Fix circle-shapes area in measure_obs: use pi*r**2, not shapely Point.area (=0)

Circles are stored as `Point` geometries with a `radius` column, for which
shapely `.area` is 0 — so `measure_obs` wrote area=0 and equivalent_diameter=0
for every circle (surfaced on the real Visium spots dataset, all circles).
Compute their area as `pi * r**2`; equivalent diameter then equals the true
diameter `2*r`. Polygons/multipolygons still use the geometric area. Adds a
regression test on `blobs_circles`.

Author: timtreis

src/spatialdata_plot/pl/utils.py

@@ -4527,12 +4527,15 @@ def _compute_element_measurements(sdata: SpatialData, element_name: str) -> pd.D
     model = get_model(element)
     if model is ShapesModel:
         centroids = element.geometry.centroid
+        # Circles are stored as ``Point`` geometries with a ``radius`` column, for which
+        # shapely ``.area`` is 0; their area is ``pi * r**2``. Polygons/multipolygons use
+        # the true geometric area.
+        if "radius" in element.columns:
+            area = np.pi * np.asarray(element["radius"], dtype=float) ** 2
+        else:
+            area = element.geometry.area.to_numpy()
         return pd.DataFrame(
-            {
-                "x": centroids.x.to_numpy(),
-                "y": centroids.y.to_numpy(),
-                "area": element.geometry.area.to_numpy(),
-            },
+            {"x": centroids.x.to_numpy(), "y": centroids.y.to_numpy(), "area": area},
             index=element.index,
         )
     if model is Labels2DModel:

tests/pl/test_utils.py

@@ -554,6 +554,18 @@ def test_writes_for_shapes(self, sdata_blobs: SpatialData) -> None:
             rtol=1e-9,
         )
 
+    def test_circles_area_is_pi_r_squared(self, sdata_blobs: SpatialData) -> None:
+        # Circles are stored as Point geometries (radius column); shapely .area is 0 for them,
+        # so area must be pi * r**2 and equivalent diameter must equal the true diameter 2*r.
+        _add_shapes_table(sdata_blobs, "blobs_circles", name="circles_table")
+        measure_obs(sdata_blobs, "blobs_circles", table_name="circles_table")
+        table = sdata_blobs["circles_table"]
+        gdf = sdata_blobs["blobs_circles"]
+        order = table.obs["instance_id"].to_numpy()
+        r = gdf["radius"].to_numpy()[[list(gdf.index).index(i) for i in order]]
+        np.testing.assert_allclose(table.obs["area"].to_numpy(), np.pi * r**2, rtol=1e-9)
+        np.testing.assert_allclose(table.obs["equivalent_diameter"].to_numpy(), 2.0 * r, rtol=1e-9)
+
     def test_inplace_false_leaves_original_untouched(self, sdata_blobs: SpatialData) -> None:
         out = measure_obs(sdata_blobs, "blobs_labels", inplace=False)
         assert isinstance(out, SpatialData)