Merge pull request #6 from seung-lab/wms_2d_ops

feat: 2D operations for multilabel dilate and erode + fix

automated_test.py

@@ -77,7 +77,7 @@ def test_spherical_close():
 	assert res[5,5,5] == True
 
 
-def test_multilabel_dilate():
+def test_multilabel_dilate_3d():
 	labels = np.zeros((3,3,3), dtype=bool)
 
 	out = fastmorph.dilate(labels)
@@ -116,8 +116,46 @@ def test_multilabel_dilate():
 	ans[1:,:,:] = 2
 	assert np.all(ans == out)
 
+def test_multilabel_dilate_2d():
+	labels = np.zeros((3,3), dtype=bool)
 
-def test_multilabel_erode():
+	out = fastmorph.dilate(labels)
+	assert not np.any(out)
+
+	labels[1,1] = True
+
+	out = fastmorph.dilate(labels)
+	assert np.all(out)
+
+	labels = np.zeros((3,3), dtype=bool)
+	labels[0,0] = True
+	out = fastmorph.dilate(labels)
+
+	ans = np.zeros((3,3), dtype=bool)
+	ans[:2,:2] = True
+
+	assert np.all(out == ans)
+
+	labels = np.zeros((3,3), dtype=int)
+	labels[0,1] = 1
+	labels[2,1] = 2
+
+	out = fastmorph.dilate(labels)
+	ans = np.ones((3,3), dtype=int)
+	ans[2,:] = 2
+	assert np.all(ans == out)
+
+	labels = np.zeros((3,3), dtype=int, order="F")
+	labels[0,1] = 1
+	labels[1,1] = 2
+	labels[2,1] = 2
+
+	out = fastmorph.dilate(labels)
+	ans = np.ones((3,3), dtype=int, order="F")
+	ans[1:,:] = 2
+	assert np.all(ans == out)
+
+def test_multilabel_erode_3d():
 	labels = np.ones((3,3,3), dtype=bool)
 	out = fastmorph.erode(labels)
 	assert np.sum(out) == 1 and out[1,1,1] == True
@@ -147,11 +185,54 @@ def test_multilabel_erode():
 	out = fastmorph.erode(labels)
 	assert np.sum(out) == 27
 
+def test_multilabel_erode_2d():
+	labels = np.ones((3,3), dtype=bool)
+	out = fastmorph.erode(labels)
+	assert np.sum(out) == 1 and out[1,1] == True
+
+	out = fastmorph.erode(out)
+	assert not np.any(out)
+
+	out = fastmorph.erode(out)
+	assert not np.any(out)
+
+	labels = np.ones((3,3), dtype=int, order="F")
+	labels[0,:] = 1
+	labels[1,:] = 2
+	labels[2,:] = 3
+
+	out = fastmorph.erode(labels)
+	ans = np.zeros((3,3), dtype=int, order="F")
+
+	assert np.all(ans == out)
+
+	labels = np.zeros((5,5), dtype=bool)
+	labels[1:4,1:4] = True
+	out = fastmorph.erode(labels)
+	assert np.sum(out) == 1 and out[2,2] == True
+
+	labels = np.ones((5,5), dtype=bool)
+	out = fastmorph.erode(labels)
+	assert np.sum(out) == 9
+
 @pytest.mark.parametrize('dtype', [
 	np.uint8,np.uint16,np.uint32,np.uint64,
 	np.int8,np.int16,np.int32,np.int64,
 ])
 def test_grey_erode(dtype):
+	labels = np.arange(9, dtype=dtype).reshape((3,3), order="F")
+	out = fastmorph.erode(labels, mode=fastmorph.Mode.grey)
+
+	ans = np.array([
+		[0, 0, 1],
+		[0, 0, 1],
+		[3, 3, 4],
+	], dtype=dtype).T
+	assert np.all(out == ans)
+
+	out = fastmorph.erode(out, mode=fastmorph.Mode.grey)
+	assert np.all(out == 0)
+
 	labels = np.arange(27, dtype=dtype).reshape((3,3,3), order="F")
 	out = fastmorph.erode(labels, mode=fastmorph.Mode.grey)
 
@@ -186,6 +267,20 @@ def test_grey_dilate(dtype):
 	L = 5
 	H = 10
 
+	labels = np.zeros((3,3), dtype=dtype)
+	labels[0,0] = L
+	labels[2,2] = H
+
+	out = fastmorph.dilate(labels, mode=fastmorph.Mode.grey)
+
+	ans = np.array([
+		[L, L, 0],
+		[L, H, H],
+		[0, H, H],
+	], dtype=dtype).T
+
+	assert np.all(out == ans)
+
 	labels = np.zeros((3,3,3), dtype=dtype)
 	labels[0,0,0] = L
 	labels[2,2,2] = H
@@ -222,4 +317,10 @@ def test_grey_dilate_bool():
 	out = fastmorph.dilate(labels, mode=fastmorph.Mode.grey)
 	assert np.all(out == True)
 
+	labels = np.zeros((3,3), dtype=bool)
+	labels[1,1] = True
+
+	out = fastmorph.dilate(labels, mode=fastmorph.Mode.grey)
+	assert np.all(out == True)
+
 

fastmorph/__init__.py

@@ -41,8 +41,9 @@ def dilate(
   parallel = min(parallel, mp.cpu_count())
 
   labels = np.asfortranarray(labels)
-  while labels.ndim < 3:
+  while labels.ndim < 2:
     labels = labels[..., np.newaxis]
+
   if mode == Mode.multilabel:
     output = fastmorphops.multilabel_dilate(labels, background_only, parallel)
   else:
@@ -66,7 +67,7 @@ def erode(
   parallel = min(parallel, mp.cpu_count())
 
   labels = np.asfortranarray(labels)
-  while labels.ndim < 3:
+  while labels.ndim < 2:
     labels = labels[..., np.newaxis]
 
   if mode == Mode.multilabel:
@@ -264,7 +265,7 @@ def fill_holes(
 
   if return_fill_count:
     for label in removed_set:
-      del fill_counts[label]
+      fill_counts.pop(label, None)
     ret.append(fill_counts)
 
   if return_removed: