Add a warning for undersized objects in Texture

src/zedprofiler/featurization/texture.py

@@ -7,7 +7,7 @@
 We want this module to be python api callable and scalable.
 """
 
-import contextlib
+import warnings
 
 import mahotas
 import numpy
@@ -112,7 +112,7 @@ def resample_to_isotropic(
     )
 
 
-def compute_texture(  # noqa: C901
+def compute_texture(  # noqa: C901, PLR0915
     object_loader: ObjectLoader,
     distance: int = 1,
     grayscale: int = 256,
@@ -261,7 +261,7 @@ def compute_texture(  # noqa: C901
         image_object[~resampled_mask.astype(bool)] = 0
 
         image_object = scale_image(image_object, num_gray_levels=grayscale)
-        with contextlib.suppress(ValueError):
+        try:
             # calculates 13 Haralick features for each direction (13)
             #  and each object, and stores them in a 3D array
             features[:, :, idx] = mahotas.features.haralick(
@@ -270,6 +270,15 @@ def compute_texture(  # noqa: C901
                 distance=distance,
                 compute_14th_feature=False,
             )
+        except ValueError:
+            # mahotas cannot compute GLCM features when an object's extent
+            # is smaller than the distance parameter; the object's texture
+            # values remain NaN in this case.
+            warnings.warn(
+                f"Object {label} is smaller than distance={distance}; "
+                "Texture features are undefined (NaN) for this object.",
+                stacklevel=2,
+            )
     # iterate through the direction, feature, and object dimensions
     # of the features array to populate the output dictionary
     for direction, direction_features in enumerate(features):

tests/featurization/test_texture.py

@@ -159,6 +159,38 @@ def test_value_error_in_one_object_does_not_corrupt_others() -> None:
     assert np.isnan(obj2_asm), "Object 2 (single pixel) should have NaN texture values"
 
 
+def test_undersized_object_warns() -> None:
+    """An object smaller than the distance parameter must trigger a warning.
+
+    mahotas cannot compute GLCM features for an object below a minimum pixel
+    extent for the given distance; this is expected, but it must not happen
+    silently. Regression test for compute_texture previously swallowing the
+    resulting ValueError via contextlib.suppress with no warning at all.
+    """
+    shape = (20, 20, 20)
+    image = np.zeros(shape, dtype=np.uint8)
+    label = np.zeros(shape, dtype=np.int32)
+
+    # single pixel — no neighbour pairs → ValueError from mahotas
+    image[15, 15, 15] = 100
+    label[15, 15, 15] = LABEL_OBJ_2
+
+    imgset = ImageSetLoaderModel()
+    loader = ObjectLoaderModel(
+        image=image,
+        label_image=label,
+        object_ids=[LABEL_OBJ_2],
+        image_set_loader=imgset,
+    )
+
+    with pytest.warns(UserWarning, match=r"Object 2 is smaller than distance=1"):
+        df = compute_texture(loader, distance=1, grayscale=256)
+
+    asm_cols = [c for c in df.columns if "AngularSecondMoment" in c and "-00-" in c]
+    assert asm_cols
+    assert np.isnan(df[asm_cols[0]].iloc[0])
+
+
 def test_texture_values_correct_per_object() -> None:
     """Each object must receive its own Haralick values, not another object's.