careamics 0.1.0rc6__py3-none-any.whl → 0.1.0rc8__py3-none-any.whl

careamics/config/tile_information.py

@@ -2,9 +2,7 @@
 
 from __future__ import annotations
 
-from typing import Optional, Tuple
-
-from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
+from pydantic import BaseModel, ConfigDict, field_validator
 
 
 class TileInformation(BaseModel):
@@ -13,30 +11,43 @@ class TileInformation(BaseModel):
 
     This model is used to represent the information required to stitch back a tile into
     a larger image. It is used throughout the prediction pipeline of CAREamics.
+
+    Array shape should be (C)(Z)YX, where C and Z are optional dimensions, and must not
+    contain singleton dimensions.
     """
 
     model_config = ConfigDict(validate_default=True)
 
-    array_shape: Tuple[int, ...]
-    tiled: bool = False
+    array_shape: tuple[int, ...]
+    """Shape of the original (untiled) array."""
+
     last_tile: bool = False
-    overlap_crop_coords: Optional[Tuple[Tuple[int, ...], ...]] = Field(default=None)
-    stitch_coords: Optional[Tuple[Tuple[int, ...], ...]] = Field(default=None)
+    """Whether this tile is the last one of the array."""
+
+    overlap_crop_coords: tuple[tuple[int, ...], ...]
+    """Inner coordinates of the tile where to crop the prediction in order to stitch
+    it back into the original image."""
+
+    stitch_coords: tuple[tuple[int, ...], ...]
+    """Coordinates in the original image where to stitch the cropped tile back."""
+
+    sample_id: int
+    """Sample ID of the tile."""
 
     @field_validator("array_shape")
     @classmethod
-    def no_singleton_dimensions(cls, v: Tuple[int, ...]):
+    def no_singleton_dimensions(cls, v: tuple[int, ...]):
         """
         Check that the array shape does not have any singleton dimensions.
 
         Parameters
         ----------
-        v : Tuple[int, ...]
+        v : tuple of int
             Array shape to check.
 
         Returns
         -------
-        Tuple[int, ...]
+        tuple of int
             The array shape if it does not contain singleton dimensions.
 
         Raises
@@ -48,59 +59,26 @@ class TileInformation(BaseModel):
             raise ValueError("Array shape must not contain singleton dimensions.")
         return v
 
-    @field_validator("last_tile")
-    @classmethod
-    def only_if_tiled(cls, v: bool, values: ValidationInfo):
-        """
-        Check that the last tile flag is only set if tiling is enabled.
+    def __eq__(self, other_tile: object):
+        """Check if two tile information objects are equal.
 
         Parameters
         ----------
-        v : bool
-            Last tile flag.
-        values : ValidationInfo
-            Validation information.
+        other_tile : object
+            Tile information object to compare with.
 
         Returns
         -------
         bool
-            The last tile flag.
-        """
-        if not values.data["tiled"]:
-            return False
-        return v
-
-    @field_validator("overlap_crop_coords", "stitch_coords")
-    @classmethod
-    def mandatory_if_tiled(
-        cls, v: Optional[Tuple[int, ...]], values: ValidationInfo
-    ) -> Optional[Tuple[int, ...]]:
+            Whether the two tile information objects are equal.
         """
-        Check that the coordinates are not `None` if tiling is enabled.
-
-        The method also return `None` if tiling is not enabled.
-
-        Parameters
-        ----------
-        v : Optional[Tuple[int, ...]]
-            Coordinates to check.
-        values : ValidationInfo
-            Validation information.
-
-        Returns
-        -------
-        Optional[Tuple[int, ...]]
-            The coordinates if tiling is enabled, otherwise `None`.
-
-        Raises
-        ------
-        ValueError
-            If the coordinates are `None` and tiling is enabled.
-        """
-        if values.data["tiled"]:
-            if v is None:
-                raise ValueError("Value must be specified if tiling is enabled.")
-
-            return v
-        else:
-            return None
+        if not isinstance(other_tile, TileInformation):
+            return NotImplemented
+
+        return (
+            self.array_shape == other_tile.array_shape
+            and self.last_tile == other_tile.last_tile
+            and self.overlap_crop_coords == other_tile.overlap_crop_coords
+            and self.stitch_coords == other_tile.stitch_coords
+            and self.sample_id == other_tile.sample_id
+        )

careamics/config/training_model.py

@@ -35,15 +35,19 @@ class TrainingConfig(BaseModel):
     )
 
     num_epochs: int = Field(default=20, ge=1)
+    """Number of epochs, greater than 0."""
 
     logger: Optional[Literal["wandb", "tensorboard"]] = None
+    """Logger to use during training. If None, no logger will be used. Available
+    loggers are defined in SupportedLogger."""
 
     checkpoint_callback: CheckpointModel = CheckpointModel()
+    """Checkpoint callback configuration."""
 
     early_stopping_callback: Optional[EarlyStoppingModel] = Field(
         default=None, validate_default=True
     )
-    # precision: Literal["64", "32", "16", "bf16"] = 32
+    """Early stopping callback configuration."""
 
     def __str__(self) -> str:
         """Pretty string reprensenting the configuration.

careamics/config/transformations/normalize_model.py

@@ -1,8 +1,9 @@
 """Pydantic model for the Normalize transform."""
 
-from typing import Literal
+from typing import Literal, Optional
 
-from pydantic import ConfigDict, Field
+from pydantic import ConfigDict, Field, model_validator
+from typing_extensions import Self
 
 from .transform_model import TransformModel
 
@@ -28,5 +29,32 @@ class NormalizeModel(TransformModel):
     )
 
     name: Literal["Normalize"] = "Normalize"
-    mean: float = Field(default=0.485)  # albumentations defaults
-    std: float = Field(default=0.229)
+    image_means: list = Field(..., min_length=0, max_length=32)
+    image_stds: list = Field(..., min_length=0, max_length=32)
+    target_means: Optional[list] = Field(default=None, min_length=0, max_length=32)
+    target_stds: Optional[list] = Field(default=None, min_length=0, max_length=32)
+
+    @model_validator(mode="after")
+    def validate_means_stds(self: Self) -> Self:
+        """Validate that the means and stds have the same length.
+
+        Returns
+        -------
+        Self
+            The instance of the model.
+        """
+        if len(self.image_means) != len(self.image_stds):
+            raise ValueError("The number of image means and stds must be the same.")
+
+        if (self.target_means is None) != (self.target_stds is None):
+            raise ValueError(
+                "Both target means and stds must be provided together, or bot None."
+            )
+
+        if self.target_means is not None and self.target_stds is not None:
+            if len(self.target_means) != len(self.target_stds):
+                raise ValueError(
+                    "The number of target means and stds must be the same."
+                )
+
+        return self

careamics/config/validators/validator_utils.py

@@ -72,7 +72,7 @@ def value_ge_than_8_power_of_2(
         If the value is not a power of 2.
     """
     if value < 8:
-        raise ValueError(f"Value must be non-zero positive (got {value}).")
+        raise ValueError(f"Value must be greater than 8 (got {value}).")
 
     if (value & (value - 1)) != 0:
         raise ValueError(f"Value must be a power of 2 (got {value}).")

careamics/dataset/__init__.py

@@ -1,6 +1,17 @@
 """Dataset module."""
 
-__all__ = ["InMemoryDataset", "PathIterableDataset"]
+__all__ = [
+    "InMemoryDataset",
+    "InMemoryPredDataset",
+    "InMemoryTiledPredDataset",
+    "PathIterableDataset",
+    "IterableTiledPredDataset",
+    "IterablePredDataset",
+]
 
 from .in_memory_dataset import InMemoryDataset
+from .in_memory_pred_dataset import InMemoryPredDataset
+from .in_memory_tiled_pred_dataset import InMemoryTiledPredDataset
 from .iterable_dataset import PathIterableDataset
+from .iterable_pred_dataset import IterablePredDataset
+from .iterable_tiled_pred_dataset import IterableTiledPredDataset

careamics/dataset/dataset_utils/__init__.py

@@ -2,17 +2,18 @@
 
 __all__ = [
     "reshape_array",
+    "compute_normalization_stats",
     "get_files_size",
     "list_files",
     "validate_source_target_files",
-    "read_tiff",
-    "get_read_func",
-    "read_zarr",
+    "iterate_over_files",
+    "WelfordStatistics",
 ]
 
 
-from .dataset_utils import reshape_array
+from .dataset_utils import (
+    reshape_array,
+)
 from .file_utils import get_files_size, list_files, validate_source_target_files
-from .read_tiff import read_tiff
-from .read_utils import get_read_func
-from .read_zarr import read_zarr
+from .iterate_over_files import iterate_over_files
+from .running_stats import WelfordStatistics, compute_normalization_stats

careamics/dataset/dataset_utils/file_utils.py

@@ -33,7 +33,7 @@ def list_files(
     data_type: Union[str, SupportedData],
     extension_filter: str = "",
 ) -> List[Path]:
-    """Create a recursive list of files in `data_path`.
+    """List recursively files in `data_path` and return a sorted list.
 
     If `data_path` is a file, its name is validated against the `data_type` using
     `fnmatch`, and the method returns `data_path` itself.
@@ -75,7 +75,7 @@ def list_files(
         raise FileNotFoundError(f"Data path {data_path} does not exist.")
 
     # get extension compatible with fnmatch and rglob search
-    extension = SupportedData.get_extension(data_type)
+    extension = SupportedData.get_extension_pattern(data_type)
 
     if data_type == SupportedData.CUSTOM and extension_filter != "":
         extension = extension_filter

careamics/dataset/dataset_utils/iterate_over_files.py

@@ -0,0 +1,83 @@
+"""Function to iterate over files."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Callable, Generator, Optional, Union
+
+from numpy.typing import NDArray
+from torch.utils.data import get_worker_info
+
+from careamics.config import DataConfig, InferenceConfig
+from careamics.file_io.read import read_tiff
+from careamics.utils.logging import get_logger
+
+from .dataset_utils import reshape_array
+
+logger = get_logger(__name__)
+
+
+def iterate_over_files(
+    data_config: Union[DataConfig, InferenceConfig],
+    data_files: list[Path],
+    target_files: Optional[list[Path]] = None,
+    read_source_func: Callable = read_tiff,
+) -> Generator[tuple[NDArray, Optional[NDArray]], None, None]:
+    """Iterate over data source and yield whole reshaped images.
+
+    Parameters
+    ----------
+    data_config : CAREamics DataConfig or InferenceConfig
+        Configuration.
+    data_files : list of pathlib.Path
+        List of data files.
+    target_files : list of pathlib.Path, optional
+        List of target files, by default None.
+    read_source_func : Callable, optional
+        Function to read the source, by default read_tiff.
+
+    Yields
+    ------
+    NDArray
+        Image.
+    """
+    # When num_workers > 0, each worker process will have a different copy of the
+    # dataset object
+    # Configuring each copy independently to avoid having duplicate data returned
+    # from the workers
+    worker_info = get_worker_info()
+    worker_id = worker_info.id if worker_info is not None else 0
+    num_workers = worker_info.num_workers if worker_info is not None else 1
+
+    # iterate over the files
+    for i, filename in enumerate(data_files):
+        # retrieve file corresponding to the worker id
+        if i % num_workers == worker_id:
+            try:
+                # read data
+                sample = read_source_func(filename, data_config.axes)
+
+                # reshape array
+                reshaped_sample = reshape_array(sample, data_config.axes)
+
+                # read target, if available
+                if target_files is not None:
+                    if filename.name != target_files[i].name:
+                        raise ValueError(
+                            f"File {filename} does not match target file "
+                            f"{target_files[i]}. Have you passed sorted "
+                            f"arrays?"
+                        )
+
+                    # read target
+                    target = read_source_func(target_files[i], data_config.axes)
+
+                    # reshape target
+                    reshaped_target = reshape_array(target, data_config.axes)
+
+                    yield reshaped_sample, reshaped_target
+                else:
+                    yield reshaped_sample, None
+
+            except Exception as e:
+                logger.error(f"Error reading file {filename}: {e}")

careamics/dataset/dataset_utils/running_stats.py

@@ -0,0 +1,186 @@
+"""Computing data statistics."""
+
+import numpy as np
+from numpy.typing import NDArray
+
+
+def compute_normalization_stats(image: NDArray) -> tuple[NDArray, NDArray]:
+    """
+    Compute mean and standard deviation of an array.
+
+    Expected input shape is (S, C, (Z), Y, X). The mean and standard deviation are
+    computed per channel.
+
+    Parameters
+    ----------
+    image : NDArray
+        Input array.
+
+    Returns
+    -------
+    tuple of (list of floats, list of floats)
+        Lists of mean and standard deviation values per channel.
+    """
+    # Define the list of axes excluding the channel axis
+    axes = tuple(np.delete(np.arange(image.ndim), 1))
+    return np.mean(image, axis=axes), np.std(image, axis=axes)
+
+
+def update_iterative_stats(
+    count: NDArray, mean: NDArray, m2: NDArray, new_values: NDArray
+) -> tuple[NDArray, NDArray, NDArray]:
+    """Update the mean and variance of an array iteratively.
+
+    Parameters
+    ----------
+    count : NDArray
+        Number of elements in the array.
+    mean : NDArray
+        Mean of the array.
+    m2 : NDArray
+        Variance of the array.
+    new_values : NDArray
+        New values to add to the mean and variance.
+
+    Returns
+    -------
+    tuple[NDArray, NDArray, NDArray]
+        Updated count, mean, and variance.
+    """
+    count += np.array([np.prod(channel.shape) for channel in new_values])
+    # newvalues - oldMean
+    delta = [
+        np.subtract(v.flatten(), [m] * len(v.flatten()))
+        for v, m in zip(new_values, mean)
+    ]
+
+    mean += np.array([np.sum(d / c) for d, c in zip(delta, count)])
+    # newvalues - newMeant
+    delta2 = [
+        np.subtract(v.flatten(), [m] * len(v.flatten()))
+        for v, m in zip(new_values, mean)
+    ]
+
+    m2 += np.array([np.sum(d * d2) for d, d2 in zip(delta, delta2)])
+
+    return (count, mean, m2)
+
+
+def finalize_iterative_stats(
+    count: NDArray, mean: NDArray, m2: NDArray
+) -> tuple[NDArray, NDArray]:
+    """Finalize the mean and variance computation.
+
+    Parameters
+    ----------
+    count : NDArray
+        Number of elements in the array.
+    mean : NDArray
+        Mean of the array.
+    m2 : NDArray
+        Variance of the array.
+
+    Returns
+    -------
+    tuple[NDArray, NDArray]
+        Final mean and standard deviation.
+    """
+    std = np.array([np.sqrt(m / c) for m, c in zip(m2, count)])
+    if any(c < 2 for c in count):
+        return np.full(mean.shape, np.nan), np.full(std.shape, np.nan)
+    else:
+        return mean, std
+
+
+class WelfordStatistics:
+    """Compute Welford statistics iteratively.
+
+    The Welford algorithm is used to compute the mean and variance of an array
+    iteratively. Based on the implementation from:
+    https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Welford's_online_algorithm
+    """
+
+    def update(self, array: NDArray, sample_idx: int) -> None:
+        """Update the Welford statistics.
+
+        Parameters
+        ----------
+        array : NDArray
+            Input array.
+        sample_idx : int
+            Current sample number.
+        """
+        self.sample_idx = sample_idx
+        sample_channels = np.array(np.split(array, array.shape[1], axis=1))
+
+        # Initialize the statistics
+        if self.sample_idx == 0:
+            # Compute the mean and standard deviation
+            self.mean, _ = compute_normalization_stats(array)
+            # Initialize the count and m2 with zero-valued arrays of shape (C,)
+            self.count, self.mean, self.m2 = update_iterative_stats(
+                count=np.zeros(array.shape[1]),
+                mean=self.mean,
+                m2=np.zeros(array.shape[1]),
+                new_values=sample_channels,
+            )
+        else:
+            # Update the statistics
+            self.count, self.mean, self.m2 = update_iterative_stats(
+                count=self.count, mean=self.mean, m2=self.m2, new_values=sample_channels
+            )
+
+        self.sample_idx += 1
+
+    def finalize(self) -> tuple[NDArray, NDArray]:
+        """Finalize the Welford statistics.
+
+        Returns
+        -------
+        tuple or numpy arrays
+            Final mean and standard deviation.
+        """
+        return finalize_iterative_stats(self.count, self.mean, self.m2)
+
+
+# from multiprocessing import Value
+# from typing import tuple
+
+# import numpy as np
+
+
+# class RunningStats:
+#     """Calculates running mean and std."""
+
+#     def __init__(self) -> None:
+#         self.reset()
+
+#     def reset(self) -> None:
+#         """Reset the running stats."""
+#         self.avg_mean = Value("d", 0)
+#         self.avg_std = Value("d", 0)
+#         self.m2 = Value("d", 0)
+#         self.count = Value("i", 0)
+
+#     def init(self, mean: float, std: float) -> None:
+#         """Initialize running stats."""
+#         with self.avg_mean.get_lock():
+#             self.avg_mean.value += mean
+#         with self.avg_std.get_lock():
+#             self.avg_std.value = std
+
+#     def compute_std(self) -> tuple[float, float]:
+#         """Compute std."""
+#         if self.count.value >= 2:
+#             self.avg_std.value = np.sqrt(self.m2.value / self.count.value)
+
+#     def update(self, value: float) -> None:
+#         """Update running stats."""
+#         with self.count.get_lock():
+#             self.count.value += 1
+#         delta = value - self.avg_mean.value
+#         with self.avg_mean.get_lock():
+#             self.avg_mean.value += delta / self.count.value
+#         delta2 = value - self.avg_mean.value
+#         with self.m2.get_lock():
+#             self.m2.value += delta * delta2