add tests

- also exclude solidity cause it also relies on convex_area

napari_skimage_regionprops/_regionprops.py

@@ -74,13 +74,13 @@ def standard_deviation_intensity(region, intensities):
             warnings.warn("Perimeter measurements are not supported in 3D")
 
     if shape:
-        properties = properties + ['solidity', 'extent', 'local_centroid']
+        properties = properties + ['extent', 'local_centroid']
         # Workaround to avoid existing scikit-image bug
         # See https://github.com/scikit-image/scikit-image/issues/6432
         if (len(labels.shape) == 3) and (_check_2D_labels_in_3D_images(labels)):
-            warnings.warn("2D labels are present in 3D label image, 'feret_diameter_max' not calculated")
+            warnings.warn("2D labels are present in 3D label image, 'feret_diameter_max' and 'solidity' not calculated")
         else:
-            properties = properties + ['feret_diameter_max']
+            properties = properties + ['solidity', 'feret_diameter_max']
         if len(labels.shape) == 2:
             properties = properties + ['major_axis_length', 'minor_axis_length', 'orientation', 'eccentricity']
             # we need these two to compute some shape descriptors
@@ -108,7 +108,7 @@ def standard_deviation_intensity(region, intensities):
     # weighted_moments_central
     # weighted_moments_hu
     # weighted_moments_normalized
-
+    print('PROPERTIES = ', properties)
     # quantitative analysis using scikit-image's regionprops
     from skimage.measure import regionprops_table as sk_regionprops_table
     table = sk_regionprops_table(np.asarray(labels).astype(int), intensity_image=np.asarray(image),

napari_skimage_regionprops/_tests/test_function.py

@@ -397,3 +397,21 @@ def test_measure_points():
     points = np.random.random((100, 2)) * 99
 
     nsr.measure_points(points, image)
+
+def test_2d_labels_in_3d_image():
+    import numpy as np
+    labels = np.zeros((6,6,6), dtype=np.uint8)
+    labels[1:4, 1:4, 1:4] = 1 # 3D label
+    labels[4, 1:4, 1:4] = 2 # 2D label
+
+    from napari_skimage_regionprops import regionprops_table
+    table = regionprops_table(labels, labels, size=True, intensity=True, perimeter=True, shape=True, position=True,
+                moments=True)
+
+    # check one measurement
+    assert np.array_equal(table['area'], [27, 9])
+
+    # check that measurements that depend on convex_area are absent in this case
+    assert "convex_area" not in table.keys()
+    assert "feret_max_diameter" not in table.keys()
+    assert "solidity" not in table.keys()