refactor: updated doubles filtering

Author: anna-grim

src/neuron_proofreader/proposal_graph.py

@@ -27,7 +27,7 @@
 )
 from neuron_proofreader.split_proofreading.proposal_generation import (
     ProposalGenerator,
-    trim_endpoints_at_proposal
+    trim_proposal_endpoints
 )
 from neuron_proofreader.utils import (
     geometry_util as geometry,
@@ -350,7 +350,7 @@ def trim_proposals(self):
             is_simple = self.is_simple(proposal)
             is_single = self.is_single_proposal(proposal)
             if is_simple and is_single:
-                trim_endpoints_at_proposal(self, proposal)
+                trim_proposal_endpoints(self, proposal)
 
     # --- Proposal Feature Generation ---
     def proposal_attr(self, proposal, key):

src/neuron_proofreader/skeleton_graph.py

@@ -13,14 +13,13 @@
 from collections import defaultdict
 from io import StringIO
 from scipy.spatial import KDTree
+from scipy.spatial import distance
 
 import networkx as nx
 import numpy as np
 import zipfile
 
-from neuron_proofreader.utils import (
-    geometry_util, graph_util as gutil, img_util, util
-)
+from neuron_proofreader.utils import graph_util as gutil, img_util, util
 
 
 class SkeletonGraph(nx.Graph):
@@ -113,6 +112,7 @@ def load(self, swc_pointer):
         self.node_component_id = np.zeros((n), dtype=int)
         self.node_radius = np.zeros((n), dtype=np.float16)
         self.node_xyz = np.zeros((n, 3), dtype=np.float32)
+        self.set_kdtree()
 
         # Add irreducibles to graph
         component_id = 0
@@ -191,8 +191,8 @@ def _add_edge(self, edge_id, attrs, component_id):
         """
         # Determine orientation of attributes
         i, j = tuple(edge_id)
-        dist_i = geometry_util.dist(self.node_xyz[i], attrs["xyz"][0])
-        dist_j = geometry_util.dist(self.node_xyz[j], attrs["xyz"][0])
+        dist_i = distance.euclidean(self.node_xyz[i], attrs["xyz"][0])
+        dist_j = distance.euclidean(self.node_xyz[j], attrs["xyz"][0])
         if dist_i < dist_j:
             start = i
             end = j
@@ -704,7 +704,7 @@ def dist(self, i, j):
         float
             Euclidean distance between nodes "i" and "j".
         """
-        return geometry_util.dist(self.node_xyz[i], self.node_xyz[j])
+        return distance.euclidean(self.node_xyz[i], self.node_xyz[j])
 
     def get_irreducible_edge(self, node):
         # Check node is non-branhching

src/neuron_proofreader/split_proofreading/proposal_generation.py

@@ -141,7 +141,7 @@ def find_node_candidates(self, leaf, radius):
         """
         node_candidates = list()
         for node in self.get_nearby_nodes(leaf, radius):
-            # check whether to move to leaf if allowing leaf-branch connections
+            # UPDATE - check whether to move to leaf if allowing leaf-branch connections
             if self.is_valid_proposal(leaf, node):
                 node_candidates.append(node)
         return node_candidates
@@ -257,7 +257,7 @@ def set_kdtree(self):
 
 
 # --- Trim Endpoints ---
-def trim_endpoints_at_proposal(graph, proposal, max_depth=20):
+def trim_proposal_endpoints(graph, proposal, max_depth=20):
     """
     Trims branch endpoints corresponding to the given proposal.