Update graph_util.py

src/deep_neurographs/utils/graph_util.py

@@ -126,15 +126,10 @@ def run(
         irreducibles = self.schedule_processes(swc_dicts)
 
         # Build FragmentsGraph
-        if self.progress_bar:
-            pbar = tqdm(total=len(irreducibles), desc="Combine Graphs")
-
         fragments_graph = FragmentsGraph(node_spacing=self.node_spacing)
         while len(irreducibles):
             irreducible_set = irreducibles.pop()
             fragments_graph.add_component(irreducible_set)
-            if self.progress_bar:
-                pbar.update(1)
         return fragments_graph
 
     # --- Graph structure extraction ---
@@ -204,7 +199,8 @@ def get_irreducibles(self, swc_dict):
 
         # Extract irreducibles
         irreducibles = list()
-        if graph.number_of_nodes() > 1:
+        path_length = compute_path_length(graph)
+        if path_length > min_size and graph.number_of_nodes() > 1:
             for nodes in nx.connected_components(graph):
                 if len(nodes) > 1:
                     result = self.get_component_irreducibles(
@@ -303,7 +299,6 @@ def get_component_irreducibles(self, graph, swc_dict):
         edges = dict()
         nbs = defaultdict(list)
         root = None
-        total_length = 0
         branch_length = 0
         for (i, j) in nx.dfs_edges(graph, source=util.sample_once(leafs)):
             # Check if starting new or continuing current path
@@ -333,19 +328,15 @@ def get_component_irreducibles(self, graph, swc_dict):
                 nbs[root].append(j)
                 nbs[j].append(root)
                 root = None
-                total_length += branch_length
 
         # Output
-        if total_length > self.min_size:
-            irreducibles = {
-                "leaf": set_node_attrs(swc_dict, leafs),
-                "branching": set_node_attrs(swc_dict, branchings),
-                "edge": edges,
-                "swc_id": swc_dict["swc_id"],
-            }
-            return irreducibles
-        else:
-            return False
+        irreducibles = {
+            "leaf": set_node_attrs(swc_dict, leafs),
+            "branching": set_node_attrs(swc_dict, branchings),
+            "edge": edges,
+            "swc_id": swc_dict["swc_id"],
+        }
+        return irreducibles
 
 
 # --- Utils ---
@@ -630,6 +621,13 @@ def upd_node_attrs(swc_dict, leafs, branchings, i):
     return leafs, branchings
 
 
+def compute_path_length(self, graph):
+    path_length = 0
+    for i, j in nx.dfs_edges(graph):
+        path_length += compute_dist(graph, i, j)
+    return path_length
+
+
 def compute_dist(graph, i, j):
     """
     Computes Euclidean distance between nodes i and j.