careamics 0.0.19__py3-none-any.whl

careamics/config/__init__.py

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+"""CAREamics Pydantic configurations."""
+
+__all__ = [
+    "CAREAlgorithm",
+    "CheckpointConfig",
+    "Configuration",
+    "DataConfig",
+    "GaussianMixtureNMConfig",
+    "HDNAlgorithm",
+    "InferenceConfig",
+    "LVAEConfig",
+    "LVAELossConfig",
+    "MicroSplitAlgorithm",
+    "MultiChannelNMConfig",
+    "N2NAlgorithm",
+    "N2VAlgorithm",
+    "NGDataConfig",
+    "PN2VAlgorithm",
+    "TrainingConfig",
+    "UNetBasedAlgorithm",
+    "UNetConfig",
+    "VAEBasedAlgorithm",
+    "algorithm_factory",
+    "create_care_configuration",
+    "create_hdn_configuration",
+    "create_microsplit_configuration",
+    "create_n2n_configuration",
+    "create_n2v_configuration",
+    "create_ng_data_configuration",
+    "create_pn2v_configuration",
+    "load_configuration",
+    "save_configuration",
+]
+
+from .algorithms import (
+    CAREAlgorithm,
+    HDNAlgorithm,
+    MicroSplitAlgorithm,
+    N2NAlgorithm,
+    N2VAlgorithm,
+    PN2VAlgorithm,
+    UNetBasedAlgorithm,
+    VAEBasedAlgorithm,
+)
+from .architectures import LVAEConfig, UNetConfig
+from .configuration import Configuration
+from .configuration_factories import (
+    algorithm_factory,
+    create_care_configuration,
+    create_hdn_configuration,
+    create_microsplit_configuration,
+    create_n2n_configuration,
+    create_n2v_configuration,
+    create_pn2v_configuration,
+)
+from .data import DataConfig, NGDataConfig
+from .data.inference_config import InferenceConfig
+from .lightning.callbacks import CheckpointConfig
+from .lightning.training_config import TrainingConfig
+from .losses.loss_config import LVAELossConfig
+from .ng_factories.data_factory import create_ng_data_configuration
+from .noise_model import (
+    GaussianMixtureNMConfig,
+    MultiChannelNMConfig,
+)
+from .utils.configuration_io import load_configuration, save_configuration

careamics/config/algorithms/__init__.py

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+"""Algorithm configurations."""
+
+__all__ = [
+    "CAREAlgorithm",
+    "HDNAlgorithm",
+    "MicroSplitAlgorithm",
+    "N2NAlgorithm",
+    "N2VAlgorithm",
+    "PN2VAlgorithm",
+    "UNetBasedAlgorithm",
+    "VAEBasedAlgorithm",
+]
+
+from .care_algorithm_config import CAREAlgorithm
+from .hdn_algorithm_config import HDNAlgorithm
+from .microsplit_algorithm_config import MicroSplitAlgorithm
+from .n2n_algorithm_config import N2NAlgorithm
+from .n2v_algorithm_config import N2VAlgorithm
+from .pn2v_algorithm_config import PN2VAlgorithm
+from .unet_algorithm_config import UNetBasedAlgorithm
+from .vae_algorithm_config import VAEBasedAlgorithm

careamics/config/algorithms/care_algorithm_config.py

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+"""CARE algorithm configuration."""
+
+from typing import Annotated, Literal
+
+from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import AfterValidator
+
+from careamics.config.architectures import UNetConfig
+from careamics.config.validators import (
+    model_without_final_activation,
+    model_without_n2v2,
+)
+
+from .unet_algorithm_config import UNetBasedAlgorithm
+
+CARE = "CARE"
+
+CARE_DESCRIPTION = (
+    "Content-aware image restoration (CARE) is a deep-learning-based "
+    "algorithm that uses a U-Net architecture to restore images. CARE "
+    "is a supervised algorithm that requires pairs of noisy and "
+    "clean images to train the network. The algorithm learns to "
+    "predict the clean image from the noisy image. CARE is "
+    "particularly useful for denoising images acquired in low-light "
+    "conditions, such as fluorescence microscopy images."
+)
+CARE_REF = 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",
+)
+
+
+class CAREAlgorithm(UNetBasedAlgorithm):
+    """CARE algorithm configuration.
+
+    Attributes
+    ----------
+    algorithm : "care"
+        CARE Algorithm name.
+    loss : {"mae", "mse"}
+        CARE-compatible loss function.
+    """
+
+    algorithm: Literal["care"] = "care"
+    """CARE Algorithm name."""
+
+    loss: Literal["mae", "mse"] = "mae"
+    """CARE-compatible loss function."""
+
+    model: Annotated[
+        UNetConfig,
+        AfterValidator(model_without_n2v2),
+        AfterValidator(model_without_final_activation),
+    ]
+    """UNet without a final activation function and without the `n2v2` modifications."""
+
+    def get_algorithm_friendly_name(self) -> str:
+        """
+        Get the algorithm friendly name.
+
+        Returns
+        -------
+        str
+            Friendly name of the algorithm.
+        """
+        return CARE
+
+    def get_algorithm_keywords(self) -> list[str]:
+        """
+        Get algorithm keywords.
+
+        Returns
+        -------
+        list[str]
+            List of keywords.
+        """
+        return [
+            "restoration",
+            "UNet",
+            "3D" if self.model.is_3D() else "2D",
+            "CAREamics",
+            "pytorch",
+            CARE,
+        ]
+
+    def get_algorithm_references(self) -> str:
+        """
+        Get the algorithm references.
+
+        This is used to generate the README of the BioImage Model Zoo export.
+
+        Returns
+        -------
+        str
+            Algorithm references.
+        """
+        return CARE_REF.text + " doi: " + CARE_REF.doi
+
+    def get_algorithm_citations(self) -> list[CiteEntry]:
+        """
+        Return a list of citation entries of the current algorithm.
+
+        This is used to generate the model description for the BioImage Model Zoo.
+
+        Returns
+        -------
+        List[CiteEntry]
+            List of citation entries.
+        """
+        return [CARE_REF]
+
+    def get_algorithm_description(self) -> str:
+        """
+        Get the algorithm description.
+
+        Returns
+        -------
+        str
+            Algorithm description.
+        """
+        return CARE_DESCRIPTION

careamics/config/algorithms/hdn_algorithm_config.py

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+"""HDN algorithm configuration."""
+
+from typing import Literal
+
+from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import ConfigDict
+
+from careamics.config.algorithms.vae_algorithm_config import VAEBasedAlgorithm
+from careamics.config.architectures import LVAEConfig
+from careamics.config.losses.loss_config import LVAELossConfig
+
+HDN = "Hierarchical DivNoising"
+
+HDN_DESCRIPTION = (
+    "HDN leverages a hierarchical VAE to perform image "
+    "restoration. It is designed to be interpretable and unsupervised, "
+    "making it suitable for a wide range of microscopy images."
+)
+HDN_REF = CiteEntry(
+    text='Prakash, M., Delbracio, M., Milanfar, P., Jug, F. 2022. "Interpretable '
+    'Unsupervised Diversity Denoising and Artefact Removal." The International '
+    "Conference on Learning Representations (ICLR).",
+    doi="10.1561/2200000056",
+)
+
+
+class HDNAlgorithm(VAEBasedAlgorithm):
+    """HDN algorithm configuration."""
+
+    model_config = ConfigDict(validate_assignment=True)
+
+    algorithm: Literal["hdn"] = "hdn"
+
+    loss: LVAELossConfig
+
+    model: LVAEConfig  # TODO add validators
+
+    is_supervised: bool = False
+
+    def get_algorithm_friendly_name(self) -> str:
+        """
+        Get the algorithm friendly name.
+
+        Returns
+        -------
+        str
+            Friendly name of the algorithm.
+        """
+        return HDN
+
+    def get_algorithm_keywords(self) -> list[str]:
+        """
+        Get algorithm keywords.
+
+        Returns
+        -------
+        list[str]
+            List of keywords.
+        """
+        return [
+            "restoration",
+            "VAE",
+            "3D" if self.model.is_3D() else "2D",
+            "CAREamics",
+            "pytorch",
+        ]
+
+    def get_algorithm_references(self) -> str:
+        """
+        Get the algorithm references.
+
+        This is used to generate the README of the BioImage Model Zoo export.
+
+        Returns
+        -------
+        str
+            Algorithm references.
+        """
+        return HDN_REF.text + " doi: " + HDN_REF.doi
+
+    def get_algorithm_citations(self) -> list[CiteEntry]:
+        """
+        Return a list of citation entries of the current algorithm.
+
+        This is used to generate the model description for the BioImage Model Zoo.
+
+        Returns
+        -------
+        List[CiteEntry]
+            List of citation entries.
+        """
+        return [HDN_REF]
+
+    def get_algorithm_description(self) -> str:
+        """
+        Get the algorithm description.
+
+        Returns
+        -------
+        str
+            Algorithm description.
+        """
+        return HDN_DESCRIPTION

careamics/config/algorithms/microsplit_algorithm_config.py

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+"""MicroSplit algorithm configuration."""
+
+from typing import Literal
+
+from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import ConfigDict
+
+from careamics.config.algorithms.vae_algorithm_config import VAEBasedAlgorithm
+from careamics.config.architectures import LVAEConfig
+from careamics.config.losses.loss_config import LVAELossConfig
+
+MICROSPLIT = "MicroSplit"
+
+MICROSPLIT_DESCRIPTION = """MicroSplit is a self-supervised deep learning method for
+microscopy image splitting that combines the strengths of both denoising and
+representation learning approaches."""
+
+MICROSPLIT_REF = CiteEntry(
+    text='Prakash, M., Delbracio, M., Milanfar, P., Jug, F. 2022. "Interpretable '
+    'Unsupervised Diversity Denoising and Artefact Removal." The International '
+    "Conference on Learning Representations (ICLR).",
+    doi="10.1561/2200000056",
+)
+
+
+class MicroSplitAlgorithm(VAEBasedAlgorithm):
+    """MicroSplit algorithm configuration."""
+
+    model_config = ConfigDict(validate_assignment=True)
+
+    algorithm: Literal["microsplit"] = "microsplit"
+
+    loss: LVAELossConfig
+
+    model: LVAEConfig  # TODO add validators
+
+    is_supervised: bool = True
+
+    def get_algorithm_friendly_name(self) -> str:
+        """
+        Get the algorithm friendly name.
+
+        Returns
+        -------
+        str
+            Friendly name of the algorithm.
+        """
+        return MICROSPLIT
+
+    def get_algorithm_keywords(self) -> list[str]:
+        """
+        Get algorithm keywords.
+
+        Returns
+        -------
+        list[str]
+            List of keywords.
+        """
+        return [
+            "restoration",
+            "VAE",
+            "self-supervised",
+            "3D" if self.model.is_3D() else "2D",
+            "CAREamics",
+            "pytorch",
+        ]
+
+    def get_algorithm_references(self) -> str:
+        """
+        Get the algorithm references.
+
+        This is used to generate the README of the BioImage Model Zoo export.
+
+        Returns
+        -------
+        str
+            Algorithm references.
+        """
+        return MICROSPLIT_REF.text + " doi: " + MICROSPLIT_REF.doi
+
+    def get_algorithm_citations(self) -> list[CiteEntry]:
+        """
+        Return a list of citation entries of the current algorithm.
+
+        This is used to generate the model description for the BioImage Model Zoo.
+
+        Returns
+        -------
+        List[CiteEntry]
+            List of citation entries.
+        """
+        return [MICROSPLIT_REF]
+
+    def get_algorithm_description(self) -> str:
+        """
+        Get the algorithm description.
+
+        Returns
+        -------
+        str
+            Algorithm description.
+        """
+        return MICROSPLIT_DESCRIPTION

careamics/config/algorithms/n2n_algorithm_config.py

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+"""N2N Algorithm configuration."""
+
+from typing import Annotated, Literal
+
+from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import AfterValidator
+
+from careamics.config.architectures import UNetConfig
+from careamics.config.validators import (
+    model_without_final_activation,
+    model_without_n2v2,
+)
+
+from .unet_algorithm_config import UNetBasedAlgorithm
+
+N2N = "Noise2Noise"
+
+N2N_DESCRIPTION = (
+    "Noise2Noise is a deep-learning-based algorithm that uses a U-Net "
+    "architecture to restore images. Noise2Noise is a self-supervised "
+    "algorithm that requires only noisy images to train the network. "
+    "The algorithm learns to predict the clean image from the noisy "
+    "image. Noise2Noise is particularly useful when clean images are "
+    "not available for training."
+)
+
+N2N_REF = 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",
+)
+
+
+class N2NAlgorithm(UNetBasedAlgorithm):
+    """Noise2Noise Algorithm configuration."""
+
+    algorithm: Literal["n2n"] = "n2n"
+    """N2N Algorithm name."""
+
+    loss: Literal["mae", "mse"] = "mae"
+    """N2N-compatible loss function."""
+
+    model: Annotated[
+        UNetConfig,
+        AfterValidator(model_without_n2v2),
+        AfterValidator(model_without_final_activation),
+    ]
+    """UNet without a final activation function and without the `n2v2` modifications."""
+
+    def get_algorithm_friendly_name(self) -> str:
+        """
+        Get the algorithm friendly name.
+
+        Returns
+        -------
+        str
+            Friendly name of the algorithm.
+        """
+        return N2N
+
+    def get_algorithm_keywords(self) -> list[str]:
+        """
+        Get algorithm keywords.
+
+        Returns
+        -------
+        list[str]
+            List of keywords.
+        """
+        return [
+            "restoration",
+            "UNet",
+            "3D" if self.model.is_3D() else "2D",
+            "CAREamics",
+            "pytorch",
+            N2N,
+        ]
+
+    def get_algorithm_references(self) -> str:
+        """
+        Get the algorithm references.
+
+        This is used to generate the README of the BioImage Model Zoo export.
+
+        Returns
+        -------
+        str
+            Algorithm references.
+        """
+        return N2N_REF.text + " doi: " + N2N_REF.doi
+
+    def get_algorithm_citations(self) -> list[CiteEntry]:
+        """
+        Return a list of citation entries of the current algorithm.
+
+        This is used to generate the model description for the BioImage Model Zoo.
+
+        Returns
+        -------
+        List[CiteEntry]
+            List of citation entries.
+        """
+        return [N2N_REF]
+
+    def get_algorithm_description(self) -> str:
+        """
+        Get the algorithm description.
+
+        Returns
+        -------
+        str
+            Algorithm description.
+        """
+        return N2N_DESCRIPTION