Add emtpy mask handling within threshold.otsu

plantcv/plantcv/threshold/threshold_methods.py

@@ -170,6 +170,12 @@ def otsu(gray_img, object_type="light"):
 
     params.device += 1
 
+    # If the grayscale image is all zeros, return copy of input image.
+    if np.count_nonzero(gray_img) == 0:
+        bin_img = np.copy(gray_img)
+        _debug(visual=bin_img, filename=os.path.join(params.debug_outdir, f"{params.device}_otsu_empty.png"))
+        return bin_img
+
     # Threshold the image
     bin_img = _call_threshold(gray_img, 0, threshold_method, "_otsu_threshold_")
 

tests/plantcv/threshold/test_threshold_methods.py

@@ -255,3 +255,10 @@ def test_dual_channels_bad_channel():
     pts = [(0, 0), (255, 255)]
     with pytest.raises(RuntimeError):
         _ = dual_channels(img, x_channel='wrong_ch', y_channel='index', points=pts, above=True)
+
+def test_otsu_empty_mask():
+    """Test for PlantCV."""
+    mask = np.zeros((100, 100))
+    fmask = otsu(mask)
+    assert np.sum(fmask) == 0
+