swcgeom 0.11.1__py3-none-any.whl → 0.13.0__py3-none-any.whl

swcgeom/utils/geometry_object.py

@@ -0,0 +1,299 @@
+"""Geometry object."""
+
+from abc import ABC, abstractmethod
+from functools import lru_cache
+from typing import List, Tuple
+
+import numpy as np
+import numpy.typing as npt
+from sympy import Eq, solve, symbols
+
+__all__ = ["GeomObject", "GeomSphere", "GeomFrustumCone"]
+
+eps = 1e-6
+
+
+class GeomObject(ABC):
+    """Geometry object."""
+
+    @abstractmethod
+    def get_volume(self) -> float:
+        """Get volume."""
+        raise NotImplementedError()
+
+    @abstractmethod
+    def get_intersect_volume(self, obj: "GeomObject") -> float:
+        """Get intersect volume.
+
+        Parameters
+        ----------
+        obj : GeometryObject
+            Another geometry object.
+
+        Returns
+        -------
+        volume : float
+            Intersect volume.
+        """
+        raise NotImplementedError()
+
+
+class GeomSphere(GeomObject):
+    """Geometry Sphere."""
+
+    def __init__(self, center: npt.ArrayLike, radius: float):
+        super().__init__()
+
+        self.center = np.array(center)
+        assert len(self.center) == 3
+
+        self.radius = radius
+
+    def get_volume(self) -> float:
+        return self.calc_volume(self.radius)
+
+    def get_volume_spherical_cap(self, h: float) -> float:
+        return self.calc_volume_spherical_cap(self.radius, h)
+
+    def get_intersect_volume_sphere(self, obj: "GeomSphere") -> float:
+        return self.calc_intersect_volume_sphere(self, obj)
+
+    def get_intersect_volume_sphere_frustum_cone(
+        self, frustum_cone: "GeomFrustumCone"
+    ) -> float:
+        return calc_intersect_volume_sphere_frustum_cone(self, frustum_cone)
+
+    def get_intersect_volume(self, obj: GeomObject) -> float:
+        if isinstance(obj, GeomSphere):
+            return self.get_intersect_volume_sphere(obj)
+
+        if isinstance(obj, GeomFrustumCone):
+            return self.get_intersect_volume_sphere_frustum_cone(obj)
+
+        classname = obj.__class__.__name__
+        raise NotImplementedError(f"unsupported geometry object: {classname}")
+
+    @staticmethod
+    def calc_volume(radius: float) -> float:
+        r"""Calculate volume of sphere.
+
+        \being{equation}
+        V = \frac{4}{3} * π * r^3
+        \end{equation}
+
+        Returns
+        -------
+        volume : float
+            Volume.
+        """
+        return 4 / 3 * np.pi * radius**3
+
+    @staticmethod
+    def calc_volume_spherical_cap(r: float, h: float) -> float:
+        r"""Calculate the volume of a spherical cap.
+
+        \being{equation}
+        V = π * h^2 * (3r - h) / 3
+        \end{equation}
+
+        Parameters
+        ----------
+        r : float
+            radius of the sphere
+        h : float
+            height of the spherical cap
+
+        Returns
+        -------
+        volume : float
+            volume of the spherical cap
+        """
+        return np.pi * h**2 * (3 * r - h) / 3
+
+    @classmethod
+    def calc_intersect_volume_sphere(
+        cls, obj1: "GeomSphere", obj2: "GeomSphere"
+    ) -> float:
+        r"""Calculate intersect volume of two spheres.
+
+        \being{equation}
+        V = \frac{\pi}{12d} * (r_1 + r_2 - d)^2 (d^2 + 2d r_1 - 3r_1^2 + 2d r_2 - 3r_2^2 + 6 r_1r_2)
+        \end{equation}
+
+        Returns
+        -------
+        volume : float
+            Intersect volume.
+        """
+
+        r1, r2 = obj1.radius, obj2.radius
+        d = np.linalg.norm(obj1.center - obj2.center).item()
+        if d > r1 + r2:
+            return 0
+
+        if d <= abs(r1 - r2):
+            return cls.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
+        )
+        return part1 * part2
+
+
+class GeomFrustumCone(GeomObject):
+    """Geometry Frustum."""
+
+    def __init__(self, c1: npt.ArrayLike, r1: float, c2: npt.ArrayLike, r2: float):
+        super().__init__()
+
+        self.c1 = np.array(c1)
+        assert len(self.c1) == 3
+
+        self.c2 = np.array(c2)
+        assert len(self.c2) == 3
+
+        self.r1 = r1
+        self.r2 = r2
+
+    def height(self) -> float:
+        """Get height of frustum."""
+        return np.linalg.norm(self.c1 - self.c2).item()
+
+    def get_volume(self) -> float:
+        return self.calc_volume(self.r1, self.r2, self.height())
+
+    def get_intersect_volume_sphere(self, sphere: GeomSphere) -> float:
+        return calc_intersect_volume_sphere_frustum_cone(sphere, self)
+
+    def get_intersect_volume(self, obj: GeomObject) -> float:
+        if isinstance(obj, GeomSphere):
+            return self.get_intersect_volume_sphere(obj)
+
+        classname = obj.__class__.__name__
+        raise NotImplementedError(f"unsupported geometry object: {classname}")
+
+    @staticmethod
+    def calc_volume(r1: float, r2: float, height: float) -> float:
+        r"""Calculate volume of frustum.
+
+        \being{equation}
+        V = \frac{1}{3} * π * h * (r^2 + r * R + R^2)
+        \end{equation}
+
+        Returns
+        -------
+        volume : float
+            Volume.
+        """
+        return (1 / 3) * np.pi * height * (r1**2 + r1 * r2 + r2**2)
+
+
+@lru_cache
+def calc_intersect_volume_sphere_frustum_cone(
+    sphere: GeomSphere, frustum_cone: GeomFrustumCone
+) -> float:
+    r"""Calculate intersect volume of sphere and frustum cone.
+
+    Returns
+    -------
+    volume : float
+        Intersect volume.
+    """
+    h = frustum_cone.height()
+    c1, r1 = sphere.center, sphere.radius
+    if np.allclose(c1, frustum_cone.c1) and np.allclose(r1, frustum_cone.r1):
+        c2, r2 = frustum_cone.c2, frustum_cone.r2
+    elif np.allclose(c1, frustum_cone.c2) and np.allclose(r1, frustum_cone.r2):
+        c2, r2 = frustum_cone.c1, frustum_cone.r1
+    else:
+        raise NotImplementedError("unsupported to calculate intersect volume")
+
+    # Fast-Path: The surface of the frustum concentric with the sphere
+    # is the surface with smaller radius
+    if r2 >= r1:
+        if h >= r1:
+            # The hemisphere is completely inside the frustum cone
+            return GeomSphere.calc_volume_spherical_cap(r1, r1)
+
+        # The frustum cone is lower than the hemisphere
+        v_himisphere = GeomSphere.calc_volume_spherical_cap(r1, r1)
+        v_cap = GeomSphere.calc_volume_spherical_cap(r1, r1 - h)
+        return v_himisphere - v_cap
+
+    up = (c2 - c1) / np.linalg.norm(c2 - c1)
+    v = _find_unit_vector_on_plane(up)
+
+    intersections = _find_sphere_line_intersection(c1, r1, c1 + r1 * v, c2 + r2 * v)
+    assert len(intersections) == 2
+    t, p = max(intersections, key=lambda x: x[0])
+
+    # Fast-Path: The frustum cone is completely inside the sphere
+    if t > 1 + eps:
+        return frustum_cone.get_volume()
+
+    M = _project_point_on_line(c1, up, p)
+    h1 = np.linalg.norm(M - c1).item()
+    r3 = np.linalg.norm(M - p).item()
+    v_cap1 = GeomSphere.calc_volume_spherical_cap(r1, r1 - h1)
+    v_frustum = GeomFrustumCone.calc_volume(r1, r3, h1)
+
+    # Fast-Path: The frustum cone is higher than the sphere
+    if h >= r1:
+        return v_cap1 + v_frustum
+
+    v_cap2 = GeomSphere.calc_volume_spherical_cap(r1, r1 - h)
+    return v_cap1 + v_frustum - v_cap2
+
+
+def _find_unit_vector_on_plane(normal_vec3: npt.NDArray) -> npt.NDArray:
+    r = np.random.rand(3)
+    while np.allclose(r, normal_vec3) or np.allclose(r, -normal_vec3):
+        r = np.random.rand(3)
+
+    u = np.cross(r, normal_vec3)
+    unit_vector = u / np.linalg.norm(u)
+    return unit_vector
+
+
+def _find_sphere_line_intersection(
+    sphere_center: npt.NDArray,
+    sphere_radius: float,
+    line_point_a: npt.NDArray,
+    line_point_b: npt.NDArray,
+) -> List[Tuple[float, npt.NDArray[np.float64]]]:
+    x1, y1, z1 = sphere_center
+    x2, y2, z2 = line_point_a
+    x3, y3, z3 = line_point_b
+    t = symbols("t")
+
+    # line
+    x = x2 + t * (x3 - x2)
+    y = y2 + t * (y3 - y2)
+    z = z2 + t * (z3 - z2)
+
+    # sphere
+    sphere_eq = Eq((x - x1) ** 2 + (y - y1) ** 2 + (z - z1) ** 2, sphere_radius**2)
+
+    # solve
+    t_values = solve(sphere_eq, t)
+    intersections = [
+        np.array(
+            [float(x.subs(t, t_val)), float(y.subs(t, t_val)), float(z.subs(t, t_val))]
+        )
+        for t_val in t_values
+    ]
+    return list(zip(t_values, intersections))
+
+
+def _project_point_on_line(
+    point_a: npt.ArrayLike, direction_vector: npt.ArrayLike, point_p: npt.ArrayLike
+) -> npt.NDArray:
+    A = np.array(point_a)
+    n = np.array(direction_vector)
+    P = np.array(point_p)
+    print(A.dtype, n.dtype, P.dtype)
+
+    AP = P - A
+    projection = A + np.dot(AP, n) / np.dot(n, n) * n
+    return projection

swcgeom/utils/neuromorpho.py

@@ -83,6 +83,8 @@ import os
 import urllib.parse
 from typing import Any, Callable, Dict, Iterable, List, Optional
 
+from swcgeom.utils import FileReader
+
 __all__ = [
     "neuromorpho_is_valid",
     "neuromorpho_convert_lmdb_to_swc",
@@ -95,14 +97,19 @@ URL_CNG_VERSION = (
 )
 API_NEURON_MAX_SIZE = 500
 
-# about 1.1 GB and 18 GB in version 8.5.25 released in 2023-08-01
 KB = 1024
 MB = 1024 * KB
 GB = 1024 * MB
+
+# Test version: 8.5.25 (2023-08-01)
+# About 1.1 GB and 18 GB
+# No ETAs for future version
 SIZE_METADATA = 2 * GB
 SIZE_DATA = 20 * GB
 
 # fmt:off
+# Test version: 8.5.25 (2023-08-01)
+# No ETAs for future version
 invalid_ids = [
     # bad file
     81062, 86970, 79791,
@@ -132,6 +139,7 @@ def neuromorpho_convert_lmdb_to_swc(
     *,
     group_by: Optional[str | Callable[[Dict[str, Any]], str | None]] = None,
     where: Optional[Callable[[Dict[str, Any]], bool]] = None,
+    encoding: str | None = "utf-8",
     verbose: bool = False,
 ) -> None:
     """Convert lmdb format to SWCs.
@@ -147,6 +155,9 @@ def neuromorpho_convert_lmdb_to_swc(
         attribute name for grouping, e.g.: `archive`, `species`.
     where : (metadata: Dict[str, Any]) -> bool, optional
         Filter neurons by metadata.
+    encoding : str | None, default to `utf-8`
+        Change swc encoding, part of the original data is not utf-8
+        encoded. If is None, keep the original encoding format.
     verbose : bool, default False
         Print verbose info.
 
@@ -165,7 +176,7 @@ def neuromorpho_convert_lmdb_to_swc(
     See Also
     --------
     neuromorpho_is_valid :
-        Recommend filter function, use `where=neuromorpho_is_valid`
+        Recommended filter function, try `where=neuromorpho_is_valid`
     """
     import lmdb
     from tqdm import tqdm
@@ -196,21 +207,31 @@ def neuromorpho_convert_lmdb_to_swc(
     env_c = lmdb.Environment(os.path.join(root, "cng_version"), readonly=True)
     with env_c.begin() as tx_c:
         for k, grp in tqdm(items) if verbose else items:
+            kk = k.decode("utf-8")
             try:
                 bs = tx_c.get(k)
                 if bs is None:
-                    logging.warning("cng version of '%s' not exists", k.decode("utf-8"))
+                    logging.warning("cng version of '%s' not exists", kk)
                     continue
 
                 fs = (
-                    os.path.join(dest, grp, k.decode("utf-8") + ".swc")
+                    os.path.join(dest, grp, f"{kk}.swc")
                     if grp is not None
-                    else os.path.join(dest, k.decode("utf-8") + ".swc")
+                    else os.path.join(dest, f"{kk}.swc")
                 )
-                with open(fs, "wb") as f:
-                    f.write(bs)  # type: ignore
+
+                if encoding is None:
+                    with open(fs, "wb") as f:
+                        f.write(bs)  # type: ignore
+                else:
+                    bs = io.BytesIO(bs)  # type: ignore
+                    with (
+                        open(fs, "w", encoding=encoding) as fw,
+                        FileReader(bs, encoding="detect") as fr,
+                    ):
+                        fw.writelines(fr.readlines())
             except Exception as e:  # pylint: disable=broad-exception-caught
-                logging.warning("fails to convert of %s, err: %s", k.decode("utf-8"), e)
+                logging.warning("fails to convert of %s, err: %s", kk, e)
 
     env_c.close()
 
@@ -432,16 +453,17 @@ if __name__ == "__main__":
     sub.add_argument("--retry", type=int, default=3)
     sub.add_argument("--proxy", type=str, default=None)
     sub.add_argument("--verbose", type=bool, default=True)
-    sub.set_defaults(func=lambda args: download_neuromorpho(**vars(args)))
+    sub.set_defaults(func=download_neuromorpho)
 
     sub = subparsers.add_parser("convert")
     sub.add_argument("-i", "--root", type=str, required=True)
     sub.add_argument("-o", "--dest", type=str, default=None)
     sub.add_argument("--group_by", type=str, default=None)
+    sub.add_argument("--encoding", type=str, default="utf-8")
     sub.add_argument("--verbose", type=bool, default=True)
-    sub.set_defaults(func=lambda args: neuromorpho_convert_lmdb_to_swc(**vars(args)))
+    sub.set_defaults(func=neuromorpho_convert_lmdb_to_swc)
 
     args = parser.parse_args()
     func = args.func
     del args.func  # type: ignore
-    func(args)
+    func(**vars(args))

swcgeom/utils/renderer.py

@@ -9,12 +9,12 @@ import numpy.typing as npt
 from matplotlib import cm
 from matplotlib.axes import Axes
 from matplotlib.collections import LineCollection, PatchCollection
-from matplotlib.colors import Normalize
+from matplotlib.colors import Colormap, Normalize
 from matplotlib.figure import Figure
 from matplotlib.patches import Circle
 from typing_extensions import Self
 
-from .transforms import (
+from swcgeom.utils.transforms import (
     Vec3f,
     model_view_transformation,
     orthographic_projection_simple,
@@ -208,14 +208,15 @@ def draw_circles(
     *,
     y_min: Optional[float] = None,
     y_max: Optional[float] = None,
-    cmap: str = "viridis",
+    cmap: str | Colormap = "viridis",
 ) -> PatchCollection:
     """Draw a sequential of circles."""
+
     y_min = y.min() if y_min is None else y_min
     y_max = y.max() if y_max is None else y_max
     norm = Normalize(y_min, y_max)
 
-    color_map = cm.get_cmap(name=cmap)
+    color_map = cmap if isinstance(cmap, Colormap) else cm.get_cmap(name=cmap)
     colors = color_map(norm(y))
 
     circles = [

swcgeom/utils/transforms.py

@@ -212,6 +212,31 @@ def to_homogeneous(xyz: npt.ArrayLike, w: float) -> npt.NDArray[np.float32]:
     Parameters
     ----------
     xyz : ArrayLike
+        Coordinate of shape (..., 3)
+    w : float
+        w of homogeneous coordinate, 1 for dot, 0 for vector.
+
+    Returns
+    -------
+    xyz4 : npt.NDArray[np.float32]
+        Array of shape (..., 4)
+    """
+    xyz = np.array(xyz)
+    if xyz.ndim == 1:
+        return _to_homogeneous(xyz[None, ...], w)[0]
+
+    shape = xyz.shape[:-1]
+    xyz = xyz.reshape(-1, xyz.shape[-1])
+    xyz4 = _to_homogeneous(xyz, w).reshape(*shape, 4)
+    return xyz4
+
+
+def _to_homogeneous(xyz: npt.NDArray, w: float) -> npt.NDArray[np.float32]:
+    """Fill xyz to homogeneous coordinates.
+
+    Parameters
+    ----------
+    xyz : npt.NDArray
         Coordinate of shape (N, 3)
     w : float
         w of homogeneous coordinate, 1 for dot, 0 for vector.
@@ -221,10 +246,10 @@ def to_homogeneous(xyz: npt.ArrayLike, w: float) -> npt.NDArray[np.float32]:
     xyz4 : npt.NDArray[np.float32]
         Array of shape (N, 4)
     """
-    xyz = np.array(xyz)
     if xyz.shape[1] == 4:
         return xyz
 
+    assert xyz.shape[1] == 3
     filled = np.full((xyz.shape[0], 1), fill_value=w)
     xyz4 = np.concatenate([xyz, filled], axis=1)
     return xyz4

{swcgeom-0.11.1.dist-info → swcgeom-0.13.0.dist-info}/METADATA

@@ -1,15 +1,14 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.11.1
-Summary: A neuron geometry library for swc format
+Version: 0.13.0
+Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: CC4.0 BY-NC-SA
 Project-URL: repository, https://github.com/yzx9/swcgeom
-Keywords: neuron,swc,geom
+Keywords: neuronscience,neuron,neuroanatomy,neuron-morphology
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: chardet >=5.2.0
 Requires-Dist: imagecodecs >=2023.3.16
 Requires-Dist: matplotlib >=3.5.2
 Requires-Dist: numpy >=1.22.3
@@ -17,31 +16,32 @@ Requires-Dist: pandas >=1.4.2
 Requires-Dist: pynrrd >=1.0.0
 Requires-Dist: scipy >=1.9.1
 Requires-Dist: seaborn >=0.12.0
+Requires-Dist: sympy >=1.12
 Requires-Dist: tifffile >=2022.8.12
 Requires-Dist: typing-extensions >=4.4.0
+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'
+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'
 
-# SWC GEOM
+# SWCGEOM
 
 <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a><br />
 
 [![Release to GitHub](https://github.com/yzx9/swcgeom/actions/workflows/github-publish.yml/badge.svg)](https://github.com/yzx9/swcgeom/releases)
-
 [![Release to PyPI](https://github.com/yzx9/swcgeom/actions/workflows/pypi-publish.yml/badge.svg)](https://pypi.org/project/swcgeom/)
-
 [![Release to Test PyPI](https://github.com/yzx9/swcgeom/actions/workflows/test-pypi-publish.yml/badge.svg)](https://test.pypi.org/project/swcgeom/)
 
 A neuron geometry library for swc format.
 
 ## Usage
 
-See documents for details.
+See examples for details.
 
 ## Development
 

swcgeom-0.13.0.dist-info/RECORD

@@ -0,0 +1,61 @@
+swcgeom/__init__.py,sha256=z88Zwcjv-ii7c7dYd9QPg9XrUVorQjtrgGbQCsEnQhc,265
+swcgeom/_version.py,sha256=Y4u7iBqF7QJAbpBNSFA2tk5t2mrMGrI-nonxUAhVkPU,413
+swcgeom/analysis/__init__.py,sha256=c8X_oMxaOijEVjHexFseYs49WMalG_mSxmlQZr5CZeI,339
+swcgeom/analysis/branch_features.py,sha256=s6PTMwwvxrVtZXRZlQbUSIw4M9-1IG63kf-Nxc0tMB0,1958
+swcgeom/analysis/feature_extractor.py,sha256=coe07_bJau96BkimcnXzuf4KqjY5_QRLwqaumFsu_tQ,14031
+swcgeom/analysis/node_features.py,sha256=fevnyrF-t4PX39ifLypiDW6EUWB8i-a3PpBnQZU3VOc,3407
+swcgeom/analysis/path_features.py,sha256=iE21HBxAoGLxk_qK7MBwQhyUOBqNPcnk4urVHr9SVqk,889
+swcgeom/analysis/sholl.py,sha256=9hSW8rZm1gvSIgcEZg8IVPT8kzBgBfwqbwP4E8R7L44,6390
+swcgeom/analysis/trunk.py,sha256=L2tjUIUmrRQpah_W3ZETGWd16bDXJ5F8Sk2XBNGms0Q,5558
+swcgeom/analysis/visualization.py,sha256=mKOpzTPkLpr1ggGL1MZPZRTG92GEg4idLT4eN5z5KOs,5654
+swcgeom/analysis/volume.py,sha256=bMQ9N9Ow1-h27SLQ9AzUm9dyF_jhoTNBMNVqQWDcHMw,2103
+swcgeom/core/__init__.py,sha256=ZUudZavxAIUU6Q0lBHrQ4ybmL5lBfvzyYsTtpuih9wg,332
+swcgeom/core/branch.py,sha256=uuJCxaByRu-OdDZVWEffSFcmZWY-6ZWUhHN1M2Awj1s,3980
+swcgeom/core/branch_tree.py,sha256=sN0viBVg5A4r9dMCkGNAaVttrdR4bEoZZBbHZFKdXj4,1892
+swcgeom/core/node.py,sha256=HvfgsW4WU01hkRIPci8KF4bQMAkwtAxOGfUL4yUbuBs,3623
+swcgeom/core/path.py,sha256=CsEelHiDR0JPBP1dTvoCSRvX3kBlZxkQilosnncV4nQ,4188
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 Wheel-Version: 1.0
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 Root-Is-Purelib: true
 Tag: py3-none-any
 

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