Merge pull request #109 from clbarnes/default_tags

Add tags=None to TreeNeurons

navis/core/skeleton.py

@@ -119,6 +119,8 @@ class TreeNeuron(BaseNeuron):
     # Set default function for soma finding. Default = :func:`navis.morpho.find_soma`
     _soma: Union[Callable[['TreeNeuron'], Sequence[int]], int] = morpho.find_soma
 
+    tags: Optional[Dict[str, List[int]]] = None
+
     #: Attributes to be used when comparing two neurons.
     EQ_ATTRIBUTES = ['n_nodes', 'n_connectors', 'soma', 'root',
                      'n_branches', 'n_leafs', 'cable_length', 'name']

navis/graph/graph_utils.py

@@ -1180,6 +1180,9 @@ def reroot_skeleton(x: 'core.NeuronObject',
 
         # If new root is a tag, rather than a ID, try finding that node
         if isinstance(root, str):
+            if x.tags is None:
+                raise ValueError("Neuron does not have tags")
+
             if root not in x.tags:
                 raise ValueError(f'#{x.id}: Found no nodes with tag {root}'
                                  ' - please double check!')
@@ -1416,6 +1419,8 @@ def cut_skeleton(x: 'core.NeuronObject',
     for cn in where:
         # If cut_node is a tag (rather than an ID), try finding that node
         if isinstance(cn, str):
+            if x.tags is None:
+                raise ValueError(f"Neuron {x.id} has no tags")
             if cn not in x.tags:
                 raise ValueError(f'#{x.id}: Found no node with tag {cn}'
                                  ' - please double check!')

navis/morpho/manipulation.py

@@ -1085,7 +1085,7 @@ def stitch_skeletons(*x: Union[Sequence[NeuronObject], 'core.NeuronList'],
                 if n.has_connectors:
                     n.connectors['node_id'] = n.connectors.node_id.map(lambda x: new_map.get(x, x))
 
-                if hasattr(n, 'tags'):
+                if getattr(n, 'tags', None) is not None:
                     n.tags = {new_map.get(k, k): v for k, v in n.tags.items()}  # type: ignore
 
                 # Remap parent IDs
@@ -1110,7 +1110,7 @@ def stitch_skeletons(*x: Union[Sequence[NeuronObject], 'core.NeuronList'],
         m.tags = {}  # type: ignore  # TreeNeuron has no tags
 
     for n in nl:
-        for k, v in getattr(n, 'tags', {}).items():
+        for k, v in (getattr(n, 'tags', None) or {}).items():
             m.tags[k] = m.tags.get(k, []) + list(utils.make_iterable(v))
 
     # Reset temporary attributes of our final neuron

navis/morpho/subset.py

@@ -283,7 +283,7 @@ def _subset_treeneuron(x, subset, keep_disc_cn, prevent_fragments):
         x._connectors = x.connectors[x.connectors.node_id.isin(subset)]
         x._connectors.reset_index(inplace=True, drop=True)
 
-    if hasattr(x, 'tags'):
+    if getattr(x, 'tags', None) is not None:
         # Filter tags
         x.tags = {t: [tn for tn in x.tags[t] if tn in subset] for t in x.tags}  # type: ignore  # TreeNeuron has no tags