swcgeom 0.18.1__py3-none-any.whl → 0.19.0__py3-none-any.whl

swcgeom/analysis/lmeasure.py

@@ -20,6 +20,7 @@ from typing import Literal
 
 import numpy as np
 import numpy.typing as npt
+
 from swcgeom.core import Branch, Compartment, Node, Tree
 
 __all__ = ["LMeasure"]
@@ -28,30 +29,26 @@ __all__ = ["LMeasure"]
 class LMeasure:
     """L-Measure analysis.
 
-    The L-Measure analysis provide a set of morphometric features for
-    multiple levels analysis, as described in the paper [1]_
+    The L-Measure analysis provide a set of morphometric features for multiple levels
+    analysis, as described in the paper [1]_
 
-    References
-    ----------
-    .. [1] Scorcioni R, Polavaram S, Ascoli GA. L-Measure: a
-       web-accessible tool for the analysis, comparison and search of
-       digital reconstructions of neuronal morphologies. Nat Protoc.
-       2008;3(5):866-76. doi: 10.1038/nprot.2008.51. PMID: 18451794;
-       PMCID: PMC4340709.
+    References:
+    .. [1] Scorcioni R, Polavaram S, Ascoli GA. L-Measure: a web-accessible tool for
+       the analysis, comparison and search of digital reconstructions of neuronal
+       morphologies. Nat Protoc. 2008;3(5):866-76. doi: 10.1038/nprot.2008.51.
+       PMID: 18451794; PMCID: PMC4340709.
 
-    See Also
-    --------
-    L-Measure: http://cng.gmu.edu:8080/Lm/help/index.htm
+    See Also:
+        L-Measure: http://cng.gmu.edu:8080/Lm/help/index.htm
     """
 
     def __init__(self, compartment_point: Literal[0, -1] = -1):
         """
-        Parameters
-        ----------
-        compartment_point : 0 | -1, default=-1
-            The point of the compartment to be used for the measurements.
-            If 0, the first point of the compartment is used. If -1, the
-            last point of the compartment is used.
+        Args:
+            compartment_point:
+                The point of the compartment to be used for the measurements. If 0, the
+                first point of the compartment is used. If -1, the last point of the
+                compartment is used.
         """
         super().__init__()
         self.compartment_point = compartment_point
@@ -61,78 +58,69 @@ class LMeasure:
     def n_stems(self, tree: Tree) -> int:
         """Number of stems that is connected to soma.
 
-        This function returns the number of stems attached to the soma.
-        When the type of the Compartment changes from type=1 to others
-        it is labeled a stem. These stems can also be considered as
-        independent subtrees for subtree level analysis.
+        This function returns the number of stems attached to the soma. When the type
+        of the Compartment changes from type=1 to others it is labeled a stem. These
+        stems can also be considered as independent subtrees for subtree level analysis.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/N_stems.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/N_stems.htm
         """
         return len(tree.soma().children())
 
     def n_bifs(self, tree: Tree) -> int:
         """Number of bifurcations.
 
-        This function returns the number of bifurcations for the given
-        input neuron. A bifurcation point has two daughters.
+        This function returns the number of bifurcations for the given input neuron. A
+        bifurcation point has two daughters.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/N_bifs.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/N_bifs.htm
         """
         return len(tree.get_furcations())
 
     def n_branch(self, tree: Tree) -> int:
         """Number of branches.
 
-        This function returns the number of branches in the given input
-        neuron. A branch is one or more compartments that lie between
-        two branching points or between one branching point and a
-        termination point.
+        This function returns the number of branches in the given input neuron. A
+        branch is one or more compartments that lie between two branching points or
+        between one branching point and a termination point.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/N_branch.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/N_branch.htm
         """
         return len(tree.get_branches())
 
     def n_tips(self, tree: Tree) -> int:
         """Number of terminal tips.
 
-        This function returns the number of terminal tips for the given
-        input neuron. This function counts the number of compartments
-        that terminate as terminal endpoints.
+        This function returns the number of terminal tips for the given input neuron.
+        This function counts the number of compartments that terminate as terminal
+        endpoints.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/N_tips.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/N_tips.htm
         """
         return len(tree.get_tips())
 
     def terminal_segment(self) -> int:
         """Terminal Segment.
 
-        TerminalSegment is the branch that ends as a terminal branch.
-        This function returns "1" for all the compartments in the
-        terminal branch.
+        TerminalSegment is the branch that ends as a terminal branch. This function
+        returns "1" for all the compartments in the terminal branch.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/TerminalSegment.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/TerminalSegment.htm
         """
         raise NotImplementedError()
 
     def branch_pathlength(self, branch: Branch) -> float:
         """Length of the branch.
 
-        This function returns the sum of the length of all compartments
-        forming the giveN_branch.
+        This function returns the sum of the length of all compartments forming the
+        giveN_branch.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Branch_pathlength.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Branch_pathlength.htm
         """
         # ? as a topological measurement, this should accept a tree
         return branch.length()
@@ -140,12 +128,11 @@ class LMeasure:
     def contraction(self, branch: Branch) -> float:
         """Contraction of the branch.
 
-        This function returns the ratio between Euclidean distance of a
-        branch and its path length.
+        This function returns the ratio between Euclidean distance of a branch and its
+        path length.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Contraction.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Contraction.htm
         """
         # ? as a topological measurement, this should accept a tree
         euclidean = branch[0].distance(branch[-1])
@@ -154,13 +141,11 @@ class LMeasure:
     def fragmentation(self, branch: Branch) -> int:
         """Number of compartments.
 
-        This function returns the total number of compartments that
-        constitute a branch between two bifurcation points or between a
-        bifurcation point and a terminal tip.
+        This function returns the total number of compartments that constitute a branch
+        between two bifurcation points or between a bifurcation point and a terminal tip.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Fragmentation.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Fragmentation.htm
         """
         # ? as a topological measurement, this should accept a tree
         return branch.number_of_edges()
@@ -168,19 +153,17 @@ class LMeasure:
     def partition_asymmetry(self, n: Tree.Node) -> float:
         """Partition asymmetry.
 
-        This is computed only on bifurcation. If n1 is the number of
-        tips on the left and n2 on the right. Asymmetry return
-        abs(n1-n2)/(n1+n2-2).
+        This is computed only on bifurcation. If `n1` is the number of tips on the left
+        and `n2` on the right. Asymmetry return `abs(n1-n2)/(n1+n2-2)`.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Partition_asymmetry.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Partition_asymmetry.htm
         """
 
         children = n.children()
-        assert (
-            len(children) == 2
-        ), "Partition asymmetry is only defined for bifurcations"
+        assert len(children) == 2, (
+            "Partition asymmetry is only defined for bifurcations"
+        )
         n1 = len(children[0].subtree().get_tips())
         n2 = len(children[1].subtree().get_tips())
         if n1 == n2:
@@ -190,27 +173,24 @@ class LMeasure:
     def fractal_dim(self):
         """Fractal dimension.
 
-        Fractal dimension (D) of neuronal branches is computedas the
-        slope of linear fit of regression line obtained from the
-        log-log plot of Path distance vs Euclidean distance.
+        Fractal dimension (D) of neuronal branches is computedas the slope of linear
+        fit of regression line obtained from the log-log plot of Path distance vs
+        Euclidean distance.
 
-        This method of measuring the fractal follows the reference
-        given below by Marks & Burke, J Comp Neurol. 2007. [1]_
+        This method of measuring the fractal follows the reference given below by
+        Marks & Burke, J Comp Neurol. 2007. [1]_
         - When D = 1, the particle moves in a straight line.
         - When D = 2, the motion is a space-filling random walk
-        - When D is only slightly larger than 1, the particle
-          trajectory resembles a country road or a dendrite branch.
+        - When D is only slightly larger than 1, the particle trajectory resembles a
+          country road or a dendrite branch.
 
-        References
-        ----------
-        .. [1] Marks WB, Burke RE. Simulation of motoneuron morphology
-           in three dimensions. I. Building individual dendritic trees.
-           J Comp Neurol. 2007 Aug 10;503(5):685-700.
-           doi: 10.1002/cne.21418. PMID: 17559104.
+        References:
+        .. [1] Marks WB, Burke RE. Simulation of motoneuron morphology in three
+           dimensions. I. Building individual dendritic trees. J Comp Neurol. 2007 Aug
+           10;503(5):685-700. doi: 10.1002/cne.21418. PMID: 17559104.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Fractal_Dim.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Fractal_Dim.htm
         """
         raise NotImplementedError()
 
@@ -219,12 +199,11 @@ class LMeasure:
     def taper_1(self, branch: Branch) -> float:
         """The Burke Taper.
 
-        This function returns the Burke Taper. This function is
-        measured between two bifurcation points.
+        This function returns the Burke Taper. This function is measured between two
+        bifurcation points.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Taper_1.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Taper_1.htm
         """
         da, db = 2 * branch[0].r, 2 * branch[-1].r
         return (da - db) / branch.length()
@@ -232,12 +211,11 @@ class LMeasure:
     def taper_2(self, branch: Branch) -> float:
         """The Hillman taper.
 
-        This function returns the Hillman taper. This is measured
-        between two bifurcation points.
+        This function returns the Hillman taper. This is measured between two
+        bifurcation points.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Taper_2.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Taper_2.htm
         """
         da, db = 2 * branch[0].r, 2 * branch[-1].r
         return (da - db) / da
@@ -245,26 +223,22 @@ class LMeasure:
     def daughter_ratio(self):
         """Daughter ratio.
 
-        The function returns the ratio between the bigger daughter and
-        the other one. A daughter is the next immediate compartment
-        connected to a bifurcation point.
+        The function returns the ratio between the bigger daughter and the other one. A
+        daughter is the next immediate compartment connected to a bifurcation point.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Daughter_Ratio.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Daughter_Ratio.htm
         """
         raise NotImplementedError()
 
     def parent_daughter_ratio(self) -> float:
         """Parent daughter ratio.
 
-        This function returns the ratio between the diameter of a
-        daughter and its father. One values for each daughter is
-        returned at each bifurcation point.
+        This function returns the ratio between the diameter of a daughter and its
+        father. One values for each daughter is returned at each bifurcation point.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Parent_Daughter_Ratio.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Parent_Daughter_Ratio.htm
         """
         raise NotImplementedError()
 
@@ -272,21 +246,17 @@ class LMeasure:
         """Rall Power.
 
         Rall value is computed as the best value that fits the equation
-        (Bif_Dia)^Rall=(Daughter1_dia^Rall+Daughter2_dia^Rall).
-        According to Rall’s rule we compute rall’s power by linking the
-        diameter of two daughter branches to the diameter of the
-        bifurcating parent. We compute the best fit rall’s power within
-        the boundary values of [0, 5] at incremental steps of 1000
-        compartments. The final rall value is the idealistic n value
-        that can propagate the signal transmission without loss from
-        the starting point to the terminal point in a cable model
-        assumption.
+        `(Bif_Dia)^Rall=(Daughter1_dia^Rall+Daughter2_dia^Rall)`. According to Rall’s
+        rule we compute rall’s power by linking the diameter of two daughter branches
+        to the diameter of the bifurcating parent. We compute the best fit rall’s power
+        within the boundary values of `[0, 5]` at incremental steps of 1000
+        compartments. The final rall value is the idealistic n value that can propagate
+        the signal transmission without loss from the starting point to the terminal
+        point in a cable model assumption.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Rall_Power.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Rall_Power.htm
         """
-
         rall_power, _, _, _ = self._rall_power(bif)
         return rall_power
 
@@ -310,28 +280,23 @@ class LMeasure:
     def pk(self, bif: Tree.Node) -> float:
         """Ratio of rall power increased.
 
-        After computing the average value for Rall_Power, this function
-        returns the ratio of (d1^rall+d2^rall)/(bifurcDiam^rall).
+        After computing the average value for Rall_Power, this function returns the
+        ratio of `(d1^rall+d2^rall)/(bifurcDiam^rall)`.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Pk.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Pk.htm
         """
-
         rall_power, dp, da, db = self._rall_power(bif)
         return (da**rall_power + db**rall_power) / dp**rall_power
 
     def pk_classic(self, bif: Tree.Node) -> float:
         """Ratio of rall power increased with fixed rall power 1.5.
 
-        This function returns the same value as Pk, but with Rall_Power
-        sets to 1.5.
+        This function returns the same value as Pk, but with `Rall_Power` sets to 1.5.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Pk_classic.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Pk_classic.htm
         """
-
         dp, da, db = self._rall_power_d(bif)
         rall_power = 1.5
         return (da**rall_power + db**rall_power) / dp**rall_power
@@ -339,14 +304,11 @@ class LMeasure:
     def pk_2(self, bif: Tree.Node) -> float:
         """Ratio of rall power increased with fixed rall power 2.
 
-        This function returns the same value as Pk, but with Rall_Power
-        sets to 2 .
+        This function returns the same value as Pk, but with `Rall_Power` sets to 2 .
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Pk_2.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Pk_2.htm
         """
-
         dp, da, db = self._rall_power_d(bif)
         rall_power = 2
         return (da**rall_power + db**rall_power) / dp**rall_power
@@ -354,53 +316,44 @@ class LMeasure:
     def bif_ampl_local(self, bif: Tree.Node) -> float:
         """Bifurcation angle.
 
-        Given a bifurcation, this function returns the angle between
-        the first two compartments (in degree).
+        Given a bifurcation, this function returns the angle between the first two
+        compartments (in degree).
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_ampl_local.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_ampl_local.htm
         """
-
         v1, v2 = self._bif_vector_local(bif)
         return np.degrees(angle(v1, v2))
 
     def bif_ampl_remote(self, bif: Tree.Node) -> float:
         """Bifurcation angle.
 
-        This function returns the angle between two bifurcation points
-        or between bifurcation point and terminal point or between two
-        terminal points.
+        This function returns the angle between two bifurcation points or between
+        bifurcation point and terminal point or between two terminal points.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_ampl_remote.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_ampl_remote.htm
         """
-
         v1, v2 = self._bif_vector_remote(bif)
         return np.degrees(angle(v1, v2))
 
     def bif_tilt_local(self, bif: Tree.Node) -> float:
         """Bifuarcation tilt.
 
-        This function returns the angle between the previous
-        compartment of bifurcating father and the two daughter
-        compartments of the same bifurcation. The smaller of the two
-        angles is returned as the result.
+        This function returns the angle between the previous compartment of bifurcating
+        father and the two daughter compartments of the same bifurcation. The smaller
+        of the two angles is returned as the result.
 
-        Tilt is measured as outer angle between parent and child
-        compartments. L-Measure returns smaller angle of the two
-        children, but intuitively this can be viewed as the angle of
-        deflection of the parent orientation compared to the
+        Tilt is measured as outer angle between parent and child compartments.
+        L-Measure returns smaller angle of the two children, but intuitively this can
+        be viewed as the angle of deflection of the parent orientation compared to the
         orientation of the mid line of the bifurcation amplitude angle.
 
         (i.e.) new tilt(NT) = pi - 1/2 Bif_amp_remote - old tilt(OT)
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_tilt_local.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_tilt_local.htm
         """
-
         parent = bif.parent()
         assert parent is not None, "Bifurcation tilt is not defined for root"
         v = parent.xyz() - bif.xyz()
@@ -413,25 +366,21 @@ class LMeasure:
     def bif_tilt_remote(self, bif: Tree.Node) -> float:
         """Bifuarcation tilt.
 
-        This function returns the angle between the previous father
-        node of the current bifurcating father and its two daughter
-        nodes. A node is a terminating point or a bifurcation point or
-        a root point. Smaller of the two angles is returned as the
-        result. This angle is not computed for the root node.
+        This function returns the angle between the previous father node of the current
+        bifurcating father and its two daughter nodes. A node is a terminating point or
+        a bifurcation point or a root point. Smaller of the two angles is returned as
+        the result. This angle is not computed for the root node.
 
-        Tilt is measured as outer angle between parent and child
-        compartments. L-Measure returns smaller angle of the two
-        children, but intuitively this can be viewed as the angle of
-        deflection of the parent orientation compared to the
-        orientation of the mid line of the bifurcation amplitude angle.
+        Tilt is measured as outer angle between parent and child compartments. L-Measure
+        returns smaller angle of the two children, but intuitively this can be viewed as
+        the angle of deflection of the parent orientation compared to the orientation of
+        the mid line of the bifurcation amplitude angle.
 
         (i.e.) new tilt(NT) = pi - 1/2 Bif_amp_remote - old tilt(OT)
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_tilt_remote.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_tilt_remote.htm
         """
-
         parent = bif.parent()
         assert parent is not None, "Bifurcation tilt is not defined for root"
         v = parent.xyz() - bif.xyz()
@@ -444,27 +393,22 @@ class LMeasure:
     def bif_torque_local(self, bif: Tree.Node) -> float:
         """Bifurcation torque.
 
-        This function returns the angle between the plane of previous
-        bifurcation and the current bifurcation. Bifurcation plane is
-        identified by the two daughter compartments leaving the
-        bifurcation.
+        This function returns the angle between the plane of previous bifurcation and
+        the current bifurcation. Bifurcation plane is identified by the two daughter
+        compartments leaving the bifurcation.
 
-        A torque is the inner angle measured between two planes
-        (current & parent) of bifurcations. Plane DCE has current
-        bifurcation and plane CAB has parent bifurcation. Although LM
-        returns the absolute angle between CAB and DCE as the result,
-        it must be noted that intuitively what we are measuring is
-        relative change in the angle of second plane (DCE) with respect
-        to the first plane (CAB). Therefore, angles > 90 degrees should
-        be considered as pi - angle.
+        A torque is the inner angle measured between two planes (current & parent) of
+        bifurcations. Plane DCE has current bifurcation and plane CAB has parent
+        bifurcation. Although LM returns the absolute angle between CAB and DCE as the
+        result, it must be noted that intuitively what we are measuring is relative
+        change in the angle of second plane (DCE) with respect to the first plane (CAB).
+        Therefore, angles > 90 degrees should be considered as pi - angle.
 
         i.e. in Example1 tilt = 30deg. and in Example2 tilt = 180-110 = 70deg.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_torque_local.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_torque_local.htm
         """
-
         parent = bif.parent()
         assert parent is not None, "Bifurcation torque is not defined for root"
         idx = parent.branch().origin_id()[0]
@@ -480,29 +424,24 @@ class LMeasure:
     def bif_torque_remote(self, bif: Tree.Node) -> float:
         """Bifurcation torque.
 
-        This function returns the angle between, current plane of
-        bifurcation and previous plane of bifurcation. This is a
-        bifurcation level metric and from the figure, the current
-        plane of bifurcation is formed between C D and E where all
-        three are bifurcation points and the previous plane is formed
-        between A B and C bifurcation points.
-
-        A torque is the inner angle measured between two planes
-        (current & parent) of bifurcations. Plane DCE has current
-        bifurcation and plane CAB has parent bifurcation. Although LM
-        returns the absolute angle between CAB and DCE as the result,
-        it must be noted that intuitively what we are measuring is
-        relative change in the angle of second plane (DCE) with respect
-        to the first plane (CAB). Therefore, angles > 90 degrees should
-        be considered as pi - angle.
+        This function returns the angle between, current plane of bifurcation and
+        previous plane of bifurcation. This is a bifurcation level metric and from the
+        figure, the current plane of bifurcation is formed between C D and E where all
+        three are bifurcation points and the previous plane is formed between A B and
+        C bifurcation points.
+
+        A torque is the inner angle measured between two planes (current & parent) of
+        bifurcations. Plane DCE has current bifurcation and plane CAB has parent
+        bifurcation. Although LM returns the absolute angle between CAB and DCE as the
+        result, it must be noted that intuitively what we are measuring is relative
+        change in the angle of second plane (DCE) with respect to the first plane (CAB).
+        Therefore, angles > 90 degrees should be considered as pi - angle.
 
         i.e. in Example1 tilt = 30deg. and in Example2 tilt = 180-110 = 70deg.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_torque_remote.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_torque_remote.htm
         """
-
         parent = bif.parent()
         assert parent is not None, "Bifurcation torque is not defined for root"
         idx = parent.branch().origin_id()[0]
@@ -538,12 +477,10 @@ class LMeasure:
     def last_parent_diam(self, branch: Branch) -> float:
         """The diameter of last bifurcation before the terminal tips.
 
-        This function returns the diameter of last bifurcation before
-        the terminal tips.
+        This function returns the diameter of last bifurcation before the terminal tips.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Last_parent_diam.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Last_parent_diam.htm
         """
 
         raise NotImplementedError()
@@ -551,27 +488,23 @@ class LMeasure:
     def diam_threshold(self, branch: Branch) -> float:
         """
 
-        This function returns Diameter of first compartment after the
-        last bifurcation leading to a terminal tip.
+        This function returns Diameter of first compartment after the last bifurcation
+        leading to a terminal tip.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Diam_threshold.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Diam_threshold.htm
         """
-
         raise NotImplementedError()
 
     def hillman_threshold(self, branch: Branch) -> float:
         """Hillman Threshold.
 
-        Computes the weighted average between 50% of father and 25% of
-        daughter diameters of the terminal bifurcation.
+        Computes the weighted average between 50% of father and 25% of daughter
+        diameters of the terminal bifurcation.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/HillmanThreshold.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/HillmanThreshold.htm
         """
-
         raise NotImplementedError()
 
     # Compartment level geometrical measurements
@@ -579,41 +512,35 @@ class LMeasure:
     def diameter(self, node: Node) -> float:
         """This function returns diameter of each compartment the neuron.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Diameter.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Diameter.htm
         """
-
         return 2 * node.r
 
     def diameter_pow(self, node: Node) -> float:
         """Computes the diameter raised to the power 1.5 for each compartment.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Diameter_pow.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Diameter_pow.htm
         """
-
         return self.diameter(node) ** 1.5
 
     def length(self, compartment: Compartment) -> float:
         """Length of the compartment.
 
-        This function returns the length of compartments by computing
-        the distance between the two end points of a compartment.
+        This function returns the length of compartments by computing the distance
+        between the two end points of a compartment.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Length.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Length.htm
         """
         return compartment.length()
 
     def surface(self, compartment: Compartment) -> float:
         """This function returns surface of the compartment.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Surface.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Surface.htm
         """
         p = compartment[self.compartment_point]
         return cylinder_side_surface_area(p.r, compartment.length())
@@ -621,18 +548,16 @@ class LMeasure:
     def section_area(self, node: Node) -> float:
         """This function returns the SectionArea of the compartment.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/SectionArea.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/SectionArea.htm
         """
         return circle_area(node.r)
 
     def volume(self, compartment: Compartment) -> float:
         """This function returns the volume of the compartment.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Volume.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Volume.htm
         """
         p = compartment[self.compartment_point]
         return cylinder_volume(p.r, compartment.length())
@@ -640,12 +565,11 @@ class LMeasure:
     def euc_distance(self, node: Tree.Node) -> float:
         """Euclidean distance from compartment to soma.
 
-        This function returns the Euclidean distance of a compartment
-        with respect to soma.
+        This function returns the Euclidean distance of a compartment with respect to
+        soma.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/EucDistance.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/EucDistance.htm
         """
 
         soma = node.attach.soma()
@@ -656,11 +580,9 @@ class LMeasure:
 
         This function returns the PathDistance of a compartment.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/PathDistance.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/PathDistance.htm
         """
-
         n = node
         length = 0
         while (parent := n.parent()) is not None:
@@ -673,11 +595,9 @@ class LMeasure:
 
         This function returns the order of the branch with respect to soma.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Branch_Order.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Branch_Order.htm
         """
-
         n = node
         order = 0
         while n is not None:
@@ -687,30 +607,26 @@ class LMeasure:
         return order
 
     def terminal_degree(self, node: Tree.Node) -> int:
-        """The number of tips of the comparment.
+        """The number of tips of the compartment.
 
-        This function gives the total number of tips that each
-        compartment will terminate into.
+        This function gives the total number of tips that each compartment will
+        terminate into.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Terminal_degree.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Terminal_degree.htm
         """
-
         return len(node.subtree().get_tips())
 
     def helix(self, compartment: Tree.Compartment) -> float:
         """Helix of the compartment.
 
-        The function computes the helix by choosing the 3 segments at a
-        time (or four points at a time) and computes the normal form on
-        the 3 vectors to find the 4th vector.
+        The function computes the helix by choosing the 3 segments at a time (or four
+        points at a time) and computes the normal form on the 3 vectors to find the 4th
+        vector.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Helix.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Helix.htm
         """
-
         n1 = compartment.attach.node(compartment.origin_id()[0])
         n2 = compartment.attach.node(compartment.origin_id()[1])
         parent = n1.parent()
@@ -730,42 +646,36 @@ class LMeasure:
     def width(self, tree: Tree) -> float:
         """With of the neuron.
 
-        Width is computed on the x-coordinates and it is the difference
-        of minimum and maximum x-values after eliminating the outer
-        points on the either ends by using the 95% approximation of the
-        x-values of the given input neuron.
+        Width is computed on the x-coordinates and it is the difference of minimum and
+        maximum x-values after eliminating the outer points on the either ends by using
+        the 95% approximation of the x-values of the given input neuron.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Width.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Width.htm
         """
         return max_filtered_difference(tree.x(), 95)
 
     def height(self, tree: Tree) -> float:
         """Height of the neuron.
 
-        Height is computed on the y-coordinates and it is the
-        difference of minimum and maximum y-values after eliminating
-        the outer points on the either ends by using the 95%
-        approximation of the y-values of the given input neuron.
+        Height is computed on the y-coordinates and it is the difference of minimum and
+        maximum y-values after eliminating the outer points on the either ends by using
+        the 95% approximation of the y-values of the given input neuron.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Height.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Height.htm
         """
         return max_filtered_difference(tree.y(), 95)
 
     def depth(self, tree: Tree) -> float:
         """Depth of the neuron.
 
-        Depth is computed on the x-coordinates and it is the difference
-        of minimum and maximum x-values after eliminating the outer
-        points on the either ends by using the 95% approximation of the
-        x-values of the given input neuron.
+        Depth is computed on the x-coordinates and it is the difference of minimum and
+        maximum x-values after eliminating the outer points on the either ends by using
+        the 95% approximation of the x-values of the given input neuron.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Depth.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Depth.htm
         """
         return max_filtered_difference(tree.z(), 95)
 
@@ -774,29 +684,25 @@ class LMeasure:
     def soma_surface(self, tree: Tree) -> float:
         """Soma surface area.
 
-        This function computes the surface of the soma (Type=1). If the
-        soma is composed of just one compartment, then it uses the
-        sphere assumption, otherwise it returns the sum of the external
-        cylindrical surfaces of compartments forming the soma. There
-        can be multiple soma's, one soma or no soma at all.
+        This function computes the surface of the soma (Type=1). If the soma is
+        composed of just one compartment, then it uses the sphere assumption, otherwise
+        it returns the sum of the external cylindrical surfaces of compartments forming
+        the soma. There can be multiple soma's, one soma or no soma at all.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Soma_Surface.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Soma_Surface.htm
         """
         return sphere_surface_area(tree.soma().r)  # TODO: handle multiple soma
 
     def type(self):
         """The type of compartment.
 
-        This function returns type of compartment. Each compartment of
-        the neuron is of a particular type; soma = 1, axon = 2, basal
-        dendrites = 3, apical dendrites= 4. The type values are
-        assigned directly from the given input neuron.
+        This function returns type of compartment. Each compartment of the neuron is of
+        a particular type; soma = 1, axon = 2, basal dendrites = 3, apical dendrites= 4.
+        The type values are assigned directly from the given input neuron.
 
-        See Also
-        --------
-        L-Measure: http://cng.gmu.edu:8080/Lm/help/Type.htm
+        See Also:
+            L-Measure: http://cng.gmu.edu:8080/Lm/help/Type.htm
         """
         raise NotImplementedError()
 
@@ -841,10 +747,8 @@ def pill_surface_area(ra: float, rb: float, h: float) -> float:
 def angle(a: npt.ArrayLike, b: npt.ArrayLike) -> float:
     """Get the angle of vectors.
 
-    Returns
-    -------
-    angle : float
-        Angle [0, PI) in radians.
+    Returns:
+        angle: Angle [0, PI) in radians.
     """
 
     a, b = np.array(a), np.array(b)