From e23d767662418fc14736942a652c24a6e1c7d8e2 Mon Sep 17 00:00:00 2001
From: Akhilesh Halageri <akhileshhalageri@gmail.com>
Date: Thu, 26 Sep 2024 14:45:14 +0000
Subject: [PATCH] fix(upgrade): use hierarchy from supervoxels

---
 pychunkedgraph/__init__.py                    | 2 +-
 pychunkedgraph/graph/edits.py                 | 7 ++++---
 pychunkedgraph/ingest/upgrade/parent_layer.py | 4 +++-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/pychunkedgraph/__init__.py b/pychunkedgraph/__init__.py
index 8e10cb462..e94f36fe8 100644
--- 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
index 340cefadd..afe1b3abf 100644
--- 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
index 0606ff674..2869fcf85 100644
--- 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():