nettracer3d 1.2.5__py3-none-any.whl → 1.3.1__py3-none-any.whl

nettracer3d/modularity.py

@@ -103,7 +103,7 @@ def read_excel_to_lists(file_path, sheet_name=0):
 
 
 
-def show_communities_flex(G, master_list, normalized_weights, geo_info=None, geometric=False, directory=None, weighted=True, partition=None, style=0):
+def show_communities_flex(G, master_list, normalized_weights, geo_info=None, geometric=False, directory=None, weighted=True, partition=None, style=0, show_labels = True):
 
     if normalized_weights is None:
         G, edge_weights = network_analysis.weighted_network(master_list)
@@ -179,7 +179,8 @@ def show_communities_flex(G, master_list, normalized_weights, geo_info=None, geo
                 normalized_weight = G[edge[0]][edge[1]]['weight']
                 nx.draw_networkx_edges(G, pos, edgelist=[edge], width=5 * normalized_weight, edge_color='black')
 
-            nx.draw_networkx_labels(G, pos)
+            if show_labels:
+                nx.draw_networkx_labels(G, pos)
 
         else:
             pos = nx.spring_layout(G)
@@ -195,20 +196,28 @@ def show_communities_flex(G, master_list, normalized_weights, geo_info=None, geo
                 normalized_weight = G[edge[0]][edge[1]]['weight']
                 nx.draw_networkx_edges(G, pos, edgelist=[edge], width=5 * normalized_weight, edge_color='black')
 
-            nx.draw_networkx_labels(G, pos)
+            if show_labels:
+                nx.draw_networkx_labels(G, pos)
 
     else:
         # Create node color list based on partition and the same color mapping
-        node_colors = [colors_matplotlib[partition[node]] for node in G.nodes()]
+        node_colors = []
+        for node in G.nodes():
+            try:
+                node_colors.append(colors_matplotlib[partition[node]])
+            except:
+                node_colors.append((1, 1, 1))
+
+        #node_colors = [colors_matplotlib[partition[node]] for node in G.nodes()]
 
         if geometric:
             pos, z_pos = simple_network.geometric_positions(geo_info[0], geo_info[1])
             node_sizes_list = [z_pos[node] for node in G.nodes()]
-            nx.draw(G, pos, with_labels=True, font_color='black', font_weight='bold', 
+            nx.draw(G, pos, with_labels=show_labels, font_color='black', font_weight='bold', 
                    node_size=node_sizes_list, node_color=node_colors, alpha=0.8, font_size=12)
         else:
             pos = nx.spring_layout(G)
-            nx.draw(G, pos, with_labels=True, font_color='black', font_weight='bold', 
+            nx.draw(G, pos, with_labels=show_labels, font_color='black', font_weight='bold', 
                    node_size=100, node_color=node_colors, alpha=0.8)
 
     plt.axis('off')

nettracer3d/morphology.py

@@ -337,7 +337,7 @@ def search_neighbor_ids(nodes, targets, id_dict, neighborhood_dict, totals, sear
     targets = np.isin(nodes, targets)
     targets = nettracer.binarize(targets)
         
-    dilated = nettracer.dilate(targets, search, xy_scale = xy_scale, z_scale = z_scale, fast_dil = fastdil)
+    dilated = nettracer.dilate_3D_dt(targets, search, xy_scaling = xy_scale, z_scaling = z_scale, fast_dil = fastdil)
     dilated = dilated - targets #technically we dont need the cores
     search_vol = np.count_nonzero(dilated) * xy_scale * xy_scale * z_scale #need this for density
     targets = dilated != 0