Fix submission.json output path and filter NaNs in hybrid_merge

script.py

@@ -234,6 +234,21 @@ def hybrid_merge(pred_v, pred_e, track_v, track_e, merge_radius=0.8):
     pred_v = np.array(pred_v) if isinstance(pred_v, list) else pred_v
     track_v = np.array(track_v)
     
+    # Filter out NaNs and Infs from track_v
+    valid_mask = np.isfinite(track_v).all(axis=1)
+    if not valid_mask.all():
+        valid_indices = np.where(valid_mask)[0]
+        idx_map = {old_idx: new_idx for new_idx, old_idx in enumerate(valid_indices)}
+        track_v = track_v[valid_mask]
+        new_track_e = []
+        for u, v in track_e:
+            if u in idx_map and v in idx_map:
+                new_track_e.append((idx_map[u], idx_map[v]))
+        track_e = new_track_e
+        
+    if len(track_v) == 0:
+        return pred_v, pred_e
+    
     # We will append track vertices that are NOT close to any pred_v
     if len(pred_v) > 0:
         from scipy.spatial import cKDTree
@@ -381,7 +396,8 @@ if __name__ == "__main__":
                       f"{elapsed:.0f}s elapsed, ~{remaining:.0f}s remaining")
 
     # Save
-    with open("submission.json", "w") as f:
+    output_path = Path(params.get('output_path', '.'))
+    with open(output_path / "submission.json", "w") as f:
         json.dump(solution, f)
 
     elapsed = time.time() - t_start