careamics 0.1.0rc5__py3-none-any.whl → 0.1.0rc6__py3-none-any.whl

careamics/config/inference_model.py

@@ -7,12 +7,8 @@ from typing import Any, List, Literal, Optional, Union
 from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
 from typing_extensions import Self
 
-from .support import SupportedTransform
-from .transformations.normalize_model import NormalizeModel
 from .validators import check_axes_validity, patch_size_ge_than_8_power_of_2
 
-TRANSFORMS_UNION = Union[NormalizeModel]
-
 
 class InferenceConfig(BaseModel):
     """Configuration class for the prediction model."""
@@ -33,15 +29,6 @@ class InferenceConfig(BaseModel):
     mean: float
     std: float = Field(..., ge=0.0)
 
-    transforms: List[TRANSFORMS_UNION] = Field(
-        default=[
-            {
-                "name": SupportedTransform.NORMALIZE.value,
-            },
-        ],
-        validate_default=True,
-    )
-
     # only default TTAs are supported for now
     tta_transforms: bool = Field(default=True)
 
@@ -149,39 +136,6 @@ class InferenceConfig(BaseModel):
 
         return axes
 
-    @field_validator("transforms")
-    @classmethod
-    def validate_transforms(
-        cls, transforms: List[TRANSFORMS_UNION]
-    ) -> List[TRANSFORMS_UNION]:
-        """
-        Validate that transforms do not have N2V pixel manipulate transforms.
-
-        Parameters
-        ----------
-        transforms : List[TRANSFORMS_UNION]
-            Transforms.
-
-        Returns
-        -------
-        List[TRANSFORMS_UNION]
-            Validated transforms.
-
-        Raises
-        ------
-        ValueError
-            If transforms contain N2V pixel manipulate transforms.
-        """
-        if transforms is not None:
-            for transform in transforms:
-                if transform.name == SupportedTransform.N2V_MANIPULATE.value:
-                    raise ValueError(
-                        "N2V_Manipulate transform is not allowed in "
-                        "prediction transforms."
-                    )
-
-        return transforms
-
     @model_validator(mode="after")
     def validate_dimensions(self: Self) -> Self:
         """
@@ -235,25 +189,6 @@ class InferenceConfig(BaseModel):
 
         return self
 
-    @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.
-
-        Returns
-        -------
-        Self
-            Inference model with mean and std added to the Normalize transform.
-        """
-        if self.mean is not None or 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
-
-        return self
-
     def _update(self, **kwargs: Any) -> None:
         """
         Update multiple arguments at once.

careamics/config/optimizer_models.py

@@ -1,3 +1,5 @@
+"""Optimizers and schedulers Pydantic models."""
+
 from __future__ import annotations
 
 from typing import Dict, Literal
@@ -19,8 +21,7 @@ from .support import SupportedOptimizer
 
 
 class OptimizerModel(BaseModel):
-    """
-    Torch optimizer.
+    """Torch optimizer Pydantic model.
 
     Only parameters supported by the corresponding torch optimizer will be taken
     into account. For more details, check:
@@ -115,8 +116,7 @@ class OptimizerModel(BaseModel):
 
 
 class LrSchedulerModel(BaseModel):
-    """
-    Torch learning rate scheduler.
+    """Torch learning rate scheduler Pydantic model.
 
     Only parameters supported by the corresponding torch lr scheduler will be taken
     into account. For more details, check:

careamics/config/support/__init__.py

@@ -14,7 +14,6 @@ __all__ = [
     "SupportedPixelManipulation",
     "SupportedTransform",
     "SupportedData",
-    "SupportedExtractionStrategy",
     "SupportedStructAxis",
     "SupportedLogger",
 ]
@@ -24,7 +23,6 @@ from .supported_activations import SupportedActivation
 from .supported_algorithms import SupportedAlgorithm
 from .supported_architectures import SupportedArchitecture
 from .supported_data import SupportedData
-from .supported_extraction_strategies import SupportedExtractionStrategy
 from .supported_loggers import SupportedLogger
 from .supported_losses import SupportedLoss
 from .supported_optimizers import SupportedOptimizer, SupportedScheduler

careamics/config/support/supported_activations.py

@@ -1,3 +1,5 @@
+"""Activations supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

careamics/config/support/supported_algorithms.py

@@ -1,3 +1,5 @@
+"""Algorithms supported by CAREamics."""
+
 from __future__ import annotations
 
 from careamics.utils import BaseEnum
@@ -10,9 +12,9 @@ class SupportedAlgorithm(str, BaseEnum):
     """
 
     N2V = "n2v"
-    CUSTOM = "custom"
     CARE = "care"
     N2N = "n2n"
+    CUSTOM = "custom"
     # PN2V = "pn2v"
     # HDN = "hdn"
     # SEG = "segmentation"

careamics/config/support/supported_architectures.py

@@ -1,3 +1,5 @@
+"""Architectures supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

careamics/config/support/supported_data.py

@@ -1,3 +1,5 @@
+"""Data supported by CAREamics."""
+
 from __future__ import annotations
 
 from typing import Union

careamics/config/support/supported_loggers.py

@@ -1,3 +1,5 @@
+"""Logger supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

careamics/config/support/supported_losses.py

@@ -1,3 +1,5 @@
+"""Losses supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

careamics/config/support/supported_optimizers.py

@@ -1,3 +1,5 @@
+"""Optimizers and schedulers supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

careamics/config/support/supported_pixel_manipulations.py

@@ -1,15 +1,15 @@
+"""Pixel manipulation methods supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 
 class SupportedPixelManipulation(str, BaseEnum):
-    """_summary_.
+    """Supported Noise2Void pixel manipulations.
 
     - Uniform: Replace masked pixel value by a (uniformly) randomly selected neighbor
         pixel value.
     - Median: Replace masked pixel value by the mean of the neighborhood.
     """
 
-    # TODO docs
-
     UNIFORM = "uniform"
     MEDIAN = "median"

careamics/config/support/supported_struct_axis.py

@@ -1,3 +1,5 @@
+"""StructN2V axes supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

careamics/config/support/supported_transforms.py

@@ -1,23 +1,12 @@
+"""Transforms supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 
 class SupportedTransform(str, BaseEnum):
-    """Transforms officially supported by CAREamics.
-
-    - Flip: from Albumentations, randomly flip the input horizontally, vertically or
-        both, parameter `p` can be used to set the probability to apply the transform.
-    - XYRandomRotate90: #TODO
-    - Normalize # TODO add details, in particular about the parameters
-    - ManipulateN2V # TODO add details, in particular about the parameters
-    - NDFlip
-
-    Note that while any Albumentations (see https://albumentations.ai/) transform can be
-    used in CAREamics, no check are implemented to verify the compatibility of any other
-    transforms than the ones officially supported.
-    """
+    """Transforms officially supported by CAREamics."""
 
-    NDFLIP = "NDFlip"
+    XY_FLIP = "XYFlip"
     XY_RANDOM_ROTATE90 = "XYRandomRotate90"
     NORMALIZE = "Normalize"
     N2V_MANIPULATE = "N2VManipulate"
-    # CUSTOM = "Custom"

careamics/config/tile_information.py

@@ -1,3 +1,5 @@
+"""Pydantic model representing the metadata of a prediction tile."""
+
 from __future__ import annotations
 
 from typing import Optional, Tuple

careamics/config/transformations/__init__.py

@@ -2,13 +2,14 @@
 
 __all__ = [
     "N2VManipulateModel",
-    "NDFlipModel",
+    "XYFlipModel",
     "NormalizeModel",
     "XYRandomRotate90Model",
+    "XorYFlipModel",
 ]
 
 
 from .n2v_manipulate_model import N2VManipulateModel
-from .nd_flip_model import NDFlipModel
 from .normalize_model import NormalizeModel
+from .xy_flip_model import XYFlipModel
 from .xy_random_rotate90_model import XYRandomRotate90Model

careamics/config/transformations/xy_flip_model.py

@@ -0,0 +1,43 @@
+"""Pydantic model for the XYFlip transform."""
+
+from typing import Literal, Optional
+
+from pydantic import ConfigDict, Field
+
+from .transform_model import TransformModel
+
+
+class XYFlipModel(TransformModel):
+    """
+    Pydantic model used to represent XYFlip transformation.
+
+    Attributes
+    ----------
+    name : Literal["XYFlip"]
+        Name of the transformation.
+    p : float
+        Probability of applying the transform, by default 0.5.
+    seed : Optional[int]
+        Seed for the random number generator,  by default None.
+    """
+
+    model_config = ConfigDict(
+        validate_assignment=True,
+    )
+
+    name: Literal["XYFlip"] = "XYFlip"
+    flip_x: bool = Field(
+        True,
+        description="Whether to flip along the X axis.",
+    )
+    flip_y: bool = Field(
+        True,
+        description="Whether to flip along the Y axis.",
+    )
+    p: float = Field(
+        0.5,
+        description="Probability of applying the transform.",
+        ge=0,
+        le=1,
+    )
+    seed: Optional[int] = None

careamics/config/transformations/xy_random_rotate90_model.py

@@ -2,21 +2,23 @@
 
 from typing import Literal, Optional
 
-from pydantic import ConfigDict
+from pydantic import ConfigDict, Field
 
 from .transform_model import TransformModel
 
 
 class XYRandomRotate90Model(TransformModel):
     """
-    Pydantic model used to represent NDFlip transformation.
+    Pydantic model used to represent the XY random 90 degree rotation transformation.
 
     Attributes
     ----------
     name : Literal["XYRandomRotate90"]
         Name of the transformation.
+    p : float
+        Probability of applying the transform, by default 0.5.
     seed : Optional[int]
-        Seed for the random number generator.
+        Seed for the random number generator, by default None.
     """
 
     model_config = ConfigDict(
@@ -24,4 +26,10 @@ class XYRandomRotate90Model(TransformModel):
     )
 
     name: Literal["XYRandomRotate90"] = "XYRandomRotate90"
+    p: float = Field(
+        0.5,
+        description="Probability of applying the transform.",
+        ge=0,
+        le=1,
+    )
     seed: Optional[int] = None

careamics/conftest.py

@@ -14,6 +14,18 @@ from sybil.parsers.doctest import DocTestParser
 
 @pytest.fixture(scope="module")
 def my_path(tmpdir_factory: TempPathFactory) -> Path:
+    """Fixture used in doctest to create a temporary directory.
+
+    Parameters
+    ----------
+    tmpdir_factory : TempPathFactory
+        Temporary path factory from pytest.
+
+    Returns
+    -------
+    Path
+        Temporary directory path.
+    """
     return tmpdir_factory.mktemp("my_path")
 
 

careamics/dataset/dataset_utils/dataset_utils.py

@@ -1,4 +1,4 @@
-"""Convenience methods for datasets."""
+"""Dataset utilities."""
 
 from typing import List, Tuple
 
@@ -17,12 +17,12 @@ def _get_shape_order(
 
     Parameters
     ----------
-    shape_in : Tuple
+    shape_in : Tuple[int, ...]
         Input shape.
-    ref_axes : str
-        Reference axes.
     axes_in : str
         Input axes.
+    ref_axes : str
+        Reference axes.
 
     Returns
     -------

careamics/dataset/dataset_utils/file_utils.py

@@ -1,3 +1,5 @@
+"""File utilities."""
+
 from fnmatch import fnmatch
 from pathlib import Path
 from typing import List, Union
@@ -11,8 +13,7 @@ logger = get_logger(__name__)
 
 
 def get_files_size(files: List[Path]) -> float:
-    """
-    Get files size in MB.
+    """Get files size in MB.
 
     Parameters
     ----------
@@ -32,7 +33,7 @@ def list_files(
     data_type: Union[str, SupportedData],
     extension_filter: str = "",
 ) -> List[Path]:
-    """Creates a recursive list of files in `data_path`.
+    """Create a recursive list of files in `data_path`.
 
     If `data_path` is a file, its name is validated against the `data_type` using
     `fnmatch`, and the method returns `data_path` itself.

careamics/dataset/dataset_utils/read_tiff.py

@@ -1,3 +1,5 @@
+"""Funtions to read tiff images."""
+
 import logging
 from fnmatch import fnmatch
 from pathlib import Path
@@ -19,8 +21,10 @@ def read_tiff(file_path: Path, *args: list, **kwargs: dict) -> np.ndarray:
     ----------
     file_path : Path
         Path to a file.
-    axes : str
-        Description of axes in format STCZYX.
+    *args : list
+        Additional arguments.
+    **kwargs : dict
+        Additional keyword arguments.
 
     Returns
     -------

careamics/dataset/dataset_utils/read_utils.py

@@ -1,3 +1,5 @@
+"""Read function utilities."""
+
 from typing import Callable, Union
 
 from careamics.config.support import SupportedData

careamics/dataset/dataset_utils/read_zarr.py

@@ -1,3 +1,5 @@
+"""Function to read zarr images."""
+
 from typing import Union
 
 from zarr import Group, core, hierarchy, storage
@@ -6,26 +8,28 @@ from zarr import Group, core, hierarchy, storage
 def read_zarr(
     zarr_source: Group, axes: str
 ) -> Union[core.Array, storage.DirectoryStore, hierarchy.Group]:
-    """Reads a file and returns a pointer.
+    """Read a file and returns a pointer.
 
     Parameters
     ----------
-    file_path : Path
-        pathlib.Path object containing a path to a file
+    zarr_source : Group
+        Zarr storage.
+    axes : str
+        Axes of the data.
 
     Returns
     -------
     np.ndarray
-        Pointer to zarr storage
+        Pointer to zarr storage.
 
     Raises
     ------
     ValueError, OSError
-        if a file is not a valid tiff or damaged
+        if a file is not a valid tiff or damaged.
     ValueError
-        if data dimensions are not 2, 3 or 4
+        if data dimensions are not 2, 3 or 4.
     ValueError
-        if axes parameter from config is not consistent with data dimensions
+        if axes parameter from config is not consistent with data dimensions.
     """
     if isinstance(zarr_source, hierarchy.Group):
         array = zarr_source[0]