careamics 0.0.11__py3-none-any.whl → 0.0.13__py3-none-any.whl

careamics/lightning/dataset_ng/data_module.py

@@ -0,0 +1,678 @@
+"""Next-Generation CAREamics DataModule."""
+
+from collections.abc import Callable
+from pathlib import Path
+from typing import Any, Optional, Union, overload
+
+import numpy as np
+import pytorch_lightning as L
+from numpy.typing import NDArray
+from torch.utils.data import DataLoader
+from torch.utils.data._utils.collate import default_collate
+
+from careamics.config.data.ng_data_model import NGDataConfig
+from careamics.config.support import SupportedData
+from careamics.dataset.dataset_utils import list_files, validate_source_target_files
+from careamics.dataset_ng.dataset import Mode
+from careamics.dataset_ng.factory import create_dataset
+from careamics.dataset_ng.patch_extractor import ImageStackLoader
+from careamics.utils import get_logger
+
+logger = get_logger(__name__)
+
+ItemType = Union[Path, str, NDArray[Any]]
+"""Type of input items passed to the dataset."""
+
+InputType = Union[ItemType, list[ItemType], None]
+"""Type of input data passed to the dataset."""
+
+
+class CareamicsDataModule(L.LightningDataModule):
+    """Data module for Careamics dataset.
+
+    Parameters
+    ----------
+    data_config : DataConfig
+        Pydantic model for CAREamics data configuration.
+    train_data : Optional[InputType]
+        Training data, can be a path to a folder, a list of paths, or a numpy array.
+    train_data_target : Optional[InputType]
+        Training data target, can be a path to a folder,
+        a list of paths, or a numpy array.
+    val_data : Optional[InputType]
+        Validation data, can be a path to a folder,
+        a list of paths, or a numpy array.
+    val_data_target : Optional[InputType]
+        Validation data target, can be a path to a folder,
+        a list of paths, or a numpy array.
+    pred_data : Optional[InputType]
+        Prediction data, can be a path to a folder, a list of paths,
+        or a numpy array.
+    pred_data_target : Optional[InputType]
+        Prediction data target, can be a path to a folder,
+        a list of paths, or a numpy array.
+    read_source_func : Optional[Callable], default=None
+        Function to read the source data. Only used for `custom`
+        data type (see DataModel).
+    read_kwargs : Optional[dict[str, Any]]
+        The kwargs for the read source function.
+    image_stack_loader : Optional[ImageStackLoader]
+        The image stack loader.
+    image_stack_loader_kwargs : Optional[dict[str, Any]]
+        The image stack loader kwargs.
+    extension_filter : str, default=""
+        Filter for file extensions. Only used for `custom` data types
+        (see DataModel).
+    val_percentage : Optional[float]
+        Percentage of the training data to use for validation. Only
+        used if `val_data` is None.
+    val_minimum_split : int, default=5
+        Minimum number of patches or files to split from the training data for
+        validation. Only used if `val_data` is None.
+    use_in_memory : bool
+        Load data in memory dataset if possible, by default True.
+
+
+    Attributes
+    ----------
+    config : DataConfig
+        Pydantic model for CAREamics data configuration.
+    data_type : str
+        Type of data, one of SupportedData.
+    batch_size : int
+        Batch size for the dataloaders.
+    use_in_memory : bool
+        Whether to load data in memory if possible.
+    extension_filter : str
+        Filter for file extensions, by default "".
+    read_source_func : Optional[Callable], default=None
+        Function to read the source data.
+    read_kwargs : Optional[dict[str, Any]], default=None
+        The kwargs for the read source function.
+    val_percentage : Optional[float]
+        Percentage of the training data to use for validation.
+    val_minimum_split : int, default=5
+        Minimum number of patches or files to split from the training data for
+        validation.
+    train_data : Optional[Any]
+        Training data, can be a path to a folder, a list of paths, or a numpy array.
+    train_data_target : Optional[Any]
+        Training data target, can be a path to a folder, a list of paths, or a numpy
+        array.
+    val_data : Optional[Any]
+        Validation data, can be a path to a folder, a list of paths, or a numpy array.
+    val_data_target : Optional[Any]
+        Validation data target, can be a path to a folder, a list of paths, or a numpy
+        array.
+    pred_data : Optional[Any]
+        Prediction data, can be a path to a folder, a list of paths, or a numpy array.
+    pred_data_target : Optional[Any]
+        Prediction data target, can be a path to a folder, a list of paths, or a numpy
+        array.
+
+    Raises
+    ------
+    ValueError
+        If at least one of train_data, val_data or pred_data is not provided.
+    ValueError
+        If input and target data types are not consistent.
+    """
+
+    # standard use
+    @overload
+    def __init__(
+        self,
+        data_config: NGDataConfig,
+        *,
+        train_data: Optional[InputType] = None,
+        train_data_target: Optional[InputType] = None,
+        val_data: Optional[InputType] = None,
+        val_data_target: Optional[InputType] = None,
+        pred_data: Optional[InputType] = None,
+        pred_data_target: Optional[InputType] = None,
+        extension_filter: str = "",
+        val_percentage: Optional[float] = None,
+        val_minimum_split: int = 5,
+        use_in_memory: bool = True,
+    ) -> None: ...
+
+    # custom read function
+    @overload
+    def __init__(
+        self,
+        data_config: NGDataConfig,
+        *,
+        train_data: Optional[InputType] = None,
+        train_data_target: Optional[InputType] = None,
+        val_data: Optional[InputType] = None,
+        val_data_target: Optional[InputType] = None,
+        pred_data: Optional[InputType] = None,
+        pred_data_target: Optional[InputType] = None,
+        read_source_func: Callable,
+        read_kwargs: Optional[dict[str, Any]] = None,
+        extension_filter: str = "",
+        val_percentage: Optional[float] = None,
+        val_minimum_split: int = 5,
+        use_in_memory: bool = True,
+    ) -> None: ...
+
+    @overload
+    def __init__(
+        self,
+        data_config: NGDataConfig,
+        *,
+        train_data: Optional[Any] = None,
+        train_data_target: Optional[Any] = None,
+        val_data: Optional[Any] = None,
+        val_data_target: Optional[Any] = None,
+        pred_data: Optional[Any] = None,
+        pred_data_target: Optional[Any] = None,
+        image_stack_loader: ImageStackLoader,
+        image_stack_loader_kwargs: Optional[dict[str, Any]] = None,
+        extension_filter: str = "",
+        val_percentage: Optional[float] = None,
+        val_minimum_split: int = 5,
+        use_in_memory: bool = True,
+    ) -> None: ...
+
+    def __init__(
+        self,
+        data_config: NGDataConfig,
+        *,
+        train_data: Optional[Any] = None,
+        train_data_target: Optional[Any] = None,
+        val_data: Optional[Any] = None,
+        val_data_target: Optional[Any] = None,
+        pred_data: Optional[Any] = None,
+        pred_data_target: Optional[Any] = None,
+        read_source_func: Optional[Callable] = None,
+        read_kwargs: Optional[dict[str, Any]] = None,
+        image_stack_loader: Optional[ImageStackLoader] = None,
+        image_stack_loader_kwargs: Optional[dict[str, Any]] = None,
+        extension_filter: str = "",
+        val_percentage: Optional[float] = None,
+        val_minimum_split: int = 5,
+        use_in_memory: bool = True,
+    ) -> None:
+        """
+        Data module for Careamics dataset initialization.
+
+        Create a lightning datamodule that handles creating datasets for training,
+        validation, and prediction.
+
+        Parameters
+        ----------
+        data_config : NGDataConfig
+            Pydantic model for CAREamics data configuration.
+        train_data : Optional[InputType]
+            Training data, can be a path to a folder, a list of paths, or a numpy array.
+        train_data_target : Optional[InputType]
+            Training data target, can be a path to a folder,
+            a list of paths, or a numpy array.
+        val_data : Optional[InputType]
+            Validation data, can be a path to a folder,
+            a list of paths, or a numpy array.
+        val_data_target : Optional[InputType]
+            Validation data target, can be a path to a folder,
+            a list of paths, or a numpy array.
+        pred_data : Optional[InputType]
+            Prediction data, can be a path to a folder, a list of paths,
+            or a numpy array.
+        pred_data_target : Optional[InputType]
+            Prediction data target, can be a path to a folder,
+            a list of paths, or a numpy array.
+        read_source_func : Optional[Callable]
+            Function to read the source data, by default None. Only used for `custom`
+            data type (see DataModel).
+        read_kwargs : Optional[dict[str, Any]]
+            The kwargs for the read source function.
+        image_stack_loader : Optional[ImageStackLoader]
+            The image stack loader.
+        image_stack_loader_kwargs : Optional[dict[str, Any]]
+            The image stack loader kwargs.
+        extension_filter : str
+            Filter for file extensions, by default "". Only used for `custom` data types
+            (see DataModel).
+        val_percentage : Optional[float]
+            Percentage of the training data to use for validation. Only
+            used if `val_data` is None.
+        val_minimum_split : int
+            Minimum number of patches or files to split from the training data for
+            validation, by default 5. Only used if `val_data` is None.
+        use_in_memory : bool
+            Load data in memory dataset if possible, by default True.
+        """
+        super().__init__()
+
+        if train_data is None and val_data is None and pred_data is None:
+            raise ValueError(
+                "At least one of train_data, val_data or pred_data must be provided."
+            )
+
+        self.config: NGDataConfig = data_config
+        self.data_type: str = data_config.data_type
+        self.batch_size: int = data_config.batch_size
+        self.use_in_memory: bool = use_in_memory
+        self.extension_filter: str = extension_filter
+        self.read_source_func = read_source_func
+        self.read_kwargs = read_kwargs
+        self.image_stack_loader = image_stack_loader
+        self.image_stack_loader_kwargs = image_stack_loader_kwargs
+
+        # TODO: implement the validation split logic
+        self.val_percentage = val_percentage
+        self.val_minimum_split = val_minimum_split
+        if self.val_percentage is not None:
+            raise NotImplementedError("Validation split not implemented")
+
+        self.train_data, self.train_data_target = self._initialize_data_pair(
+            train_data, train_data_target
+        )
+        self.val_data, self.val_data_target = self._initialize_data_pair(
+            val_data, val_data_target
+        )
+
+        # The pred_data_target can be needed to count metrics on the prediction
+        self.pred_data, self.pred_data_target = self._initialize_data_pair(
+            pred_data, pred_data_target
+        )
+
+    def _validate_input_target_type_consistency(
+        self,
+        input_data: InputType,
+        target_data: Optional[InputType],
+    ) -> None:
+        """Validate if the input and target data types are consistent.
+
+        Parameters
+        ----------
+        input_data : InputType
+            Input data, can be a path to a folder, a list of paths, or a numpy array.
+        target_data : Optional[InputType]
+            Target data, can be None, a path to a folder, a list of paths, or a numpy
+            array.
+        """
+        if input_data is not None and target_data is not None:
+            if not isinstance(input_data, type(target_data)):
+                raise ValueError(
+                    f"Inputs for input and target must be of the same type or None. "
+                    f"Got {type(input_data)} and {type(target_data)}."
+                )
+        if isinstance(input_data, list) and isinstance(target_data, list):
+            if len(input_data) != len(target_data):
+                raise ValueError(
+                    f"Inputs and targets must have the same length. "
+                    f"Got {len(input_data)} and {len(target_data)}."
+                )
+            if not isinstance(input_data[0], type(target_data[0])):
+                raise ValueError(
+                    f"Inputs and targets must have the same type. "
+                    f"Got {type(input_data[0])} and {type(target_data[0])}."
+                )
+
+    def _list_files_in_directory(
+        self,
+        input_data,
+        target_data=None,
+    ) -> tuple[list[Path], Optional[list[Path]]]:
+        """List files from input and target directories.
+
+        Parameters
+        ----------
+        input_data : InputType
+            Input data, can be a path to a folder, a list of paths, or a numpy array.
+        target_data : Optional[InputType]
+            Target data, can be None, a path to a folder, a list of paths, or a numpy
+            array.
+
+        Returns
+        -------
+        (list[Path], Optional[list[Path]])
+            A tuple containing lists of file paths for input and target data.
+            If target_data is None, the second element will be None.
+        """
+        input_data = Path(input_data)
+        input_files = list_files(input_data, self.data_type, self.extension_filter)
+        if target_data is None:
+            return input_files, None
+        else:
+            target_data = Path(target_data)
+            target_files = list_files(
+                target_data, self.data_type, self.extension_filter
+            )
+            validate_source_target_files(input_files, target_files)
+            return input_files, target_files
+
+    def _convert_paths_to_pathlib(
+        self,
+        input_data,
+        target_data=None,
+    ) -> tuple[list[Path], Optional[list[Path]]]:
+        """Create a list of file paths from the input and target data.
+
+        Parameters
+        ----------
+        input_data : InputType
+            Input data, can be a path to a folder, a list of paths, or a numpy array.
+        target_data : Optional[InputType]
+            Target data, can be None, a path to a folder, a list of paths, or a numpy
+            array.
+
+        Returns
+        -------
+        (list[Path], Optional[list[Path]])
+            A tuple containing lists of file paths for input and target data.
+            If target_data is None, the second element will be None.
+        """
+        input_files = [
+            Path(item) if isinstance(item, str) else item for item in input_data
+        ]
+        if target_data is None:
+            return input_files, None
+        else:
+            target_files = [
+                Path(item) if isinstance(item, str) else item for item in target_data
+            ]
+            validate_source_target_files(input_files, target_files)
+            return input_files, target_files
+
+    def _validate_array_input(
+        self,
+        input_data: InputType,
+        target_data: Optional[InputType],
+    ) -> tuple[Any, Any]:
+        """Validate if the input data is a numpy array.
+
+        Parameters
+        ----------
+        input_data : InputType
+            Input data, can be a path to a folder, a list of paths, or a numpy array.
+        target_data : Optional[InputType]
+            Target data, can be None, a path to a folder, a list of paths, or a numpy
+            array.
+
+        Returns
+        -------
+        (Any, Any)
+            A tuple containing the input and target.
+        """
+        if isinstance(input_data, np.ndarray):
+            input_array = [input_data]
+            target_array = [target_data] if target_data is not None else None
+            return input_array, target_array
+        elif isinstance(input_data, list):
+            return input_data, target_data
+        else:
+            raise ValueError(
+                f"Unsupported input type for {self.data_type}: {type(input_data)}"
+            )
+
+    def _validate_path_input(
+        self, input_data: InputType, target_data: Optional[InputType]
+    ) -> tuple[list[Path], Optional[list[Path]]]:
+        """Validate if the input data is a path or a list of paths.
+
+        Parameters
+        ----------
+        input_data : InputType
+            Input data, can be a path to a folder, a list of paths, or a numpy array.
+        target_data : Optional[InputType]
+            Target data, can be None, a path to a folder, a list of paths, or a numpy
+            array.
+
+        Returns
+        -------
+        (list[Path], Optional[list[Path]])
+            A tuple containing lists of file paths for input and target data.
+            If target_data is None, the second element will be None.
+        """
+        if isinstance(input_data, str | Path):
+            if target_data is not None:
+                assert isinstance(target_data, str | Path)
+            input_list, target_list = self._list_files_in_directory(
+                input_data, target_data
+            )
+            return input_list, target_list
+        elif isinstance(input_data, list):
+            if target_data is not None:
+                assert isinstance(target_data, list)
+            input_list, target_list = self._convert_paths_to_pathlib(
+                input_data, target_data
+            )
+            return input_list, target_list
+        else:
+            raise ValueError(
+                f"Unsupported input type for {self.data_type}: {type(input_data)}"
+            )
+
+    def _validate_custom_input(self, input_data, target_data) -> tuple[Any, Any]:
+        """Convert custom input data to a list of file paths.
+
+        Parameters
+        ----------
+        input_data : InputType
+            Input data, can be a path to a folder, a list of paths, or a numpy array.
+        target_data : Optional[InputType]
+            Target data, can be None, a path to a folder, a list of paths, or a numpy
+            array.
+
+        Returns
+        -------
+        (Any, Any)
+            A tuple containing lists of file paths for input and target data.
+            If target_data is None, the second element will be None.
+        """
+        if self.image_stack_loader is not None:
+            return input_data, target_data
+        elif isinstance(input_data, str | Path):
+            if target_data is not None:
+                assert isinstance(target_data, str | Path)
+            input_list, target_list = self._list_files_in_directory(
+                input_data, target_data
+            )
+            return input_list, target_list
+        elif isinstance(input_data, list):
+            if isinstance(input_data[0], str | Path):
+                if target_data is not None:
+                    assert isinstance(target_data, list)
+                input_list, target_list = self._convert_paths_to_pathlib(
+                    input_data, target_data
+                )
+                return input_list, target_list
+        else:
+            raise ValueError(
+                f"If using {self.data_type}, pass a custom "
+                f"image_stack_loader or read_source_func"
+            )
+        return input_data, target_data
+
+    def _initialize_data_pair(
+        self,
+        input_data: Optional[InputType],
+        target_data: Optional[InputType],
+    ) -> tuple[Any, Any]:
+        """
+        Initialize a pair of input and target data.
+
+        Parameters
+        ----------
+        input_data : InputType
+            Input data, can be None, a path to a folder, a list of paths, or a numpy
+            array.
+        target_data : Optional[InputType]
+            Target data, can be None, a path to a folder, a list of paths, or a numpy
+            array.
+
+        Returns
+        -------
+        (list of numpy.ndarray or list of pathlib.Path, None or list of numpy.ndarray or
+        list of pathlib.Path)
+            A tuple containing the initialized input and target data. For file paths,
+            returns lists of Path objects. For numpy arrays, returns the arrays
+            directly.
+        """
+        if input_data is None:
+            return None, None
+
+        self._validate_input_target_type_consistency(input_data, target_data)
+
+        if self.data_type == SupportedData.ARRAY:
+            if isinstance(input_data, np.ndarray):
+                return self._validate_array_input(input_data, target_data)
+            elif isinstance(input_data, list):
+                if isinstance(input_data[0], np.ndarray):
+                    return self._validate_array_input(input_data, target_data)
+                else:
+                    raise ValueError(
+                        f"Unsupported input type for {self.data_type}: "
+                        f"{type(input_data[0])}"
+                    )
+            else:
+                raise ValueError(
+                    f"Unsupported input type for {self.data_type}: {type(input_data)}"
+                )
+        elif self.data_type in (SupportedData.TIFF, SupportedData.CZI):
+            if isinstance(input_data, str | Path):
+                return self._validate_path_input(input_data, target_data)
+            elif isinstance(input_data, list):
+                if isinstance(input_data[0], str | Path):
+                    return self._validate_path_input(input_data, target_data)
+                else:
+                    raise ValueError(
+                        f"Unsupported input type for {self.data_type}: "
+                        f"{type(input_data[0])}"
+                    )
+            else:
+                raise ValueError(
+                    f"Unsupported input type for {self.data_type}: {type(input_data)}"
+                )
+        elif self.data_type == SupportedData.CUSTOM:
+            return self._validate_custom_input(input_data, target_data)
+        else:
+            raise NotImplementedError(f"Unsupported data type: {self.data_type}")
+
+    def setup(self, stage: str) -> None:
+        """
+        Setup datasets.
+
+        Lightning hook that is called at the beginning of fit (train + validate),
+        validate, test, or predict. Creates the datasets for a given stage.
+
+        Parameters
+        ----------
+        stage : str
+            The stage to set up datasets for.
+            Is either 'fit', 'validate', 'test', or 'predict'.
+
+        Raises
+        ------
+        NotImplementedError
+            If stage is not one of "fit", "validate" or "predict".
+        """
+        if stage == "fit":
+            self.train_dataset = create_dataset(
+                mode=Mode.TRAINING,
+                inputs=self.train_data,
+                targets=self.train_data_target,
+                config=self.config,
+                in_memory=self.use_in_memory,
+                read_func=self.read_source_func,
+                read_kwargs=self.read_kwargs,
+                image_stack_loader=self.image_stack_loader,
+                image_stack_loader_kwargs=self.image_stack_loader_kwargs,
+            )
+            # TODO: ugly, need to find a better solution
+            self.stats = self.train_dataset.input_stats
+            self.config.set_means_and_stds(
+                self.train_dataset.input_stats.means,
+                self.train_dataset.input_stats.stds,
+                self.train_dataset.target_stats.means,
+                self.train_dataset.target_stats.stds,
+            )
+            self.val_dataset = create_dataset(
+                mode=Mode.VALIDATING,
+                inputs=self.val_data,
+                targets=self.val_data_target,
+                config=self.config,
+                in_memory=self.use_in_memory,
+                read_func=self.read_source_func,
+                read_kwargs=self.read_kwargs,
+                image_stack_loader=self.image_stack_loader,
+                image_stack_loader_kwargs=self.image_stack_loader_kwargs,
+            )
+        elif stage == "validate":
+            self.val_dataset = create_dataset(
+                mode=Mode.VALIDATING,
+                inputs=self.val_data,
+                targets=self.val_data_target,
+                config=self.config,
+                in_memory=self.use_in_memory,
+                read_func=self.read_source_func,
+                read_kwargs=self.read_kwargs,
+                image_stack_loader=self.image_stack_loader,
+                image_stack_loader_kwargs=self.image_stack_loader_kwargs,
+            )
+            self.stats = self.val_dataset.input_stats
+        elif stage == "predict":
+            self.predict_dataset = create_dataset(
+                mode=Mode.PREDICTING,
+                inputs=self.pred_data,
+                targets=self.pred_data_target,
+                config=self.config,
+                in_memory=self.use_in_memory,
+                read_func=self.read_source_func,
+                read_kwargs=self.read_kwargs,
+                image_stack_loader=self.image_stack_loader,
+                image_stack_loader_kwargs=self.image_stack_loader_kwargs,
+            )
+            self.stats = self.predict_dataset.input_stats
+        else:
+            raise NotImplementedError(f"Stage {stage} not implemented")
+
+    def train_dataloader(self) -> DataLoader:
+        """
+        Create a dataloader for training.
+
+        Returns
+        -------
+        DataLoader
+            Training dataloader.
+        """
+        return DataLoader(
+            self.train_dataset,
+            batch_size=self.batch_size,
+            collate_fn=default_collate,
+            **self.config.train_dataloader_params,
+        )
+
+    def val_dataloader(self) -> DataLoader:
+        """
+        Create a dataloader for validation.
+
+        Returns
+        -------
+        DataLoader
+            Validation dataloader.
+        """
+        return DataLoader(
+            self.val_dataset,
+            batch_size=self.batch_size,
+            collate_fn=default_collate,
+            **self.config.val_dataloader_params,
+        )
+
+    def predict_dataloader(self) -> DataLoader:
+        """
+        Create a dataloader for prediction.
+
+        Returns
+        -------
+        DataLoader
+            Prediction dataloader.
+        """
+        return DataLoader(
+            self.predict_dataset,
+            batch_size=self.batch_size,
+            collate_fn=default_collate,
+            **self.config.test_dataloader_params,
+        )

careamics/lightning/dataset_ng/lightning_modules/__init__.py

@@ -0,0 +1,9 @@
+"""CAREamics PyTorch Lightning modules."""
+
+from .care_module import CAREModule
+from .n2v_module import N2VModule
+
+__all__ = [
+    "CAREModule",
+    "N2VModule",
+]