configuration_factories

def algorithm_factory(
    algorithm: dict[str, Any]
) -> Union[N2VAlgorithm, N2NAlgorithm, CAREAlgorithm]:
    """
    Create an algorithm model for training CAREamics.

    Parameters
    ----------
    algorithm : dict
        Algorithm dictionary.

    Returns
    -------
    N2VAlgorithm or N2NAlgorithm or CAREAlgorithm
        Algorithm model for training CAREamics.
    """
    adapter: TypeAdapter = TypeAdapter(
        Annotated[
            Union[N2VAlgorithm, N2NAlgorithm, CAREAlgorithm],
            Field(discriminator="algorithm"),
        ]
    )
    return adapter.validate_python(algorithm)

def create_care_configuration(
    experiment_name: str,
    data_type: Literal["array", "tiff", "custom"],
    axes: str,
    patch_size: list[int],
    batch_size: int,
    num_epochs: int,
    augmentations: Optional[list[Union[XYFlipModel, XYRandomRotate90Model]]] = None,
    independent_channels: bool = True,
    loss: Literal["mae", "mse"] = "mae",
    n_channels_in: Optional[int] = None,
    n_channels_out: Optional[int] = None,
    logger: Literal["wandb", "tensorboard", "none"] = "none",
    model_params: Optional[dict] = None,
    train_dataloader_params: Optional[dict[str, Any]] = None,
    val_dataloader_params: Optional[dict[str, Any]] = None,
) -> Configuration:
    """
    Create a configuration for training CARE.

    If "Z" is present in `axes`, then `path_size` must be a list of length 3, otherwise
    2.

    If "C" is present in `axes`, then you need to set `n_channels_in` to the number of
    channels. Likewise, if you set the number of channels, then "C" must be present in
    `axes`.

    To set the number of output channels, use the `n_channels_out` parameter. If it is
    not specified, it will be assumed to be equal to `n_channels_in`.

    By default, all channels are trained together. To train all channels independently,
    set `independent_channels` to True.

    By setting `augmentations` to `None`, the default transformations (flip in X and Y,
    rotations by 90 degrees in the XY plane) are applied. Rather than the default
    transforms, a list of transforms can be passed to the `augmentations` parameter. To
    disable the transforms, simply pass an empty list.

    Parameters
    ----------
    experiment_name : str
        Name of the experiment.
    data_type : Literal["array", "tiff", "custom"]
        Type of the data.
    axes : str
        Axes of the data (e.g. SYX).
    patch_size : List[int]
        Size of the patches along the spatial dimensions (e.g. [64, 64]).
    batch_size : int
        Batch size.
    num_epochs : int
        Number of epochs.
    augmentations : list of transforms, default=None
        List of transforms to apply, either both or one of XYFlipModel and
        XYRandomRotate90Model. By default, it applies both XYFlip (on X and Y)
        and XYRandomRotate90 (in XY) to the images.
    independent_channels : bool, optional
        Whether to train all channels independently, by default False.
    loss : Literal["mae", "mse"], default="mae"
        Loss function to use.
    n_channels_in : int or None, default=None
        Number of channels in.
    n_channels_out : int or None, default=None
        Number of channels out.
    logger : Literal["wandb", "tensorboard", "none"], default="none"
        Logger to use.
    model_params : dict, default=None
        UNetModel parameters.
    train_dataloader_params : dict, optional
        Parameters for the training dataloader, see the PyTorch docs for `DataLoader`.
        If left as `None`, the dict `{"shuffle": True}` will be used, this is set in
        the `GeneralDataConfig`.
    val_dataloader_params : dict, optional
        Parameters for the validation dataloader, see PyTorch the docs for `DataLoader`.
        If left as `None`, the empty dict `{}` will be used, this is set in the
        `GeneralDataConfig`.

    Returns
    -------
    Configuration
        Configuration for training CARE.

    Examples
    --------
    Minimum example:
    >>> config = create_care_configuration(
    ...     experiment_name="care_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100
    ... )

    To disable transforms, simply set `augmentations` to an empty list:
    >>> config = create_care_configuration(
    ...     experiment_name="care_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     augmentations=[]
    ... )

    A list of transforms can be passed to the `augmentations` parameter to replace the
    default augmentations:
    >>> from careamics.config.transformations import XYFlipModel
    >>> config = create_care_configuration(
    ...     experiment_name="care_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     augmentations=[
    ...         # No rotation and only Y flipping
    ...         XYFlipModel(flip_x = False, flip_y = True)
    ...     ]
    ... )

    If you are training multiple channels they will be trained independently by default,
    you simply need to specify the number of channels input (and optionally, the number
    of channels output):
    >>> config = create_care_configuration(
    ...     experiment_name="care_experiment",
    ...     data_type="array",
    ...     axes="YXC", # channels must be in the axes
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     n_channels_in=3, # number of input channels
    ...     n_channels_out=1 # if applicable
    ... )

    If instead you want to train multiple channels together, you need to turn off the
    `independent_channels` parameter:
    >>> config = create_care_configuration(
    ...     experiment_name="care_experiment",
    ...     data_type="array",
    ...     axes="YXC", # channels must be in the axes
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     independent_channels=False,
    ...     n_channels_in=3,
    ...     n_channels_out=1 # if applicable
    ... )
    """
    return Configuration(
        **_create_supervised_config_dict(
            algorithm="care",
            experiment_name=experiment_name,
            data_type=data_type,
            axes=axes,
            patch_size=patch_size,
            batch_size=batch_size,
            num_epochs=num_epochs,
            augmentations=augmentations,
            independent_channels=independent_channels,
            loss=loss,
            n_channels_in=n_channels_in,
            n_channels_out=n_channels_out,
            logger=logger,
            model_params=model_params,
            train_dataloader_params=train_dataloader_params,
            val_dataloader_params=val_dataloader_params,
        )
    )

def create_n2n_configuration(
    experiment_name: str,
    data_type: Literal["array", "tiff", "custom"],
    axes: str,
    patch_size: list[int],
    batch_size: int,
    num_epochs: int,
    augmentations: Optional[list[Union[XYFlipModel, XYRandomRotate90Model]]] = None,
    independent_channels: bool = True,
    loss: Literal["mae", "mse"] = "mae",
    n_channels_in: Optional[int] = None,
    n_channels_out: Optional[int] = None,
    logger: Literal["wandb", "tensorboard", "none"] = "none",
    model_params: Optional[dict] = None,
    train_dataloader_params: Optional[dict[str, Any]] = None,
    val_dataloader_params: Optional[dict[str, Any]] = None,
) -> Configuration:
    """
    Create a configuration for training Noise2Noise.

    If "Z" is present in `axes`, then `path_size` must be a list of length 3, otherwise
    2.

    If "C" is present in `axes`, then you need to set `n_channels_in` to the number of
    channels. Likewise, if you set the number of channels, then "C" must be present in
    `axes`.

    To set the number of output channels, use the `n_channels_out` parameter. If it is
    not specified, it will be assumed to be equal to `n_channels_in`.

    By default, all channels are trained together. To train all channels independently,
    set `independent_channels` to True.

    By setting `augmentations` to `None`, the default transformations (flip in X and Y,
    rotations by 90 degrees in the XY plane) are applied. Rather than the default
    transforms, a list of transforms can be passed to the `augmentations` parameter. To
    disable the transforms, simply pass an empty list.

    Parameters
    ----------
    experiment_name : str
        Name of the experiment.
    data_type : Literal["array", "tiff", "custom"]
        Type of the data.
    axes : str
        Axes of the data (e.g. SYX).
    patch_size : List[int]
        Size of the patches along the spatial dimensions (e.g. [64, 64]).
    batch_size : int
        Batch size.
    num_epochs : int
        Number of epochs.
    augmentations : list of transforms, default=None
        List of transforms to apply, either both or one of XYFlipModel and
        XYRandomRotate90Model. By default, it applies both XYFlip (on X and Y)
        and XYRandomRotate90 (in XY) to the images.
    independent_channels : bool, optional
        Whether to train all channels independently, by default False.
    loss : Literal["mae", "mse"], optional
        Loss function to use, by default "mae".
    n_channels_in : int or None, default=None
        Number of channels in.
    n_channels_out : int or None, default=None
        Number of channels out.
    logger : Literal["wandb", "tensorboard", "none"], optional
        Logger to use, by default "none".
    model_params : dict, optional
        UNetModel parameters, by default {}.
    train_dataloader_params : dict, optional
        Parameters for the training dataloader, see the PyTorch docs for `DataLoader`.
        If left as `None`, the dict `{"shuffle": True}` will be used, this is set in
        the `GeneralDataConfig`.
    val_dataloader_params : dict, optional
        Parameters for the validation dataloader, see PyTorch the docs for `DataLoader`.
        If left as `None`, the empty dict `{}` will be used, this is set in the
        `GeneralDataConfig`.

    Returns
    -------
    Configuration
        Configuration for training Noise2Noise.

    Examples
    --------
    Minimum example:
    >>> config = create_n2n_configuration(
    ...     experiment_name="n2n_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100
    ... )

    To disable transforms, simply set `augmentations` to an empty list:
    >>> config = create_n2n_configuration(
    ...     experiment_name="n2n_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     augmentations=[]
    ... )

    A list of transforms can be passed to the `augmentations` parameter to replace the
    default augmentations:
    >>> from careamics.config.transformations import XYFlipModel
    >>> config = create_n2n_configuration(
    ...     experiment_name="n2n_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     augmentations=[
    ...         # No rotation and only Y flipping
    ...         XYFlipModel(flip_x = False, flip_y = True)
    ...     ]
    ... )

    If you are training multiple channels they will be trained independently by default,
    you simply need to specify the number of channels input (and optionally, the number
    of channels output):
    >>> config = create_n2n_configuration(
    ...     experiment_name="n2n_experiment",
    ...     data_type="array",
    ...     axes="YXC", # channels must be in the axes
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     n_channels_in=3, # number of input channels
    ...     n_channels_out=1 # if applicable
    ... )

    If instead you want to train multiple channels together, you need to turn off the
    `independent_channels` parameter:
    >>> config = create_n2n_configuration(
    ...     experiment_name="n2n_experiment",
    ...     data_type="array",
    ...     axes="YXC", # channels must be in the axes
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     independent_channels=False,
    ...     n_channels_in=3,
    ...     n_channels_out=1 # if applicable
    ... )
    """
    return Configuration(
        **_create_supervised_config_dict(
            algorithm="n2n",
            experiment_name=experiment_name,
            data_type=data_type,
            axes=axes,
            patch_size=patch_size,
            batch_size=batch_size,
            num_epochs=num_epochs,
            augmentations=augmentations,
            independent_channels=independent_channels,
            loss=loss,
            n_channels_in=n_channels_in,
            n_channels_out=n_channels_out,
            logger=logger,
            model_params=model_params,
            train_dataloader_params=train_dataloader_params,
            val_dataloader_params=val_dataloader_params,
        )
    )

def create_n2v_configuration(
    experiment_name: str,
    data_type: Literal["array", "tiff", "custom"],
    axes: str,
    patch_size: list[int],
    batch_size: int,
    num_epochs: int,
    augmentations: Optional[list[Union[XYFlipModel, XYRandomRotate90Model]]] = None,
    independent_channels: bool = True,
    use_n2v2: bool = False,
    n_channels: Optional[int] = None,
    roi_size: int = 11,
    masked_pixel_percentage: float = 0.2,
    struct_n2v_axis: Literal["horizontal", "vertical", "none"] = "none",
    struct_n2v_span: int = 5,
    logger: Literal["wandb", "tensorboard", "none"] = "none",
    model_params: Optional[dict] = None,
    train_dataloader_params: Optional[dict[str, Any]] = None,
    val_dataloader_params: Optional[dict[str, Any]] = None,
) -> Configuration:
    """
    Create a configuration for training Noise2Void.

    N2V uses a UNet model to denoise images in a self-supervised manner. To use its
    variants structN2V and N2V2, set the `struct_n2v_axis` and `struct_n2v_span`
    (structN2V) parameters, or set `use_n2v2` to True (N2V2).

    N2V2 modifies the UNet architecture by adding blur pool layers and removes the skip
    connections, thus removing checkboard artefacts. StructN2V is used when vertical
    or horizontal correlations are present in the noise; it applies an additional mask
    to the manipulated pixel neighbors.

    If "Z" is present in `axes`, then `path_size` must be a list of length 3, otherwise
    2.

    If "C" is present in `axes`, then you need to set `n_channels` to the number of
    channels.

    By default, all channels are trained independently. To train all channels together,
    set `independent_channels` to False.

    By default, the transformations applied are a random flip along X or Y, and a random
    90 degrees rotation in the XY plane. Normalization is always applied, as well as the
    N2V manipulation.

    By setting `augmentations` to `None`, the default transformations (flip in X and Y,
    rotations by 90 degrees in the XY plane) are applied. Rather than the default
    transforms, a list of transforms can be passed to the `augmentations` parameter. To
    disable the transforms, simply pass an empty list.

    The `roi_size` parameter specifies the size of the area around each pixel that will
    be manipulated by N2V. The `masked_pixel_percentage` parameter specifies how many
    pixels per patch will be manipulated.

    The parameters of the UNet can be specified in the `model_params` (passed as a
    parameter-value dictionary). Note that `use_n2v2` and 'n_channels' override the
    corresponding parameters passed in `model_params`.

    If you pass "horizontal" or "vertical" to `struct_n2v_axis`, then structN2V mask
    will be applied to each manipulated pixel.

    Parameters
    ----------
    experiment_name : str
        Name of the experiment.
    data_type : Literal["array", "tiff", "custom"]
        Type of the data.
    axes : str
        Axes of the data (e.g. SYX).
    patch_size : List[int]
        Size of the patches along the spatial dimensions (e.g. [64, 64]).
    batch_size : int
        Batch size.
    num_epochs : int
        Number of epochs.
    augmentations : list of transforms, default=None
        List of transforms to apply, either both or one of XYFlipModel and
        XYRandomRotate90Model. By default, it applies both XYFlip (on X and Y)
        and XYRandomRotate90 (in XY) to the images.
    independent_channels : bool, optional
        Whether to train all channels together, by default True.
    use_n2v2 : bool, optional
        Whether to use N2V2, by default False.
    n_channels : int or None, default=None
        Number of channels (in and out).
    roi_size : int, optional
        N2V pixel manipulation area, by default 11.
    masked_pixel_percentage : float, optional
        Percentage of pixels masked in each patch, by default 0.2.
    struct_n2v_axis : Literal["horizontal", "vertical", "none"], optional
        Axis along which to apply structN2V mask, by default "none".
    struct_n2v_span : int, optional
        Span of the structN2V mask, by default 5.
    logger : Literal["wandb", "tensorboard", "none"], optional
        Logger to use, by default "none".
    model_params : dict, optional
        UNetModel parameters, by default None.
    train_dataloader_params : dict, optional
        Parameters for the training dataloader, see the PyTorch docs for `DataLoader`.
        If left as `None`, the dict `{"shuffle": True}` will be used, this is set in
        the `GeneralDataConfig`.
    val_dataloader_params : dict, optional
        Parameters for the validation dataloader, see PyTorch the docs for `DataLoader`.
        If left as `None`, the empty dict `{}` will be used, this is set in the
        `GeneralDataConfig`.

    Returns
    -------
    Configuration
        Configuration for training N2V.

    Examples
    --------
    Minimum example:
    >>> config = create_n2v_configuration(
    ...     experiment_name="n2v_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100
    ... )

    To disable transforms, simply set `augmentations` to an empty list:
    >>> config = create_n2v_configuration(
    ...     experiment_name="n2v_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     augmentations=[]
    ... )

    A list of transforms can be passed to the `augmentations` parameter:
    >>> from careamics.config.transformations import XYFlipModel
    >>> config = create_n2v_configuration(
    ...     experiment_name="n2v_experiment",
    ...     data_type="array",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     augmentations=[
    ...         # No rotation and only Y flipping
    ...         XYFlipModel(flip_x = False, flip_y = True)
    ...     ]
    ... )

    To use N2V2, simply pass the `use_n2v2` parameter:
    >>> config = create_n2v_configuration(
    ...     experiment_name="n2v2_experiment",
    ...     data_type="tiff",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     use_n2v2=True
    ... )

    For structN2V, there are two parameters to set, `struct_n2v_axis` and
    `struct_n2v_span`:
    >>> config = create_n2v_configuration(
    ...     experiment_name="structn2v_experiment",
    ...     data_type="tiff",
    ...     axes="YX",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     struct_n2v_axis="horizontal",
    ...     struct_n2v_span=7
    ... )

    If you are training multiple channels they will be trained independently by default,
    you simply need to specify the number of channels:
    >>> config = create_n2v_configuration(
    ...     experiment_name="n2v_experiment",
    ...     data_type="array",
    ...     axes="YXC",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     n_channels=3
    ... )

    If instead you want to train multiple channels together, you need to turn off the
    `independent_channels` parameter:
    >>> config = create_n2v_configuration(
    ...     experiment_name="n2v_experiment",
    ...     data_type="array",
    ...     axes="YXC",
    ...     patch_size=[64, 64],
    ...     batch_size=32,
    ...     num_epochs=100,
    ...     independent_channels=False,
    ...     n_channels=3
    ... )
    """
    # if there are channels, we need to specify their number
    if "C" in axes and n_channels is None:
        raise ValueError("Number of channels must be specified when using channels.")
    elif "C" not in axes and (n_channels is not None and n_channels > 1):
        raise ValueError(
            f"C is not present in the axes, but number of channels is specified "
            f"(got {n_channels} channel)."
        )

    if n_channels is None:
        n_channels = 1

    # augmentations
    spatial_transforms = _list_spatial_augmentations(augmentations)

    # create the N2VManipulate transform using the supplied parameters
    n2v_transform = N2VManipulateModel(
        name=SupportedTransform.N2V_MANIPULATE.value,
        strategy=(
            SupportedPixelManipulation.MEDIAN.value
            if use_n2v2
            else SupportedPixelManipulation.UNIFORM.value
        ),
        roi_size=roi_size,
        masked_pixel_percentage=masked_pixel_percentage,
        struct_mask_axis=struct_n2v_axis,
        struct_mask_span=struct_n2v_span,
    )

    # algorithm
    algorithm_params = _create_algorithm_configuration(
        axes=axes,
        algorithm="n2v",
        loss="n2v",
        independent_channels=independent_channels,
        n_channels_in=n_channels,
        n_channels_out=n_channels,
        use_n2v2=use_n2v2,
        model_params=model_params,
    )
    algorithm_params["n2v_config"] = n2v_transform

    # data
    data_params = _create_data_configuration(
        data_type=data_type,
        axes=axes,
        patch_size=patch_size,
        batch_size=batch_size,
        augmentations=spatial_transforms,
        train_dataloader_params=train_dataloader_params,
        val_dataloader_params=val_dataloader_params,
    )

    # training
    training_params = _create_training_configuration(
        num_epochs=num_epochs,
        logger=logger,
    )

    return Configuration(
        experiment_name=experiment_name,
        algorithm_config=algorithm_params,
        data_config=data_params,
        training_config=training_params,
    )