careamics 0.0.5__py3-none-any.whl → 0.0.6__py3-none-any.whl

careamics/config/fcn_algorithm_model.py

@@ -1,152 +0,0 @@
-"""Module containing `FCNAlgorithmConfig` class."""
-
-from pprint import pformat
-from typing import Literal, Union
-
-from pydantic import BaseModel, ConfigDict, Field, model_validator
-from typing_extensions import Self
-
-from careamics.config.architectures import CustomModel, UNetModel
-from careamics.config.optimizer_models import LrSchedulerModel, OptimizerModel
-
-
-class FCNAlgorithmConfig(BaseModel):
-    """Algorithm configuration.
-
-    This Pydantic model validates the parameters governing the components of the
-    training algorithm: which algorithm, loss function, model architecture, optimizer,
-    and learning rate scheduler to use.
-
-    Currently, we only support N2V, CARE, N2N and custom models. The `n2v` algorithm is
-    only compatible with `n2v` loss and `UNet` architecture. The `custom` algorithm
-    allows you to register your own architecture and select it using its name as
-    `name` in the custom pydantic model.
-
-    Attributes
-    ----------
-    algorithm : {"n2v", "care", "n2n", "custom"}
-        Algorithm to use.
-    loss : {"n2v", "mae", "mse"}
-        Loss function to use.
-    model : UNetModel or CustomModel
-        Model architecture to use.
-    optimizer : OptimizerModel, optional
-        Optimizer to use.
-    lr_scheduler : LrSchedulerModel, optional
-        Learning rate scheduler to use.
-
-    Raises
-    ------
-    ValueError
-        Algorithm parameter type validation errors.
-    ValueError
-        If the algorithm, loss and model are not compatible.
-
-    Examples
-    --------
-    Minimum example:
-    >>> from careamics.config import FCNAlgorithmConfig
-    >>> config_dict = {
-    ...     "algorithm": "n2v",
-    ...     "loss": "n2v",
-    ...     "model": {
-    ...         "architecture": "UNet",
-    ...     }
-    ... }
-    >>> config = FCNAlgorithmConfig(**config_dict)
-    """
-
-    # Pydantic class configuration
-    model_config = ConfigDict(
-        protected_namespaces=(),  # allows to use model_* as a field name
-        validate_assignment=True,
-        extra="allow",
-    )
-
-    # Mandatory fields
-    algorithm: Literal["n2v", "care", "n2n", "custom"]
-    """Name of the algorithm, as defined in SupportedAlgorithm. Use `custom` for custom
-    model architecture."""
-
-    loss: Literal["n2v", "mae", "mse"]
-    """Loss function to use, as defined in SupportedLoss."""
-
-    model: Union[UNetModel, CustomModel] = Field(discriminator="architecture")
-    """Model architecture to use, along with its parameters. Compatible architectures
-    are defined in SupportedArchitecture, and their Pydantic models in
-    `careamics.config.architectures`."""
-    # TODO supported architectures are now all the architectures but does not warn users
-    # of the compatibility with the algorithm
-
-    # Optional fields
-    optimizer: OptimizerModel = OptimizerModel()
-    """Optimizer to use, defined in SupportedOptimizer."""
-
-    lr_scheduler: LrSchedulerModel = LrSchedulerModel()
-    """Learning rate scheduler to use, defined in SupportedLrScheduler."""
-
-    @model_validator(mode="after")
-    def algorithm_cross_validation(self: Self) -> Self:
-        """Validate the algorithm model based on `algorithm`.
-
-        N2V:
-        - loss must be n2v
-        - model must be a `UNetModel`
-
-        Returns
-        -------
-        Self
-            The validated model.
-        """
-        # N2V
-        if self.algorithm == "n2v":
-            # n2v is only compatible with the n2v loss
-            if self.loss != "n2v":
-                raise ValueError(
-                    f"Algorithm {self.algorithm} only supports loss `n2v`."
-                )
-
-            # n2v 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`."
-                )
-
-            # n2v requires the number of input and output channels to be the same
-            if self.model.in_channels != self.model.num_classes:
-                raise ValueError(
-                    "N2V 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`.")
-
-        if (self.algorithm == "custom") != (self.model.architecture == "custom"):
-            raise ValueError(
-                "Algorithm and model architecture must be both `custom` or not."
-            )
-
-        return self
-
-    def __str__(self) -> str:
-        """Pretty string representing the configuration.
-
-        Returns
-        -------
-        str
-            Pretty string.
-        """
-        return pformat(self.model_dump())
-
-    @classmethod
-    def get_compatible_algorithms(cls) -> list[str]:
-        """Get the list of compatible algorithms.
-
-        Returns
-        -------
-        list of str
-            List of compatible algorithms.
-        """
-        return ["n2v", "care", "n2n"]

careamics/config/references/__init__.py

@@ -1,45 +0,0 @@
-"""Module containing references to the algorithm used in CAREamics."""
-
-__all__ = [
-    "N2V2Ref",
-    "N2VRef",
-    "StructN2VRef",
-    "N2VDescription",
-    "N2V2Description",
-    "StructN2VDescription",
-    "StructN2V2Description",
-    "N2V",
-    "N2V2",
-    "STRUCT_N2V",
-    "STRUCT_N2V2",
-    "CUSTOM",
-    "N2N",
-    "CARE",
-    "CAREDescription",
-    "N2NDescription",
-    "CARERef",
-    "N2NRef",
-]
-
-from .algorithm_descriptions import (
-    CARE,
-    CUSTOM,
-    N2N,
-    N2V,
-    N2V2,
-    STRUCT_N2V,
-    STRUCT_N2V2,
-    CAREDescription,
-    N2NDescription,
-    N2V2Description,
-    N2VDescription,
-    StructN2V2Description,
-    StructN2VDescription,
-)
-from .references import (
-    CARERef,
-    N2NRef,
-    N2V2Ref,
-    N2VRef,
-    StructN2VRef,
-)

careamics/config/references/algorithm_descriptions.py

@@ -1,132 +0,0 @@
-"""Descriptions of the algorithms used in CAREmics."""
-
-from pydantic import BaseModel
-
-CUSTOM = "Custom"
-N2V = "Noise2Void"
-N2V2 = "N2V2"
-STRUCT_N2V = "StructN2V"
-STRUCT_N2V2 = "StructN2V2"
-N2N = "Noise2Noise"
-CARE = "CARE"
-
-
-N2V_DESCRIPTION = (
-    "Noise2Void is a UNet-based self-supervised algorithm that "
-    "uses blind-spot training to denoise images. In short, in every "
-    "patches during training, random pixels are selected and their "
-    "value replaced by a neighboring pixel value. The network is then "
-    "trained to predict the original pixel value. The algorithm "
-    "relies on the continuity of the signal (neighboring pixels have "
-    "similar values) and the pixel-wise independence of the noise "
-    "(the noise in a pixel is not correlated with the noise in "
-    "neighboring pixels)."
-)
-
-
-class AlgorithmDescription(BaseModel):
-    """Description of an algorithm.
-
-    Attributes
-    ----------
-    description : str
-        Description of the algorithm.
-    """
-
-    description: str
-
-
-class N2VDescription(AlgorithmDescription):
-    """Description of Noise2Void.
-
-    Attributes
-    ----------
-    description : str
-        Description of Noise2Void.
-    """
-
-    description: str = N2V_DESCRIPTION
-
-
-class N2V2Description(AlgorithmDescription):
-    """Description of N2V2.
-
-    Attributes
-    ----------
-    description : str
-        Description of N2V2.
-    """
-
-    description: str = (
-        "N2V2 is a variant of Noise2Void. "
-        + N2V_DESCRIPTION
-        + "\nN2V2 introduces blur-pool layers and removed skip "
-        "connections in the UNet architecture to remove checkboard "
-        "artefacts, a common artefacts ocurring in Noise2Void."
-    )
-
-
-class StructN2VDescription(AlgorithmDescription):
-    """Description of StructN2V.
-
-    Attributes
-    ----------
-    description : str
-        Description of StructN2V.
-    """
-
-    description: str = (
-        "StructN2V is a variant of Noise2Void. "
-        + N2V_DESCRIPTION
-        + "\nStructN2V uses a linear mask (horizontal or vertical) to replace "
-        "the pixel values of neighbors of the masked pixels by a random "
-        "value. Such masking allows removing 1D structured noise from the "
-        "the images, the main failure case of the original N2V."
-    )
-
-
-class StructN2V2Description(AlgorithmDescription):
-    """Description of StructN2V2.
-
-    Attributes
-    ----------
-    description : str
-        Description of StructN2V2.
-    """
-
-    description: str = (
-        "StructN2V2 is a a variant of Noise2Void that uses both "
-        "structN2V and N2V2. "
-        + N2V_DESCRIPTION
-        + "\nStructN2V2 uses a linear mask (horizontal or vertical) to replace "
-        "the pixel values of neighbors of the masked pixels by a random "
-        "value. Such masking allows removing 1D structured noise from the "
-        "the images, the main failure case of the original N2V."
-        "\nN2V2 introduces blur-pool layers and removed skip connections in "
-        "the UNet architecture to remove checkboard artefacts, a common "
-        "artefacts ocurring in Noise2Void."
-    )
-
-
-class N2NDescription(AlgorithmDescription):
-    """Description of Noise2Noise.
-
-    Attributes
-    ----------
-    description : str
-        Description of Noise2Noise.
-    """
-
-    description: str = "Noise2Noise"  # TODO
-
-
-class CAREDescription(AlgorithmDescription):
-    """Description of CARE.
-
-    Attributes
-    ----------
-    description : str
-        Description of CARE.
-    """
-
-    description: str = "CARE"  # TODO

careamics/config/references/references.py

@@ -1,39 +0,0 @@
-"""References for the CAREamics algorithms."""
-
-from bioimageio.spec.generic.v0_3 import CiteEntry
-
-N2VRef = CiteEntry(
-    text='Krull, A., Buchholz, T.O. and Jug, F., 2019. "Noise2Void - Learning '
-    'denoising from single noisy images". In Proceedings of the IEEE/CVF '
-    "conference on computer vision and pattern recognition (pp. 2129-2137).",
-    doi="10.1109/cvpr.2019.00223",
-)
-
-N2V2Ref = CiteEntry(
-    text="Höck, E., Buchholz, T.O., Brachmann, A., Jug, F. and Freytag, A., "
-    '2022. "N2V2 - Fixing Noise2Void checkerboard artifacts with modified '
-    'sampling strategies and a tweaked network architecture". In European '
-    "Conference on Computer Vision (pp. 503-518).",
-    doi="10.1007/978-3-031-25069-9_33",
-)
-
-StructN2VRef = CiteEntry(
-    text="Broaddus, C., Krull, A., Weigert, M., Schmidt, U. and Myers, G., 2020."
-    '"Removing structured noise with self-supervised blind-spot '
-    'networks". In 2020 IEEE 17th International Symposium on Biomedical '
-    "Imaging (ISBI) (pp. 159-163).",
-    doi="10.1109/isbi45749.2020.9098336",
-)
-
-N2NRef = CiteEntry(
-    text="Lehtinen, J., Munkberg, J., Hasselgren, J., Laine, S., Karras, T., "
-    'Aittala, M. and Aila, T., 2018. "Noise2Noise: Learning image restoration '
-    'without clean data". arXiv preprint arXiv:1803.04189.',
-    doi="10.48550/arXiv.1803.04189",
-)
-
-CARERef = CiteEntry(
-    text='Weigert, Martin, et al. "Content-aware image restoration: pushing the '
-    'limits of fluorescence microscopy." Nature methods 15.12 (2018): 1090-1097.',
-    doi="10.1038/s41592-018-0216-7",
-)

careamics/config/transformations/transform_union.py

@@ -1,20 +0,0 @@
-"""Type used to represent all transformations users can create."""
-
-from typing import Union
-
-from pydantic import Discriminator
-from typing_extensions import Annotated
-
-from .n2v_manipulate_model import N2VManipulateModel
-from .xy_flip_model import XYFlipModel
-from .xy_random_rotate90_model import XYRandomRotate90Model
-
-TRANSFORMS_UNION = Annotated[
-    Union[
-        XYFlipModel,
-        XYRandomRotate90Model,
-        N2VManipulateModel,
-    ],
-    Discriminator("name"),  # used to tell the different transform models apart
-]
-"""Available transforms in CAREamics."""