monai-weekly 1.5.dev2505__py3-none-any.whl → 1.5.dev2507__py3-none-any.whl

tests/apps/pathology/transforms/post/test_generate_instance_contour.py

@@ -0,0 +1,58 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.array import GenerateInstanceContour
+from monai.transforms import BoundingRect
+from monai.utils import min_version, optional_import
+from tests.test_utils import TEST_NDARRAYS, assert_allclose
+
+_, has_skimage = optional_import("skimage", "0.19.3", min_version)
+
+y, x = np.ogrid[0:30, 0:30]
+get_bbox = BoundingRect()
+
+TEST_CASE_1 = [(x - 2) ** 2 + (y - 2) ** 2 <= 2**2, 3, [0, 0], [[2, 0], [0, 2], [2, 4], [4, 2]]]
+
+TEST_CASE_2 = [(x - 8) ** 2 + (y - 8) ** 2 <= 2**2, 3, [8, 8], [[10, 8], [8, 10], [10, 12], [12, 10]]]
+
+TEST_CASE_3 = [
+    (x - 5) ** 2 / 3**2 + (y - 5) ** 2 / 2**2 <= 1,
+    3,
+    [2, 3],
+    [[5, 3], [4, 4], [3, 4], [2, 5], [3, 6], [4, 6], [5, 7], [6, 6], [7, 6], [8, 5], [7, 4], [6, 4]],
+]
+
+TEST_CASE = []
+for p in TEST_NDARRAYS:
+    TEST_CASE.append([p, *TEST_CASE_1])
+    TEST_CASE.append([p, *TEST_CASE_2])
+    TEST_CASE.append([p, *TEST_CASE_3])
+
+
+@unittest.skipUnless(has_skimage, "Requires scikit-image library.")
+class TestGenerateInstanceContour(unittest.TestCase):
+    @parameterized.expand(TEST_CASE)
+    def test_shape(self, in_type, test_data, min_num_points, offset, expected):
+        inst_bbox = get_bbox(test_data[None])
+        inst_map = test_data[inst_bbox[0][0] : inst_bbox[0][1], inst_bbox[0][2] : inst_bbox[0][3]]
+        result = GenerateInstanceContour(min_num_points=min_num_points)(in_type(inst_map[None]), offset=offset)
+        assert_allclose(result, expected, type_test=False)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_instance_contourd.py

@@ -0,0 +1,61 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.dictionary import GenerateInstanceContourd
+from monai.transforms import BoundingRect
+from monai.utils import min_version, optional_import
+from tests.test_utils import TEST_NDARRAYS, assert_allclose
+
+_, has_skimage = optional_import("skimage", "0.19.3", min_version)
+
+y, x = np.ogrid[0:30, 0:30]
+get_bbox = BoundingRect()
+
+TEST_CASE_1 = [(x - 2) ** 2 + (y - 2) ** 2 <= 2**2, 3, [0, 0], [[2, 0], [0, 2], [2, 4], [4, 2]]]
+
+TEST_CASE_2 = [(x - 10) ** 2 + (y - 10) ** 2 <= 2**2, 3, [8, 8], [[10, 8], [8, 10], [10, 12], [12, 10]]]
+
+TEST_CASE_3 = [
+    (x - 5) ** 2 / 3**2 + (y - 5) ** 2 / 2**2 <= 1,
+    3,
+    [2, 3],
+    [[5, 3], [4, 4], [3, 4], [2, 5], [3, 6], [4, 6], [5, 7], [6, 6], [7, 6], [8, 5], [7, 4], [6, 4]],
+]
+
+TEST_CASE = []
+for p in TEST_NDARRAYS:
+    TEST_CASE.append([p, *TEST_CASE_1])
+    TEST_CASE.append([p, *TEST_CASE_2])
+    TEST_CASE.append([p, *TEST_CASE_3])
+
+
+@unittest.skipUnless(has_skimage, "Requires scikit-image library.")
+class TestGenerateInstanceContourd(unittest.TestCase):
+    @parameterized.expand(TEST_CASE)
+    def test_shape(self, in_type, test_data, min_num_points, offset, expected):
+        inst_bbox = get_bbox(test_data[None])
+        inst_map = test_data[inst_bbox[0][0] : inst_bbox[0][1], inst_bbox[0][2] : inst_bbox[0][3]]
+        test_data = {"image": in_type(inst_map[None]), "offset": offset}
+        result = GenerateInstanceContourd(
+            keys="image", contour_key_postfix="contour", offset_key="offset", min_num_points=min_num_points
+        )(test_data)
+        assert_allclose(result["image_contour"], expected, type_test=False)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_instance_type.py

@@ -0,0 +1,51 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.array import GenerateInstanceType
+from tests.test_utils import TEST_NDARRAYS, assert_allclose
+
+y, x = np.ogrid[0:30, 0:30]
+
+TEST_CASE_1 = [
+    (x - 2) ** 2 + (y - 2) ** 2 <= 2**2,
+    (x - 2) ** 2 + (y - 3) ** 2 <= 2**2,
+    np.array([[0, 5, 0, 5]]),
+    [1, 0.6666666111111158],
+]
+
+TEST_CASE_2 = [
+    (x - 8) ** 2 / 3**2 + (y - 8) ** 2 / 2**2 <= 1,
+    (x - 7) ** 2 / 3**2 + (y - 7) ** 2 / 2**2 <= 1,
+    np.array([[6, 11, 5, 12]]),
+    [1, 0.7058823114186875],
+]
+TEST_CASE = []
+for p in TEST_NDARRAYS:
+    TEST_CASE.append([p, *TEST_CASE_1])
+    TEST_CASE.append([p, *TEST_CASE_2])
+
+
+class TestGenerateInstanceType(unittest.TestCase):
+    @parameterized.expand(TEST_CASE)
+    def test_shape(self, in_type, type_pred, seg_pred, bbox, expected):
+        result = GenerateInstanceType()(in_type(type_pred[None]), in_type(seg_pred[None]), bbox, 1)
+        assert_allclose(result, expected)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_instance_typed.py

@@ -0,0 +1,53 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.dictionary import GenerateInstanceTyped
+from tests.test_utils import TEST_NDARRAYS, assert_allclose
+
+y, x = np.ogrid[0:30, 0:30]
+
+TEST_CASE_1 = [
+    (x - 2) ** 2 + (y - 2) ** 2 <= 2**2,
+    (x - 2) ** 2 + (y - 3) ** 2 <= 2**2,
+    np.array([[0, 5, 0, 5]]),
+    [1, 0.6666666111111158],
+]
+
+TEST_CASE_2 = [
+    (x - 8) ** 2 / 3**2 + (y - 8) ** 2 / 2**2 <= 1,
+    (x - 7) ** 2 / 3**2 + (y - 7) ** 2 / 2**2 <= 1,
+    np.array([[6, 11, 5, 12]]),
+    [1, 0.7058823114186875],
+]
+TEST_CASE = []
+for p in TEST_NDARRAYS:
+    TEST_CASE.append([p, *TEST_CASE_1])
+    TEST_CASE.append([p, *TEST_CASE_2])
+
+
+class TestGenerateInstanceTyped(unittest.TestCase):
+    @parameterized.expand(TEST_CASE)
+    def test_shape(self, in_type, type_pred, seg_pred, bbox, expected):
+        test_data = {"type_pred": in_type(type_pred[None]), "seg": in_type(seg_pred[None]), "bbox": bbox, "id": 1}
+        result = GenerateInstanceTyped(keys="type_pred")(test_data)
+        assert_allclose(result["type_info"]["inst_type"], expected[0])
+        assert_allclose(result["type_info"]["type_prob"], expected[1])
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_succinct_contour.py

@@ -0,0 +1,55 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.array import GenerateSuccinctContour
+
+TEST_CASE_1 = [
+    [
+        np.array([[1.5, 0.0], [1.0, 0.5], [0.5, 1.0], [0.0, 1.5]]),
+        np.array([[0.0, 2.5], [0.5, 3.0], [1.0, 3.5], [1.5, 4.0]]),
+        np.array([[4.0, 1.5], [3.5, 1.0], [3.0, 0.5], [2.5, 0.0]]),
+        np.array([[2.5, 4.0], [3.0, 3.5], [3.5, 3.0], [4.0, 2.5]]),
+    ],
+    5,
+    5,
+    [[2, 0], [0, 2], [2, 4], [4, 2]],
+]
+
+TEST_CASE_2 = [
+    [
+        np.array([[1.5, 0.0], [1.0, 0.5], [0.5, 1.0], [0.5, 2.0], [0.0, 2.5]]),
+        np.array([[0.0, 3.5], [0.5, 4.0], [0.5, 5.0], [1.0, 5.5], [1.5, 6.0]]),
+        np.array([[4.0, 2.5], [3.5, 2.0], [3.5, 1.0], [3.0, 0.5], [2.5, 0.0]]),
+        np.array([[2.5, 6.0], [3.0, 5.5], [3.5, 5.0], [3.5, 4.0], [4.0, 3.5]]),
+    ],
+    5,
+    7,
+    [[3, 0], [2, 1], [1, 1], [0, 2], [1, 3], [2, 3], [3, 4], [4, 3], [5, 3], [6, 2], [5, 1], [4, 1]],
+]
+
+
+class TestGenerateSuccinctContour(unittest.TestCase):
+
+    @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
+    def test_shape(self, test_data, height, width, expected):
+        result = GenerateSuccinctContour(height=height, width=width)(test_data)
+        np.testing.assert_allclose(result, expected)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py

@@ -0,0 +1,57 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.dictionary import GenerateSuccinctContourd
+
+y, x = np.ogrid[0:5, 0:5]
+TEST_CASE_1 = [
+    [
+        np.array([[1.5, 0.0], [1.0, 0.5], [0.5, 1.0], [0.0, 1.5]]),
+        np.array([[0.0, 2.5], [0.5, 3.0], [1.0, 3.5], [1.5, 4.0]]),
+        np.array([[4.0, 1.5], [3.5, 1.0], [3.0, 0.5], [2.5, 0.0]]),
+        np.array([[2.5, 4.0], [3.0, 3.5], [3.5, 3.0], [4.0, 2.5]]),
+    ],
+    5,
+    5,
+    [[2, 0], [0, 2], [2, 4], [4, 2]],
+]
+
+TEST_CASE_2 = [
+    [
+        np.array([[1.5, 0.0], [1.0, 0.5], [0.5, 1.0], [0.5, 2.0], [0.0, 2.5]]),
+        np.array([[0.0, 3.5], [0.5, 4.0], [0.5, 5.0], [1.0, 5.5], [1.5, 6.0]]),
+        np.array([[4.0, 2.5], [3.5, 2.0], [3.5, 1.0], [3.0, 0.5], [2.5, 0.0]]),
+        np.array([[2.5, 6.0], [3.0, 5.5], [3.5, 5.0], [3.5, 4.0], [4.0, 3.5]]),
+    ],
+    5,
+    7,
+    [[3, 0], [2, 1], [1, 1], [0, 2], [1, 3], [2, 3], [3, 4], [4, 3], [5, 3], [6, 2], [5, 1], [4, 1]],
+]
+
+
+class TestGenerateSuccinctContour(unittest.TestCase):
+
+    @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
+    def test_shape(self, data, height, width, expected):
+        test_data = {"contour": data}
+        result = GenerateSuccinctContourd(keys="contour", height=height, width=width)(test_data)
+        np.testing.assert_allclose(result["contour"], expected)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_watershed_markers.py

@@ -0,0 +1,53 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.array import GenerateWatershedMarkers
+from monai.utils import min_version, optional_import
+from tests.test_utils import TEST_NDARRAYS
+
+_, has_skimage = optional_import("skimage", "0.19.3", min_version)
+_, has_scipy = optional_import("scipy", "1.8.1", min_version)
+
+EXCEPTION_TESTS = []
+TESTS = []
+
+np.random.RandomState(123)
+
+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])
+
+    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, arguments, mask, probmap, exception_type):
+        with self.assertRaises(exception_type):
+            GenerateWatershedMarkers(**arguments)(mask, probmap)
+
+    @parameterized.expand(TESTS)
+    def test_value2(self, arguments, mask, probmap, expected_shape):
+        result = GenerateWatershedMarkers(**arguments)(mask, probmap)
+        self.assertEqual(result.shape, expected_shape)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py

@@ -0,0 +1,83 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.dictionary import GenerateWatershedMarkersd
+from monai.utils import min_version, optional_import
+from tests.test_utils import TEST_NDARRAYS
+
+_, has_skimage = optional_import("skimage", "0.19.3", min_version)
+_, has_scipy = optional_import("scipy", "1.8.1", min_version)
+
+EXCEPTION_TESTS = []
+TESTS = []
+
+np.random.RandomState(123)
+
+for p in TEST_NDARRAYS:
+    EXCEPTION_TESTS.append(
+        [
+            {"mask_key": "mask", "border_key": "border"},
+            p(np.random.rand(2, 5, 5)),
+            p(np.random.rand(1, 5, 5)),
+            ValueError,
+        ]
+    )
+    EXCEPTION_TESTS.append(
+        [
+            {"mask_key": "mask", "border_key": "border"},
+            p(np.random.rand(1, 5, 5)),
+            p(np.random.rand(2, 5, 5)),
+            ValueError,
+        ]
+    )
+    EXCEPTION_TESTS.append(
+        [
+            {"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,
+        ]
+    )
+
+    TESTS.append([{}, p(np.random.rand(1, 5, 5)), p(np.random.rand(1, 5, 5)), (1, 5, 5)])
+    TESTS.append(
+        [
+            {"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, arguments, mask, border_map, exception_type):
+        with self.assertRaises(exception_type):
+            GenerateWatershedMarkersd(**arguments)({"mask": mask, "border": border_map, "old_markers": 1})
+
+    @parameterized.expand(TESTS)
+    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)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_watershed_mask.py

@@ -0,0 +1,77 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+import torch
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.array import GenerateWatershedMask
+from monai.utils import min_version, optional_import
+from tests.test_utils import TEST_NDARRAYS
+
+_, has_scipy = optional_import("scipy", "1.8.1", min_version)
+
+EXCEPTION_TESTS = []
+TESTS = []
+
+np.random.RandomState(123)
+
+for p in TEST_NDARRAYS:
+    EXCEPTION_TESTS.append([{"activation": "incorrect"}, ValueError])
+    EXCEPTION_TESTS.append([{"activation": 1}, ValueError])
+
+    TESTS.append(
+        [
+            {"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]],
+                    [[0.5000, 0.3400, 0.9900], [0.8900, 0.5600, 0.2700], [0.6100, 0.6300, 0.0600]],
+                ]
+            ),
+            (1, 3, 3),
+            [0, 1],
+        ]
+    )
+
+    TESTS.append(
+        [
+            {"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],
+        ]
+    )
+
+
+@unittest.skipUnless(has_scipy, "Requires scipy library.")
+class TestGenerateWatershedMask(unittest.TestCase):
+    @parameterized.expand(EXCEPTION_TESTS)
+    def test_value(self, arguments, exception_type):
+        with self.assertRaises(exception_type):
+            GenerateWatershedMask(**arguments)
+
+    @parameterized.expand(TESTS)
+    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):
+            result = result.cpu().numpy()
+        self.assertEqual(np.unique(result).tolist(), expected_value)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py

@@ -0,0 +1,77 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+import torch
+from parameterized import parameterized
+
+from monai.apps.pathology.transforms.post.dictionary import GenerateWatershedMaskd
+from monai.utils import min_version, optional_import
+from tests.test_utils import TEST_NDARRAYS
+
+_, has_scipy = optional_import("scipy", "1.8.1", min_version)
+
+EXCEPTION_TESTS = []
+TESTS = []
+
+np.random.RandomState(123)
+
+for p in TEST_NDARRAYS:
+    EXCEPTION_TESTS.append([{"keys": "img", "activation": "incorrect"}, ValueError])
+    EXCEPTION_TESTS.append([{"keys": "img", "activation": 1}, ValueError])
+
+    TESTS.append(
+        [
+            {"keys": "img", "mask_key": "mask", "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]],
+                    [[0.5000, 0.3400, 0.9900], [0.8900, 0.5600, 0.2700], [0.6100, 0.6300, 0.0600]],
+                ]
+            ),
+            (1, 3, 3),
+            [0, 1],
+        ]
+    )
+
+    TESTS.append(
+        [
+            {"keys": "img", "mask_key": "mask", "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],
+        ]
+    )
+
+
+@unittest.skipUnless(has_scipy, "Requires scipy library.")
+class TestGenerateWatershedMaskd(unittest.TestCase):
+    @parameterized.expand(EXCEPTION_TESTS)
+    def test_value(self, arguments, exception_type):
+        with self.assertRaises(exception_type):
+            GenerateWatershedMaskd(**arguments)
+
+    @parameterized.expand(TESTS)
+    def test_value2(self, arguments, image, expected_shape, expected_value):
+        result = GenerateWatershedMaskd(**arguments)({"img": image})
+        self.assertEqual(result["mask"].shape, expected_shape)
+
+        if isinstance(result["mask"], torch.Tensor):
+            result["mask"] = result["mask"].cpu().numpy()
+        self.assertEqual(np.unique(result["mask"]).tolist(), expected_value)
+
+
+if __name__ == "__main__":
+    unittest.main()