Explicit handling of empty masks in label images

If there is an empty intermediate label it's unclear what the correct behaviour should be, so let the user choose between an exception and empty mask

src/omero_metadata/rois.py

@@ -33,7 +33,8 @@ def __init__(self, msg='Invalid labels found'):
 
 
 def mask_from_binary_image(
-        binim, rgba=None, z=None, c=None, t=None, text=None):
+        binim, rgba=None, z=None, c=None, t=None, text=None,
+        raise_on_no_mask=True):
     """
     Create a mask shape from a binary image (background=0)
     :param numpy.array binim: Binary 2D array, must contain values [0, 1] only
@@ -42,23 +43,31 @@ def mask_from_binary_image(
     :param c: Optional C-index for the mask
     :param t: Optional T-index for the mask
     :param text: Optional text for the mask
+    :param raise_on_no_mask: If True (default) throw an exception if no mask
+           found, otherwise return an empty Mask
     :return: An OMERO mask
     :raises NoMaskFound: If no labels were found
     :raises InvalidBinaryImage: If the maximum labels is greater than 1
     """
     # Find bounding box to minimise size of mask
     xmask = binim.sum(0).nonzero()[0]
     ymask = binim.sum(1).nonzero()[0]
-    if not any(xmask) and not any(ymask):
-        raise NoMaskFound()
-
-    x0 = min(xmask)
-    w = max(xmask) - x0 + 1
-    y0 = min(ymask)
-    h = max(ymask) - y0 + 1
-    submask = binim[y0:(y0 + h), x0:(x0 + w)]
-    if not np.array_equal(np.unique(submask), [0, 1]):
-        raise InvalidBinaryImage()
+    if any(xmask) and any(ymask):
+        x0 = min(xmask)
+        w = max(xmask) - x0 + 1
+        y0 = min(ymask)
+        h = max(ymask) - y0 + 1
+        submask = binim[y0:(y0 + h), x0:(x0 + w)]
+        if not np.array_equal(np.unique(submask), [0, 1]):
+            raise InvalidBinaryImage()
+    else:
+        if raise_on_no_mask:
+            raise NoMaskFound()
+        x0 = 0
+        w = 0
+        y0 = 0
+        h = 0
+        submask = []
 
     mask = MaskI()
     # BUG in older versions of Numpy:
@@ -87,7 +96,8 @@ def mask_from_binary_image(
 
 
 def masks_from_label_image(
-        labelim, rgba=None, z=None, c=None, t=None, text=None):
+        labelim, rgba=None, z=None, c=None, t=None, text=None,
+        raise_on_no_mask=True):
     """
     Create mask shapes from a label image (background=0)
     :param numpy.array labelim: 2D label array
@@ -96,13 +106,13 @@ def masks_from_label_image(
     :param c: Optional C-index for the mask
     :param t: Optional T-index for the mask
     :param text: Optional text for the mask
+    :param raise_on_no_mask: If True (default) throw an exception if no mask
+           found, otherwise return an empty Mask
     :return: A list of OMERO masks in label order ([] if no labels found)
     """
     masks = []
     for i in xrange(1, labelim.max() + 1):
-        try:
-            mask = mask_from_binary_image(labelim == i, rgba, z, c, t, text)
-            masks.append(mask)
-        except NoMaskFound:
-            pass
+        mask = mask_from_binary_image(labelim == i, rgba, z, c, t, text,
+                                      raise_on_no_mask)
+        masks.append(mask)
     return masks

test/unit/test_masks.py

@@ -14,6 +14,7 @@
 from omero_metadata import (
     mask_from_binary_image,
     masks_from_label_image,
+    NoMaskFound,
 )
 
 
@@ -96,3 +97,39 @@ def test_masks_from_label_image(self, label_image, args):
                 assert unwrap(mask.getTheC()) is None
                 assert unwrap(mask.getTheT()) is None
                 assert unwrap(mask.getTextValue()) is None
+
+    @pytest.mark.parametrize('args', [
+        {},
+        {'rgba': (255, 128, 64, 128), 'z': 1, 'c': 2, 't': 3, 'text': 'test'}
+    ])
+    @pytest.mark.parametrize('raise_on_no_mask', [
+        True,
+        False,
+    ])
+    def test_empty_mask_from_binary_image(self, args, raise_on_no_mask):
+        empty_binary_image = np.array([[0]])
+        if raise_on_no_mask:
+            with pytest.raises(NoMaskFound):
+                mask = mask_from_binary_image(
+                    empty_binary_image, raise_on_no_mask=raise_on_no_mask,
+                    **args)
+        else:
+            mask = mask_from_binary_image(
+                empty_binary_image, raise_on_no_mask=raise_on_no_mask,
+                **args)
+            assert unwrap(mask.getWidth()) == 0
+            assert unwrap(mask.getHeight()) == 0
+            assert unwrap(mask.getX()) == 0
+            assert unwrap(mask.getY()) == 0
+            assert np.array_equal(mask.getBytes(), [])
+
+            if args:
+                assert unwrap(mask.getTheZ()) == 1
+                assert unwrap(mask.getTheC()) == 2
+                assert unwrap(mask.getTheT()) == 3
+                assert unwrap(mask.getTextValue()) == 'test'
+            else:
+                assert unwrap(mask.getTheZ()) is None
+                assert unwrap(mask.getTheC()) is None
+                assert unwrap(mask.getTheT()) is None
+                assert unwrap(mask.getTextValue()) is None