Refactor HoVerNet post-processing

docs/source/apps.rst

@@ -155,6 +155,8 @@ Applications
     :members:
 .. autoclass:: HoVerNetNuclearTypePostProcessing
     :members:
+.. autoclass:: HoVerNetInstanceMapPostProcessing
+    :members:
 
 .. automodule:: monai.apps.pathology.transforms.post.dictionary
 .. autoclass:: GenerateSuccinctContourd
@@ -175,6 +177,8 @@ Applications
     :members:
 .. autoclass:: GenerateWatershedMarkersd
     :members:
+.. autoclass:: HoVerNetInstanceMapPostProcessingd
+    :members:
 .. autoclass:: HoVerNetNuclearTypePostProcessingd
     :members:
 

monai/apps/pathology/transforms/__init__.py

@@ -18,6 +18,7 @@
     GenerateSuccinctContour,
     GenerateWatershedMarkers,
     GenerateWatershedMask,
+    HoVerNetInstanceMapPostProcessing,
     HoVerNetNuclearTypePostProcessing,
     Watershed,
 )
@@ -46,6 +47,9 @@
     GenerateWatershedMaskD,
     GenerateWatershedMaskd,
     GenerateWatershedMaskDict,
+    HoVerNetInstanceMapPostProcessingD,
+    HoVerNetInstanceMapPostProcessingd,
+    HoVerNetInstanceMapPostProcessingDict,
     HoVerNetNuclearTypePostProcessingD,
     HoVerNetNuclearTypePostProcessingd,
     HoVerNetNuclearTypePostProcessingDict,

monai/apps/pathology/transforms/post/__init__.py

@@ -18,6 +18,7 @@
     GenerateSuccinctContour,
     GenerateWatershedMarkers,
     GenerateWatershedMask,
+    HoVerNetInstanceMapPostProcessing,
     HoVerNetNuclearTypePostProcessing,
     Watershed,
 )
@@ -46,6 +47,9 @@
     GenerateWatershedMaskD,
     GenerateWatershedMaskd,
     GenerateWatershedMaskDict,
+    HoVerNetInstanceMapPostProcessingD,
+    HoVerNetInstanceMapPostProcessingd,
+    HoVerNetInstanceMapPostProcessingDict,
     HoVerNetNuclearTypePostProcessingD,
     HoVerNetNuclearTypePostProcessingd,
     HoVerNetNuclearTypePostProcessingDict,

monai/transforms/post/array.py

@@ -360,7 +360,7 @@ class RemoveSmallObjects(Transform):
     Data should be one-hotted.
 
     Args:
-        min_size: objects smaller than this size are removed.
+        min_size: objects smaller than this size (in pixel) are removed.
         connectivity: Maximum number of orthogonal hops to consider a pixel/voxel as a neighbor.
             Accepted values are ranging from  1 to input.ndim. If ``None``, a full
             connectivity of ``input.ndim`` is used. For more details refer to linked scikit-image

tests/test_generate_distance_map.py

@@ -25,10 +25,8 @@
 
 for p in TEST_NDARRAYS:
     EXCEPTION_TESTS.append([{}, p(np.random.rand(2, 5, 5)), p(np.random.rand(1, 5, 5)), ValueError])
-
     EXCEPTION_TESTS.append([{}, p(np.random.rand(1, 5, 5)), p(np.random.rand(2, 5, 5)), ValueError])
 
-for p in TEST_NDARRAYS:
     TESTS.append([{}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), (1, 5, 5)])
     TESTS.append(
         [{"smooth_fn": GaussianSmooth(sigma=0.4)}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), (1, 5, 5)]

tests/test_generate_distance_mapd.py

@@ -25,20 +25,26 @@
 
 for p in TEST_NDARRAYS:
     EXCEPTION_TESTS.append(
-        [{"keys": "mask", "border_key": "border"}, p(np.random.rand(2, 5, 5)), p(np.random.rand(1, 5, 5)), ValueError]
+        [
+            {"mask_key": "mask", "border_key": "border"},
+            p(np.random.rand(2, 5, 5)),
+            p(np.random.rand(1, 5, 5)),
+            ValueError,
+        ]
     )
-
     EXCEPTION_TESTS.append(
-        [{"keys": "mask", "border_key": "border"}, p(np.random.rand(1, 5, 5)), p(np.random.rand(2, 5, 5)), ValueError]
+        [
+            {"mask_key": "mask", "border_key": "border"},
+            p(np.random.rand(1, 5, 5)),
+            p(np.random.rand(2, 5, 5)),
+            ValueError,
+        ]
     )
 
-for p in TEST_NDARRAYS:
-    TESTS.append(
-        [{"keys": "mask", "border_key": "border"}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), (1, 5, 5)]
-    )
+    TESTS.append([{}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), (1, 5, 5)])
     TESTS.append(
         [
-            {"keys": "mask", "border_key": "border", "smooth_fn": GaussianSmooth(sigma=0.4)},
+            {"mask_key": "mask", "border_key": "border", "smooth_fn": GaussianSmooth(sigma=0.4)},
             p(np.random.rand(1, 5, 5)),
             p(np.random.rand(1, 5, 5)),
             (1, 5, 5),
@@ -55,7 +61,7 @@ def test_value(self, argments, mask, border_map, exception_type):
     @parameterized.expand(TESTS)
     def test_value2(self, argments, mask, border_map, expected_shape):
         result = GenerateDistanceMapd(**argments)({"mask": mask, "border": border_map})
-        self.assertEqual(result["dist"].shape, expected_shape)
+        self.assertEqual(result["dist_map"].shape, expected_shape)
 
 
 if __name__ == "__main__":

tests/test_generate_instance_border.py

@@ -23,61 +23,23 @@
 np.random.RandomState(123)
 
 for p in TEST_NDARRAYS:
-    EXCEPTION_TESTS.append(
-        [
-            {"kernel_size": 3, "remove_small_objects": False},
-            p(np.random.rand(1, 5, 5, 5)),
-            p(np.random.rand(2, 5, 5)),
-            ValueError,
-        ]
-    )
+    EXCEPTION_TESTS.append([{"kernel_size": 3}, p(np.random.rand(1, 5, 5, 5)), p(np.random.rand(2, 5, 5)), ValueError])
+    EXCEPTION_TESTS.append([{"kernel_size": 3}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), ValueError])
+    EXCEPTION_TESTS.append([{"kernel_size": 3}, p(np.random.rand(2, 5, 5)), p(np.random.rand(2, 5, 5)), ValueError])
 
-    EXCEPTION_TESTS.append(
-        [
-            {"kernel_size": 3, "remove_small_objects": False},
-            p(np.random.rand(1, 5, 5)),
-            p(np.random.rand(1, 5, 5)),
-            ValueError,
-        ]
-    )
-
-    EXCEPTION_TESTS.append(
-        [
-            {"kernel_size": 3, "remove_small_objects": False},
-            p(np.random.rand(2, 5, 5)),
-            p(np.random.rand(2, 5, 5)),
-            ValueError,
-        ]
-    )
-
-for p in TEST_NDARRAYS:
-    TESTS.append(
-        [
-            {"kernel_size": 3, "remove_small_objects": False},
-            p(np.random.rand(1, 5, 5)),
-            p(np.random.rand(2, 5, 5)),
-            (1, 5, 5),
-        ]
-    )
-    TESTS.append(
-        [
-            {"kernel_size": 3, "remove_small_objects": False},
-            p(np.random.rand(1, 5, 5)),
-            p(np.random.rand(2, 5, 5)),
-            (1, 5, 5),
-        ]
-    )
+    TESTS.append([{"kernel_size": 3}, p(np.random.rand(1, 5, 5)), p(np.random.rand(2, 5, 5)), (1, 5, 5)])
+    TESTS.append([{"kernel_size": 3}, p(np.random.rand(1, 5, 5)), p(np.random.rand(2, 5, 5)), (1, 5, 5)])
 
 
 class TestGenerateInstanceBorder(unittest.TestCase):
     @parameterized.expand(EXCEPTION_TESTS)
-    def test_value(self, argments, mask, hover_map, exception_type):
+    def test_value(self, arguments, mask, hover_map, exception_type):
         with self.assertRaises(exception_type):
-            GenerateInstanceBorder(**argments)(mask, hover_map)
+            GenerateInstanceBorder(**arguments)(mask, hover_map)
 
     @parameterized.expand(TESTS)
-    def test_value2(self, argments, mask, hover_map, expected_shape):
-        result = GenerateInstanceBorder(**argments)(mask, hover_map)
+    def test_value2(self, arguments, mask, hover_map, expected_shape):
+        result = GenerateInstanceBorder(**arguments)(mask, hover_map)
         self.assertEqual(result.shape, expected_shape)
 
 

tests/test_generate_instance_borderd.py

@@ -24,48 +24,20 @@
 
 for p in TEST_NDARRAYS:
     EXCEPTION_TESTS.append(
-        [
-            {"keys": "mask", "kernel_size": 3, "remove_small_objects": True, "min_size": 10},
-            p(np.random.rand(1, 5, 5, 5)),
-            p(np.random.rand(2, 5, 5)),
-            ValueError,
-        ]
+        [{"mask_key": "mask", "kernel_size": 3}, p(np.random.rand(1, 5, 5, 5)), p(np.random.rand(2, 5, 5)), ValueError]
     )
-
     EXCEPTION_TESTS.append(
-        [
-            {"keys": "mask", "kernel_size": 3, "remove_small_objects": True, "min_size": 10},
-            p(np.random.rand(1, 5, 5)),
-            p(np.random.rand(1, 5, 5)),
-            ValueError,
-        ]
+        [{"mask_key": "mask", "kernel_size": 3}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), ValueError]
     )
-
     EXCEPTION_TESTS.append(
-        [
-            {"keys": "mask", "kernel_size": 3, "remove_small_objects": True, "min_size": 10},
-            p(np.random.rand(2, 5, 5)),
-            p(np.random.rand(2, 5, 5)),
-            ValueError,
-        ]
+        [{"mask_key": "mask", "kernel_size": 3}, p(np.random.rand(2, 5, 5)), p(np.random.rand(2, 5, 5)), ValueError]
     )
 
-for p in TEST_NDARRAYS:
     TESTS.append(
-        [
-            {"keys": "mask", "kernel_size": 3, "remove_small_objects": False, "min_size": 10},
-            p(np.random.rand(1, 5, 5)),
-            p(np.random.rand(2, 5, 5)),
-            (1, 5, 5),
-        ]
+        [{"mask_key": "mask", "kernel_size": 3}, p(np.random.rand(1, 5, 5)), p(np.random.rand(2, 5, 5)), (1, 5, 5)]
     )
     TESTS.append(
-        [
-            {"keys": "mask", "kernel_size": 3, "remove_small_objects": True, "min_size": 10},
-            p(np.random.rand(1, 5, 5)),
-            p(np.random.rand(2, 5, 5)),
-            (1, 5, 5),
-        ]
+        [{"mask_key": "mask", "kernel_size": 3}, p(np.random.rand(1, 5, 5)), p(np.random.rand(2, 5, 5)), (1, 5, 5)]
     )
 
 

tests/test_generate_watershed_markers.py

@@ -28,24 +28,22 @@
 
 for p in TEST_NDARRAYS:
     EXCEPTION_TESTS.append([{}, p(np.random.rand(2, 5, 5)), p(np.random.rand(1, 5, 5)), ValueError])
-
     EXCEPTION_TESTS.append([{}, p(np.random.rand(1, 5, 5)), p(np.random.rand(2, 5, 5)), ValueError])
 
-for p in TEST_NDARRAYS:
     TESTS.append([{}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), (1, 5, 5)])
 
 
 @unittest.skipUnless(has_skimage, "Requires scikit-image library.")
 @unittest.skipUnless(has_scipy, "Requires scipy library.")
 class TestGenerateWatershedMarkers(unittest.TestCase):
     @parameterized.expand(EXCEPTION_TESTS)
-    def test_value(self, argments, mask, probmap, exception_type):
+    def test_value(self, arguments, mask, probmap, exception_type):
         with self.assertRaises(exception_type):
-            GenerateWatershedMarkers(**argments)(mask, probmap)
+            GenerateWatershedMarkers(**arguments)(mask, probmap)
 
     @parameterized.expand(TESTS)
-    def test_value2(self, argments, mask, probmap, expected_shape):
-        result = GenerateWatershedMarkers(**argments)(mask, probmap)
+    def test_value2(self, arguments, mask, probmap, expected_shape):
+        result = GenerateWatershedMarkers(**arguments)(mask, probmap)
         self.assertEqual(result.shape, expected_shape)
 
 

tests/test_generate_watershed_markersd.py

@@ -28,39 +28,52 @@
 
 for p in TEST_NDARRAYS:
     EXCEPTION_TESTS.append(
-        [{"keys": "mask", "border_key": "border"}, p(np.random.rand(2, 5, 5)), p(np.random.rand(1, 5, 5)), ValueError]
+        [
+            {"mask_key": "mask", "border_key": "border"},
+            p(np.random.rand(2, 5, 5)),
+            p(np.random.rand(1, 5, 5)),
+            ValueError,
+        ]
     )
-
     EXCEPTION_TESTS.append(
-        [{"keys": "mask", "border_key": "border"}, p(np.random.rand(1, 5, 5)), p(np.random.rand(2, 5, 5)), ValueError]
+        [
+            {"mask_key": "mask", "border_key": "border"},
+            p(np.random.rand(1, 5, 5)),
+            p(np.random.rand(2, 5, 5)),
+            ValueError,
+        ]
     )
-
     EXCEPTION_TESTS.append(
         [
-            {"keys": "mask", "border_key": "border", "markers_key": "old_markers"},
+            {"mask_key": "mask", "border_key": "border", "markers_key": "old_markers"},
             p(np.random.rand(1, 5, 5)),
             p(np.random.rand(1, 5, 5)),
             KeyError,
         ]
     )
 
-for p in TEST_NDARRAYS:
+    TESTS.append([{}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), (1, 5, 5)])
     TESTS.append(
-        [{"keys": "mask", "border_key": "border"}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), (1, 5, 5)]
+        [
+            {"threshold": 0.4, "radius": 1, "min_object_size": 0},
+            p(np.random.rand(1, 5, 5)),
+            p(np.random.rand(1, 5, 5)),
+            (1, 5, 5),
+        ]
     )
 
 
 @unittest.skipUnless(has_skimage, "Requires scikit-image library.")
 @unittest.skipUnless(has_scipy, "Requires scipy library.")
 class TestGenerateWatershedMarkersd(unittest.TestCase):
     @parameterized.expand(EXCEPTION_TESTS)
-    def test_value(self, argments, mask, border_map, exception_type):
+    def test_value(self, arguments, mask, border_map, exception_type):
         with self.assertRaises(exception_type):
-            GenerateWatershedMarkersd(**argments)({"mask": mask, "border": border_map, "old_markers": 1})
+            GenerateWatershedMarkersd(**arguments)({"mask": mask, "border": border_map, "old_markers": 1})
 
     @parameterized.expand(TESTS)
-    def test_value2(self, argments, mask, border_map, expected_shape):
-        result = GenerateWatershedMarkersd(**argments)({"mask": mask, "border": border_map})
+    def test_value2(self, arguments, mask, border_map, expected_shape):
+        result = GenerateWatershedMarkersd(**arguments)({"mask": mask, "border": border_map})
         self.assertEqual(result["markers"].shape, expected_shape)
 
 

tests/test_generate_watershed_mask.py

@@ -27,18 +27,12 @@
 np.random.RandomState(123)
 
 for p in TEST_NDARRAYS:
-    EXCEPTION_TESTS.append(
-        [
-            {"softmax": False, "sigmoid": True, "remove_small_objects": True, "min_size": 10},
-            p(np.random.rand(1, 5, 5)),
-            ValueError,
-        ]
-    )
+    EXCEPTION_TESTS.append([{"activation": "incorrect"}, ValueError])
+    EXCEPTION_TESTS.append([{"activation": 1}, ValueError])
 
-for p in TEST_NDARRAYS:
     TESTS.append(
         [
-            {"softmax": True, "sigmoid": False, "threshold": None, "remove_small_objects": False, "min_size": 10},
+            {"activation": "softmax", "min_object_size": 0},
             p(
                 [
                     [[0.5022, 0.3403, 0.9997], [0.8793, 0.5514, 0.2697], [0.6134, 0.6389, 0.0680]],
@@ -52,7 +46,7 @@
 
     TESTS.append(
         [
-            {"softmax": False, "sigmoid": True, "threshold": 0.5, "remove_small_objects": False, "min_size": 10},
+            {"activation": "sigmoid", "threshold": 0.5, "min_object_size": 0},
             p([[[0.5022, 0.3403, 0.9997], [0.8793, 0.5514, 0.2697], [-0.1134, -0.0389, -0.0680]]]),
             (1, 3, 3),
             [0, 1],
@@ -63,13 +57,13 @@
 @unittest.skipUnless(has_scipy, "Requires scipy library.")
 class TestGenerateWatershedMask(unittest.TestCase):
     @parameterized.expand(EXCEPTION_TESTS)
-    def test_value(self, argments, image, exception_type):
+    def test_value(self, arguments, exception_type):
         with self.assertRaises(exception_type):
-            GenerateWatershedMask(**argments)(image)
+            GenerateWatershedMask(**arguments)
 
     @parameterized.expand(TESTS)
-    def test_value2(self, argments, image, expected_shape, expected_value):
-        result = GenerateWatershedMask(**argments)(image)
+    def test_value2(self, arguments, image, expected_shape, expected_value):
+        result = GenerateWatershedMask(**arguments)(image)
         self.assertEqual(result.shape, expected_shape)
 
         if isinstance(result, torch.Tensor):