refactor!: rename bifurcation to furcation

swcgeom/analysis/feature_extractor.py

@@ -19,8 +19,8 @@
 from matplotlib.axes import Axes
 
 from swcgeom.analysis.features import (
-    BifurcationFeatures,
     BranchFeatures,
+    FurcationFeatures,
     NodeFeatures,
     PathFeatures,
     TipFeatures,
@@ -40,6 +40,9 @@
     "node_count",
     "node_radial_distance",
     "node_branch_order",
+    # furcation nodes
+    "furcation_count",
+    "furcation_radial_distance",
     # bifurcation nodes
     "bifurcation_count",
     "bifurcation_radial_distance",
@@ -57,7 +60,7 @@
 NDArrayf32 = npt.NDArray[np.float32]
 FeatAndKwargs = Feature | tuple[Feature, dict[str, Any]]
 
-Feature1D = set(["length", "volume", "node_count", "bifurcation_count", "tip_count"])
+Feature1D = set(["length", "volume", "node_count", "furcation_count", "tip_count"])
 
 
 class Features:
@@ -70,7 +73,7 @@ class Features:
     @cached_property
     def node_features(self) -> NodeFeatures: return NodeFeatures(self.tree)
     @cached_property
-    def bifurcation_features(self) -> BifurcationFeatures: return BifurcationFeatures(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)
     @cached_property
@@ -214,6 +217,12 @@ def _plot_histogram_impl(
     ) -> Axes:
         raise NotImplementedError()
 
+    def get_bifurcation_count(self, **kwargs):
+        raise DeprecationWarning("Use `furcation_count` instead.")
+
+    def get_bifurcation_radial_distance(self, **kwargs):
+        raise DeprecationWarning("Use `furcation_radial_distance` instead.")
+
 
 class TreeFeatureExtractor(FeatureExtractor):
     """Extract feature from tree."""

swcgeom/analysis/features.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 import numpy.typing as npt
-from typing_extensions import Self
+from typing_extensions import Self, deprecated
 
 from swcgeom.core import Branch, BranchTree, Tree
 
@@ -121,12 +121,24 @@ def from_tree(cls, tree: Tree) -> Self:
         return cls(NodeFeatures(tree))
 
 
-class BifurcationFeatures(_SubsetNodesFeatures):
-    """Evaluate bifurcation node feature of tree."""
+class FurcationFeatures(_SubsetNodesFeatures):
+    """Evaluate furcation node feature of tree."""
 
     @cached_property
     def nodes(self) -> npt.NDArray[np.bool_]:
-        return np.array([n.is_bifurcation() for n in self._features.tree])
+        return np.array([n.is_furcation() for n in self._features.tree])
+
+
+@deprecated("Use FurcationFeatures instead")
+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.
+    """
 
 
 class TipFeatures(_SubsetNodesFeatures):

swcgeom/analysis/lmeasure.py

@@ -69,7 +69,7 @@ def n_bifs(self, tree: Tree) -> int:
         --------
         L-Measure: http://cng.gmu.edu:8080/Lm/help/N_bifs.htm
         """
-        return len(tree.get_bifurcations())
+        return len(tree.get_furcations())
 
     def n_branch(self, tree: Tree) -> int:
         """Number of branches.
@@ -339,7 +339,7 @@ def pk_2(self, bif: Tree.Node) -> float:
         return (da**rall_power + db**rall_power) / dp**rall_power
 
     def bif_ampl_local(self, bif: Tree.Node) -> float:
-        """Bifuraction angle.
+        """Bifurcation angle.
 
         Given a bifurcation, this function returns the angle between
         the first two compartments (in degree).
@@ -353,7 +353,7 @@ def bif_ampl_local(self, bif: Tree.Node) -> float:
         return np.degrees(angle(v1, v2))
 
     def bif_ampl_remote(self, bif: Tree.Node) -> float:
-        """Bifuraction angle.
+        """Bifurcation angle.
 
         This function returns the angle between two bifurcation points
         or between bifurcation point and terminal point or between two
@@ -668,7 +668,7 @@ def branch_order(self, node: Tree.Node) -> int:
         n = node
         order = 0
         while n is not None:
-            if n.is_bifurcation():
+            if n.is_furcation():
                 order += 1
             n = n.parent()
         return order

swcgeom/core/node.py

@@ -5,6 +5,7 @@
 
 import numpy as np
 import numpy.typing as npt
+from typing_extensions import deprecated
 
 from swcgeom.core.swc import DictSWC, SWCTypeVar
 from swcgeom.core.swc_utils import SWCNames
@@ -95,9 +96,22 @@ def format_swc(self) -> str:
         items = [self.id, self.type, x, y, z, r, self.pid]
         return " ".join(map(str, items))
 
-    def is_bifurcation(self) -> bool:
+    def is_furcation(self) -> bool:
+        """Is furcation node."""
         return np.count_nonzero(self.attach.pid() == self.id) > 1
 
+    @deprecated("Use is_furcation instead")
+    def is_bifurcation(self) -> bool:
+        """Is furcation node.
+
+        Notes
+        -----
+        Deprecated due to the wrong spelling of furcation. For now, it
+        is just an alias of `is_furcation` and raise a warning. It will
+        be change to raise an error in the future.
+        """
+        return self.is_furcation()
+
     def is_tip(self) -> bool:
         return self.id not in self.attach.pid()
 

swcgeom/core/path.py

@@ -16,7 +16,7 @@
 class Path(SWCLike, Generic[SWCTypeVar]):
     """Neuron path.
 
-    A path is a linear set of points without bifurcations.
+    A path is a linear set of points without furcations.
     """
 
     attach: SWCTypeVar

swcgeom/core/tree.py

@@ -8,6 +8,7 @@
 import numpy as np
 import numpy.typing as npt
 import pandas as pd
+from typing_extensions import deprecated
 
 from swcgeom.core.branch import Branch
 from swcgeom.core.compartment import Compartment, Compartments
@@ -38,11 +39,11 @@ def children(self) -> list["Tree.Node"]:
 
         def branch(self) -> "Tree.Branch":
             ns: list["Tree.Node"] = [self]
-            while not ns[-1].is_bifurcation() and (p := ns[-1].parent()) is not None:
+            while not ns[-1].is_furcation() and (p := ns[-1].parent()) is not None:
                 ns.append(p)
 
             ns.reverse()
-            while not (ns[-1].is_bifurcation() or ns[-1].is_tip()):
+            while not (ns[-1].is_furcation() or ns[-1].is_tip()):
                 ns.append(ns[-1].children()[0])
 
             return Tree.Branch(self.attach, [n.id for n in ns])
@@ -187,16 +188,28 @@ def soma(self, type_check: bool = True) -> Node:
             raise ValueError(f"no soma found in: {self.source}")
         return n
 
-    def get_bifurcations(self) -> list[Node]:
-        """Get all node of bifurcations."""
-        bifurcations: list[int] = []
+    def get_furcations(self) -> list[Node]:
+        """Get all node of furcations."""
+        furcations: list[int] = []
 
-        def collect_bifurcations(n: Tree.Node, children: list[None]) -> None:
+        def collect_furcations(n: Tree.Node, children: list[None]) -> None:
             if len(children) > 1:
-                bifurcations.append(n.id)
+                furcations.append(n.id)
+
+        self.traverse(leave=collect_furcations)
+        return [self.node(i) for i in furcations]
 
-        self.traverse(leave=collect_bifurcations)
-        return [self.node(i) for i in bifurcations]
+    @deprecated("Use `get_furcations` instead")
+    def get_bifurcations(self) -> list[Node]:
+        """Get all node of furcations.
+
+        Notes
+        -----
+        Deprecated due to the wrong spelling of furcation. For now, it
+        is just an alias of `get_furcations` and raise a warning. It
+        will be change to raise an error in the future.
+        """
+        return self.get_furcations()
 
     def get_tips(self) -> list[Node]:
         """Get all node of tips."""

swcgeom/transforms/tree.py

@@ -20,7 +20,7 @@
     "CutByType",
     "CutAxonTree",
     "CutDendriteTree",
-    "CutByBifurcationOrder",
+    "CutByFurcationOrder",
     "CutShortTipBranch",
 ]
 
@@ -124,28 +124,48 @@ def __init__(self, types: Optional[SWCTypes] = None) -> None:
         super().__init__(type=types.basal_dendrite)  # TODO: apical dendrite
 
 
-class CutByBifurcationOrder(Transform[Tree, Tree]):
-    """Cut tree by bifurcation order."""
+class CutByFurcationOrder(Transform[Tree, Tree]):
+    """Cut tree by furcation order."""
 
-    max_bifurcation_order: int
+    max_furcation_order: int
 
     def __init__(self, max_bifurcation_order: int) -> None:
-        self.max_bifurcation_order = max_bifurcation_order
+        self.max_furcation_order = max_bifurcation_order
 
     def __call__(self, x: Tree) -> Tree:
         return cut_tree(x, enter=self._enter)
 
     def __repr__(self) -> str:
-        return f"CutByBifurcationOrder-{self.max_bifurcation_order}"
+        return f"CutByBifurcationOrder-{self.max_furcation_order}"
 
     def _enter(self, n: Tree.Node, parent_level: int | None) -> tuple[int, bool]:
         if parent_level is None:
             level = 0
-        elif n.is_bifurcation():
+        elif n.is_furcation():
             level = parent_level + 1
         else:
             level = parent_level
-        return (level, level >= self.max_bifurcation_order)
+        return (level, level >= self.max_furcation_order)
+
+
+@deprecated("Use CutByFurcationOrder instead")
+class CutByBifurcationOrder(CutByFurcationOrder):
+    """Cut tree by bifurcation order.
+
+    Notes
+    -----
+    Deprecated due to the wrong spelling of furcation. For now, it
+    is just an alias of `CutByFurcationOrder` and raise a warning. It
+    will be change to raise an error in the future.
+    """
+
+    max_furcation_order: int
+
+    def __init__(self, max_bifurcation_order: int) -> None:
+        super().__init__(max_bifurcation_order)
+
+    def __repr__(self) -> str:
+        return f"CutByBifurcationOrder-{self.max_furcation_order}"
 
 
 class CutShortTipBranch(Transform[Tree, Tree]):