swcgeom 0.17.0__py3-none-any.whl → 0.17.1__py3-none-any.whl
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- swcgeom/_version.py +2 -2
- swcgeom/analysis/feature_extractor.py +13 -12
- swcgeom/analysis/features.py +4 -4
- swcgeom/analysis/lmeasure.py +5 -5
- swcgeom/analysis/sholl.py +4 -4
- swcgeom/analysis/trunk.py +12 -11
- swcgeom/analysis/visualization.py +9 -9
- swcgeom/analysis/visualization3d.py +85 -0
- swcgeom/analysis/volume.py +4 -4
- swcgeom/core/branch.py +4 -3
- swcgeom/core/branch_tree.py +3 -4
- swcgeom/core/compartment.py +3 -2
- swcgeom/core/node.py +2 -2
- swcgeom/core/path.py +3 -2
- swcgeom/core/population.py +16 -27
- swcgeom/core/swc.py +11 -10
- swcgeom/core/swc_utils/base.py +8 -17
- swcgeom/core/swc_utils/io.py +7 -6
- swcgeom/core/swc_utils/normalizer.py +4 -3
- swcgeom/core/swc_utils/subtree.py +2 -2
- swcgeom/core/tree.py +22 -34
- swcgeom/core/tree_utils.py +11 -10
- swcgeom/core/tree_utils_impl.py +3 -3
- swcgeom/images/augmentation.py +3 -3
- swcgeom/images/folder.py +10 -16
- swcgeom/images/io.py +19 -30
- swcgeom/transforms/image_stack.py +6 -5
- swcgeom/transforms/images.py +2 -3
- swcgeom/transforms/neurolucida_asc.py +4 -6
- swcgeom/transforms/population.py +1 -3
- swcgeom/transforms/tree.py +8 -7
- swcgeom/transforms/tree_assembler.py +4 -3
- swcgeom/utils/ellipse.py +3 -4
- swcgeom/utils/neuromorpho.py +17 -16
- swcgeom/utils/plotter_2d.py +12 -6
- swcgeom/utils/plotter_3d.py +31 -0
- swcgeom/utils/renderer.py +6 -6
- swcgeom/utils/sdf.py +2 -2
- swcgeom/utils/solid_geometry.py +1 -3
- swcgeom/utils/transforms.py +1 -3
- swcgeom/utils/volumetric_object.py +8 -10
- {swcgeom-0.17.0.dist-info → swcgeom-0.17.1.dist-info}/METADATA +1 -1
- swcgeom-0.17.1.dist-info/RECORD +67 -0
- swcgeom-0.17.0.dist-info/RECORD +0 -65
- {swcgeom-0.17.0.dist-info → swcgeom-0.17.1.dist-info}/LICENSE +0 -0
- {swcgeom-0.17.0.dist-info → swcgeom-0.17.1.dist-info}/WHEEL +0 -0
- {swcgeom-0.17.0.dist-info → swcgeom-0.17.1.dist-info}/top_level.txt +0 -0
swcgeom/utils/renderer.py
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"""Rendering related utils."""
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from functools import cached_property
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from typing import
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from typing import Literal, cast
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import numpy as np
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import numpy.typing as npt
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__all__ = ["CameraOptions", "Camera", "SimpleCamera", "palette"]
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CameraOption = Vec3f |
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CameraOption = Vec3f | tuple[Vec3f, Vec3f] | tuple[Vec3f, Vec3f, Vec3f]
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CameraPreset = Literal["xy", "yz", "zx", "yx", "zy", "xz"]
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CameraPresets:
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CameraPresets: dict[CameraPreset, tuple[Vec3f, Vec3f, Vec3f]] = {
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"xy": ((0.0, 0.0, 0.0), (+0.0, +0.0, -1.0), (+0.0, +1.0, +0.0)),
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"yz": ((0.0, 0.0, 0.0), (-1.0, +0.0, +0.0), (+0.0, +0.0, +1.0)),
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"zx": ((0.0, 0.0, 0.0), (+0.0, -1.0, +0.0), (+1.0, +0.0, +0.0)),
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if isinstance(camera[0], tuple):
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return cls((0, 0, 0), cast(Vec3f, camera), (0, 1, 0))
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return cls(*cast(
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return cls(*cast(tuple[Vec3f, Vec3f, Vec3f], camera))
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class Palette:
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# pylint: disable=too-few-public-methods
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default:
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vaa3d:
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default: dict[int, str]
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vaa3d: dict[int, str]
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def __init__(self):
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default = [
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swcgeom/utils/sdf.py
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import warnings
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from abc import ABC, abstractmethod
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from
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from collections.abc import Iterable
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import numpy as np
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import numpy.typing as npt
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# Axis-aligned bounding box, tuple of array of shape (3,)
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AABB =
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AABB = tuple[npt.NDArray[np.float32], npt.NDArray[np.float32]]
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class SDF(ABC):
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swcgeom/utils/solid_geometry.py
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"""Solid Geometry."""
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from typing import List, Tuple
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sphere_radius: float,
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line_point_a: npt.NDArray,
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line_point_b: npt.NDArray,
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) ->
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) -> list[tuple[float, npt.NDArray[np.float64]]]:
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A = np.array(line_point_a)
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B = np.array(line_point_b)
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C = np.array(sphere_center)
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swcgeom/utils/transforms.py
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"""3D geometry transformations."""
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"orthographic_projection_simple",
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Vec3f =
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Vec3f = tuple[float, float, float]
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def angle(a: npt.ArrayLike, b: npt.ArrayLike) -> float:
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from typing import Generic, Optional,
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from typing import Generic, Optional, TypeVar
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def sample(self, n: int) -> tuple[npt.NDArray[np.float32], float]:
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def sample(self, n: int) -> tuple[npt.NDArray[np.float32], float]:
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(min_x, min_y, min_z), (max_x, max_y, max_z) = self.sdf.bounding_box()
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samples = np.random.uniform(
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def union(self, obj: VolObject) -> VolObject:
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def intersect(self, obj: VolObject) -> VolObject:
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swcgeom/__init__.py,sha256=z88Zwcjv-ii7c7dYd9QPg9XrUVorQjtrgGbQCsEnQhc,265
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swcgeom/_version.py,sha256=_lgKa5p_bLODIZJPNplciMDP-zYDU8I4ZC5LbeKWQ08,413
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swcgeom/analysis/__init__.py,sha256=NurxIAyjsxjYv9rbzNf65y2sv-iBcGTmLap645hYq9Y,280
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swcgeom/analysis/feature_extractor.py,sha256=Sx9jiRWNEssFJtivrgjUSRfcVxj04KZ2AbR62PuINTU,13956
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swcgeom/analysis/features.py,sha256=7VfCadvlEDhMoLF7NqfZ4St2GGI4yZgaJ60IfUDv-7o,5959
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swcgeom/analysis/lmeasure.py,sha256=as34yoFQz-aNcM1qUpkheRH6-Otwy38Y-_1aWP_h4xs,27552
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swcgeom/analysis/sholl.py,sha256=w9c4OQYf2VIHtLZi6bXT1znmUdm-I_PVNCDeR760WIY,7236
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swcgeom/analysis/trunk.py,sha256=fMHnLDxm2jP_bKBM8ATbTQvBVS5G92ITbgMAm1pIK20,5566
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swcgeom/analysis/visualization.py,sha256=C18J45btqM8kikXyIEZODk4PYgAK1-9pN2Hf6j3QCzs,5635
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swcgeom/analysis/visualization3d.py,sha256=CTUcWBa2cMyDdKimMEtDBmbVzYf3-cTp-6UskPP6Erg,2513
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swcgeom/analysis/volume.py,sha256=y-GVlK8gB7JPS4DpBq1jIjl9Wd-0zryZ9qo8zHGE6_k,4616
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swcgeom/core/__init__.py,sha256=BEfFBnpaKnJOBID5G5kpGcL7_E1Fj0eZZDITDVwvmRY,445
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swcgeom/core/branch.py,sha256=Jwv30pF5bfdZ7B9pl1yP2IYGczdzQtdHKYT2qNmxigE,4183
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swcgeom/core/branch_tree.py,sha256=D8Yb4sz2TniQyeUIqoYW78ZBxLFXyumPuhgmQdff0yI,1843
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swcgeom/core/compartment.py,sha256=5ZLlbsgHouwiRxtl9xLKD02IvsyjlvmIyaXG7IySAZ0,3269
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swcgeom/core/node.py,sha256=alMZENhDQ3wYg6OYElTqS3dz19_y9_C4F2Jj38MNZ3k,3340
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swcgeom/core/path.py,sha256=oS4gIW6LC--vcvCOacNzTxpmWXnxLqAusZaOc5z6t4I,4600
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swcgeom/core/population.py,sha256=DRzHMh7G6sMcmvp_zYan74Qu4N2sQ_3HXomrAMW61cA,9790
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swcgeom/core/swc.py,sha256=sq9-Fg5-d8Yxc2-ITu__LzN5k1hxQNkVTdmee1gpGME,6803
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swcgeom/core/tree.py,sha256=5hynlhuHFdyOmm-2R2fHHQFi5SGGLGcW5_92t1Oecak,12138
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swcgeom/core/tree_utils.py,sha256=Adxggh6tusPRAxEIcwoWbMstojZVKcgGOWPhTFJYjoM,7757
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swcgeom/core/tree_utils_impl.py,sha256=MFCrd34VZE1oSJjt9xo5L7Oyf5-ERS8ifW8zUw6isNE,1597
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swcgeom/core/swc_utils/__init__.py,sha256=qghRxjtzvq5KKfN4HhvLpZNsGPfZQu-Jj2x62_5-TbQ,575
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swcgeom/core/swc_utils/assembler.py,sha256=XtjEWz_iAOMpQzLnErCiCjbnqrbB7JA4t2-LLi2R4rQ,889
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swcgeom/core/swc_utils/base.py,sha256=CJWQioScS1L17KIJlpZMDgu68ZTCF_82nJeg25z7SRI,4731
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swcgeom/core/swc_utils/checker.py,sha256=yuLPRoSt9c7No4GGePa05kxjGFCs0zYS7oB1HadNeMI,2852
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swcgeom/core/swc_utils/io.py,sha256=xA5zvpM4gccsodKCruD-XInlC3NfvA1SgEDnqI5cjY8,6458
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swcgeom/core/swc_utils/normalizer.py,sha256=BN4UOatAo869L1EqXM8IGz0oy0bXPu9KJfZwCGz_PkM,5097
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swcgeom/core/swc_utils/subtree.py,sha256=iX0K90d4iEDdLx6NZ-4HJ-kY_NPE4XkcKn8xwXnYhQo,1988
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swcgeom/images/__init__.py,sha256=QBP1ZGGo2nWAcV7Krz-vbvW_jN4ChqXrrpoScXcUURs,96
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swcgeom/images/augmentation.py,sha256=DfSaEs57aY50O6IKDNupmLI8fHyOvNVmH8uXtdd45iQ,4167
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swcgeom/images/contrast.py,sha256=ViZVW6XI-l2sLVTODLRLtHinv_7lVgtH-xZmaw1nQLw,2160
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swcgeom/images/folder.py,sha256=-EYx_uZ4wwzoCsh9KjFsTl3Hr8aIDgfY76vi-3JeZcc,6749
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swcgeom/images/io.py,sha256=6ITCUB3wtV96UHpfSPewnbeNacBQ9WTfGc9gA8eTDNw,20669
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swcgeom/transforms/__init__.py,sha256=1rr4X--qY_lBi7l7_NHyvvkoWpQOQOqkioRT8I20olI,562
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swcgeom/transforms/base.py,sha256=gN5Iqi-OHkYrsjllSOdxI6Yzav3jJGoi6kUPy-38FAs,4101
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swcgeom/transforms/branch.py,sha256=R0rVti--u70IiUKyHSx6MsDYJyy6zSCf18Uia2Cmh28,5410
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swcgeom/transforms/geometry.py,sha256=XR73fO_8T7otUFIllqKOWW0OnrsXBc7yA01oDT99yMc,7385
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swcgeom/transforms/image_preprocess.py,sha256=ZVPpRoO69dmLF5K7CWsGaQJXB2G5gxdvA-FcDmfz4yQ,3662
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swcgeom/transforms/image_stack.py,sha256=Pb2AwSB_ecnd747Z2aQm5l0CcaiSO8BtHw51j_uWtc0,5789
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swcgeom/transforms/images.py,sha256=L4WSinFQsB9RJ5f2UhLlmKiEEhJtH5hlJ1DrXA_1H8Q,5735
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swcgeom/transforms/mst.py,sha256=Oc_HnaXjg5EXC7ZnOPneHX0-rXizDAEUcjq63GTj-ac,6251
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swcgeom/transforms/neurolucida_asc.py,sha256=zxXZ_LltO1BTILWGU9yZKoXbMPW6ldXpZZryYf3X6Jw,14120
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