careamics 0.1.0rc6__py3-none-any.whl → 0.1.0rc7__py3-none-any.whl

careamics/config/algorithm_model.py

@@ -134,21 +134,6 @@ class AlgorithmConfig(BaseModel):
                     "sure that `in_channels` and `num_classes` are the same."
                 )
 
-        # N2N
-        if self.algorithm == "n2n":
-            # n2n is only compatible with the UNet model
-            if not isinstance(self.model, UNetModel):
-                raise ValueError(
-                    f"Model for algorithm {self.algorithm} must be a `UNetModel`."
-                )
-
-            # n2n requires the number of input and output channels to be the same
-            if self.model.in_channels != self.model.num_classes:
-                raise ValueError(
-                    "N2N requires the same number of input and output channels. Make "
-                    "sure that `in_channels` and `num_classes` are the same."
-                )
-
         if self.algorithm == "care" or self.algorithm == "n2n":
             if self.loss == "n2v":
                 raise ValueError("Supervised algorithms do not support loss `n2v`.")

careamics/config/architectures/custom_model.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from pprint import pformat
-from typing import Any, Dict, Literal
+from typing import Any, Literal
 
 from pydantic import ConfigDict, field_validator, model_validator
 from torch.nn import Module
@@ -136,7 +136,7 @@ class CustomModel(ArchitectureModel):
         """
         return pformat(self.model_dump())
 
-    def model_dump(self, **kwargs: Any) -> Dict[str, Any]:
+    def model_dump(self, **kwargs: Any) -> dict[str, Any]:
         """Dump the model configuration.
 
         Parameters
@@ -146,7 +146,7 @@ class CustomModel(ArchitectureModel):
 
         Returns
         -------
-        Dict[str, Any]
+        dict[str, Any]
             Model configuration.
         """
         model_dict = super().model_dump()

careamics/config/configuration_example.py

@@ -54,9 +54,6 @@ def full_configuration_example() -> Configuration:
         batch_size=8,
         axes="YX",
         transforms=[
-            {
-                "name": SupportedTransform.NORMALIZE.value,
-            },
             {
                 "name": SupportedTransform.XY_FLIP.value,
             },

careamics/config/configuration_factory.py

@@ -107,9 +107,6 @@ def _create_supervised_configuration(
     # augmentations
     if use_augmentations:
         transforms: List[Dict[str, Any]] = [
-            {
-                "name": SupportedTransform.NORMALIZE.value,
-            },
             {
                 "name": SupportedTransform.XY_FLIP.value,
             },
@@ -118,11 +115,7 @@ def _create_supervised_configuration(
             },
         ]
     else:
-        transforms = [
-            {
-                "name": SupportedTransform.NORMALIZE.value,
-            },
-        ]
+        transforms = []
 
     # data model
     data = DataConfig(
@@ -250,7 +243,8 @@ def create_n2n_configuration(
     use_augmentations: bool = True,
     independent_channels: bool = False,
     loss: Literal["mae", "mse"] = "mae",
-    n_channels: int = 1,
+    n_channels_in: int = 1,
+    n_channels_out: int = -1,
     logger: Literal["wandb", "tensorboard", "none"] = "none",
     model_kwargs: Optional[dict] = None,
 ) -> Configuration:
@@ -260,10 +254,13 @@ def create_n2n_configuration(
     If "Z" is present in `axes`, then `path_size` must be a list of length 3, otherwise
     2.
 
-    If "C" is present in `axes`, then you need to set `n_channels` to the number of
+    If "C" is present in `axes`, then you need to set `n_channels_in` to the number of
     channels. Likewise, if you set the number of channels, then "C" must be present in
     `axes`.
 
+    To set the number of output channels, use the `n_channels_out` parameter. If it is
+    not specified, it will be assumed to be equal to `n_channels_in`.
+
     By default, all channels are trained together. To train all channels independently,
     set `independent_channels` to True.
 
@@ -290,8 +287,10 @@ def create_n2n_configuration(
         Whether to train all channels independently, by default False.
     loss : Literal["mae", "mse"], optional
         Loss function to use, by default "mae".
-    n_channels : int, optional
-        Number of channels (in and out), by default 1.
+    n_channels_in : int, optional
+        Number of channels in, by default 1.
+    n_channels_out : int, optional
+        Number of channels out, by default -1.
     logger : Literal["wandb", "tensorboard", "none"], optional
         Logger to use, by default "none".
     model_kwargs : dict, optional
@@ -302,6 +301,9 @@ def create_n2n_configuration(
     Configuration
         Configuration for training Noise2Noise.
     """
+    if n_channels_out == -1:
+        n_channels_out = n_channels_in
+
     return _create_supervised_configuration(
         algorithm="n2n",
         experiment_name=experiment_name,
@@ -313,8 +315,8 @@ def create_n2n_configuration(
         use_augmentations=use_augmentations,
         independent_channels=independent_channels,
         loss=loss,
-        n_channels_in=n_channels,
-        n_channels_out=n_channels,
+        n_channels_in=n_channels_in,
+        n_channels_out=n_channels_out,
         logger=logger,
         model_kwargs=model_kwargs,
     )
@@ -522,9 +524,6 @@ def create_n2v_configuration(
     # augmentations
     if use_augmentations:
         transforms: List[Dict[str, Any]] = [
-            {
-                "name": SupportedTransform.NORMALIZE.value,
-            },
             {
                 "name": SupportedTransform.XY_FLIP.value,
             },
@@ -533,11 +532,7 @@ def create_n2v_configuration(
             },
         ]
     else:
-        transforms = [
-            {
-                "name": SupportedTransform.NORMALIZE.value,
-            },
-        ]
+        transforms = []
 
     # n2v2 and structn2v
     nv2_transform = {
@@ -618,7 +613,10 @@ def create_inference_configuration(
     InferenceConfiguration
         Configuration used to configure CAREamicsPredictData.
     """
-    if configuration.data_config.mean is None or configuration.data_config.std is None:
+    if (
+        configuration.data_config.image_means is None
+        or configuration.data_config.image_stds is None
+    ):
         raise ValueError("Mean and std must be provided in the configuration.")
 
     # tile size for UNets
@@ -648,8 +646,8 @@ def create_inference_configuration(
         tile_size=tile_size,
         tile_overlap=tile_overlap,
         axes=axes or configuration.data_config.axes,
-        mean=configuration.data_config.mean,
-        std=configuration.data_config.std,
+        image_means=configuration.data_config.image_means,
+        image_stds=configuration.data_config.image_stds,
         tta_transforms=tta_transforms,
         batch_size=batch_size,
     )

careamics/config/configuration_model.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 import re
 from pathlib import Path
 from pprint import pformat
-from typing import Dict, List, Literal, Union
+from typing import Literal, Union
 
 import yaml
 from bioimageio.spec.generic.v0_3 import CiteEntry
@@ -269,7 +269,7 @@ class Configuration(BaseModel):
         """
         return pformat(self.model_dump())
 
-    def set_3D(self, is_3D: bool, axes: str, patch_size: List[int]) -> None:
+    def set_3D(self, is_3D: bool, axes: str, patch_size: list[int]) -> None:
         """
         Set 3D flag and axes.
 
@@ -279,7 +279,7 @@ class Configuration(BaseModel):
             Whether the algorithm is 3D or not.
         axes : str
             Axes of the data.
-        patch_size : List[int]
+        patch_size : list[int]
             Patch size.
         """
         # set the flag and axes (this will not trigger validation at the config level)
@@ -389,7 +389,7 @@ class Configuration(BaseModel):
 
         return ""
 
-    def get_algorithm_citations(self) -> List[CiteEntry]:
+    def get_algorithm_citations(self) -> list[CiteEntry]:
         """
         Return a list of citation entries of the current algorithm.
 
@@ -455,13 +455,13 @@ class Configuration(BaseModel):
 
         return ""
 
-    def get_algorithm_keywords(self) -> List[str]:
+    def get_algorithm_keywords(self) -> list[str]:
         """
         Get algorithm keywords.
 
         Returns
         -------
-        List[str]
+        list[str]
             List of keywords.
         """
         if self.algorithm_config.algorithm == SupportedAlgorithm.N2V:
@@ -491,8 +491,8 @@ class Configuration(BaseModel):
         self,
         exclude_defaults: bool = False,
         exclude_none: bool = True,
-        **kwargs: Dict,
-    ) -> Dict:
+        **kwargs: dict,
+    ) -> dict:
         """
         Override model_dump method in order to set default values.
 
@@ -503,7 +503,7 @@ class Configuration(BaseModel):
             True.
         exclude_none : bool, optional
             Whether to exclude fields with None values or not, by default True.
-        **kwargs : Dict
+        **kwargs : dict
             Keyword arguments.
 
         Returns
@@ -524,7 +524,7 @@ def load_configuration(path: Union[str, Path]) -> Configuration:
 
     Parameters
     ----------
-    path : Union[str, Path]
+    path : str or Path
         Path to the configuration.
 
     Returns
@@ -556,7 +556,7 @@ def save_configuration(config: Configuration, path: Union[str, Path]) -> Path:
     ----------
     config : Configuration
         Configuration to save.
-    path : Union[str, Path]
+    path : str or Path
         Path to a existing folder in which to save the configuration or to an existing
         configuration file.
 

careamics/config/data_model.py

@@ -3,8 +3,9 @@
 from __future__ import annotations
 
 from pprint import pformat
-from typing import Any, List, Literal, Optional, Union
+from typing import Any, Literal, Optional, Union
 
+from numpy.typing import NDArray
 from pydantic import (
     BaseModel,
     ConfigDict,
@@ -17,7 +18,6 @@ from typing_extensions import Annotated, Self
 
 from .support import SupportedTransform
 from .transformations.n2v_manipulate_model import N2VManipulateModel
-from .transformations.normalize_model import NormalizeModel
 from .transformations.xy_flip_model import XYFlipModel
 from .transformations.xy_random_rotate90_model import XYRandomRotate90Model
 from .validators import check_axes_validity, patch_size_ge_than_8_power_of_2
@@ -26,7 +26,6 @@ TRANSFORMS_UNION = Annotated[
     Union[
         XYFlipModel,
         XYRandomRotate90Model,
-        NormalizeModel,
         N2VManipulateModel,
     ],
     Discriminator("name"),  # used to tell the different transform models apart
@@ -39,7 +38,9 @@ class DataConfig(BaseModel):
 
     If std is specified, mean must be specified as well. Note that setting the std first
     and then the mean (if they were both `None` before) will raise a validation error.
-    Prefer instead `set_mean_and_std` to set both at once.
+    Prefer instead `set_mean_and_std` to set both at once. Means and stds are expected
+    to be lists of floats, one for each channel. For supervised tasks, the mean and std
+    of the target could be different from the input data.
 
     All supported transforms are defined in the SupportedTransform enum.
 
@@ -55,7 +56,7 @@ class DataConfig(BaseModel):
     ... )
 
     To change the mean and std of the data:
-    >>> data.set_mean_and_std(mean=214.3, std=84.5)
+    >>> data.set_mean_and_std(image_means=[214.3], image_stds=[84.5])
 
     One can pass also a list of transformations, by keyword, using the
     SupportedTransform value:
@@ -67,11 +68,6 @@ class DataConfig(BaseModel):
     ...     axes="YX",
     ...     transforms=[
     ...         {
-    ...             "name": SupportedTransform.NORMALIZE.value,
-    ...             "mean": 167.6,
-    ...             "std": 47.2,
-    ...         },
-    ...         {
     ...             "name": "XYFlip",
     ...         }
     ...     ]
@@ -85,19 +81,24 @@ class DataConfig(BaseModel):
 
     # Dataset configuration
     data_type: Literal["array", "tiff", "custom"]  # As defined in SupportedData
-    patch_size: Union[List[int]] = Field(..., min_length=2, max_length=3)
+    patch_size: Union[list[int]] = Field(..., min_length=2, max_length=3)
     batch_size: int = Field(default=1, ge=1, validate_default=True)
     axes: str
 
     # Optional fields
-    mean: Optional[float] = None
-    std: Optional[float] = None
+    image_means: Optional[list[float]] = Field(
+        default=None, min_length=0, max_length=32
+    )
+    image_stds: Optional[list[float]] = Field(default=None, min_length=0, max_length=32)
+    target_means: Optional[list[float]] = Field(
+        default=None, min_length=0, max_length=32
+    )
+    target_stds: Optional[list[float]] = Field(
+        default=None, min_length=0, max_length=32
+    )
 
-    transforms: List[TRANSFORMS_UNION] = Field(
+    transforms: list[TRANSFORMS_UNION] = Field(
         default=[
-            {
-                "name": SupportedTransform.NORMALIZE.value,
-            },
             {
                 "name": SupportedTransform.XY_FLIP.value,
             },
@@ -116,8 +117,8 @@ class DataConfig(BaseModel):
     @field_validator("patch_size")
     @classmethod
     def all_elements_power_of_2_minimum_8(
-        cls, patch_list: Union[List[int]]
-    ) -> Union[List[int]]:
+        cls, patch_list: Union[list[int]]
+    ) -> Union[list[int]]:
         """
         Validate patch size.
 
@@ -125,12 +126,12 @@ class DataConfig(BaseModel):
 
         Parameters
         ----------
-        patch_list : Union[List[int]]
+        patch_list : list of int
             Patch size.
 
         Returns
         -------
-        Union[List[int]]
+        list of int
             Validated patch size.
 
         Raises
@@ -180,19 +181,19 @@ class DataConfig(BaseModel):
     @field_validator("transforms")
     @classmethod
     def validate_prediction_transforms(
-        cls, transforms: List[TRANSFORMS_UNION]
-    ) -> List[TRANSFORMS_UNION]:
+        cls, transforms: list[TRANSFORMS_UNION]
+    ) -> list[TRANSFORMS_UNION]:
         """
         Validate N2VManipulate transform position in the transform list.
 
         Parameters
         ----------
-        transforms : List[Transformations_Union]
+        transforms : list[Transformations_Union]
             Transforms.
 
         Returns
         -------
-        List[TRANSFORMS_UNION]
+        list of transforms
             Validated transforms.
 
         Raises
@@ -235,29 +236,33 @@ class DataConfig(BaseModel):
             If std is not None and mean is None.
         """
         # check that mean and std are either both None, or both specified
-        if (self.mean is None) != (self.std is None):
+        if (self.image_means and not self.image_stds) or (
+            self.image_stds and not self.image_means
+        ):
             raise ValueError(
                 "Mean and std must be either both None, or both specified."
             )
 
-        return self
+        elif (self.image_means is not None and self.image_stds is not None) and (
+            len(self.image_means) != len(self.image_stds)
+        ):
+            raise ValueError(
+                "Mean and std must be specified for each " "input channel."
+            )
 
-    @model_validator(mode="after")
-    def add_std_and_mean_to_normalize(self: Self) -> Self:
-        """
-        Add mean and std to the Normalize transform if it is present.
+        if (self.target_means and not self.target_stds) or (
+            self.target_stds and not self.target_means
+        ):
+            raise ValueError(
+                "Mean and std must be either both None, or both specified "
+            )
 
-        Returns
-        -------
-        Self
-            Data model with mean and std added to the Normalize transform.
-        """
-        if self.mean is not None and self.std is not None:
-            # search in the transforms for Normalize and update parameters
-            for transform in self.transforms:
-                if transform.name == SupportedTransform.NORMALIZE.value:
-                    transform.mean = self.mean
-                    transform.std = self.std
+        elif self.target_means is not None and self.target_stds is not None:
+            if len(self.target_means) != len(self.target_stds):
+                raise ValueError(
+                    "Mean and std must be either both None, or both specified for each "
+                    "target channel."
+                )
 
         return self
 
@@ -341,7 +346,13 @@ class DataConfig(BaseModel):
         if self.has_n2v_manipulate():
             self.transforms.pop(-1)
 
-    def set_mean_and_std(self, mean: float, std: float) -> None:
+    def set_mean_and_std(
+        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,
+    ) -> None:
         """
         Set mean and standard deviation of the data.
 
@@ -350,14 +361,33 @@ class DataConfig(BaseModel):
 
         Parameters
         ----------
-        mean : float
-            Mean of the data.
-        std : float
-            Standard deviation of the data.
+        image_means : NDArray or tuple or list
+            Mean values for normalization.
+        image_stds : NDArray or tuple or list
+            Standard deviation values for normalization.
+        target_means : NDArray or tuple or list, optional
+            Target mean values for normalization, by default ().
+        target_stds : NDArray or tuple or list, optional
+            Target standard deviation values for normalization, by default ().
         """
-        self._update(mean=mean, std=std)
+        # make sure we pass a list
+        if image_means is not None:
+            image_means = list(image_means)
+        if image_stds is not None:
+            image_stds = list(image_stds)
+        if target_means is not None:
+            target_means = list(target_means)
+        if target_stds is not None:
+            target_stds = list(target_stds)
+
+        self._update(
+            image_means=image_means,
+            image_stds=image_stds,
+            target_means=target_means,
+            target_stds=target_stds,
+        )
 
-    def set_3D(self, axes: str, patch_size: List[int]) -> None:
+    def set_3D(self, axes: str, patch_size: list[int]) -> None:
         """
         Set 3D parameters.
 
@@ -365,7 +395,7 @@ class DataConfig(BaseModel):
         ----------
         axes : str
             Axes.
-        patch_size : List[int]
+        patch_size : list of int
             Patch size.
         """
         self._update(axes=axes, patch_size=patch_size)

careamics/config/inference_model.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import Any, List, Literal, Optional, Union
+from typing import Any, Literal, Optional, Union
 
 from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
 from typing_extensions import Self
@@ -17,17 +17,17 @@ class InferenceConfig(BaseModel):
 
     # Mandatory fields
     data_type: Literal["array", "tiff", "custom"]  # As defined in SupportedData
-    tile_size: Optional[Union[List[int]]] = Field(
+    tile_size: Optional[Union[list[int]]] = Field(
         default=None, min_length=2, max_length=3
     )
-    tile_overlap: Optional[Union[List[int]]] = Field(
+    tile_overlap: Optional[Union[list[int]]] = Field(
         default=None, min_length=2, max_length=3
     )
 
     axes: str
 
-    mean: float
-    std: float = Field(..., ge=0.0)
+    image_means: list = Field(..., min_length=0, max_length=32)
+    image_stds: list = Field(..., min_length=0, max_length=32)
 
     # only default TTAs are supported for now
     tta_transforms: bool = Field(default=True)
@@ -38,8 +38,8 @@ class InferenceConfig(BaseModel):
     @field_validator("tile_overlap")
     @classmethod
     def all_elements_non_zero_even(
-        cls, tile_overlap: Optional[Union[List[int]]]
-    ) -> Optional[Union[List[int]]]:
+        cls, tile_overlap: Optional[list[int]]
+    ) -> Optional[list[int]]:
         """
         Validate tile overlap.
 
@@ -47,12 +47,12 @@ class InferenceConfig(BaseModel):
 
         Parameters
         ----------
-        tile_overlap : Optional[Union[List[int]]]
+        tile_overlap : list[int] or None
             Patch size.
 
         Returns
         -------
-        Optional[Union[List[int]]]
+        list[int] or None
             Validated tile overlap.
 
         Raises
@@ -77,19 +77,19 @@ class InferenceConfig(BaseModel):
     @field_validator("tile_size")
     @classmethod
     def tile_min_8_power_of_2(
-        cls, tile_list: Optional[Union[List[int]]]
-    ) -> Optional[Union[List[int]]]:
+        cls, tile_list: Optional[list[int]]
+    ) -> Optional[list[int]]:
         """
         Validate that each entry is greater or equal than 8 and a power of 2.
 
         Parameters
         ----------
-        tile_list : List[int]
+        tile_list : list of int
             Patch size.
 
         Returns
         -------
-        List[int]
+        list of int
             Validated patch size.
 
         Raises
@@ -182,11 +182,23 @@ class InferenceConfig(BaseModel):
             If std is not None and mean is None.
         """
         # check that mean and std are either both None, or both specified
-        if (self.mean is None) != (self.std is None):
+        if not self.image_means and not self.image_stds:
+            raise ValueError("Mean and std must be specified during inference.")
+
+        if (self.image_means and not self.image_stds) or (
+            self.image_stds and not self.image_means
+        ):
             raise ValueError(
                 "Mean and std must be either both None, or both specified."
             )
 
+        elif (self.image_means is not None and self.image_stds is not None) and (
+            len(self.image_means) != len(self.image_stds)
+        ):
+            raise ValueError(
+                "Mean and std must be specified for each " "input channel."
+            )
+
         return self
 
     def _update(self, **kwargs: Any) -> None:
@@ -201,7 +213,7 @@ class InferenceConfig(BaseModel):
         self.__dict__.update(kwargs)
         self.__class__.model_validate(self.__dict__)
 
-    def set_3D(self, axes: str, tile_size: List[int], tile_overlap: List[int]) -> None:
+    def set_3D(self, axes: str, tile_size: list[int], tile_overlap: list[int]) -> None:
         """
         Set 3D parameters.
 
@@ -209,9 +221,9 @@ class InferenceConfig(BaseModel):
         ----------
         axes : str
             Axes.
-        tile_size : List[int]
+        tile_size : list of int
             Tile size.
-        tile_overlap : List[int]
+        tile_overlap : list of int
             Tile overlap.
         """
         self._update(axes=axes, tile_size=tile_size, tile_overlap=tile_overlap)