Fix radius bug

navis-org · Nov 23, 2022 · 00017e1 · 00017e1
1 parent e74f3d4
commit 00017e1
Showing 1 changed file with 8 additions and 3 deletions.
diff --git a/navis/io/swc_io.py b/navis/io/swc_io.py
@@ -593,7 +593,7 @@ def _write_swc(x: 'core.TreeNeuron',
         return node_map
 
 
-def sort_swc(df: pd.DataFrame, roots, sort_children=True, inplace=False):
+def _sort_swc_dfs(df: pd.DataFrame, roots, sort_children=True, inplace=False):
     """Depth-first search tree to ensure parents are always defined before children."""
     children = defaultdict(list)
     node_id_to_orig_idx = dict()
@@ -631,6 +631,10 @@ def sort_swc(df: pd.DataFrame, roots, sort_children=True, inplace=False):
     return df
 
 
+def _sort_swc_parent(df, inplace=False):
+    return df.sort_values("parent_id", inplace=inplace)
+
+
 def make_swc_table(x: 'core.TreeNeuron',
                    labels: Union[str, dict, bool] = None,
                    export_connectors: bool = False,
@@ -671,7 +675,8 @@ def make_swc_table(x: 'core.TreeNeuron',
 
     """
     # Work on a copy sorted in depth-first order
-    swc = sort_swc(x.nodes, x.root, inplace=False)
+    # swc = _sort_swc_dfs(x.nodes, x.root, inplace=False)
+    swc = _sort_swc_dfs(x.nodes, x.root, inplace=False)
 
     # Add labels
     swc['label'] = 0
@@ -707,7 +712,7 @@ def make_swc_table(x: 'core.TreeNeuron',
 
     # Make sure radius has no `None` or negative
     swc['radius'] = swc.radius.fillna(0)
-    swc['radius'][swc['radius'] < 0] = 0
+    swc.loc[swc["radius"] < 0, "radius"] = 0
 
     if return_node_map is not None:
         # remap IDs