Fix pre-commit

panimg/image_builders/metaio_mhd_mha.py

@@ -7,7 +7,7 @@
 from collections import defaultdict
 from collections.abc import Iterator, Mapping
 from pathlib import Path
-from typing import DefaultDict, Union
+from typing import DefaultDict
 
 from panimg.exceptions import UnconsumedFilesException, ValidationError
 from panimg.image_builders.metaio_utils import load_sitk_image, parse_mh_header
@@ -57,7 +57,7 @@ def detect_mhd_file(headers: dict[str, str], path: Path) -> bool:
             raise ValueError("Data container of mhd file is missing")
         return True
 
-    def detect_mha_file(headers: Mapping[str, Union[str, None]]) -> bool:
+    def detect_mha_file(headers: Mapping[str, str | None]) -> bool:
         data_file = headers.get(element_data_file_key, None)
         return data_file == "LOCAL"
 

panimg/image_builders/oct.py

@@ -118,7 +118,7 @@ def _create_itk_fundus_image(
     )
 
 
-def _extract_slice_size(*, img: Union[FDS, FDA]) -> OctDimensions:
+def _extract_slice_size(*, img: FDS | FDA) -> OctDimensions:
     slice_size_meta_data = Struct(
         "unknown" / PaddedString(12, "utf16"),
         "xmm" / Float64l,

panimg/image_builders/tiff.py

@@ -1,11 +1,11 @@
 import os
 import re
 from collections import defaultdict
-from collections.abc import Iterator
+from collections.abc import Callable, Iterator
 from dataclasses import dataclass, field
 from pathlib import Path
 from tempfile import TemporaryDirectory
-from typing import Callable, DefaultDict, Optional
+from typing import DefaultDict
 from uuid import UUID, uuid4
 
 import tifffile
@@ -42,12 +42,12 @@ class GrandChallengeTiffFile:
     image_width: int = 0
     image_height: int = 0
     resolution_levels: int = 0
-    color_space: Optional[ColorSpace] = None
+    color_space: ColorSpace | None = None
     voxel_width_mm: float = 0
     voxel_height_mm: float = 0
     associated_files: list[Path] = field(default_factory=list)
-    min_voxel_value: Optional[int] = None
-    max_voxel_value: Optional[int] = None
+    min_voxel_value: int | None = None
+    max_voxel_value: int | None = None
 
     def validate(self) -> None:
         if not self.image_width:
@@ -76,7 +76,7 @@ def validate(self) -> None:
             )
 
     @property
-    def segments(self) -> Optional[frozenset[int]]:
+    def segments(self) -> frozenset[int] | None:
         if self.min_voxel_value is None or self.max_voxel_value is None:
             return None
         if (
@@ -209,7 +209,7 @@ def _extract_tags(
     return gc_file
 
 
-def _get_color_space(*, color_space_string) -> Optional[ColorSpace]:
+def _get_color_space(*, color_space_string) -> ColorSpace | None:
     color_space_string = color_space_string.upper()
 
     if color_space_string == "MINISBLACK":
@@ -319,7 +319,7 @@ def _get_vms_files(vms_file: Path):
 def _convert(
     *,
     files: list[Path],
-    associated_files_getter: Optional[Callable[[Path], list[Path]]],
+    associated_files_getter: Callable[[Path], list[Path]] | None,
     converter,
     output_directory: Path,
     file_errors: dict[Path, list[str]],

panimg/models.py

@@ -5,7 +5,7 @@
 from enum import Enum
 from functools import cached_property
 from pathlib import Path
-from typing import Any, NamedTuple, Optional
+from typing import Any, NamedTuple
 from uuid import UUID, uuid4
 
 import numpy as np
@@ -132,35 +132,35 @@ class PanImg:
     name: str
     width: int
     height: int
-    depth: Optional[int]
-    voxel_width_mm: Optional[float]
-    voxel_height_mm: Optional[float]
-    voxel_depth_mm: Optional[float]
-    timepoints: Optional[int]
-    resolution_levels: Optional[int]
-    window_center: Optional[float]
-    window_width: Optional[float]
+    depth: int | None
+    voxel_width_mm: float | None
+    voxel_height_mm: float | None
+    voxel_depth_mm: float | None
+    timepoints: int | None
+    resolution_levels: int | None
+    window_center: float | None
+    window_width: float | None
     color_space: ColorSpace
     eye_choice: EyeChoice
     patient_id: str = ""
     patient_name: str = ""
-    patient_birth_date: Optional[datetime.date] = None
+    patient_birth_date: datetime.date | None = None
     patient_age: str = ""
     patient_sex: PatientSex = PatientSex.EMPTY
-    study_date: Optional[datetime.date] = None
+    study_date: datetime.date | None = None
     study_instance_uid: str = ""
     series_instance_uid: str = ""
     study_description: str = ""
     series_description: str = ""
-    segments: Optional[frozenset[int]] = None
+    segments: frozenset[int] | None = None
 
 
 @dataclass(frozen=True)
 class PanImgFile:
     image_id: UUID
     image_type: ImageType
     file: Path
-    directory: Optional[Path] = None
+    directory: Path | None = None
 
 
 @dataclass
@@ -196,7 +196,7 @@ def height(self) -> int:
         return int(self.image.GetHeight())
 
     @property
-    def depth(self) -> Optional[int]:
+    def depth(self) -> int | None:
         try:
             depth = int(self.image.GetDepth())
         except (RuntimeError, ValueError):
@@ -212,7 +212,7 @@ def _extract_first_float(value: str) -> float:
             return float(value)
 
     @property
-    def window_center(self) -> Optional[float]:
+    def window_center(self) -> float | None:
         try:
             return self._extract_first_float(
                 self.image.GetMetaData("WindowCenter")
@@ -221,7 +221,7 @@ def window_center(self) -> Optional[float]:
             return None
 
     @property
-    def window_width(self) -> Optional[float]:
+    def window_width(self) -> float | None:
         try:
             return self._extract_first_float(
                 self.image.GetMetaData("WindowWidth")
@@ -230,7 +230,7 @@ def window_width(self) -> Optional[float]:
             return None
 
     @property
-    def timepoints(self) -> Optional[int]:
+    def timepoints(self) -> int | None:
         if self.image.GetDimension() == 4 and self.segments is None:
             # Only 4D files that are non-segmentations have timepoints
             return int(self.image.GetSize()[3])
@@ -265,7 +265,7 @@ def add_value_range_meta_data(cls, image: Image):  # noqa: B902, N805
         return image
 
     @cached_property
-    def segments(self) -> Optional[frozenset[int]]:
+    def segments(self) -> frozenset[int] | None:
         if (
             self.image.GetNumberOfComponentsPerPixel() != 1
             or self.image.GetPixelIDValue() not in MASK_TYPE_PIXEL_IDS
@@ -305,21 +305,21 @@ def color_space(self) -> ColorSpace:
         return ITK_COLOR_SPACE_MAP[self.image.GetNumberOfComponentsPerPixel()]
 
     @property
-    def voxel_width_mm(self) -> Optional[float]:
+    def voxel_width_mm(self) -> float | None:
         if self.spacing_valid:
             return float(self.image.GetSpacing()[0])
         else:
             return None
 
     @property
-    def voxel_height_mm(self) -> Optional[float]:
+    def voxel_height_mm(self) -> float | None:
         if self.spacing_valid:
             return float(self.image.GetSpacing()[1])
         else:
             return None
 
     @property
-    def voxel_depth_mm(self) -> Optional[float]:
+    def voxel_depth_mm(self) -> float | None:
         if self.spacing_valid:
             try:
                 return float(self.image.GetSpacing()[2])
@@ -406,7 +406,7 @@ class TIFFImage(BaseModel):
     resolution_levels: int
     color_space: ColorSpace
     eye_choice: EyeChoice = EyeChoice.NOT_APPLICABLE
-    segments: Optional[frozenset[int]] = None
+    segments: frozenset[int] | None = None
 
     model_config = ConfigDict(frozen=True)
 

panimg/panimg.py

@@ -2,7 +2,7 @@
 from collections import defaultdict
 from collections.abc import Iterable
 from pathlib import Path
-from typing import DefaultDict, Optional
+from typing import DefaultDict
 
 from panimg.exceptions import UnconsumedFilesException
 from panimg.image_builders import DEFAULT_IMAGE_BUILDERS
@@ -17,8 +17,8 @@ def convert(
     *,
     input_directory: Path,
     output_directory: Path,
-    builders: Optional[Iterable[ImageBuilder]] = None,
-    post_processors: Optional[Iterable[PostProcessor]] = None,
+    builders: Iterable[ImageBuilder] | None = None,
+    post_processors: Iterable[PostProcessor] | None = None,
     recurse_subdirectories: bool = True,
 ) -> PanImgResult:
     new_images: set[PanImg] = set()

panimg/types.py

@@ -1,6 +1,6 @@
 from collections.abc import Iterator
 from pathlib import Path
-from typing import Protocol, Union
+from typing import Protocol
 
 from panimg.models import (
     PanImgFile,
@@ -13,7 +13,7 @@
 class ImageBuilder(Protocol):
     def __call__(  # noqa: E704
         self, *, files: set[Path]
-    ) -> Union[Iterator[SimpleITKImage], Iterator[TIFFImage]]: ...
+    ) -> Iterator[SimpleITKImage] | Iterator[TIFFImage]: ...
 
 
 class PostProcessor(Protocol):

tests/test_background_tasks.py

@@ -119,6 +119,7 @@ def test_staged_mhd_upload_with_additional_headers(
             for original, new in zip(
                 extract_header_listing(key, original_headers),
                 extract_header_listing(key, headers),
+                strict=True,
             ):
                 assert original == new, key
         else:

tests/test_mhd.py

@@ -1,7 +1,6 @@
 import shutil
 import zlib
 from pathlib import Path
-from typing import Union
 
 import pytest
 import SimpleITK
@@ -198,8 +197,8 @@ def test_load_sitk_image_with_additional_meta_data(tmpdir, test_img: str):
 )
 def test_load_sitk_image_with_various_window_formats(
     test_img: str,
-    center: Union[float, list[float]],
-    width: Union[float, list[float]],
+    center: float | list[float],
+    width: float | list[float],
 ):
     src = MHD_WINDOW_DIR / test_img
     sitk_image = load_sitk_image(src)