swcgeom 0.15.0__py3-none-any.whl → 0.18.3__py3-none-any.whl

swcgeom/utils/volumetric_object.py

@@ -1,3 +1,18 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Volumetric object.
 
 This library implements the calculation of volumes for any shape
@@ -16,7 +31,7 @@ computations.
 
 import warnings
 from abc import ABC, abstractmethod
-from typing import Generic, Optional, Tuple, TypeVar
+from typing import Generic, Optional, TypeVar
 
 import numpy as np
 import numpy.typing as npt
@@ -95,7 +110,7 @@ class VolMCObject(VolObject, ABC):
             self.n_samples = n_samples
 
     @abstractmethod
-    def sample(self, n: int) -> Tuple[npt.NDArray[np.float32], float]:
+    def sample(self, n: int) -> tuple[npt.NDArray[np.float32], float]:
         """Sample points.
 
         Parameters
@@ -172,7 +187,7 @@ class VolSDFObject(VolMCObject):
         super().__init__(**kwargs)
         self.sdf = sdf
 
-    def sample(self, n: int) -> Tuple[npt.NDArray[np.float32], float]:
+    def sample(self, n: int) -> tuple[npt.NDArray[np.float32], float]:
         (min_x, min_y, min_z), (max_x, max_y, max_z) = self.sdf.bounding_box()
         samples = np.random.uniform(
             (min_x, min_y, min_z), (max_x, max_y, max_z), size=(n, 3)
@@ -186,17 +201,17 @@ class VolSDFObject(VolMCObject):
     def union(self, obj: VolObject) -> VolObject:
         if isinstance(obj, VolSDFObject):
             return VolSDFUnion(self, obj)
-        return super().union(obj)
+        raise NotImplementedError()
 
     def intersect(self, obj: VolObject) -> VolObject:
         if isinstance(obj, VolSDFObject):
             return VolSDFIntersection(self, obj)
-        return super().intersect(obj)
+        raise NotImplementedError()
 
     def subtract(self, obj: VolObject) -> VolObject:
         if isinstance(obj, VolSDFObject):
             return VolSDFDifference(self, obj)
-        return super().subtract(obj)
+        raise NotImplementedError()
 
 
 T = TypeVar("T", bound=VolSDFObject)
@@ -386,9 +401,7 @@ class VolSphere2Intersection(VolSDFIntersection[VolSphere, VolSphere]):
             return VolSphere.calc_volume(min(r1, r2))
 
         part1 = (np.pi / (12 * d)) * (r1 + r2 - d) ** 2
-        part2 = (
-            d**2 + 2 * d * r1 - 3 * r1**2 + 2 * d * r2 - 3 * r2**2 + 6 * r1 * r2
-        )
+        part2 = d**2 + 2 * d * r1 - 3 * r1**2 + 2 * d * r2 - 3 * r2**2 + 6 * r1 * r2
         return part1 * part2
 
 
@@ -497,7 +510,7 @@ class VolSphereFrustumConeUnion(VolSDFUnion[VolSphere, VolFrustumCone]):
         )
 
 
-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

{swcgeom-0.15.0.dist-info → swcgeom-0.18.3.dist-info}/LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [2024] [Zexin Yuan]
+   Copyright [yyyy] [name of copyright owner]
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

{swcgeom-0.15.0.dist-info → swcgeom-0.18.3.dist-info}/METADATA

@@ -1,33 +1,33 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: swcgeom
-Version: 0.15.0
+Version: 0.18.3
 Summary: Neuron geometry library for swc format
-Author-email: yzx9 <yuan.zx@outlook.com>
+Author-email: yzx9 <pypi@yzx9.xyz>
 License: Apache-2.0
 Project-URL: repository, https://github.com/yzx9/swcgeom
 Keywords: neuronscience,neuron,neuroanatomy,neuron-morphology
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: imagecodecs >=2023.3.16
-Requires-Dist: matplotlib >=3.5.2
-Requires-Dist: numpy >=1.22.3
-Requires-Dist: pandas >=1.4.2
-Requires-Dist: pynrrd >=1.0.0
-Requires-Dist: scipy >=1.9.1
-Requires-Dist: sdflit >=0.2.1
-Requires-Dist: seaborn >=0.12.0
-Requires-Dist: tifffile >=2022.8.12
-Requires-Dist: typing-extensions >=4.4.0
-Requires-Dist: v3d-py-helper >=0.1.0
+Requires-Dist: imagecodecs>=2023.3.16
+Requires-Dist: matplotlib>=3.5.2
+Requires-Dist: numpy>=1.22.3
+Requires-Dist: pandas>=1.4.2
+Requires-Dist: pynrrd>=1.1.0
+Requires-Dist: scipy>=1.9.1
+Requires-Dist: sdflit>=0.2.1
+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>=0.4.1
 Provides-Extra: all
-Requires-Dist: beautifulsoup4 >=4.11.1 ; extra == 'all'
-Requires-Dist: certifi >=2023.5.7 ; extra == 'all'
-Requires-Dist: chardet >=5.2.0 ; extra == 'all'
-Requires-Dist: lmdb >=1.4.1 ; extra == 'all'
-Requires-Dist: pycurl >=7.0.0 ; extra == 'all'
-Requires-Dist: tqdm >=4.46.1 ; extra == 'all'
-Requires-Dist: urllib3 >=1.26.0 ; extra == 'all'
+Requires-Dist: beautifulsoup4>=4.11.1; extra == "all"
+Requires-Dist: certifi>=2023.5.7; extra == "all"
+Requires-Dist: chardet>=5.2.0; extra == "all"
+Requires-Dist: lmdb>=1.4.1; extra == "all"
+Requires-Dist: requests>=2.0.0; extra == "all"
+Requires-Dist: urllib3>=1.26.0; extra == "all"
 
 # SWCGEOM
 
@@ -56,16 +56,20 @@ pip install build
 pip install --editable .
 ```
 
-Static analysis don't support import hook used in editable install for [PEP660](https://peps.python.org/pep-0660/) since upgrade to setuptools v64+, detail infomation at [setuptools#3518](https://github.com/pypa/setuptools/issues/3518), a workaround for vscode with pylance:
+Static analysis don't support import hook used in editable install for
+[PEP660](https://peps.python.org/pep-0660/) since upgrade to setuptools v64+,
+detail information at [setuptools#3518](https://github.com/pypa/setuptools/issues/3518),
+a workaround for vscode with pylance:
 
 ```json
 {
-    "python.analysis.extraPaths": ["/path/to/this/project"]
+  "python.analysis.extraPaths": ["/path/to/this/project"]
 }
 ```
 
 ## LICENSE
 
-This work is licensed under a <a rel="license" href="https://www.apache.org/licenses/">Apache-2.0</a>.
+This work is licensed under a
+<a rel="license" href="https://www.apache.org/licenses/">Apache-2.0</a>.
 
 Copyright (c) 2022-present, Zexin Yuan

swcgeom-0.18.3.dist-info/RECORD

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+swcgeom-0.18.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+swcgeom-0.18.3.dist-info/METADATA,sha256=jAOt9X1yBoGfypR3HTr0NkiyoHpNPmuQ_rtoqJN1LSo,2301
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{swcgeom-0.15.0.dist-info → swcgeom-0.18.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

swcgeom/_version.py

@@ -1,16 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple, Union
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-else:
-    VERSION_TUPLE = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-
-__version__ = version = '0.15.0'
-__version_tuple__ = version_tuple = (0, 15, 0)

swcgeom/analysis/branch_features.py

@@ -1,67 +0,0 @@
-"""Branch anlysis of tree."""
-
-from functools import cached_property
-from typing import List, TypeVar
-
-import numpy as np
-import numpy.typing as npt
-
-from swcgeom.core import Branch, Tree
-
-__all__ = ["BranchFeatures"]
-
-T = TypeVar("T", bound=Branch)
-
-
-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/analysis/node_features.py

@@ -1,121 +0,0 @@
-"""Depth distribution of tree."""
-
-from abc import ABC, abstractmethod
-from functools import cached_property
-
-import numpy as np
-import numpy.typing as npt
-from typing_extensions import Self
-
-from swcgeom.core import BranchTree, Tree
-
-__all__ = ["NodeFeatures", "BifurcationFeatures", "TipFeatures"]
-
-
-class NodeFeatures:
-    """Evaluate node feature of tree."""
-
-    tree: Tree
-
-    @cached_property
-    def _branch_tree(self) -> BranchTree:
-        return BranchTree.from_tree(self.tree)
-
-    def __init__(self, tree: Tree) -> None:
-        self.tree = tree
-
-    def get_count(self) -> npt.NDArray[np.float32]:
-        """Get number of nodes.
-
-        Returns
-        -------
-        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]:
-        """Get the end-to-end straight-line distance to soma.
-
-        Returns
-        -------
-        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
-
-    def get_branch_order(self) -> npt.NDArray[np.int32]:
-        """Get branch order of criticle nodes of tree.
-
-        Branch order is the number of bifurcations between current
-        position and the root.
-
-        Criticle node means that soma, bifucation nodes, tips.
-
-        Returns
-        -------
-        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:
-            cur_order = pre_depth + 1 if pre_depth is not None else 0
-            order[n.id] = cur_order
-            return cur_order
-
-        self._branch_tree.traverse(enter=assign_depth)
-        return order
-
-
-class _SubsetNodesFeatures(ABC):
-    _features: NodeFeatures
-
-    @property
-    @abstractmethod
-    def nodes(self) -> npt.NDArray[np.bool_]:
-        raise NotImplementedError()
-
-    def __init__(self, features: NodeFeatures) -> None:
-        self._features = features
-
-    def get_count(self) -> npt.NDArray[np.float32]:
-        """Get number of nodes.
-
-        Returns
-        -------
-        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]:
-        """Get the end-to-end straight-line distance to soma.
-
-        Returns
-        -------
-        radial_distance : npt.NDArray[np.float32]
-            Array of shape (N,).
-        """
-        return self._features.get_radial_distance()[self.nodes]
-
-    @classmethod
-    def from_tree(cls, tree: Tree) -> Self:
-        return cls(NodeFeatures(tree))
-
-
-class BifurcationFeatures(_SubsetNodesFeatures):
-    """Evaluate bifurcation 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])
-
-
-class TipFeatures(_SubsetNodesFeatures):
-    """Evaluate tip node feature of tree."""
-
-    @cached_property
-    def nodes(self) -> npt.NDArray[np.bool_]:
-        return np.array([n.is_tip() for n in self._features.tree])

swcgeom/analysis/path_features.py

@@ -1,37 +0,0 @@
-"""Depth distribution of tree."""
-
-
-from functools import cached_property
-from typing import List
-
-import numpy as np
-import numpy.typing as npt
-
-from swcgeom.core import Tree
-
-__all__ = ["PathFeatures"]
-
-
-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()

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