swcgeom 0.16.0__tar.gz → 0.17.1__tar.gz

{swcgeom-0.16.0 → swcgeom-0.17.1}/CHANGELOG.md

@@ -1,5 +1,36 @@
 # Changelog
 
+## **0.17.1**&emsp;<sub><sup>2024-04-05 ([a8007ac...0ef3c2b](https://github.com/yzx9/swcgeom/compare/a8007ac6c5eb7de03298dbdcc6be59d3c282e125...0ef3c2b370a570366a79ef456c1125d12f006409?diff=split))</sup></sub>
+
+### Features
+
+##### &ensp;`utils`
+
+- set round style ([90030e3](https://github.com/yzx9/swcgeom/commit/90030e3af1dc7ba763e04c313cb93f154e2f052c))
+
+<br>
+
+
+## **0.17.0**&emsp;<sub><sup>2024-04-04 ([59257cb...2072139](https://github.com/yzx9/swcgeom/compare/59257cbfb6264afd3ca31fcba002f692bbb69ed0...20721393086e5a890b097b3ae32aaa1e4ad6b898?diff=split))</sup></sub>
+
+### Features
+
+##### &ensp;`images`
+
+- handle raw file in terafly ([67ecd63](https://github.com/yzx9/swcgeom/commit/67ecd63bf4124d49b00e779c2702a7b939ef710b))
+- add image stack dtype support ([7313ead](https://github.com/yzx9/swcgeom/commit/7313ead09ec61970f221b9e0c3691d31c269b591))
+
+##### &ensp;`transforms`
+
+- add new image transformation classes ([7b5d805](https://github.com/yzx9/swcgeom/commit/7b5d805a1aa0deac3f9d7576a9aecab36b59774b))
+- add image flip and notes ([5f2a4d1](https://github.com/yzx9/swcgeom/commit/5f2a4d1a9c2b5fb68e8221c7b024a411b247ab6d))
+
+
+### BREAKING CHANGES
+- `images` remove deprecated \`swap\_xy\` and \`filp\_xy\` flag ([2072139](https://github.com/yzx9/swcgeom/commit/20721393086e5a890b097b3ae32aaa1e4ad6b898))
+<br>
+
+
 ## **0.16.0**&emsp;<sub><sup>2024-03-16 ([bf2bf95...7029483](https://github.com/yzx9/swcgeom/compare/bf2bf95ee9fbfb7eba871db7303292f1dfcc7b8f...70294836643e51ca43d039887bbd71de3a9b561b?diff=split))</sup></sub>
 
 ### Features

{swcgeom-0.16.0/swcgeom.egg-info → swcgeom-0.17.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.16.0
+Version: 0.17.1
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: Apache-2.0

{swcgeom-0.16.0 → swcgeom-0.17.1}/examples/CollectTips.ipynb

@@ -23,7 +23,6 @@
     "import os\n",
     "from functools import reduce\n",
     "from operator import add\n",
-    "from typing import List\n",
     "\n",
     "import numpy as np\n",
     "\n",
@@ -37,11 +36,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def collect_tips(cur: swcgeom.Tree.Node, children: List[int]) -> int:\n",
+    "def collect_tips(cur: swcgeom.Tree.Node, children: list[int]) -> int:\n",
     "    cur[\"tips\"] = max(1, reduce(add, children, 0))\n",
     "    return cur[\"tips\"]\n",
     "\n",
-    "def collect_length(cur: swcgeom.Tree.Node, children: List[swcgeom.Tree.Node]) -> swcgeom.Tree.Node:\n",
+    "def collect_length(cur: swcgeom.Tree.Node, children: list[swcgeom.Tree.Node]) -> swcgeom.Tree.Node:\n",
     "    def length(acc: float, child: swcgeom.Tree.Node) -> float:\n",
     "        return acc + cur.distance(child) + child[\"length\"]\n",
     "\n",

{swcgeom-0.16.0 → swcgeom-0.17.1}/examples/CutTree.ipynb

@@ -30,7 +30,6 @@
    "outputs": [],
    "source": [
     "import math\n",
-    "from typing import List\n",
     "\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
@@ -138,7 +137,7 @@
     "\n",
     "    removals = []\n",
     "\n",
-    "    def collect_cut(n: Tree.Node, children: List[int]) -> int:\n",
+    "    def collect_cut(n: Tree.Node, children: list[int]) -> int:\n",
     "        if len(children) <= 1:\n",
     "            return n.id\n",
     "\n",

{swcgeom-0.16.0 → swcgeom-0.17.1}/examples/Features.ipynb

@@ -20,7 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from typing import Any, cast, Dict\n",
+    "from typing import Any, cast\n",
     "\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
@@ -88,7 +88,7 @@
    ],
    "source": [
     "features = extract_feature(tree3)\n",
-    "all_features: Dict[Feature, Dict] = {\n",
+    "all_features: dict[Feature, dict] = {\n",
     "    \"length\": {},\n",
     "    \"node_radial_distance\": {},\n",
     "    \"node_branch_order\": {},\n",

{swcgeom-0.16.0 → swcgeom-0.17.1}/examples/dgl/graph.py

@@ -1,6 +1,6 @@
 """Dgl grapth transforms."""
 
-from typing import List, cast
+from typing import cast
 
 import dgl
 
@@ -19,13 +19,13 @@ class ToDGLGraph(Transform[Tree, dgl.DGLGraph]):
     this class is more of a toy and template.
     """
 
-    keys: List[str] | None
+    keys: list[str] | None
     to_bidirected: bool
 
     def __init__(
         self,
         to_bidirected: bool = False,
-        keys: List[str] | None = None,
+        keys: list[str] | None = None,
     ) -> None:
         """Transofrm tree to dgl graph.
 
@@ -33,7 +33,7 @@ class ToDGLGraph(Transform[Tree, dgl.DGLGraph]):
         ----------
         to_bidirected : bool, default to `False`
             If True, return bidirected graph.
-        keys : List[str], optional
+        keys : list[str], optional
             Copy these keys as ndata of graph.
         """
 

{swcgeom-0.16.0 → swcgeom-0.17.1}/examples/pytorch/branch.py

@@ -1,6 +1,7 @@
 """Transformations in branch requires pytorch."""
 
-from typing import Callable, Literal
+from collections.abc import Callable
+from typing import Literal
 
 import numpy as np
 import numpy.typing as npt

{swcgeom-0.16.0 → swcgeom-0.17.1}/examples/pytorch/branch_dataset.py

@@ -2,7 +2,8 @@
 
 import os
 import warnings
-from typing import Generic, Iterable, TypeVar, cast
+from collections.abc import Iterable
+from typing import Generic, TypeVar, cast
 
 import torch
 import torch.utils.data

{swcgeom-0.16.0 → swcgeom-0.17.1}/swcgeom/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.16.0'
-__version_tuple__ = version_tuple = (0, 16, 0)
+__version__ = version = '0.17.1'
+__version_tuple__ = version_tuple = (0, 17, 1)

{swcgeom-0.16.0 → swcgeom-0.17.1}/swcgeom/analysis/__init__.py

@@ -1,9 +1,7 @@
 """Analysis for neuron trees."""
 
-from swcgeom.analysis.branch_features import *
 from swcgeom.analysis.feature_extractor import *
-from swcgeom.analysis.node_features import *
-from swcgeom.analysis.path_features import *
+from swcgeom.analysis.features import *
 from swcgeom.analysis.sholl import *
 from swcgeom.analysis.trunk import *
 from swcgeom.analysis.visualization import *

{swcgeom-0.16.0 → swcgeom-0.17.1}/swcgeom/analysis/feature_extractor.py

@@ -7,23 +7,24 @@ naming specification.
 """
 
 from abc import ABC, abstractmethod
+from collections.abc import Callable
 from functools import cached_property
 from itertools import chain
 from os.path import basename
-from typing import Any, Callable, Dict, List, Literal, Tuple, overload
+from typing import Any, Literal, overload
 
 import numpy as np
 import numpy.typing as npt
 import seaborn as sns
 from matplotlib.axes import Axes
 
-from swcgeom.analysis.branch_features import BranchFeatures
-from swcgeom.analysis.node_features import (
+from swcgeom.analysis.features import (
     BifurcationFeatures,
+    BranchFeatures,
     NodeFeatures,
+    PathFeatures,
     TipFeatures,
 )
-from swcgeom.analysis.path_features import PathFeatures
 from swcgeom.analysis.sholl import Sholl
 from swcgeom.analysis.volume import get_volume
 from swcgeom.core import Population, Populations, Tree
@@ -54,7 +55,7 @@ Feature = Literal[
 ]
 
 NDArrayf32 = npt.NDArray[np.float32]
-FeatAndKwargs = Feature | Tuple[Feature, Dict[str, Any]]
+FeatAndKwargs = Feature | tuple[Feature, dict[str, Any]]
 
 Feature1D = set(["length", "volume", "node_count", "bifurcation_count", "tip_count"])
 
@@ -121,9 +122,9 @@ class FeatureExtractor(ABC):
     @overload
     def get(self, feature: Feature, **kwargs) -> NDArrayf32: ...
     @overload
-    def get(self, feature: List[FeatAndKwargs]) -> List[NDArrayf32]: ...
+    def get(self, feature: list[FeatAndKwargs]) -> list[NDArrayf32]: ...
     @overload
-    def get(self, feature: Dict[Feature, Dict[str, Any]]) -> Dict[str, NDArrayf32]: ...
+    def get(self, feature: dict[Feature, dict[str, Any]]) -> dict[str, NDArrayf32]: ...
     # fmt:on
     def get(self, feature, **kwargs):
         """Get feature.
@@ -168,7 +169,7 @@ class FeatureExtractor(ABC):
 
     # Custom Plots
 
-    def plot_node_branch_order(self, feature_kwargs: Dict[str, Any], **kwargs) -> Axes:
+    def plot_node_branch_order(self, feature_kwargs: dict[str, Any], **kwargs) -> Axes:
         vals = self._get("node_branch_order", **feature_kwargs)
         bin_edges = np.arange(int(np.ceil(vals.max() + 1))) + 0.5
         return self._plot_histogram_impl(vals, bin_edges, **kwargs)
@@ -234,7 +235,7 @@ class TreeFeatureExtractor(FeatureExtractor):
 
     def plot_sholl(
         self,
-        feature_kwargs: Dict[str, Any],  # pylint: disable=unused-argument
+        feature_kwargs: dict[str, Any],  # pylint: disable=unused-argument
         **kwargs,
     ) -> Axes:
         _, ax = self._features.sholl.plot(**kwargs)
@@ -264,7 +265,7 @@ class PopulationFeatureExtractor(FeatureExtractor):
     """Extract features from population."""
 
     _population: Population
-    _features: List[Features]
+    _features: list[Features]
 
     def __init__(self, population: Population) -> None:
         super().__init__()
@@ -279,7 +280,7 @@ class PopulationFeatureExtractor(FeatureExtractor):
 
     # Custom Plots
 
-    def plot_sholl(self, feature_kwargs: Dict[str, Any], **kwargs) -> Axes:
+    def plot_sholl(self, feature_kwargs: dict[str, Any], **kwargs) -> Axes:
         vals, rs = self._get_sholl_impl(**feature_kwargs)
         ax = self._lineplot(xs=rs, ys=vals.flatten(), **kwargs)
         ax.set_ylabel("Count of Intersections")
@@ -295,7 +296,7 @@ class PopulationFeatureExtractor(FeatureExtractor):
 
     def _get_sholl_impl(
         self, steps: int = 20, **kwargs
-    ) -> Tuple[NDArrayf32, NDArrayf32]:
+    ) -> tuple[NDArrayf32, NDArrayf32]:
         rmax = max(t.sholl.rmax for t in self._features)
         rs = Sholl.get_rs(rmax=rmax, steps=steps)
         vals = self._get_impl("sholl", steps=rs, **kwargs)
@@ -333,7 +334,7 @@ class PopulationsFeatureExtractor(FeatureExtractor):
     """Extract feature from population."""
 
     _populations: Populations
-    _features: List[List[Features]]
+    _features: list[list[Features]]
 
     def __init__(self, populations: Populations) -> None:
         super().__init__()
@@ -348,7 +349,7 @@ class PopulationsFeatureExtractor(FeatureExtractor):
 
     # Custom Plots
 
-    def plot_sholl(self, feature_kwargs: Dict[str, Any], **kwargs) -> Axes:
+    def plot_sholl(self, feature_kwargs: dict[str, Any], **kwargs) -> Axes:
         vals, rs = self._get_sholl_impl(**feature_kwargs)
         ax = self._lineplot(xs=rs, ys=vals, **kwargs)
         ax.set_ylabel("Count of Intersections")
@@ -369,7 +370,7 @@ class PopulationsFeatureExtractor(FeatureExtractor):
 
     def _get_sholl_impl(
         self, steps: int = 20, **kwargs
-    ) -> Tuple[NDArrayf32, NDArrayf32]:
+    ) -> tuple[NDArrayf32, NDArrayf32]:
         rmaxs = chain.from_iterable((t.sholl.rmax for t in p) for p in self._features)
         rmax = max(rmaxs)
         rs = Sholl.get_rs(rmax=rmax, steps=steps)

swcgeom-0.16.0/swcgeom/analysis/node_features.py → swcgeom-0.17.1/swcgeom/analysis/features.py

@@ -1,15 +1,26 @@
-"""Depth distribution of tree."""
+"""Feature anlysis of tree."""
 
 from abc import ABC, abstractmethod
 from functools import cached_property
+from typing import TypeVar
 
 import numpy as np
 import numpy.typing as npt
 from typing_extensions import Self
 
-from swcgeom.core import BranchTree, Tree
+from swcgeom.core import Branch, BranchTree, Tree
 
-__all__ = ["NodeFeatures", "BifurcationFeatures", "TipFeatures"]
+__all__ = [
+    "NodeFeatures",
+    "BifurcationFeatures",
+    "TipFeatures",
+    "PathFeatures",
+    "BranchFeatures",
+]
+
+T = TypeVar("T", bound=Branch)
+
+# Node Level
 
 
 class NodeFeatures:
@@ -31,6 +42,7 @@ class NodeFeatures:
         -------
         count : array of shape (1,)
         """
+
         return np.array([self.tree.number_of_nodes()], dtype=np.float32)
 
     def get_radial_distance(self) -> npt.NDArray[np.float32]:
@@ -41,6 +53,7 @@ class NodeFeatures:
         radial_distance : npt.NDArray[np.float32]
             Array of shape (N,).
         """
+
         xyz = self.tree.xyz() - self.tree.soma().xyz()
         radial_distance = np.linalg.norm(xyz, axis=1)
         return radial_distance
@@ -58,6 +71,7 @@ class NodeFeatures:
         order : npt.NDArray[np.int32]
             Array of shape (N,), which k is the number of branchs.
         """
+
         order = np.zeros_like(self._branch_tree.id(), dtype=np.int32)
 
         def assign_depth(n: Tree.Node, pre_depth: int | None) -> int:
@@ -88,6 +102,7 @@ class _SubsetNodesFeatures(ABC):
         count : npt.NDArray[np.float32]
             Array of shape (1,).
         """
+
         return np.array([np.count_nonzero(self.nodes)], dtype=np.float32)
 
     def get_radial_distance(self) -> npt.NDArray[np.float32]:
@@ -98,6 +113,7 @@ class _SubsetNodesFeatures(ABC):
         radial_distance : npt.NDArray[np.float32]
             Array of shape (N,).
         """
+
         return self._features.get_radial_distance()[self.nodes]
 
     @classmethod
@@ -119,3 +135,89 @@ class TipFeatures(_SubsetNodesFeatures):
     @cached_property
     def nodes(self) -> npt.NDArray[np.bool_]:
         return np.array([n.is_tip() for n in self._features.tree])
+
+
+# Path Level
+
+
+class PathFeatures:
+    """Path analysis of tree."""
+
+    tree: Tree
+
+    def __init__(self, tree: Tree) -> None:
+        self.tree = tree
+
+    def get_count(self) -> int:
+        return len(self._paths)
+
+    def get_length(self) -> npt.NDArray[np.float32]:
+        """Get length of paths."""
+
+        length = [path.length() for path in self._paths]
+        return np.array(length, dtype=np.float32)
+
+    def get_tortuosity(self) -> npt.NDArray[np.float32]:
+        """Get tortuosity of path."""
+
+        return np.array([path.tortuosity() for path in self._paths], dtype=np.float32)
+
+    @cached_property
+    def _paths(self) -> list[Tree.Path]:
+        return self.tree.get_paths()
+
+
+class BranchFeatures:
+    """Analysis bransh of tree."""
+
+    tree: Tree
+
+    def __init__(self, tree: Tree) -> None:
+        self.tree = tree
+
+    def get_count(self) -> int:
+        return len(self._branches)
+
+    def get_length(self) -> npt.NDArray[np.float32]:
+        """Get length of branches."""
+
+        length = [br.length() for br in self._branches]
+        return np.array(length, dtype=np.float32)
+
+    def get_tortuosity(self) -> npt.NDArray[np.float32]:
+        """Get tortuosity of path."""
+
+        return np.array([br.tortuosity() for br in self._branches], dtype=np.float32)
+
+    def get_angle(self, eps: float = 1e-7) -> npt.NDArray[np.float32]:
+        """Get agnle between branches.
+
+        Returns
+        -------
+        angle : npt.NDArray[np.float32]
+            An array of shape (N, N), which N is length of branches.
+        """
+
+        return self.calc_angle(self._branches, eps=eps)
+
+    @staticmethod
+    def calc_angle(branches: list[T], eps: float = 1e-7) -> npt.NDArray[np.float32]:
+        """Calc agnle between branches.
+
+        Returns
+        -------
+        angle : npt.NDArray[np.float32]
+            An array of shape (N, N), which N is length of branches.
+        """
+
+        vector = np.array([br[-1].xyz() - br[0].xyz() for br in branches])
+        vector_dot = np.matmul(vector, vector.T)
+        vector_norm = np.linalg.norm(vector, ord=2, axis=1, keepdims=True)
+        vector_norm_dot = np.matmul(vector_norm, vector_norm.T) + eps
+        arccos = np.clip(vector_dot / vector_norm_dot, -1, 1)
+        angle = np.arccos(arccos)
+        return angle
+
+    @cached_property
+    def _branches(self) -> list[Tree.Branch]:
+        return self.tree.get_branches()

{swcgeom-0.16.0 → swcgeom-0.17.1}/swcgeom/analysis/lmeasure.py

@@ -1,7 +1,7 @@
 """L-Measure analysis."""
 
 import math
-from typing import Literal, Tuple
+from typing import Literal
 
 import numpy as np
 import numpy.typing as npt
@@ -274,7 +274,7 @@ class LMeasure:
         rall_power, _, _, _ = self._rall_power(bif)
         return rall_power
 
-    def _rall_power_d(self, bif: Tree.Node) -> Tuple[float, float, float]:
+    def _rall_power_d(self, bif: Tree.Node) -> tuple[float, float, float]:
         children = bif.children()
         assert len(children) == 2, "Rall Power is only defined for bifurcations"
         parent = bif.parent()
@@ -284,7 +284,7 @@ class LMeasure:
         da, db = 2 * children[0].r, 2 * children[1].r
         return dp, da, db
 
-    def _rall_power(self, bif: Tree.Node) -> Tuple[float, float, float, float]:
+    def _rall_power(self, bif: Tree.Node) -> tuple[float, float, float, float]:
         dp, da, db = self._rall_power_d(bif)
         start, stop, step = 0, 5, 5 / 1000
         xs = np.arange(start, stop, step)
@@ -501,7 +501,7 @@ class LMeasure:
 
     def _bif_vector_local(
         self, bif: Tree.Node
-    ) -> Tuple[npt.NDArray[np.float32], npt.NDArray[np.float32]]:
+    ) -> tuple[npt.NDArray[np.float32], npt.NDArray[np.float32]]:
         children = bif.children()
         assert len(children) == 2, "Only defined for bifurcations"
 
@@ -511,7 +511,7 @@ class LMeasure:
 
     def _bif_vector_remote(
         self, bif: Tree.Node
-    ) -> Tuple[npt.NDArray[np.float32], npt.NDArray[np.float32]]:
+    ) -> tuple[npt.NDArray[np.float32], npt.NDArray[np.float32]]:
         children = bif.children()
         assert len(children) == 2, "Only defined for bifurcations"
 

{swcgeom-0.16.0 → swcgeom-0.17.1}/swcgeom/analysis/sholl.py

@@ -1,7 +1,7 @@
 """Sholl analysis."""
 
 import warnings
-from typing import List, Literal, Optional, Tuple
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -84,18 +84,18 @@ class Sholl:
 
     def plot(  # pylint: disable=too-many-arguments
         self,
-        steps: List[float] | int = 20,
+        steps: list[float] | int = 20,
         plot_type: str | None = None,
         kind: Literal["bar", "linechart", "circles"] = "circles",
         fig: Figure | None = None,
         ax: Axes | None = None,
         **kwargs,
-    ) -> Tuple[Figure, Axes]:
+    ) -> tuple[Figure, Axes]:
         """Plot Sholl analysis.
 
         Parameters
         ----------
-        steps : int or List[float], default to 20
+        steps : int or list[float], default to 20
             Steps of raius of circle. If steps is int, then it will be
             evenly divided into n radii.
         kind : "bar" | "linechart" | "circles", default `circles`

{swcgeom-0.16.0 → swcgeom-0.17.1}/swcgeom/analysis/trunk.py

@@ -2,8 +2,9 @@
 
 # pylint: disable=invalid-name
 
+from collections.abc import Iterable
 from itertools import chain
-from typing import Any, Dict, Iterable, List, Literal, Optional, Tuple, cast
+from typing import Any, Literal, Optional, cast
 
 import numpy as np
 import numpy.typing as npt
@@ -28,28 +29,28 @@ def draw_trunk(
     *,
     fig: Optional[Figure] = None,
     ax: Optional[Axes] = None,
-    bound: Bounds | Tuple[Bounds, Dict[str, Any]] | None = "ellipse",
-    point: bool | Dict[str, Any] = True,
+    bound: Bounds | tuple[Bounds, dict[str, Any]] | None = "ellipse",
+    point: bool | dict[str, Any] = True,
     projection: Projection = "2d",
     cmap: Any = "viridis",
     **kwargs,
-) -> Tuple[Figure, Axes]:
+) -> tuple[Figure, Axes]:
     """Draw trunk tree.
 
     Parameters
     ----------
     t : Tree
-    florets : List of (int | List of int)
+    florets : List of (int | list of int)
         The florets that needs to be removed, each floret can be a
         subtree or multiple subtrees (e.g., dendrites are a bunch of
         subtrees), each number is the id of a tree node.
     fig : ~matplotlib.figure.Figure, optional
     ax : ~matplotlib.axes.Axes, optional
-    bound : Bounds | (Bounds, Dict[str, Any]) | None, default 'ellipse'
+    bound : Bounds | (Bounds, dict[str, Any]) | None, default 'ellipse'
         Kind of bound, support 'aabb', 'ellipse'. If bound is None, no
         bound will be drawn. If bound is a tuple, the second item will
         used as kwargs and forward to draw function.
-    point : bool | Dict[str, Any], default True
+    point : bool | dict[str, Any], default True
         Draw point at the start of a subtree. If point is False, no
         point will be drawn. If point is a dict, this will used a
         kwargs and forward to draw function.
@@ -57,7 +58,7 @@ def draw_trunk(
         Colormap, any value supported by ~matplotlib.cm.Colormap. We
         will use the ratio of the length of the subtree to the total
         length of the tree to determine the color.
-    **kwargs : Dict[str, Any]
+    **kwargs : dict[str, Any]
         Forward to ~swcgeom.analysis.draw.
     """
     # pylint: disable=too-many-locals
@@ -83,14 +84,14 @@ def draw_trunk(
 
 def split_florets(
     t: Tree, florets: Iterable[int | Iterable[int]]
-) -> Tuple[Tree, List[List[Tree]]]:
+) -> tuple[Tree, list[list[Tree]]]:
     florets = [[i] if isinstance(i, (int, np.integer)) else i for i in florets]
     subtrees = [[get_subtree(t, ff) for ff in f] for f in florets]
     trunk = to_subtree(t, chain(*florets))
     return trunk, subtrees
 
 
-def get_length_ratio(t: Tree, tss: List[List[Tree]]) -> Any:
+def get_length_ratio(t: Tree, tss: list[list[Tree]]) -> Any:
     lens = np.array([sum(t.length() for t in ts) for ts in tss])
     return lens / t.length()
 
@@ -101,7 +102,7 @@ def get_length_ratio(t: Tree, tss: List[List[Tree]]) -> Any:
 def draw_bound(
     ts: Iterable[Tree],
     ax: Axes,
-    bound: Bounds | Tuple[Bounds, Dict[str, Any]],
+    bound: Bounds | tuple[Bounds, dict[str, Any]],
     projection: Projection,
     **kwargs,
 ) -> None:

{swcgeom-0.16.0 → swcgeom-0.17.1}/swcgeom/analysis/visualization.py

@@ -2,7 +2,7 @@
 
 import os
 import weakref
-from typing import Any, Dict, List, Literal, Optional, Tuple
+from typing import Any, Literal, Optional
 
 import numpy as np
 from matplotlib.axes import Axes
@@ -21,15 +21,15 @@ from swcgeom.utils import (
 
 __all__ = ["draw"]
 
-Positions = Literal["lt", "lb", "rt", "rb"] | Tuple[float, float]
-locations: Dict[Literal["lt", "lb", "rt", "rb"], Tuple[float, float]] = {
+Positions = Literal["lt", "lb", "rt", "rb"] | tuple[float, float]
+locations: dict[Literal["lt", "lb", "rt", "rb"], tuple[float, float]] = {
     "lt": (0.10, 0.90),
     "lb": (0.10, 0.10),
     "rt": (0.90, 0.90),
     "rb": (0.90, 0.10),
 }
 
-ax_weak_memo = weakref.WeakKeyDictionary[Axes, Dict[str, Any]]({})
+ax_weak_memo = weakref.WeakKeyDictionary[Axes, dict[str, Any]]({})
 
 
 def draw(
@@ -39,7 +39,7 @@ def draw(
     ax: Optional[Axes] = None,
     show: bool | None = None,
     camera: CameraOptions = "xy",
-    color: Optional[Dict[int, str] | str] = None,
+    color: Optional[dict[int, str] | str] = None,
     label: str | bool = True,
     direction_indicator: Positions | Literal[False] = "rb",
     unit: Optional[str] = None,
@@ -64,7 +64,7 @@ def draw(
         vector, then then threat it as (look-at, up), so camera is
         ((0, 0, 0), look-at, up). An easy way is to use the presets
         "xy", "yz" and "zx".
-    color : Dict[int, str] | "vaa3d" | str, optional
+    color : dict[int, str] | "vaa3d" | str, optional
         Color map. If is dict, segments will be colored by the type of
         parent node.If is string, the value will be use for any type.
     label : str | bool, default True
@@ -120,14 +120,14 @@ def draw(
     return fig, ax
 
 
-def get_ax_swc(ax: Axes) -> List[SWCLike]:
+def get_ax_swc(ax: Axes) -> list[SWCLike]:
     ax_weak_memo.setdefault(ax, {})
     return ax_weak_memo[ax]["swc"]
 
 
 def get_ax_color(
-    ax: Axes, swc: SWCLike, color: Optional[Dict[int, str] | str] = None
-) -> str | List[str]:
+    ax: Axes, swc: SWCLike, color: Optional[dict[int, str] | str] = None
+) -> str | list[str]:
     if color == "vaa3d":
         color = palette.vaa3d
     elif isinstance(color, str):