careamics 0.0.4.2__py3-none-any.whl → 0.0.6__py3-none-any.whl

careamics/dataset/dataset_utils/file_utils.py

@@ -2,7 +2,7 @@
 
 from fnmatch import fnmatch
 from pathlib import Path
-from typing import List, Union
+from typing import Union
 
 import numpy as np
 
@@ -12,12 +12,12 @@ from careamics.utils.logging import get_logger
 logger = get_logger(__name__)
 
 
-def get_files_size(files: List[Path]) -> float:
+def get_files_size(files: list[Path]) -> float:
     """Get files size in MB.
 
     Parameters
     ----------
-    files : List[Path]
+    files : list of pathlib.Path
         List of files.
 
     Returns
@@ -32,7 +32,7 @@ def list_files(
     data_path: Union[str, Path],
     data_type: Union[str, SupportedData],
     extension_filter: str = "",
-) -> List[Path]:
+) -> list[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
@@ -55,8 +55,8 @@ def list_files(
 
     Returns
     -------
-    List[Path]
-        List of pathlib.Path objects.
+    list[Path]
+        list of pathlib.Path objects.
 
     Raises
     ------
@@ -105,7 +105,7 @@ def list_files(
     return files
 
 
-def validate_source_target_files(src_files: List[Path], tar_files: List[Path]) -> None:
+def validate_source_target_files(src_files: list[Path], tar_files: list[Path]) -> None:
     """
     Validate source and target path lists.
 
@@ -113,9 +113,9 @@ def validate_source_target_files(src_files: List[Path], tar_files: List[Path]) -
 
     Parameters
     ----------
-    src_files : List[Path]
+    src_files : list of pathlib.Path
         List of source files.
-    tar_files : List[Path]
+    tar_files : list of pathlib.Path
         List of target files.
 
     Raises

careamics/dataset/dataset_utils/iterate_over_files.py

@@ -2,13 +2,14 @@
 
 from __future__ import annotations
 
+from collections.abc import Generator
 from pathlib import Path
-from typing import Callable, Generator, Optional, Union
+from typing import Callable, Optional, Union
 
 from numpy.typing import NDArray
 from torch.utils.data import get_worker_info
 
-from careamics.config import DataConfig, InferenceConfig
+from careamics.config import GeneralDataConfig, InferenceConfig
 from careamics.file_io.read import read_tiff
 from careamics.utils.logging import get_logger
 
@@ -18,7 +19,7 @@ logger = get_logger(__name__)
 
 
 def iterate_over_files(
-    data_config: Union[DataConfig, InferenceConfig],
+    data_config: Union[GeneralDataConfig, InferenceConfig],
     data_files: list[Path],
     target_files: Optional[list[Path]] = None,
     read_source_func: Callable = read_tiff,

careamics/dataset/dataset_utils/running_stats.py

@@ -34,36 +34,35 @@ def update_iterative_stats(
     Parameters
     ----------
     count : NDArray
-        Number of elements in the array.
+        Number of elements in the array. Shape: (C,).
     mean : NDArray
-        Mean of the array.
+        Mean of the array. Shape: (C,).
     m2 : NDArray
-        Variance of the array.
+        Variance of the array. Shape: (C,).
     new_values : NDArray
-        New values to add to the mean and variance.
+        New values to add to the mean and variance. Shape: (C, 1, 1, Z, Y, X).
 
     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)
-    ]
+    num_channels = len(new_values)
 
-    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)
-    ]
+    # --- update channel-wise counts ---
+    count += np.ones_like(count) * np.prod(new_values.shape[1:])
 
-    m2 += np.array([np.sum(d * d2) for d, d2 in zip(delta, delta2)])
+    # --- update channel-wise mean ---
+    # compute (new_values - old_mean) -> shape: (C, Z*Y*X)
+    delta = new_values.reshape(num_channels, -1) - mean.reshape(num_channels, 1)
+    mean += np.sum(delta / count.reshape(num_channels, 1), axis=1)
 
-    return (count, mean, m2)
+    # --- update channel-wise SoS ---
+    # compute (new_values - new_mean) -> shape: (C, Z*Y*X)
+    delta2 = new_values.reshape(num_channels, -1) - mean.reshape(num_channels, 1)
+    m2 += np.sum(delta * delta2, axis=1)
+
+    return count, mean, m2
 
 
 def finalize_iterative_stats(
@@ -74,18 +73,18 @@ def finalize_iterative_stats(
     Parameters
     ----------
     count : NDArray
-        Number of elements in the array.
+        Number of elements in the array. Shape: (C,).
     mean : NDArray
-        Mean of the array.
+        Mean of the array. Shape: (C,).
     m2 : NDArray
-        Variance of the array.
+        Variance of the array. Shape: (C,).
 
     Returns
     -------
     tuple[NDArray, NDArray]
-        Final mean and standard deviation.
+        Final channel-wise mean and standard deviation.
     """
-    std = np.array([np.sqrt(m / c) for m, c in zip(m2, count)])
+    std = np.sqrt(m2 / count)
     if any(c < 2 for c in count):
         return np.full(mean.shape, np.nan), np.full(std.shape, np.nan)
     else:

careamics/dataset/in_memory_dataset.py

@@ -9,13 +9,9 @@ from typing import Any, Callable, Optional, Union
 import numpy as np
 from torch.utils.data import Dataset
 
-from careamics.file_io.read import read_tiff
-from careamics.transforms import Compose
-
-from ..config import DataConfig
-from ..config.transformations import NormalizeModel
-from ..utils.logging import get_logger
-from .patching.patching import (
+from careamics.config import GeneralDataConfig, N2VDataConfig
+from careamics.config.transformations import NormalizeModel
+from careamics.dataset.patching.patching import (
     PatchedOutput,
     Stats,
     prepare_patches_supervised,
@@ -23,6 +19,9 @@ from .patching.patching import (
     prepare_patches_unsupervised,
     prepare_patches_unsupervised_array,
 )
+from careamics.file_io.read import read_tiff
+from careamics.transforms import Compose
+from careamics.utils.logging import get_logger
 
 logger = get_logger(__name__)
 
@@ -47,7 +46,7 @@ class InMemoryDataset(Dataset):
 
     def __init__(
         self,
-        data_config: DataConfig,
+        data_config: GeneralDataConfig,
         inputs: Union[np.ndarray, list[Path]],
         input_target: Optional[Union[np.ndarray, list[Path]]] = None,
         read_source_func: Callable = read_tiff,
@@ -58,7 +57,7 @@ class InMemoryDataset(Dataset):
 
         Parameters
         ----------
-        data_config : DataConfig
+        data_config : GeneralDataConfig
             Data configuration.
         inputs : numpy.ndarray or list[pathlib.Path]
             Input data.
@@ -124,7 +123,7 @@ class InMemoryDataset(Dataset):
                     target_stds=self.target_stats.stds,
                 )
             ]
-            + self.data_config.transforms,
+            + list(self.data_config.transforms),
         )
 
     def _prepare_patches(self, supervised: bool) -> PatchedOutput:
@@ -219,12 +218,12 @@ class InMemoryDataset(Dataset):
 
             return self.patch_transform(patch=patch, target=target)
 
-        elif self.data_config.has_n2v_manipulate():  # TODO not compatible with HDN
+        elif isinstance(self.data_config, N2VDataConfig):
             return self.patch_transform(patch=patch)
         else:
             raise ValueError(
                 "Something went wrong! No target provided (not supervised training) "
-                "and no N2V manipulation (no N2V training)."
+                "while the algorithm is not Noise2Void."
             )
 
     def get_data_statistics(self) -> tuple[list[float], list[float]]:

careamics/dataset/iterable_dataset.py

@@ -10,7 +10,7 @@ from typing import Callable, Optional
 import numpy as np
 from torch.utils.data import IterableDataset
 
-from careamics.config import DataConfig
+from careamics.config import GeneralDataConfig
 from careamics.config.transformations import NormalizeModel
 from careamics.file_io.read import read_tiff
 from careamics.transforms import Compose
@@ -49,7 +49,7 @@ class PathIterableDataset(IterableDataset):
 
     def __init__(
         self,
-        data_config: DataConfig,
+        data_config: GeneralDataConfig,
         src_files: list[Path],
         target_files: Optional[list[Path]] = None,
         read_source_func: Callable = read_tiff,
@@ -58,7 +58,7 @@ class PathIterableDataset(IterableDataset):
 
         Parameters
         ----------
-        data_config : DataConfig
+        data_config : GeneralDataConfig
             Data configuration.
         src_files : list[Path]
             List of data files.
@@ -115,7 +115,7 @@ class PathIterableDataset(IterableDataset):
                     target_stds=self.target_stats.stds,
                 )
             ]
-            + data_config.transforms
+            + list(data_config.transforms)
         )
 
     def _calculate_mean_and_std(self) -> tuple[Stats, Stats]:

careamics/dataset/iterable_pred_dataset.py

@@ -2,8 +2,9 @@
 
 from __future__ import annotations
 
+from collections.abc import Generator
 from pathlib import Path
-from typing import Any, Callable, Generator
+from typing import Any, Callable
 
 from numpy.typing import NDArray
 from torch.utils.data import IterableDataset

careamics/dataset/iterable_tiled_pred_dataset.py

@@ -2,8 +2,9 @@
 
 from __future__ import annotations
 
+from collections.abc import Generator
 from pathlib import Path
-from typing import Any, Callable, Generator
+from typing import Any, Callable
 
 from numpy.typing import NDArray
 from torch.utils.data import IterableDataset

careamics/dataset/patching/random_patching.py

@@ -1,6 +1,7 @@
 """Random patching utilities."""
 
-from typing import Generator, List, Optional, Tuple, Union
+from collections.abc import Generator
+from typing import Optional, Union
 
 import numpy as np
 import zarr
@@ -11,10 +12,10 @@ from .validate_patch_dimension import validate_patch_dimensions
 # TOOD split in testable functions
 def extract_patches_random(
     arr: np.ndarray,
-    patch_size: Union[List[int], Tuple[int, ...]],
+    patch_size: Union[list[int], tuple[int, ...]],
     target: Optional[np.ndarray] = None,
     seed: Optional[int] = None,
-) -> Generator[Tuple[np.ndarray, Optional[np.ndarray]], None, None]:
+) -> Generator[tuple[np.ndarray, Optional[np.ndarray]], None, None]:
     """
     Generate patches from an array in a random manner.
 
@@ -31,12 +32,12 @@ def extract_patches_random(
     ----------
     arr : np.ndarray
         Input image array.
-    patch_size : Tuple[int]
+    patch_size : tuple of int
         Patch sizes in each dimension.
     target : Optional[np.ndarray], optional
         Target array, by default None.
-    seed : Optional[int], optional
-        Random seed, by default None.
+    seed : int or None, default=None
+        Random seed.
 
     Yields
     ------
@@ -112,8 +113,8 @@ def extract_patches_random(
 
 def extract_patches_random_from_chunks(
     arr: zarr.Array,
-    patch_size: Union[List[int], Tuple[int, ...]],
-    chunk_size: Union[List[int], Tuple[int, ...]],
+    patch_size: Union[list[int], tuple[int, ...]],
+    chunk_size: Union[list[int], tuple[int, ...]],
     chunk_limit: Optional[int] = None,
     seed: Optional[int] = None,
 ) -> Generator[np.ndarray, None, None]:
@@ -127,9 +128,9 @@ def extract_patches_random_from_chunks(
     ----------
     arr : np.ndarray
         Input image array.
-    patch_size : Union[List[int], Tuple[int, ...]]
+    patch_size : Union[list[int], tuple[int, ...]]
         Patch sizes in each dimension.
-    chunk_size : Union[List[int], Tuple[int, ...]]
+    chunk_size : Union[list[int], tuple[int, ...]]
         Chunk sizes to load from the.
     chunk_limit : Optional[int], optional
         Number of chunks to load, by default None.

careamics/dataset/patching/sequential_patching.py

@@ -1,6 +1,6 @@
 """Sequential patching functions."""
 
-from typing import List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import numpy as np
 from skimage.util import view_as_windows
@@ -9,21 +9,21 @@ from .validate_patch_dimension import validate_patch_dimensions
 
 
 def _compute_number_of_patches(
-    arr_shape: Tuple[int, ...], patch_sizes: Union[List[int], Tuple[int, ...]]
-) -> Tuple[int, ...]:
+    arr_shape: tuple[int, ...], patch_sizes: Union[list[int], tuple[int, ...]]
+) -> tuple[int, ...]:
     """
     Compute the number of patches that fit in each dimension.
 
     Parameters
     ----------
-    arr_shape : Tuple[int, ...]
+    arr_shape : tuple[int, ...]
         Shape of the input array.
-    patch_sizes : Union[List[int], Tuple[int, ...]
+    patch_sizes : Union[list[int], tuple[int, ...]
         Shape of the patches.
 
     Returns
     -------
-    Tuple[int, ...]
+    tuple[int, ...]
         Number of patches in each dimension.
     """
     if len(arr_shape) != len(patch_sizes):
@@ -47,8 +47,8 @@ def _compute_number_of_patches(
 
 
 def _compute_overlap(
-    arr_shape: Tuple[int, ...], patch_sizes: Union[List[int], Tuple[int, ...]]
-) -> Tuple[int, ...]:
+    arr_shape: tuple[int, ...], patch_sizes: Union[list[int], tuple[int, ...]]
+) -> tuple[int, ...]:
     """
     Compute the overlap between patches in each dimension.
 
@@ -57,14 +57,14 @@ def _compute_overlap(
 
     Parameters
     ----------
-    arr_shape : Tuple[int, ...]
+    arr_shape : tuple[int, ...]
         Input array shape.
-    patch_sizes : Union[List[int], Tuple[int, ...]]
+    patch_sizes : Union[list[int], tuple[int, ...]]
         Size of the patches.
 
     Returns
     -------
-    Tuple[int, ...]
+    tuple[int, ...]
         Overlap between patches in each dimension.
     """
     n_patches = _compute_number_of_patches(arr_shape, patch_sizes)
@@ -80,21 +80,21 @@ def _compute_overlap(
 
 
 def _compute_patch_steps(
-    patch_sizes: Union[List[int], Tuple[int, ...]], overlaps: Tuple[int, ...]
-) -> Tuple[int, ...]:
+    patch_sizes: Union[list[int], tuple[int, ...]], overlaps: tuple[int, ...]
+) -> tuple[int, ...]:
     """
     Compute steps between patches.
 
     Parameters
     ----------
-    patch_sizes : Tuple[int]
+    patch_sizes : tuple[int]
         Size of the patches.
-    overlaps : Tuple[int]
+    overlaps : tuple[int]
         Overlap between patches.
 
     Returns
     -------
-    Tuple[int]
+    tuple[int]
         Steps between patches.
     """
     steps = [
@@ -107,9 +107,9 @@ def _compute_patch_steps(
 # TODO why stack the target here and not on a different dimension before this function?
 def _compute_patch_views(
     arr: np.ndarray,
-    window_shape: List[int],
-    step: Tuple[int, ...],
-    output_shape: List[int],
+    window_shape: list[int],
+    step: tuple[int, ...],
+    output_shape: list[int],
     target: Optional[np.ndarray] = None,
 ) -> np.ndarray:
     """
@@ -119,11 +119,11 @@ def _compute_patch_views(
     ----------
     arr : np.ndarray
         Array from which the views are extracted.
-    window_shape : Tuple[int]
+    window_shape : tuple[int]
         Shape of the views.
-    step : Tuple[int]
+    step : tuple[int]
         Steps between views.
-    output_shape : Tuple[int]
+    output_shape : tuple[int]
         Shape of the output array.
     target : Optional[np.ndarray], optional
         Target array, by default None.
@@ -150,9 +150,9 @@ def _compute_patch_views(
 
 def extract_patches_sequential(
     arr: np.ndarray,
-    patch_size: Union[List[int], Tuple[int, ...]],
+    patch_size: Union[list[int], tuple[int, ...]],
     target: Optional[np.ndarray] = None,
-) -> Tuple[np.ndarray, Optional[np.ndarray]]:
+) -> tuple[np.ndarray, Optional[np.ndarray]]:
     """
     Generate patches from an array in a sequential manner.
 
@@ -163,14 +163,14 @@ def extract_patches_sequential(
     ----------
     arr : np.ndarray
         Input image array.
-    patch_size : Tuple[int]
+    patch_size : tuple[int]
         Patch sizes in each dimension.
     target : Optional[np.ndarray], optional
         Target array, by default None.
 
     Returns
     -------
-    Tuple[np.ndarray, Optional[np.ndarray]]
+    tuple[np.ndarray, Optional[np.ndarray]]
         Patches.
     """
     is_3d_patch = len(patch_size) == 3

careamics/dataset/patching/validate_patch_dimension.py

@@ -1,13 +1,13 @@
 """Patch validation functions."""
 
-from typing import List, Tuple, Union
+from typing import Union
 
 import numpy as np
 
 
 def validate_patch_dimensions(
     arr: np.ndarray,
-    patch_size: Union[List[int], Tuple[int, ...]],
+    patch_size: Union[list[int], tuple[int, ...]],
     is_3d_patch: bool,
 ) -> None:
     """
@@ -26,7 +26,7 @@ def validate_patch_dimensions(
     ----------
     arr : np.ndarray
         Input array.
-    patch_size : Union[List[int], Tuple[int, ...]]
+    patch_size : Union[list[int], tuple[int, ...]]
         Size of the patches along each dimension of the array, except the first.
     is_3d_patch : bool
         Whether the patch is 3D or not.

careamics/dataset/tiling/__init__.py

@@ -1,9 +1,9 @@
 """Tiling functions."""
 
 __all__ = [
-    "stitch_prediction",
-    "extract_tiles",
     "collate_tiles",
+    "extract_tiles",
+    "stitch_prediction",
 ]
 
 from .collate_tiles import collate_tiles

careamics/dataset/tiling/collate_tiles.py

@@ -1,6 +1,6 @@
 """Collate function for tiling."""
 
-from typing import Any, List, Tuple
+from typing import Any
 
 import numpy as np
 from torch.utils.data.dataloader import default_collate
@@ -8,7 +8,7 @@ from torch.utils.data.dataloader import default_collate
 from careamics.config.tile_information import TileInformation
 
 
-def collate_tiles(batch: List[Tuple[np.ndarray, TileInformation]]) -> Any:
+def collate_tiles(batch: list[tuple[np.ndarray, TileInformation]]) -> Any:
     """
     Collate tiles received from CAREamics prediction dataloader.
 
@@ -19,7 +19,7 @@ def collate_tiles(batch: List[Tuple[np.ndarray, TileInformation]]) -> Any:
 
     Parameters
     ----------
-    batch : List[Tuple[np.ndarray, TileInformation], ...]
+    batch : list[tuple[np.ndarray, TileInformation], ...]
         Batch of tiles.
 
     Returns

careamics/dataset/tiling/lvae_tiled_patching.py

@@ -2,7 +2,8 @@
 
 import builtins
 import itertools
-from typing import Any, Generator, Optional, Union
+from collections.abc import Generator
+from typing import Any, Optional, Union
 
 import numpy as np
 from numpy.typing import NDArray

careamics/dataset/tiling/tiled_patching.py

@@ -1,7 +1,8 @@
 """Tiled patching utilities."""
 
 import itertools
-from typing import Generator, List, Tuple, Union
+from collections.abc import Generator
+from typing import Union
 
 import numpy as np
 
@@ -10,7 +11,7 @@ from careamics.config.tile_information import TileInformation
 
 def _compute_crop_and_stitch_coords_1d(
     axis_size: int, tile_size: int, overlap: int
-) -> Tuple[List[Tuple[int, int]], List[Tuple[int, int]], List[Tuple[int, int]]]:
+) -> tuple[list[tuple[int, int]], list[tuple[int, int]], list[tuple[int, int]]]:
     """
     Compute the coordinates of each tile along an axis, given the overlap.
 
@@ -25,8 +26,8 @@ def _compute_crop_and_stitch_coords_1d(
 
     Returns
     -------
-    Tuple[Tuple[int, ...], ...]
-        Tuple of all coordinates for given axis.
+    tuple[tuple[int, ...], ...]
+        tuple of all coordinates for given axis.
     """
     # Compute the step between tiles
     step = tile_size - overlap
@@ -81,9 +82,9 @@ def _compute_crop_and_stitch_coords_1d(
 
 def extract_tiles(
     arr: np.ndarray,
-    tile_size: Union[List[int], Tuple[int, ...]],
-    overlaps: Union[List[int], Tuple[int, ...]],
-) -> Generator[Tuple[np.ndarray, TileInformation], None, None]:
+    tile_size: Union[list[int], tuple[int, ...]],
+    overlaps: Union[list[int], tuple[int, ...]],
+) -> Generator[tuple[np.ndarray, TileInformation], None, None]:
     """Generate tiles from the input array with specified overlap.
 
     The tiles cover the whole array. The method returns a generator that yields
@@ -98,14 +99,14 @@ def extract_tiles(
     ----------
     arr : np.ndarray
         Array of shape (S, C, (Z), Y, X).
-    tile_size : Union[List[int], Tuple[int]]
+    tile_size : Union[list[int], tuple[int]]
         Tile sizes in each dimension, of length 2 or 3.
-    overlaps : Union[List[int], Tuple[int]]
+    overlaps : Union[list[int], tuple[int]]
         Overlap values in each dimension, of length 2 or 3.
 
     Yields
     ------
-    Generator[Tuple[np.ndarray, TileInformation], None, None]
+    Generator[tuple[np.ndarray, TileInformation], None, None]
         Tile generator, yields the tile and additional information.
     """
     # Iterate over num samples (S)

careamics/file_io/__init__.py

@@ -1,13 +1,13 @@
 """Functions relating reading and writing image files."""
 
 __all__ = [
-    "read",
-    "write",
-    "get_read_func",
-    "get_write_func",
     "ReadFunc",
-    "WriteFunc",
     "SupportedWriteType",
+    "WriteFunc",
+    "get_read_func",
+    "get_write_func",
+    "read",
+    "write",
 ]
 
 from . import read, write

careamics/file_io/read/__init__.py

@@ -1,10 +1,10 @@
 """Functions relating to reading image files of different formats."""
 
 __all__ = [
+    "ReadFunc",
     "get_read_func",
     "read_tiff",
     "read_zarr",
-    "ReadFunc",
 ]
 
 from .get_func import ReadFunc, get_read_func