Skip to content

289 circular graph error #159

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
AnniekStok wants to merge 3 commits into
base: main
Choose a base branch
from
Open

289 circular graph error #159

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
53c8a55
check for duplicate nodes when creating candidate graph from seg
AnniekStok Feb 9, 2026
9178572
add test for checking for duplicate nodes when creating candgraph fro…
AnniekStok Feb 9, 2026
fe1533e
move test for duplicates indies nodes_from_segmentation, raise ValueE…
AnniekStok Feb 11, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions src/funtracks/candidate_graph/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,8 @@ def nodes_from_segmentation(
attrs[NodeAttr.SEG_ID.value] = regionprop.label
centroid = regionprop.centroid # [z,] y, x
attrs[NodeAttr.POS.value] = centroid
if node_id in cand_graph.nodes:
raise ValueError("Duplicate values found among nodes")
cand_graph.add_node(node_id, **attrs)
nodes_in_frame.append(node_id)
if nodes_in_frame:
Expand Down
9 changes: 9 additions & 0 deletions tests/candidate_graph/test_compute_graph.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,15 @@ def test_graph_from_segmentation_3d(segmentation_3d, graph_3d):
assert pytest.approx(cand_graph.edges[edge], abs=0.01) == graph_3d.edges[edge]


def test_graph_from_segmentation_with_duplicate_nodes(segmentation_2d):
segmentation_2d[1][20:25, 20:25] = 1 # add a duplicate label to another time point
with pytest.raises(ValueError, match="Duplicate values found among nodes"):
compute_graph_from_seg(
segmentation=segmentation_2d,
max_edge_distance=100,
)


def test_graph_from_points_list():
points_list = np.array(
[
Expand Down