swcgeom 0.18.1__py3-none-any.whl → 0.19.0__py3-none-any.whl

swcgeom/core/tree_utils_impl.py

@@ -15,12 +15,10 @@
 
 """SWC util wrapper for tree, split to avoid circle imports.
 
-Notes
------
-Do not import `Tree` and keep this file minimized.
+NOTE: Do not import `Tree` and keep this file minimized.
 """
 
-from typing import Any, Optional
+from typing import Any
 
 import numpy as np
 import numpy.typing as npt
@@ -35,7 +33,7 @@ TreeArgs = tuple[int, dict[str, npt.NDArray[Any]], str, SWCNames]
 
 
 def get_subtree_impl(
-    swc_like: SWCLike, n: int, *, out_mapping: Optional[Mapping] = None
+    swc_like: SWCLike, n: int, *, out_mapping: Mapping | None = None
 ) -> TreeArgs:
     ids = []
     topo = (swc_like.id(), swc_like.pid())
@@ -51,7 +49,7 @@ def to_subtree_impl(
     swc_like: SWCLike,
     sub: Topology,
     *,
-    out_mapping: Optional[Mapping] = None,
+    out_mapping: Mapping | None = None,
 ) -> TreeArgs:
     (new_id, new_pid), mapping = to_sub_topology(sub)
 

swcgeom/images/__init__.py

@@ -15,5 +15,5 @@
 
 """Image Stack Related."""
 
-from swcgeom.images.folder import *
-from swcgeom.images.io import *
+from swcgeom.images.folder import *  # noqa: F403
+from swcgeom.images.io import *  # noqa: F403

swcgeom/images/augmentation.py

@@ -15,13 +15,11 @@
 
 """Play augment in image stack.
 
-Notes
------
-This is expremental code, and the API is subject to change.
+NOTE: This is expremental code, and the API is subject to change.
 """
 
 import random
-from typing import Literal, Optional
+from typing import Literal
 
 import numpy as np
 import numpy.typing as npt
@@ -67,7 +65,7 @@ class Augmentation:
         self.seed = seed
         self.rand = random.Random(seed)
 
-    def swapaxes(self, x, mode: Optional[Literal["xy", "xz", "yz"]] = None) -> NDArrf32:
+    def swapaxes(self, x, mode: Literal["xy", "xz", "yz"] | None = None) -> NDArrf32:
         if mode is None:
             modes: list[Literal["xy", "xz", "yz"]] = ["xy", "xz", "yz"]
             mode = modes[self.rand.randint(0, 2)]
@@ -82,7 +80,7 @@ class Augmentation:
             case _:
                 raise ValueError(f"invalid mode: {mode}")
 
-    def flip(self, x, mode: Optional[Literal["xy", "xz", "yz"]] = None) -> NDArrf32:
+    def flip(self, x, mode: Literal["xy", "xz", "yz"] | None = None) -> NDArrf32:
         if mode is None:
             modes: list[Literal["xy", "xz", "yz"]] = ["xy", "xz", "yz"]
             mode = modes[random.randint(0, 2)]
@@ -101,16 +99,13 @@ class Augmentation:
 fns = list(augs.keys())
 
 
-def play_augment(x: NDArrf32, method: Optional[Augmentation | int] = None) -> NDArrf32:
+def play_augment(x: NDArrf32, method: Augmentation | int | None = None) -> NDArrf32:
     """Play augment in x.
 
-    Parameters
-    ----------
-    x : Array
-        Array of shape (X, Y, Z, C)
-    method : int or str, optional
-        Augmentation method index / name. if not provided, a random
-        augment will be apply.
+    Args
+        x: Array of shape (X, Y, Z, C)
+        method: Augmentation method index / name.
+            If not provided, a random augment will be apply.
     """
 
     if isinstance(method, str):
@@ -132,31 +127,20 @@ def random_augmentations(
 ) -> npt.NDArray[np.int64]:
     """Generate a sequence of augmentations.
 
-    Parameters
-    ----------
-    n : int
-        Size of image stacks.
-    k : int
-        Each image stack augmented to K image stack.
-    seed : int | None, optional
-        Random seed, forwarding to `random.Random`
-    include_identity : bool, default `True`
-        Include identity transform.
-
-    Returns
-    -------
-    augmentations : List of (int, int)
-        Sequence of length N * K, contains image index and augmentation
-        method index.
-
-    Examples
-    --------
-    ```python
-    xs = os.listdir("path_to_imgs")
-    augs = generate_random_augmentations(len(xs), 5)
-    for i, j in range(augs):
-        x = play_augment(read_imgs(os.path.join("path_to_imgs", xs[i])), j)
-    ```
+    >>> xs = os.listdir("path_to_imgs")  # doctest: +SKIP
+    >>> augs = generate_random_augmentations(len(xs), 5)  # doctest: +SKIP
+    >>> for i, j in range(augs):  # doctest: +SKIP
+    ...     x = play_augment(read_imgs(os.path.join("path_to_imgs", xs[i])), j)
+
+    Args:
+        n: Size of image stacks.
+        k: Each image stack augmented to K image stack.
+        seed: Random seed, forwarding to `random.Random`
+        include_identity: Include identity transform.
+
+    Returns:
+        augmentations: List of (int, int)
+            Sequence of length N * K, contains index of image and augmentation method.
     """
 
     rand = random.Random(seed)

swcgeom/images/contrast.py

@@ -15,12 +15,10 @@
 
 """The contrast of an image.
 
-Notes
------
-This is expremental code, and the API is subject to change.
+NOTE: This is expremental code, and the API is subject to change.
 """
 
-from typing import Optional, overload
+from typing import overload
 
 import numpy as np
 import numpy.typing as npt
@@ -34,13 +32,11 @@ Array3D = npt.NDArray[np.float32]
 def contrast_std(image: Array3D) -> float:
     """Get the std contrast of an image stack.
 
-    Parameters
-    ----------
-    imgs : ndarray
+    Args:
+        imgs: ndarray
 
-    Returns
-    -------
-    contrast : float
+    Returns:
+        contrast
     """
     ...
 
@@ -49,21 +45,17 @@ def contrast_std(image: Array3D) -> float:
 def contrast_std(image: Array3D, contrast: float) -> Array3D:
     """Adjust the contrast of an image stack.
 
-    Parameters
-    ----------
-    imgs : ndarray
-    constrast : float
-        The contrast adjustment factor. 1.0 leaves the image unchanged.
+    Args:
+        imgs: ndarray
+        contrast: The contrast adjustment factor. 1.0 leaves the image unchanged.
 
-    Returns
-    -------
-    imgs : ndarray
-        The adjusted image.
+    Returns:
+        imgs: The adjusted image.
     """
     ...
 
 
-def contrast_std(image: Array3D, contrast: Optional[float] = None):
+def contrast_std(image: Array3D, contrast: float | None = None):
     if contrast is None:
         return np.std(image).item()
     else:
@@ -73,15 +65,9 @@ def contrast_std(image: Array3D, contrast: Optional[float] = None):
 def contrast_michelson(image: Array3D) -> float:
     """Get the Michelson contrast of an image stack.
 
-    Parameters
-    ----------
-    imgs : ndarray
-
-    Returns
-    -------
-    contrast : float
+    Returns:
+        contrast: float
     """
-
     vmax = np.max(image)
     vmin = np.min(image)
     return ((vmax - vmin) / (vmax + vmin)).item()
@@ -90,33 +76,23 @@ def contrast_michelson(image: Array3D) -> float:
 def contrast_rms(imgs: npt.NDArray[np.float32]) -> float:
     """Get the RMS contrast of an image stack.
 
-    Parameters
-    ----------
-    imgs : ndarray
-
-    Returns
-    -------
-    contrast : float
+    Returns:
+        contrast
     """
-
     return np.sqrt(np.mean(imgs**2)).item()
 
 
 def contrast_weber(imgs: Array3D, mask: npt.NDArray[np.bool_]) -> float:
     """Get the Weber contrast of an image stack.
 
-    Parameters
-    ----------
-    imgs : ndarray
-    mask : ndarray of bool
-        The mask to segment the foreground and background. 1 for
-        foreground, 0 for background.
+    Args:
+        imgs: ndarray
+        mask: The mask to segment the foreground and background.
+            1 for foreground, 0 for background.
 
-    Returns
-    -------
-    contrast : float
+    Returns:
+        contrast
     """
-
     l_foreground = np.mean(imgs, where=mask)
     l_background = np.mean(imgs, where=np.logical_not(mask))
     return ((l_foreground - l_background) / l_background).item()

swcgeom/images/folder.py

@@ -20,7 +20,7 @@ import os
 import re
 from collections.abc import Callable, Iterable
 from dataclasses import dataclass
-from typing import Generic, Literal, Optional, TypeVar, overload
+from typing import Generic, Literal, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -41,13 +41,21 @@ class ImageStackFolderBase(Generic[ScalarType, T]):
     files: list[str]
     transform: Transform[npt.NDArray[ScalarType], T]
 
-    # fmt: off
     @overload
-    def __init__(self, files: Iterable[str], *, dtype: None = ..., transform: Optional[Transform[npt.NDArray[np.float32], T]] = None) -> None: ...
+    def __init__(
+        self,
+        files: Iterable[str],
+        *,
+        transform: Transform[npt.NDArray[np.float32], T] | None = ...,
+    ) -> None: ...
     @overload
-    def __init__(self, files: Iterable[str], *, dtype: ScalarType, transform: Optional[Transform[npt.NDArray[ScalarType], T]] = None) -> None: ...
-    # fmt: on
-
+    def __init__(
+        self,
+        files: Iterable[str],
+        *,
+        dtype: ScalarType,
+        transform: Transform[npt.NDArray[ScalarType], T] | None = ...,
+    ) -> None: ...
     def __init__(self, files: Iterable[str], *, dtype=None, transform=None) -> None:
         super().__init__()
         self.files = list(files)
@@ -66,7 +74,7 @@ class ImageStackFolderBase(Generic[ScalarType, T]):
         return read_imgs(fname, dtype=self.dtype).get_full()  # type: ignore
 
     @staticmethod
-    def scan(root: str, *, pattern: Optional[str] = None) -> list[str]:
+    def scan(root: str, *, pattern: str | None = None) -> list[str]:
         if not os.path.isdir(root):
             raise NotADirectoryError(f"not a directory: {root}")
 
@@ -108,16 +116,12 @@ class ImageStackFolder(ImageStackFolderBase[ScalarType, T]):
     def stat(self, *, transform: bool = False, verbose: bool = False) -> Statistics:
         """Statistics of folder.
 
-        Parameters
-        ----------
-        transform : bool, default to False
-            Apply transform to the images. If True, you need to make
-            sure the transformed data is a ndarray.
-        verbose : bool, optional
+        NOTE: We are asserting that the images are of the same shape.
 
-        Notes
-        -----
-        We are asserting that the images are of the same shape.
+        Args:
+            transform: Apply transform to the images.
+                If True, you need to make sure the transformed data is a ndarray.
+            verbose: Show progress bar.
         """
 
         vmin, vmax = math.inf, -math.inf
@@ -134,7 +138,7 @@ class ImageStackFolder(ImageStackFolderBase[ScalarType, T]):
                 M2 = np.zeros_like(imgs)
 
             n += 1
-            delta = imgs - mean  # type: ignore
+            delta = imgs - mean
             mean += delta / n
             delta2 = imgs - mean
             M2 += delta * delta2
@@ -152,15 +156,12 @@ class ImageStackFolder(ImageStackFolderBase[ScalarType, T]):
         )
 
     @classmethod
-    def from_dir(cls, root: str, *, pattern: Optional[str] = None, **kwargs) -> Self:
+    def from_dir(cls, root: str, *, pattern: str | None = None, **kwargs) -> Self:
         """
-        Parameters
-        ----------
-        root : str
-        pattern : str, optional
-            Filter files by pattern.
-        **kwargs
-            Pass to `cls.__init__`
+        Args:
+            root: str
+            pattern: Filter files by pattern.
+            **kwargs: Pass to `cls.__init__`
         """
 
         return cls(cls.scan(root, pattern=pattern), **kwargs)
@@ -184,7 +185,7 @@ class LabeledImageStackFolder(ImageStackFolderBase[ScalarType, T]):
         root: str,
         label: int | Callable[[str], int],
         *,
-        pattern: Optional[str] = None,
+        pattern: str | None = None,
         **kwargs,
     ) -> Self:
         files = cls.scan(root, pattern=pattern)
@@ -211,15 +212,12 @@ class PathImageStackFolder(ImageStackFolderBase[ScalarType, T]):
         return self._get(self.files[idx]), relpath
 
     @classmethod
-    def from_dir(cls, root: str, *, pattern: Optional[str] = None, **kwargs) -> Self:
+    def from_dir(cls, root: str, *, pattern: str | None = None, **kwargs) -> Self:
         """
-        Parameters
-        ----------
-        root : str
-        pattern : str, optional
-            Filter files by pattern.
-        **kwargs
-            Pass to `cls.__init__`
+        Args:
+            root: str
+            pattern: Filter files by pattern.
+            **kwargs: Pass to `cls.__init__`
         """
 
         return cls(cls.scan(root, pattern=pattern), root=root, **kwargs)