swcgeom 0.15.0__py3-none-any.whl → 0.17.0__py3-none-any.whl

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/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/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/analysis/{node_features.py → 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()