careamics 0.0.1__py3-none-any.whl → 0.0.3__py3-none-any.whl

careamics/config/configuration_model.py

@@ -0,0 +1,604 @@
+"""Pydantic CAREamics configuration."""
+
+from __future__ import annotations
+
+import re
+from pathlib import Path
+from pprint import pformat
+from typing import Literal, Union
+
+import yaml
+from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
+from typing_extensions import Self
+
+from .data_model import DataConfig
+from .fcn_algorithm_model import FCNAlgorithmConfig
+from .references import (
+    CARE,
+    CUSTOM,
+    N2N,
+    N2V,
+    N2V2,
+    STRUCT_N2V,
+    STRUCT_N2V2,
+    CAREDescription,
+    CARERef,
+    N2NDescription,
+    N2NRef,
+    N2V2Description,
+    N2V2Ref,
+    N2VDescription,
+    N2VRef,
+    StructN2V2Description,
+    StructN2VDescription,
+    StructN2VRef,
+)
+from .support import SupportedAlgorithm, SupportedPixelManipulation, SupportedTransform
+from .training_model import TrainingConfig
+from .transformations.n2v_manipulate_model import (
+    N2VManipulateModel,
+)
+from .vae_algorithm_model import VAEAlgorithmConfig
+
+
+class Configuration(BaseModel):
+    """
+    CAREamics configuration.
+
+    The configuration defines all parameters used to build and train a CAREamics model.
+    These parameters are validated to ensure that they are compatible with each other.
+
+    It contains three sub-configurations:
+
+    - AlgorithmModel: configuration for the algorithm training, which includes the
+        architecture, loss function, optimizer, and other hyperparameters.
+    - DataModel: configuration for the dataloader, which includes the type of data,
+        transformations, mean/std and other parameters.
+    - TrainingModel: configuration for the training, which includes the number of
+        epochs or the callbacks.
+
+    Attributes
+    ----------
+    experiment_name : str
+        Name of the experiment, used when saving logs and checkpoints.
+    algorithm : AlgorithmModel
+        Algorithm configuration.
+    data : DataModel
+        Data configuration.
+    training : TrainingModel
+        Training configuration.
+
+    Methods
+    -------
+    set_3D(is_3D: bool, axes: str, patch_size: List[int]) -> None
+        Switch configuration between 2D and 3D.
+    set_N2V2(use_n2v2: bool) -> None
+        Switch N2V algorithm between N2V and N2V2.
+    set_structN2V(
+        mask_axis: Literal["horizontal", "vertical", "none"], mask_span: int) -> None
+        Set StructN2V parameters.
+    model_dump(
+        exclude_defaults: bool = False, exclude_none: bool = True, **kwargs: Dict
+        ) -> Dict
+        Export configuration to a dictionary.
+
+    Raises
+    ------
+    ValueError
+        Configuration parameter type validation errors.
+    ValueError
+        If the experiment name contains invalid characters or is empty.
+    ValueError
+        If the algorithm is 3D but there is not "Z" in the data axes, or 2D algorithm
+        with "Z" in data axes.
+    ValueError
+        Algorithm, data or training validation errors.
+
+    Notes
+    -----
+    We provide convenience methods to create standards configurations, for instance
+    for N2V, in the `careamics.config.configuration_factory` module.
+    >>> from careamics.config.configuration_factory import create_n2v_configuration
+    >>> config = create_n2v_configuration(
+    ...     experiment_name="n2v_experiment",
+    ...     data_type="array",
+    ...     axes="YX",
+    ...     patch_size=[64, 64],
+    ...     batch_size=32,
+    ...     num_epochs=100
+    ... )
+
+    The configuration can be exported to a dictionary using the model_dump method:
+    >>> config_dict = config.model_dump()
+
+    Configurations can also be exported or imported from yaml files:
+    >>> from careamics.config import save_configuration, load_configuration
+    >>> path_to_config = save_configuration(config, my_path / "config.yml")
+    >>> other_config = load_configuration(path_to_config)
+
+    Examples
+    --------
+    Minimum example:
+    >>> from careamics.config import Configuration
+    >>> config_dict = {
+    ...         "experiment_name": "N2V_experiment",
+    ...         "algorithm_config": {
+    ...             "algorithm_type": "fcn",
+    ...             "algorithm": "n2v",
+    ...             "loss": "n2v",
+    ...             "model": {
+    ...                 "architecture": "UNet",
+    ...             },
+    ...         },
+    ...         "training_config": {
+    ...             "num_epochs": 200,
+    ...         },
+    ...         "data_config": {
+    ...             "data_type": "tiff",
+    ...             "patch_size": [64, 64],
+    ...             "axes": "SYX",
+    ...         },
+    ...     }
+    >>> config = Configuration(**config_dict)
+    """
+
+    model_config = ConfigDict(
+        validate_assignment=True,
+        set_arbitrary_types_allowed=True,
+    )
+
+    # version
+    version: Literal["0.1.0"] = "0.1.0"
+    """CAREamics configuration version."""
+
+    # required parameters
+    experiment_name: str
+    """Name of the experiment, used to name logs and checkpoints."""
+
+    # Sub-configurations
+    algorithm_config: Union[FCNAlgorithmConfig, VAEAlgorithmConfig] = Field(
+        discriminator="algorithm_type"
+    )
+    """Algorithm configuration, holding all parameters required to configure the
+    model."""
+
+    data_config: DataConfig
+    """Data configuration, holding all parameters required to configure the training
+    data loader."""
+
+    training_config: TrainingConfig
+    """Training configuration, holding all parameters required to configure the
+    training process."""
+
+    @field_validator("experiment_name")
+    @classmethod
+    def no_symbol(cls, name: str) -> str:
+        """
+        Validate experiment name.
+
+        A valid experiment name is a non-empty string with only contains letters,
+        numbers, underscores, dashes and spaces.
+
+        Parameters
+        ----------
+        name : str
+            Name to validate.
+
+        Returns
+        -------
+        str
+            Validated name.
+
+        Raises
+        ------
+        ValueError
+            If the name is empty or contains invalid characters.
+        """
+        if len(name) == 0 or name.isspace():
+            raise ValueError("Experiment name is empty.")
+
+        # Validate using a regex that it contains only letters, numbers, underscores,
+        # dashes and spaces
+        if not re.match(r"^[a-zA-Z0-9_\- ]*$", name):
+            raise ValueError(
+                f"Experiment name contains invalid characters (got {name}). "
+                f"Only letters, numbers, underscores, dashes and spaces are allowed."
+            )
+
+        return name
+
+    @model_validator(mode="after")
+    def validate_3D(self: Self) -> Self:
+        """
+        Change algorithm dimensions to match data.axes.
+
+        Only for non-custom algorithms.
+
+        Returns
+        -------
+        Self
+            Validated configuration.
+        """
+        if self.algorithm_config.algorithm != SupportedAlgorithm.CUSTOM:
+            if "Z" in self.data_config.axes and not self.algorithm_config.model.is_3D():
+                # change algorithm to 3D
+                self.algorithm_config.model.set_3D(True)
+            elif (
+                "Z" not in self.data_config.axes and self.algorithm_config.model.is_3D()
+            ):
+                # change algorithm to 2D
+                self.algorithm_config.model.set_3D(False)
+
+        return self
+
+    @model_validator(mode="after")
+    def validate_algorithm_and_data(self: Self) -> Self:
+        """
+        Validate algorithm and data compatibility.
+
+        In particular, the validation does the following:
+
+        - If N2V is used, it enforces the presence of N2V_Maniuplate in the transforms
+        - If N2V2 is used, it enforces the correct manipulation strategy
+
+        Returns
+        -------
+        Self
+            Validated configuration.
+        """
+        if self.algorithm_config.algorithm == SupportedAlgorithm.N2V:
+            # missing N2V_MANIPULATE
+            if not self.data_config.has_n2v_manipulate():
+                self.data_config.transforms.append(
+                    N2VManipulateModel(
+                        name=SupportedTransform.N2V_MANIPULATE.value,
+                    )
+                )
+
+            median = SupportedPixelManipulation.MEDIAN.value
+            uniform = SupportedPixelManipulation.UNIFORM.value
+            strategy = median if self.algorithm_config.model.n2v2 else uniform
+            self.data_config.set_N2V2_strategy(strategy)
+        else:
+            # remove N2V manipulate if present
+            if self.data_config.has_n2v_manipulate():
+                self.data_config.remove_n2v_manipulate()
+
+        return self
+
+    def __str__(self) -> str:
+        """
+        Pretty string reprensenting the configuration.
+
+        Returns
+        -------
+        str
+            Pretty string.
+        """
+        return pformat(self.model_dump())
+
+    def set_3D(self, is_3D: bool, axes: str, patch_size: list[int]) -> None:
+        """
+        Set 3D flag and axes.
+
+        Parameters
+        ----------
+        is_3D : bool
+            Whether the algorithm is 3D or not.
+        axes : str
+            Axes of the data.
+        patch_size : list[int]
+            Patch size.
+        """
+        # set the flag and axes (this will not trigger validation at the config level)
+        self.algorithm_config.model.set_3D(is_3D)
+        self.data_config.set_3D(axes, patch_size)
+
+        # cheap hack: trigger validation
+        self.algorithm_config = self.algorithm_config
+
+    def set_N2V2(self, use_n2v2: bool) -> None:
+        """
+        Switch N2V algorithm between N2V and N2V2.
+
+        Parameters
+        ----------
+        use_n2v2 : bool
+            Whether to use N2V2 or not.
+
+        Raises
+        ------
+        ValueError
+            If the algorithm is not N2V.
+        """
+        if self.algorithm_config.algorithm == SupportedAlgorithm.N2V:
+            self.algorithm_config.model.n2v2 = use_n2v2
+            strategy = (
+                SupportedPixelManipulation.MEDIAN.value
+                if use_n2v2
+                else SupportedPixelManipulation.UNIFORM.value
+            )
+            self.data_config.set_N2V2_strategy(strategy)
+        else:
+            raise ValueError("N2V2 can only be set for N2V algorithm.")
+
+    def set_structN2V(
+        self, mask_axis: Literal["horizontal", "vertical", "none"], mask_span: int
+    ) -> None:
+        """
+        Set StructN2V parameters.
+
+        Parameters
+        ----------
+        mask_axis : Literal["horizontal", "vertical", "none"]
+            Axis of the structural mask.
+        mask_span : int
+            Span of the structural mask.
+        """
+        self.data_config.set_structN2V_mask(mask_axis, mask_span)
+
+    def get_algorithm_flavour(self) -> str:
+        """
+        Get the algorithm name.
+
+        Returns
+        -------
+        str
+            Algorithm name.
+        """
+        if self.algorithm_config.algorithm == SupportedAlgorithm.N2V:
+            use_n2v2 = self.algorithm_config.model.n2v2
+            use_structN2V = self.data_config.transforms[-1].struct_mask_axis != "none"
+
+            # return the n2v flavour
+            if use_n2v2 and use_structN2V:
+                return STRUCT_N2V2
+            elif use_n2v2:
+                return N2V2
+            elif use_structN2V:
+                return STRUCT_N2V
+            else:
+                return N2V
+        elif self.algorithm_config.algorithm == SupportedAlgorithm.N2N:
+            return N2N
+        elif self.algorithm_config.algorithm == SupportedAlgorithm.CARE:
+            return CARE
+        else:
+            return CUSTOM
+
+    def get_algorithm_description(self) -> str:
+        """
+        Return a description of the algorithm.
+
+        This method is used to generate the README of the BioImage Model Zoo export.
+
+        Returns
+        -------
+        str
+            Description of the algorithm.
+        """
+        algorithm_flavour = self.get_algorithm_flavour()
+
+        if algorithm_flavour == CUSTOM:
+            return f"Custom algorithm, named {self.algorithm_config.model.name}"
+        else:  # currently only N2V flavours
+            if algorithm_flavour == N2V:
+                return N2VDescription().description
+            elif algorithm_flavour == N2V2:
+                return N2V2Description().description
+            elif algorithm_flavour == STRUCT_N2V:
+                return StructN2VDescription().description
+            elif algorithm_flavour == STRUCT_N2V2:
+                return StructN2V2Description().description
+            elif algorithm_flavour == N2N:
+                return N2NDescription().description
+            elif algorithm_flavour == CARE:
+                return CAREDescription().description
+
+        return ""
+
+    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.
+        """
+        if self.algorithm_config.algorithm == SupportedAlgorithm.N2V:
+            use_n2v2 = self.algorithm_config.model.n2v2
+            use_structN2V = self.data_config.transforms[-1].struct_mask_axis != "none"
+
+            # return the (struct)N2V(2) references
+            if use_n2v2 and use_structN2V:
+                return [N2VRef, N2V2Ref, StructN2VRef]
+            elif use_n2v2:
+                return [N2VRef, N2V2Ref]
+            elif use_structN2V:
+                return [N2VRef, StructN2VRef]
+            else:
+                return [N2VRef]
+        elif self.algorithm_config.algorithm == SupportedAlgorithm.N2N:
+            return [N2NRef]
+        elif self.algorithm_config.algorithm == SupportedAlgorithm.CARE:
+            return [CARERef]
+
+        raise ValueError("Citation not available for custom algorithm.")
+
+    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.
+        """
+        if self.algorithm_config.algorithm == SupportedAlgorithm.N2V:
+            use_n2v2 = self.algorithm_config.model.n2v2
+            use_structN2V = self.data_config.transforms[-1].struct_mask_axis != "none"
+
+            references = [
+                N2VRef.text + " doi: " + N2VRef.doi,
+                N2V2Ref.text + " doi: " + N2V2Ref.doi,
+                StructN2VRef.text + " doi: " + StructN2VRef.doi,
+            ]
+
+            # return the (struct)N2V(2) references
+            if use_n2v2 and use_structN2V:
+                return "".join(references)
+            elif use_n2v2:
+                references.pop(-1)
+                return "".join(references)
+            elif use_structN2V:
+                references.pop(-2)
+                return "".join(references)
+            else:
+                return references[0]
+
+        return ""
+
+    def get_algorithm_keywords(self) -> list[str]:
+        """
+        Get algorithm keywords.
+
+        Returns
+        -------
+        list[str]
+            List of keywords.
+        """
+        if self.algorithm_config.algorithm == SupportedAlgorithm.N2V:
+            use_n2v2 = self.algorithm_config.model.n2v2
+            use_structN2V = self.data_config.transforms[-1].struct_mask_axis != "none"
+
+            keywords = [
+                "denoising",
+                "restoration",
+                "UNet",
+                "3D" if "Z" in self.data_config.axes else "2D",
+                "CAREamics",
+                "pytorch",
+                N2V,
+            ]
+
+            if use_n2v2:
+                keywords.append(N2V2)
+            if use_structN2V:
+                keywords.append(STRUCT_N2V)
+        else:
+            keywords = ["CAREamics"]
+
+        return keywords
+
+    def model_dump(
+        self,
+        exclude_defaults: bool = False,
+        exclude_none: bool = True,
+        **kwargs: dict,
+    ) -> dict:
+        """
+        Override model_dump method in order to set default values.
+
+        Parameters
+        ----------
+        exclude_defaults : bool, optional
+            Whether to exclude fields with default values or not, by default
+            True.
+        exclude_none : bool, optional
+            Whether to exclude fields with None values or not, by default True.
+        **kwargs : dict
+            Keyword arguments.
+
+        Returns
+        -------
+        dict
+            Dictionary containing the model parameters.
+        """
+        dictionary = super().model_dump(
+            exclude_none=exclude_none, exclude_defaults=exclude_defaults, **kwargs
+        )
+
+        return dictionary
+
+
+def load_configuration(path: Union[str, Path]) -> Configuration:
+    """
+    Load configuration from a yaml file.
+
+    Parameters
+    ----------
+    path : str or Path
+        Path to the configuration.
+
+    Returns
+    -------
+    Configuration
+        Configuration.
+
+    Raises
+    ------
+    FileNotFoundError
+        If the configuration file does not exist.
+    """
+    # load dictionary from yaml
+    if not Path(path).exists():
+        raise FileNotFoundError(
+            f"Configuration file {path} does not exist in " f" {Path.cwd()!s}"
+        )
+
+    dictionary = yaml.load(Path(path).open("r"), Loader=yaml.SafeLoader)
+
+    return Configuration(**dictionary)
+
+
+def save_configuration(config: Configuration, path: Union[str, Path]) -> Path:
+    """
+    Save configuration to path.
+
+    Parameters
+    ----------
+    config : Configuration
+        Configuration to save.
+    path : str or Path
+        Path to a existing folder in which to save the configuration or to an existing
+        configuration file.
+
+    Returns
+    -------
+    Path
+        Path object representing the configuration.
+
+    Raises
+    ------
+    ValueError
+        If the path does not point to an existing directory or .yml file.
+    """
+    # make sure path is a Path object
+    config_path = Path(path)
+
+    # check if path is pointing to an existing directory or .yml file
+    if config_path.exists():
+        if config_path.is_dir():
+            config_path = Path(config_path, "config.yml")
+        elif config_path.suffix != ".yml" and config_path.suffix != ".yaml":
+            raise ValueError(
+                f"Path must be a directory or .yml or .yaml file (got {config_path})."
+            )
+    else:
+        if config_path.suffix != ".yml" and config_path.suffix != ".yaml":
+            raise ValueError(
+                f"Path must be a directory or .yml or .yaml file (got {config_path})."
+            )
+
+    # save configuration as dictionary to yaml
+    with open(config_path, "w") as f:
+        # dump configuration
+        yaml.dump(config.model_dump(), f, default_flow_style=False, sort_keys=False)
+
+    return config_path