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fix: clear error when aggregating by labels without instances #1264

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fix: clear error when aggregating by labels without instances #1264

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4 changes: 4 additions & 0 deletions src/spatialdata/_core/operations/aggregate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -317,6 +317,10 @@ def _aggregate_image_by_labels(
zones: ArrayLike = out["zone"].to_numpy()
outs.append(out.drop(columns=["zone"])) # remove the 0 (background)
df = pd.concat(outs, axis=1)
if len(df) == 0:
raise ValueError(
"No labelled instances (non-zero label ids) found in `by`, so there is nothing to aggregate by."
)

X = sparse.csr_matrix(df.values)

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7 changes: 7 additions & 0 deletions tests/core/operations/test_aggregations.py
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Expand Up @@ -359,6 +359,13 @@ def test_aggregate_image_by_labels(labels_blobs, image_schema, labels_schema) ->
assert len(out) == 3


def test_aggregate_image_by_background_only_labels() -> None:
image = Image2DModel.parse(RNG.normal(size=(2, 16, 16)))
labels = Labels2DModel.parse(np.zeros((16, 16), dtype=np.int32))
with pytest.raises(ValueError, match="No labelled instances"):
aggregate(values=image, by=labels, agg_func="mean")


@pytest.mark.parametrize("values", ["blobs_image", "blobs_points", "blobs_circles", "blobs_polygons"])
@pytest.mark.parametrize("by", ["blobs_labels", "blobs_circles", "blobs_polygons"])
def test_aggregate_requiring_alignment(sdata_blobs: SpatialData, values, by) -> None:
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