fix(edits/split): filter out inactive cross edges

Author: akhileshh

pychunkedgraph/graph/chunkedgraph.py

@@ -657,7 +657,11 @@ def copy_fake_edges(self, chunk_id: np.uint64) -> None:
         self.client.write(mutations)
 
     def get_l2_agglomerations(
-        self, level2_ids: np.ndarray, edges_only: bool = False
+        self,
+        level2_ids: np.ndarray,
+        edges_only: bool = False,
+        active: bool = False,
+        time_stamp: typing.Optional[datetime.datetime] = None,
     ) -> typing.Tuple[typing.Dict[int, types.Agglomeration], typing.Tuple[Edges]]:
         """
         Children of Level 2 Node IDs and edges.
@@ -703,6 +707,15 @@ def get_l2_agglomerations(
                     raise ValueError("Found conflicting parents.")
             sv_parent_d.update(dict(zip(svs.tolist(), [l2id] * len(svs))))
 
+        if active:
+            n1, n2 = all_chunk_edges.node_ids1, all_chunk_edges.node_ids2
+            layers = self.get_cross_chunk_edges_layer(all_chunk_edges.get_pairs())
+            max_layer = np.max(layers) + 1
+            parents1 = self.get_roots(n1, stop_layer=max_layer, time_stamp=time_stamp)
+            parents2 = self.get_roots(n2, stop_layer=max_layer, time_stamp=time_stamp)
+            mask = parents1 == parents2
+            all_chunk_edges = all_chunk_edges[mask]
+
         in_edges, out_edges, cross_edges = edge_utils.categorize_edges_v2(
             self.meta, all_chunk_edges, sv_parent_d
         )

pychunkedgraph/graph/edits.py

@@ -313,7 +313,6 @@ def remove_edges(
     cg,
     *,
     atomic_edges: Iterable[np.ndarray],
-    l2id_agglomeration_d: Dict,
     operation_id: basetypes.OPERATION_ID = None,
     time_stamp: datetime.datetime = None,
     parent_ts: datetime.datetime = None,
@@ -323,6 +322,9 @@ def remove_edges(
     roots = cg.get_roots(l2ids, assert_roots=True, time_stamp=parent_ts)
     assert np.unique(roots).size == 1, "L2 IDs must belong to same root."
 
+    l2id_agglomeration_d, _ = cg.get_l2_agglomerations(
+        l2ids, active=True, time_stamp=parent_ts
+    )
     new_old_id_d = defaultdict(set)
     old_new_id_d = defaultdict(set)
     old_hierarchy_d = _init_old_hierarchy(cg, l2ids, parent_ts=parent_ts)
@@ -409,7 +411,6 @@ def _get_descendants(cg, new_id):
     return result
 
 
-
 def _update_neighbor_cross_edges_single(
     cg, new_id: int, cx_edges_d: dict, node_map: dict, *, parent_ts
 ) -> dict:
@@ -498,7 +499,7 @@ def _update_neighbor_cross_edges(
 
 def _get_supervoxels(cg, node_ids):
     """Returns the first supervoxel found for each node_id."""
-    result  = {}
+    result = {}
     node_ids_copy = np.copy(node_ids)
     children = np.copy(node_ids)
     children_d = cg.get_children(node_ids)

pychunkedgraph/graph/operation.py

@@ -640,7 +640,7 @@ def _apply(
                 operation_id=operation_id,
                 time_stamp=timestamp,
                 parent_ts=self.parent_ts,
-                allow_same_segment_merge=self.allow_same_segment_merge
+                allow_same_segment_merge=self.allow_same_segment_merge,
             )
         return new_roots, new_l2_ids, fake_edge_rows + new_entries
 
@@ -751,18 +751,11 @@ def _apply(
         ):
             raise PreconditionError("Supervoxels must belong to the same object.")
 
-        with TimeIt("subgraph", self.cg.graph_id, operation_id):
-            l2id_agglomeration_d, _ = self.cg.get_l2_agglomerations(
-                self.cg.get_parents(
-                    self.removed_edges.ravel(), time_stamp=self.parent_ts
-                ),
-            )
         with TimeIt("remove_edges", self.cg.graph_id, operation_id):
             return edits.remove_edges(
                 self.cg,
                 operation_id=operation_id,
                 atomic_edges=self.removed_edges,
-                l2id_agglomeration_d=l2id_agglomeration_d,
                 time_stamp=timestamp,
                 parent_ts=self.parent_ts,
             )
@@ -929,7 +922,6 @@ def _apply(
                 self.cg,
                 operation_id=operation_id,
                 atomic_edges=self.removed_edges,
-                l2id_agglomeration_d=l2id_agglomeration_d,
                 time_stamp=timestamp,
                 parent_ts=self.parent_ts,
             )

pychunkedgraph/repair/edits.py

@@ -7,6 +7,13 @@
 from pychunkedgraph.graph.operation import GraphEditOperation
 
 
+def _get_previous_log_ts(cg, operation):
+    log, previous_ts = cg.client.read_log_entry(operation - 1)
+    if log:
+        return previous_ts
+    return _get_previous_log_ts(cg, operation-1)
+
+
 def repair_operation(
     cg: ChunkedGraph,
     operation_id: int,
@@ -20,8 +27,8 @@ def repair_operation(
     _, current_ts = cg.client.read_log_entry(operation_id)
     parent_ts = current_ts - timedelta(milliseconds=10)
     if operation_id > 1 and use_preceding_edit_ts:
-        _, previous_ts = cg.client.read_log_entry(operation_id - 1)
-        parent_ts = previous_ts + timedelta(milliseconds=200)
+        previous_ts = _get_previous_log_ts(cg, operation_id)
+        parent_ts = previous_ts + timedelta(milliseconds=100)
 
     result = operation.execute(
         operation_id=operation_id,