swcgeom 0.17.0__py3-none-any.whl → 0.17.1__py3-none-any.whl

swcgeom/images/folder.py

@@ -4,18 +4,9 @@ import math
 import os
 import re
 import warnings
+from collections.abc import Callable, Iterable
 from dataclasses import dataclass
-from typing import (
-    Callable,
-    Generic,
-    Iterable,
-    List,
-    Literal,
-    Optional,
-    Tuple,
-    TypeVar,
-    overload,
-)
+from typing import Generic, Literal, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -33,7 +24,7 @@ T = TypeVar("T")
 class ImageStackFolderBase(Generic[ScalarType, T]):
     """Image stack folder base."""
 
-    files: List[str]
+    files: list[str]
     transform: Transform[npt.NDArray[ScalarType], T]
 
     # fmt: off
@@ -61,7 +52,10 @@ 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: Optional[str] = None) -> list[str]:
+        if not os.path.isdir(root):
+            raise NotADirectoryError(f"not a directory: {root}")
+
         is_valid = re.compile(pattern).match if pattern is not None else truthly
 
         fs = []
@@ -168,13 +162,13 @@ class ImageStackFolder(ImageStackFolderBase[ScalarType, T]):
 class LabeledImageStackFolder(ImageStackFolderBase[ScalarType, T]):
     """Image stack folder with label."""
 
-    labels: List[int]
+    labels: list[int]
 
     def __init__(self, files: Iterable[str], labels: Iterable[int], **kwargs):
         super().__init__(files, **kwargs)
         self.labels = list(labels)
 
-    def __getitem__(self, idx: int) -> Tuple[T, int]:
+    def __getitem__(self, idx: int) -> tuple[T, int]:
         return self._get(self.files[idx]), self.labels[idx]
 
     @classmethod
@@ -205,7 +199,7 @@ class PathImageStackFolder(ImageStackFolderBase[ScalarType, T]):
         super().__init__(files, **kwargs)
         self.root = root
 
-    def __getitem__(self, idx: int) -> Tuple[T, str]:
+    def __getitem__(self, idx: int) -> tuple[T, str]:
         relpath = os.path.relpath(self.files[idx], self.root)
         return self._get(self.files[idx]), relpath
 

swcgeom/images/io.py

@@ -4,20 +4,9 @@ import os
 import re
 import warnings
 from abc import ABC, abstractmethod
+from collections.abc import Callable, Iterable
 from functools import cache, lru_cache
-from typing import (
-    Any,
-    Callable,
-    Generic,
-    Iterable,
-    List,
-    Literal,
-    Optional,
-    Tuple,
-    TypeVar,
-    cast,
-    overload,
-)
+from typing import Any, Generic, Literal, Optional, TypeVar, cast, overload
 
 import nrrd
 import numpy as np
@@ -27,7 +16,7 @@ from v3dpy.loaders import PBD, Raw
 
 __all__ = ["read_imgs", "save_tiff", "read_images"]
 
-Vec3i = Tuple[int, int, int]
+Vec3i = tuple[int, int, int]
 ScalarType = TypeVar("ScalarType", bound=np.generic, covariant=True)
 
 RE_TERAFLY_ROOT = re.compile(r"^RES\((\d+)x(\d+)x(\d+)\)$")
@@ -58,17 +47,17 @@ class ImageStack(ABC, Generic[ScalarType]):
     def __getitem__(self, key: int) -> npt.NDArray[ScalarType]: ...                     # array of shape (Y, Z, C)
     @overload
     @abstractmethod
-    def __getitem__(self, key: Tuple[int, int]) -> npt.NDArray[ScalarType]: ...         # array of shape (Z, C)
+    def __getitem__(self, key: tuple[int, int]) -> npt.NDArray[ScalarType]: ...         # array of shape (Z, C)
     @overload
     @abstractmethod
-    def __getitem__(self, key: Tuple[int, int, int]) -> npt.NDArray[ScalarType]: ...    # array of shape (C,)
+    def __getitem__(self, key: tuple[int, int, int]) -> npt.NDArray[ScalarType]: ...    # array of shape (C,)
     @overload
     @abstractmethod
-    def __getitem__(self, key: Tuple[int, int, int, int]) -> ScalarType: ...            # value
+    def __getitem__(self, key: tuple[int, int, int, int]) -> ScalarType: ...            # value
     @overload
     @abstractmethod
     def __getitem__(
-        self, key: slice | Tuple[slice, slice] | Tuple[slice, slice, slice] |  Tuple[slice, slice, slice, slice],
+        self, key: slice | tuple[slice, slice] | tuple[slice, slice, slice] |  tuple[slice, slice, slice, slice],
     ) -> npt.NDArray[ScalarType]: ... # array of shape (X, Y, Z, C)
     @overload
     @abstractmethod
@@ -95,7 +84,7 @@ class ImageStack(ABC, Generic[ScalarType]):
         return self[:, :, :, :]
 
     @property
-    def shape(self) -> Tuple[int, int, int, int]:
+    def shape(self) -> tuple[int, int, int, int]:
         raise NotImplementedError()
 
 
@@ -118,7 +107,7 @@ def read_imgs(fname: str, **kwargs):  # type: ignore
         Casting data to specified dtype. If integer and float
         conversions occur, they will be scaled (assuming floats are
         between 0 and 1).
-    **kwargs : Dict[str, Any]
+    **kwargs : dict[str, Any]
         Forwarding to the corresponding reader.
     """
 
@@ -169,7 +158,7 @@ def save_tiff(
         Compression algorithm, forwarding to `tifffile.imwrite`. If no
         algorithnm is specify specified, we will use the zlib algorithm
         with compression level 6 by default.
-    **kwargs : Dict[str, Any]
+    **kwargs : dict[str, Any]
         Forwarding to `tifffile.imwrite`
     """
     if isinstance(data, ImageStack):
@@ -245,8 +234,8 @@ class NDArrayImageStack(ImageStack[ScalarType]):
         return self.imgs
 
     @property
-    def shape(self) -> Tuple[int, int, int, int]:
-        return cast(Tuple[int, int, int, int], self.imgs.shape)
+    def shape(self) -> tuple[int, int, int, int]:
+        return cast(tuple[int, int, int, int], self.imgs.shape)
 
 
 class TiffImageStack(NDArrayImageStack[ScalarType]):
@@ -324,7 +313,7 @@ class TeraflyImageStack(ImageStack[ScalarType]):
     use its coordinate system, remember to FLIP Y-AXIS BACK.
     """
 
-    _listdir: Callable[[str], List[str]]
+    _listdir: Callable[[str], list[str]]
     _read_patch: Callable[[str], npt.NDArray]
 
     def __init__(
@@ -350,7 +339,7 @@ class TeraflyImageStack(ImageStack[ScalarType]):
         self.res, self.res_dirs, self.res_patch_sizes = self.get_resolutions(root)
 
         @cache
-        def listdir(path: str) -> List[str]:
+        def listdir(path: str) -> list[str]:
             return os.listdir(path)
 
         @lru_cache(maxsize=lru_maxsize)
@@ -429,19 +418,19 @@ class TeraflyImageStack(ImageStack[ScalarType]):
         raise NotImplementedError()  # TODO
 
     @property
-    def shape(self) -> Tuple[int, int, int, int]:
+    def shape(self) -> tuple[int, int, int, int]:
         res_max = self.res[-1]
         return res_max[0], res_max[1], res_max[2], 1
 
     @classmethod
-    def get_resolutions(cls, root: str) -> Tuple[List[Vec3i], List[str], List[Vec3i]]:
+    def get_resolutions(cls, root: str) -> tuple[list[Vec3i], list[str], list[Vec3i]]:
         """Get all resolutions.
 
         Returns
         -------
         resolutions : List of (int, int, int)
             Sequence of sorted resolutions (from small to large).
-        roots : List[str]
+        roots : list[str]
             Sequence of root of resolutions respectively.
         patch_sizes : List of (int, int, int)
             Sequence of patch size of resolutions respectively.
@@ -581,7 +570,7 @@ class GrayImageStack:
     @overload
     def __getitem__(self, key: npt.NDArray[np.integer[Any]]) -> np.float32: ...
     @overload
-    def __getitem__(self, key: slice | Tuple[slice, slice] | Tuple[slice, slice, slice]) -> npt.NDArray[np.float32]: ...
+    def __getitem__(self, key: slice | tuple[slice, slice] | tuple[slice, slice, slice]) -> npt.NDArray[np.float32]: ...
     # fmt: on
     def __getitem__(self, key):
         """Get pixel/patch of image stack."""
@@ -608,7 +597,7 @@ class GrayImageStack:
         return self.imgs.get_full()[:, :, :, 0]
 
     @property
-    def shape(self) -> Tuple[int, int, int]:
+    def shape(self) -> tuple[int, int, int]:
         return self.imgs.shape[:-1]
 
 

swcgeom/transforms/image_stack.py

@@ -12,7 +12,8 @@ pip install swcgeom[all]
 import os
 import re
 import time
-from typing import Iterable, List, Optional, Tuple
+from collections.abc import Iterable
+from typing import Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -69,7 +70,7 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
         x: Tree,
         verbose: bool = True,
         *,
-        ranges: Optional[Tuple[npt.ArrayLike, npt.ArrayLike]] = None,
+        ranges: Optional[tuple[npt.ArrayLike, npt.ArrayLike]] = None,
     ) -> Iterable[npt.NDArray[np.uint8]]:
         if verbose:
             print("To image stack: " + x.source)
@@ -133,7 +134,7 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
         scene = ObjectsScene()
         scene.set_background((0, 0, 0))
 
-        def leave(n: Tree.Node, children: List[Tree.Node]) -> Tree.Node:
+        def leave(n: Tree.Node, children: list[Tree.Node]) -> Tree.Node:
             for c in children:
                 sdf = RoundCone(_tp3f(n.xyz()), _tp3f(c.xyz()), n.r, c.r).into()
                 scene.add_object(SDFObject(sdf, material).into())
@@ -175,7 +176,7 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
     def save_tif(
         fname: str,
         frames: Iterable[npt.NDArray[np.uint8]],
-        resolution: Tuple[float, float] = (1, 1),
+        resolution: tuple[float, float] = (1, 1),
     ) -> None:
         with tifffile.TiffWriter(fname) as tif:
             for frame in frames:
@@ -191,7 +192,7 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
                 )
 
 
-def _tp3f(x: npt.NDArray) -> Tuple[float, float, float]:
+def _tp3f(x: npt.NDArray) -> tuple[float, float, float]:
     """Convert to tuple of 3 floats."""
     assert len(x) == 3
     return (float(x[0]), float(x[1]), float(x[2]))

swcgeom/transforms/images.py

@@ -1,7 +1,6 @@
 """Image stack related transform."""
 
 import warnings
-from typing import Tuple
 
 import numpy as np
 import numpy.typing as npt
@@ -28,7 +27,7 @@ NDArrayf32 = npt.NDArray[np.float32]
 class ImagesCenterCrop(Transform[NDArrayf32, NDArrayf32]):
     """Get image stack center."""
 
-    def __init__(self, shape_out: int | Tuple[int, int, int]):
+    def __init__(self, shape_out: int | tuple[int, int, int]):
         super().__init__()
         self.shape_out = (
             shape_out
@@ -53,7 +52,7 @@ class Center(ImagesCenterCrop):
         Use :class:`ImagesCenterCrop` instead.
     """
 
-    def __init__(self, shape_out: int | Tuple[int, int, int]):
+    def __init__(self, shape_out: int | tuple[int, int, int]):
         warnings.warn(
             "`Center` is deprecated, use `ImagesCenterCrop` instead",
             DeprecationWarning,

swcgeom/transforms/neurolucida_asc.py

@@ -4,9 +4,7 @@ import os
 import re
 from enum import Enum, auto
 from io import TextIOBase
-from typing import Any, List, NamedTuple, Optional, cast
-
-import numpy as np
+from typing import Any, NamedTuple, Optional, cast
 
 from swcgeom.core import Tree
 from swcgeom.core.swc_utils import SWCNames, SWCTypes, get_names, get_types
@@ -116,8 +114,8 @@ class ASTNode:
         self,
         type: ASTType,
         value: Any = None,
-        tokens: Optional[List["Token"]] = None,
-        children: Optional[List["ASTNode"]] = None,
+        tokens: Optional[list["Token"]] = None,
+        children: Optional[list["ASTNode"]] = None,
     ):
         self.type = type
         self.value = value
@@ -149,7 +147,7 @@ class ASTNode:
 
 
 class AST(ASTNode):
-    def __init__(self, children: Optional[List[ASTNode]] = None, source: str = ""):
+    def __init__(self, children: Optional[list[ASTNode]] = None, source: str = ""):
         super().__init__(ASTType.ROOT, children=children)
         self.source = source
 

swcgeom/transforms/population.py

@@ -1,7 +1,5 @@
 """Transformation in population."""
 
-from typing import List
-
 from swcgeom.core import Population, Tree
 from swcgeom.transforms.base import Transform
 
@@ -16,7 +14,7 @@ class PopulationTransform(Transform[Population, Population]):
         self.transform = transform
 
     def __call__(self, population: Population) -> Population:
-        trees: List[Tree] = []
+        trees: list[Tree] = []
         for t in population:
             new_t = self.transform(t)
             if new_t.source == "":

swcgeom/transforms/tree.py

@@ -1,7 +1,8 @@
 """Transformation in tree."""
 
 import warnings
-from typing import Callable, List, Optional, Tuple
+from collections.abc import Callable
+from typing import Optional
 
 import numpy as np
 
@@ -102,7 +103,7 @@ class CutByType(Transform[Tree, Tree]):
     def __call__(self, x: Tree) -> Tree:
         removals = set(x.id()[x.type() != self.type])
 
-        def leave(n: Tree.Node, keep_children: List[bool]) -> bool:
+        def leave(n: Tree.Node, keep_children: list[bool]) -> bool:
             if n.id in removals and any(keep_children):
                 removals.remove(n.id)
             return n.id not in removals
@@ -145,7 +146,7 @@ class CutByBifurcationOrder(Transform[Tree, Tree]):
     def __repr__(self) -> str:
         return f"CutByBifurcationOrder-{self.max_bifurcation_order}"
 
-    def _enter(self, n: Tree.Node, parent_level: int | None) -> Tuple[int, bool]:
+    def _enter(self, n: Tree.Node, parent_level: int | None) -> tuple[int, bool]:
         if parent_level is None:
             level = 0
         elif n.is_bifurcation():
@@ -164,7 +165,7 @@ class CutShortTipBranch(Transform[Tree, Tree]):
     """
 
     thre: float
-    callbacks: List[Callable[[Tree.Branch], None]]
+    callbacks: list[Callable[[Tree.Branch], None]]
 
     def __init__(
         self, thre: float = 5, callback: Optional[Callable[[Tree.Branch], None]] = None
@@ -176,7 +177,7 @@ class CutShortTipBranch(Transform[Tree, Tree]):
             self.callbacks.append(callback)
 
     def __call__(self, x: Tree) -> Tree:
-        removals: List[int] = []
+        removals: list[int] = []
         self.callbacks.append(lambda br: removals.append(br[1].id))
         x.traverse(leave=self._leave)
         self.callbacks.pop()
@@ -186,8 +187,8 @@ class CutShortTipBranch(Transform[Tree, Tree]):
         return f"threshold={self.thre}"
 
     def _leave(
-        self, n: Tree.Node, children: List[Tuple[float, Tree.Node] | None]
-    ) -> Tuple[float, Tree.Node] | None:
+        self, n: Tree.Node, children: list[tuple[float, Tree.Node] | None]
+    ) -> tuple[float, Tree.Node] | None:
         if len(children) == 0:  # tip
             return 0, n
 

swcgeom/transforms/tree_assembler.py

@@ -1,7 +1,8 @@
 """Assemble a tree."""
 
+from collections.abc import Iterable
 from copy import copy
-from typing import Iterable, List, Optional, Tuple
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -18,7 +19,7 @@ from swcgeom.transforms.base import Transform
 EPS = 1e-5
 
 
-class LinesToTree(Transform[List[pd.DataFrame], Tree]):
+class LinesToTree(Transform[list[pd.DataFrame], Tree]):
     """Assemble lines to swc."""
 
     def __init__(self, *, thre: float = 0.2, undirected: bool = True):
@@ -97,7 +98,7 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
         undirected: bool = True,
         sort_nodes: bool = True,
         names: Optional[SWCNames] = None,
-    ) -> Tuple[pd.DataFrame, List[pd.DataFrame]]:
+    ) -> tuple[pd.DataFrame, list[pd.DataFrame]]:
         """Trying assemble lines to a tree.
 
         Treat the first line as a tree, find a line whose shortest distance

swcgeom/utils/ellipse.py

@@ -3,7 +3,6 @@
 # pylint: disable=invalid-name
 
 from functools import cached_property
-from typing import Tuple
 
 import numpy as np
 import numpy.linalg as la
@@ -22,7 +21,7 @@ class Ellipse:
         self.centroid = centroid
 
     @property
-    def radii(self) -> Tuple[float, float]:
+    def radii(self) -> tuple[float, float]:
         # x, y radii.
         _U, D, _V = self.svd
         rx, ry = 1.0 / np.sqrt(D)
@@ -39,7 +38,7 @@ class Ellipse:
         return b
 
     @property
-    def axes(self) -> Tuple[float, float]:
+    def axes(self) -> tuple[float, float]:
         # Major and minor semi-axis of the ellipse.
         rx, ry = self.radii
         dx, dy = 2 * rx, 2 * ry
@@ -77,7 +76,7 @@ def mvee(points: npt.NDArray[np.floating], tol: float = 1e-3) -> Ellipse:
 
 def _mvee(
     points: npt.NDArray[np.floating], tol: float = 1e-3
-) -> Tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
+) -> tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
     """Finds the Minimum Volume Enclosing Ellipsoid.
 
     Returns

swcgeom/utils/neuromorpho.py

@@ -81,7 +81,8 @@ import logging
 import math
 import os
 import urllib.parse
-from typing import Any, Callable, Dict, Iterable, List, Literal, Optional, Tuple
+from collections.abc import Callable, Iterable
+from typing import Any, Literal, Optional
 
 from tqdm import tqdm
 
@@ -116,7 +117,7 @@ SIZE_METADATA = 2 * GB
 SIZE_DATA = 20 * GB
 
 RESOURCES = Literal["morpho_cng", "morpho_source", "log_cng", "log_source"]
-DOWNLOAD_CONFIGS: Dict[RESOURCES, Tuple[str, int]] = {
+DOWNLOAD_CONFIGS: dict[RESOURCES, tuple[str, int]] = {
     # name/path: (url, size)
     "morpho_cng": (URL_MORPHO_CNG, 20 * GB),
     "morpho_source": (URL_LOG_CNG, 512 * GB),
@@ -145,7 +146,7 @@ invalid_ids = [
 # fmt: on
 
 
-def neuromorpho_is_valid(metadata: Dict[str, Any]) -> bool:
+def neuromorpho_is_valid(metadata: dict[str, Any]) -> bool:
     return metadata["neuron_id"] not in invalid_ids
 
 
@@ -209,7 +210,7 @@ class NeuroMorpho:
             self._info("skip download metadata")
 
         # file
-        def dumps(keys: List[bytes]) -> str:
+        def dumps(keys: list[bytes]) -> str:
             return json.dumps([i.decode("utf-8") for i in keys])
 
         for name in resources:
@@ -238,8 +239,8 @@ class NeuroMorpho:
         self,
         dest: Optional[str] = None,
         *,
-        group_by: Optional[str | Callable[[Dict[str, Any]], str | None]] = None,
-        where: Optional[Callable[[Dict[str, Any]], bool]] = None,
+        group_by: Optional[str | Callable[[dict[str, Any]], str | None]] = None,
+        where: Optional[Callable[[dict[str, Any]], bool]] = None,
         encoding: str | None = "utf-8",
     ) -> None:
         r"""Convert lmdb format to SWCs.
@@ -249,11 +250,11 @@ class NeuroMorpho:
         path : str
         dest : str, optional
             If None, use `path/swc`.
-        group_by : str | (metadata: Dict[str, Any]) -> str | None, optional
+        group_by : str | (metadata: dict[str, Any]) -> str | None, optional
             Group neurons by metadata. If a None is returned then no
             grouping. If a string is entered, use it as a metadata
             attribute name for grouping, e.g.: `archive`, `species`.
-        where : (metadata: Dict[str, Any]) -> bool, optional
+        where : (metadata: dict[str, Any]) -> bool, optional
             Filter neurons by metadata.
         encoding : str | None, default to `utf-8`
             Change swc encoding, part of the original data is not utf-8
@@ -346,14 +347,14 @@ class NeuroMorpho:
         pages: Optional[Iterable[int]] = None,
         page_size: int = API_PAGE_SIZE_MAX,
         **kwargs,
-    ) -> List[int]:
+    ) -> list[int]:
         r"""Download all neuron metadata.
 
         Parameters
         ----------
         path : str
             Path to save data.
-        pages : list of int, optional
+        pages : List of int, optional
             If is None, download all pages.
         verbose : bool, default False
             Show verbose log.
@@ -362,7 +363,7 @@ class NeuroMorpho:
 
         Returns
         -------
-        err_pages : list of int
+        err_pages : List of int
             Failed pages.
         """
 
@@ -402,7 +403,7 @@ class NeuroMorpho:
         override: bool = False,
         map_size: int = 512 * GB,
         **kwargs,
-    ) -> List[bytes]:
+    ) -> list[bytes]:
         """Download files.
 
         Parameters
@@ -412,7 +413,7 @@ class NeuroMorpho:
             Path to save data.
         path_metadata : str
             Path to lmdb of metadata.
-        keys : list of bytes, optional
+        keys : List of bytes, optional
             If exist, ignore `override` option. If None, download all key.
         override : bool, default False
             Override even exists.
@@ -422,7 +423,7 @@ class NeuroMorpho:
 
         Returns
         -------
-        err_keys : list of str
+        err_keys : List of str
             Failed keys.
         """
 
@@ -459,7 +460,7 @@ class NeuroMorpho:
 
     def _get_metadata(
         self, page: int, page_size: int = API_PAGE_SIZE_MAX, **kwargs
-    ) -> Dict[str, Any]:
+    ) -> dict[str, Any]:
         params = {
             "page": page,
             "size": page_size,
@@ -470,7 +471,7 @@ class NeuroMorpho:
         resp = self._get(url, **kwargs)
         return json.loads(resp)
 
-    def _get_file(self, url: str, metadata: Dict[str, Any], **kwargs) -> bytes:
+    def _get_file(self, url: str, metadata: dict[str, Any], **kwargs) -> bytes:
         """Get file.
 
         Returns

swcgeom/utils/plotter_2d.py

@@ -1,6 +1,6 @@
-"""Rendering related utils."""
+"""2D Plotting utils."""
 
-from typing import Optional, Tuple
+from typing import Optional
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -19,7 +19,12 @@ __all__ = ["draw_lines", "draw_direction_indicator", "draw_circles", "get_fig_ax
 
 
 def draw_lines(
-    ax: Axes, lines: npt.NDArray[np.floating], camera: Camera, **kwargs
+    ax: Axes,
+    lines: npt.NDArray[np.floating],
+    camera: Camera,
+    joinstyle="round",
+    capstyle="round",
+    **kwargs,
 ) -> LineCollection:
     """Draw lines.
 
@@ -43,11 +48,12 @@ def draw_lines(
     starts, ends = np.dot(T, starts.T).T[:, 0:2], np.dot(T, ends.T).T[:, 0:2]
 
     edges = np.stack([starts, ends], axis=1)
-    return ax.add_collection(LineCollection(edges, **kwargs))  # type: ignore
+    collection = LineCollection(edges, joinstyle=joinstyle, capstyle=capstyle, **kwargs)  # type: ignore
+    return ax.add_collection(collection)  # type: ignore
 
 
 def draw_direction_indicator(
-    ax: Axes, camera: Camera, loc: Tuple[float, float]
+    ax: Axes, camera: Camera, loc: tuple[float, float]
 ) -> None:
     x, y = loc
     direction = camera.MV.dot(
@@ -120,7 +126,7 @@ def draw_circles(
 
 def get_fig_ax(
     fig: Optional[Figure] = None, ax: Optional[Axes] = None
-) -> Tuple[Figure, Axes]:
+) -> tuple[Figure, Axes]:
     if fig is None and ax is not None:
         fig = ax.get_figure()
         assert fig is not None, "expecting a figure from the axes"

swcgeom/utils/plotter_3d.py

@@ -0,0 +1,31 @@
+"""3D Plotting utils."""
+
+import numpy as np
+import numpy.typing as npt
+from mpl_toolkits.mplot3d import Axes3D
+from mpl_toolkits.mplot3d.art3d import Line3DCollection
+
+__all__ = ["draw_lines_3d"]
+
+
+def draw_lines_3d(
+    ax: Axes3D,
+    lines: npt.NDArray[np.floating],
+    joinstyle="round",
+    capstyle="round",
+    **kwargs,
+):
+    """Draw lines.
+
+    Parameters
+    ----------
+    ax : ~matplotlib.axes.Axes
+    lines : A collection of coords of lines
+        Excepting a ndarray of shape (N, 2, 3), the axis-2 holds two points,
+        and the axis-3 holds the coordinates (x, y, z).
+    **kwargs : dict[str, Unknown]
+        Forwarded to `~mpl_toolkits.mplot3d.art3d.Line3DCollection`.
+    """
+
+    line_collection = Line3DCollection(lines, joinstyle=joinstyle, capstyle=capstyle, **kwargs)  # type: ignore
+    return ax.add_collection3d(line_collection)