minor upds

src/deep_neurographs/groundtruth_generation.py

@@ -15,7 +15,6 @@
 import numpy as np
 
 from deep_neurographs import geometry
-from deep_neurographs.geometry import dist as get_dist
 from deep_neurographs.utils import util
 
 ALIGNED_THRESHOLD = 4.5
@@ -141,7 +140,7 @@ def is_component_aligned(target_graph, pred_graph, nodes, kdtree):
         for xyz in pred_graph.edges[edge]["xyz"]:
             hat_xyz = geometry.kdtree_query(kdtree, xyz)
             hat_swc_id = target_graph.xyz_to_swc(hat_xyz)
-            d = get_dist(hat_xyz, xyz)
+            d = geometry.dist(hat_xyz, xyz)
             dists[hat_swc_id].append(d)
 
     # Deterine whether aligned

src/deep_neurographs/inference.py

@@ -132,7 +132,6 @@ def __init__(
         )
 
         # Set output directory
-        date = datetime.today().strftime("%Y-%m-%d")
         self.output_dir = output_dir
         util.mkdir(self.output_dir, delete=True)
         if self.log_runtimes:

src/deep_neurographs/neurograph.py

@@ -9,9 +9,7 @@
 NOTE: SAVE LABEL UPDATES --- THERE IS A BUG IN FEATURE GENERATION
 
 """
-import os
 import zipfile
-from concurrent.futures import ThreadPoolExecutor
 from copy import deepcopy
 from io import StringIO
 
@@ -21,10 +19,8 @@
 from scipy.spatial import KDTree
 
 from deep_neurographs import generate_proposals, geometry
-from deep_neurographs.geometry import dist as get_dist
 from deep_neurographs.groundtruth_generation import init_targets
-from deep_neurographs.utils import graph_util as gutil
-from deep_neurographs.utils import img_util, swc_util, util
+from deep_neurographs.utils import graph_util as gutil, img_util, util
 
 
 class NeuroGraph(nx.Graph):
@@ -808,7 +804,7 @@ def dist(self, i, j):
             Euclidean distance between nodes "i" and "j".
 
         """
-        return get_dist(self.nodes[i]["xyz"], self.nodes[j]["xyz"])
+        return geometry.dist(self.nodes[i]["xyz"], self.nodes[j]["xyz"])
 
     def branches(self, i, ignore_reducibles=True, key="xyz"):
         branches = list()

src/deep_neurographs/utils/util.py

@@ -10,19 +10,20 @@
 
 import json
 import math
-import networkx as nx
 import os
 import shutil
 from io import BytesIO
 from random import sample
 from zipfile import ZipFile
 
 import boto3
+import networkx as nx
 import numpy as np
 import psutil
 from google.cloud import storage
 
-from deep_neurographs.utils import graph_util as gutil, swc_util
+from deep_neurographs.utils import graph_util as gutil
+
 
 # --- os utils ---
 def mkdir(path, delete=False):