swcgeom 0.17.0__tar.gz → 0.17.2__tar.gz

{swcgeom-0.17.0 → swcgeom-0.17.2}/CHANGELOG.md

@@ -1,5 +1,36 @@
 # Changelog
 
+## **0.17.2**&emsp;<sub><sup>2024-08-07 ([9d5347d...59a5cbf](https://github.com/yzx9/swcgeom/compare/9d5347d0a427f460b92fd86c596e40a23812e48d...59a5cbfbe78f18a95ff8f35e72a4a0f0cdbc5009?diff=split))</sup></sub>
+
+### Bug Fixes
+
+##### &ensp;`analysis`
+
+- handle zero partition asymmetry in lmeasure ([1f332f2](https://github.com/yzx9/swcgeom/commit/1f332f22f465ea1ec7ff0b5e4013ddb6d64ffa5d))
+- workaround with angle ([05d2ff7](https://github.com/yzx9/swcgeom/commit/05d2ff77ba5f4b4331daca0bade89e10a56f564d))
+
+##### &ensp;`utils`
+
+- download with multiprocessing should avoid locals func ([6aff3e0](https://github.com/yzx9/swcgeom/commit/6aff3e0ee06fb527f759e6ec9ac09ab1ca745dad))
+
+
+### BREAKING CHANGES
+-  rename bifurcation to furcation ([26e9dec](https://github.com/yzx9/swcgeom/commit/26e9dec2db5b7d457dfe52d9a8e0177d26bc5b07))
+- `core` lazy loading in range indexing ([7d38ea8](https://github.com/yzx9/swcgeom/commit/7d38ea80fefc907c3f55663c052db9b81f144d68))
+<br>
+
+
+## **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

{swcgeom-0.17.0/swcgeom.egg-info → swcgeom-0.17.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.17.0
+Version: 0.17.2
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: Apache-2.0
@@ -20,7 +20,7 @@ Requires-Dist: seaborn>=0.12.0
 Requires-Dist: tifffile>=2022.8.12
 Requires-Dist: typing_extensions>=4.4.0
 Requires-Dist: tqdm>=4.46.1
-Requires-Dist: v3d-py-helper>=0.1.0
+Requires-Dist: v3d-py-helper==0.1.0
 Provides-Extra: all
 Requires-Dist: beautifulsoup4>=4.11.1; extra == "all"
 Requires-Dist: certifi>=2023.5.7; extra == "all"

{swcgeom-0.17.0 → swcgeom-0.17.2}/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-0.17.0 → swcgeom-0.17.2}/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-0.17.0 → swcgeom-0.17.2}/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-0.17.0 → swcgeom-0.17.2}/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-0.17.0 → swcgeom-0.17.2}/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-0.17.0 → swcgeom-0.17.2}/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
@@ -40,7 +41,7 @@ class BranchDataset(torch.utils.data.Dataset, Generic[T]):
         save : Union[str, bool], default `True`
             Save branch data to file if not False. If `True`, automatically
             generate file name.
-        transfroms : Transfroms[Branch, T], optional
+        transforms : Transforms[Branch, T], optional
             Branch transformations.
 
         See Also

{swcgeom-0.17.0 → swcgeom-0.17.2}/examples/pytorch/tree_folder_dataset.py

@@ -30,7 +30,7 @@ class TreeFolderDataset(torch.utils.data.Dataset, Generic[T]):
         ----------
         swc_dir : str
             Path of SWC file directory.
-        transfroms : Transfroms[Tree, T], optional
+        transforms : Transforms[Tree, T], optional
             Branch transformations.
 
         See Also

{swcgeom-0.17.0 → swcgeom-0.17.2}/pyproject.toml

@@ -23,7 +23,7 @@ dependencies = [
     "tifffile>=2022.8.12",
     "typing_extensions>=4.4.0",
     "tqdm>=4.46.1",
-    "v3d-py-helper>=0.1.0",
+    "v3d-py-helper==0.1.0",
 ]
 
 [project.optional-dependencies]

{swcgeom-0.17.0 → swcgeom-0.17.2}/swcgeom/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.17.0'
-__version_tuple__ = version_tuple = (0, 17, 0)
+__version__ = version = '0.17.2'
+__version_tuple__ = version_tuple = (0, 17, 2)

{swcgeom-0.17.0 → swcgeom-0.17.2}/swcgeom/analysis/feature_extractor.py

@@ -7,10 +7,11 @@ 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
@@ -18,8 +19,8 @@ import seaborn as sns
 from matplotlib.axes import Axes
 
 from swcgeom.analysis.features import (
-    BifurcationFeatures,
     BranchFeatures,
+    FurcationFeatures,
     NodeFeatures,
     PathFeatures,
     TipFeatures,
@@ -39,6 +40,9 @@ Feature = Literal[
     "node_count",
     "node_radial_distance",
     "node_branch_order",
+    # furcation nodes
+    "furcation_count",
+    "furcation_radial_distance",
     # bifurcation nodes
     "bifurcation_count",
     "bifurcation_radial_distance",
@@ -54,9 +58,9 @@ 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"])
+Feature1D = set(["length", "volume", "node_count", "furcation_count", "tip_count"])
 
 
 class Features:
@@ -69,7 +73,7 @@ class Features:
     @cached_property
     def node_features(self) -> NodeFeatures: return NodeFeatures(self.tree)
     @cached_property
-    def bifurcation_features(self) -> BifurcationFeatures: return BifurcationFeatures(self.node_features)
+    def furcation_features(self) -> FurcationFeatures: return FurcationFeatures(self.node_features)
     @cached_property
     def tip_features(self) -> TipFeatures: return TipFeatures(self.node_features)
     @cached_property
@@ -121,9 +125,9 @@ 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 +172,7 @@ 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)
@@ -213,6 +217,12 @@ class FeatureExtractor(ABC):
     ) -> Axes:
         raise NotImplementedError()
 
+    def get_bifurcation_count(self, **kwargs):
+        raise DeprecationWarning("Use `furcation_count` instead.")
+
+    def get_bifurcation_radial_distance(self, **kwargs):
+        raise DeprecationWarning("Use `furcation_radial_distance` instead.")
+
 
 class TreeFeatureExtractor(FeatureExtractor):
     """Extract feature from tree."""
@@ -234,7 +244,7 @@ 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 +274,7 @@ 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 +289,7 @@ 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 +305,7 @@ 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 +343,7 @@ 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 +358,7 @@ 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 +379,7 @@ 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-0.17.0 → swcgeom-0.17.2}/swcgeom/analysis/features.py

@@ -2,11 +2,11 @@
 
 from abc import ABC, abstractmethod
 from functools import cached_property
-from typing import List, TypeVar
+from typing import TypeVar
 
 import numpy as np
 import numpy.typing as npt
-from typing_extensions import Self
+from typing_extensions import Self, deprecated
 
 from swcgeom.core import Branch, BranchTree, Tree
 
@@ -121,12 +121,24 @@ class _SubsetNodesFeatures(ABC):
         return cls(NodeFeatures(tree))
 
 
-class BifurcationFeatures(_SubsetNodesFeatures):
-    """Evaluate bifurcation node feature of tree."""
+class FurcationFeatures(_SubsetNodesFeatures):
+    """Evaluate furcation node feature of tree."""
 
     @cached_property
     def nodes(self) -> npt.NDArray[np.bool_]:
-        return np.array([n.is_bifurcation() for n in self._features.tree])
+        return np.array([n.is_furcation() for n in self._features.tree])
+
+
+@deprecated("Use FurcationFeatures instead")
+class BifurcationFeatures(FurcationFeatures):
+    """Evaluate bifurcation node feature of tree.
+
+    Notes
+    -----
+    Deprecated due to the wrong spelling of furcation. For now, it
+    is just an alias of `FurcationFeatures` and raise a warning. It
+    will be change to raise an error in the future.
+    """
 
 
 class TipFeatures(_SubsetNodesFeatures):
@@ -163,7 +175,7 @@ class PathFeatures:
         return np.array([path.tortuosity() for path in self._paths], dtype=np.float32)
 
     @cached_property
-    def _paths(self) -> List[Tree.Path]:
+    def _paths(self) -> list[Tree.Path]:
         return self.tree.get_paths()
 
 
@@ -201,7 +213,7 @@ class BranchFeatures:
         return self.calc_angle(self._branches, eps=eps)
 
     @staticmethod
-    def calc_angle(branches: List[T], eps: float = 1e-7) -> npt.NDArray[np.float32]:
+    def calc_angle(branches: list[T], eps: float = 1e-7) -> npt.NDArray[np.float32]:
         """Calc agnle between branches.
 
         Returns
@@ -219,5 +231,5 @@ class BranchFeatures:
         return angle
 
     @cached_property
-    def _branches(self) -> List[Tree.Branch]:
+    def _branches(self) -> list[Tree.Branch]:
         return self.tree.get_branches()

{swcgeom-0.17.0 → swcgeom-0.17.2}/swcgeom/analysis/lmeasure.py

@@ -1,13 +1,11 @@
 """L-Measure analysis."""
 
 import math
-from typing import Literal, Tuple
+from typing import Literal
 
 import numpy as np
 import numpy.typing as npt
-
 from swcgeom.core import Branch, Compartment, Node, Tree
-from swcgeom.utils import angle
 
 __all__ = ["LMeasure"]
 
@@ -69,7 +67,7 @@ class LMeasure:
         --------
         L-Measure: http://cng.gmu.edu:8080/Lm/help/N_bifs.htm
         """
-        return len(tree.get_bifurcations())
+        return len(tree.get_furcations())
 
     def n_branch(self, tree: Tree) -> int:
         """Number of branches.
@@ -163,12 +161,15 @@ class LMeasure:
         --------
         L-Measure: http://cng.gmu.edu:8080/Lm/help/Partition_asymmetry.htm
         """
+
         children = n.children()
         assert (
             len(children) == 2
         ), "Partition asymmetry is only defined for bifurcations"
         n1 = len(children[0].subtree().get_tips())
         n2 = len(children[1].subtree().get_tips())
+        if n1 == n2:
+            return 0
         return abs(n1 - n2) / (n1 + n2 - 2)
 
     def fractal_dim(self):
@@ -274,7 +275,7 @@ 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 +285,7 @@ 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)
@@ -336,7 +337,7 @@ class LMeasure:
         return (da**rall_power + db**rall_power) / dp**rall_power
 
     def bif_ampl_local(self, bif: Tree.Node) -> float:
-        """Bifuraction angle.
+        """Bifurcation angle.
 
         Given a bifurcation, this function returns the angle between
         the first two compartments (in degree).
@@ -350,7 +351,7 @@ class LMeasure:
         return np.degrees(angle(v1, v2))
 
     def bif_ampl_remote(self, bif: Tree.Node) -> float:
-        """Bifuraction angle.
+        """Bifurcation angle.
 
         This function returns the angle between two bifurcation points
         or between bifurcation point and terminal point or between two
@@ -361,7 +362,7 @@ class LMeasure:
         L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_ampl_remote.htm
         """
 
-        v1, v2 = self._bif_vector_local(bif)
+        v1, v2 = self._bif_vector_remote(bif)
         return np.degrees(angle(v1, v2))
 
     def bif_tilt_local(self, bif: Tree.Node) -> float:
@@ -501,7 +502,7 @@ 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 +512,7 @@ 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"
 
@@ -665,7 +666,7 @@ class LMeasure:
         n = node
         order = 0
         while n is not None:
-            if n.is_bifurcation():
+            if n.is_furcation():
                 order += 1
             n = n.parent()
         return order
@@ -819,3 +820,23 @@ def pill_surface_area(ra: float, rb: float, h: float) -> float:
     bottom_hemisphere_area = 2 * math.pi * rb**2
     total_area = lateral_area + top_hemisphere_area + bottom_hemisphere_area
     return total_area
+
+
+# TODO: move to `utils`
+def angle(a: npt.ArrayLike, b: npt.ArrayLike) -> float:
+    """Get the angle of vectors.
+
+    Returns
+    -------
+    angle : float
+        Angle [0, PI) in radians.
+    """
+
+    a, b = np.array(a), np.array(b)
+    if np.linalg.norm(a) == 0 or np.linalg.norm(b) == 0:
+        raise ValueError("Input vectors must not be zero vectors.")
+
+    costheta = np.dot(a, b) / (np.linalg.norm(a) * np.linalg.norm(b))
+    costheta = np.clip(costheta, -1, 1)  # avoid numerical errors
+    theta = np.arccos(costheta)
+    return theta

{swcgeom-0.17.0 → swcgeom-0.17.2}/swcgeom/analysis/sholl.py

@@ -1,13 +1,14 @@
 """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
 import seaborn as sns
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
+from typing_extensions import deprecated
 
 from swcgeom.analysis.visualization import draw
 from swcgeom.core import Tree
@@ -84,18 +85,18 @@ 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`
@@ -160,20 +161,17 @@ class Sholl:
 
         return self.get_rs(self.rmax, steps)
 
+    @deprecated("Use `Sholl.get(x)` instead")
     def get_count(self) -> npt.NDArray[np.int32]:
         """Get the count of intersection.
 
         .. deprecated:: 0.5.0
-            Use :meth:`Sholl.get` instead.
+            Use :meth:`Sholl(x).get()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.get_count` has been renamed to `get` since v0.5.0, "
-            "and will be removed in next version",
-            DeprecationWarning,
-        )
         return self.get().astype(np.int32)
 
+    @deprecated("Use `Shool(x).get().mean()` instead")
     def avg(self) -> float:
         """Get the average of the count of intersection.
 
@@ -181,14 +179,9 @@ class Sholl:
             Use :meth:`Shool(x).get().mean()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.avg` has been deprecated since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().mean()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().mean()
 
+    @deprecated("Use `Shool(x).get().std()` instead")
     def std(self) -> float:
         """Get the std of the count of intersection.
 
@@ -196,14 +189,9 @@ class Sholl:
             Use :meth:`Shool(x).get().std()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.std` has been deprecate since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().std()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().std()
 
+    @deprecated("Use `Shool(x).get().sum()` instead")
     def sum(self) -> int:
         """Get the sum of the count of intersection.
 
@@ -211,10 +199,4 @@ class Sholl:
             Use :meth:`Shool(x).get().sum()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.sum` has been deprecate since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().sum()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().sum()