refactor: migrate all type annotations from Python 3.9 to 3.10 syntax

Replaced typing module generics like List, Dict, Tuple with built-in alternatives (list, dict, tuple).
Updated code to use new union syntax (X | Y) instead of Union[X, Y].

config/config.py

@@ -1,5 +1,5 @@
 import json
-from typing import Any, Dict, Optional
+from typing import Any
 from pydantic import BaseModel
 
 from .wandb_config import WandbConfig
@@ -13,7 +13,7 @@ class ComponentConfig(BaseModel):
     name: str
     params: BaseModel
 
-    def dump(self) -> Dict[str, Any]:
+    def dump(self) -> dict[str, Any]:
         """
         Recursively serializes the component into a dictionary.
 
@@ -24,22 +24,18 @@ class ComponentConfig(BaseModel):
             params_dump = self.params.model_dump()
         else:
             params_dump = self.params
-        return {
-            "name": self.name,
-            "params": params_dump
-        }
-        
+        return {"name": self.name, "params": params_dump}
 
 
 class Config(BaseModel):
     model: ComponentConfig
     dataset_config: DatasetConfig
     wandb_config: WandbConfig
-    criterion: Optional[ComponentConfig] = None
-    optimizer: Optional[ComponentConfig] = None
-    scheduler: Optional[ComponentConfig] = None
+    criterion: ComponentConfig | None = None
+    optimizer: ComponentConfig | None = None
+    scheduler: ComponentConfig | None = None
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """
         Produce a JSON‐serializable dict of this config, including nested
         ComponentConfig and DatasetConfig entries. Useful for saving to file
@@ -49,7 +45,7 @@ class Config(BaseModel):
             A dict with keys 'model', 'dataset_config', and (if set)
             'criterion', 'optimizer', 'scheduler'.
         """
-        data: Dict[str, Any] = {
+        data: dict[str, Any] = {
             "model": self.model.dump(),
             "dataset_config": self.dataset_config.model_dump(),
         }
@@ -62,7 +58,6 @@ class Config(BaseModel):
         data["wandb"] = self.wandb_config.model_dump()
         return data
 
-
     def save_json(self, file_path: str, indent: int = 4) -> None:
         """
         Save this config to a JSON file.
@@ -75,7 +70,6 @@ class Config(BaseModel):
         with open(file_path, "w", encoding="utf-8") as f:
             f.write(json.dumps(config_dict, indent=indent))
 
-
     @classmethod
     def load_json(cls, file_path: str) -> "Config":
         """
@@ -96,7 +90,9 @@ class Config(BaseModel):
         wandb_config = WandbConfig(**data.get("wandb", {}))
 
         # Helper function to parse registry fields.
-        def parse_field(component_data: Dict[str, Any], registry_getter) -> Optional[ComponentConfig]:
+        def parse_field(
+            component_data: dict[str, Any], registry_getter
+        ) -> ComponentConfig | None:
             name = component_data.get("name")
             params_data = component_data.get("params", {})
 
@@ -107,16 +103,31 @@ class Config(BaseModel):
             return None
 
         from core import (
-            ModelRegistry, CriterionRegistry, OptimizerRegistry, SchedulerRegistry
+            ModelRegistry,
+            CriterionRegistry,
+            OptimizerRegistry,
+            SchedulerRegistry,
         )
 
-        parsed_model = parse_field(data.get("model", {}), lambda key: ModelRegistry.get_model_params(key))
-        parsed_criterion = parse_field(data.get("criterion", {}), lambda key: CriterionRegistry.get_criterion_params(key))
-        parsed_optimizer = parse_field(data.get("optimizer", {}), lambda key: OptimizerRegistry.get_optimizer_params(key))
-        parsed_scheduler = parse_field(data.get("scheduler", {}), lambda key: SchedulerRegistry.get_scheduler_params(key))
+        parsed_model = parse_field(
+            data.get("model", {}),
+            lambda key: ModelRegistry.get_model_params(key),
+        )
+        parsed_criterion = parse_field(
+            data.get("criterion", {}),
+            lambda key: CriterionRegistry.get_criterion_params(key),
+        )
+        parsed_optimizer = parse_field(
+            data.get("optimizer", {}),
+            lambda key: OptimizerRegistry.get_optimizer_params(key),
+        )
+        parsed_scheduler = parse_field(
+            data.get("scheduler", {}),
+            lambda key: SchedulerRegistry.get_scheduler_params(key),
+        )
 
         if parsed_model is None:
-            raise ValueError('Failed to load model information')
+            raise ValueError("Failed to load model information")
 
         return cls(
             model=parsed_model,
@@ -124,5 +135,5 @@ class Config(BaseModel):
             criterion=parsed_criterion,
             optimizer=parsed_optimizer,
             scheduler=parsed_scheduler,
-            wandb_config=wandb_config
+            wandb_config=wandb_config,
         )

config/dataset_config.py

@@ -1,5 +1,5 @@
 from pydantic import BaseModel, model_validator, field_validator
-from typing import Any, Dict, Optional, Union
+from typing import Any
 import os
 
 
@@ -7,7 +7,7 @@ class DatasetCommonConfig(BaseModel):
     """
     Common configuration fields shared by both training and testing.
     """
-    seed: Optional[int] = 0         # Seed for splitting if data is not pre-split (and all random operations)
+    seed: int | None = 0            # Seed for splitting if data is not pre-split (and all random operations)
     device: str = "cuda:0"          # Device used for training/testing (e.g., 'cpu' or 'cuda')
     use_amp: bool = False           # Flag to use Automatic Mixed Precision (AMP)
     roi_size: int = 512             # The size of the square window for cropping
@@ -65,9 +65,9 @@ class DatasetTrainingConfig(BaseModel):
     pre_split: TrainingPreSplitInfo = TrainingPreSplitInfo()
     split: TrainingSplitInfo = TrainingSplitInfo()
 
-    train_size: Union[int, float] = 0.7    # Training data size (int for static, float in (0,1] for dynamic)
-    valid_size: Union[int, float] = 0.1    # Validation data size (int for static, float in (0,1] for dynamic)
-    test_size: Union[int, float] = 0.2     # Testing data size (int for static, float in (0,1] for dynamic)
+    train_size: int | float = 0.7    # Training data size (int for static, float in (0,1] for dynamic)
+    valid_size: int | float = 0.1    # Validation data size (int for static, float in (0,1] for dynamic)
+    test_size: int | float = 0.2     # Testing data size (int for static, float in (0,1] for dynamic)
     train_offset: int = 0           # Offset for training data
     valid_offset: int = 0           # Offset for validation data
     test_offset: int = 0            # Offset for testing data 
@@ -78,7 +78,7 @@ class DatasetTrainingConfig(BaseModel):
 
 
     @field_validator("train_size", "valid_size", "test_size", mode="before")
-    def validate_sizes(cls, v: Union[int, float]) -> Union[int, float]:
+    def validate_sizes(cls, v: int | float) -> int | float:
         """
         Validates size values:
         - If provided as a float, must be in the range (0, 1].
@@ -145,12 +145,12 @@ class DatasetTestingConfig(BaseModel):
     Configuration fields used only in testing mode.
     """
     test_dir: str = "."                    # Test data directory; must be non-empty
-    test_size: Union[int, float] = 1.0     # Testing data size (int for static, float in (0,1] for dynamic)
+    test_size: int | float = 1.0     # Testing data size (int for static, float in (0,1] for dynamic)
     test_offset: int = 0                # Offset for testing data 
     shuffle: bool = True                # Shuffle data
 
     @field_validator("test_size", mode="before")
-    def validate_test_size(cls, v: Union[int, float]) -> Union[int, float]:
+    def validate_test_size(cls, v: int | float) -> int | float:
         """
         Validates the test_size value.
         """
@@ -224,7 +224,7 @@ class DatasetConfig(BaseModel):
                 raise ValueError(f"Path for pretrained_weights does not exist: {self.common.pretrained_weights}")
         return self
 
-    def model_dump(self, **kwargs) -> Dict[str, Any]:
+    def model_dump(self, **kwargs) -> dict[str, Any]:
         """
         Dumps only the relevant configuration depending on the is_training flag.
         Only the nested configuration (training or testing) along with common fields is returned.

config/wandb_config.py

@@ -1,5 +1,5 @@
 from pydantic import BaseModel, model_validator
-from typing import Any, Dict, Optional
+from typing import Any
 
 
 class WandbConfig(BaseModel):
@@ -7,12 +7,12 @@ class WandbConfig(BaseModel):
     Configuration for Weights & Biases logging.
     """
     use_wandb: bool = False         # Whether to enable WandB logging
-    project: Optional[str] = None      # WandB project name
-    group: Optional[str] = None        # WandB group name
-    entity: Optional[str] = None       # WandB entity (user or team)
-    name: Optional[str] = None         # Name of the run
-    tags: Optional[list[str]] = None   # List of tags for the run
-    notes: Optional[str] = None        # Notes or description for the run
+    project: str | None = None      # WandB project name
+    group: str | None = None        # WandB group name
+    entity: str | None = None       # WandB entity (user or team)
+    name: str | None = None         # Name of the run
+    tags: list[str] | None = None   # List of tags for the run
+    notes: str | None = None        # Notes or description for the run
     save_code: bool = True          # Whether to save the code to WandB
 
     @model_validator(mode="after")
@@ -22,7 +22,7 @@ class WandbConfig(BaseModel):
                 raise ValueError("When use_wandb=True, 'project' must be provided")
         return self
     
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """
         Return a dict of all W&B parameters, excluding 'use_wandb' and any None values.
         """

core/data/transforms/__init__.py

@@ -1,6 +1,6 @@
 from .cell_aware import IntensityDiversification
-from .load_image import CustomLoadImage, CustomLoadImaged
-from .normalize_image import CustomNormalizeImage, CustomNormalizeImaged
+from .load_image import CustomLoadImaged
+from .normalize_image import CustomNormalizeImaged
 
 from monai.transforms import * # type: ignore
 

core/data/transforms/cell_aware.py

@@ -1,7 +1,7 @@
 import copy
 import torch
 import numpy as np
-from typing import Dict, Sequence, Tuple, Union
+from typing import Sequence
 from skimage.segmentation import find_boundaries
 from monai.transforms import RandScaleIntensity, Compose, MapTransform # type: ignore
 
@@ -26,14 +26,14 @@ class BoundaryExclusion(MapTransform):
     def __init__(self, keys: Sequence[str] = ("mask",), allow_missing_keys: bool = False) -> None:
         """
         Args:
-            keys (Sequence[str]): Keys in the input dictionary corresponding to the label image.
+            keys (Sequence(str)): Keys in the input dictionary corresponding to the label image.
                                   Default is ("mask",).
             allow_missing_keys (bool): If True, missing keys in the input will be ignored.
                                        Default is False.
         """
         super().__init__(keys=keys, allow_missing_keys=allow_missing_keys)
 
-    def __call__(self, data: Dict[str, np.ndarray]) -> Dict[str, np.ndarray]:
+    def __call__(self, data: dict[str, np.ndarray]) -> dict[str, np.ndarray]:
         """
         Apply the boundary exclusion transform to the label image.
 
@@ -46,10 +46,10 @@ class BoundaryExclusion(MapTransform):
           6. Assigning the transformed label back into the input dictionary.
 
         Args:
-            data (Dict[str, np.ndarray]): Dictionary containing at least the "mask" key with a label image.
+            data (Dict(str, np.ndarray)): Dictionary containing at least the "mask" key with a label image.
 
         Returns:
-            Dict[str, np.ndarray]: The input dictionary with the "mask" key updated after boundary exclusion.
+            Dict(str, np.ndarray): The input dictionary with the "mask" key updated after boundary exclusion.
         """
         # Retrieve the original label image.
         label_original: np.ndarray = data["mask"]
@@ -100,17 +100,17 @@ class IntensityDiversification(MapTransform):
         self,
         keys: Sequence[str] = ("image",),
         change_cell_ratio: float = 0.4,
-        scale_factors: Union[Tuple[float, float], float] = (0.0, 0.7),
+        scale_factors: tuple[float, float] | float = (0.0, 0.7),
         allow_missing_keys: bool = False,
     ) -> None:
         """
         Args:
-            keys (Sequence[str]): Keys in the input dictionary corresponding to the image.
+            keys (Sequence(str)): Keys in the input dictionary corresponding to the image.
                                   Default is ("image",).
             change_cell_ratio (float): Ratio of cells to apply the intensity scaling.
                                        For example, 0.4 means 40% of the cells will be transformed.
                                        Default is 0.4.
-            scale_factors (Sequence[float]): Factors used for random intensity scaling.
+            scale_factors (tuple(float, float) | float): Factors used for random intensity scaling.
                                              Default is (0.0, 0.7).
             allow_missing_keys (bool): If True, missing keys in the input will be ignored.
                                        Default is False.
@@ -120,7 +120,7 @@ class IntensityDiversification(MapTransform):
         # Compose a random intensity scaling transform with 100% probability.
         self.randscale_intensity = Compose([RandScaleIntensity(prob=1.0, factors=scale_factors)])
 
-    def __call__(self, data: Dict[str, np.ndarray]) -> Dict[str, np.ndarray]:
+    def __call__(self, data: dict[str, np.ndarray]) -> dict[str, np.ndarray]:
         """
         Apply a cell-wise intensity diversification transform to an input image.
 
@@ -141,12 +141,12 @@ class IntensityDiversification(MapTransform):
         9. Combine the unchanged and modified parts to update the image for that channel.
 
         Args:
-            data (Dict[str, np.ndarray]): A dictionary containing:
+            data (dict(str, np.ndarray)): A dictionary containing:
                 - "image": The original image array.
                 - "mask": The corresponding cell label image array.
 
         Returns:
-            Dict[str, np.ndarray]: The updated dictionary with the "image" key modified after applying 
+            dict(str, np.ndarray): The updated dictionary with the "image" key modified after applying 
                                 the intensity transformation.
 
         Raises:

core/data/transforms/load_image.py

@@ -1,7 +1,7 @@
 import numpy as np
 import tifffile as tif
 import skimage.io as io
-from typing import Final, List, Optional, Sequence, Type, Union
+from typing import Final, Sequence, Type
 
 from monai.utils.enums import PostFix
 from monai.utils.module import optional_import
@@ -45,7 +45,7 @@ class CustomLoadImage(LoadImage):
     """
     def __init__(
         self,
-        reader: Optional[Union[ImageReader, Type[ImageReader], str]] = None,
+        reader: ImageReader | Type[ImageReader] | str | None = None,
         image_only: bool = False,
         dtype: DtypeLike = np.float32,
         ensure_channel_first: bool = False,
@@ -75,9 +75,9 @@ class CustomLoadImaged(LoadImaged):
     def __init__(
         self,
         keys: KeysCollection,
-        reader: Optional[Union[Type[ImageReader], str]] = None,
+        reader: Type[ImageReader] | str | None = None,
         dtype: DtypeLike = np.float32,
-        meta_keys: Optional[KeysCollection] = None,
+        meta_keys: KeysCollection | None = None,
         meta_key_postfix: str = DEFAULT_POST_FIX,
         overwriting: bool = False,
         image_only: bool = False,
@@ -141,13 +141,13 @@ class UniversalImageReader(NumpyReader):
     (e.g., repeating or cropping channels).
     """
     def __init__(
-        self, channel_dim: Optional[int] = None, **kwargs,
-    ):
+        self, channel_dim: int | None = None, **kwargs,
+    ) -> None:
         super().__init__(channel_dim=channel_dim, **kwargs)
         self.kwargs = kwargs
         self.channel_dim = channel_dim
 
-    def verify_suffix(self, filename: Union[Sequence[PathLike], PathLike]) -> bool:
+    def verify_suffix(self, filename: Sequence[PathLike] | PathLike) -> bool:
         """
         Check if the file format is supported for reading.
         
@@ -155,7 +155,7 @@ class UniversalImageReader(NumpyReader):
         """
         return has_itk or is_supported_format(filename, SUPPORTED_IMAGE_FORMATS)
 
-    def read(self, data: Union[Sequence[PathLike], PathLike], **kwargs):
+    def read(self, data: Sequence[PathLike] | PathLike, **kwargs):
         """
         Read image(s) from the given path.
         
@@ -166,7 +166,7 @@ class UniversalImageReader(NumpyReader):
         Returns:
           A single image or a list of images depending on the number of paths provided.
         """
-        images: List[np.ndarray] = []  # List to store the loaded images
+        images: list[np.ndarray] = []  # List to store the loaded images
 
         # Convert data to a tuple to support multiple files
         filenames: Sequence[PathLike] = ensure_tuple(data)

core/data/transforms/normalize_image.py

@@ -2,7 +2,7 @@ import numpy as np
 from skimage import exposure
 from monai.config.type_definitions import KeysCollection
 from monai.transforms.transform import Transform, MapTransform
-from typing import Dict, Hashable, Mapping, Sequence
+from typing import Hashable, Mapping, Sequence
 
 __all__ = [
     "CustomNormalizeImage",
@@ -23,7 +23,7 @@ class CustomNormalizeImage(Transform):
     def __init__(self, percentiles: Sequence[float] = (0, 99), channel_wise: bool = False) -> None:
         """
         Args:
-            percentiles (Sequence[float]): Lower and upper percentiles used for intensity scaling.
+            percentiles (Sequence(float)): Lower and upper percentiles used for intensity scaling.
                                            Default is (0, 99).
             channel_wise (bool): Whether to apply normalization on each channel individually.
                                  Default is False.
@@ -106,7 +106,7 @@ class CustomNormalizeImaged(MapTransform):
         """
         Args:
             keys (KeysCollection): Keys identifying the image entries in the dictionary.
-            percentiles (Sequence[float]): Lower and upper percentiles used for intensity scaling.
+            percentiles (Sequence(float)): Lower and upper percentiles used for intensity scaling.
                                            Default is (1, 99).
             channel_wise (bool): Whether to apply normalization on each channel individually.
                                  Default is False.
@@ -117,7 +117,7 @@ class CustomNormalizeImaged(MapTransform):
         # Create an instance of the normalization transform with specified parameters.
         self.normalizer: CustomNormalizeImage = CustomNormalizeImage(percentiles, channel_wise)
 
-    def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
+    def __call__(self, data: Mapping[Hashable, np.ndarray]) -> dict[Hashable, np.ndarray]:
         """
         Apply the normalization transform to each image in the input dictionary.
 
@@ -125,10 +125,10 @@ class CustomNormalizeImaged(MapTransform):
             data (Mapping[Hashable, np.ndarray]): A dictionary mapping keys to numpy arrays representing images.
 
         Returns:
-            Dict[Hashable, np.ndarray]: A dictionary with the same keys where the images have been normalized.
+            dict(Hashable, np.ndarray): A dictionary with the same keys where the images have been normalized.
         """
         # Copy the input dictionary to avoid modifying the original data.
-        d: Dict[Hashable, np.ndarray] = dict(data)
+        d: dict[Hashable, np.ndarray] = dict(data)
         # Iterate over each key specified in the transform and normalize the corresponding image.
         for key in self.keys:
             d[key] = self.normalizer(d[key])

core/data/transforms/random_crop.py

@@ -1,6 +1,6 @@
 import torch
 import numpy as np
-from typing import Hashable, List, Sequence, Optional, Tuple
+from typing import Sequence
 
 from monai.utils.misc import fall_back_tuple
 from monai.data.meta_tensor import MetaTensor
@@ -14,7 +14,7 @@ logger = get_logger(__name__)
 
 def _compute_multilabel_bbox(
     mask: np.ndarray
-) -> Optional[Tuple[List[int], List[int], List[int], List[int]]]:
+) -> tuple[list[int], list[int], list[int], list[int]] | None:
     """
     Compute per-channel bounding-box constraints and return lists of limits for each axis.
 
@@ -33,10 +33,10 @@ def _compute_multilabel_bbox(
     if channels.size == 0:
         return None
 
-    top_mins: List[int] = []
-    top_maxs: List[int] = []
-    left_mins: List[int] = []
-    left_maxs: List[int] = []
+    top_mins: list[int] = []
+    top_maxs: list[int] = []
+    left_mins: list[int] = []
+    left_maxs: list[int] = []
     C = mask.shape[0]
     for ch in range(C):
         rs, cs = np.nonzero(mask[ch])
@@ -74,7 +74,7 @@ class SpatialCropAllClasses(Randomizable, Crop):
         super().__init__(lazy=lazy)
         self.roi_size = tuple(roi_size)
         self.num_candidates = num_candidates
-        self._slices: Optional[Tuple[slice, ...]] = None
+        self._slices: tuple[slice, ...] | None = None
 
     def randomize(self, img_size: Sequence[int]) -> None: # type: ignore
         """
@@ -139,7 +139,7 @@ class SpatialCropAllClasses(Randomizable, Crop):
             slice(left, left + crop_w),
         )
 
-    def __call__(self, img: torch.Tensor, lazy: Optional[bool] = None) -> torch.Tensor: # type: ignore
+    def __call__(self, img: torch.Tensor, lazy: bool | None = None) -> torch.Tensor: # type: ignore
         """
         On first call (mask), computes crop. On subsequent (image), just applies.
         Raises if mask not provided first.

core/losses/__init__.py

@@ -1,4 +1,4 @@
-from typing import Dict, Final, Tuple, Type, List, Any, Union
+from typing import Final, Type, Any
 from pydantic import BaseModel
 
 from .base import BaseLoss
@@ -16,7 +16,7 @@ __all__ = [
 class CriterionRegistry:
     """Registry of loss functions and their parameter classes with case-insensitive lookup."""
     
-    __CRITERIONS: Final[Dict[str, Dict[str, Any]]] = {
+    __CRITERIONS: Final[dict[str, dict[str, Any]]] = {
         "CrossEntropyLoss": {
             "class": CrossEntropyLoss,
             "params": CrossEntropyLossParams,
@@ -36,7 +36,7 @@ class CriterionRegistry:
     }
     
     @classmethod
-    def __get_entry(cls, name: str) -> Dict[str, Any]:
+    def __get_entry(cls, name: str) -> dict[str, Any]:
         """
         Private method to retrieve the criterion entry from the registry using case-insensitive lookup.
         
@@ -44,7 +44,7 @@ class CriterionRegistry:
             name (str): The name of the loss function.
         
         Returns:
-            Dict[str, Any]: A dictionary containing the keys 'class' and 'params'.
+            dict(str, Any): A dictionary containing the keys 'class' and 'params'.
         
         Raises:
             ValueError: If the loss function is not found.
@@ -67,7 +67,7 @@ class CriterionRegistry:
             name (str): Name of the loss function.
         
         Returns:
-            Type[BaseLoss]: The loss function class.
+            Type(BaseLoss): The loss function class.
         """
         entry = cls.__get_entry(name)
         return entry["class"]
@@ -81,17 +81,17 @@ class CriterionRegistry:
             name (str): Name of the loss function.
         
         Returns:
-            Type[BaseModel]: The loss function parameter class.
+            Type(BaseModel): The loss function parameter class.
         """
         entry = cls.__get_entry(name)
         return entry["params"]
     
     @classmethod
-    def get_available_criterions(cls) -> Tuple[str, ...]:
+    def get_available_criterions(cls) -> tuple[str, ...]:
         """
         Returns a tuple of available loss function names in their original case.
         
         Returns:
-            Tuple[str]: Tuple of available loss function names.
+            tuple(str): Tuple of available loss function names.
         """
         return tuple(cls.__CRITERIONS.keys())

core/losses/base.py

@@ -1,15 +1,12 @@
 import abc
 import torch
-import torch.nn as nn
 from pydantic import BaseModel
-from typing import Dict, Any, Optional
-from monai.metrics.cumulative_average import CumulativeAverage
 
 
-class BaseLoss(nn.Module, abc.ABC):
+class BaseLoss(torch.nn.Module, abc.ABC):
     """Custom loss function combining BCEWithLogitsLoss and MSE losses for cell recognition and distinction."""
 
-    def __init__(self, params: Optional[BaseModel] = None):
+    def __init__(self, params: BaseModel | None = None) -> None:
         super().__init__()
         
         
@@ -28,16 +25,16 @@ class BaseLoss(nn.Module, abc.ABC):
         
 
     @abc.abstractmethod
-    def get_loss_metrics(self) -> Dict[str, float]:
+    def get_loss_metrics(self) -> dict[str, float]:
         """
         Retrieves the tracked loss metrics.
 
         Returns:
-            Dict[str, float]: A dictionary containing the loss name and average loss value.
+            dict(str, float): A dictionary containing the loss name and average loss value.
         """
         
 
     @abc.abstractmethod
-    def reset_metrics(self):
+    def reset_metrics(self) -> None:
         """Resets the stored loss metrics."""
     

core/losses/bce.py

@@ -1,6 +1,8 @@
-from .base import *
-from typing import List, Literal, Union
+from .base import BaseLoss
+import torch
+from typing import Any, Literal
 from pydantic import BaseModel, ConfigDict
+from monai.metrics.cumulative_average import CumulativeAverage
 
 
 class BCELossParams(BaseModel):
@@ -11,11 +13,11 @@ class BCELossParams(BaseModel):
     
     with_logits: bool = False
     
-    weight: Optional[List[Union[int, float]]] = None  # Sample weights
+    weight: list[int | float] | None = None  # Sample weights
     reduction: Literal["none", "mean", "sum"] = "mean"  # Reduction method
-    pos_weight: Optional[List[Union[int, float]]] = None  # Used only for BCEWithLogitsLoss
+    pos_weight: list[int | float] | None = None  # Used only for BCEWithLogitsLoss
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """
         Returns a dictionary of valid parameters for `nn.BCEWithLogitsLoss` and `nn.BCELoss`.
 
@@ -23,7 +25,7 @@ class BCELossParams(BaseModel):
         - Ensures only the valid parameters are passed based on the loss function.
 
         Returns:
-            Dict[str, Any]: Filtered dictionary of parameters.
+            dict(str, Any): Filtered dictionary of parameters.
         """
         loss_kwargs = self.model_dump()
         if not self.with_logits:
@@ -47,19 +49,23 @@ class BCELoss(BaseLoss):
     Custom loss function wrapper for `nn.BCELoss and nn.BCEWithLogitsLoss` with tracking of loss metrics.
     """
 
-    def __init__(self, params: Optional[BCELossParams] = None):
+    def __init__(self, params: BCELossParams | None = None) -> None:
         """
         Initializes the loss function with optional BCELoss parameters.
 
         Args:
-            params (Optional[Dict[str, Any]]): Parameters for nn.BCELoss (default: None).
+            params (BCELossParams | None): Parameters for nn.BCELoss (default: None).
         """
         super().__init__(params=params)
         with_logits = params.with_logits if params is not None else False
         _bce_params = params.asdict() if params is not None else {}
         
         # Initialize loss functions with user-provided parameters or PyTorch defaults
-        self.bce_loss = nn.BCEWithLogitsLoss(**_bce_params) if with_logits else nn.BCELoss(**_bce_params)
+        self.bce_loss = (
+            torch.nn.BCEWithLogitsLoss(**_bce_params) 
+            if with_logits 
+            else torch.nn.BCELoss(**_bce_params)
+        )
         
         # Using CumulativeAverage from MONAI to track loss metrics
         self.loss_bce_metric = CumulativeAverage()
@@ -90,18 +96,18 @@ class BCELoss(BaseLoss):
         return loss
 
 
-    def get_loss_metrics(self) -> Dict[str, float]:
+    def get_loss_metrics(self) -> dict[str, float]:
         """
         Retrieves the tracked loss metrics.
 
         Returns:
-            Dict[str, float]: A dictionary containing the average BCE loss.
+            dict(str, float): A dictionary containing the average BCE loss.
         """
         return {
             "loss": round(self.loss_bce_metric.aggregate().item(), 4),
         }
 
 
-    def reset_metrics(self):
+    def reset_metrics(self) -> None:
         """Resets the stored loss metrics."""
         self.loss_bce_metric.reset()

core/losses/ce.py

@@ -1,6 +1,8 @@
-from .base import *
-from typing import List, Literal, Union
+from .base import BaseLoss
+import torch
+from typing import Any, Literal
 from pydantic import BaseModel, ConfigDict
+from monai.metrics.cumulative_average import CumulativeAverage
 
 
 class CrossEntropyLossParams(BaseModel):
@@ -9,17 +11,17 @@ class CrossEntropyLossParams(BaseModel):
     """
     model_config = ConfigDict(frozen=True)
     
-    weight: Optional[List[Union[int, float]]] = None
+    weight: list[int | float] | None = None
     ignore_index: int = -100
     reduction: Literal["none", "mean", "sum"] = "mean"
     label_smoothing: float = 0.0
     
-    def asdict(self):
+    def asdict(self) -> dict[str, Any]:
         """
         Returns a dictionary of valid parameters for `nn.CrossEntropyLoss`.
 
         Returns:
-            Dict[str, Any]: Dictionary of parameters for nn.CrossEntropyLoss.
+            dict(str, Any): Dictionary of parameters for nn.CrossEntropyLoss.
         """
         loss_kwargs = self.model_dump()
         
@@ -36,18 +38,18 @@ class CrossEntropyLoss(BaseLoss):
     Custom loss function wrapper for `nn.CrossEntropyLoss` with tracking of loss metrics.
     """
 
-    def __init__(self, params: Optional[CrossEntropyLossParams] = None):
+    def __init__(self, params: CrossEntropyLossParams | None = None) -> None:
         """
         Initializes the loss function with optional CrossEntropyLoss parameters.
 
         Args:
-            params (Optional[Dict[str, Any]]): Parameters for nn.CrossEntropyLoss (default: None).
+            params (CrossEntropyLossParams | None): Parameters for nn.CrossEntropyLoss (default: None).
         """
         super().__init__(params=params)
         _ce_params = params.asdict() if params is not None else {}
         
         # Initialize loss functions with user-provided parameters or PyTorch defaults
-        self.ce_loss = nn.CrossEntropyLoss(**_ce_params)
+        self.ce_loss = torch.nn.CrossEntropyLoss(**_ce_params)
         
         # Using CumulativeAverage from MONAI to track loss metrics
         self.loss_ce_metric = CumulativeAverage()
@@ -78,18 +80,18 @@ class CrossEntropyLoss(BaseLoss):
         return loss
 
 
-    def get_loss_metrics(self) -> Dict[str, float]:
+    def get_loss_metrics(self) -> dict[str, float]:
         """
         Retrieves the tracked loss metrics.
 
         Returns:
-            Dict[str, float]: A dictionary containing the average CrossEntropy loss.
+            dict(str, float): A dictionary containing the average CrossEntropy loss.
         """
         return {
             "loss": round(self.loss_ce_metric.aggregate().item(), 4),
         }
 
 
-    def reset_metrics(self):
+    def reset_metrics(self) -> None:
         """Resets the stored loss metrics."""
         self.loss_ce_metric.reset()

core/losses/mse.py

@@ -1,6 +1,8 @@
-from .base import *
-from typing import Literal
+from .base import BaseLoss
+import torch
+from typing import Any, Literal
 from pydantic import BaseModel, ConfigDict
+from monai.metrics.cumulative_average import CumulativeAverage
 
 
 class MSELossParams(BaseModel):
@@ -11,12 +13,12 @@ class MSELossParams(BaseModel):
     
     reduction: Literal["none", "mean", "sum"] = "mean"
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """
         Returns a dictionary of valid parameters for `nn.MSELoss`.
 
         Returns:
-            Dict[str, Any]: Dictionary of parameters for `nn.MSELoss`.
+            dict(str, Any): Dictionary of parameters for `nn.MSELoss`.
         """
         loss_kwargs = self.model_dump()
         return {k: v for k, v in loss_kwargs.items() if v is not None}  # Remove None values
@@ -27,18 +29,18 @@ class MSELoss(BaseLoss):
     Custom loss function wrapper for `nn.MSELoss` with tracking of loss metrics.
     """
 
-    def __init__(self, params: Optional[MSELossParams] = None):
+    def __init__(self, params: MSELossParams | None = None):
         """
         Initializes the loss function with optional MSELoss parameters.
 
         Args:
-            params (Optional[MSELossParams]): Parameters for `nn.MSELoss` (default: None).
+            params (MSELossParams | None): Parameters for `nn.MSELoss` (default: None).
         """
         super().__init__(params=params)
         _mse_params = params.asdict() if params is not None else {}
 
         # Initialize MSE loss with user-provided parameters or PyTorch defaults
-        self.mse_loss = nn.MSELoss(**_mse_params)
+        self.mse_loss = torch.nn.MSELoss(**_mse_params)
 
         # Using CumulativeAverage from MONAI to track loss metrics
         self.loss_mse_metric = CumulativeAverage()
@@ -67,12 +69,12 @@ class MSELoss(BaseLoss):
 
         return loss
 
-    def get_loss_metrics(self) -> Dict[str, float]:
+    def get_loss_metrics(self) -> dict[str, float]:
         """
         Retrieves the tracked loss metrics.
 
         Returns:
-            Dict[str, float]: A dictionary containing the average MSE loss.
+            dict(str, float): A dictionary containing the average MSE loss.
         """
         return {
             "loss": round(self.loss_mse_metric.aggregate().item(), 4),

core/losses/mse_with_bce.py

@@ -1,8 +1,11 @@
-from .base import *
+from .base import BaseLoss
 from .bce import BCELossParams
 from .mse import MSELossParams
 
+import torch
+from typing import Any
 from pydantic import BaseModel, ConfigDict
+from monai.metrics.cumulative_average import CumulativeAverage
 
 
 class BCE_MSE_LossParams(BaseModel):
@@ -15,12 +18,12 @@ class BCE_MSE_LossParams(BaseModel):
     bce_params: BCELossParams = BCELossParams()
     mse_params: MSELossParams = MSELossParams()
     
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """
         Returns a dictionary of valid parameters for `nn.BCELoss` and `nn.MSELoss`.
 
         Returns:
-            Dict[str, Any]: Dictionary of parameters.
+            dict(str, Any): Dictionary of parameters.
         """
         
         return {
@@ -35,7 +38,7 @@ class BCE_MSE_Loss(BaseLoss):
     Custom loss function combining BCE (with or without logits) and MSE losses for cell recognition and distinction.
     """
 
-    def __init__(self, params: Optional[BCE_MSE_LossParams]):
+    def __init__(self, params: BCE_MSE_LossParams | None = None):
         """
         Initializes the loss function with optional BCE and MSE parameters.
         """
@@ -50,14 +53,16 @@ class BCE_MSE_Loss(BaseLoss):
 
         # Choose BCE loss function
         self.bce_loss = (
-            nn.BCEWithLogitsLoss(**_bce_params) if _params.bce_params.with_logits else nn.BCELoss(**_bce_params)
+            torch.nn.BCEWithLogitsLoss(**_bce_params)
+            if _params.bce_params.with_logits 
+            else torch.nn.BCELoss(**_bce_params)
         )
 
         # Process MSE parameters
         _mse_params = _params.mse_params.asdict()
 
         # Initialize MSE loss
-        self.mse_loss = nn.MSELoss(**_mse_params)
+        self.mse_loss = torch.nn.MSELoss(**_mse_params)
 
         # Using CumulativeAverage from MONAI to track loss metrics
         self.loss_bce_metric = CumulativeAverage()
@@ -101,12 +106,12 @@ class BCE_MSE_Loss(BaseLoss):
 
         return total_loss
 
-    def get_loss_metrics(self) -> Dict[str, float]:
+    def get_loss_metrics(self) -> dict[str, float]:
         """
         Retrieves the tracked loss metrics.
 
         Returns:
-            Dict[str, float]: A dictionary containing the average BCE and MSE loss.
+            dict(str, float): A dictionary containing the average BCE and MSE loss.
         """
         return {
             "bce_loss": round(self.loss_bce_metric.aggregate().item(), 4),

core/models/__init__.py

@@ -1,5 +1,5 @@
-import torch.nn as nn
-from typing import Dict, Final, Tuple, Type, Any, List, Union
+from torch import nn
+from typing import Final, Type, Any
 from pydantic import BaseModel
 
 from .model_v import ModelV, ModelVParams
@@ -16,7 +16,7 @@ class ModelRegistry:
     """Registry for models and their parameter classes with case-insensitive lookup."""
     
     # Single dictionary storing both model classes and parameter classes.
-    __MODELS: Final[Dict[str, Dict[str, Type[Any]]]] = {
+    __MODELS: Final[dict[str, dict[str, Type[Any]]]] = {
         "ModelV": {
             "class": ModelV,
             "params": ModelVParams,
@@ -24,7 +24,7 @@ class ModelRegistry:
     }
     
     @classmethod
-    def __get_entry(cls, name: str) -> Dict[str, Type[Any]]:
+    def __get_entry(cls, name: str) -> dict[str, Type[Any]]:
         """
         Private method to retrieve the model entry from the registry using case-insensitive lookup.
         
@@ -32,7 +32,7 @@ class ModelRegistry:
             name (str): The name of the model.
         
         Returns:
-            Dict[str, Type[Any]]: A dictionary containing the keys 'class' and 'params'.
+            dict(str, Type[Any]): A dictionary containing the keys 'class' and 'params'.
         
         Raises:
             ValueError: If the model is not found.
@@ -55,7 +55,7 @@ class ModelRegistry:
             name (str): Name of the model.
         
         Returns:
-            Type[nn.Module]: The model class.
+            Type(torch.nn.Module): The model class.
         """
         entry = cls.__get_entry(name)
         return entry["class"]
@@ -69,17 +69,17 @@ class ModelRegistry:
             name (str): Name of the model.
         
         Returns:
-            Type[BaseModel]: The model parameter class.
+            Type(BaseModel): The model parameter class.
         """
         entry = cls.__get_entry(name)
         return entry["params"]
     
     @classmethod
-    def get_available_models(cls) -> Tuple[str, ...]:
+    def get_available_models(cls) -> tuple[str, ...]:
         """
         Returns a tuple of available model names in their original case.
         
         Returns:
-            Tuple[str]: Tuple of available model names.
+            Tuple(str): Tuple of available model names.
         """
         return tuple(cls.__MODELS.keys())

core/models/model_v.py

@@ -1,8 +1,7 @@
-from typing import List, Optional
-
 import torch
-import torch.nn as nn
+from torch import nn
 
+from typing import Any
 from segmentation_models_pytorch import MAnet
 from segmentation_models_pytorch.base.modules import Activation
 
@@ -15,18 +14,18 @@ class ModelVParams(BaseModel):
     model_config = ConfigDict(frozen=True)
     
     encoder_name: str = "mit_b5"                               # Default encoder
-    encoder_weights: Optional[str] = "imagenet"                # Pre-trained weights
-    decoder_channels: List[int] = [1024, 512, 256, 128, 64]    # Decoder configuration
+    encoder_weights: str | None = "imagenet"                   # Pre-trained weights
+    decoder_channels: list[int] = [1024, 512, 256, 128, 64]    # Decoder configuration
     decoder_pab_channels: int = 256                            # Decoder Pyramid Attention Block channels
     in_channels: int = 3                                       # Number of input channels
     out_classes: int = 1                                       # Number of output classes
     
-    def asdict(self):
+    def asdict(self) -> dict[str, Any]:
         """
         Returns a dictionary of valid parameters for `nn.ModelV`.
 
         Returns:
-            Dict[str, Any]: Dictionary of parameters for nn.ModelV.
+            dict(str, Any): Dictionary of parameters for nn.ModelV.
         """
         loss_kwargs = self.model_dump()
         return {k: v for k, v in loss_kwargs.items() if v is not None}  # Remove None values
@@ -84,11 +83,11 @@ class DeepSegmentationHead(nn.Sequential):
         in_channels: int,
         out_channels: int,
         kernel_size: int = 3,
-        activation: Optional[str] = None,
+        activation: str | None = None,
         upsampling: int = 1,
     ) -> None:
         # Define a sequence of layers for the segmentation head
-        layers: List[nn.Module] = [
+        layers: list[nn.Module] = [
             nn.Conv2d(
                 in_channels,
                 in_channels // 2,

core/optimizers/__init__.py

@@ -1,5 +1,5 @@
 from pydantic import BaseModel
-from typing import Dict, Final, Tuple, Type, List, Any, Union
+from typing import Final, Type, Any
 
 from .base import BaseOptimizer
 from .adam import AdamParams, AdamOptimizer
@@ -16,7 +16,7 @@ class OptimizerRegistry:
     """Registry for optimizers and their parameter classes with case-insensitive lookup."""
     
     # Single dictionary storing both optimizer classes and parameter classes.
-    __OPTIMIZERS: Final[Dict[str, Dict[str, Type[Any]]]] = {
+    __OPTIMIZERS: Final[dict[str, dict[str, Type[Any]]]] = {
         "SGD": {
             "class": SGDOptimizer,
             "params": SGDParams,
@@ -32,7 +32,7 @@ class OptimizerRegistry:
     }
     
     @classmethod
-    def __get_entry(cls, name: str) -> Dict[str, Type[Any]]:
+    def __get_entry(cls, name: str) -> dict[str, Type[Any]]:
         """
         Private method to retrieve the optimizer entry from the registry using case-insensitive lookup.
         
@@ -40,7 +40,7 @@ class OptimizerRegistry:
             name (str): The name of the optimizer.
         
         Returns:
-            Dict[str, Type[Any]]: A dictionary containing the keys 'class' and 'params'.
+            dict(str, Type(Any)): A dictionary containing the keys 'class' and 'params'.
         
         Raises:
             ValueError: If the optimizer is not found.
@@ -63,7 +63,7 @@ class OptimizerRegistry:
             name (str): Name of the optimizer.
         
         Returns:
-            Type[BaseOptimizer]: The optimizer class.
+            Type(BaseOptimizer): The optimizer class.
         """
         entry = cls.__get_entry(name)
         return entry["class"]
@@ -77,17 +77,17 @@ class OptimizerRegistry:
             name (str): Name of the optimizer.
         
         Returns:
-            Type[BaseModel]: The optimizer parameter class.
+            Type(BaseModel): The optimizer parameter class.
         """
         entry = cls.__get_entry(name)
         return entry["params"]
     
     @classmethod
-    def get_available_optimizers(cls) -> Tuple[str, ...]:
+    def get_available_optimizers(cls) -> tuple[str, ...]:
         """
         Returns a tuple of available optimizer names in their original case.
         
         Returns:
-            Tuple[str]: Tuple of available optimizer names.
+            Tuple(str): Tuple of available optimizer names.
         """
         return tuple(cls.__OPTIMIZERS.keys())

core/optimizers/adam.py

@@ -1,6 +1,6 @@
 import torch
 from torch import optim
-from typing import Any, Dict, Iterable, Optional, Tuple
+from typing import Any, Iterable
 from pydantic import BaseModel, ConfigDict
 
 from .base import BaseOptimizer
@@ -10,12 +10,12 @@ class AdamParams(BaseModel):
     model_config = ConfigDict(frozen=True)
 
     lr: float = 1e-3                            # Learning rate
-    betas: Tuple[float, float] = (0.9, 0.999)   # Coefficients for computing running averages
+    betas: tuple[float, float] = (0.9, 0.999)   # Coefficients for computing running averages
     eps: float = 1e-8                           # Term added to denominator for numerical stability
     weight_decay: float = 0.0                   # L2 regularization
     amsgrad: bool = False                       # Whether to use the AMSGrad variant
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """Returns a dictionary of valid parameters for `torch.optim.Adam`."""
         return self.model_dump()
     
@@ -25,7 +25,7 @@ class AdamOptimizer(BaseOptimizer):
     Wrapper around torch.optim.Adam.
     """
 
-    def __init__(self, model_params: Iterable[torch.nn.Parameter], optim_params: AdamParams):
+    def __init__(self, model_params: Iterable[torch.nn.Parameter], optim_params: AdamParams) -> None:
         """
         Initializes the Adam optimizer with given parameters.
 

core/optimizers/adamw.py

@@ -1,6 +1,6 @@
 import torch
 from torch import optim
-from typing import Any, Dict, Iterable, Optional, Tuple
+from typing import Any, Iterable
 from pydantic import BaseModel, ConfigDict
 
 from .base import BaseOptimizer
@@ -10,12 +10,12 @@ class AdamWParams(BaseModel):
     model_config = ConfigDict(frozen=True)
 
     lr: float = 1e-3                            # Learning rate
-    betas: Tuple[float, ...] = (0.9, 0.999)   # Adam coefficients
+    betas: tuple[float, ...] = (0.9, 0.999)   # Adam coefficients
     eps: float = 1e-8                           # Numerical stability
     weight_decay: float = 1e-2                  # L2 penalty (AdamW uses decoupled weight decay)
     amsgrad: bool = False                       # Whether to use the AMSGrad variant
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """Returns a dictionary of valid parameters for `torch.optim.AdamW`."""
         return self.model_dump()
     
@@ -25,7 +25,7 @@ class AdamWOptimizer(BaseOptimizer):
     Wrapper around torch.optim.AdamW.
     """
 
-    def __init__(self, model_params: Iterable[torch.nn.Parameter], optim_params: AdamWParams):
+    def __init__(self, model_params: Iterable[torch.nn.Parameter], optim_params: AdamWParams) -> None:
         """
         Initializes the AdamW optimizer with given parameters.
 

core/optimizers/base.py

@@ -1,15 +1,15 @@
 import torch
-import torch.optim as optim
+from torch import optim
 from pydantic import BaseModel
-from typing import Any, Iterable, Optional
+from typing import Any, Iterable
 
 
 class BaseOptimizer:
     """Custom loss function combining BCEWithLogitsLoss and MSE losses for cell recognition and distinction."""
 
-    def __init__(self, model_params: Iterable[torch.nn.Parameter], optim_params: BaseModel):
+    def __init__(self, model_params: Iterable[torch.nn.Parameter], optim_params: BaseModel) -> None:
         super().__init__()
-        self.optim: Optional[optim.Optimizer] = None
+        self.optim: optim.Optimizer | None = None
         
 
     def zero_grad(self, set_to_none: bool = True) -> None:
@@ -25,12 +25,12 @@ class BaseOptimizer:
             self.optim.zero_grad(set_to_none=set_to_none)
 
 
-    def step(self, closure: Optional[Any] = None) -> Any:
+    def step(self, closure: Any | None = None) -> Any:
         """
         Performs a single optimization step (parameter update).
 
         Args:
-            closure (Optional[Callable]): A closure that reevaluates the model and returns the loss.
+            closure (Any | None): A closure that reevaluates the model and returns the loss.
                                           This is required for optimizers like LBFGS that need multiple forward passes.
 
         Returns:

core/optimizers/sgd.py

@@ -1,6 +1,6 @@
 import torch
 from torch import optim
-from typing import Any, Dict, Iterable, Optional
+from typing import Any, Iterable
 from pydantic import BaseModel, ConfigDict
 
 from .base import BaseOptimizer
@@ -16,7 +16,7 @@ class SGDParams(BaseModel):
     weight_decay: float = 0.0                   # L2 penalty
     nesterov: bool = False                      # Enables Nesterov momentum
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """Returns a dictionary of valid parameters for `torch.optim.SGD`."""
         return self.model_dump()
     
@@ -26,7 +26,7 @@ class SGDOptimizer(BaseOptimizer):
     Wrapper around torch.optim.SGD.
     """
 
-    def __init__(self, model_params: Iterable[torch.nn.Parameter], optim_params: SGDParams):
+    def __init__(self, model_params: Iterable[torch.nn.Parameter], optim_params: SGDParams) -> None:
         """
         Initializes the SGD optimizer with given parameters.
 

core/schedulers/__init__.py

@@ -1,5 +1,4 @@
-import torch.optim.lr_scheduler as lr_scheduler
-from typing import Dict, Final, Tuple, Type, List, Any, Union
+from typing import Final, Type, Any
 from pydantic import BaseModel
 
 from .base import BaseScheduler
@@ -17,7 +16,7 @@ __all__ = [
 class SchedulerRegistry:
     """Registry for learning rate schedulers and their parameter classes with case-insensitive lookup."""
     
-    __SCHEDULERS: Final[Dict[str, Dict[str, Type[Any]]]] = {
+    __SCHEDULERS: Final[dict[str, dict[str, Type[Any]]]] = {
         "Step": {
             "class": StepLRScheduler,
             "params": StepLRParams,
@@ -37,7 +36,7 @@ class SchedulerRegistry:
     }
     
     @classmethod
-    def __get_entry(cls, name: str) -> Dict[str, Type[Any]]:
+    def __get_entry(cls, name: str) -> dict[str, Type[Any]]:
         """
         Private method to retrieve the scheduler entry from the registry using case-insensitive lookup.
         
@@ -45,7 +44,7 @@ class SchedulerRegistry:
             name (str): The name of the scheduler.
         
         Returns:
-            Dict[str, Type[Any]]: A dictionary containing the keys 'class' and 'params'.
+            dict(str, Type(Any)): A dictionary containing the keys 'class' and 'params'.
         
         Raises:
             ValueError: If the scheduler is not found.
@@ -68,7 +67,7 @@ class SchedulerRegistry:
             name (str): Name of the scheduler.
         
         Returns:
-            Type[BaseScheduler]: The scheduler class.
+            Type(BaseScheduler): The scheduler class.
         """
         entry = cls.__get_entry(name)
         return entry["class"]
@@ -82,17 +81,17 @@ class SchedulerRegistry:
             name (str): Name of the scheduler.
         
         Returns:
-            Type[BaseModel]: The scheduler parameter class.
+            Type(BaseModel): The scheduler parameter class.
         """
         entry = cls.__get_entry(name)
         return entry["params"]
     
     @classmethod
-    def get_available_schedulers(cls) -> Tuple[str, ...]:
+    def get_available_schedulers(cls) -> tuple[str, ...]:
         """
         Returns a tuple of available scheduler names in their original case.
         
         Returns:
-            Tuple[str]: Tuple of available scheduler names.
+            Tuple(str): Tuple of available scheduler names.
         """
         return tuple(cls.__SCHEDULERS.keys())

core/schedulers/base.py

@@ -1,6 +1,5 @@
-import torch.optim as optim
+from torch import optim
 from pydantic import BaseModel
-from typing import List, Optional
 
 
 class BaseScheduler:
@@ -9,8 +8,8 @@ class BaseScheduler:
     Wraps a PyTorch LR scheduler and provides a unified interface.
     """
 
-    def __init__(self, optimizer: optim.Optimizer, params: BaseModel):
-        self.scheduler: Optional[optim.lr_scheduler.LRScheduler] = None
+    def __init__(self, optimizer: optim.Optimizer, params: BaseModel) -> None:
+        self.scheduler: optim.lr_scheduler.LRScheduler | None = None
 
     def step(self) -> None:
         """
@@ -20,7 +19,7 @@ class BaseScheduler:
         if self.scheduler is not None:
             self.scheduler.step()
 
-    def get_last_lr(self) -> List[float]:
+    def get_last_lr(self) -> list[float]:
         """
         Returns the most recent learning rate(s).
         """

core/schedulers/cosine_annealing.py

@@ -1,10 +1,9 @@
-from typing import Any, Dict
-from pydantic import BaseModel, ConfigDict
-from torch import optim
-from torch.optim.lr_scheduler import CosineAnnealingLR
-
 from .base import BaseScheduler
 
+from typing import Any
+from torch import optim
+from torch.optim.lr_scheduler import CosineAnnealingLR
+from pydantic import BaseModel, ConfigDict
 
 
 class CosineAnnealingLRParams(BaseModel):
@@ -16,7 +15,7 @@ class CosineAnnealingLRParams(BaseModel):
     last_epoch: int = -1
 
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """Returns a dictionary of valid parameters for `torch.optim.lr_scheduler.CosineAnnealingLR`."""
         return self.model_dump()
 
@@ -26,7 +25,7 @@ class CosineAnnealingLRScheduler(BaseScheduler):
     Wrapper around torch.optim.lr_scheduler.CosineAnnealingLR.
     """
 
-    def __init__(self, optimizer: optim.Optimizer, params: CosineAnnealingLRParams):
+    def __init__(self, optimizer: optim.Optimizer, params: CosineAnnealingLRParams) -> None:
         """
         Args:
             optimizer (Optimizer): Wrapped optimizer.

core/schedulers/exponential.py

@@ -1,9 +1,9 @@
-from typing import Any, Dict
-from pydantic import BaseModel, ConfigDict
+from .base import BaseScheduler
+
+from typing import Any
 from torch import optim
 from torch.optim.lr_scheduler import ExponentialLR
-
-from .base import BaseScheduler
+from pydantic import BaseModel, ConfigDict
 
 
 class ExponentialLRParams(BaseModel):
@@ -13,7 +13,7 @@ class ExponentialLRParams(BaseModel):
     gamma: float = 0.95 # Multiplicative factor of learning rate decay
     last_epoch: int = -1
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """Returns a dictionary of valid parameters for `torch.optim.lr_scheduler.ExponentialLR`."""
         return self.model_dump()
 
@@ -23,7 +23,7 @@ class ExponentialLRScheduler(BaseScheduler):
     Wrapper around torch.optim.lr_scheduler.ExponentialLR.
     """
 
-    def __init__(self, optimizer: optim.Optimizer, params: ExponentialLRParams):
+    def __init__(self, optimizer: optim.Optimizer, params: ExponentialLRParams) -> None:
         """
         Args:
             optimizer (Optimizer): Wrapped optimizer.

core/schedulers/multi_step.py

@@ -1,20 +1,20 @@
-from typing import Any, Dict, Tuple
-from pydantic import BaseModel, ConfigDict
+from .base import BaseScheduler
+
+from typing import Any
 from torch import optim
 from torch.optim.lr_scheduler import MultiStepLR
-
-from .base import BaseScheduler
+from pydantic import BaseModel, ConfigDict
 
 
 class MultiStepLRParams(BaseModel):
     """Configuration for `torch.optim.lr_scheduler.MultiStepLR`."""
     model_config = ConfigDict(frozen=True)
 
-    milestones: Tuple[int, ...] = (30, 80)   # List of epoch indices for LR decay
+    milestones: tuple[int, ...] = (30, 80)   # List of epoch indices for LR decay
     gamma: float = 0.1                     # Multiplicative factor of learning rate decay
     last_epoch: int = -1
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """Returns a dictionary of valid parameters for `torch.optim.lr_scheduler.MultiStepLR`."""
         return self.model_dump()
 
@@ -24,7 +24,7 @@ class MultiStepLRScheduler(BaseScheduler):
     Wrapper around torch.optim.lr_scheduler.MultiStepLR.
     """
 
-    def __init__(self, optimizer: optim.Optimizer, params: MultiStepLRParams):
+    def __init__(self, optimizer: optim.Optimizer, params: MultiStepLRParams) -> None:
         """
         Args:
             optimizer (Optimizer): Wrapped optimizer.

core/schedulers/step.py

@@ -1,9 +1,9 @@
-from typing import Any, Dict
-from pydantic import BaseModel, ConfigDict
+from .base import BaseScheduler
+
+from typing import Any
 from torch import optim
 from torch.optim.lr_scheduler import StepLR
-
-from .base import BaseScheduler
+from pydantic import BaseModel, ConfigDict
 
 
 class StepLRParams(BaseModel):
@@ -14,7 +14,7 @@ class StepLRParams(BaseModel):
     gamma: float = 0.1      # Multiplicative factor of learning rate decay
     last_epoch: int = -1
 
-    def asdict(self) -> Dict[str, Any]:
+    def asdict(self) -> dict[str, Any]:
         """Returns a dictionary of valid parameters for `torch.optim.lr_scheduler.StepLR`."""
         return self.model_dump()
     
@@ -25,7 +25,7 @@ class StepLRScheduler(BaseScheduler):
     Wrapper around torch.optim.lr_scheduler.StepLR.
     """
 
-    def __init__(self, optimizer: optim.Optimizer, params: StepLRParams):
+    def __init__(self, optimizer: optim.Optimizer, params: StepLRParams) -> None:
         """
         Args:
             optimizer (Optimizer): Wrapped optimizer.

core/segmentator.py

@@ -19,15 +19,14 @@ from torch.utils.data import DataLoader
 import fastremap
 
 import fill_voids
-from skimage import morphology
+# from skimage import morphology
 from skimage.segmentation import find_boundaries
 from scipy.special import expit
 from scipy.ndimage import mean, find_objects
 
 from monai.data.dataset import Dataset
-from monai.transforms import * # type: ignore
+from monai.transforms.compose import Compose
 from monai.inferers.utils import sliding_window_inference
-from monai.metrics.cumulative_average import CumulativeAverage
 
 import matplotlib.pyplot as plt
 import matplotlib.colors as mcolors
@@ -42,16 +41,16 @@ from itertools import chain
 
 from pprint import pformat
 from tabulate import tabulate
-from typing import Any, Dict, Literal, Optional, Tuple, List, Union
+from typing import Any, Literal
 
 from tqdm import tqdm
 import wandb
 
 from config import Config
-from core.models import *
-from core.losses import *
-from core.optimizers import *
-from core.schedulers import *
+from core.models import ModelRegistry
+from core.losses import CriterionRegistry
+from core.optimizers import OptimizerRegistry
+from core.schedulers import SchedulerRegistry
 from core.utils import (
     compute_batch_segmentation_tp_fp_fn,
     compute_f1_score,
@@ -78,30 +77,30 @@ class CellSegmentator:
             else None
         )
         
-        self._train_dataloader:     Optional[DataLoader] = None
-        self._valid_dataloader:     Optional[DataLoader] = None
-        self._test_dataloader:      Optional[DataLoader] = None
-        self._predict_dataloader:   Optional[DataLoader] = None
+        self._train_dataloader:     DataLoader | None = None
+        self._valid_dataloader:     DataLoader | None = None
+        self._test_dataloader:      DataLoader | None = None
+        self._predict_dataloader:   DataLoader | None = None
         
         self._best_weights = None
 
 
     def create_dataloaders(
         self,
-        train_transforms: Optional[Compose] = None,
-        valid_transforms: Optional[Compose] = None,
-        test_transforms: Optional[Compose] = None,
-        predict_transforms: Optional[Compose] = None
+        train_transforms: Compose | None = None,
+        valid_transforms: Compose | None = None,
+        test_transforms: Compose | None = None,
+        predict_transforms: Compose | None = None
     ) -> None:
         """
         Creates train, validation, test, and prediction dataloaders based on dataset configuration
         and provided transforms.
 
         Args:
-            train_transforms (Optional[Compose]): Transformations for training data.
-            valid_transforms (Optional[Compose]): Transformations for validation data.
-            test_transforms (Optional[Compose]): Transformations for testing data.
-            predict_transforms (Optional[Compose]): Transformations for prediction data.
+            train_transforms (Compose | None): Transformations for training data.
+            valid_transforms (Compose | None): Transformations for validation data.
+            test_transforms (Compose | None): Transformations for testing data.
+            predict_transforms (Compose | None): Transformations for prediction data.
 
         Raises:
             ValueError: If required transforms are missing.
@@ -257,7 +256,7 @@ class CellSegmentator:
     def print_data_info(
         self,
         loader_type: Literal["train", "valid", "test", "predict"],
-        index: Optional[int] = None
+        index: int | None = None
     ) -> None:
         """
         Prints statistics for a single sample from the specified dataloader.
@@ -267,7 +266,7 @@ class CellSegmentator:
             index: The sample index; if None, a random index is selected.
         """
         # Retrieve the dataloader attribute, e.g., self._train_dataloader
-        loader: Optional[torch.utils.data.DataLoader] = getattr(self, f"_{loader_type}_dataloader", None)
+        loader: DataLoader | None = getattr(self, f"_{loader_type}_dataloader", None)
         if loader is None:
             logger.error(f"Dataloader '{loader_type}' is not initialized.")
             return
@@ -326,8 +325,8 @@ class CellSegmentator:
         lines.append("=" * 40)
 
         # Output via logger
-        for l in lines:
-            logger.info(l)
+        for line in lines:
+            logger.info(line)
 
     
     def train(self, save_results: bool = True, only_masks: bool = False) -> None:
@@ -661,16 +660,16 @@ class CellSegmentator:
             logger.info(f"├─ Validation frequency: {training.val_freq}")
 
             if training.is_split:
-                logger.info(f"├─ Using pre-split directories:")
+                logger.info( "├─ Using pre-split directories:")
                 logger.info(f"│  ├─ Train dir: {training.pre_split.train_dir}")
                 logger.info(f"│  ├─ Valid dir: {training.pre_split.valid_dir}")
                 logger.info(f"│  └─ Test dir:  {training.pre_split.test_dir}")
             else:
-                logger.info(f"├─ Using unified dataset with splits:")
-                logger.info(f"│  ├─ All data dir: {training.split.all_data_dir}")
+                logger.info( "├─ Using unified dataset with splits:")
+                logger.info( "│  ├─ All data dir: {training.split.all_data_dir}")
                 logger.info(f"│  └─ Shuffle: {'yes' if training.split.shuffle else 'no'}")
 
-            logger.info(f"└─ Dataset split:")
+            logger.info( "└─ Dataset split:")
             logger.info(f"   ├─ Train size: {training.train_size}, offset: {training.train_offset}")
             logger.info(f"   ├─ Valid size: {training.valid_size}, offset: {training.valid_offset}")
             logger.info(f"   └─ Test size:  {training.test_size}, offset: {training.test_offset}")
@@ -703,12 +702,12 @@ class CellSegmentator:
         logger.info("===================================")
 
 
-    def __set_seed(self, seed: Optional[int]) -> None:
+    def __set_seed(self, seed: int | None) -> None:
         """
         Sets the random seed for reproducibility across Python, NumPy, and PyTorch.
 
         Args:
-            seed (Optional[int]): Seed value. If None, no seeding is performed.
+            seed (int | None): Seed value. If None, no seeding is performed.
         """
         if seed is not None:
             random.seed(seed)
@@ -724,9 +723,9 @@ class CellSegmentator:
     def __get_dataset(
         self,
         images_dir: str,
-        masks_dir: Optional[str],
+        masks_dir: str | None,
         transforms: Compose,
-        size: Union[int, float],
+        size: int | float,
         offset: int,
         shuffle: bool
     ) -> Dataset:
@@ -735,9 +734,9 @@ class CellSegmentator:
 
         Args:
             images_dir (str): Path to directory or glob pattern for input images.
-            masks_dir (Optional[str]): Path to directory or glob pattern for masks.
+            masks_dir (str | None): Path to directory or glob pattern for masks.
             transforms (Compose): Transformations to apply to each image or pair.
-            size (Union[int, float]): Either an integer or a fraction of the dataset.
+            size (int | float): Either an integer or a fraction of the dataset.
             offset (int): Number of images to skip from the start.
             shuffle (bool): Whether to shuffle the dataset before slicing.
 
@@ -806,12 +805,12 @@ class CellSegmentator:
         return Dataset(data, transforms)
     
     
-    def __print_with_logging(self, metrics: Dict[str, Union[float, np.ndarray]], step: int) -> None:
+    def __print_with_logging(self, metrics: dict[str, float | np.ndarray], step: int) -> None:
         """
         Print metrics in a tabular format and log to W&B.
 
         Args:
-            metrics (Dict[str, Union[float, np.ndarray]]): Mapping from metric names 
+            metrics (dict(str, float | np.ndarray)): Mapping from metric names 
                 to either a float or a ND numpy array.
             step (int): epoch index.
         """
@@ -846,14 +845,14 @@ class CellSegmentator:
     
     def __save_metrics_to_csv(
         self,
-        metrics: Dict[str, Union[float, np.ndarray]],
+        metrics: dict[str, float | np.ndarray],
         output_path: str
     ) -> None:
         """
         Saves a dictionary of metrics to a CSV file with columns 'Metric' and 'Value'.
 
         Args:
-            metrics (Dict[str, Union[float, np.ndarray]]):
+            metrics (dict(str, float | np.ndarray)):
                 Mapping from metric names to scalar values or numpy arrays.
             output_path (str):
                 Path to the output CSV file.
@@ -874,22 +873,22 @@ class CellSegmentator:
     
     def __run_epoch(self,
         mode: Literal["train", "valid", "test"],
-        epoch: Optional[int] = None,
+        epoch: int | None = None,
         save_results: bool = True,
         only_masks: bool = False
-    ) -> Dict[str, Union[float, np.ndarray]]:
+    ) -> dict[str, float | np.ndarray]:
         """
         Execute one epoch of training, validation, or testing.
 
         Args:
             mode (str): One of 'train', 'valid', or 'test'.
-            epoch (int, optional): Current epoch number for logging.
+            epoch (int | None): Current epoch number for logging.
             save_results (bool): If True, the predicted masks and test metrics will be saved.
             only_masks (bool): If True and save_results is True, only raw predicted masks are saved,
                           without visualization overlays.
 
         Returns:
-            Dict[str, Union[float, np.ndarray]]: Metrics for valid/test.
+            dict(str, float | np.ndarray): Metrics for valid/test.
         """
         # Ensure required components are available
         if mode in ("train", "valid") and (self._optimizer is None or self._criterion is None):
@@ -988,7 +987,7 @@ class CellSegmentator:
 
         if self._criterion is not None:
             # Collect loss metrics
-            epoch_metrics: Dict[str, Union[float, np.ndarray]] = {
+            epoch_metrics: dict[str, float | np.ndarray] = {
                 f"{mode}_{name}": value for name, value in self._criterion.get_loss_metrics().items()
             }
             # Reset internal loss metrics accumulator
@@ -1051,17 +1050,17 @@ class CellSegmentator:
     def __post_process_predictions(
         self,
         raw_outputs: torch.Tensor,
-        ground_truth: Optional[torch.Tensor] = None
-    ) -> Tuple[np.ndarray, Optional[np.ndarray]]:
+        ground_truth: torch.Tensor | None = None
+    ) -> tuple[np.ndarray, np.ndarray | None]:
         """
         Post-process raw network outputs to extract instance segmentation masks.
 
         Args:
             raw_outputs (torch.Tensor): Raw model outputs of shape (B, С, H, W).
-            ground_truth (torch.Tensor): Ground truth masks of shape (B, С, H, W).
+            ground_truth (torch.Tensor | None): Ground truth masks of shape (B, С, H, W).
 
         Returns:
-            Tuple[np.ndarray, Optional[np.ndarray]]:
+            tuple(np.ndarray, np.ndarray | None):
                 - instance_masks: Instance-wise masks array of shape (B, С, H, W).
                 - labels_np: Converted ground truth of shape (B, С, H, W) or None if 
                 ground_truth was not provided.
@@ -1097,8 +1096,8 @@ class CellSegmentator:
         ground_truth_masks: np.ndarray,
         iou_threshold: float = 0.5,
         return_error_masks: bool = False
-    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray,
-               Optional[np.ndarray], Optional[np.ndarray], Optional[np.ndarray]]:
+    ) -> tuple[np.ndarray, np.ndarray, np.ndarray,
+               np.ndarray | None, np.ndarray | None, np.ndarray | None]:
         """
         Compute batch-wise true positives, false positives, and false negatives
         for instance segmentation, using a configurable IoU threshold.
@@ -1111,7 +1110,7 @@ class CellSegmentator:
             return_error_masks (bool): Whether to also return binary error masks.
 
         Returns:
-            Tuple(np.ndarray, np.ndarray, np.ndarray,
+            tuple(np.ndarray, np.ndarray, np.ndarray,
             np.ndarray | None, np.ndarray | None, np.ndarray | None):
                 - tp: True positives per batch and class, shape (B, C)
                 - fp: False positives per batch and class, shape (B, C)
@@ -1143,7 +1142,7 @@ class CellSegmentator:
         false_positives: np.ndarray,
         false_negatives: np.ndarray,
         reduction: Literal["micro", "macro", "weighted", "imagewise", "per_class", "none"] = "micro"
-    ) -> Union[float, np.ndarray]:
+    ) -> float | np.ndarray:
         """
         Compute F1-score from batch-wise TP/FP/FN using various aggregation schemes.
 
@@ -1266,7 +1265,7 @@ class CellSegmentator:
         false_positives: np.ndarray,
         false_negatives: np.ndarray,
         reduction: Literal["micro", "macro", "weighted", "imagewise", 'per_class', "none"] = "micro"
-    ) -> Union[float, np.ndarray]:
+    ) -> float | np.ndarray:
         """
         Compute Average Precision (AP) from batch-wise TP/FP/FN using various aggregation schemes.
 
@@ -1399,23 +1398,23 @@ class CellSegmentator:
     
     def __save_prediction_masks(
         self,
-        sample: Dict[str, Any],
-        predicted_mask: Union[np.ndarray, torch.Tensor],
+        sample: dict[str, Any],
+        predicted_mask: np.ndarray | torch.Tensor,
         start_index: int = 0,
         only_masks: bool = False,
-        masks: Optional[Tuple[np.ndarray, np.ndarray, np.ndarray]] = None
+        masks: tuple[np.ndarray, np.ndarray, np.ndarray] | None = None
     ) -> None:
         """
         Save multi-channel predicted masks as TIFFs and 
         corresponding visualizations as PNGs in separate folders.
 
         Args:
-            sample (Dict[str, Any]): Batch sample from MONAI 
+            sample (dict(str, Any)): Batch sample from MONAI 
                 LoadImaged (contains 'image', optional 'mask', and 'image_meta_dict').
-            predicted_mask (np.ndarray or torch.Tensor): Array of shape (C, H, W) or (B, C, H, W).
+            predicted_mask (np.ndarray | torch.Tensor): Array of shape (C, H, W) or (B, C, H, W).
             start_index (int): Starting index for naming when metadata is missing.
             only_masks (bool): If True, save only the raw predicted mask TIFFs and skip PNG visualizations.
-            masks (Tuple[np.ndarray, np.ndarray, np.ndarray] | None): 
+            masks (tuple[np.ndarray, np.ndarray, np.ndarray] | None): 
                 A tuple (tp_masks, fp_masks, fn_masks), each of shape (B, C, H, W). Defaults to None.
         """
         # Base directories (created once per call)
@@ -1428,14 +1427,14 @@ class CellSegmentator:
         os.makedirs(evaluate_dir, exist_ok=True)
 
         # Convert tensors to numpy if necessary
-        def to_numpy(x: Union[np.ndarray, torch.Tensor]) -> np.ndarray:
+        def to_numpy(x: np.ndarray | torch.Tensor) -> np.ndarray:
             return x.cpu().numpy() if isinstance(x, torch.Tensor) else x
 
         pred_array = to_numpy(predicted_mask).astype(np.uint16)
 
         # Handle batch dimension
         for idx in range(pred_array.shape[0]):
-            batch_sample: Dict[str, Any] = {}
+            batch_sample: dict[str, Any] = {}
             # copy per-sample image and meta
             img = to_numpy(sample["image"])
             if img.ndim == 4:
@@ -1467,21 +1466,21 @@ class CellSegmentator:
 
     def __save_single_prediction_mask(
         self,
-        sample: Dict[str, Any],
+        sample: dict[str, Any],
         pred_array: np.ndarray,
         start_index: int,
         masks_dir: str,
         plots_dir: str,
         evaluate_dir: str,
         only_masks: bool = False,
-        masks: Optional[Tuple[np.ndarray, np.ndarray, np.ndarray]] = None
+        masks: tuple[np.ndarray, np.ndarray, np.ndarray] | None = None
     ) -> None:
         """
         Save a single sample's predicted mask and optional TP/FP/FN masks and visualizations.
         Assumes output directories already exist.
 
         Args:
-            sample (Dict[str, Any]): Dictionary containing 'image', 'mask',
+            sample (dict(str, Any)): Dictionary containing 'image', 'mask',
                 and optional 'image_meta_dict' for metadata.
             pred_array (np.ndarray): Predicted mask array of shape (C,H,W).
             start_index (int): Base index for generating filenames when metadata is missing.
@@ -1489,7 +1488,7 @@ class CellSegmentator:
             plots_dir (str): Directory for saving PNG visualizations.
             evaluate_dir (str): Directory for saving PNG visualizations of evaluation results.
             only_masks (bool): If True, saves only TIFF mask files; skips PNG plots.
-            masks (Tuple[np.ndarray, np.ndarray, np.ndarray], optional): A tuple of
+            masks (tuple[np.ndarray, np.ndarray, np.ndarray] | None): A tuple of
                 true-positive, false-positive, and false-negative mask arrays,
                 each of shape (C,H,W). Defaults to None.
         """
@@ -1510,7 +1509,7 @@ class CellSegmentator:
                 "Expected 2D (H,W) or 3D (C,H,W)."
             )
                 
-        true_mask_array: Optional[np.ndarray] = sample.get("mask")
+        true_mask_array: np.ndarray | None = sample.get("mask")
         if isinstance(true_mask_array, np.ndarray):
             if true_mask_array.ndim == 2:
                 true_mask_array = np.expand_dims(true_mask_array, axis=0)
@@ -1562,7 +1561,7 @@ class CellSegmentator:
         file_path: str,
         image_data: np.ndarray,
         predicted_mask: np.ndarray,
-        true_mask: Optional[np.ndarray] = None,
+        true_mask: np.ndarray | None = None,
     ) -> None:
         """
         Create and save grid visualization: 1x3 if no true mask, or 2x3 if true mask provided.
@@ -1572,7 +1571,7 @@ class CellSegmentator:
             image_data (np.ndarray): The original input image array, expected shape (C, H, W).
             predicted_mask (np.ndarray): The predicted mask array, shape (H, W),
                 depending on the task.
-            true_mask (Optional[np.ndarray], optional): The ground-truth mask array.
+            true_mask (np.ndarray | None): The ground-truth mask array.
                 If provided, an additional row with true mask and overlap visualization 
                 will be added to the plot. Default is None.
 
@@ -1603,7 +1602,7 @@ class CellSegmentator:
         img: np.ndarray,
         mask: np.ndarray,
         contour_color: str,
-        titles: Tuple[str, ...]
+        titles: tuple[str, ...]
     ):
         """
         Plot a row of three panels: original image, mask, and mask boundaries on image.
@@ -1618,7 +1617,8 @@ class CellSegmentator:
         # Panel 1: Original image
         ax0, ax1, ax2 = axes
         ax0.imshow(img, cmap='gray' if img.ndim == 2 else None)
-        ax0.set_title(titles[0]); ax0.axis('off')
+        ax0.set_title(titles[0])
+        ax0.axis('off')
         
         # Compute boundaries once
         boundaries = find_boundaries(mask, mode='thick')
@@ -1793,7 +1793,8 @@ class CellSegmentator:
 
                 # Get coordinates of all non-zero pixels in the padded mask
                 y, x = torch.nonzero(masks_padded, as_tuple=True)
-                y = y.int();  x = x.int()   # ensure integer type
+                y = y.int()
+                x = x.int()   # ensure integer type
 
                 # Generate 8-connected neighbors (including center) via broadcasted offsets
                 offsets = torch.tensor([
@@ -1830,9 +1831,12 @@ class CellSegmentator:
                 ], dtype=np.int16)
                 
                 # Compute centers (pixel indices) and extents via the provided helper
-                centers, ext = self.__get_mask_centers_and_extents(mask_channel, slices_arr)
+                centers, ext = self.__get_mask_centers_and_extents(
+                    mask_channel, slices_arr
+                )
                 # Move centers to GPU and shift by +1 for padding
-                meds_p = torch.from_numpy(centers).to(self._device).long() + 1    # (M, 2); +1 for padding
+                # (M, 2); +1 for padding
+                meds_p = torch.from_numpy(centers).to(self._device).long() + 1
 
                 # Determine number of diffusion iterations
                 n_iter = 2 * ext.max()
@@ -1865,7 +1869,7 @@ class CellSegmentator:
     def __get_mask_centers_and_extents(
         label_map: np.ndarray,
         slices_arr: np.ndarray
-    ) -> Tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[np.ndarray, np.ndarray]:
         """
         Compute the centroids and extents of labeled regions in a 2D mask array.
 
@@ -1923,7 +1927,7 @@ class CellSegmentator:
         neighbor_indices: torch.Tensor,
         center_indices: torch.Tensor,
         valid_neighbor_mask: torch.Tensor,
-        output_shape: Tuple[int, int],
+        output_shape: tuple[int, int],
         num_iterations: int = 200
     ) -> np.ndarray:
         """
@@ -1933,7 +1937,7 @@ class CellSegmentator:
             neighbor_indices (torch.Tensor): Tensor of shape (2, 9, N) containing row and column indices for 9 neighbors per pixel.
             center_indices (torch.Tensor): Tensor of shape (2, N) with row and column indices of mask centers.
             valid_neighbor_mask (torch.Tensor): Boolean tensor of shape (9, N) indicating if each neighbor is valid.
-            output_shape (Tuple[int, int]): Desired 2D shape of the diffusion tensor, e.g., (H, W).
+            output_shape (tuple(int, int)): Desired 2D shape of the diffusion tensor, e.g., (H, W).
             num_iterations (int, optional): Number of diffusion iterations. Defaults to 200.
             
         Returns:
@@ -2242,7 +2246,7 @@ class CellSegmentator:
         flow_field: np.ndarray,
         initial_coords: np.ndarray,
         num_iters: int = 200
-    ) -> Union[np.ndarray, torch.Tensor]:
+    ) -> np.ndarray | torch.Tensor:
         """
         Trace pixel positions through a flow field via iterative interpolation.
 
@@ -2252,7 +2256,7 @@ class CellSegmentator:
             num_iters (int): Number of integration steps.
 
         Returns:
-            np.ndarray or torch.Tensor: Final (y, x) positions of each point.
+            (np.ndarray | torch.Tensor): Final (y, x) positions of each point.
         """
         dims = 2
         # Extract spatial dimensions
@@ -2383,7 +2387,7 @@ class CellSegmentator:
         self,
         pixel_positions: torch.Tensor,
         valid_indices: np.ndarray,
-        original_shape: Tuple[int, ...],
+        original_shape: tuple[int, ...],
         pad_radius: int = 20,
         max_size_fraction: float = 0.4
     ) -> np.ndarray:
@@ -2534,7 +2538,7 @@ class CellSegmentator:
         input_tensor: Tensor,
         kernel_size: int = 5,
         axis: int = 1,
-        output_tensor: Optional[Tensor] = None
+        output_tensor: Tensor | None = None
     ) -> Tensor:
         """
         Memory-efficient 1D max pooling along a specified axis using in-place updates.
@@ -2547,7 +2551,7 @@ class CellSegmentator:
             input_tensor (Tensor): Source tensor for pooling.
             kernel_size (int): Size of the pooling window (must be odd and >= 3).
             axis (int): Axis along which to compute 1D max pooling.
-            output_tensor (Optional[Tensor]): Tensor to store the result.
+            output_tensor (Tensor | None): Tensor to store the result.
                 If None, a clone of input_tensor is used.
 
         Returns:
@@ -2691,7 +2695,7 @@ class CellSegmentator:
         self,
         mask: np.ndarray,
         flow_network: np.ndarray
-    ) -> Tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[np.ndarray, np.ndarray]:
         """
         Compute mean squared error between network-predicted flows and flows derived from masks.
 
@@ -2700,7 +2704,7 @@ class CellSegmentator:
             flow_network (np.ndarray): Network predicted flows of shape [axis, ...].
 
         Returns:
-            Tuple[np.ndarray, np.ndarray]:
+            tuple(np.ndarray, np.ndarray):
                 - flow_errors: 1D array (length = max label) of mean squared error per label.
                 - computed_flows: Array of flows derived from the mask, same shape as flow_network.
 

core/utils/measures.py

@@ -8,7 +8,7 @@ from numpy.typing import NDArray
 from numba import jit
 from skimage import segmentation
 from scipy.optimize import linear_sum_assignment
-from typing import Dict, List, Tuple, Any, Union
+from typing import Any
 
 from core.logger import get_logger
 
@@ -27,7 +27,7 @@ def compute_f1_score(
     true_positives: int,
     false_positives: int,
     false_negatives: int
-) -> Tuple[float, float, float]:
+) -> tuple[float, float, float]:
     """
     Computes the precision, recall, and F1-score given the numbers of
     true positives, false positives, and false negatives.
@@ -76,7 +76,7 @@ def compute_confusion_matrix(
     ground_truth_mask: np.ndarray,
     predicted_mask: np.ndarray,
     iou_threshold: float = 0.5
-) -> Tuple[int, int, int]:
+) -> tuple[int, int, int]:
     """
     Computes the confusion matrix elements (true positives, false positives, false negatives)
     for a single image given the ground truth and predicted masks.
@@ -114,7 +114,7 @@ def compute_segmentation_tp_fp_fn(
     iou_threshold: float = 0.5,
     return_error_masks: bool = False,
     remove_boundary_objects: bool = True
-) -> Dict[str, np.ndarray]:
+) -> dict[str, np.ndarray]:
     """
     Computes TP, FP and FN for segmentation on a single image.
     
@@ -176,7 +176,7 @@ def compute_segmentation_tp_fp_fn(
             false_positive_mask_list.append(results.get('fp_mask')) # type: ignore
             false_negative_mask_list.append(results.get('fn_mask')) # type: ignore
 
-    output: Dict[str, np.ndarray] = {
+    output: dict[str, np.ndarray] = {
         'tp': np.array(true_positive_list),
         'fp': np.array(false_positive_list),
         'fn': np.array(false_negative_list)
@@ -194,7 +194,7 @@ def compute_segmentation_f1_metrics(
     iou_threshold: float = 0.5,
     return_error_masks: bool = False,
     remove_boundary_objects: bool = True
-) -> Dict[str, np.ndarray]:
+) -> dict[str, np.ndarray]:
     """
     Computes F1 metrics (precision, recall, F1-score) for segmentation on a single image.
     
@@ -240,7 +240,7 @@ def compute_segmentation_f1_metrics(
         recall_list.append(recall)
         f1_score_list.append(f1_score)
 
-    output: Dict[str, np.ndarray] = {
+    output: dict[str, np.ndarray] = {
         'precision': np.array(precision_list),
         'recall': np.array(recall_list),
         'f1_score': np.array(f1_score_list),
@@ -255,7 +255,7 @@ def compute_segmentation_average_precision_metrics(
     iou_threshold: float = 0.5,
     return_error_masks: bool = False,
     remove_boundary_objects: bool = True
-) -> Dict[str, np.ndarray]:
+) -> dict[str, np.ndarray]:
     """
     Computes the average precision (AP) for segmentation on a single image.
     
@@ -298,7 +298,7 @@ def compute_segmentation_average_precision_metrics(
         )
         avg_precision_list.append(avg_precision)
         
-    output: Dict[str, np.ndarray] = {
+    output: dict[str, np.ndarray] = {
         'avg_precision': np.array(avg_precision_list)
     }
     output.update(results)
@@ -311,7 +311,7 @@ def compute_batch_segmentation_tp_fp_fn(
     iou_threshold: float = 0.5,
     return_error_masks: bool = False,
     remove_boundary_objects: bool = True
-) -> Dict[str, np.ndarray]:
+) -> dict[str, np.ndarray]:
     """
     Computes segmentation TP, FP and FN for a batch of images.
     
@@ -361,7 +361,7 @@ def compute_batch_segmentation_tp_fp_fn(
             fp_mask_list.append(result.get('fp_mask')) # type: ignore
             fn_mask_list.append(result.get('fn_mask')) # type: ignore
 
-    output: Dict[str, np.ndarray] = {
+    output: dict[str, np.ndarray] = {
         'tp': np.stack(tp_list, axis=0),
         'fp': np.stack(fp_list, axis=0),
         'fn': np.stack(fn_list, axis=0)
@@ -379,7 +379,7 @@ def compute_batch_segmentation_f1_metrics(
     iou_threshold: float = 0.5,
     return_error_masks: bool = False,
     remove_boundary_objects: bool = True
-) -> Dict[str, np.ndarray]:
+) -> dict[str, np.ndarray]:
     """
     Computes segmentation F1 metrics for a batch of images.
     
@@ -435,7 +435,7 @@ def compute_batch_segmentation_f1_metrics(
             fp_mask_list.append(result.get('fp_mask')) # type: ignore
             fn_mask_list.append(result.get('fn_mask')) # type: ignore
 
-    output: Dict[str, np.ndarray] = {
+    output: dict[str, np.ndarray] = {
         'precision': np.stack(precision_list, axis=0),
         'recall': np.stack(recall_list, axis=0),
         'f1_score': np.stack(f1_score_list, axis=0),
@@ -456,7 +456,7 @@ def compute_batch_segmentation_average_precision_metrics(
     iou_threshold: float = 0.5,
     return_error_masks: bool = False,
     remove_boundary_objects: bool = True
-) -> Dict[str, NDArray]:
+) -> dict[str, np.ndarray]:
     """
     Computes segmentation average precision metrics for a batch of images.
     
@@ -508,7 +508,7 @@ def compute_batch_segmentation_average_precision_metrics(
             fp_mask_list.append(result.get('fp_mask')) # type: ignore
             fn_mask_list.append(result.get('fn_mask')) # type: ignore
 
-    output: Dict[str, NDArray] = {
+    output: dict[str, np.ndarray] = {
         'avg_precision': np.stack(avg_precision_list, axis=0),
         'tp': np.stack(tp_list, axis=0),
         'fp': np.stack(fp_list, axis=0),
@@ -555,7 +555,7 @@ def _process_instance_matching(
     iou_threshold: float = 0.5,
     return_masks: bool = False,
     without_boundary_objects: bool = True
-) -> Dict[str, Union[int, NDArray[np.uint8]]]:
+) -> dict[str, int | NDArray[np.uint8]]:
     """
     Processes instance matching on a full image by performing the following steps:
       - Removes objects that touch the image boundary and reindexes the masks.
@@ -597,8 +597,8 @@ def _process_instance_matching(
             fn_mask = np.zeros_like(ground_truth_mask, dtype=np.uint8)
             # Mark all ground truth objects as false negatives.
             fn_mask[ground_truth_mask > 0] = 1
-            result.update({'tp_mask': tp_mask, 'fp_mask': fp_mask, 'fn_mask': fn_mask})
-        return result
+            result.update({'tp_mask': tp_mask, 'fp_mask': fp_mask, 'fn_mask': fn_mask}) # type: ignore
+        return result # type: ignore
 
     # Compute the IoU matrix for the processed masks.
     iou_matrix = _calculate_iou(processed_ground_truth, processed_prediction)
@@ -640,11 +640,11 @@ def _process_instance_matching(
         for pred_label in (all_prediction_labels - matched_prediction_labels):
             fp_mask[processed_prediction == pred_label] = 1
 
-        result.update({'tp_mask': tp_mask, 'fp_mask': fp_mask, 'fn_mask': fn_mask})
-    return result
+        result.update({'tp_mask': tp_mask, 'fp_mask': fp_mask, 'fn_mask': fn_mask}) # type: ignore
+    return result # type: ignore
 
 
-def _compute_optimal_matching_pairs(iou_matrix: np.ndarray, iou_threshold: float) -> List[Any]:
+def _compute_optimal_matching_pairs(iou_matrix: np.ndarray, iou_threshold: float) -> list[Any]:
     """
     Computes the optimal matching pairs between ground truth and predicted masks using the IoU matrix.
     
@@ -687,7 +687,7 @@ def _compute_patch_based_metrics(
     iou_threshold: float = 0.5,
     return_masks: bool = False,
     without_boundary_objects: bool = True
-) -> Dict[str, Union[int, NDArray[np.uint8]]]:
+) -> dict[str, int | NDArray[np.uint8]]:
     """
     Computes segmentation metrics using a patch-based approach for very large images.
     
@@ -747,7 +747,7 @@ def _compute_patch_based_metrics(
                 padded_fp_mask[y_start:y_end, x_start:x_end] = patch_results.get('fp_mask', 0) # type: ignore
                 padded_fn_mask[y_start:y_end, x_start:x_end] = patch_results.get('fn_mask', 0) # type: ignore
 
-    results: Dict[str, Union[int, np.ndarray]] = {'tp': total_tp, 'fp': total_fp, 'fn': total_fn}
+    results: dict[str, int | np.ndarray] = {'tp': total_tp, 'fp': total_fp, 'fn': total_fn}
     if return_masks:
         # Crop the padded masks back to the original image size.
         results.update({

generate_config.py

@@ -1,5 +1,4 @@
 import os
-from typing import Tuple
 
 from config import Config, WandbConfig, DatasetConfig, ComponentConfig
 
@@ -8,7 +7,7 @@ from core import (
 )
 
 
-def prompt_choice(prompt_message: str, options: Tuple[str, ...]) -> str:
+def prompt_choice(prompt_message: str, options: tuple[str, ...]) -> str:
     """
     Prompt the user with a list of options and return the selected option.
     """

main.py

@@ -1,20 +1,25 @@
 import os
+import sys
 import argparse
 import wandb
 
 from config import Config
-from core.data import *
+from core.data import (
+    get_train_transforms,
+    get_valid_transforms,
+    get_test_transforms,
+    get_predict_transforms
+)
 from core.segmentator import CellSegmentator
 
 
-def main():
+def main() -> None:
     parser = argparse.ArgumentParser(
         description="Train or predict cell segmentator with specified config file."
     )
     parser.add_argument(
         '-c', '--config',
         type=str,
-        default='config/templates/train/ModelV_BCE_MSE_Loss_AdamW_CosineAnnealing.json',
         help='Path to the JSON config file'
     )
     parser.add_argument(
@@ -36,6 +41,10 @@ def main():
               ' masks without additional visualizations')
     )
 
+    if len(sys.argv) == 1:
+        parser.print_help()
+        sys.exit(0)
+
     args = parser.parse_args()
 
     mode = args.mode
@@ -44,7 +53,7 @@ def main():
 
     if mode == 'train' and not config.dataset_config.is_training:
         raise ValueError(
-            f"Config is not set for training (is_training=False), but mode 'train' was requested."
+            "Config is not set for training (is_training=False), but mode 'train' was requested."
         )
     if mode in ('test', 'predict') and config.dataset_config.is_training:
         raise ValueError(