careamics 0.0.14__py3-none-any.whl → 0.0.15__py3-none-any.whl

careamics/config/data/ng_data_model.py

@@ -4,7 +4,7 @@ from __future__ import annotations
 
 from collections.abc import Sequence
 from pprint import pformat
-from typing import Annotated, Any, Literal, Optional, Union
+from typing import Annotated, Any, Literal, Union
 from warnings import warn
 
 import numpy as np
@@ -106,22 +106,16 @@ class NGDataConfig(BaseModel):
     batch_size: int = Field(default=1, ge=1, validate_default=True)
     """Batch size for training."""
 
-    image_means: Optional[list[Float]] = Field(
-        default=None, min_length=0, max_length=32
-    )
+    image_means: list[Float] | None = Field(default=None, min_length=0, max_length=32)
     """Means of the data across channels, used for normalization."""
 
-    image_stds: Optional[list[Float]] = Field(default=None, min_length=0, max_length=32)
+    image_stds: list[Float] | None = Field(default=None, min_length=0, max_length=32)
     """Standard deviations of the data across channels, used for normalization."""
 
-    target_means: Optional[list[Float]] = Field(
-        default=None, min_length=0, max_length=32
-    )
+    target_means: list[Float] | None = Field(default=None, min_length=0, max_length=32)
     """Means of the target data across channels, used for normalization."""
 
-    target_stds: Optional[list[Float]] = Field(
-        default=None, min_length=0, max_length=32
-    )
+    target_stds: list[Float] | None = Field(default=None, min_length=0, max_length=32)
     """Standard deviations of the target data across channels, used for
     normalization."""
 
@@ -148,7 +142,7 @@ class NGDataConfig(BaseModel):
     test_dataloader_params: dict[str, Any] = Field(default={})
     """Dictionary of PyTorch test dataloader parameters."""
 
-    seed: Optional[int] = Field(default=None, gt=0)
+    seed: int | None = Field(default=None, gt=0)
     """Random seed for reproducibility."""
 
     @field_validator("axes")
@@ -330,8 +324,8 @@ class NGDataConfig(BaseModel):
         self,
         image_means: Union[NDArray, tuple, list, None],
         image_stds: Union[NDArray, tuple, list, None],
-        target_means: Optional[Union[NDArray, tuple, list, None]] = None,
-        target_stds: Optional[Union[NDArray, tuple, list, None]] = None,
+        target_means: Union[NDArray, tuple, list, None] | None = None,
+        target_stds: Union[NDArray, tuple, list, None] | None = None,
     ) -> None:
         """
         Set mean and standard deviation of the data across channels.

careamics/config/data/patching_strategies/_overlapping_patched_model.py

@@ -1,7 +1,6 @@
 """Sequential patching Pydantic model."""
 
 from collections.abc import Sequence
-from typing import Optional
 
 from pydantic import Field, ValidationInfo, field_validator
 
@@ -24,7 +23,7 @@ class _OverlappingPatchedModel(_PatchedModel):
         dimension, and the number of dimensions be either 2 or 3.
     """
 
-    overlaps: Optional[Sequence[int]] = Field(
+    overlaps: Sequence[int] | None = Field(
         default=None,
         min_length=2,
         max_length=3,
@@ -37,8 +36,8 @@ class _OverlappingPatchedModel(_PatchedModel):
     @field_validator("overlaps")
     @classmethod
     def overlap_smaller_than_patch_size(
-        cls, overlaps: Optional[Sequence[int]], values: ValidationInfo
-    ) -> Optional[Sequence[int]]:
+        cls, overlaps: Sequence[int] | None, values: ValidationInfo
+    ) -> Sequence[int] | None:
         """
         Validate overlap.
 
@@ -78,7 +77,7 @@ class _OverlappingPatchedModel(_PatchedModel):
 
     @field_validator("overlaps")
     @classmethod
-    def overlap_even(cls, overlaps: Optional[Sequence[int]]) -> Optional[Sequence[int]]:
+    def overlap_even(cls, overlaps: Sequence[int] | None) -> Sequence[int] | None:
         """
         Validate overlaps.
 

careamics/config/inference_model.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import Any, Literal, Optional, Union
+from typing import Any, Literal, Union
 
 from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
 from typing_extensions import Self
@@ -18,12 +18,10 @@ class InferenceConfig(BaseModel):
     data_type: Literal["array", "tiff", "czi", "custom"]  # As defined in SupportedData
     """Type of input data: numpy.ndarray (array) or path (tiff, czi, or custom)."""
 
-    tile_size: Optional[Union[list[int]]] = Field(
-        default=None, min_length=2, max_length=3
-    )
+    tile_size: Union[list[int]] | None = Field(default=None, min_length=2, max_length=3)
     """Tile size of prediction, only effective if `tile_overlap` is specified."""
 
-    tile_overlap: Optional[Union[list[int]]] = Field(
+    tile_overlap: Union[list[int]] | None = Field(
         default=None, min_length=2, max_length=3
     )
     """Overlap between tiles, only effective if `tile_size` is specified."""
@@ -48,8 +46,8 @@ class InferenceConfig(BaseModel):
     @field_validator("tile_overlap")
     @classmethod
     def all_elements_non_zero_even(
-        cls, tile_overlap: Optional[list[int]]
-    ) -> Optional[list[int]]:
+        cls, tile_overlap: list[int] | None
+    ) -> list[int] | None:
         """
         Validate tile overlap.
 
@@ -86,9 +84,7 @@ class InferenceConfig(BaseModel):
 
     @field_validator("tile_size")
     @classmethod
-    def tile_min_8_power_of_2(
-        cls, tile_list: Optional[list[int]]
-    ) -> Optional[list[int]]:
+    def tile_min_8_power_of_2(cls, tile_list: list[int] | None) -> list[int] | None:
         """
         Validate that each entry is greater or equal than 8 and a power of 2.
 

careamics/config/likelihood_model.py

@@ -1,6 +1,6 @@
 """Likelihood model."""
 
-from typing import Annotated, Literal, Optional, Union
+from typing import Annotated, Literal, Union
 
 import numpy as np
 import torch
@@ -31,7 +31,7 @@ class GaussianLikelihoodConfig(BaseModel):
 
     model_config = ConfigDict(validate_assignment=True)
 
-    predict_logvar: Optional[Literal["pixelwise"]] = None
+    predict_logvar: Literal["pixelwise"] | None = None
     """If `pixelwise`, log-variance is computed for each pixel, else log-variance
     is not computed."""
 

careamics/config/nm_model.py

@@ -1,7 +1,7 @@
 """Noise models config."""
 
 from pathlib import Path
-from typing import Annotated, Literal, Optional, Union
+from typing import Annotated, Literal, Union
 
 import numpy as np
 import torch
@@ -42,21 +42,19 @@ class GaussianMixtureNMConfig(BaseModel):
     # model type
     model_type: Literal["GaussianMixtureNoiseModel"]
 
-    path: Optional[Union[Path, str]] = None
+    path: Union[Path, str] | None = None
     """Path to the directory where the trained noise model (*.npz) is saved in the
     `train` method."""
 
     # TODO remove and use as parameters to the NM functions?
-    signal: Optional[Union[str, Path, np.ndarray]] = Field(default=None, exclude=True)
+    signal: Union[str, Path, np.ndarray] | None = Field(default=None, exclude=True)
     """Path to the file containing signal or respective numpy array."""
 
     # TODO remove and use as parameters to the NM functions?
-    observation: Optional[Union[str, Path, np.ndarray]] = Field(
-        default=None, exclude=True
-    )
+    observation: Union[str, Path, np.ndarray] | None = Field(default=None, exclude=True)
     """Path to the file containing observation or respective numpy array."""
 
-    weight: Optional[Array] = None
+    weight: Array | None = None
     """A [3*n_gaussian, n_coeff] sized array containing the values of the weights
     describing the GMM noise model, with each row corresponding to one
     parameter of each gaussian, namely [mean, standard deviation and weight].

careamics/config/training_model.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from pprint import pformat
-from typing import Literal, Optional, Union
+from typing import Literal, Union
 
 from pydantic import BaseModel, ConfigDict, Field, field_validator
 
@@ -41,11 +41,11 @@ class TrainingConfig(BaseModel):
     """Validation step frequency."""
     accumulate_grad_batches: int = Field(default=1, ge=1)
     """Number of batches to accumulate gradients over before stepping the optimizer."""
-    gradient_clip_val: Optional[Union[int, float]] = None
+    gradient_clip_val: Union[int, float] | None = None
     """The value to which to clip the gradient"""
     gradient_clip_algorithm: Literal["value", "norm"] = "norm"
     """The algorithm to use for gradient clipping (see lightning `Trainer`)."""
-    logger: Optional[Literal["wandb", "tensorboard"]] = None
+    logger: Literal["wandb", "tensorboard"] | None = None
     """Logger to use during training. If None, no logger will be used. Available
     loggers are defined in SupportedLogger."""
 
@@ -53,7 +53,7 @@ class TrainingConfig(BaseModel):
     """Checkpoint callback configuration, following PyTorch Lightning Checkpoint
     callback."""
 
-    early_stopping_callback: Optional[EarlyStoppingModel] = Field(
+    early_stopping_callback: EarlyStoppingModel | None = Field(
         default=None, validate_default=True
     )
     """Early stopping callback configuration, following PyTorch Lightning Checkpoint

careamics/config/transformations/normalize_model.py

@@ -1,6 +1,6 @@
 """Pydantic model for the Normalize transform."""
 
-from typing import Literal, Optional
+from typing import Literal
 
 from pydantic import ConfigDict, Field, model_validator
 from typing_extensions import Self
@@ -31,8 +31,8 @@ class NormalizeModel(TransformModel):
     name: Literal["Normalize"] = "Normalize"
     image_means: list = Field(..., min_length=0, max_length=32)
     image_stds: list = Field(..., min_length=0, max_length=32)
-    target_means: Optional[list] = Field(default=None, min_length=0, max_length=32)
-    target_stds: Optional[list] = Field(default=None, min_length=0, max_length=32)
+    target_means: list | None = Field(default=None, min_length=0, max_length=32)
+    target_stds: list | None = Field(default=None, min_length=0, max_length=32)
 
     @model_validator(mode="after")
     def validate_means_stds(self: Self) -> Self:

careamics/config/transformations/xy_flip_model.py

@@ -1,6 +1,6 @@
 """Pydantic model for the XYFlip transform."""
 
-from typing import Literal, Optional
+from typing import Literal
 
 from pydantic import ConfigDict, Field
 
@@ -40,4 +40,4 @@ class XYFlipModel(TransformModel):
         ge=0,
         le=1,
     )
-    seed: Optional[int] = None
+    seed: int | None = None

careamics/config/transformations/xy_random_rotate90_model.py

@@ -1,6 +1,6 @@
 """Pydantic model for the XYRandomRotate90 transform."""
 
-from typing import Literal, Optional
+from typing import Literal
 
 from pydantic import ConfigDict, Field
 
@@ -32,4 +32,4 @@ class XYRandomRotate90Model(TransformModel):
         ge=0,
         le=1,
     )
-    seed: Optional[int] = None
+    seed: int | None = None

careamics/config/validators/validator_utils.py

@@ -5,7 +5,6 @@ These functions are used to validate dimensions and axes of inputs.
 """
 
 from collections.abc import Sequence
-from typing import Optional
 
 _AXES = "STCZYX"
 
@@ -80,7 +79,7 @@ def value_ge_than_8_power_of_2(
 
 
 def patch_size_ge_than_8_power_of_2(
-    patch_list: Optional[Sequence[int]],
+    patch_list: Sequence[int] | None,
 ) -> None:
     """
     Validate that each entry is greater or equal than 8 and a power of 2.

careamics/dataset/dataset_utils/iterate_over_files.py

@@ -4,7 +4,7 @@ from __future__ import annotations
 
 from collections.abc import Callable, Generator
 from pathlib import Path
-from typing import Optional, Union
+from typing import Union
 
 from numpy.typing import NDArray
 from torch.utils.data import get_worker_info
@@ -21,9 +21,9 @@ logger = get_logger(__name__)
 def iterate_over_files(
     data_config: Union[DataConfig, InferenceConfig],
     data_files: list[Path],
-    target_files: Optional[list[Path]] = None,
+    target_files: list[Path] | None = None,
     read_source_func: Callable = read_tiff,
-) -> Generator[tuple[NDArray, Optional[NDArray]], None, None]:
+) -> Generator[tuple[NDArray, NDArray | None], None, None]:
     """Iterate over data source and yield whole reshaped images.
 
     Parameters

careamics/dataset/in_memory_dataset.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 import copy
 from collections.abc import Callable
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any, Union
 
 import numpy as np
 from torch.utils.data import Dataset
@@ -49,7 +49,7 @@ class InMemoryDataset(Dataset):
         self,
         data_config: DataConfig,
         inputs: Union[np.ndarray, list[Path]],
-        input_target: Optional[Union[np.ndarray, list[Path]]] = None,
+        input_target: Union[np.ndarray, list[Path]] | None = None,
         read_source_func: Callable = read_tiff,
         **kwargs: Any,
     ) -> None:

careamics/dataset/iterable_dataset.py

@@ -5,7 +5,6 @@ from __future__ import annotations
 import copy
 from collections.abc import Callable, Generator
 from pathlib import Path
-from typing import Optional
 
 import numpy as np
 from torch.utils.data import IterableDataset
@@ -51,7 +50,7 @@ class PathIterableDataset(IterableDataset):
         self,
         data_config: DataConfig,
         src_files: list[Path],
-        target_files: Optional[list[Path]] = None,
+        target_files: list[Path] | None = None,
         read_source_func: Callable = read_tiff,
     ) -> None:
         """Constructors.

careamics/dataset/patching/random_patching.py

@@ -1,7 +1,7 @@
 """Random patching utilities."""
 
 from collections.abc import Generator
-from typing import Optional, Union
+from typing import Union
 
 import numpy as np
 import zarr
@@ -13,9 +13,9 @@ from .validate_patch_dimension import validate_patch_dimensions
 def extract_patches_random(
     arr: np.ndarray,
     patch_size: Union[list[int], tuple[int, ...]],
-    target: Optional[np.ndarray] = None,
-    seed: Optional[int] = None,
-) -> Generator[tuple[np.ndarray, Optional[np.ndarray]], None, None]:
+    target: np.ndarray | None = None,
+    seed: int | None = None,
+) -> Generator[tuple[np.ndarray, np.ndarray | None], None, None]:
     """
     Generate patches from an array in a random manner.
 
@@ -115,8 +115,8 @@ def extract_patches_random_from_chunks(
     arr: zarr.Array,
     patch_size: Union[list[int], tuple[int, ...]],
     chunk_size: Union[list[int], tuple[int, ...]],
-    chunk_limit: Optional[int] = None,
-    seed: Optional[int] = None,
+    chunk_limit: int | None = None,
+    seed: int | None = None,
 ) -> Generator[np.ndarray, None, None]:
     """
     Generate patches from an array in a random manner.

careamics/dataset/patching/sequential_patching.py

@@ -1,6 +1,6 @@
 """Sequential patching functions."""
 
-from typing import Optional, Union
+from typing import Union
 
 import numpy as np
 from skimage.util import view_as_windows
@@ -110,7 +110,7 @@ def _compute_patch_views(
     window_shape: list[int],
     step: tuple[int, ...],
     output_shape: list[int],
-    target: Optional[np.ndarray] = None,
+    target: np.ndarray | None = None,
 ) -> np.ndarray:
     """
     Compute views of an array corresponding to patches.
@@ -151,8 +151,8 @@ def _compute_patch_views(
 def extract_patches_sequential(
     arr: np.ndarray,
     patch_size: Union[list[int], tuple[int, ...]],
-    target: Optional[np.ndarray] = None,
-) -> tuple[np.ndarray, Optional[np.ndarray]]:
+    target: np.ndarray | None = None,
+) -> tuple[np.ndarray, np.ndarray | None]:
     """
     Generate patches from an array in a sequential manner.
 

careamics/dataset/tiling/lvae_tiled_patching.py

@@ -3,7 +3,7 @@
 import builtins
 import itertools
 from collections.abc import Generator
-from typing import Any, Optional, Union
+from typing import Any, Union
 
 import numpy as np
 from numpy.typing import NDArray
@@ -16,7 +16,7 @@ def extract_tiles(
     arr: NDArray,
     tile_size: NDArray[np.int_],
     overlaps: NDArray[np.int_],
-    padding_kwargs: Optional[dict[str, Any]] = None,
+    padding_kwargs: dict[str, Any] | None = None,
 ) -> Generator[tuple[NDArray, TileInformation], None, None]:
     """Generate tiles from the input array with specified overlap.
 

careamics/dataset_ng/dataset.py

@@ -1,7 +1,7 @@
 from collections.abc import Sequence
 from enum import Enum
 from pathlib import Path
-from typing import Any, Generic, Literal, NamedTuple, Optional, Union
+from typing import Any, Generic, Literal, NamedTuple, Union
 
 import numpy as np
 from numpy.typing import NDArray
@@ -51,7 +51,7 @@ class CareamicsDataset(Dataset, Generic[GenericImageStack]):
         data_config: NGDataConfig,
         mode: Mode,
         input_extractor: PatchExtractor[GenericImageStack],
-        target_extractor: Optional[PatchExtractor[GenericImageStack]] = None,
+        target_extractor: PatchExtractor[GenericImageStack] | None = None,
     ):
         self.config = data_config
         self.mode = mode
@@ -115,7 +115,7 @@ class CareamicsDataset(Dataset, Generic[GenericImageStack]):
 
         return patching_strategy
 
-    def _initialize_transforms(self) -> Optional[Compose]:
+    def _initialize_transforms(self) -> Compose | None:
         normalize = NormalizeModel(
             image_means=self.input_stats.means,
             image_stds=self.input_stats.stds,

careamics/dataset_ng/factory.py

@@ -1,7 +1,7 @@
 from collections.abc import Sequence
 from enum import Enum
 from pathlib import Path
-from typing import Any, Optional
+from typing import Any
 
 from numpy.typing import NDArray
 from typing_extensions import ParamSpec
@@ -48,8 +48,8 @@ class DatasetType(Enum):
 def determine_dataset_type(
     data_type: SupportedData,
     in_memory: bool,
-    read_func: Optional[ReadFunc] = None,
-    image_stack_loader: Optional[ImageStackLoader] = None,
+    read_func: ReadFunc | None = None,
+    image_stack_loader: ImageStackLoader | None = None,
 ) -> DatasetType:
     """Determine what the dataset type should be based on the input arguments.
 
@@ -121,10 +121,10 @@ def create_dataset(
     inputs: Any,
     targets: Any,
     in_memory: bool,
-    read_func: Optional[ReadFunc] = None,
-    read_kwargs: Optional[dict[str, Any]] = None,
-    image_stack_loader: Optional[ImageStackLoader] = None,
-    image_stack_loader_kwargs: Optional[dict[str, Any]] = None,
+    read_func: ReadFunc | None = None,
+    read_kwargs: dict[str, Any] | None = None,
+    image_stack_loader: ImageStackLoader | None = None,
+    image_stack_loader_kwargs: dict[str, Any] | None = None,
 ) -> CareamicsDataset[ImageStack]:
     """
     Convenience function to create the CAREamicsDataset.
@@ -201,7 +201,7 @@ def create_array_dataset(
     config: NGDataConfig,
     mode: Mode,
     inputs: Sequence[NDArray[Any]],
-    targets: Optional[Sequence[NDArray[Any]]],
+    targets: Sequence[NDArray[Any]] | None,
 ) -> CareamicsDataset[InMemoryImageStack]:
     """
     Create a CAREamicsDataset from array data.
@@ -223,7 +223,7 @@ def create_array_dataset(
         A CAREamicsDataset.
     """
     input_extractor = create_array_extractor(source=inputs, axes=config.axes)
-    target_extractor: Optional[PatchExtractor[InMemoryImageStack]]
+    target_extractor: PatchExtractor[InMemoryImageStack] | None
     if targets is not None:
         target_extractor = create_array_extractor(source=targets, axes=config.axes)
     else:
@@ -235,7 +235,7 @@ def create_tiff_dataset(
     config: NGDataConfig,
     mode: Mode,
     inputs: Sequence[Path],
-    targets: Optional[Sequence[Path]],
+    targets: Sequence[Path] | None,
 ) -> CareamicsDataset[InMemoryImageStack]:
     """
     Create a CAREamicsDataset from tiff files that will be all loaded into memory.
@@ -260,7 +260,7 @@ def create_tiff_dataset(
         source=inputs,
         axes=config.axes,
     )
-    target_extractor: Optional[PatchExtractor[InMemoryImageStack]]
+    target_extractor: PatchExtractor[InMemoryImageStack] | None
     if targets is not None:
         target_extractor = create_tiff_extractor(source=targets, axes=config.axes)
     else:
@@ -273,7 +273,7 @@ def create_czi_dataset(
     config: NGDataConfig,
     mode: Mode,
     inputs: Sequence[Path],
-    targets: Optional[Sequence[Path]],
+    targets: Sequence[Path] | None,
 ) -> CareamicsDataset[CziImageStack]:
     """
     Create a dataset from CZI files.
@@ -296,7 +296,7 @@ def create_czi_dataset(
     """
 
     input_extractor = create_czi_extractor(source=inputs, axes=config.axes)
-    target_extractor: Optional[PatchExtractor[CziImageStack]]
+    target_extractor: PatchExtractor[CziImageStack] | None
     if targets is not None:
         target_extractor = create_czi_extractor(source=targets, axes=config.axes)
     else:
@@ -309,7 +309,7 @@ def create_ome_zarr_dataset(
     config: NGDataConfig,
     mode: Mode,
     inputs: Sequence[Path],
-    targets: Optional[Sequence[Path]],
+    targets: Sequence[Path] | None,
 ) -> CareamicsDataset[ZarrImageStack]:
     """
     Create a dataset from OME ZARR files.
@@ -332,7 +332,7 @@ def create_ome_zarr_dataset(
     """
 
     input_extractor = create_ome_zarr_extractor(source=inputs, axes=config.axes)
-    target_extractor: Optional[PatchExtractor[ZarrImageStack]]
+    target_extractor: PatchExtractor[ZarrImageStack] | None
     if targets is not None:
         target_extractor = create_ome_zarr_extractor(source=targets, axes=config.axes)
     else:
@@ -345,7 +345,7 @@ def create_custom_file_dataset(
     config: NGDataConfig,
     mode: Mode,
     inputs: Sequence[Path],
-    targets: Optional[Sequence[Path]],
+    targets: Sequence[Path] | None,
     *,
     read_func: ReadFunc,
     read_kwargs: dict[str, Any],
@@ -378,7 +378,7 @@ def create_custom_file_dataset(
     input_extractor = create_custom_file_extractor(
         source=inputs, axes=config.axes, read_func=read_func, read_kwargs=read_kwargs
     )
-    target_extractor: Optional[PatchExtractor[InMemoryImageStack]]
+    target_extractor: PatchExtractor[InMemoryImageStack] | None
     if targets is not None:
         target_extractor = create_custom_file_extractor(
             source=targets,
@@ -396,7 +396,7 @@ def create_custom_image_stack_dataset(
     config: NGDataConfig,
     mode: Mode,
     inputs: Any,
-    targets: Optional[Any],
+    targets: Any | None,
     image_stack_loader: ImageStackLoader[P, GenericImageStack],
     *args: P.args,
     **kwargs: P.kwargs,
@@ -436,7 +436,7 @@ def create_custom_image_stack_dataset(
         *args,
         **kwargs,
     )
-    target_extractor: Optional[PatchExtractor[GenericImageStack]]
+    target_extractor: PatchExtractor[GenericImageStack] | None
     if targets is not None:
         target_extractor = create_custom_image_stack_extractor(
             targets,

careamics/dataset_ng/patching_strategies/random_patching.py

@@ -1,7 +1,6 @@
 """A module for random patching strategies."""
 
 from collections.abc import Sequence
-from typing import Optional
 
 import numpy as np
 
@@ -31,7 +30,7 @@ class RandomPatchingStrategy:
         self,
         data_shapes: Sequence[Sequence[int]],
         patch_size: Sequence[int],
-        seed: Optional[int] = None,
+        seed: int | None = None,
     ):
         """
         A patching strategy for sampling random patches.
@@ -193,7 +192,7 @@ class FixedRandomPatchingStrategy:
         self,
         data_shapes: Sequence[Sequence[int]],
         patch_size: Sequence[int],
-        seed: Optional[int] = None,
+        seed: int | None = None,
     ):
         """A patching strategy for sampling random patches.
 

careamics/dataset_ng/patching_strategies/sequential_patching.py

@@ -1,6 +1,5 @@
 import itertools
 from collections.abc import Sequence
-from typing import Optional
 
 import numpy as np
 from typing_extensions import ParamSpec
@@ -18,7 +17,7 @@ class SequentialPatchingStrategy:
         self,
         data_shapes: Sequence[Sequence[int]],
         patch_size: Sequence[int],
-        overlaps: Optional[Sequence[int]] = None,
+        overlaps: Sequence[int] | None = None,
     ):
         self.data_shapes = data_shapes
         self.patch_size = patch_size

careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py

@@ -4,7 +4,7 @@ from __future__ import annotations
 
 from collections.abc import Sequence
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any, Union
 
 from pytorch_lightning import LightningModule, Trainer
 from pytorch_lightning.callbacks import BasePredictionWriter
@@ -84,9 +84,9 @@ class PredictionWriterCallback(BasePredictionWriter):
         cls,
         write_type: SupportedWriteType,
         tiled: bool,
-        write_func: Optional[WriteFunc] = None,
-        write_extension: Optional[str] = None,
-        write_func_kwargs: Optional[dict[str, Any]] = None,
+        write_func: WriteFunc | None = None,
+        write_extension: str | None = None,
+        write_func_kwargs: dict[str, Any] | None = None,
         dirpath: Union[Path, str] = "predictions",
     ) -> PredictionWriterCallback:  # TODO: change type hint to self (find out how)
         """
@@ -172,7 +172,7 @@ class PredictionWriterCallback(BasePredictionWriter):
         trainer: Trainer,
         pl_module: LightningModule,
         prediction: Any,  # TODO: change to expected type
-        batch_indices: Optional[Sequence[int]],
+        batch_indices: Sequence[int] | None,
         batch: Any,  # TODO: change to expected type
         batch_idx: int,
         dataloader_idx: int,