minor upds

src/deep_neurographs/fragment_filtering.py

@@ -25,7 +25,7 @@
 def remove_curvy(graph, max_length, ratio=0.5):
     deleted_ids = set()
     components = [c for c in connected_components(graph) if len(c) == 2]
-    for nodes in tqdm(components, desc="Curvy Fragment Filtering"):
+    for nodes in tqdm(components, desc="Filter Curvy Fragment"):
         if len(nodes) == 2:
             i, j = tuple(nodes)
             length = graph.edges[i, j]["length"]
@@ -67,7 +67,7 @@ def remove_doubles(graph, max_length, node_spacing, output_dir=None):
         util.mkdir(output_dir, delete=True)
 
     # Main
-    desc = "Doubled Fragment Filtering"
+    desc = "Filter Doubled Fragment"
     for idx in tqdm(np.argsort([len(c) for c in components]), desc=desc):
         i, j = tuple(components[idx])
         swc_id = graph.nodes[i]["swc_id"]

src/deep_neurographs/machine_learning/heterograph_models.py

@@ -59,6 +59,7 @@ def __init__(
 
         self.input_edges = nn.ModuleDict()
         for key, d in edge_dict.items():
+            key = str(key)
             self.input_edges[str(key)] = nn.Linear(d, hidden_dim, device=device)
 
         # Layer dimensions
@@ -154,7 +155,7 @@ def forward(self, x_dict, edge_index_dict, edge_attr_dict):
 
         # Input - Edges
         for key, f in self.input_edges.items():
-            #key = reformat_edge_key(key)
+            key = reformat_edge_key(key)
             edge_attr_dict[key] = f(edge_attr_dict[key])
         edge_attr_dict = self.activation(edge_attr_dict)
 

src/deep_neurographs/utils/swc_util.py

@@ -172,7 +172,7 @@ def load_from_gcs(self, gcs_dict):
         with ProcessPoolExecutor() as executor:
             # Assign processes
             processes = list()
-            for path in tqdm(zip_paths, desc="Downloading SWCs"):
+            for path in tqdm(zip_paths, desc="Download SWCs"):
                 zip_content = bucket.blob(path).download_as_bytes()
                 processes.append(
                     executor.submit(self.load_from_cloud_zip, zip_content)