swcgeom 0.18.3__py3-none-any.whl → 0.19.1__py3-none-any.whl

swcgeom/analysis/feature_extractor.py

@@ -15,10 +15,8 @@
 
 """Easy way to compute and visualize common features for feature.
 
-Notes
------
-For development, see method `Features.get_evaluator` to confirm the
-naming specification.
+NOTE: For development, see method `Features.get_evaluator` to confirm the naming
+specification.
 """
 
 from abc import ABC, abstractmethod
@@ -83,23 +81,31 @@ class Features:
 
     tree: Tree
 
-    # fmt:off
     # Modules
     @cached_property
-    def node_features(self) -> NodeFeatures: return NodeFeatures(self.tree)
+    def node_features(self) -> NodeFeatures:
+        return NodeFeatures(self.tree)
+
     @cached_property
-    def furcation_features(self) -> FurcationFeatures: return FurcationFeatures(self.node_features)
+    def furcation_features(self) -> FurcationFeatures:
+        return FurcationFeatures(self.node_features)
+
     @cached_property
-    def tip_features(self) -> TipFeatures: return TipFeatures(self.node_features)
+    def tip_features(self) -> TipFeatures:
+        return TipFeatures(self.node_features)
+
     @cached_property
-    def branch_features(self) -> BranchFeatures: return BranchFeatures(self.tree)
+    def branch_features(self) -> BranchFeatures:
+        return BranchFeatures(self.tree)
+
     @cached_property
-    def path_features(self) -> PathFeatures: return PathFeatures(self.tree)
+    def path_features(self) -> PathFeatures:
+        return PathFeatures(self.tree)
 
     # Caches
     @cached_property
-    def sholl(self) -> Sholl: return Sholl(self.tree)
-    # fmt:on
+    def sholl(self) -> Sholl:
+        return Sholl(self.tree)
 
     def __init__(self, tree: Tree) -> None:
         self.tree = tree
@@ -136,22 +142,17 @@ class Features:
 class FeatureExtractor(ABC):
     """Extract features from tree."""
 
-    # fmt:off
     @overload
     def get(self, feature: Feature, **kwargs) -> NDArrayf32: ...
     @overload
     def get(self, feature: list[FeatAndKwargs]) -> list[NDArrayf32]: ...
     @overload
     def get(self, feature: dict[Feature, dict[str, Any]]) -> dict[str, NDArrayf32]: ...
-    # fmt:on
     def get(self, feature, **kwargs):
         """Get feature.
 
-        Notes
-        -----
-        Shape of returned array is not uniform, `TreeFeatureExtractor`
-        returns array of shape (L, ), `PopulationFeatureExtracor`
-        returns array of shape (N, L).
+        NOTE: Shape of returned array is not uniform, `TreeFeatureExtractor` returns
+        array of shape (L, ), `PopulationFeatureExtracor` returns array of shape (N, L).
         """
         if isinstance(feature, dict):
             return {k: self._get(k, **v) for k, v in feature.items()}
@@ -164,11 +165,8 @@ class FeatureExtractor(ABC):
     def plot(self, feature: FeatAndKwargs, title: str | bool = True, **kwargs) -> Axes:
         """Plot feature with appropriate way.
 
-        Notes
-        -----
-        The drawing method is different in different classes, different
-        in different features, and may different between versions,
-        there are NO guarantees.
+        NOTE: The drawing method is different in different classes, different in
+        different features, and may different between versions, there are NO guarantees.
         """
         feat, feat_kwargs = _get_feat_and_kwargs(feature)
         if callable(custom_plot := getattr(self, f"plot_{feat}", None)):

swcgeom/analysis/features.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 
-"""Feature anlysis of tree."""
+"""Feature analysis of tree."""
 
 from abc import ABC, abstractmethod
 from functools import cached_property
@@ -53,22 +53,17 @@ class NodeFeatures:
     def get_count(self) -> npt.NDArray[np.float32]:
         """Get number of nodes.
 
-        Returns
-        -------
-        count : array of shape (1,)
+        Args:
+            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]:
         """Get the end-to-end straight-line distance to soma.
 
-        Returns
-        -------
-        radial_distance : npt.NDArray[np.float32]
-            Array of shape (N,).
+        Returns:
+            radial_distance: Array of shape (N,).
         """
-
         xyz = self.tree.xyz() - self.tree.soma().xyz()
         radial_distance = np.linalg.norm(xyz, axis=1)
         return radial_distance
@@ -81,12 +76,9 @@ class NodeFeatures:
 
         Criticle node means that soma, bifucation nodes, tips.
 
-        Returns
-        -------
-        order : npt.NDArray[np.int32]
-            Array of shape (N,), which k is the number of branchs.
+        Returns:
+            order: Array of shape (N,), which k is the number of branches.
         """
-
         order = np.zeros_like(self._branch_tree.id(), dtype=np.int32)
 
         def assign_depth(n: Tree.Node, pre_depth: int | None) -> int:
@@ -112,23 +104,17 @@ class _SubsetNodesFeatures(ABC):
     def get_count(self) -> npt.NDArray[np.float32]:
         """Get number of nodes.
 
-        Returns
-        -------
-        count : npt.NDArray[np.float32]
-            Array of shape (1,).
+        Returns:
+            count: Array of shape (1,).
         """
-
         return np.array([np.count_nonzero(self.nodes)], dtype=np.float32)
 
     def get_radial_distance(self) -> npt.NDArray[np.float32]:
         """Get the end-to-end straight-line distance to soma.
 
-        Returns
-        -------
-        radial_distance : npt.NDArray[np.float32]
-            Array of shape (N,).
+        Returns:
+            radial_distance: Array of shape (N,).
         """
-
         return self._features.get_radial_distance()[self.nodes]
 
     @classmethod
@@ -148,11 +134,9 @@ class FurcationFeatures(_SubsetNodesFeatures):
 class BifurcationFeatures(FurcationFeatures):
     """Evaluate bifurcation node feature of tree.
 
-    Notes
-    -----
-    Deprecated due to the wrong spelling of furcation. For now, it
-    is just an alias of `FurcationFeatures` and raise a warning. It
-    will be change to raise an error in the future.
+    NOTE: Deprecated due to the wrong spelling of furcation. For now, it is just an
+    alias of `FurcationFeatures` and raise a warning. It will be change to raise an
+    error in the future.
     """
 
 
@@ -219,24 +203,18 @@ class BranchFeatures:
     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.
+        Returns:
+            angle: 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.
+        Returns:
+            angle: 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)