Fix mask isub + tracksdata update

pyproject.toml

@@ -38,7 +38,7 @@ dependencies =[
     "dask>=2025.5.0",
     "pandas>=2.3.3",
     "zarr>=2.18,<4",
-    "tracksdata[spatial]>=0.1.0rc6",
+    "tracksdata[spatial]>=0.1.0rc7",
     "tqdm>=4.66.1",
     # zarr 2.x's util.py imports cbuffer_sizes/cbuffer_metainfo from
     # numcodecs.blosc, which numcodecs >= 0.16 removed. Pin numcodecs per

src/funtracks/actions/update_segmentation.py

@@ -60,9 +60,15 @@ def _apply(self) -> None:
         mask_new = self.mask
 
         if value == 0:
-            # val=0 means deleting (part of) the mask
+            # val=0 means deleting (part of) the mask.
+            # Mask.__isub__ subtracts *in place* and returns the same object, which
+            # would mutate the mask still stored in the graph. Downstream consumers
+            # (e.g. GraphArrayView's cache invalidation) diff the graph's previous
+            # mask against the new one, so the previous mask must stay intact.
+            # Subtract on a fresh copy so the graph receives a distinct new object.
             mask_old = self.tracks.graph.nodes[self.node][self.mask_key]
-            mask_subtracted = mask_old.__isub__(mask_new)
+            mask_subtracted = Mask(mask_old.mask.copy(), bbox=mask_old.bbox.copy())
+            mask_subtracted -= mask_new
             self.tracks.update_mask(self.node, mask_subtracted, mask_key=self.mask_key)
 
         elif self.tracks.graph.has_node(value):

tests/actions/test_update_node_segs.py

@@ -50,3 +50,30 @@ def test_update_node_segs(get_tracks, ndim):
     assert tracks.graph.nodes[1]["area"] == original_area + 1
     assert not np.allclose(tracks.graph.nodes[1]["pos"], original_pos)
     assert_array_almost_equal(tracks.segmentation, new_seg)
+
+
+def test_update_node_segs_erase_interior_pixel(get_tracks):
+    """Erasing a pixel *interior* to a node must clear it in the segmentation view.
+
+    Node 1 is a disk centred at (50, 50); erasing its centre pixel does not shrink
+    the bbox, so it exercises exactly the bbox-unchanged path that regressed.
+    """
+    tracks = get_tracks(ndim=3, with_seg=True, is_solution=True)
+    node = 1
+    time = tracks.get_time(node)
+
+    original_bbox = np.asarray(tracks.graph.nodes[node]["bbox"]).copy()
+    original_area = tracks.graph.nodes[node]["area"]
+    # Precondition: the interior pixel currently belongs to the node.
+    assert int(np.asarray(tracks.segmentation[time, 50, 50])) == node
+
+    # Erase the single interior pixel (50, 50).
+    erase_mask = Mask(np.ones((1, 1), dtype=bool), np.array([50, 50, 51, 51]))
+    UpdateNodeSeg(tracks, node, mask=erase_mask, added=False)
+
+    # The bbox must be unchanged (the erased pixel was interior), which is the
+    # condition under which the stale-readback bug manifested.
+    assert np.array_equal(np.asarray(tracks.graph.nodes[node]["bbox"]), original_bbox)
+    assert tracks.graph.nodes[node]["area"] == original_area - 1
+    # The segmentation view must reflect the erase.
+    assert int(np.asarray(tracks.segmentation[time, 50, 50])) == 0

tests/data_model/test_solution_tracks.py

@@ -44,7 +44,10 @@ def test_from_tracks_cls(graph_2d_with_segmentation):
     )
     solution_tracks = SolutionTracks.from_tracks(tracks)
     assert solution_tracks.graph == tracks.graph
-    assert solution_tracks.segmentation == tracks.segmentation
+    # from_tracks reuses the same segmentation instance. Assert identity rather
+    # than `==`: on newer tracksdata GraphArrayView.__eq__ is element-wise and
+    # returns an array, which makes a truthiness assert ambiguous.
+    assert solution_tracks.segmentation is tracks.segmentation
     assert solution_tracks.features.time_key == tracks.features.time_key
     assert solution_tracks.features.position_key == tracks.features.position_key
     assert solution_tracks.scale == tracks.scale