careamics 0.1.0rc1__py3-none-any.whl → 0.1.0rc3__py3-none-any.whl

careamics/config/callback_model.py

@@ -0,0 +1,92 @@
+"""Checkpoint saving configuration."""
+from __future__ import annotations
+
+from datetime import timedelta
+from typing import Literal, Optional
+
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+)
+
+
+class CheckpointModel(BaseModel):
+    """_summary_.
+
+    Parameters
+    ----------
+    BaseModel : _type_
+        _description_
+    """
+
+    model_config = ConfigDict(
+        validate_assignment=True,
+    )
+
+    monitor: Literal["val_loss"] = Field(default="val_loss", validate_default=True)
+    verbose: bool = Field(default=False, validate_default=True)
+    save_weights_only: bool = Field(default=False, validate_default=True)
+    mode: Literal["min", "max"] = Field(default="min", validate_default=True)
+    auto_insert_metric_name: bool = Field(default=False, validate_default=True)
+    every_n_train_steps: Optional[int] = Field(
+        default=None, ge=1, le=10, validate_default=True
+    )
+    train_time_interval: Optional[timedelta] = Field(
+        default=None, validate_default=True
+    )
+    every_n_epochs: Optional[int] = Field(
+        default=None, ge=1, le=10, validate_default=True
+    )
+    save_last: Optional[Literal[True, False, "link"]] = Field(
+        default=True, validate_default=True
+    )
+    save_top_k: int = Field(default=3, ge=1, le=10, validate_default=True)
+
+
+class EarlyStoppingModel(BaseModel):
+    """_summary_.
+
+    Parameters
+    ----------
+    BaseModel : _type_
+        _description_
+    """
+
+    model_config = ConfigDict(
+        validate_assignment=True,
+    )
+
+    monitor: Literal["val_loss"] = Field(default="val_loss", validate_default=True)
+    patience: int = Field(default=3, ge=1, le=10, validate_default=True)
+    mode: Literal["min", "max", "auto"] = Field(default="min", validate_default=True)
+    min_delta: float = Field(default=0.0, ge=0.0, le=1.0, validate_default=True)
+    check_finite: bool = Field(default=True, validate_default=True)
+    stop_on_nan: bool = Field(default=True, validate_default=True)
+    verbose: bool = Field(default=False, validate_default=True)
+    restore_best_weights: bool = Field(default=True, validate_default=True)
+    auto_lr_find: bool = Field(default=False, validate_default=True)
+    auto_lr_find_patience: int = Field(default=3, ge=1, le=10, validate_default=True)
+    auto_lr_find_mode: Literal["min", "max", "auto"] = Field(
+        default="min", validate_default=True
+    )
+    auto_lr_find_direction: Literal["forward", "backward"] = Field(
+        default="backward", validate_default=True
+    )
+    auto_lr_find_max_lr: float = Field(
+        default=10.0, ge=0.0, le=1e6, validate_default=True
+    )
+    auto_lr_find_min_lr: float = Field(
+        default=1e-8, ge=0.0, le=1e6, validate_default=True
+    )
+    auto_lr_find_num_training: int = Field(
+        default=100, ge=1, le=1e6, validate_default=True
+    )
+    auto_lr_find_divergence_threshold: float = Field(
+        default=5.0, ge=0.0, le=1e6, validate_default=True
+    )
+    auto_lr_find_accumulate_grad_batches: int = Field(
+        default=1, ge=1, le=1e6, validate_default=True
+    )
+    auto_lr_find_stop_divergence: bool = Field(default=True, validate_default=True)
+    auto_lr_find_step_scale: float = Field(default=0.1, ge=0.0, le=10)

careamics/config/configuration_factory.py

@@ -0,0 +1,460 @@
+"""Convenience functions to create configurations for training and inference."""
+
+from typing import Any, Dict, List, Literal, Optional, Tuple, Union
+
+from albumentations import Compose
+
+from .algorithm_model import AlgorithmModel
+from .architectures import UNetModel
+from .configuration_model import Configuration
+from .data_model import DataModel
+from .inference_model import InferenceModel
+from .support import (
+    SupportedAlgorithm,
+    SupportedArchitecture,
+    SupportedLoss,
+    SupportedPixelManipulation,
+    SupportedTransform,
+)
+from .training_model import TrainingModel
+
+
+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,
+    use_augmentations: bool = True,
+    use_n2v2: bool = False,
+    n_channels: int = 1,
+    logger: Literal["wandb", "tensorboard", "none"] = "none",
+    model_kwargs: Optional[dict] = None,
+) -> Configuration:
+    """
+    Create a configuration for training N2V.
+
+    If "Z" is present in `axes`, then `path_size` must be a list of length 3, otherwise
+    2.
+
+    By setting `use_augmentations` to False, the only transformation applied will be
+    normalization and N2V manipulation.
+
+    The parameter `use_n2v2` overrides the corresponding `n2v2` that can be passed
+    in `model_kwargs`.
+
+    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.
+    use_augmentations : bool, optional
+        Whether to use augmentations, by default True.
+    use_n2v2 : bool, optional
+        Whether to use N2V2, by default False.
+    n_channels : int, optional
+        Number of channels (in and out), by default 1.
+    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_kwargs : dict, optional
+        UNetModel parameters, by default {}.
+
+    Returns
+    -------
+    Configuration
+        Configuration for training N2V.
+    """
+    # model
+    if model_kwargs is None:
+        model_kwargs = {}
+    model_kwargs["n2v2"] = use_n2v2
+    model_kwargs["conv_dims"] = 3 if "Z" in axes else 2
+    model_kwargs["in_channels"] = n_channels
+    model_kwargs["num_classes"] = n_channels
+
+    unet_model = UNetModel(
+        architecture=SupportedArchitecture.UNET.value,
+        **model_kwargs,
+    )
+
+    # algorithm model
+    algorithm = AlgorithmModel(
+        algorithm=SupportedAlgorithm.N2V.value,
+        loss=SupportedLoss.N2V.value,
+        model=unet_model,
+    )
+
+    # augmentations
+    if use_augmentations:
+        transforms: List[Dict[str, Any]] = [
+            {
+                "name": SupportedTransform.NORMALIZE.value,
+            },
+            {
+                "name": SupportedTransform.NDFLIP.value,
+            },
+            {
+                "name": SupportedTransform.XY_RANDOM_ROTATE90.value,
+            },
+        ]
+    else:
+        transforms = [
+            {
+                "name": SupportedTransform.NORMALIZE.value,
+            },
+        ]
+
+    # data model
+    data = DataModel(
+        data_type=data_type,
+        axes=axes,
+        patch_size=patch_size,
+        batch_size=batch_size,
+        transforms=transforms,
+    )
+
+    # training model
+    training = TrainingModel(
+        num_epochs=num_epochs,
+        batch_size=batch_size,
+        logger=None if logger == "none" else logger,
+    )
+
+    # create configuration
+    configuration = Configuration(
+        experiment_name=experiment_name,
+        algorithm_config=algorithm,
+        data_config=data,
+        training_config=training,
+    )
+
+    return configuration
+
+
+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,
+    use_augmentations: bool = True,
+    use_n2v2: bool = False,
+    n_channels: int = -1,
+    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_kwargs: Optional[dict] = None,
+) -> Configuration:
+    """
+    Create a configuration for training N2V.
+
+    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 "C" is present in `axes`, then you need to set `n_channels` to the number of
+    channels.
+
+    If "Z" is present in `axes`, then `path_size` must be a list of length 3, otherwise
+    2.
+
+    By setting `use_augmentations` to False, the only transformations applied will be
+    normalization and N2V manipulation.
+
+    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_kwargs` (passed as a
+    parameter-value dictionary). Note that `use_n2v2` and 'n_channels' override the
+    corresponding parameters passed in `model_kwargs`.
+
+    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.
+    use_augmentations : bool, optional
+        Whether to use augmentations, by default True.
+    use_n2v2 : bool, optional
+        Whether to use N2V2, by default False.
+    n_channels : int, optional
+        Number of channels (in and out), by default -1.
+    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_kwargs : dict, optional
+        UNetModel parameters, by default {}.
+
+    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 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 together, then you 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
+    ... )
+
+    To turn off the augmentations, except normalization and N2V manipulation, use the
+    relevant keyword argument:
+    >>> config = create_n2v_configuration(
+    ...     experiment_name="n2v_experiment",
+    ...     data_type="array",
+    ...     axes="YX",
+    ...     patch_size=[64, 64],
+    ...     batch_size=32,
+    ...     num_epochs=100,
+    ...     use_augmentations=False
+    ... )
+    """
+    # if there are channels, we need to specify their number
+    if "C" in axes and n_channels == -1:
+        raise ValueError(
+            f"Number of channels must be specified when using channels "
+            f"(got {n_channels} channel)."
+        )
+    elif "C" not in axes 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)."
+        )
+    elif n_channels == -1:
+        n_channels = 1
+
+    # model
+    if model_kwargs is None:
+        model_kwargs = {}
+    model_kwargs["n2v2"] = use_n2v2
+    model_kwargs["conv_dims"] = 3 if "Z" in axes else 2
+    model_kwargs["in_channels"] = n_channels
+    model_kwargs["num_classes"] = n_channels
+
+    unet_model = UNetModel(
+        architecture=SupportedArchitecture.UNET.value,
+        **model_kwargs,
+    )
+
+    # algorithm model
+    algorithm = AlgorithmModel(
+        algorithm=SupportedAlgorithm.N2V.value,
+        loss=SupportedLoss.N2V.value,
+        model=unet_model,
+    )
+
+    # augmentations
+    if use_augmentations:
+        transforms: List[Dict[str, Any]] = [
+            {
+                "name": SupportedTransform.NORMALIZE.value,
+            },
+            {
+                "name": SupportedTransform.NDFLIP.value,
+            },
+            {
+                "name": SupportedTransform.XY_RANDOM_ROTATE90.value,
+            },
+        ]
+    else:
+        transforms = [
+            {
+                "name": SupportedTransform.NORMALIZE.value,
+            },
+        ]
+
+    # n2v2 and structn2v
+    nv2_transform = {
+        "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,
+    }
+    transforms.append(nv2_transform)
+
+    # data model
+    data = DataModel(
+        data_type=data_type,
+        axes=axes,
+        patch_size=patch_size,
+        batch_size=batch_size,
+        transforms=transforms,
+    )
+
+    # training model
+    training = TrainingModel(
+        num_epochs=num_epochs,
+        batch_size=batch_size,
+        logger=None if logger == "none" else logger,
+    )
+
+    # create configuration
+    configuration = Configuration(
+        experiment_name=experiment_name,
+        algorithm_config=algorithm,
+        data_config=data,
+        training_config=training,
+    )
+
+    return configuration
+
+
+# TODO add tests
+def create_inference_configuration(
+    training_configuration: Configuration,
+    tile_size: Optional[Tuple[int, ...]] = None,
+    tile_overlap: Optional[Tuple[int, ...]] = None,
+    data_type: Optional[Literal["array", "tiff", "custom"]] = None,
+    axes: Optional[str] = None,
+    transforms: Optional[Union[List[Dict[str, Any]], Compose]] = None,
+    tta_transforms: bool = True,
+    batch_size: Optional[int] = 1,
+) -> InferenceModel:
+    """
+    Create a configuration for inference with N2V.
+
+    If not provided, `data_type` and `axes` are taken from the training
+    configuration. If `transforms` are not provided, only normalization is applied.
+
+    Parameters
+    ----------
+    training_configuration : Configuration
+        Configuration used for training.
+    tile_size : Tuple[int, ...], optional
+        Size of the tiles.
+    tile_overlap : Tuple[int, ...], optional
+        Overlap of the tiles.
+    data_type : str, optional
+        Type of the data, by default "tiff".
+    axes : str, optional
+        Axes of the data, by default "YX".
+    transforms : List[Dict[str, Any]] or Compose, optional
+        Transformations to apply to the data, by default None.
+    tta_transforms : bool, optional
+        Whether to apply test-time augmentations, by default True.
+    batch_size : int, optional
+        Batch size, by default 1.
+
+    Returns
+    -------
+    InferenceConfiguration
+        Configuration for inference with N2V.
+    """
+    if (
+        training_configuration.data_config.mean is None
+        or training_configuration.data_config.std is None
+    ):
+        raise ValueError("Mean and std must be provided in the training configuration.")
+
+    if transforms is None:
+        transforms = [
+            {
+                "name": SupportedTransform.NORMALIZE.value,
+            },
+        ]
+
+    return InferenceModel(
+        data_type=data_type or training_configuration.data_config.data_type,
+        tile_size=tile_size,
+        tile_overlap=tile_overlap,
+        axes=axes or training_configuration.data_config.axes,
+        mean=training_configuration.data_config.mean,
+        std=training_configuration.data_config.std,
+        transforms=transforms,
+        tta_transforms=tta_transforms,
+        batch_size=batch_size,
+    )