swcgeom 0.12.0__tar.gz → 0.13.0__tar.gz

{swcgeom-0.12.0 → swcgeom-0.13.0}/.vscode/settings.json

@@ -11,5 +11,10 @@
     ],
     "[python]": {
         "editor.defaultFormatter": "ms-python.black-formatter"
-    }
+    },
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
 }

{swcgeom-0.12.0 → swcgeom-0.13.0}/CHANGELOG.md

@@ -1,5 +1,30 @@
 # Changelog
 
+## **0.13.0**&emsp;<sub><sup>2023-12-14 ([e2add59...06239bd](https://github.com/yzx9/swcgeom/compare/e2add59652bfc02d802f6770ea2c5fbc3fd7d729...06239bd129e6fab329ec80326352b48049fb504e?diff=split))</sup></sub>
+
+### Features
+
+##### `analysis`
+* import sholl plot ([b03b45c](https://github.com/yzx9/swcgeom/commit/b03b45c4f20f2ed57263b1c2398316533b45b837))
+* calc volume of tree \(close \#9\) ([a5004da](https://github.com/yzx9/swcgeom/commit/a5004dab71e71e68fd4a512757c9310f557878cf))
+
+##### `core`
+* check if it has a cyclic \(\#1\) ([e2add59](https://github.com/yzx9/swcgeom/commit/e2add59652bfc02d802f6770ea2c5fbc3fd7d729))
+
+##### `utils`
+* transform batch of vec3 to vec4 ([d2d660c](https://github.com/yzx9/swcgeom/commit/d2d660ca53b9886a81b02193ea77f76da4620ffa))
+
+### Bug Fixes
+
+##### `utils`
+* should support \`StringIO\` ([de439db](https://github.com/yzx9/swcgeom/commit/de439dba00ce7407d4ae18c9427eab1e5af4d95e))
+
+### Performance Improvements
+* improve dsu ([8b414c3](https://github.com/yzx9/swcgeom/commit/8b414c37f4fc3f4ded9c8b19eb8ee0ad52dedd53))
+
+<br>
+
+
 ## **0.12.0**&emsp;<sub><sup>2023-10-12 ([d9ba943...0824e9b](https://github.com/yzx9/swcgeom/compare/d9ba9433735c69edf979013632278e5f498a6fe0...0824e9b4110f820cd11c469ca6e319c1b2f14145?diff=split))</sup></sub>
 
 ### Features

{swcgeom-0.12.0/swcgeom.egg-info → swcgeom-0.13.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.12.0
+Version: 0.13.0
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: CC4.0 BY-NC-SA
@@ -16,6 +16,7 @@ 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

{swcgeom-0.12.0 → swcgeom-0.13.0}/pyproject.toml

@@ -19,6 +19,7 @@ dependencies = [
     "pynrrd>=1.0.0",
     "scipy>=1.9.1",
     "seaborn>=0.12.0",
+    "sympy>=1.12",
     "tifffile>=2022.8.12",
     "typing_extensions>=4.4.0",
     "v3d-py-helper-0.1.0",

{swcgeom-0.12.0 → swcgeom-0.13.0}/swcgeom/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.12.0'
-__version_tuple__ = version_tuple = (0, 12, 0)
+__version__ = version = '0.13.0'
+__version_tuple__ = version_tuple = (0, 13, 0)

{swcgeom-0.12.0 → swcgeom-0.13.0}/swcgeom/analysis/feature_extractor.py

@@ -25,6 +25,7 @@ from swcgeom.analysis.node_features import (
 )
 from swcgeom.analysis.path_features import PathFeatures
 from swcgeom.analysis.sholl import Sholl
+from swcgeom.analysis.volume import get_volume
 from swcgeom.core import Population, Populations, Tree
 from swcgeom.utils import padding1d
 
@@ -32,6 +33,7 @@ __all__ = ["Feature", "extract_feature"]
 
 Feature = Literal[
     "length",
+    "volume",
     "sholl",
     # node
     "node_count",
@@ -54,7 +56,7 @@ Feature = Literal[
 NDArrayf32 = npt.NDArray[np.float32]
 FeatAndKwargs = Feature | Tuple[Feature, Dict[str, Any]]
 
-Feature1D = set(["length", "node_count", "bifurcation_count", "tip_count"])
+Feature1D = set(["length", "volume", "node_count", "bifurcation_count", "tip_count"])
 
 
 class Features:
@@ -105,6 +107,9 @@ class Features:
     def get_length(self, **kwargs) -> NDArrayf32:
         return np.array([self.tree.length(**kwargs)], dtype=np.float32)
 
+    def get_volume(self, **kwargs) -> NDArrayf32:
+        return np.array([get_volume(self.tree, **kwargs)], dtype=np.float32)
+
     def get_sholl(self, **kwargs) -> NDArrayf32:
         return self.sholl.get(**kwargs).astype(np.float32)
 
@@ -288,9 +293,11 @@ class PopulationFeatureExtractor(FeatureExtractor):
         v = np.stack([padding1d(len_max, v, dtype=np.float32) for v in vals])
         return v
 
-    def _get_sholl_impl(self, **kwargs) -> Tuple[NDArrayf32, NDArrayf32]:
+    def _get_sholl_impl(
+        self, steps: int = 20, **kwargs
+    ) -> Tuple[NDArrayf32, NDArrayf32]:
         rmax = max(t.sholl.rmax for t in self._features)
-        rs = Sholl.get_rs(rmax=rmax, steps=20)
+        rs = Sholl.get_rs(rmax=rmax, steps=steps)
         vals = self._get_impl("sholl", steps=rs, **kwargs)
         return vals, rs
 
@@ -360,10 +367,12 @@ class PopulationsFeatureExtractor(FeatureExtractor):
 
         return out
 
-    def _get_sholl_impl(self, **kwargs) -> Tuple[NDArrayf32, NDArrayf32]:
+    def _get_sholl_impl(
+        self, steps: int = 20, **kwargs
+    ) -> Tuple[NDArrayf32, NDArrayf32]:
         rmaxs = chain.from_iterable((t.sholl.rmax for t in p) for p in self._features)
         rmax = max(rmaxs)
-        rs = Sholl.get_rs(rmax=rmax, steps=20)
+        rs = Sholl.get_rs(rmax=rmax, steps=steps)
         vals = self._get_impl("sholl", steps=rs, **kwargs)
         return vals, rs
 
@@ -408,7 +417,7 @@ class PopulationsFeatureExtractor(FeatureExtractor):
         return ax
 
 
-def extract_feature(obj: Tree | Population) -> FeatureExtractor:
+def extract_feature(obj: Tree | Population | Populations) -> FeatureExtractor:
     if isinstance(obj, Tree):
         return TreeFeatureExtractor(obj)
 

{swcgeom-0.12.0 → swcgeom-0.13.0}/swcgeom/analysis/sholl.py

@@ -42,9 +42,12 @@ class Sholl:
         step: Optional[float] = None,
     ) -> None:
         tree = Tree.from_swc(tree) if isinstance(tree, str) else tree
-        self.tree = TranslateOrigin.transform(tree)  # shift
-        self.rs = np.linalg.norm(self.tree.get_segments().xyz(), axis=2)
-        self.rmax = self.rs.max()
+        try:
+            self.tree = TranslateOrigin.transform(tree)  # shift
+            self.rs = np.linalg.norm(self.tree.get_segments().xyz(), axis=2)
+            self.rmax = self.rs.max()
+        except Exception as e:
+            raise ValueError(f"invalid tree: {tree.source or ''}") from e
 
         if step is not None:
             warnings.warn(
@@ -96,6 +99,7 @@ class Sholl:
         **kwargs :
             Forwarding to plot method.
         """
+
         if plot_type is not None:
             warnings.warn(
                 "`plot_type` has been renamed to `kind` since v0.5.0, "

swcgeom-0.13.0/swcgeom/analysis/volume.py

@@ -0,0 +1,80 @@
+"""Analysis of volume of a SWC tree."""
+
+from typing import List
+
+from swcgeom.core import Tree
+from swcgeom.utils import GeomFrustumCone, GeomSphere
+
+__all__ = ["get_volume"]
+
+
+def get_volume(tree: Tree):
+    """Get the volume of the tree.
+
+    Parameters
+    ----------
+    tree : Tree
+        SWC tree.
+
+    Returns
+    -------
+    volume : float
+        Volume of the tree.
+
+    Notes
+    -----
+    The SWC format is a method for representing neurons, which includes
+    both the radius of individual points and their interconnectivity.
+    Consequently, there are multiple distinct approaches to
+    representation within this framework.
+
+    Currently, we support a standard approach to volume calculation.
+    This method involves treating each node as a sphere and
+    representing the connections between them as truncated cone-like
+    structures, or frustums, with varying radii at their top and bottom
+    surfaces.
+
+    More representation methods will be supported in the future.
+    """
+    volume = 0.0
+
+    def leave(node: Tree.Node, children: List[GeomSphere]) -> GeomSphere:
+        sphere = GeomSphere(node.xyz(), node.r)
+        frustum_cones = [
+            GeomFrustumCone(node.xyz(), node.r, c.center, c.radius) for c in children
+        ]
+
+        v = sphere.get_volume()
+        v += sum(fc.get_volume() for fc in frustum_cones)
+        v -= sum(sphere.get_intersect_volume(fc) for fc in frustum_cones)
+        v -= sum(s.get_intersect_volume(fc) for s, fc in zip(children, frustum_cones))
+
+        # TODO
+        # remove volume of intersection between frustum cones
+        # v -= sum(
+        #     fc1.get_intersect_volume(fc2)
+        #     for fc1 in frustum_cones
+        #     for fc2 in frustum_cones
+        #     if fc1 != fc2
+        # )
+
+        nonlocal volume
+        volume += v
+        return sphere
+
+    tree.traverse(leave=leave)
+    return volume
+
+
+if __name__ == "__main__":
+    from io import StringIO
+
+    swc = """
+1 1 0 0 0 1 -1
+2 1 2 0 0 1  1
+3 1 4 0 0 1  2
+"""
+
+    tree = Tree.from_swc(StringIO(swc))
+    volume = get_volume(tree)
+    print(volume)

{swcgeom-0.12.0 → swcgeom-0.13.0}/swcgeom/core/swc_utils/checker.py

@@ -1,17 +1,22 @@
 """Check common """
 
 import warnings
+from collections import defaultdict
 from typing import Optional
 
 import numpy as np
 import pandas as pd
 
 from swcgeom.core.swc_utils.base import SWCNames, Topology, get_dsu, get_names, traverse
+from swcgeom.utils import DisjointSetUnion
+
 
 __all__ = [
     "is_single_root",
     "is_bifurcate",
     "is_sorted",
+    "has_cyclic",
+    # legacy
     "is_binary_tree",
     "check_single_root",
 ]
@@ -25,13 +30,11 @@ def is_single_root(df: pd.DataFrame, *, names: Optional[SWCNames] = None) -> boo
 def is_bifurcate(topology: Topology, *, exclude_root: bool = True) -> bool:
     """Check is it a bifurcate topology."""
 
-    children = {}
+    children = defaultdict(list)
     for idx, pid in zip(*topology):
-        s = children.get(pid, [])
-        s.append(idx)
-        children[pid] = s
+        children[pid].append(idx)
 
-    root = children.get(-1, [])
+    root = children[-1]
     for k, v in children.items():
         if len(v) > 1 and (not exclude_root or k in root):
             return False
@@ -58,6 +61,27 @@ def is_sorted(topology: Topology) -> bool:
     return flag
 
 
+def has_cyclic(topology: Topology) -> bool:
+    """Has cyclic in topology."""
+    node_num = len(topology[0])
+    dsu = DisjointSetUnion(node_number=node_num)
+
+    for i in range(node_num):
+        node_a = topology[0][i]
+        node_b = topology[1][i]
+        # skip the root node
+        if node_b == -1:
+            continue
+
+        # check whether it is circle
+        if dsu.is_same_set(node_a, node_b):
+            return True
+
+        dsu.union_sets(node_a, node_b)
+
+    return False
+
+
 def check_single_root(*args, **kwargs) -> bool:
     warnings.warn(
         "`check_single_root` has been renamed to `is_single_root` since"

{swcgeom-0.12.0 → swcgeom-0.13.0}/swcgeom/core/swc_utils/io.py

@@ -35,7 +35,7 @@ def read_swc(
 
     Parameters
     ----------
-    swc_file : str
+    swc_file : PathOrIO
         Path of swc file, the id should be consecutively incremented.
     extra_cols : Iterable[str], optional
         Read more cols in swc file.
@@ -142,7 +142,7 @@ def parse_swc(
 
     Parameters
     ----------
-    fname : str
+    fname : PathOrIO
     names : SWCNames
     extra_cols : list of str, optional
     encoding : str | 'detect', default `utf-8`

{swcgeom-0.12.0 → swcgeom-0.13.0}/swcgeom/utils/__init__.py

@@ -1,8 +1,10 @@
 """Utils."""
 
 from swcgeom.utils.debug import *
+from swcgeom.utils.dsu import *
 from swcgeom.utils.ellipse import *
 from swcgeom.utils.file import *
+from swcgeom.utils.geometry_object import *
 from swcgeom.utils.neuromorpho import *
 from swcgeom.utils.numpy_helper import *
 from swcgeom.utils.renderer import *

swcgeom-0.13.0/swcgeom/utils/dsu.py

@@ -0,0 +1,42 @@
+"""Disjoint Set Union Impl."""
+
+__all__ = ["DisjointSetUnion"]
+
+
+class DisjointSetUnion:
+    """Disjoint Set Union.
+
+    DSU with path compression and union by rank.
+    """
+
+    def __init__(self, node_number: int):
+        self.element_parent = [i for i in range(node_number)]
+        self.rank = [0 for _ in range(node_number)]
+
+    def find_parent(self, node_id: int) -> int:
+        if node_id != self.element_parent[node_id]:
+            self.element_parent[node_id] = self.find_parent(
+                self.element_parent[node_id]
+            )
+        return self.element_parent[node_id]
+
+    def union_sets(self, node_a: int, node_b: int) -> None:
+        assert self.validate_node(node_a) and self.validate_node(node_b)
+
+        root_a = self.find_parent(node_a)
+        root_b = self.find_parent(node_b)
+        if root_a != root_b:
+            # union by rank
+            if self.rank[root_a] < self.rank[root_b]:
+                self.element_parent[root_a] = root_b
+            elif self.rank[root_a] > self.rank[root_b]:
+                self.element_parent[root_b] = root_a
+            else:
+                self.element_parent[root_b] = root_a
+                self.rank[root_a] += 1
+
+    def is_same_set(self, node_a: int, node_b: int) -> bool:
+        return self.find_parent(node_a) == self.find_parent(node_b)
+
+    def validate_node(self, node_id: int) -> bool:
+        return 0 <= node_id < len(self.element_parent)

{swcgeom-0.12.0 → swcgeom-0.13.0}/swcgeom/utils/file.py

@@ -11,12 +11,12 @@ pip install swcgeom[all]
 """
 
 import warnings
-from io import BytesIO, TextIOWrapper
+from io import BytesIO, TextIOBase, TextIOWrapper
 from typing import Literal
 
 __all__ = ["FileReader", "PathOrIO"]
 
-PathOrIO = int | str | bytes | BytesIO | TextIOWrapper
+PathOrIO = int | str | bytes | BytesIO | TextIOBase
 
 
 class FileReader:
@@ -32,7 +32,7 @@ class FileReader:
 
         Parameters
         ----------
-        fname : str
+        fname : PathOrIO
         encoding : str | 'detect', default `utf-8`
             The name of the encoding used to decode the file. If is
             `detect`, we will try to detect the character encoding.
@@ -40,8 +40,9 @@ class FileReader:
             Used for detect character endocing, raising warning when
             parsing with low confidence.
         """
+        # TODO: support StringIO
         self.fname, self.fb, self.f = "", None, None
-        if isinstance(fname, TextIOWrapper):
+        if isinstance(fname, TextIOBase):
             self.f = fname
             encoding = fname.encoding  # skip detect
         elif isinstance(fname, BytesIO):
@@ -54,7 +55,7 @@ class FileReader:
         self.encoding = encoding
         self.kwargs = kwargs
 
-    def __enter__(self) -> TextIOWrapper:
+    def __enter__(self) -> TextIOBase:
         if isinstance(self.fb, BytesIO):
             self.f = TextIOWrapper(self.fb, encoding=self.encoding)
         elif self.f is None:
@@ -71,7 +72,7 @@ class FileReader:
 def detect_encoding(fname: PathOrIO, *, low_confidence: float = 0.9) -> str:
     import chardet
 
-    if isinstance(fname, TextIOWrapper):
+    if isinstance(fname, TextIOBase):
         return fname.encoding
     elif isinstance(fname, BytesIO):
         data = fname.read()