careamics 0.1.0rc4__py3-none-any.whl → 0.1.0rc5__py3-none-any.whl

careamics/config/data_model.py

@@ -1,10 +1,10 @@
 """Data configuration."""
+
 from __future__ import annotations
 
 from pprint import pformat
 from typing import Any, List, Literal, Optional, Union
 
-from albumentations import Compose
 from pydantic import (
     BaseModel,
     ConfigDict,
@@ -71,8 +71,6 @@ class DataConfig(BaseModel):
     ...         },
     ...         {
     ...             "name": "NDFlip",
-    ...             "is_3D": True,
-    ...             "flip_z": True,
     ...         }
     ...     ]
     ... )
@@ -81,7 +79,6 @@ class DataConfig(BaseModel):
     # Pydantic class configuration
     model_config = ConfigDict(
         validate_assignment=True,
-        arbitrary_types_allowed=True,  # Allow Compose declaration
     )
 
     # Dataset configuration
@@ -94,7 +91,7 @@ class DataConfig(BaseModel):
     mean: Optional[float] = None
     std: Optional[float] = None
 
-    transforms: Union[List[TRANSFORMS_UNION], Compose] = Field(
+    transforms: List[TRANSFORMS_UNION] = Field(
         default=[
             {
                 "name": SupportedTransform.NORMALIZE.value,
@@ -181,19 +178,19 @@ class DataConfig(BaseModel):
     @field_validator("transforms")
     @classmethod
     def validate_prediction_transforms(
-        cls, transforms: Union[List[TRANSFORMS_UNION], Compose]
-    ) -> Union[List[TRANSFORMS_UNION], Compose]:
+        cls, transforms: List[TRANSFORMS_UNION]
+    ) -> List[TRANSFORMS_UNION]:
         """
         Validate N2VManipulate transform position in the transform list.
 
         Parameters
         ----------
-        transforms : Union[List[Transformations_Union], Compose]
+        transforms : List[Transformations_Union]
             Transforms.
 
         Returns
         -------
-        Union[List[Transformations_Union], Compose]
+        List[TRANSFORMS_UNION]
             Validated transforms.
 
         Raises
@@ -201,23 +198,22 @@ class DataConfig(BaseModel):
         ValueError
             If multiple instances of N2VManipulate are found.
         """
-        if not isinstance(transforms, Compose):
-            transform_list = [t.name for t in transforms]
-
-            if SupportedTransform.N2V_MANIPULATE in transform_list:
-                # multiple N2V_MANIPULATE
-                if transform_list.count(SupportedTransform.N2V_MANIPULATE) > 1:
-                    raise ValueError(
-                        f"Multiple instances of "
-                        f"{SupportedTransform.N2V_MANIPULATE} transforms "
-                        f"are not allowed."
-                    )
-
-                # N2V_MANIPULATE not the last transform
-                elif transform_list[-1] != SupportedTransform.N2V_MANIPULATE:
-                    index = transform_list.index(SupportedTransform.N2V_MANIPULATE)
-                    transform = transforms.pop(index)
-                    transforms.append(transform)
+        transform_list = [t.name for t in transforms]
+
+        if SupportedTransform.N2V_MANIPULATE in transform_list:
+            # multiple N2V_MANIPULATE
+            if transform_list.count(SupportedTransform.N2V_MANIPULATE) > 1:
+                raise ValueError(
+                    f"Multiple instances of "
+                    f"{SupportedTransform.N2V_MANIPULATE} transforms "
+                    f"are not allowed."
+                )
+
+            # N2V_MANIPULATE not the last transform
+            elif transform_list[-1] != SupportedTransform.N2V_MANIPULATE:
+                index = transform_list.index(SupportedTransform.N2V_MANIPULATE)
+                transform = transforms.pop(index)
+                transforms.append(transform)
 
         return transforms
 
@@ -256,11 +252,10 @@ class DataConfig(BaseModel):
         """
         if self.mean is not None or self.std is not None:
             # search in the transforms for Normalize and update parameters
-            if self.has_transform_list():
-                for transform in self.transforms:
-                    if transform.name == SupportedTransform.NORMALIZE.value:
-                        transform.mean = self.mean
-                        transform.std = self.std
+            for transform in self.transforms:
+                if transform.name == SupportedTransform.NORMALIZE.value:
+                    transform.mean = self.mean
+                    transform.std = self.std
 
         return self
 
@@ -286,13 +281,6 @@ class DataConfig(BaseModel):
                     f"({self.axes})."
                 )
 
-            if self.has_transform_list():
-                for transform in self.transforms:
-                    if transform.name == SupportedTransform.NDFLIP:
-                        transform.is_3D = True
-                    elif transform.name == SupportedTransform.XY_RANDOM_ROTATE90:
-                        transform.is_3D = True
-
         else:
             if len(self.patch_size) != 2:
                 raise ValueError(
@@ -300,13 +288,6 @@ class DataConfig(BaseModel):
                     f"({self.axes})."
                 )
 
-            if self.has_transform_list():
-                for transform in self.transforms:
-                    if transform.name == SupportedTransform.NDFLIP:
-                        transform.is_3D = False
-                    elif transform.name == SupportedTransform.XY_RANDOM_ROTATE90:
-                        transform.is_3D = False
-
         return self
 
     def __str__(self) -> str:
@@ -332,84 +313,31 @@ class DataConfig(BaseModel):
         self.__dict__.update(kwargs)
         self.__class__.model_validate(self.__dict__)
 
-    def has_transform_list(self) -> bool:
-        """
-        Check if the transforms are a list, as opposed to a Compose object.
-
-        Returns
-        -------
-        bool
-            True if the transforms are a list, False otherwise.
-        """
-        return isinstance(self.transforms, list)
-
     def has_n2v_manipulate(self) -> bool:
         """
         Check if the transforms contain N2VManipulate.
 
-        Use `has_transform_list` to check if the transforms are a list.
-
         Returns
         -------
         bool
             True if the transforms contain N2VManipulate, False otherwise.
-
-        Raises
-        ------
-        ValueError
-            If the transforms are a Compose object.
         """
-        if self.has_transform_list():
-            return any(
-                transform.name == SupportedTransform.N2V_MANIPULATE.value
-                for transform in self.transforms
-            )
-        else:
-            raise ValueError(
-                "Checking for N2VManipulate with Compose transforms is not allowed. "
-                "Check directly in the Compose."
-            )
+        return any(
+            transform.name == SupportedTransform.N2V_MANIPULATE.value
+            for transform in self.transforms
+        )
 
     def add_n2v_manipulate(self) -> None:
-        """
-        Add N2VManipulate to the transforms.
-
-        Use `has_transform_list` to check if the transforms are a list.
-
-        Raises
-        ------
-        ValueError
-            If the transforms are a Compose object.
-        """
-        if self.has_transform_list():
-            if not self.has_n2v_manipulate():
-                self.transforms.append(
-                    N2VManipulateModel(name=SupportedTransform.N2V_MANIPULATE.value)
-                )
-        else:
-            raise ValueError(
-                "Adding N2VManipulate with Compose transforms is not allowed. Add "
-                "N2VManipulate directly to the transform in the Compose."
+        """Add N2VManipulate to the transforms."""
+        if not self.has_n2v_manipulate():
+            self.transforms.append(
+                N2VManipulateModel(name=SupportedTransform.N2V_MANIPULATE.value)
             )
 
     def remove_n2v_manipulate(self) -> None:
-        """
-        Remove N2VManipulate from the transforms.
-
-        Use `has_transform_list` to check if the transforms are a list.
-
-        Raises
-        ------
-        ValueError
-            If the transforms are a Compose object.
-        """
-        if self.has_transform_list() and self.has_n2v_manipulate():
+        """Remove N2VManipulate from the transforms."""
+        if self.has_n2v_manipulate():
             self.transforms.pop(-1)
-        else:
-            raise ValueError(
-                "Removing N2VManipulate with Compose transforms is not allowed. Remove "
-                "N2VManipulate directly from the transform in the Compose."
-            )
 
     def set_mean_and_std(self, mean: float, std: float) -> None:
         """
@@ -428,16 +356,10 @@ class DataConfig(BaseModel):
         self._update(mean=mean, std=std)
 
         # search in the transforms for Normalize and update parameters
-        if self.has_transform_list():
-            for transform in self.transforms:
-                if transform.name == SupportedTransform.NORMALIZE.value:
-                    transform.mean = mean
-                    transform.std = std
-        else:
-            raise ValueError(
-                "Setting mean and std with Compose transforms is not allowed. Add "
-                "mean and std parameters directly to the transform in the Compose."
-            )
+        for transform in self.transforms:
+            if transform.name == SupportedTransform.NORMALIZE.value:
+                transform.mean = mean
+                transform.std = std
 
     def set_3D(self, axes: str, patch_size: List[int]) -> None:
         """
@@ -465,8 +387,6 @@ class DataConfig(BaseModel):
         ------
         ValueError
             If the N2V pixel manipulate transform is not found in the transforms.
-        ValueError
-            If the transforms are a Compose object.
         """
         if use_n2v2:
             self.set_N2V2_strategy("median")
@@ -486,28 +406,19 @@ class DataConfig(BaseModel):
         ------
         ValueError
             If the N2V pixel manipulate transform is not found in the transforms.
-        ValueError
-            If the transforms are a Compose object.
         """
-        if isinstance(self.transforms, list):
-            found_n2v = False
+        found_n2v = False
 
-            for transform in self.transforms:
-                if transform.name == SupportedTransform.N2V_MANIPULATE.value:
-                    transform.strategy = strategy
-                    found_n2v = True
-
-            if not found_n2v:
-                transforms = [t.name for t in self.transforms]
-                raise ValueError(
-                    f"N2V_Manipulate transform not found in the transforms list "
-                    f"({transforms})."
-                )
+        for transform in self.transforms:
+            if transform.name == SupportedTransform.N2V_MANIPULATE.value:
+                transform.strategy = strategy
+                found_n2v = True
 
-        else:
+        if not found_n2v:
+            transforms = [t.name for t in self.transforms]
             raise ValueError(
-                "Setting N2V2 strategy with Compose transforms is not allowed. Add "
-                "N2V2 strategy parameters directly to the transform in the Compose."
+                f"N2V_Manipulate transform not found in the transforms list "
+                f"({transforms})."
             )
 
     def set_structN2V_mask(
@@ -529,27 +440,18 @@ class DataConfig(BaseModel):
         ------
         ValueError
             If the N2V pixel manipulate transform is not found in the transforms.
-        ValueError
-            If the transforms are a Compose object.
         """
-        if isinstance(self.transforms, list):
-            found_n2v = False
+        found_n2v = False
 
-            for transform in self.transforms:
-                if transform.name == SupportedTransform.N2V_MANIPULATE.value:
-                    transform.struct_mask_axis = mask_axis
-                    transform.struct_mask_span = mask_span
-                    found_n2v = True
+        for transform in self.transforms:
+            if transform.name == SupportedTransform.N2V_MANIPULATE.value:
+                transform.struct_mask_axis = mask_axis
+                transform.struct_mask_span = mask_span
+                found_n2v = True
 
-            if not found_n2v:
-                transforms = [t.name for t in self.transforms]
-                raise ValueError(
-                    f"N2V pixel manipulate transform not found in the transforms "
-                    f"({transforms})."
-                )
-
-        else:
+        if not found_n2v:
+            transforms = [t.name for t in self.transforms]
             raise ValueError(
-                "Setting structN2VMask with Compose transforms is not allowed. Add "
-                "structN2VMask parameters directly to the transform in the Compose."
+                f"N2V pixel manipulate transform not found in the transforms "
+                f"({transforms})."
             )

careamics/config/inference_model.py

@@ -1,9 +1,9 @@
 """Pydantic model representing CAREamics prediction configuration."""
+
 from __future__ import annotations
 
 from typing import Any, List, Literal, Optional, Union
 
-from albumentations import Compose
 from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
 from typing_extensions import Self
 
@@ -33,7 +33,7 @@ class InferenceConfig(BaseModel):
     mean: float
     std: float = Field(..., ge=0.0)
 
-    transforms: Union[List[TRANSFORMS_UNION], Compose] = Field(
+    transforms: List[TRANSFORMS_UNION] = Field(
         default=[
             {
                 "name": SupportedTransform.NORMALIZE.value,
@@ -51,22 +51,22 @@ class InferenceConfig(BaseModel):
     @field_validator("tile_overlap")
     @classmethod
     def all_elements_non_zero_even(
-        cls, patch_list: Optional[Union[List[int]]]
+        cls, tile_overlap: Optional[Union[List[int]]]
     ) -> Optional[Union[List[int]]]:
         """
-        Validate patch size.
+        Validate tile overlap.
 
-        Patch size must be non-zero, positive and even.
+        Overlaps must be non-zero, positive and even.
 
         Parameters
         ----------
-        patch_list : Optional[Union[List[int]]]
+        tile_overlap : Optional[Union[List[int]]]
             Patch size.
 
         Returns
         -------
         Optional[Union[List[int]]]
-            Validated patch size.
+            Validated tile overlap.
 
         Raises
         ------
@@ -75,8 +75,8 @@ class InferenceConfig(BaseModel):
         ValueError
             If the patch size is not even.
         """
-        if patch_list is not None:
-            for dim in patch_list:
+        if tile_overlap is not None:
+            for dim in tile_overlap:
                 if dim < 1:
                     raise ValueError(
                         f"Patch size must be non-zero positive (got {dim})."
@@ -85,7 +85,7 @@ class InferenceConfig(BaseModel):
                 if dim % 2 != 0:
                     raise ValueError(f"Patch size must be even (got {dim}).")
 
-        return patch_list
+        return tile_overlap
 
     @field_validator("tile_size")
     @classmethod
@@ -152,19 +152,19 @@ class InferenceConfig(BaseModel):
     @field_validator("transforms")
     @classmethod
     def validate_transforms(
-        cls, transforms: Union[List[TRANSFORMS_UNION], Compose]
-    ) -> Union[List[TRANSFORMS_UNION], Compose]:
+        cls, transforms: List[TRANSFORMS_UNION]
+    ) -> List[TRANSFORMS_UNION]:
         """
         Validate that transforms do not have N2V pixel manipulate transforms.
 
         Parameters
         ----------
-        transforms : Union[List[TransformModel], Compose]
+        transforms : List[TRANSFORMS_UNION]
             Transforms.
 
         Returns
         -------
-        Union[List[Transformations_Union], Compose]
+        List[TRANSFORMS_UNION]
             Validated transforms.
 
         Raises
@@ -172,7 +172,7 @@ class InferenceConfig(BaseModel):
         ValueError
             If transforms contain N2V pixel manipulate transforms.
         """
-        if not isinstance(transforms, Compose) and transforms is not None:
+        if transforms is not None:
             for transform in transforms:
                 if transform.name == SupportedTransform.N2V_MANIPULATE.value:
                     raise ValueError(
@@ -247,11 +247,10 @@ class InferenceConfig(BaseModel):
         """
         if self.mean is not None or self.std is not None:
             # search in the transforms for Normalize and update parameters
-            if not isinstance(self.transforms, Compose):
-                for transform in self.transforms:
-                    if transform.name == SupportedTransform.NORMALIZE.value:
-                        transform.mean = self.mean
-                        transform.std = self.std
+            for transform in self.transforms:
+                if transform.name == SupportedTransform.NORMALIZE.value:
+                    transform.mean = self.mean
+                    transform.std = self.std
 
         return self
 

careamics/config/references/algorithm_descriptions.py

@@ -1,4 +1,5 @@
 """Descriptions of the algorithms used in CAREmics."""
+
 from pydantic import BaseModel
 
 CUSTOM = "Custom"

careamics/config/references/references.py

@@ -1,4 +1,5 @@
 """References for the CAREamics algorithms."""
+
 from bioimageio.spec.generic.v0_3 import CiteEntry
 
 N2VRef = CiteEntry(

careamics/config/support/supported_extraction_strategies.py

@@ -3,6 +3,7 @@ Extraction strategy module.
 
 This module defines the various extraction strategies available in CAREamics.
 """
+
 from careamics.utils import BaseEnum
 
 

careamics/config/training_model.py

@@ -1,4 +1,5 @@
 """Training configuration."""
+
 from __future__ import annotations
 
 from pprint import pformat

careamics/config/transformations/n2v_manipulate_model.py

@@ -1,4 +1,5 @@
 """Pydantic model for the N2VManipulate transform."""
+
 from typing import Literal
 
 from pydantic import ConfigDict, Field, field_validator

careamics/config/transformations/nd_flip_model.py

@@ -1,7 +1,8 @@
 """Pydantic model for the NDFlip transform."""
-from typing import Literal
 
-from pydantic import ConfigDict, Field
+from typing import Literal, Optional
+
+from pydantic import ConfigDict
 
 from .transform_model import TransformModel
 
@@ -14,12 +15,8 @@ class NDFlipModel(TransformModel):
     ----------
     name : Literal["NDFlip"]
         Name of the transformation.
-    p : float
-        Probability of applying the transformation, by default 0.5.
-    is_3D : bool
-        Whether the transformation should be applied in 3D, by default False.
-    flip_z : bool
-        Whether to flip the z axis, by default True.
+    seed : Optional[int]
+        Seed for the random number generator.
     """
 
     model_config = ConfigDict(
@@ -27,6 +24,4 @@ class NDFlipModel(TransformModel):
     )
 
     name: Literal["NDFlip"] = "NDFlip"
-    p: float = Field(default=0.5, ge=0.0, le=1.0)
-    is_3D: bool = Field(default=False)
-    flip_z: bool = Field(default=True)
+    seed: Optional[int] = None

careamics/config/transformations/normalize_model.py

@@ -1,4 +1,5 @@
 """Pydantic model for the Normalize transform."""
+
 from typing import Literal
 
 from pydantic import ConfigDict, Field

careamics/config/transformations/transform_model.py

@@ -1,4 +1,5 @@
 """Parent model for the transforms."""
+
 from typing import Any, Dict
 
 from pydantic import BaseModel, ConfigDict

careamics/config/transformations/xy_random_rotate90_model.py

@@ -1,7 +1,8 @@
 """Pydantic model for the XYRandomRotate90 transform."""
-from typing import Literal
 
-from pydantic import ConfigDict, Field
+from typing import Literal, Optional
+
+from pydantic import ConfigDict
 
 from .transform_model import TransformModel
 
@@ -14,10 +15,8 @@ class XYRandomRotate90Model(TransformModel):
     ----------
     name : Literal["XYRandomRotate90"]
         Name of the transformation.
-    p : float
-        Probability of applying the transformation, by default 0.5.
-    is_3D : bool
-        Whether the transformation should be applied in 3D, by default False.
+    seed : Optional[int]
+        Seed for the random number generator.
     """
 
     model_config = ConfigDict(
@@ -25,5 +24,4 @@ class XYRandomRotate90Model(TransformModel):
     )
 
     name: Literal["XYRandomRotate90"] = "XYRandomRotate90"
-    p: float = Field(default=0.5, ge=0.0, le=1.0)
-    is_3D: bool = Field(default=False)
+    seed: Optional[int] = None

careamics/config/validators/validator_utils.py

@@ -3,6 +3,7 @@ Validator functions.
 
 These functions are used to validate dimensions and axes of inputs.
 """
+
 from typing import List, Optional, Tuple, Union
 
 _AXES = "STCZYX"

careamics/conftest.py

@@ -2,6 +2,7 @@
 
 See https://sybil.readthedocs.io/en/latest/use.html#pytest
 """
+
 from pathlib import Path
 
 import pytest

careamics/dataset/dataset_utils/__init__.py

@@ -1,6 +1,5 @@
 """Files and arrays utils used in the datasets."""
 
-
 __all__ = [
     "reshape_array",
     "get_files_size",

careamics/dataset/dataset_utils/dataset_utils.py

@@ -1,4 +1,5 @@
 """Convenience methods for datasets."""
+
 from typing import List, Tuple
 
 import numpy as np