fix(upgrade): use hierarchy from supervoxels

CAVEconnectome · Sep 26, 2024 · e23d767 · e23d767
1 parent c1af454
commit e23d767
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Showing 3 changed files with 8 additions and 5 deletions.
diff --git a/pychunkedgraph/__init__.py b/pychunkedgraph/__init__.py
@@ -1 +1 @@
-__version__ = "3.0.4"
+__version__ = "3.0.5"
diff --git a/pychunkedgraph/graph/edits.py b/pychunkedgraph/graph/edits.py
@@ -497,7 +497,7 @@ def _update_neighbor_cross_edges(
     return updated_entries
 
 
-def _get_supervoxels(cg, node_ids):
+def get_supervoxels(cg, node_ids):
     """Returns the first supervoxel found for each node_id."""
     result = {}
     node_ids_copy = np.copy(node_ids)
@@ -606,7 +606,7 @@ def _update_cross_edge_cache(self, parent, children):
         )
         cx_edges_d = concatenate_cross_edge_dicts(cx_edges_d.values())
         edge_nodes = np.unique(np.concatenate([*cx_edges_d.values(), types.empty_2d]))
-        edge_supervoxels = _get_supervoxels(self.cg, edge_nodes)
+        edge_supervoxels = get_supervoxels(self.cg, edge_nodes)
         edge_parents = self.cg.get_roots(
             edge_supervoxels,
             stop_layer=parent_layer,
@@ -671,7 +671,8 @@ def _create_new_parents(self, layer: int):
                     l2c1 = get_l2children(self.cg, c1)
                     l2c2 = get_l2children(self.cg, c2)
                     if np.intersect1d(l2c1, l2c2).size:
-                        msg = f"{self._operation_id}:{c1} {c2} have common children."
+                        c = np.intersect1d(l2c1, l2c2)
+                        msg = f"{self._operation_id}: {layer} {c1} {c2} have common children {c}"
                         raise ValueError(msg)
 
     def run(self) -> Iterable:

diff --git a/pychunkedgraph/ingest/upgrade/parent_layer.py b/pychunkedgraph/ingest/upgrade/parent_layer.py
@@ -10,6 +10,7 @@
 
 from pychunkedgraph.graph import ChunkedGraph
 from pychunkedgraph.graph.attributes import Connectivity, Hierarchy
+from pychunkedgraph.graph.edits import get_supervoxels
 from pychunkedgraph.graph.utils import serializers
 from pychunkedgraph.graph.types import empty_2d
 from pychunkedgraph.utils.general import chunked
@@ -101,7 +102,8 @@ def update_cross_edges(cg: ChunkedGraph, layer, node, node_ts, earliest_ts) -> l
         if edges.size == 0:
             continue
         nodes = np.unique(edges[:, 1])
-        parents = cg.get_roots(nodes, time_stamp=ts, stop_layer=layer, ceil=False)
+        svs = get_supervoxels(cg, nodes)
+        parents = cg.get_roots(svs, time_stamp=ts, stop_layer=layer, ceil=False)
         edge_parents_d = dict(zip(nodes, parents))
         val_dict = {}
         for _layer, layer_edges in cx_edges_d.items():