Further cleaning and removing unused functions

tmd/Topology/methods.py

@@ -217,54 +217,6 @@ def get_section_mean_radii(tree, beg, end):
     return ph
 
 
-def get_ph_branchorder(tree, feature='radial_distances', **kwargs):
-    """Returns the ph diagram enhanced with the corresponding encoded radii"""
-    ph = []
-
-    rd = getattr(tree, 'get_point_' + feature)(**kwargs)
-    bo = tree.get_point_section_branch_orders()
-
-    active = tree.get_bif_term() == 0
-
-    beg, end = tree.get_sections_2()
-
-    beg = np.array(beg)
-    end = np.array(end)
-
-    parents = {e: b for b, e in zip(beg, end)}
-    children = {b: end[np.where(beg == b)[0]] for b in np.unique(beg)}
-
-    bos = tree.get_section_branch_orders()
-    #bos = np.array(get_section_branchorder(tree, beg, end))
-
-    while len(np.where(active)[0]) > 1:
-        alive = list(np.where(active)[0])
-        for l in alive:
-
-            p = parents[l]
-            c = children[p]
-
-            if np.alltrue(active[c]):
-                active[p] = True
-                active[c] = False
-
-                mx = np.argmax(abs(rd[c]))
-                mx_id = c[mx]
-
-                c = np.delete(c, mx)
-
-                for ci in c:
-                    bosID = np.array(bos)[np.where(beg == p)[0][0]]
-                    ph.append([rd[ci], rd[p], bo[p]])
-
-                rd[p] = rd[mx_id]
-                bo[p] = bo[mx_id]
-
-    ph.append([rd[np.where(active)[0][0]], 0, bo[np.where(active)[0][0]]]) # Add the last alive component
-
-    return ph
-
-
 def get_ph_neuron(neuron, feature='radial_distances', neurite_type='all', **kwargs):
     '''Method to extract ph from a neuron that contains mutlifurcations'''
 
@@ -312,7 +264,7 @@ def get_lifetime(tree, feature='point_radial_distances'):
     This can be used as the first step for the approximation of P.H.
     of the radial distances of the neuronal branches.
     '''
-    begs, ends = tree.get_sections()
+    begs, ends = tree.get_sections_2()
     rd = getattr(tree, 'get_' + feature)()
     lifetime = np.array(len(begs) * [np.zeros(2)])
 

tmd/Tree/Tree.py

@@ -6,19 +6,14 @@
 class Tree(object):
     '''Tree class'''
     import numpy as _np
-    from tmd.Tree.methods import size
-    from tmd.Tree.methods import get_sections
     from tmd.Tree.methods import get_sections_2
     from tmd.Tree.methods import get_sections_only_points
-    from tmd.Tree.methods import get_section_points
-    from tmd.Tree.methods import get_section_number
-    from tmd.Tree.methods import get_section_lengths
-    from tmd.Tree.methods import get_section_radial_distances
-    from tmd.Tree.methods import get_section_path_distances
-    from tmd.Tree.methods import get_section_branch_orders
-    from tmd.Tree.methods import get_section_start
-    from tmd.Tree.methods import get_segment_lengths
-    from tmd.Tree.methods import get_segment_radial_distances
+    from tmd.Tree.methods import get_segments
+    from tmd.Tree.methods import get_bounding_box
+    from tmd.Tree.methods import get_pca
+    from tmd.Tree.methods import extract_simplified
+    from tmd.Tree.methods import get_type
+    from tmd.Tree.methods import get_direction_between
     from tmd.Tree.methods import get_point_radial_distances
     from tmd.Tree.methods import get_point_radial_distances_time
     from tmd.Tree.methods import get_point_weighted_radial_distances
@@ -27,25 +22,9 @@ class Tree(object):
     from tmd.Tree.methods import get_point_section_lengths
     from tmd.Tree.methods import get_point_section_branch_orders
     from tmd.Tree.methods import get_bif_term
-    from tmd.Tree.methods import get_trunk
     from tmd.Tree.methods import get_bifurcations
     from tmd.Tree.methods import get_multifurcations
     from tmd.Tree.methods import get_terminations
-    from tmd.Tree.methods import get_way_to_root
-    from tmd.Tree.methods import get_way_to_section_end
-    from tmd.Tree.methods import get_way_to_section_start
-    from tmd.Tree.methods import get_bounding_box
-    from tmd.Tree.methods import get_segments
-    from tmd.Tree.methods import get_type
-    from tmd.Tree.methods import get_children
-    from tmd.Tree.methods import get_bif_angles
-    from tmd.Tree.methods import get_direction
-    from tmd.Tree.methods import get_direction_between
-    from tmd.Tree.methods import get_pca
-    from tmd.Tree.methods import extract_simplified
-    from tmd.Tree.methods import get_angle_between
-    from tmd.Tree.methods import get_branch_order
-    from tmd.Tree.methods import get_parent_child_angles
 
 
     def __init__(self, x=_np.array([]), y=_np.array([]), z=_np.array([]),
@@ -56,19 +35,14 @@ def __init__(self, x=_np.array([]), y=_np.array([]), z=_np.array([]),
         ----------
         x : numpy array
             The x-coordinates of neuron's tree segments.
-
         y : numpy array
             The y-coordinates of neuron's tree segments.
-
         z : numpy array
             The z-coordinate of neuron's tree segments.
-
         d : numpy array
             The diameters of neuron's tree segments.
-
         t : numpy array
             The types (basal, apical, axon) of neuron's tree segments.
-
         p : numpy array
             The index of the parent of neuron's tree segments.