swcgeom 0.15.0__tar.gz → 0.17.0__tar.gz

swcgeom-0.17.0/.github/workflows/build.yml

@@ -0,0 +1,38 @@
+name: Build Python Package
+
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          git describe --tags
+          git describe --tags $(git rev-list --tags --max-count=1)
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Archive production artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: release
+          path: |
+            dist/
+            swcgeom.egg-info/

swcgeom-0.17.0/.github/workflows/github-publish.yml

@@ -0,0 +1,35 @@
+name: Release to GitHub
+
+on:
+  push:
+    tags:
+      - v*
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    uses: ./.github/workflows/build.yml
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Get version
+        id: get_version
+        run: echo ::set-output name=VERSION::${GITHUB_REF/refs\/tags\//}
+
+      - name: Download release
+        uses: actions/download-artifact@v3
+        with:
+          name: release
+
+      - name: Pack release
+        run: tar czf swcgeom-${{ steps.get_version.outputs.VERSION }}.tgz dist/
+
+      - name: Create release
+        uses: softprops/action-gh-release@v1
+        with:
+          token: ${{ secrets.GH_TOKEN }}
+          files: swcgeom-${{ steps.get_version.outputs.VERSION }}.tgz

{swcgeom-0.15.0 → swcgeom-0.17.0}/.github/workflows/pypi-publish.yml

@@ -6,26 +6,26 @@ name: Release to PyPI
 on:
   push:
     tags:
-    - v*
+      - v*
 
 permissions:
   contents: read
 
 jobs:
-  build: 
+  build:
     uses: ./.github/workflows/build.yml
 
-  release:
+  publish:
     runs-on: ubuntu-latest
     needs: build
     steps:
-    - name: Download release
-      uses: actions/download-artifact@v3
-      with:
-        name: release
+      - name: Download release
+        uses: actions/download-artifact@v3
+        with:
+          name: release
 
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

{swcgeom-0.15.0 → swcgeom-0.17.0}/.github/workflows/test.yml

@@ -3,7 +3,7 @@ name: Run tests
 on: [push]
 
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
     strategy:
       matrix:

swcgeom-0.17.0/.vscode/settings.json

@@ -0,0 +1,15 @@
+{
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter"
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "isort.args": [
+        "--profile",
+        "black"
+    ],
+}

{swcgeom-0.15.0 → swcgeom-0.17.0}/CHANGELOG.md

@@ -1,5 +1,74 @@
 # Changelog
 
+## **0.17.0**&emsp;<sub><sup>2024-04-04 ([59257cb...2072139](https://github.com/yzx9/swcgeom/compare/59257cbfb6264afd3ca31fcba002f692bbb69ed0...20721393086e5a890b097b3ae32aaa1e4ad6b898?diff=split))</sup></sub>
+
+### Features
+
+##### &ensp;`images`
+
+- handle raw file in terafly ([67ecd63](https://github.com/yzx9/swcgeom/commit/67ecd63bf4124d49b00e779c2702a7b939ef710b))
+- add image stack dtype support ([7313ead](https://github.com/yzx9/swcgeom/commit/7313ead09ec61970f221b9e0c3691d31c269b591))
+
+##### &ensp;`transforms`
+
+- add new image transformation classes ([7b5d805](https://github.com/yzx9/swcgeom/commit/7b5d805a1aa0deac3f9d7576a9aecab36b59774b))
+- add image flip and notes ([5f2a4d1](https://github.com/yzx9/swcgeom/commit/5f2a4d1a9c2b5fb68e8221c7b024a411b247ab6d))
+
+
+### BREAKING CHANGES
+- `images` remove deprecated \`swap\_xy\` and \`filp\_xy\` flag ([2072139](https://github.com/yzx9/swcgeom/commit/20721393086e5a890b097b3ae32aaa1e4ad6b898))
+<br>
+
+
+## **0.16.0**&emsp;<sub><sup>2024-03-16 ([bf2bf95...7029483](https://github.com/yzx9/swcgeom/compare/bf2bf95ee9fbfb7eba871db7303292f1dfcc7b8f...70294836643e51ca43d039887bbd71de3a9b561b?diff=split))</sup></sub>
+
+### Features
+
+##### &ensp;`analysis`
+
+- add l\-measure support \(close \#13\) ([15ddc33](https://github.com/yzx9/swcgeom/commit/15ddc333c4cdce42fe99fb2383fa0768bc2e35b2))
+
+##### &ensp;`core`
+
+- \`Tree\` accpet values with custom names ([722f84f](https://github.com/yzx9/swcgeom/commit/722f84fdd71133d07e74b5f90171b3671a4fe4c9))
+- add \`Population\.map\` parallel processing support ([a1ee5bb](https://github.com/yzx9/swcgeom/commit/a1ee5bb6344ad5ab7b6572962f3b84caedf1351f))
+
+##### &ensp;`images`
+
+- add image contrast functions ([85b881e](https://github.com/yzx9/swcgeom/commit/85b881e91e878daf6fb3aa2862b5cd62eaa3488b))
+- stat image stack folder ([ffc5e3a](https://github.com/yzx9/swcgeom/commit/ffc5e3a649a4d8203c2530b6351a7b509b262cf3))
+
+##### &ensp;`transforms`
+
+- add basic neuronlucida asc format support \(close \#12\) ([619a275](https://github.com/yzx9/swcgeom/commit/619a275aaa5a311c66e1a2438e6251ee4b9bd703))
+- add \`SGuoImPreProcess\` ([dab7481](https://github.com/yzx9/swcgeom/commit/dab74818e5ea82d27450758f868bdc633b8992bf))
+- add image stack related transforms ([7029483](https://github.com/yzx9/swcgeom/commit/70294836643e51ca43d039887bbd71de3a9b561b))
+
+##### &ensp;`utils`
+
+- \`Tree\` support array like inputs ([1f228d0](https://github.com/yzx9/swcgeom/commit/1f228d055b99c8545ba51da5af2bca8d7b760f3f))
+- download source swc and log from neuromorpho ([d4fbfb6](https://github.com/yzx9/swcgeom/commit/d4fbfb6f0b89990bf63b481333d6c3c3cb16705c))
+
+### Bug Fixes
+
+##### &ensp;`utils`
+
+- expecting a figure from the axes ([bf2bf95](https://github.com/yzx9/swcgeom/commit/bf2bf95ee9fbfb7eba871db7303292f1dfcc7b8f))
+
+### Performance Improvements
+
+##### &ensp;`core`
+
+- use NamedTuple for SWCNames and SWCTypes ([300bfea](https://github.com/yzx9/swcgeom/commit/300bfeac92b90e09f262a850ecc226257c2af2e5))
+
+
+### BREAKING CHANGES
+
+- `core` \`Tree\` accpet values with custom names ([722f84f](https://github.com/yzx9/swcgeom/commit/722f84fdd71133d07e74b5f90171b3671a4fe4c9))
+- `core` remove deprecated \`Tree\.Node\.get\_branch\` and \`Node\.child\_ids\` method ([1de86af](https://github.com/yzx9/swcgeom/commit/1de86afc21451be4c6bde5084688170d901eb625))
+
+<br>
+
 ## **0.15.0**&emsp;<sub><sup>2024-01-28 ([d300b41...8c9e0ab](https://github.com/yzx9/swcgeom/compare/d300b41689ee892fe5a23dad57f92e1054c0f9e9...8c9e0ab45c447d3d8121b0cc4178be5f65d18a56?diff=split))</sup></sub>
 
 ### Features

{swcgeom-0.15.0/swcgeom.egg-info → swcgeom-0.17.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.15.0
+Version: 0.17.0
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: Apache-2.0
@@ -19,14 +19,14 @@ 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
+Requires-Dist: tqdm>=4.46.1
 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: requests>=2.0.0; extra == "all"
 Requires-Dist: urllib3>=1.26.0; extra == "all"
 
 # SWCGEOM

{swcgeom-0.15.0 → swcgeom-0.17.0}/examples/pytorch/branch_dataset.py

@@ -8,7 +8,7 @@ import torch
 import torch.utils.data
 from tree_folder_dataset import TreeFolderDataset
 
-from swcgeom import Branch
+from swcgeom.core import Branch
 from swcgeom.transforms import Identity, Transform
 from swcgeom.utils import numpy_err
 

{swcgeom-0.15.0 → swcgeom-0.17.0}/pyproject.toml

@@ -22,6 +22,7 @@ dependencies = [
     "seaborn>=0.12.0",
     "tifffile>=2022.8.12",
     "typing_extensions>=4.4.0",
+    "tqdm>=4.46.1",
     "v3d-py-helper>=0.1.0",
 ]
 
@@ -31,8 +32,7 @@ all = [
     "certifi>=2023.5.7",
     "chardet>=5.2.0",
     "lmdb>=1.4.1",
-    "pycurl>=7.0.0",
-    "tqdm>=4.46.1",
+    "requests>=2.0.0",
     "urllib3>=1.26.0",
 ]
 

{swcgeom-0.15.0 → swcgeom-0.17.0}/swcgeom/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.15.0'
-__version_tuple__ = version_tuple = (0, 15, 0)
+__version__ = version = '0.17.0'
+__version_tuple__ = version_tuple = (0, 17, 0)

{swcgeom-0.15.0 → swcgeom-0.17.0}/swcgeom/analysis/__init__.py

@@ -1,9 +1,7 @@
 """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.features import *
 from swcgeom.analysis.sholl import *
 from swcgeom.analysis.trunk import *
 from swcgeom.analysis.visualization import *

{swcgeom-0.15.0 → swcgeom-0.17.0}/swcgeom/analysis/feature_extractor.py

@@ -17,13 +17,13 @@ import numpy.typing as npt
 import seaborn as sns
 from matplotlib.axes import Axes
 
-from swcgeom.analysis.branch_features import BranchFeatures
-from swcgeom.analysis.node_features import (
+from swcgeom.analysis.features import (
     BifurcationFeatures,
+    BranchFeatures,
     NodeFeatures,
+    PathFeatures,
     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

swcgeom-0.15.0/swcgeom/analysis/node_features.py → swcgeom-0.17.0/swcgeom/analysis/features.py

@@ -1,15 +1,26 @@
-"""Depth distribution of tree."""
+"""Feature anlysis of tree."""
 
 from abc import ABC, abstractmethod
 from functools import cached_property
+from typing import List, TypeVar
 
 import numpy as np
 import numpy.typing as npt
 from typing_extensions import Self
 
-from swcgeom.core import BranchTree, Tree
+from swcgeom.core import Branch, BranchTree, Tree
 
-__all__ = ["NodeFeatures", "BifurcationFeatures", "TipFeatures"]
+__all__ = [
+    "NodeFeatures",
+    "BifurcationFeatures",
+    "TipFeatures",
+    "PathFeatures",
+    "BranchFeatures",
+]
+
+T = TypeVar("T", bound=Branch)
+
+# Node Level
 
 
 class NodeFeatures:
@@ -31,6 +42,7 @@ class NodeFeatures:
         -------
         count : array of shape (1,)
         """
+
         return np.array([self.tree.number_of_nodes()], dtype=np.float32)
 
     def get_radial_distance(self) -> npt.NDArray[np.float32]:
@@ -41,6 +53,7 @@ class NodeFeatures:
         radial_distance : npt.NDArray[np.float32]
             Array of shape (N,).
         """
+
         xyz = self.tree.xyz() - self.tree.soma().xyz()
         radial_distance = np.linalg.norm(xyz, axis=1)
         return radial_distance
@@ -58,6 +71,7 @@ class NodeFeatures:
         order : npt.NDArray[np.int32]
             Array of shape (N,), which k is the number of branchs.
         """
+
         order = np.zeros_like(self._branch_tree.id(), dtype=np.int32)
 
         def assign_depth(n: Tree.Node, pre_depth: int | None) -> int:
@@ -88,6 +102,7 @@ class _SubsetNodesFeatures(ABC):
         count : npt.NDArray[np.float32]
             Array of shape (1,).
         """
+
         return np.array([np.count_nonzero(self.nodes)], dtype=np.float32)
 
     def get_radial_distance(self) -> npt.NDArray[np.float32]:
@@ -98,6 +113,7 @@ class _SubsetNodesFeatures(ABC):
         radial_distance : npt.NDArray[np.float32]
             Array of shape (N,).
         """
+
         return self._features.get_radial_distance()[self.nodes]
 
     @classmethod
@@ -119,3 +135,89 @@ class TipFeatures(_SubsetNodesFeatures):
     @cached_property
     def nodes(self) -> npt.NDArray[np.bool_]:
         return np.array([n.is_tip() for n in self._features.tree])
+
+
+# Path Level
+
+
+class PathFeatures:
+    """Path analysis of tree."""
+
+    tree: Tree
+
+    def __init__(self, tree: Tree) -> None:
+        self.tree = tree
+
+    def get_count(self) -> int:
+        return len(self._paths)
+
+    def get_length(self) -> npt.NDArray[np.float32]:
+        """Get length of paths."""
+
+        length = [path.length() for path in self._paths]
+        return np.array(length, dtype=np.float32)
+
+    def get_tortuosity(self) -> npt.NDArray[np.float32]:
+        """Get tortuosity of path."""
+
+        return np.array([path.tortuosity() for path in self._paths], dtype=np.float32)
+
+    @cached_property
+    def _paths(self) -> List[Tree.Path]:
+        return self.tree.get_paths()
+
+
+class BranchFeatures:
+    """Analysis bransh of tree."""
+
+    tree: Tree
+
+    def __init__(self, tree: Tree) -> None:
+        self.tree = tree
+
+    def get_count(self) -> int:
+        return len(self._branches)
+
+    def get_length(self) -> npt.NDArray[np.float32]:
+        """Get length of branches."""
+
+        length = [br.length() for br in self._branches]
+        return np.array(length, dtype=np.float32)
+
+    def get_tortuosity(self) -> npt.NDArray[np.float32]:
+        """Get tortuosity of path."""
+
+        return np.array([br.tortuosity() for br in self._branches], dtype=np.float32)
+
+    def get_angle(self, eps: float = 1e-7) -> npt.NDArray[np.float32]:
+        """Get agnle between branches.
+
+        Returns
+        -------
+        angle : npt.NDArray[np.float32]
+            An array of shape (N, N), which N is length of branches.
+        """
+
+        return self.calc_angle(self._branches, eps=eps)
+
+    @staticmethod
+    def calc_angle(branches: List[T], eps: float = 1e-7) -> npt.NDArray[np.float32]:
+        """Calc agnle between branches.
+
+        Returns
+        -------
+        angle : npt.NDArray[np.float32]
+            An array of shape (N, N), which N is length of branches.
+        """
+
+        vector = np.array([br[-1].xyz() - br[0].xyz() for br in branches])
+        vector_dot = np.matmul(vector, vector.T)
+        vector_norm = np.linalg.norm(vector, ord=2, axis=1, keepdims=True)
+        vector_norm_dot = np.matmul(vector_norm, vector_norm.T) + eps
+        arccos = np.clip(vector_dot / vector_norm_dot, -1, 1)
+        angle = np.arccos(arccos)
+        return angle
+
+    @cached_property
+    def _branches(self) -> List[Tree.Branch]:
+        return self.tree.get_branches()