swcgeom 0.16.0__py3-none-any.whl → 0.17.1__py3-none-any.whl

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/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 @@
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-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
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-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
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-swcgeom/core/swc_utils/checker.py,sha256=yuLPRoSt9c7No4GGePa05kxjGFCs0zYS7oB1HadNeMI,2852
-swcgeom/core/swc_utils/io.py,sha256=6_--Qoe8kDja4PWsjwqRAvPJZNMFILFgauHaeWeGikU,6444
-swcgeom/core/swc_utils/normalizer.py,sha256=_Ysi8bSJ2JBnIGB8o6BvAg2mcz6xuJp9rgNLZqpLuR8,5083
-swcgeom/core/swc_utils/subtree.py,sha256=43QITYvgXu3b_kfIod2Irrj3dSfrA-gTFev5VxzRafI,1995
-swcgeom/images/__init__.py,sha256=QBP1ZGGo2nWAcV7Krz-vbvW_jN4ChqXrrpoScXcUURs,96
-swcgeom/images/augmentation.py,sha256=cV4k4KR_WcsRajyr0DuhHVDRRZcN4FQ7OIzB_rb2FUo,4173
-swcgeom/images/contrast.py,sha256=ViZVW6XI-l2sLVTODLRLtHinv_7lVgtH-xZmaw1nQLw,2160
-swcgeom/images/folder.py,sha256=YY9YjF17nDwOQEXhzFe-Dj0zPTcG0WP1-gisscImmYg,6674
-swcgeom/images/io.py,sha256=s7YgzlVbl1fTI0PvW09p4_Z-hDdU9Ofh8d99nyhMyY4,21445
-swcgeom/transforms/__init__.py,sha256=1rr4X--qY_lBi7l7_NHyvvkoWpQOQOqkioRT8I20olI,562
-swcgeom/transforms/base.py,sha256=gN5Iqi-OHkYrsjllSOdxI6Yzav3jJGoi6kUPy-38FAs,4101
-swcgeom/transforms/branch.py,sha256=R0rVti--u70IiUKyHSx6MsDYJyy6zSCf18Uia2Cmh28,5410
-swcgeom/transforms/geometry.py,sha256=XR73fO_8T7otUFIllqKOWW0OnrsXBc7yA01oDT99yMc,7385
-swcgeom/transforms/image_preprocess.py,sha256=ZVPpRoO69dmLF5K7CWsGaQJXB2G5gxdvA-FcDmfz4yQ,3662
-swcgeom/transforms/image_stack.py,sha256=RIldGAOI3QeoeBtr0VKeBKJVg-fWSmzWll63SvsaTfI,5775
-swcgeom/transforms/images.py,sha256=ia6h8L7rIubNb02YlbOa-CTScttQJmiS5dHT4D2HpWg,2679
-swcgeom/transforms/mst.py,sha256=Oc_HnaXjg5EXC7ZnOPneHX0-rXizDAEUcjq63GTj-ac,6251
-swcgeom/transforms/neurolucida_asc.py,sha256=O4fK1OMropPnIEVdMenbyT_sV39gEGIv_6vIl6yUOVg,14146
-swcgeom/transforms/path.py,sha256=Gk2iunGQMX7vE83bdo8xoDO-KAT1Vvep0iZs7oFLzFQ,1089
-swcgeom/transforms/population.py,sha256=EmZ6ntuOKe8mXJxMW7nCUA-w2DVlEVe2n0IOVz49tCY,833
-swcgeom/transforms/tree.py,sha256=YzLvKUwTOj92286jHah0CtRYQIxHiNiMGKcgsc_dB0E,6333
-swcgeom/transforms/tree_assembler.py,sha256=vi_X9CNo5IxHP5J7bRl2z91PWufU6HmYlz1iyfdPUxE,5121
-swcgeom/utils/__init__.py,sha256=LXL0wqq6-ggNweZrftp2lrNHCmVJ6LHIto3DuwlYz3c,466
-swcgeom/utils/debug.py,sha256=qay2qJpViLX82mzxdndxQFn-pi1vaEj9CbLGuGt8Y9k,465
-swcgeom/utils/download.py,sha256=By2qZezo6h1Ke_4YpSIhDgcisOrpjVqRmNzbhynC2xs,2834
-swcgeom/utils/dsu.py,sha256=3aCbtpnl_D0OXnowTS8-kuwnCS4BKBYL5ECiFQ1fUW8,1435
-swcgeom/utils/ellipse.py,sha256=LB3q5CIy75GEUdTauIpKySwIHaDrwXzzkBhOCnjJ8Vw,3259
-swcgeom/utils/file.py,sha256=1hchQDsPgn-i-Vz5OQtcogxav_ajCQ_OaEZCLmqczRg,2515
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-swcgeom/utils/numpy_helper.py,sha256=xuvXpZgP-ZeuwTvPFD3DIxwJ5BK4fMCU7k5_5fUHaWE,1425
-swcgeom/utils/plotter_2d.py,sha256=R34_cLfcx_ycPuXS4D0n6ERse7mmzcnhMlkz8KU4yk4,3740
-swcgeom/utils/renderer.py,sha256=yGEu2SBvUQCVwsU8MT273HHgQ9uk5R0Pmo_bJaTN5yU,4233
-swcgeom/utils/sdf.py,sha256=zNDgwXKRNIVcV4ORMmDXup6Bhf_vlHqwa-b3WZn6KhE,10684
-swcgeom/utils/solid_geometry.py,sha256=TV02jhcoCLCqtYA9hfE50LFD_VRfixMiOSiHB5Jb2_U,2431
-swcgeom/utils/transforms.py,sha256=PmP5fL_iVguq4GR2aqXhM0TeCsiFVnrPZMZG6zLohrE,6983
-swcgeom/utils/volumetric_object.py,sha256=DVRGGmQrAL0oaW6hbNtp5TStbic9DfyJdCzsv2FNw2c,15134
-swcgeom-0.16.0.dist-info/LICENSE,sha256=JPtohhZ4XURqoKI0ZqnMYb7dobCOoZR_n5EpnaLTp3E,11344
-swcgeom-0.16.0.dist-info/METADATA,sha256=cSs43xlPOCFXa9GcEGPGUE0tjDo6vDtskZ8IvlZAcuA,2332
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-swcgeom-0.16.0.dist-info/RECORD,,