flake8 fixes

Author: anna-grim

src/segmentation_skeleton_metrics/skeleton_metric.py

@@ -156,7 +156,7 @@ def load_groundtruth(self, swc_pointer):
     def load_fragments(self, swc_pointer):
         print("\n(2) Load Fragments")
         if swc_pointer:
-            coords_only = False #not self.save_projections
+            coords_only = False  #not self.save_projections
             graph_builder = gutil.GraphBuilder(
                 anisotropy=self.anisotropy,
                 coords_only=coords_only,
@@ -551,7 +551,7 @@ def find_graph_from_label(self, label):
         for key in self.fragment_graphs:
             if label == util.get_segment_id(key):
                 return self.fragment_graphs[key]
-        
+
     def find_label_intersections(self):
         """
         Detects merges between ground truth graphs, namely distinct graphs that
@@ -873,7 +873,6 @@ def physical_dist(self, voxel_1, voxel_2):
         xyz_1 = img_util.to_physical(voxel_1, self.anisotropy)
         xyz_2 = img_util.to_physical(voxel_2, self.anisotropy)
         return distance.euclidean(xyz_1, xyz_2)
-        
 
     def init_counter(self):
         """

src/segmentation_skeleton_metrics/utils/graph_util.py

@@ -6,18 +6,15 @@
 @email: [email protected]
 
 """
-from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed
+from concurrent.futures import as_completed, ProcessPoolExecutor
 from random import sample
 from scipy.spatial import distance
 from tqdm import tqdm
 
 import networkx as nx
 import numpy as np
-import sys
 
-from segmentation_skeleton_metrics.utils import img_util, swc_util, util
-
-ANISOTROPY = np.array([0.748, 0.748, 1.0])
+from segmentation_skeleton_metrics.utils import swc_util, util
 
 
 class GraphBuilder:
@@ -42,7 +39,9 @@ def __init__(
 
         # Reader
         anisotropy = anisotropy if use_anisotropy else (1.0, 1.0, 1.0)
-        self.swc_reader = swc_util.Reader(anisotropy, selected_ids=selected_ids)
+        self.swc_reader = swc_util.Reader(
+            anisotropy, selected_ids=selected_ids
+        )
 
     def run(self, swc_pointer):
         graphs = self._build_graphs_from_swcs(swc_pointer)
@@ -51,13 +50,12 @@ def run(self, swc_pointer):
 
     # --- Build Graphs ---
     def _build_graphs_from_swcs(self, swc_pointer):
-        with ThreadPoolExecutor() as executor:
+        with ProcessPoolExecutor() as executor:
             # Assign processes
             processes = list()
             swc_dicts = self.swc_reader.load(swc_pointer)
             while len(swc_dicts) > 0:
                 swc_dict = swc_dicts.pop()
-                #if self._process_swc_dict(swc_dict["swc_id"]):
                 processes.append(executor.submit(self.to_graph, swc_dict))
 
             # Store results
@@ -97,9 +95,8 @@ def to_graph(self, swc_dict):
 
         # Build graph
         if not self.coords_only:
-            #graph.set_nodes()
+            graph.set_nodes()
             id_lookup = dict()
-            run_length = 0
             for i, id_i in enumerate(swc_dict["id"]):
                 id_lookup[id_i] = i
                 if swc_dict["pid"][i] != -1:

src/segmentation_skeleton_metrics/utils/swc_util.py

@@ -352,7 +352,7 @@ def read_voxel(self, xyz_str, offset):
         xyz = [float(xyz_str[i]) + offset[i] for i in range(3)]
         return img_util.to_voxels(xyz, self.anisotropy)
 
-    
+
 # --- Helpers ---
 def to_zipped_swc(zip_writer, graph, color=None):
     """