swcgeom 0.11.1__tar.gz → 0.13.0__tar.gz

{swcgeom-0.11.1 → 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-0.11.1 → swcgeom-0.13.0}/CHANGELOG.md

@@ -1,5 +1,78 @@
 # 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
+
+##### `core`
+
+* support read from io ([8fe9df8](https://github.com/yzx9/swcgeom/commit/8fe9df8459e8cef3cd6bde4ff3546e1a83871eda))
+* get neurites and dendrites ([a9acfde](https://github.com/yzx9/swcgeom/commit/a9acfde5ab77bac22d36e7c461089f5159e6330a))
+* add swc types ([7439288](https://github.com/yzx9/swcgeom/commit/7439288d199d558cd170600b07d1ab51a8489bc4))
+* add type check in \`Tree\.Node\.is\_soma\` ([35b53d6](https://github.com/yzx9/swcgeom/commit/35b53d68c30e444b0b8ae57519f8196c5dbdcb4d))
+
+##### `images`
+
+* support \`v3dpbd\` and \`v3draw\` \(close \#6\) ([ca8267d](https://github.com/yzx9/swcgeom/commit/ca8267d694f62abc59b9c8174efc91512a9ccec9))
+
+##### `transforms`
+
+* sort mst tree by default ([7878f3f](https://github.com/yzx9/swcgeom/commit/7878f3fdb9beeebd31ecfa7649611fdd03e34eff))
+* add path transforms ([aaa1b1e](https://github.com/yzx9/swcgeom/commit/aaa1b1e3c718017ae18a52d91918b29c02f302b3))
+
+##### `utils`
+
+* change to utf\-8 encode ([45e971e](https://github.com/yzx9/swcgeom/commit/45e971eef9cc88abb8e1fca5f26b99e46fcb5aaf))
+
+### Bug Fixes
+
+##### `core`
+
+* avoid duplicate cols comments ([f99eaf3](https://github.com/yzx9/swcgeom/commit/f99eaf3946846522d7eac1769f6a9a4fd20e8bf0))
+* inherit source ([702efab](https://github.com/yzx9/swcgeom/commit/702efabb5db9a27e8eaed9d1feb45f24e6b4e808))
+* remove original point when cat tree ([065125e](https://github.com/yzx9/swcgeom/commit/065125e7ccf0d3f6ef9ff9c7689a0e7aeb6be349))
+
+##### `images`
+
+* shape should be vec4i ([0824e9b](https://github.com/yzx9/swcgeom/commit/0824e9b4110f820cd11c469ca6e319c1b2f14145))
+
+##### `transforms`
+
+* add missing exports ([93bf8e6](https://github.com/yzx9/swcgeom/commit/93bf8e6076d8d7a3898a1ff88cbe05d855d1173c))
+
+### Performance Improvements
+
+##### `transforms`
+
+* disable \`detach\` operation ([204d44c](https://github.com/yzx9/swcgeom/commit/204d44cbab563309d85f9c6f64793e5eda028547))
+
+<br>
+
 ## **0.11.1**&emsp;<sub><sup>2023-08-12 ([36fa413...36fa413](https://github.com/yzx9/swcgeom/compare/36fa4135f2001694b8caea74e82c5ffa1118e90d...36fa4135f2001694b8caea74e82c5ffa1118e90d?diff=split))</sup></sub>
 
 *no relevant changes*

{swcgeom-0.11.1/swcgeom.egg-info → swcgeom-0.13.0}/PKG-INFO

@@ -1,31 +1,47 @@
 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
-Provides-Extra: all
 License-File: LICENSE
+Requires-Dist: imagecodecs>=2023.3.16
+Requires-Dist: matplotlib>=3.5.2
+Requires-Dist: numpy>=1.22.3
+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-0.11.1 → swcgeom-0.13.0}/README.md

@@ -1,18 +1,16 @@
-# 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-0.11.1 → swcgeom-0.13.0}/examples/pytorch/tree_folder_dataset.py

@@ -4,8 +4,8 @@ from typing import Generic, TypeVar, cast
 
 import torch.utils.data
 
-from ...core import Population, Tree
-from ...transforms import Identity, Transform
+from swcgeom import Population, Tree
+from swcgeom.transforms import Identity, Transform
 
 __all__ = ["TreeFolderDataset"]
 

swcgeom-0.13.0/pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "swcgeom"
+dynamic = ["version"]
+description = "Neuron geometry library for swc format"
+readme = "README.md"
+requires-python = ">=3.10"
+authors = [{ name = "yzx9", email = "yuan.zx@outlook.com" }]
+keywords = ["neuronscience", "neuron", "neuroanatomy", "neuron-morphology"]
+license = { text = "CC4.0 BY-NC-SA" }
+dependencies = [
+    "imagecodecs>=2023.3.16",
+    "matplotlib>=3.5.2",
+    "numpy>=1.22.3",
+    "pandas>=1.4.2",
+    "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",
+]
+
+[project.optional-dependencies]
+all = [
+    "beautifulsoup4>=4.11.1",
+    "certifi>=2023.5.7",
+    "chardet>=5.2.0",
+    "lmdb>=1.4.1",
+    "pycurl>=7.0.0",
+    "tqdm>=4.46.1",
+    "urllib3>=1.26.0",
+]
+
+[project.urls]
+repository = "https://github.com/yzx9/swcgeom"
+
+[tool.setuptools_scm]
+write_to = "swcgeom/_version.py"

swcgeom-0.13.0/swcgeom/__init__.py

@@ -0,0 +1,6 @@
+"""A neuron geometry library for swc format."""
+
+from swcgeom import analysis, core, images, transforms
+from swcgeom._version import __version__, __version_tuple__
+from swcgeom.analysis import draw
+from swcgeom.core import BranchTree, Population, Populations, Tree

swcgeom-0.13.0/swcgeom/_version.py

@@ -0,0 +1,16 @@
+# 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 = '0.13.0'
+__version_tuple__ = version_tuple = (0, 13, 0)

swcgeom-0.13.0/swcgeom/analysis/__init__.py

@@ -0,0 +1,9 @@
+"""Analysis for neuron trees."""
+
+from swcgeom.analysis.branch_features import *
+from swcgeom.analysis.feature_extractor import *
+from swcgeom.analysis.node_features import *
+from swcgeom.analysis.path_features import *
+from swcgeom.analysis.sholl import *
+from swcgeom.analysis.trunk import *
+from swcgeom.analysis.visualization import *

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/analysis/branch_features.py

@@ -6,7 +6,7 @@ from typing import List, TypeVar
 import numpy as np
 import numpy.typing as npt
 
-from ..core import Branch, Tree
+from swcgeom.core import Branch, Tree
 
 __all__ = ["BranchFeatures"]
 

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/analysis/feature_extractor.py

@@ -17,17 +17,23 @@ import numpy.typing as npt
 import seaborn as sns
 from matplotlib.axes import Axes
 
-from ..core import Population, Populations, Tree
-from ..utils import padding1d
-from .branch_features import BranchFeatures
-from .node_features import BifurcationFeatures, NodeFeatures, TipFeatures
-from .path_features import PathFeatures
-from .sholl import Sholl
+from swcgeom.analysis.branch_features import BranchFeatures
+from swcgeom.analysis.node_features import (
+    BifurcationFeatures,
+    NodeFeatures,
+    TipFeatures,
+)
+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
 
 __all__ = ["Feature", "extract_feature"]
 
 Feature = Literal[
     "length",
+    "volume",
     "sholl",
     # node
     "node_count",
@@ -50,7 +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:
@@ -101,6 +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)
 
@@ -284,9 +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
 
@@ -356,10 +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
 
@@ -404,7 +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-0.11.1 → swcgeom-0.13.0}/swcgeom/analysis/node_features.py

@@ -7,7 +7,7 @@ import numpy as np
 import numpy.typing as npt
 from typing_extensions import Self
 
-from ..core import BranchTree, Tree
+from swcgeom.core import BranchTree, Tree
 
 __all__ = ["NodeFeatures", "BifurcationFeatures", "TipFeatures"]
 

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/analysis/path_features.py

@@ -7,7 +7,7 @@ from typing import List
 import numpy as np
 import numpy.typing as npt
 
-from ..core import Tree
+from swcgeom.core import Tree
 
 __all__ = ["PathFeatures"]
 

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/analysis/sholl.py

@@ -9,10 +9,10 @@ import seaborn as sns
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
 
-from ..core import Tree
-from ..transforms import TranslateOrigin
-from ..utils import draw_circles, get_fig_ax
-from .visualization import draw
+from swcgeom.analysis.visualization import draw
+from swcgeom.core import Tree
+from swcgeom.transforms import TranslateOrigin
+from swcgeom.utils import draw_circles, get_fig_ax
 
 __all__ = ["Sholl"]
 
@@ -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-0.11.1 → swcgeom-0.13.0}/swcgeom/analysis/trunk.py

@@ -12,9 +12,9 @@ from matplotlib.axes import Axes
 from matplotlib.figure import Figure
 from matplotlib.patches import Circle, Ellipse, Patch, Rectangle
 
-from ..core import Tree, get_subtree, to_subtree
-from ..utils import get_fig_ax, mvee
-from .visualization import draw
+from swcgeom.analysis.visualization import draw
+from swcgeom.core import Tree, get_subtree, to_subtree
+from swcgeom.utils import get_fig_ax, mvee
 
 __all__ = ["draw_trunk"]
 
@@ -178,5 +178,5 @@ def create_point_2d(
 # Helpers
 
 
-def get_dendrites(tree: Tree) -> Iterable[int]:  # TODO: move to `Tree`
-    return [n.id for n in tree.soma().children() if n.type in [3, 4]]
+def get_dendrites(tree: Tree) -> Iterable[int]:
+    return (t.node(0).id for t in tree.get_dendrites())

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/analysis/visualization.py

@@ -9,8 +9,8 @@ from matplotlib.axes import Axes
 from matplotlib.figure import Figure
 from matplotlib.legend import Legend
 
-from ..core import SWCLike, Tree
-from ..utils import (
+from swcgeom.core import SWCLike, Tree
+from swcgeom.utils import (
     CameraOptions,
     SimpleCamera,
     draw_direction_indicator,

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-0.13.0/swcgeom/core/__init__.py

@@ -0,0 +1,11 @@
+"""Neuron trees."""
+
+from swcgeom.core import swc_utils
+from swcgeom.core.branch import *
+from swcgeom.core.branch_tree import *
+from swcgeom.core.node import *
+from swcgeom.core.path import *
+from swcgeom.core.population import *
+from swcgeom.core.swc import *
+from swcgeom.core.tree import *
+from swcgeom.core.tree_utils import *

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/core/branch.py

@@ -5,9 +5,9 @@ from typing import Generic, Iterable, List
 import numpy as np
 import numpy.typing as npt
 
-from .path import Path
-from .segment import Segment, Segments
-from .swc import DictSWC, SWCTypeVar
+from swcgeom.core.path import Path
+from swcgeom.core.segment import Segment, Segments
+from swcgeom.core.swc import DictSWC, SWCTypeVar
 
 __all__ = ["Branch"]
 
@@ -42,7 +42,11 @@ class Branch(Path, Generic[SWCTypeVar]):
     def detach(self) -> "Branch[DictSWC]":
         """Detach from current attached object."""
         # pylint: disable=consider-using-dict-items
-        attact = DictSWC(**{k: self[k] for k in self.keys()}, names=self.names)
+        attact = DictSWC(
+            **{k: self[k] for k in self.keys()},
+            source=self.attach.source,
+            names=self.names,
+        )
         attact.ndata[self.names.id] = self.id()
         attact.ndata[self.names.pid] = self.pid()
         return Branch(attact, self.id())

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/core/branch_tree.py

@@ -7,9 +7,9 @@ import numpy as np
 import pandas as pd
 from typing_extensions import Self
 
-from .branch import Branch
-from .swc_utils import to_sub_topology
-from .tree import Tree
+from swcgeom.core.branch import Branch
+from swcgeom.core.swc_utils import to_sub_topology
+from swcgeom.core.tree import Tree
 
 __all__ = ["BranchTree"]
 
@@ -45,8 +45,7 @@ class BranchTree(Tree):
         ndata = {k: tree.get_ndata(k)[id_map].copy() for k in tree.keys()}
         ndata.update(id=new_id, pid=new_pid)
 
-        branch_tree = cls(n_nodes, **ndata, names=tree.names)
-        branch_tree.source = tree.source  # TODO
+        branch_tree = cls(n_nodes, **ndata, source=tree.source, names=tree.names)
 
         branch_tree.branches = {}
         for br in branches:

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/core/node.py

@@ -6,8 +6,8 @@ from typing import Any, Generic, Iterable
 import numpy as np
 import numpy.typing as npt
 
-from .swc import DictSWC, SWCTypeVar
-from .swc_utils import SWCNames
+from swcgeom.core.swc import DictSWC, SWCTypeVar
+from swcgeom.core.swc_utils import SWCNames
 
 __all__ = ["Node"]
 
@@ -113,7 +113,9 @@ class Node(Generic[SWCTypeVar]):
         """Detach from current attached object."""
         # pylint: disable=consider-using-dict-items
         attact = DictSWC(
-            **{k: np.array([self[k]]) for k in self.keys()}, names=self.names
+            **{k: np.array([self[k]]) for k in self.keys()},
+            source=self.attach.source,
+            names=self.names,
         )
         attact.ndata[self.names.id] = np.array([0])
         attact.ndata[self.names.pid] = np.array([-1])

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/core/path.py

@@ -5,8 +5,8 @@ from typing import Generic, Iterable, Iterator, List, overload
 import numpy as np
 import numpy.typing as npt
 
-from .node import Node
-from .swc import DictSWC, SWCLike, SWCTypeVar
+from swcgeom.core.node import Node
+from swcgeom.core.swc import DictSWC, SWCLike, SWCTypeVar
 
 __all__ = ["Path"]
 
@@ -28,6 +28,7 @@ class Path(SWCLike, Generic[SWCTypeVar]):
         self.attach = attach
         self.names = attach.names
         self.idx = np.array(idx, dtype=np.int32)
+        self.source = self.attach.source
 
     def __iter__(self) -> Iterator[Node]:
         return (self.get_node(i) for i in range(len(self)))
@@ -79,7 +80,9 @@ class Path(SWCLike, Generic[SWCTypeVar]):
         """Detach from current attached object."""
         # pylint: disable-next=consider-using-dict-items
         attact = DictSWC(
-            **{k: self.get_ndata(k) for k in self.keys()}, names=self.names
+            **{k: self.get_ndata(k) for k in self.keys()},
+            source=self.source,
+            names=self.names,
         )
         attact.ndata[self.names.id] = self.id()
         attact.ndata[self.names.pid] = self.pid()

{swcgeom-0.11.1 → swcgeom-0.13.0}/swcgeom/core/population.py

@@ -19,8 +19,8 @@ import numpy as np
 import numpy.typing as npt
 from typing_extensions import Self
 
-from .swc import eswc_cols
-from .tree import Tree
+from swcgeom.core.swc import eswc_cols
+from swcgeom.core.tree import Tree
 
 __all__ = ["LazyLoadingTrees", "ChainTrees", "Population", "Populations"]