bug: image out of bounds error

src/deep_neurographs/graph_utils.py

@@ -86,8 +86,6 @@ def get_irreducibles(
         connector_length=connector_length,
         prune_depth=prune_depth,
     )
-    if graph.number_of_nodes() < min_size:
-        return [], []
 
     # Extract irreducibles
     irreducibles = []
@@ -308,7 +306,7 @@ def inspect_branch(graph, leaf, depth):
             return path
         elif graph.degree(j) == 2:
             path.append(j)
-    return []
+    return path[0:max(10, len(path))]
 
 
 def prune_short_connectors(graph, length=8):

src/deep_neurographs/img_utils.py

@@ -132,12 +132,16 @@ def read_tensorstore_with_bbox(img, bbox):
     """
     start = bbox["min"]
     end = bbox["max"]
-    return (
-        img[start[0]: end[0], start[1]: end[1], start[2]: end[2]]
-        .read()
-        .result()
-    )
-
+    try:
+        return (
+            img[start[0]: end[0], start[1]: end[1], start[2]: end[2]]
+            .read()
+            .result()
+        )
+    except Exception as e:
+        print(type(e), e)
+        shape = [end[i] - start[i] +1 for i in range(3)]
+        return np.zeros(shape)
 
 def read_chunk(img, xyz, shape, from_center=True):
     """

src/deep_neurographs/machine_learning/feature_generation.py

@@ -347,7 +347,7 @@ def proposal_skeletal(neurograph, proposals, search_radius):
         i, j = tuple(proposal)
         features[proposal] = np.concatenate(
             (
-                neurograph.proposal_length(proposal),
+                neurograph.proposal_length(proposal) / 2,
                 neurograph.degree[i],
                 neurograph.degree[j],
                 len(neurograph.nodes[i]["proposals"]),

src/deep_neurographs/reconstruction.py

@@ -208,7 +208,7 @@ def save_prediction(neurograph, accepted_proposals, output_dir):
 
     # Write Result
     neurograph.to_swc(swc_dir)
-    save_corrections(neurograph, accepted_proposals, corrections_dir)
+    #save_corrections(neurograph, accepted_proposals, corrections_dir)
     save_connections(neurograph, accepted_proposals, connections_path)