careamics 0.0.1__py3-none-any.whl → 0.0.2__py3-none-any.whl

careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py

@@ -0,0 +1,398 @@
+"""Module containing different strategies for writing predictions."""
+
+from pathlib import Path
+from typing import Any, Optional, Protocol, Sequence, Union
+
+import numpy as np
+from numpy.typing import NDArray
+from pytorch_lightning import LightningModule, Trainer
+from torch.utils.data import DataLoader
+
+from careamics.config.tile_information import TileInformation
+from careamics.dataset import IterablePredDataset, IterableTiledPredDataset
+from careamics.file_io import WriteFunc
+from careamics.prediction_utils import stitch_prediction_single
+
+from .file_path_utils import create_write_file_path, get_sample_file_path
+
+
+class WriteStrategy(Protocol):
+    """Protocol for write strategy classes."""
+
+    def write_batch(
+        self,
+        trainer: Trainer,
+        pl_module: LightningModule,
+        prediction: Any,  # TODO: change to expected type
+        batch_indices: Optional[Sequence[int]],
+        batch: Any,  # TODO: change to expected type
+        batch_idx: int,
+        dataloader_idx: int,
+        dirpath: Path,
+    ) -> None:
+        """
+        WriteStrategy subclasses must contain this function to write a batch.
+
+        Parameters
+        ----------
+        trainer : Trainer
+            PyTorch Lightning Trainer.
+        pl_module : LightningModule
+            PyTorch Lightning LightningModule.
+        prediction : Any
+            Predictions on `batch`.
+        batch_indices : sequence of int
+            Indices identifying the samples in the batch.
+        batch : Any
+            Input batch.
+        batch_idx : int
+            Batch index.
+        dataloader_idx : int
+            Dataloader index.
+        dirpath : Path
+            Path to directory to save predictions to.
+        """
+
+
+class CacheTiles(WriteStrategy):
+    """
+    A write strategy that will cache tiles.
+
+    Tiles are cached until a whole image is predicted on. Then the stitched
+    prediction is saved.
+
+    Parameters
+    ----------
+    write_func : WriteFunc
+        Function used to save predictions.
+    write_extension : str
+        Extension added to prediction file paths.
+    write_func_kwargs : dict of {str: Any}
+        Extra kwargs to pass to `write_func`.
+
+    Attributes
+    ----------
+    write_func : WriteFunc
+        Function used to save predictions.
+    write_extension : str
+        Extension added to prediction file paths.
+    write_func_kwargs : dict of {str: Any}
+        Extra kwargs to pass to `write_func`.
+    tile_cache : list of numpy.ndarray
+        Tiles cached for stitching prediction.
+    tile_info_cache : list of TileInformation
+        Cached tile information for stitching prediction.
+    """
+
+    def __init__(
+        self,
+        write_func: WriteFunc,
+        write_extension: str,
+        write_func_kwargs: dict[str, Any],
+    ) -> None:
+        """
+        A write strategy that will cache tiles.
+
+        Tiles are cached until a whole image is predicted on. Then the stitched
+        prediction is saved.
+
+        Parameters
+        ----------
+        write_func : WriteFunc
+            Function used to save predictions.
+        write_extension : str
+            Extension added to prediction file paths.
+        write_func_kwargs : dict of {str: Any}
+            Extra kwargs to pass to `write_func`.
+        """
+        super().__init__()
+
+        self.write_func: WriteFunc = write_func
+        self.write_extension: str = write_extension
+        self.write_func_kwargs: dict[str, Any] = write_func_kwargs
+
+        # where tiles will be cached until a whole image has been predicted
+        self.tile_cache: list[NDArray] = []
+        self.tile_info_cache: list[TileInformation] = []
+
+    @property
+    def last_tiles(self) -> list[bool]:
+        """
+        List of bool to determine whether each tile in the cache is the last tile.
+
+        Returns
+        -------
+        list of bool
+            Whether each tile in the tile cache is the last tile.
+        """
+        return [tile_info.last_tile for tile_info in self.tile_info_cache]
+
+    def write_batch(
+        self,
+        trainer: Trainer,
+        pl_module: LightningModule,
+        prediction: tuple[NDArray, list[TileInformation]],
+        batch_indices: Optional[Sequence[int]],
+        batch: tuple[NDArray, list[TileInformation]],
+        batch_idx: int,
+        dataloader_idx: int,
+        dirpath: Path,
+    ) -> None:
+        """
+        Cache tiles until the last tile is predicted; save the stitched prediction.
+
+        Parameters
+        ----------
+        trainer : Trainer
+            PyTorch Lightning Trainer.
+        pl_module : LightningModule
+            PyTorch Lightning LightningModule.
+        prediction : Any
+            Predictions on `batch`.
+        batch_indices : sequence of int
+            Indices identifying the samples in the batch.
+        batch : Any
+            Input batch.
+        batch_idx : int
+            Batch index.
+        dataloader_idx : int
+            Dataloader index.
+        dirpath : Path
+            Path to directory to save predictions to.
+        """
+        dataloaders: Union[DataLoader, list[DataLoader]] = trainer.predict_dataloaders
+        dataloader: DataLoader = (
+            dataloaders[dataloader_idx]
+            if isinstance(dataloaders, list)
+            else dataloaders
+        )
+        dataset: IterableTiledPredDataset = dataloader.dataset
+        if not isinstance(dataset, IterableTiledPredDataset):
+            raise TypeError("Prediction dataset is not `IterableTiledPredDataset`.")
+
+        # cache tiles (batches are split into single samples)
+        self.tile_cache.extend(np.split(prediction[0], prediction[0].shape[0]))
+        self.tile_info_cache.extend(prediction[1])
+
+        # save stitched prediction
+        if self._has_last_tile():
+
+            # get image tiles and remove them from the cache
+            tiles, tile_infos = self._get_image_tiles()
+            self._clear_cache()
+
+            # stitch prediction
+            prediction_image = stitch_prediction_single(
+                tiles=tiles, tile_infos=tile_infos
+            )
+
+            # write prediction
+            sample_id = tile_infos[0].sample_id  # need this to select correct file name
+            input_file_path = get_sample_file_path(dataset=dataset, sample_id=sample_id)
+            file_path = create_write_file_path(
+                dirpath=dirpath,
+                file_path=input_file_path,
+                write_extension=self.write_extension,
+            )
+            self.write_func(
+                file_path=file_path, img=prediction_image[0], **self.write_func_kwargs
+            )
+
+    def _has_last_tile(self) -> bool:
+        """
+        Whether a last tile is contained in the cached tiles.
+
+        Returns
+        -------
+        bool
+            Whether a last tile is contained in the cached tiles.
+        """
+        return any(self.last_tiles)
+
+    def _clear_cache(self) -> None:
+        """Remove the tiles in the cache up to the first last tile."""
+        index = self._last_tile_index()
+        self.tile_cache = self.tile_cache[index + 1 :]
+        self.tile_info_cache = self.tile_info_cache[index + 1 :]
+
+    def _last_tile_index(self) -> int:
+        """
+        Find the index of the last tile in the tile cache.
+
+        Returns
+        -------
+        int
+            Index of last tile.
+
+        Raises
+        ------
+        ValueError
+            If there is no last tile in the tile cache.
+        """
+        last_tiles = self.last_tiles
+        if not any(last_tiles):
+            raise ValueError("No last tile in the tile cache.")
+        index = np.where(last_tiles)[0][0]
+        return index
+
+    def _get_image_tiles(self) -> tuple[list[NDArray], list[TileInformation]]:
+        """
+        Get the tiles corresponding to a single image.
+
+        Returns
+        -------
+        tuple of (list of numpy.ndarray, list of TileInformation)
+            Tiles and tile information to stitch together a full image.
+        """
+        index = self._last_tile_index()
+        tiles = self.tile_cache[: index + 1]
+        tile_infos = self.tile_info_cache[: index + 1]
+        return tiles, tile_infos
+
+
+class WriteTilesZarr(WriteStrategy):
+    """Strategy to write tiles to Zarr file."""
+
+    def write_batch(
+        self,
+        trainer: Trainer,
+        pl_module: LightningModule,
+        prediction: Any,
+        batch_indices: Optional[Sequence[int]],
+        batch: Any,
+        batch_idx: int,
+        dataloader_idx: int,
+        dirpath: Path,
+    ) -> None:
+        """
+        Write tiles to zarr file.
+
+        Parameters
+        ----------
+        trainer : Trainer
+            PyTorch Lightning Trainer.
+        pl_module : LightningModule
+            PyTorch Lightning LightningModule.
+        prediction : Any
+            Predictions on `batch`.
+        batch_indices : sequence of int
+            Indices identifying the samples in the batch.
+        batch : Any
+            Input batch.
+        batch_idx : int
+            Batch index.
+        dataloader_idx : int
+            Dataloader index.
+        dirpath : Path
+            Path to directory to save predictions to.
+
+        Raises
+        ------
+        NotImplementedError
+        """
+        raise NotImplementedError
+
+
+class WriteImage(WriteStrategy):
+    """
+    A strategy for writing image predictions (i.e. un-tiled predictions).
+
+    Parameters
+    ----------
+    write_func : WriteFunc
+        Function used to save predictions.
+    write_extension : str
+        Extension added to prediction file paths.
+    write_func_kwargs : dict of {str: Any}
+        Extra kwargs to pass to `write_func`.
+
+    Attributes
+    ----------
+    write_func : WriteFunc
+        Function used to save predictions.
+    write_extension : str
+        Extension added to prediction file paths.
+    write_func_kwargs : dict of {str: Any}
+        Extra kwargs to pass to `write_func`.
+    """
+
+    def __init__(
+        self,
+        write_func: WriteFunc,
+        write_extension: str,
+        write_func_kwargs: dict[str, Any],
+    ) -> None:
+        """
+        A strategy for writing image predictions (i.e. un-tiled predictions).
+
+        Parameters
+        ----------
+        write_func : WriteFunc
+            Function used to save predictions.
+        write_extension : str
+            Extension added to prediction file paths.
+        write_func_kwargs : dict of {str: Any}
+            Extra kwargs to pass to `write_func`.
+        """
+        super().__init__()
+
+        self.write_func: WriteFunc = write_func
+        self.write_extension: str = write_extension
+        self.write_func_kwargs: dict[str, Any] = write_func_kwargs
+
+    def write_batch(
+        self,
+        trainer: Trainer,
+        pl_module: LightningModule,
+        prediction: NDArray,
+        batch_indices: Optional[Sequence[int]],
+        batch: NDArray,
+        batch_idx: int,
+        dataloader_idx: int,
+        dirpath: Path,
+    ) -> None:
+        """
+        Save full images.
+
+        Parameters
+        ----------
+        trainer : Trainer
+            PyTorch Lightning Trainer.
+        pl_module : LightningModule
+            PyTorch Lightning LightningModule.
+        prediction : Any
+            Predictions on `batch`.
+        batch_indices : sequence of int
+            Indices identifying the samples in the batch.
+        batch : Any
+            Input batch.
+        batch_idx : int
+            Batch index.
+        dataloader_idx : int
+            Dataloader index.
+        dirpath : Path
+            Path to directory to save predictions to.
+
+        Raises
+        ------
+        TypeError
+            If trainer prediction dataset is not `IterablePredDataset`.
+        """
+        dls: Union[DataLoader, list[DataLoader]] = trainer.predict_dataloaders
+        dl: DataLoader = dls[dataloader_idx] if isinstance(dls, list) else dls
+        ds: IterablePredDataset = dl.dataset
+        if not isinstance(ds, IterablePredDataset):
+            raise TypeError("Prediction dataset is not `IterablePredDataset`.")
+
+        for i in range(prediction.shape[0]):
+            prediction_image = prediction[0]
+            sample_id = batch_idx * dl.batch_size + i
+            input_file_path = get_sample_file_path(dataset=ds, sample_id=sample_id)
+            file_path = create_write_file_path(
+                dirpath=dirpath,
+                file_path=input_file_path,
+                write_extension=self.write_extension,
+            )
+            self.write_func(
+                file_path=file_path, img=prediction_image, **self.write_func_kwargs
+            )

careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py

@@ -0,0 +1,215 @@
+"""Module containing convienience function to create `WriteStrategy`."""
+
+from typing import Any, Optional
+
+from careamics.config.support import SupportedData
+from careamics.file_io import SupportedWriteType, WriteFunc, get_write_func
+
+from .write_strategy import CacheTiles, WriteImage, WriteStrategy
+
+
+def create_write_strategy(
+    write_type: SupportedWriteType,
+    tiled: bool,
+    write_func: Optional[WriteFunc] = None,
+    write_extension: Optional[str] = None,
+    write_func_kwargs: Optional[dict[str, Any]] = None,
+) -> WriteStrategy:
+    """
+    Create a write strategy from convenient parameters.
+
+    Parameters
+    ----------
+    write_type : {"tiff", "custom"}
+        The data type to save as, includes custom.
+    tiled : bool
+        Whether the prediction will be tiled or not.
+    write_func : WriteFunc, optional
+        If a known `write_type` is selected this argument is ignored. For a custom
+        `write_type` a function to save the data must be passed. See notes below.
+    write_extension : str, optional
+        If a known `write_type` is selected this argument is ignored. For a custom
+        `write_type` an extension to save the data with must be passed.
+    write_func_kwargs : dict of {str: any}, optional
+        Additional keyword arguments to be passed to the save function.
+
+    Returns
+    -------
+    WriteStrategy
+        A strategy for writing predicions.
+
+    Notes
+    -----
+    The `write_func` function signature must match that of the example below
+        ```
+        write_func(file_path: Path, img: NDArray, *args, **kwargs) -> None: ...
+        ```
+
+    The `write_func_kwargs` will be passed to the `write_func` doing the following:
+        ```
+        write_func(file_path=file_path, img=img, **kwargs)
+        ```
+    """
+    if write_func_kwargs is None:
+        write_func_kwargs = {}
+
+    write_strategy: WriteStrategy
+    if not tiled:
+        write_func = select_write_func(write_type=write_type, write_func=write_func)
+        write_extension = select_write_extension(
+            write_type=write_type, write_extension=write_extension
+        )
+        write_strategy = WriteImage(
+            write_func=write_func,
+            write_extension=write_extension,
+            write_func_kwargs=write_func_kwargs,
+        )
+    else:
+        # select CacheTiles or WriteTilesZarr (when implemented)
+        write_strategy = _create_tiled_write_strategy(
+            write_type=write_type,
+            write_func=write_func,
+            write_extension=write_extension,
+            write_func_kwargs=write_func_kwargs,
+        )
+
+    return write_strategy
+
+
+def _create_tiled_write_strategy(
+    write_type: SupportedWriteType,
+    write_func: Optional[WriteFunc],
+    write_extension: Optional[str],
+    write_func_kwargs: dict[str, Any],
+) -> WriteStrategy:
+    """
+    Create a tiled write strategy.
+
+    Either `CacheTiles` for caching tiles until a whole image is predicted or
+    `WriteTilesZarr` for writing tiles directly to disk.
+
+    Parameters
+    ----------
+    write_type : {"tiff", "custom"}
+        The data type to save as, includes custom.
+    write_func : WriteFunc, optional
+        If a known `write_type` is selected this argument is ignored. For a custom
+        `write_type` a function to save the data must be passed. See notes below.
+    write_extension : str, optional
+        If a known `write_type` is selected this argument is ignored. For a custom
+        `write_type` an extension to save the data with must be passed.
+    write_func_kwargs : dict of {str: any}
+        Additional keyword arguments to be passed to the save function.
+
+    Returns
+    -------
+    WriteStrategy
+        A strategy for writing tiled predictions.
+
+    Raises
+    ------
+    NotImplementedError
+        if `write_type="zarr" is chosen.
+    """
+    # if write_type == SupportedData.ZARR:
+    #    create *args, **kwargs
+    #    return WriteTilesZarr(*args, **kwargs)
+    # else:
+    if write_type == "zarr":
+        raise NotImplementedError("Saving to zarr is not implemented yet.")
+    else:
+        write_func = select_write_func(write_type=write_type, write_func=write_func)
+        write_extension = select_write_extension(
+            write_type=write_type, write_extension=write_extension
+        )
+        return CacheTiles(
+            write_func=write_func,
+            write_extension=write_extension,
+            write_func_kwargs=write_func_kwargs,
+        )
+
+
+def select_write_func(
+    write_type: SupportedWriteType, write_func: Optional[WriteFunc] = None
+) -> WriteFunc:
+    """
+    Return a function to write images.
+
+    If `write_type` is "custom" then `write_func`, otherwise the known write function
+    is selected.
+
+    Parameters
+    ----------
+    write_type : {"tiff", "custom"}
+        The data type to save as, includes custom.
+    write_func : WriteFunc, optional
+        If a known `write_type` is selected this argument is ignored. For a custom
+        `write_type` a function to save the data must be passed. See notes below.
+
+    Returns
+    -------
+    WriteFunc
+        A function for writing images.
+
+    Raises
+    ------
+    ValueError
+        If `write_type="custom"` but `write_func` has not been given.
+
+    Notes
+    -----
+    The `write_func` function signature must match that of the example below
+        ```
+        write_func(file_path: Path, img: NDArray, *args, **kwargs) -> None: ...
+        ```
+    """
+    if write_type == SupportedData.CUSTOM:
+        if write_func is None:
+            raise ValueError(
+                "A save function must be provided for custom data types."
+                # TODO: link to how save functions should be implemented
+            )
+        else:
+            write_func = write_func
+    else:
+        write_func = get_write_func(write_type)
+    return write_func
+
+
+def select_write_extension(
+    write_type: SupportedWriteType, write_extension: Optional[str] = None
+) -> str:
+    """
+    Return an extension to add to file paths.
+
+    If `write_type` is "custom" then `write_extension`, otherwise the known
+    write extension is selected.
+
+    Parameters
+    ----------
+    write_type : {"tiff", "custom"}
+        The data type to save as, includes custom.
+    write_extension : str, optional
+        If a known `write_type` is selected this argument is ignored. For a custom
+        `write_type` an extension to save the data with must be passed.
+
+    Returns
+    -------
+    str
+        The extension to be added to file paths.
+
+    Raises
+    ------
+    ValueError
+        If `self.save_type="custom"` but `save_extension` has not been given.
+    """
+    write_type_: SupportedData = SupportedData(write_type)  # new variable for mypy
+    if write_type_ == SupportedData.CUSTOM:
+        if write_extension is None:
+            raise ValueError("A save extension must be provided for custom data types.")
+        else:
+            write_extension = write_extension
+    else:
+        # kind of a weird pattern -> reason to move get_extension from SupportedData
+        write_extension = write_type_.get_extension(write_type_)
+    return write_extension

careamics/lightning/callbacks/progress_bar_callback.py

@@ -0,0 +1,90 @@
+"""Progressbar callback."""
+
+import sys
+from typing import Dict, Union
+
+from pytorch_lightning import LightningModule, Trainer
+from pytorch_lightning.callbacks import TQDMProgressBar
+from tqdm import tqdm
+
+
+class ProgressBarCallback(TQDMProgressBar):
+    """Progress bar for training and validation steps."""
+
+    def init_train_tqdm(self) -> tqdm:
+        """Override this to customize the tqdm bar for training.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
+        bar = tqdm(
+            desc="Training",
+            position=(2 * self.process_position),
+            disable=self.is_disabled,
+            leave=True,
+            dynamic_ncols=True,
+            file=sys.stdout,
+            smoothing=0,
+        )
+        return bar
+
+    def init_validation_tqdm(self) -> tqdm:
+        """Override this to customize the tqdm bar for validation.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
+        # The main progress bar doesn't exist in `trainer.validate()`
+        has_main_bar = self.train_progress_bar is not None
+        bar = tqdm(
+            desc="Validating",
+            position=(2 * self.process_position + has_main_bar),
+            disable=self.is_disabled,
+            leave=False,
+            dynamic_ncols=True,
+            file=sys.stdout,
+        )
+        return bar
+
+    def init_test_tqdm(self) -> tqdm:
+        """Override this to customize the tqdm bar for testing.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
+        bar = tqdm(
+            desc="Testing",
+            position=(2 * self.process_position),
+            disable=self.is_disabled,
+            leave=True,
+            dynamic_ncols=False,
+            ncols=100,
+            file=sys.stdout,
+        )
+        return bar
+
+    def get_metrics(
+        self, trainer: Trainer, pl_module: LightningModule
+    ) -> Dict[str, Union[int, str, float, Dict[str, float]]]:
+        """Override this to customize the metrics displayed in the progress bar.
+
+        Parameters
+        ----------
+        trainer : Trainer
+            The trainer object.
+        pl_module : LightningModule
+            The LightningModule object, unused.
+
+        Returns
+        -------
+        dict
+            A dictionary with the metrics to display in the progress bar.
+        """
+        pbar_metrics = trainer.progress_bar_metrics
+        return {**pbar_metrics}