dlup 0.8.1__cp310-none-win_amd64.whl

dlup/__init__.py

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+# Copyright 2024 AI for Oncology Research Group. All Rights Reserved.
+# Copyright 2024 Jonas Teuwen. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from ._image import SlideImage, SlideImageView, Resampling
+from ._region import BoundaryMode, RegionView
+
+from .annotations import SlideAnnotations, SlideAnnotationsView
+from .data.dataset import SlideDataset, TilingConfig, MaskConfig, ImageConfig, AnnotationConfig
+
+__author__ = """dlup contributors"""
+__email__ = "j.teuwen@nki.nl"
+__version__ = "0.8.1"
+__all__ = (
+    "SlideImage",
+    "SlideImageView",
+    "SlideDataset",
+    "SlideAnnotations",
+    "SlideAnnotationsView",
+    "RegionView",
+    "BoundaryMode",
+    "Resampling",
+    "TilingConfig",
+    "MaskConfig",
+    "ImageConfig",
+    "AnnotationConfig",
+)

dlup/_background.pyi

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+# Copyright 2024 AI for Oncology Research Group. All Rights Reserved.
+# Copyright 2024 Jonas Teuwen. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import numpy as np
+import numpy.typing as npt
+
+def get_foreground_indices_numpy(
+    image_width: int,
+    image_height: int,
+    image_slide_average_mpp: float,
+    background_mask: npt.NDArray[np.int_],
+    regions_array: npt.NDArray[np.float64],
+    threshold: float,
+    foreground_indices: npt.NDArray[np.int64],
+) -> int: ...

dlup/_exceptions.py

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+# Copyright 2024 AI for Oncology Research Group. All Rights Reserved.
+# Copyright 2024 Jonas Teuwen. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Custom exceptions for dlup."""
+
+from __future__ import annotations
+
+
+class DlupError(Exception):
+    """Base class for exceptions in dlup."""
+
+    pass
+
+
+class UnsupportedSlideError(DlupError):
+    """Raised when a slide is not supported."""
+
+    def __init__(self, msg: str, identifier: str | None = None):
+        msg = msg if identifier is None else f"slide '{identifier}': " + msg
+        super().__init__(self, msg)
+
+
+class SlideError(RuntimeError):
+    """Raised when an error occurs with a slide."""
+
+    def __init__(self, msg: str, identifier: str | None = None):
+        msg = msg if identifier is None else f"slide '{identifier}': " + msg
+        super().__init__(self, msg)
+
+
+class AnnotationError(DlupError):
+    """Raised when an annotation is invalid."""
+
+    def __init__(self, msg: str):
+        super().__init__(self, msg)

dlup/_geometry.pyi

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+# Copyright 2024 AI for Oncology Research Group. All Rights Reserved.
+# Copyright 2024 Jonas Teuwen. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+from typing import Callable, overload
+
+import numpy as np
+from dlup._types import GenericNumber
+from dlup.geometry import Box as Box_
+from dlup.geometry import Point as Point_
+from dlup.geometry import Polygon as Polygon_
+from numpy.typing import NDArray
+
+class Polygon:
+    @property
+    def fields(self) -> list[str]: ...
+    def get_exterior(self) -> list[tuple[float, float]]: ...
+    def get_interiors(self) -> list[list[tuple[float, float]]]: ...
+    def contains(self, other: Polygon_) -> bool: ...
+    def correct_orientation(self) -> None: ...
+    @property
+    def bounding_box(self) -> "Box": ...
+    def scale(self, scaling: float) -> None: ...
+    def clone(self) -> "Polygon": ...
+    @property
+    def area(self) -> float: ...
+
+def set_polygon_factory(factory: Callable[[Polygon_], Polygon_]) -> None: ...
+
+class Point:
+    @property
+    def fields(self) -> list[str]: ...
+    def scale(self, scaling: float) -> None: ...
+    def get_coordinates(self) -> tuple[float, float]: ...
+    @property
+    def x(self) -> float: ...
+    @property
+    def y(self) -> float: ...
+    def clone(self) -> "Point": ...
+
+def set_point_factory(factory: Callable[[Point_], Point_]) -> None: ...
+
+class Box:
+    @property
+    def fields(self) -> list[str]: ...
+    def as_polygon(self) -> Polygon_: ...
+    @property
+    def area(self) -> float: ...
+    def scale(self, scaling: float) -> None: ...
+    @property
+    def coordinates(self) -> tuple[float, float]: ...
+    @property
+    def size(self) -> tuple[float, float]: ...
+    def clone(self) -> "Box": ...
+
+def set_box_factory(factory: Callable[[Box_], Box_]) -> None: ...
+
+class LazyArray:
+    def __array__(self) -> NDArray[np.int_]: ...
+    def numpy(self) -> NDArray[np.int_]: ...
+
+class PolygonCollection:
+    def get_geometries(self) -> list[Polygon_]: ...
+    def to_mask(self) -> LazyArray: ...
+
+class AnnotationRegion:
+    @property
+    def polygons(self) -> PolygonCollection: ...
+    @property
+    def rois(self) -> PolygonCollection: ...
+    @property
+    def points(self) -> list[Point_]: ...
+    @property
+    def boxes(self) -> list[Box_]: ...
+    @property
+    def has_rois(self) -> bool: ...
+
+class GeometryCollection:
+    def add_polygon(self, polygon: Polygon) -> None: ...
+    def add_roi(self, roi: Polygon) -> None: ...
+    def add_point(self, point: Point) -> None: ...
+    def add_box(self, box: Box) -> None: ...
+    @property
+    def polygons(self) -> list[Polygon_]: ...
+    @property
+    def rois(self) -> list[Polygon_]: ...
+    @property
+    def points(self) -> list[Point_]: ...
+    @property
+    def boxes(self) -> list[Box_]: ...
+    def set_offset(self, offset: tuple[float, float]) -> None: ...
+    def rebuild_rtree(self) -> None: ...
+    def reindex_polygons(self, index_map: dict[str, int]) -> None: ...
+    @overload
+    def remove_point(self, index: int) -> None: ...
+    @overload
+    def remove_point(self, point: Point_) -> None: ...
+    @overload
+    def remove_polygon(self, index: int) -> None: ...
+    @overload
+    def remove_polygon(self, polygon: Polygon_) -> None: ...
+    @overload
+    def remove_roi(self, index: int) -> None: ...
+    @overload
+    def remove_roi(self, roi: Polygon_) -> None: ...
+    @overload
+    def remove_box(self, index: int) -> None: ...
+    @overload
+    def remove_box(self, box: Box_) -> None: ...
+    def sort_polygons(self, key: Callable[[Polygon_], int | float | str | None], reverse: bool) -> None: ...
+    @property
+    def bounding_box(self) -> tuple[tuple[float, float], tuple[float, float]]: ...
+    def size(self) -> int: ...
+    def simplify(self, tolerance: float) -> None: ...
+    def scale(self, scaling: float) -> None: ...
+    def read_region(
+        self,
+        coordinates: tuple[GenericNumber, GenericNumber],
+        scaling: float,
+        size: tuple[GenericNumber, GenericNumber],
+    ) -> AnnotationRegion: ...
+    @property
+    def rtree_invalidated(self) -> bool: ...
+    @property
+    def index_map(self) -> dict[str, int]: ...
+    @property
+    def has_rois(self) -> bool: ...