int_ | np.float_]:
     """Clip values from 0 to size boundaries."""
     return np.clip(a, (0, 0), size)
 
@@ -92,7 +100,7 @@ class SlideImage:
     >>> wsi = dlup.SlideImage.from_file_path('path/to/slide.svs')
     """
 
-    def __init__(self, wsi: AbstractSlideBackend, identifier: str | None = None, **kwargs):
+    def __init__(self, wsi: AbstractSlideBackend, identifier: str | None = None, **kwargs: Any) -> None:
         """Initialize a whole slide image and validate its properties."""
         self._wsi = wsi
         self._identifier = identifier
@@ -111,20 +119,26 @@ class SlideImage:
 
         if self._wsi.spacing is None:
             raise UnsupportedSlideError(
-                f"The spacing of {identifier} cannot be derived from image and is not explicitly set in the `overwrite_mpp` parameter."
+                f"The spacing of {identifier} cannot be derived from image and is "
+                "not explicitly set in the `overwrite_mpp` parameter."
             )
 
         check_if_mpp_is_valid(*self._wsi.spacing)
         self._avg_native_mpp = (float(self._wsi.spacing[0]) + float(self._wsi.spacing[1])) / 2
 
-    def close(self):
+    def close(self) -> None:
         """Close the underlying image."""
         self._wsi.close()
 
-    def __enter__(self):
+    def __enter__(self) -> "SlideImage":
         return self
 
-    def __exit__(self, exc_type, exc_val, exc_tb):
+    def __exit__(
+        self,
+        exc_type: Optional[Type[BaseException]],
+        exc_val: Optional[BaseException],
+        exc_tb: Optional[TracebackType],
+    ) -> Literal[False]:
         self.close()
         return False
 
@@ -133,8 +147,8 @@ class SlideImage:
         cls: Type[_TSlideImage],
         wsi_file_path: PathLike,
         identifier: str | None = None,
-        backend: str | Callable = ImageBackend.PYVIPS,
-        **kwargs,
+        backend: ImageBackend = ImageBackend.PYVIPS,
+        **kwargs: Any,
     ) -> _TSlideImage:
         wsi_file_path = pathlib.Path(wsi_file_path)
 
@@ -152,9 +166,9 @@ class SlideImage:
 
     def read_region(
         self,
-        location: np.ndarray | tuple[GenericNumber, GenericNumber],
+        location: GenericNumberArray | tuple[GenericNumber, GenericNumber],
         scaling: float,
-        size: np.ndarray | tuple[int, int],
+        size: npt.NDArray[np.int_] | tuple[int, int],
     ) -> PIL.Image.Image:
         """Return a region at a specific scaling level of the pyramid.
 
@@ -202,8 +216,8 @@ class SlideImage:
         Examples
         --------
         The locations are defined at the requested scaling (with respect to level 0), so if we want to extract at
-        location ``(location_x, location_y)`` of a scaling 0.5 (with respect to level 0), and have resulting tile size of
-         ``(tile_size, tile_size)`` with a scaling factor of 0.5, we can use:
+        location ``(location_x, location_y)`` of a scaling 0.5 (with respect to level 0), and have
+        resulting tile size of ``(tile_size, tile_size)`` with a scaling factor of 0.5, we can use:
         >>>  wsi.read_region(location=(coordinate_x, coordinate_y), scaling=0.5, size=(tile_size, tile_size))
         """
         owsi = self._wsi
@@ -247,7 +261,11 @@ class SlideImage:
         native_size_adapted = np.ceil(native_size_adapted).astype(int)
 
         # We extract the region via openslide with the required extra border
-        region = owsi.read_region(tuple(level_zero_location_adapted), native_level, tuple(native_size_adapted))
+        region = owsi.read_region(
+            (level_zero_location_adapted[0], level_zero_location_adapted[1]),
+            native_level,
+            (native_size_adapted[0], native_size_adapted[1]),
+        )
 
         # Within this region, there are a bunch of extra pixels, we interpolate to sample
         # the pixel in the right position to retain the right sample weight.
@@ -256,7 +274,11 @@ class SlideImage:
         # TODO: This clipping could be in an error in OpenSlide mirax reader, but it's a minor thing for now
         box = (
             *fractional_coordinates,
-            *np.clip((fractional_coordinates + native_size), a_min=0, a_max=np.asarray(region.size)),
+            *np.clip(
+                (fractional_coordinates + native_size),
+                a_min=0,
+                a_max=np.asarray(region.size),
+            ),
         )
         box = cast(tuple[float, float, float, float], box)
         size = cast(tuple[int, int], size)
@@ -307,7 +329,7 @@ class SlideImage:
         return self._identifier
 
     @property
-    def properties(self) -> dict:
+    def properties(self) -> dict[str, str | int | float | bool] | None:
         """Returns any extra associated properties with the image."""
         return self._wsi.properties
 
@@ -338,7 +360,7 @@ class SlideImage:
         return width / height
 
     @property
-    def slide_bounds(self):
+    def slide_bounds(self) -> tuple[tuple[int, int], tuple[int, int]]:
         """Returns the bounds of the slide. These can be smaller than the image itself.
         These bounds are in the format (x, y), (width, height), and are defined at level 0 of the image.
         """

{dlup-0.3.26 → dlup-0.3.28}/dlup/_region.py

@@ -1,13 +1,12 @@
-# coding=utf-8
+# Copyright (c) dlup contributors
 """Defines the RegionView interface."""
 from __future__ import annotations
 
 from abc import ABC, abstractmethod
 from enum import Enum
-from typing import Iterable, Union, cast
+from typing import cast
 
 import numpy as np
-import numpy.typing as npt
 import PIL.Image
 
 from dlup.types import GenericFloatArray, GenericIntArray