swcgeom 0.16.0__py3-none-any.whl → 0.18.3__py3-none-any.whl

swcgeom-0.18.3.dist-info/RECORD

@@ -0,0 +1,67 @@
+swcgeom/__init__.py,sha256=7Hjtjg2r_dRP-oUmNX_Zza1NqV6703L0XnpuhKQ3wcs,939
+swcgeom/analysis/__init__.py,sha256=1Bp93CxYzKqnTLzRdy8GpnhhBf6t8S2sgpEIhOJOj6w,945
+swcgeom/analysis/feature_extractor.py,sha256=8hmwwWCZ8c_XcnmyY--vRygo-OAovIoMuVTHnixX8KA,14855
+swcgeom/analysis/features.py,sha256=NnFRUsMO7mPoBNLQ_kwSWHSfaV1BCOYTZz6VuG2Cfi8,6905
+swcgeom/analysis/lmeasure.py,sha256=RLhRIo3VOQFqisBDetP120SntWSTE2rJ-vL5l-QGT40,28688
+swcgeom/analysis/sholl.py,sha256=uGElY5hXILON8uHX9phGwFeKMjWCtA1GTeoyKStkSPE,7203
+swcgeom/analysis/trunk.py,sha256=f6oH2Xlpn76JjKNsC0DKFsnYGn4FP4YRucCeyUaGgjg,6147
+swcgeom/analysis/visualization.py,sha256=dioNW7Y596xhUPySkr-gbcCzLFm4PPsizKAjEXgAdyI,6216
+swcgeom/analysis/visualization3d.py,sha256=OIUEtxPZpwK8eDEuy8_ezh5x2oQishQ3-aj-dGselAY,3094
+swcgeom/analysis/volume.py,sha256=KLEqE5OWKckdw2qsI8Ugmxi-_jePnE9N9ZN6QFC07y8,5197
+swcgeom/core/__init__.py,sha256=s6hYMtFY5HKviiNkENlEy4o3taxN5Ogq04ceKQgGL6o,1223
+swcgeom/core/branch.py,sha256=xu5J12FjxXSNL3Q_Uiy5qLlMozfcdnkIDO-XyDB_CYg,4764
+swcgeom/core/branch_tree.py,sha256=jFDKkBgaTCT6C4ZsGdihxBp3xC2k9v6wxE43UGW2AuY,2424
+swcgeom/core/compartment.py,sha256=neoM4nyZxPnaHDnxr-T5xItrf6gqctbo8dOawlFQRlM,3850
+swcgeom/core/node.py,sha256=ZVhAQeadPNVpVd8LAVF5i7DWkGsjsigrUdMIUDUp8BY,4376
+swcgeom/core/path.py,sha256=_j9GP7fSaDUeUeFGXPaWDyq5BcQURzTCCh9iuQKiYWM,5065
+swcgeom/core/population.py,sha256=k-sIaYC-m2S82h-rJM0iocdFpQDKuEBuaw6_WNgI_0s,11039
+swcgeom/core/swc.py,sha256=SqJdj-auOBuxOoRxg33DFcigIx8_BuWfeHyWYBQY7xk,7384
+swcgeom/core/tree.py,sha256=Hq4KOFvEWcFqFvGC3D-1f_WKRu6p6P_hfJT5vOVGKXY,13150
+swcgeom/core/tree_utils.py,sha256=2cg3HBn7-6S_J64z9F12CLGVDarpn5epCk3icVWtgEY,8192
+swcgeom/core/tree_utils_impl.py,sha256=1G1qZA7kwWifol8h5cBsFuwh6YA0ZTfpzG5brGwBFs0,2178
+swcgeom/core/swc_utils/__init__.py,sha256=B-oJffxjFZIzIG_9Jh3uG6G_DHtqqkMxIOIU4A_dLEQ,1239
+swcgeom/core/swc_utils/assembler.py,sha256=lrW0vWFSpvL3PGjA80mCSR9XH3RHX2wLyZ1v4Tux4Gw,1470
+swcgeom/core/swc_utils/base.py,sha256=bjH8AOclIAXGecUVxDOrk9jD7NAq1OdkvXgIQLj6UP0,5312
+swcgeom/core/swc_utils/checker.py,sha256=xbzUjHPR5sMHRCA1f9MAd_4xUvyb5NRsJWSB7cPXSdw,3182
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+swcgeom/core/swc_utils/normalizer.py,sha256=egYdZAex8h1SninrWkkKpU9Tu9rmB9uaHwa3u4kasO0,5673
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+swcgeom/images/__init__.py,sha256=gwBZzrsswJ2hyRQA72khFk2JPo1JfWko4-huuAYNCOU,705
+swcgeom/images/augmentation.py,sha256=6YuQpuWaarc_bD0Pjz42eFreVjhA2qmeUEK84RBcc_g,4748
+swcgeom/images/contrast.py,sha256=f5EqJJ4tGcG46dm9pMeQm_cM1fYcIXC6qYjcOFxThTc,2741
+swcgeom/images/folder.py,sha256=-WpAvCBZ5qYfFZTWI1e-O7jAGLjm_PyZWV91fegP45E,7025
+swcgeom/images/io.py,sha256=dgu69iqb_Bkk8guLt5TYSOz-lG_WemEOFrRmoZsQTg8,21137
+swcgeom/transforms/__init__.py,sha256=nE4Uyn5vpYyNiMltTiNHDRkyjYbW6B4ToyZOxUj0TU0,1370
+swcgeom/transforms/base.py,sha256=l5DEZjZhjH23Axg8ozJTFzSmNNwIlTfm0XxAOIAQtlE,4696
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+swcgeom/transforms/branch_tree.py,sha256=i2w16ny70oWbJhq5mHX7wgEVGol1AYKB3P-N5Kh3z2I,2820
+swcgeom/transforms/geometry.py,sha256=xA9RN1oWRV0S1OVC_vxGZOq8CjGLERnlR5vM4_wvUG8,8008
+swcgeom/transforms/image_preprocess.py,sha256=lT5ceaE9IzJjq6vIFh0p1YzsyBYAtqz_ElqErvZvDdE,4243
+swcgeom/transforms/image_stack.py,sha256=Zc9p5MGt8zdkla-RnKdsF64NLgS7cfK9j2qG4ggiSgI,6720
+swcgeom/transforms/images.py,sha256=bPJwtwIcHVECHV0qQBVWRFzTWLKEf31V4TiRgjFrGn8,6139
+swcgeom/transforms/mst.py,sha256=spUuXjglCBnZmR6mIyCBJJGmQbfpx7hb1nndT3_iUG4,6832
+swcgeom/transforms/neurolucida_asc.py,sha256=0WyM9B5qpJ5hjVGKpO8atWpaUhJdLQ0lKMhcJkuOsfM,14699
+swcgeom/transforms/path.py,sha256=SqBPYvCnDc1yd8UCBwyelAXnduNAvJ16pWo9lMoZVI0,1670
+swcgeom/transforms/population.py,sha256=kayuwNs8jWTrHZ4sqoH9HUcLqR0OybJbGtb7HvpFIdw,1389
+swcgeom/transforms/tree.py,sha256=qlYISDuT7DlEQ2uaa1Y-vqb2rbs9JHr9Bays546XuCI,8152
+swcgeom/transforms/tree_assembler.py,sha256=rWm7D7tAhk9UkX1PL_QfXw2-98xlI7cF3IsIyW7eOzQ,5743
+swcgeom/utils/__init__.py,sha256=sduLt0_W5KfoatIQ5Sj26DndwiCQhpPVkZhUVi7akFE,1215
+swcgeom/utils/debug.py,sha256=ZOYLfj32YDjSU1tJrtThWF2SROwYhG2z7j4Fq0q4Dsw,1046
+swcgeom/utils/download.py,sha256=VNJCsXty3NrwPv9CzyA_OkHsEQj4LArkoAuPmW-NX6c,4237
+swcgeom/utils/dsu.py,sha256=tU_hBjSFBXiraJphB_qQ7Rt1pKNFUIbh0kvU_zJ1UaI,2016
+swcgeom/utils/ellipse.py,sha256=o8CZmEhJIy2bejDX2nr92H5vootuLoIkk-sSTG19cAo,3815
+swcgeom/utils/file.py,sha256=6P_jSfpUPulJ2PSHGr-maEZotLvM35egEmH4RRO022Y,3096
+swcgeom/utils/neuromorpho.py,sha256=AE3wlDckLFYI9MuQv4XlA0LYMLpGUm8OQLNnym-DQB4,19617
+swcgeom/utils/numpy_helper.py,sha256=wsY8-4naAOMfKQ2O-dVRcblM2NrezhjsUEfUzT2holk,2006
+swcgeom/utils/plotter_2d.py,sha256=ojhEUpMbP9-7XE64CNb4kVoUS6WoFrYlmqumbGr79go,4450
+swcgeom/utils/plotter_3d.py,sha256=6IU_Oyls5chq6ol30R4zp85oK_31yHB6vVp09D6pYGA,1458
+swcgeom/utils/renderer.py,sha256=aDp2HZRUe9GDNdslewLKh6OCTKfz8G_6c4AmK14EajQ,4801
+swcgeom/utils/sdf.py,sha256=C8uH9R2qMYeXgy1icHcaGQnjqQbU-0d6gWNw7tfge10,11156
+swcgeom/utils/solid_geometry.py,sha256=2c8MNCfvkF7HAhmLPQXvHF8uexoNJBeFh6Qa9n6M8CQ,2980
+swcgeom/utils/transforms.py,sha256=UKGeCv8O109mcBk1_opnwABLYVpmfF8sT_f5Mx5APSM,7538
+swcgeom/utils/volumetric_object.py,sha256=Y_rEAzeCozJWwXicerwRElwotTgQwHlz9TChzsG9J1I,15683
+swcgeom-0.18.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+swcgeom-0.18.3.dist-info/METADATA,sha256=jAOt9X1yBoGfypR3HTr0NkiyoHpNPmuQ_rtoqJN1LSo,2301
+swcgeom-0.18.3.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+swcgeom-0.18.3.dist-info/top_level.txt,sha256=hmLyUXWS61Gxl07haswFEKKefYPBVJYlUlol8ghNkjY,8
+swcgeom-0.18.3.dist-info/RECORD,,

{swcgeom-0.16.0.dist-info → swcgeom-0.18.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+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 = '0.16.0'
-__version_tuple__ = version_tuple = (0, 16, 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()

swcgeom-0.16.0.dist-info/RECORD

@@ -1,67 +0,0 @@
-swcgeom/__init__.py,sha256=z88Zwcjv-ii7c7dYd9QPg9XrUVorQjtrgGbQCsEnQhc,265
-swcgeom/_version.py,sha256=6rRRmvuDj83YMwAXEQTx-SPTN2ocQjA6cw2_dMCfweM,413
-swcgeom/analysis/__init__.py,sha256=esL_poW8u-_bmp7vR9ldcumX3_xodtaVfM1USqxQo5w,377
-swcgeom/analysis/branch_features.py,sha256=s6PTMwwvxrVtZXRZlQbUSIw4M9-1IG63kf-Nxc0tMB0,1958
-swcgeom/analysis/feature_extractor.py,sha256=coe07_bJau96BkimcnXzuf4KqjY5_QRLwqaumFsu_tQ,14031
-swcgeom/analysis/lmeasure.py,sha256=GI5HoIXkRp_GEDHd_JXJOMeAtZ26HP6lbSfF_0L-2r8,27559
-swcgeom/analysis/node_features.py,sha256=fevnyrF-t4PX39ifLypiDW6EUWB8i-a3PpBnQZU3VOc,3407
-swcgeom/analysis/path_features.py,sha256=iE21HBxAoGLxk_qK7MBwQhyUOBqNPcnk4urVHr9SVqk,889
-swcgeom/analysis/sholl.py,sha256=KeUyEXLatHjmn4hOSs8y_0o8UKDq9VoIufJ_81SOtgw,7249
-swcgeom/analysis/trunk.py,sha256=L2tjUIUmrRQpah_W3ZETGWd16bDXJ5F8Sk2XBNGms0Q,5558
-swcgeom/analysis/visualization.py,sha256=mKOpzTPkLpr1ggGL1MZPZRTG92GEg4idLT4eN5z5KOs,5654
-swcgeom/analysis/volume.py,sha256=nWPR7wGOk3Wl5eh97YMws0X-2jk8K7lmFp4-03wL3lY,4628
-swcgeom/core/__init__.py,sha256=BEfFBnpaKnJOBID5G5kpGcL7_E1Fj0eZZDITDVwvmRY,445
-swcgeom/core/branch.py,sha256=NchxRgXpFv_ImShvQBPU_9xNzufTrPMvEYmx7d46JNA,4162
-swcgeom/core/branch_tree.py,sha256=Ece6q1VNCRLLMj29N_MjXmmlHT8h4tpWCuDE0uSgKJo,1873
-swcgeom/core/compartment.py,sha256=-2EYkGfqN12he2dsrtO1afC52Bk_fMD5aRLO_useGCQ,3248
-swcgeom/core/node.py,sha256=Kwqoh_WMBLIt2WNDwF-7EwS-C8lONG5krGPmmdHwhvY,3329
-swcgeom/core/path.py,sha256=mxexT7eEHpRaCapE4t0dzfQGgW_zPPzn6N1MkD-jLgI,4579
-swcgeom/core/population.py,sha256=MVVAgGki9SQYMuEJpWyG0eBX4ImR2wpfvWxMqAnXRa8,9824
-swcgeom/core/swc.py,sha256=lSYxAa25l6O8WZ9JtSSET-RZMr6EA1Tq_aXL_x0H9Rc,6795
-swcgeom/core/tree.py,sha256=fQM_Z5-bWsh55hS1pde52tSjKE9-aZY75wbKmDOOQcQ,12195
-swcgeom/core/tree_utils.py,sha256=WWh7uizkyG0u7Zs6ZmkSLPYBsU4XC-gqPeOiVGyaqGE,7749
-swcgeom/core/tree_utils_impl.py,sha256=kN2ByjqqQtZUfmC_ac25tXOaE-CMiV2lP58VxFphLEU,1616
-swcgeom/core/swc_utils/__init__.py,sha256=qghRxjtzvq5KKfN4HhvLpZNsGPfZQu-Jj2x62_5-TbQ,575
-swcgeom/core/swc_utils/assembler.py,sha256=XtjEWz_iAOMpQzLnErCiCjbnqrbB7JA4t2-LLi2R4rQ,889
-swcgeom/core/swc_utils/base.py,sha256=6jNf1EeMz7yJQr3rYSi5EuU2ZPjeefB9vIRFaY53PbA,4788
-swcgeom/core/swc_utils/checker.py,sha256=yuLPRoSt9c7No4GGePa05kxjGFCs0zYS7oB1HadNeMI,2852
-swcgeom/core/swc_utils/io.py,sha256=6_--Qoe8kDja4PWsjwqRAvPJZNMFILFgauHaeWeGikU,6444
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