swcgeom 0.13.2__tar.gz → 0.15.0__tar.gz

{swcgeom-0.13.2 → swcgeom-0.15.0}/.github/workflows/test.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["pypy3.10", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4

{swcgeom-0.13.2 → swcgeom-0.15.0}/.gitignore

@@ -1,5 +1,6 @@
 # Auto generated
 _version.py
+.DS_Store
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

{swcgeom-0.13.2 → swcgeom-0.15.0}/CHANGELOG.md

@@ -1,5 +1,67 @@
 # Changelog
 
+## **0.15.0**&emsp;<sub><sup>2024-01-28 ([d300b41...8c9e0ab](https://github.com/yzx9/swcgeom/compare/d300b41689ee892fe5a23dad57f92e1054c0f9e9...8c9e0ab45c447d3d8121b0cc4178be5f65d18a56?diff=split))</sup></sub>
+
+### Features
+
+##### `core`
+
+- expose subtree id mapping ([35738a3](https://github.com/yzx9/swcgeom/commit/35738a31b2373a43ab29550335a457c51b7befce))
+
+##### `images`
+
+- add dtype support ([d300b41](https://github.com/yzx9/swcgeom/commit/d300b41689ee892fe5a23dad57f92e1054c0f9e9))
+
+##### `transforms`
+
+- generate image stack patch ([decd3a1](https://github.com/yzx9/swcgeom/commit/decd3a1ee63e1657aafa24ec5dfbf7439d25a551))
+- add \`extra\_repr\` api ([ca19361](https://github.com/yzx9/swcgeom/commit/ca1936146783ebccc2ffe25596799580e89b3432))
+
+### Bug Fixes
+
+##### `core`
+
+- fix classmethod typing annotations ([0123eeb](https://github.com/yzx9/swcgeom/commit/0123eeb46142c3c3a695a5cf2495588a2effe275))
+
+##### `transforms`
+
+- should stack images ([8c9e0ab](https://github.com/yzx9/swcgeom/commit/8c9e0ab45c447d3d8121b0cc4178be5f65d18a56))
+
+
+### BREAKING CHANGES
+- `core` remove assembler module ([414533d](https://github.com/yzx9/swcgeom/commit/414533d17238ed45972dff1909cf025a19b7fa1e))
+<br>
+
+
+## **0.14.0**&emsp;<sub><sup>2023-12-26 ([b9c95f5...cc22018](https://github.com/yzx9/swcgeom/compare/b9c95f58f725490f3b624233cc0be20b31605e53...cc22018ad79af18ecd812b932812a0ff40a0fe40?diff=split))</sup></sub>
+
+### Features
+
+##### `analysis`
+* add high accuracy volume calculation ([9b51b74](https://github.com/yzx9/swcgeom/commit/9b51b7401efffc1b0cfbfecbdf3eb60300e1e114))
+
+### Bug Fixes
+
+##### `analysis`
+* subtract volume between frustum cone ([dae116e](https://github.com/yzx9/swcgeom/commit/dae116e45146428f5cb61c696ff1d6804e03993c))
+
+##### `utils`
+* avoid numerical error ([a6bd4ad](https://github.com/yzx9/swcgeom/commit/a6bd4adc87e86dcaca2bcb45aee68cea51a540c0))
+
+### Performance Improvements
+
+##### `analysis`
+* use bvh scene ([7a7b988](https://github.com/yzx9/swcgeom/commit/7a7b98864fd6d0378b0b696d2963353d0592b4d3))
+
+##### `utils`
+* use \`sdflit\` instead custom impl ([a47a190](https://github.com/yzx9/swcgeom/commit/a47a19091b46a1071140a12fb20105cdf851a85a))
+
+### BREAKING CHANGES
+* `transforms` rewrite image stack ([cc22018](https://github.com/yzx9/swcgeom/commit/cc22018ad79af18ecd812b932812a0ff40a0fe40))
+
+<br>
+
+
 ## **0.13.2**&emsp;<sub><sup>2023-12-16 ([10f330d...291ae2a](https://github.com/yzx9/swcgeom/compare/10f330d13b49aba19c043b91c42c183e1f9ad4d4...291ae2afde6d29d234e8f1b3521d3f221350e01e?diff=split))</sup></sub>
 
 ### Performance Improvements

swcgeom-0.15.0/LICENSE

@@ -0,0 +1,201 @@
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+   9. Accepting Warranty or Additional Liability. While redistributing
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+      on Your own behalf and on Your sole responsibility, not on behalf
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+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
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{swcgeom-0.13.2/swcgeom.egg-info → swcgeom-0.15.0}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.13.2
+Version: 0.15.0
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
-License: CC4.0 BY-NC-SA
+License: Apache-2.0
 Project-URL: repository, https://github.com/yzx9/swcgeom
 Keywords: neuronscience,neuron,neuroanatomy,neuron-morphology
 Requires-Python: >=3.10
@@ -15,6 +15,7 @@ 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: sdflit>=0.2.1
 Requires-Dist: seaborn>=0.12.0
 Requires-Dist: tifffile>=2022.8.12
 Requires-Dist: typing_extensions>=4.4.0
@@ -30,8 +31,6 @@ Requires-Dist: urllib3>=1.26.0; extra == "all"
 
 # 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 />
-
 [![Run tests](https://github.com/yzx9/swcgeom/actions/workflows/test.yml/badge.svg)](https://github.com/yzx9/swcgeom/actions/workflows/test.yml)
 [![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/)
@@ -67,4 +66,6 @@ Static analysis don't support import hook used in editable install for [PEP660](
 
 ## LICENSE
 
-This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.
+This work is licensed under a <a rel="license" href="https://www.apache.org/licenses/">Apache-2.0</a>.
+
+Copyright (c) 2022-present, Zexin Yuan

{swcgeom-0.13.2 → swcgeom-0.15.0}/README.md

@@ -1,7 +1,5 @@
 # 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 />
-
 [![Run tests](https://github.com/yzx9/swcgeom/actions/workflows/test.yml/badge.svg)](https://github.com/yzx9/swcgeom/actions/workflows/test.yml)
 [![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/)
@@ -37,4 +35,6 @@ Static analysis don't support import hook used in editable install for [PEP660](
 
 ## LICENSE
 
-This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.
+This work is licensed under a <a rel="license" href="https://www.apache.org/licenses/">Apache-2.0</a>.
+
+Copyright (c) 2022-present, Zexin Yuan

{swcgeom-0.13.2 → swcgeom-0.15.0}/examples/ImageStack.ipynb

@@ -22,17 +22,13 @@
    "source": [
     "\"\"\"Create image stack from morphology.\"\"\"\n",
     "\n",
-    "import numpy as np\n",
-    "import numpy.typing as npt\n",
-    "\n",
-    "import swcgeom\n",
     "from swcgeom import Tree\n",
     "from swcgeom.transforms import ToImageStack\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,18 +37,24 @@
     "swc3 = \"data/1059283677_15257_2226-X16029-Y23953.swc\"\n",
     "\n",
     "# create a tree\n",
-    "tree1 = swcgeom.Tree.from_swc(swc1)\n",
-    "tree2 = swcgeom.Tree.from_swc(swc2)\n",
-    "tree3 = swcgeom.Tree.from_swc(swc3, extra_cols=[\"seg_id\",\"level\",\"mode\",\"timestamp\",\"TFresindex\"])"
+    "tree1 = Tree.from_swc(swc1)\n",
+    "tree2 = Tree.from_swc(swc2)\n",
+    "tree3 = Tree.from_swc(swc3, extra_cols=[\"seg_id\",\"level\",\"mode\",\"timestamp\",\"TFresindex\"])"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "trans = ToImageStack(resolution=[1, 1, 1], z_per_iter=8)\n",
+    "trans = ToImageStack(resolution=[1, 1, 1])\n",
+    "\n",
+    "# load entire image stack into memory, should be avoided for large images\n",
+    "x = trans(tree1)\n",
+    "print(x.dtype, x.shape)\n",
+    "\n",
+    "# save image stack to file\n",
     "trans.transform_and_save(\"test.tif\", tree1)"
    ]
   }
@@ -73,7 +75,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.7"
+   "version": "3.12.1"
   },
   "orig_nbformat": 4,
   "vscode": {

{swcgeom-0.13.2 → swcgeom-0.15.0}/pyproject.toml

@@ -10,7 +10,7 @@ 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" }
+license = { text = "Apache-2.0" }
 dependencies = [
     "imagecodecs>=2023.3.16",
     "matplotlib>=3.5.2",
@@ -18,6 +18,7 @@ dependencies = [
     "pandas>=1.4.2",
     "pynrrd>=1.0.0",
     "scipy>=1.9.1",
+    "sdflit>=0.2.1",
     "seaborn>=0.12.0",
     "tifffile>=2022.8.12",
     "typing_extensions>=4.4.0",

{swcgeom-0.13.2 → swcgeom-0.15.0}/swcgeom/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.13.2'
-__version_tuple__ = version_tuple = (0, 13, 2)
+__version__ = version = '0.15.0'
+__version_tuple__ = version_tuple = (0, 15, 0)

swcgeom-0.15.0/swcgeom/analysis/volume.py

@@ -0,0 +1,152 @@
+"""Analysis of volume of a SWC tree."""
+
+from typing import Dict, List, Literal
+
+import numpy as np
+from sdflit import ColoredMaterial, ObjectsScene, SDFObject, UniformSampler
+
+from swcgeom.core import Tree
+from swcgeom.utils import VolFrustumCone, VolSphere
+
+__all__ = ["get_volume"]
+
+ACCURACY_LEVEL = Literal["low", "middle", "high"]
+ACCURACY_LEVELS: Dict[ACCURACY_LEVEL, int] = {"low": 3, "middle": 5, "high": 8}
+
+
+def get_volume(
+    tree: Tree,
+    *,
+    method: Literal["frustum_cone"] = "frustum_cone",
+    accuracy: int | ACCURACY_LEVEL = "middle",
+) -> float:
+    """Get the volume of the tree.
+
+    Parameters
+    ----------
+    tree : Tree
+        Neuronal tree.
+    method : {"frustum_cone"}, optional
+        Method for volume calculation.
+    accuracy : int or {"low", "middle", "high"}, optional
+        Accuracy level for volume calculation. The higher the accuracy,
+        the more accurate the volume calculation, but the slower the
+        calculation. The accuracy level can be specified either as an
+        integer or as a string.
+
+        The string values correspond to the following accuracy levels:
+
+        - "low": 3
+        - "middle": 5
+        - "high": 8
+
+    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.
+
+    We welcome additional representation methods through pull requests.
+    """
+
+    if isinstance(accuracy, str):
+        accuracy = ACCURACY_LEVELS[accuracy]
+
+    assert 0 < accuracy <= 10
+
+    match method:
+        case "frustum_cone":
+            return _get_volume_frustum_cone(tree, accuracy=accuracy)
+        case _:
+            raise ValueError(f"Unsupported method: {method}")
+
+
+def _get_volume_frustum_cone(tree: Tree, *, accuracy: int) -> float:
+    """Get the volume of the tree using the frustum cone method.
+
+    Parameters
+    ----------
+    tree : Tree
+        Neuronal tree.
+    accuracy : int
+        1 : Sphere only
+        2 : Sphere and Frustum Cone
+        3 : Sphere, Frustum Cone, and intersection in single-branch
+        5 : Above and Sphere-Frustum Cone intersection in multi-branch
+        10 : Fully calculated by Monte Carlo method
+    """
+
+    if accuracy == 10:
+        return _get_volume_frustum_cone_mc_only(tree)
+
+    volume = 0.0
+
+    def leave(n: Tree.Node, children: List[VolSphere]) -> VolSphere:
+        sphere = VolSphere(n.xyz(), n.r)
+        cones = [VolFrustumCone(n.xyz(), n.r, c.center, c.radius) for c in children]
+
+        v = sphere.get_volume()
+        if accuracy >= 2:
+            v += sum(fc.get_volume() for fc in cones)
+
+        if accuracy >= 3:
+            v -= sum(sphere.intersect(fc).get_volume() for fc in cones)
+            v -= sum(s.intersect(fc).get_volume() for s, fc in zip(children, cones))
+            v += sum(s.intersect(sphere).get_volume() for s in children)
+
+        if accuracy >= 5:
+            v -= sum(
+                cones[i].intersect(cones[j]).subtract(sphere).get_volume()
+                for i in range(len(cones))
+                for j in range(i + 1, len(cones))
+            )
+
+        nonlocal volume
+        volume += v
+        return sphere
+
+    tree.traverse(leave=leave)
+    return volume
+
+
+def _get_volume_frustum_cone_mc_only(tree: Tree) -> float:
+    if tree.number_of_nodes() == 0:
+        return 0
+
+    material = ColoredMaterial((1, 0, 0)).into()
+    scene = ObjectsScene()
+    scene.set_background((0, 0, 0))
+
+    def leave(n: Tree.Node, children: List[VolSphere]) -> VolSphere:
+        sphere = VolSphere(n.xyz(), n.r)
+        scene.add_object(SDFObject(sphere.sdf, material).into())
+
+        for c in children:
+            fc = VolFrustumCone(n.xyz(), n.r, c.center, c.radius)
+            scene.add_object(SDFObject(fc.sdf, material).into())
+
+        return sphere
+
+    tree.traverse(leave=leave)
+    scene.build_bvh()
+
+    # TODO: estimate the number of samples needed
+    n_samples = 100_000_000
+
+    vmin, vmax = scene.bounding_box()
+    sampler = UniformSampler(vmin, vmax)
+    data = sampler.sample(scene.into(), n_samples)
+    volume = data.sum() / n_samples * np.subtract(vmax, vmin).prod()
+    return volume

{swcgeom-0.13.2 → swcgeom-0.15.0}/swcgeom/core/branch_tree.py

@@ -5,7 +5,6 @@ from typing import Dict, List
 
 import numpy as np
 import pandas as pd
-from typing_extensions import Self
 
 from swcgeom.core.branch import Branch
 from swcgeom.core.swc_utils import to_sub_topology
@@ -31,7 +30,7 @@ class BranchTree(Tree):
         return self.branches[idx]
 
     @classmethod
-    def from_tree(cls, tree: Tree) -> Self:
+    def from_tree(cls, tree: Tree) -> "BranchTree":
         """Generating a branch tree from tree."""
 
         branches = tree.get_branches()
@@ -56,6 +55,6 @@ class BranchTree(Tree):
         return branch_tree
 
     @classmethod
-    def from_data_frame(cls, df: pd.DataFrame, *args, **kwargs) -> Self:
+    def from_data_frame(cls, df: pd.DataFrame, *args, **kwargs) -> "BranchTree":
         tree = super().from_data_frame(df, *args, **kwargs)
         return cls.from_tree(tree)

{swcgeom-0.13.2 → swcgeom-0.15.0}/swcgeom/core/population.py

@@ -17,7 +17,6 @@ from typing import (
 
 import numpy as np
 import numpy.typing as npt
-from typing_extensions import Self
 
 from swcgeom.core.swc import eswc_cols
 from swcgeom.core.tree import Tree
@@ -155,7 +154,7 @@ class Population:
         return f"Neuron population in '{self.root}'"
 
     @classmethod
-    def from_swc(cls, root: str, ext: str = ".swc", **kwargs) -> Self:
+    def from_swc(cls, root: str, ext: str = ".swc", **kwargs) -> "Population":
         if not os.path.exists(root):
             raise FileNotFoundError(
                 f"the root does not refers to an existing directory: {root}"
@@ -171,7 +170,7 @@ class Population:
         ext: str = ".eswc",
         extra_cols: Optional[Iterable[str]] = None,
         **kwargs,
-    ) -> Self:
+    ) -> "Population":
         extra_cols = list(extra_cols) if extra_cols is not None else []
         extra_cols.extend(k for k, t in eswc_cols)
         return cls.from_swc(root, ext, extra_cols=extra_cols, **kwargs)
@@ -244,7 +243,7 @@ class Populations:
         check_same: bool = False,
         labels: Optional[Iterable[str]] = None,
         **kwargs,
-    ) -> Self:
+    ) -> "Populations":
         """Get population from dirs.
 
         Parameters
@@ -268,7 +267,7 @@ class Populations:
 
             fs = [inter for _ in roots]
         elif check_same:
-            assert reduce(lambda a, b: a == b, fs), "not the same among populations"
+            assert [fs[0] == a for a in fs[1:]], "not the same among populations"
 
         populations = [
             Population(
@@ -276,7 +275,7 @@ class Populations:
             )
             for i, d in enumerate(roots)
         ]
-        return cls(populations, labels=labels)
+        return Populations(populations, labels=labels)
 
     @classmethod
     def from_eswc(
@@ -286,7 +285,7 @@ class Populations:
         *,
         ext: str = ".eswc",
         **kwargs,
-    ) -> Self:
+    ) -> "Populations":
         extra_cols = list(extra_cols) if extra_cols is not None else []
         extra_cols.extend(k for k, t in eswc_cols)
         return cls.from_swc(roots, extra_cols=extra_cols, ext=ext, **kwargs)