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

careamics/lightning/predict_data_module.py

@@ -0,0 +1,333 @@
+"""Prediction Lightning data modules."""
+
+from pathlib import Path
+from typing import Any, Callable, Literal, Optional, Union
+
+import numpy as np
+import pytorch_lightning as L
+from numpy.typing import NDArray
+from torch.utils.data import DataLoader
+
+from careamics.config import InferenceConfig
+from careamics.config.support import SupportedData
+from careamics.dataset import (
+    InMemoryPredDataset,
+    InMemoryTiledPredDataset,
+    IterablePredDataset,
+    IterableTiledPredDataset,
+)
+from careamics.dataset.dataset_utils import list_files
+from careamics.dataset.tiling.collate_tiles import collate_tiles
+from careamics.file_io.read import get_read_func
+from careamics.utils import get_logger
+
+PredictDatasetType = Union[
+    InMemoryPredDataset,
+    InMemoryTiledPredDataset,
+    IterablePredDataset,
+    IterableTiledPredDataset,
+]
+
+logger = get_logger(__name__)
+
+
+class PredictDataModule(L.LightningDataModule):
+    """
+    CAREamics Lightning prediction data module.
+
+    The data module can be used with Path, str or numpy arrays. The data can be either
+    a folder containing images or a single file.
+
+    To read custom data types, you can set `data_type` to `custom` in `data_config`
+    and provide a function that returns a numpy array from a path as
+    `read_source_func` parameter. The function will receive a Path object and
+    an axies string as arguments, the axes being derived from the `data_config`.
+
+    You can also provide a `fnmatch` and `Path.rglob` compatible expression (e.g.
+    "*.czi") to filter the files extension using `extension_filter`.
+
+    Parameters
+    ----------
+    pred_config : InferenceModel
+        Pydantic model for CAREamics prediction configuration.
+    pred_data : pathlib.Path or str or numpy.ndarray
+        Prediction data, can be a path to a folder, a file or a numpy array.
+    read_source_func : Callable, optional
+        Function to read custom types, by default None.
+    extension_filter : str, optional
+        Filter to filter file extensions for custom types, by default "".
+    dataloader_params : dict, optional
+        Dataloader parameters, by default {}.
+    """
+
+    def __init__(
+        self,
+        pred_config: InferenceConfig,
+        pred_data: Union[Path, str, NDArray],
+        read_source_func: Optional[Callable] = None,
+        extension_filter: str = "",
+        dataloader_params: Optional[dict] = None,
+    ) -> None:
+        """
+        Constructor.
+
+        The data module can be used with Path, str or numpy arrays. The data can be
+        either a folder containing images or a single file.
+
+        To read custom data types, you can set `data_type` to `custom` in `data_config`
+        and provide a function that returns a numpy array from a path as
+        `read_source_func` parameter. The function will receive a Path object and
+        an axies string as arguments, the axes being derived from the `data_config`.
+
+        You can also provide a `fnmatch` and `Path.rglob` compatible expression (e.g.
+        "*.czi") to filter the files extension using `extension_filter`.
+
+        Parameters
+        ----------
+        pred_config : InferenceModel
+            Pydantic model for CAREamics prediction configuration.
+        pred_data : pathlib.Path or str or numpy.ndarray
+            Prediction data, can be a path to a folder, a file or a numpy array.
+        read_source_func : Callable, optional
+            Function to read custom types, by default None.
+        extension_filter : str, optional
+            Filter to filter file extensions for custom types, by default "".
+        dataloader_params : dict, optional
+            Dataloader parameters, by default {}.
+
+        Raises
+        ------
+        ValueError
+            If the data type is `custom` and no `read_source_func` is provided.
+        ValueError
+            If the data type is `array` and the input is not a numpy array.
+        ValueError
+            If the data type is `tiff` and the input is neither a Path nor a str.
+        """
+        if dataloader_params is None:
+            dataloader_params = {}
+        if dataloader_params is None:
+            dataloader_params = {}
+        super().__init__()
+
+        # check that a read source function is provided for custom types
+        if pred_config.data_type == SupportedData.CUSTOM and read_source_func is None:
+            raise ValueError(
+                f"Data type {SupportedData.CUSTOM} is not allowed without "
+                f"specifying a `read_source_func` and an `extension_filer`."
+            )
+
+        # check correct input type
+        if (
+            isinstance(pred_data, np.ndarray)
+            and pred_config.data_type != SupportedData.ARRAY
+        ):
+            raise ValueError(
+                f"Received a numpy array as input, but the data type was set to "
+                f"{pred_config.data_type}. Set the data type "
+                f"to {SupportedData.ARRAY} to predict on numpy arrays."
+            )
+
+        # and that Path or str are passed, if tiff file type specified
+        elif (isinstance(pred_data, Path) or isinstance(pred_config, str)) and (
+            pred_config.data_type != SupportedData.TIFF
+            and pred_config.data_type != SupportedData.CUSTOM
+        ):
+            raise ValueError(
+                f"Received a path as input, but the data type was neither set to "
+                f"{SupportedData.TIFF} nor {SupportedData.CUSTOM}. Set the data type "
+                f" to {SupportedData.TIFF} or "
+                f"{SupportedData.CUSTOM} to predict on files."
+            )
+
+        # configuration data
+        self.prediction_config = pred_config
+        self.data_type = pred_config.data_type
+        self.batch_size = pred_config.batch_size
+        self.dataloader_params = dataloader_params
+
+        self.pred_data = pred_data
+        self.tile_size = pred_config.tile_size
+        self.tile_overlap = pred_config.tile_overlap
+
+        # check if it is tiled
+        self.tiled = self.tile_size is not None and self.tile_overlap is not None
+
+        # read source function
+        if pred_config.data_type == SupportedData.CUSTOM:
+            # mypy check
+            assert read_source_func is not None
+
+            self.read_source_func: Callable = read_source_func
+        elif pred_config.data_type != SupportedData.ARRAY:
+            self.read_source_func = get_read_func(pred_config.data_type)
+
+        self.extension_filter = extension_filter
+
+    def prepare_data(self) -> None:
+        """Hook used to prepare the data before calling `setup`."""
+        # if the data is a Path or a str
+        if not isinstance(self.pred_data, np.ndarray):
+            self.pred_files = list_files(
+                self.pred_data, self.data_type, self.extension_filter
+            )
+
+    def setup(self, stage: Optional[str] = None) -> None:
+        """
+        Hook called at the beginning of predict.
+
+        Parameters
+        ----------
+        stage : Optional[str], optional
+            Stage, by default None.
+        """
+        # if numpy array
+        if self.data_type == SupportedData.ARRAY:
+            if self.tiled:
+                self.predict_dataset: PredictDatasetType = InMemoryTiledPredDataset(
+                    prediction_config=self.prediction_config,
+                    inputs=self.pred_data,
+                )
+            else:
+                self.predict_dataset = InMemoryPredDataset(
+                    prediction_config=self.prediction_config,
+                    inputs=self.pred_data,
+                )
+        else:
+            if self.tiled:
+                self.predict_dataset = IterableTiledPredDataset(
+                    prediction_config=self.prediction_config,
+                    src_files=self.pred_files,
+                    read_source_func=self.read_source_func,
+                )
+            else:
+                self.predict_dataset = IterablePredDataset(
+                    prediction_config=self.prediction_config,
+                    src_files=self.pred_files,
+                    read_source_func=self.read_source_func,
+                )
+
+    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=collate_tiles if self.tiled else None,
+            **self.dataloader_params,
+        )
+
+
+def create_predict_datamodule(
+    pred_data: Union[str, Path, NDArray],
+    data_type: Union[Literal["array", "tiff", "custom"], SupportedData],
+    axes: str,
+    image_means: list[float],
+    image_stds: list[float],
+    tile_size: Optional[tuple[int, ...]] = None,
+    tile_overlap: Optional[tuple[int, ...]] = None,
+    batch_size: int = 1,
+    tta_transforms: bool = True,
+    read_source_func: Optional[Callable] = None,
+    extension_filter: str = "",
+    dataloader_params: Optional[dict] = None,
+) -> PredictDataModule:
+    """Create a CAREamics prediction Lightning datamodule.
+
+    This function is used to explicitly pass the parameters usually contained in an
+    `inference_model` configuration.
+
+    Since the lightning datamodule has no access to the model, make sure that the
+    parameters passed to the datamodule are consistent with the model's requirements
+    and are coherent. This can be done by creating a `Configuration` object beforehand
+    and passing its parameters to the different Lightning modules.
+
+    The data module can be used with Path, str or numpy arrays. To use array data, set
+    `data_type` to `array` and pass a numpy array to `train_data`.
+
+    By default, CAREamics only supports types defined in
+    `careamics.config.support.SupportedData`. To read custom data types, you can set
+    `data_type` to `custom` and provide a function that returns a numpy array from a
+    path. Additionally, pass a `fnmatch` and `Path.rglob` compatible expression
+    (e.g. "*.jpeg") to filter the files extension using `extension_filter`.
+
+    In `dataloader_params`, you can pass any parameter accepted by PyTorch
+    dataloaders, except for `batch_size`, which is set by the `batch_size`
+    parameter.
+
+    Parameters
+    ----------
+    pred_data : str or pathlib.Path or numpy.ndarray
+        Prediction data.
+    data_type : {"array", "tiff", "custom"}
+        Data type, see `SupportedData` for available options.
+    axes : str
+        Axes of the data, chosen among SCZYX.
+    image_means : list of float
+        Mean values for normalization, only used if Normalization is defined.
+    image_stds : list of float
+        Std values for normalization, only used if Normalization is defined.
+    tile_size : tuple of int, optional
+        Tile size, 2D or 3D tile size.
+    tile_overlap : tuple of int, optional
+        Tile overlap, 2D or 3D tile overlap.
+    batch_size : int
+        Batch size.
+    tta_transforms : bool, optional
+        Use test time augmentation, by default True.
+    read_source_func : Callable, optional
+        Function to read the source data, used if `data_type` is `custom`, by
+        default None.
+    extension_filter : str, optional
+        Filter for file extensions, used if `data_type` is `custom`, by default "".
+    dataloader_params : dict, optional
+        Pytorch dataloader parameters, by default {}.
+
+    Returns
+    -------
+    PredictDataModule
+        CAREamics prediction datamodule.
+
+    Notes
+    -----
+    If you are using a UNet model and tiling, the tile size must be
+    divisible in every dimension by 2**d, where d is the depth of the model. This
+    avoids artefacts arising from the broken shift invariance induced by the
+    pooling layers of the UNet. If your image has less dimensions, as it may
+    happen in the Z dimension, consider padding your image.
+    """
+    if dataloader_params is None:
+        dataloader_params = {}
+
+    prediction_dict: dict[str, Any] = {
+        "data_type": data_type,
+        "tile_size": tile_size,
+        "tile_overlap": tile_overlap,
+        "axes": axes,
+        "image_means": image_means,
+        "image_stds": image_stds,
+        "tta_transforms": tta_transforms,
+        "batch_size": batch_size,
+    }
+
+    # validate configuration
+    prediction_config = InferenceConfig(**prediction_dict)
+
+    # sanity check on the dataloader parameters
+    if "batch_size" in dataloader_params:
+        # remove it
+        del dataloader_params["batch_size"]
+
+    return PredictDataModule(
+        pred_config=prediction_config,
+        pred_data=pred_data,
+        read_source_func=read_source_func,
+        extension_filter=extension_filter,
+        dataloader_params=dataloader_params,
+    )