monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2508__py3-none-any.whl

tests/apps/pathology/test_lesion_froc.py

@@ -0,0 +1,333 @@
+# 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 os
+import unittest
+from unittest import skipUnless
+
+import numpy as np
+from parameterized import parameterized
+
+from monai.apps.pathology.metrics import LesionFROC
+from monai.utils import optional_import
+
+_cucim, has_cucim = optional_import("cucim")
+has_cucim = has_cucim and hasattr(_cucim, "CuImage")
+_, has_skimage = optional_import("skimage.measure")
+_, has_sp = optional_import("scipy.ndimage")
+imwrite, has_tif = optional_import("tifffile", name="imwrite")
+
+
+def save_as_tif(filename, array):
+    array = array[::-1, ...]  # Upside-down
+    if not filename.endswith(".tif"):
+        filename += ".tif"
+    file_path = os.path.join("tests", "testing_data", filename)
+    imwrite(file_path, array, compression="jpeg", tile=(16, 16))
+
+
+def around(val, interval=3):
+    return slice(val - interval, val + interval)
+
+
+# mask and prediction image size
+HEIGHT = 101
+WIDTH = 800
+
+
+def prepare_test_data():
+    # -------------------------------------
+    # Ground Truth - Binary Masks
+    # -------------------------------------
+    # ground truth with no tumor
+    ground_truth = np.zeros((HEIGHT, WIDTH), dtype=np.uint8)
+    save_as_tif("temp_ground_truth_0", ground_truth)
+
+    # ground truth with one tumor
+    ground_truth[around(HEIGHT // 2), around(1 * WIDTH // 7)] = 1
+    save_as_tif("temp_ground_truth_1", ground_truth)
+
+    # ground truth with two tumors
+    ground_truth[around(HEIGHT // 2), around(2 * WIDTH // 7)] = 1
+    save_as_tif("temp_ground_truth_2", ground_truth)
+
+    # ground truth with three tumors
+    ground_truth[around(HEIGHT // 2), around(3 * WIDTH // 7)] = 1
+    save_as_tif("temp_ground_truth_3", ground_truth)
+
+    # ground truth with four tumors
+    ground_truth[around(HEIGHT // 2), around(4 * WIDTH // 7)] = 1
+    save_as_tif("temp_ground_truth_4", ground_truth)
+
+    # -------------------------------------
+    # predictions - Probability Maps
+    # -------------------------------------
+
+    # prediction with no tumor
+    prob_map = np.zeros((HEIGHT, WIDTH))
+    np.save("./tests/testing_data/temp_prob_map_0_0.npy", prob_map)
+
+    # prediction with one incorrect tumor
+    prob_map[HEIGHT // 2, 5 * WIDTH // 7] = 0.6
+    np.save("./tests/testing_data/temp_prob_map_0_1.npy", prob_map)
+
+    # prediction with correct first tumors and an incorrect tumor
+    prob_map[HEIGHT // 2, 1 * WIDTH // 7] = 0.8
+    np.save("./tests/testing_data/temp_prob_map_1_1.npy", prob_map)
+
+    # prediction with correct firt two tumors and an incorrect tumor
+    prob_map[HEIGHT // 2, 2 * WIDTH // 7] = 0.8
+    np.save("./tests/testing_data/temp_prob_map_2_1.npy", prob_map)
+
+    # prediction with two incorrect tumors
+    prob_map = np.zeros((HEIGHT, WIDTH))
+    prob_map[HEIGHT // 2, 5 * WIDTH // 7] = 0.6
+    prob_map[HEIGHT // 2, 6 * WIDTH // 7] = 0.4
+    np.save("./tests/testing_data/temp_prob_map_0_2.npy", prob_map)
+
+    # prediction with correct first tumors and two incorrect tumors
+    prob_map[HEIGHT // 2, 1 * WIDTH // 7] = 0.8
+    np.save("./tests/testing_data/temp_prob_map_1_2.npy", prob_map)
+
+
+TEST_CASE_0 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_0_0.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_0.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            }
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    np.nan,
+]
+
+TEST_CASE_1 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_0_0.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_1.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            }
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    0.0,
+]
+
+TEST_CASE_2 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_1.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_1.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            }
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    1.0,
+]
+
+TEST_CASE_3 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_2_1.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_1.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            }
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    1.0,
+]
+
+TEST_CASE_4 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_2_1.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_2.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            }
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    1.0,
+]
+
+TEST_CASE_5 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_2.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_2.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            }
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    0.5,
+]
+
+TEST_CASE_6 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_1.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_1.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_2.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_2.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    2.0 / 3.0,
+]
+
+TEST_CASE_7 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_1.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_3.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_2.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_2.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    0.4,
+]
+
+TEST_CASE_8 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_0_1.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_1.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_1.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_3.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_2.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_2.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    1.0 / 3.0,
+]
+
+TEST_CASE_9 = [
+    {
+        "data": [
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_0_2.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_4.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_1.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_3.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+            {
+                "prob_map": "./tests/testing_data/temp_prob_map_1_2.npy",
+                "tumor_mask": "./tests/testing_data/temp_ground_truth_2.tif",
+                "level": 0,
+                "pixel_spacing": 1,
+            },
+        ],
+        "grow_distance": 2,
+        "itc_diameter": 0,
+    },
+    2.0 / 9.0,
+]
+
+
+class TestEvaluateTumorFROC(unittest.TestCase):
+
+    @skipUnless(has_cucim, "Requires cucim")
+    @skipUnless(has_skimage, "Requires skimage")
+    @skipUnless(has_sp, "Requires scipy")
+    @skipUnless(has_tif, "Requires tifffile")
+    def setUp(self):
+        prepare_test_data()
+
+    @parameterized.expand(
+        [
+            TEST_CASE_0,
+            TEST_CASE_1,
+            TEST_CASE_2,
+            TEST_CASE_3,
+            TEST_CASE_4,
+            TEST_CASE_5,
+            TEST_CASE_6,
+            TEST_CASE_7,
+            TEST_CASE_8,
+            TEST_CASE_9,
+        ]
+    )
+    def test_read_patches_cucim(self, input_parameters, expected):
+        froc = LesionFROC(**input_parameters)
+        froc_score = froc.evaluate()
+        if np.isnan(expected):
+            self.assertTrue(np.isnan(froc_score))
+        else:
+            self.assertAlmostEqual(froc_score, expected)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/test_pathology_prob_nms.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
+import torch
+from parameterized import parameterized
+
+from monai.apps.pathology.utils import PathologyProbNMS
+
+probs_map_2d = np.random.rand(100, 100).clip(0, 0.5)
+probs_map_2d[33, 33] = 0.7
+probs_map_2d[66, 66] = 0.9
+expected_2d = [[0.9, 133, 133], [0.7, 67, 67]]
+TEST_CASES_2D = [
+    {"spatial_dims": 2, "prob_threshold": 0.5, "box_size": [10, 10]},
+    {"resolution_level": 1},
+    probs_map_2d,
+    expected_2d,
+]
+
+probs_map_3d = torch.rand([50, 50, 50]).uniform_(0, 0.5)
+probs_map_3d[25, 25, 25] = 0.7
+probs_map_3d[45, 45, 45] = 0.9
+expected_3d = [[0.9, 91, 91, 91], [0.7, 51, 51, 51]]
+TEST_CASES_3D = [
+    {"spatial_dims": 3, "prob_threshold": 0.5, "box_size": (10, 10, 10)},
+    {"resolution_level": 1},
+    probs_map_3d,
+    expected_3d,
+]
+
+
+class TestPathologyProbNMS(unittest.TestCase):
+
+    @parameterized.expand([TEST_CASES_2D, TEST_CASES_3D])
+    def test_output(self, class_args, call_args, probs_map, expected):
+        nms = PathologyProbNMS(**class_args)
+        output = nms(probs_map, **call_args)
+        np.testing.assert_allclose(output, expected)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/apps/pathology/test_prepare_batch_hovernet.py

@@ -0,0 +1,70 @@
+# 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 torch
+from parameterized import parameterized
+
+from monai.apps.pathology.engines import PrepareBatchHoVerNet
+from monai.engines import SupervisedEvaluator
+from monai.utils.enums import HoVerNetBranch
+from tests.test_utils import assert_allclose
+
+TEST_CASE_0 = [
+    {"extra_keys": ["extra_label1", "extra_label2"]},
+    {HoVerNetBranch.NP: torch.tensor([1, 2]), HoVerNetBranch.NC: torch.tensor([4, 4]), HoVerNetBranch.HV: 16},
+]
+
+
+class TestNet(torch.nn.Module):
+    __test__ = False  # indicate to pytest that this class is not intended for collection
+
+    def forward(self, x: torch.Tensor):
+        return {HoVerNetBranch.NP: torch.tensor([1, 2]), HoVerNetBranch.NC: torch.tensor([4, 4]), HoVerNetBranch.HV: 16}
+
+
+class TestPrepareBatchHoVerNet(unittest.TestCase):
+    @parameterized.expand([TEST_CASE_0])
+    def test_content(self, input_args, expected_value):
+        device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+        dataloader = [
+            {
+                "image": torch.tensor([1, 2]),
+                "label": torch.tensor([1, 2]),
+                "extra_label1": torch.tensor([3, 4]),
+                "extra_label2": 16,
+            }
+        ]
+        # set up engine
+        evaluator = SupervisedEvaluator(
+            device=device,
+            val_data_loader=dataloader,
+            epoch_length=1,
+            network=TestNet(),
+            non_blocking=True,
+            prepare_batch=PrepareBatchHoVerNet(**input_args),
+            decollate=False,
+        )
+        evaluator.run()
+        output = evaluator.state.output
+        assert_allclose(output["image"], torch.tensor([1, 2], device=device))
+        for k, v in output["pred"].items():
+            if isinstance(v, torch.Tensor):
+                assert_allclose(v, expected_value[k].to(device))
+            else:
+                self.assertEqual(v, expected_value[k])
+
+
+if __name__ == "__main__":
+    unittest.main()