From 4865672c939371cc098744a8bceda9a9a6dc4a97 Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Thu, 12 May 2022 08:47:12 +0100 Subject: [PATCH 1/6] temp tests Signed-off-by: Wenqi Li --- .github/workflows/cron.yml | 2 +- tests/test_cross_validation.py | 9 ++------- tests/test_decathlondataset.py | 9 ++------- tests/test_mednistdataset.py | 11 ++--------- tests/test_rotated.py | 3 +++ 5 files changed, 10 insertions(+), 24 deletions(-) diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml index 5b4e2f7285..99977457d0 100644 --- a/.github/workflows/cron.yml +++ b/.github/workflows/cron.yml @@ -7,7 +7,7 @@ on: workflow_dispatch: push: branches: - - feature/MetaTensor + - feature-tests-metatensor jobs: cron-gpu: diff --git a/tests/test_cross_validation.py b/tests/test_cross_validation.py index 7ad150c290..811dcea026 100644 --- a/tests/test_cross_validation.py +++ b/tests/test_cross_validation.py @@ -14,7 +14,7 @@ from monai.apps import CrossValidation, DecathlonDataset from monai.data import MetaTensor -from monai.transforms import AddChanneld, Compose, LoadImaged, ScaleIntensityd, ToTensord +from monai.transforms import AddChanneld, Compose, LoadImaged, ScaleIntensityd from tests.utils import skip_if_downloading_fails, skip_if_quick @@ -23,12 +23,7 @@ class TestCrossValidation(unittest.TestCase): def test_values(self): testing_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "testing_data") train_transform = Compose( - [ - LoadImaged(keys=["image", "label"]), - AddChanneld(keys=["image", "label"]), - ScaleIntensityd(keys="image"), - ToTensord(keys=["image", "label"]), - ] + [LoadImaged(keys=["image", "label"]), AddChanneld(keys=["image", "label"]), ScaleIntensityd(keys="image")] ) val_transform = LoadImaged(keys=["image", "label"]) diff --git a/tests/test_decathlondataset.py b/tests/test_decathlondataset.py index 6693ca3673..49280f6fa6 100644 --- a/tests/test_decathlondataset.py +++ b/tests/test_decathlondataset.py @@ -16,7 +16,7 @@ from monai.apps import DecathlonDataset from monai.data import MetaTensor -from monai.transforms import AddChanneld, Compose, LoadImaged, ScaleIntensityd, ToTensord +from monai.transforms import AddChanneld, Compose, LoadImaged, ScaleIntensityd from tests.utils import skip_if_downloading_fails, skip_if_quick @@ -25,12 +25,7 @@ class TestDecathlonDataset(unittest.TestCase): def test_values(self): testing_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "testing_data") transform = Compose( - [ - LoadImaged(keys=["image", "label"]), - AddChanneld(keys=["image", "label"]), - ScaleIntensityd(keys="image"), - ToTensord(keys=["image", "label"]), - ] + [LoadImaged(keys=["image", "label"]), AddChanneld(keys=["image", "label"]), ScaleIntensityd(keys="image")] ) def _test_dataset(dataset): diff --git a/tests/test_mednistdataset.py b/tests/test_mednistdataset.py index 4d2f01c24c..c4ac7fa30d 100644 --- a/tests/test_mednistdataset.py +++ b/tests/test_mednistdataset.py @@ -16,7 +16,7 @@ from monai.apps import MedNISTDataset from monai.data import MetaTensor -from monai.transforms import AddChanneld, Compose, LoadImaged, ScaleIntensityd, ToTensord +from monai.transforms import AddChanneld, Compose, LoadImaged, ScaleIntensityd from tests.utils import skip_if_downloading_fails, skip_if_quick MEDNIST_FULL_DATASET_LENGTH = 58954 @@ -26,14 +26,7 @@ class TestMedNISTDataset(unittest.TestCase): @skip_if_quick def test_values(self): testing_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "testing_data") - transform = Compose( - [ - LoadImaged(keys="image"), - AddChanneld(keys="image"), - ScaleIntensityd(keys="image"), - ToTensord(keys=["image", "label"]), - ] - ) + transform = Compose([LoadImaged(keys="image"), AddChanneld(keys="image"), ScaleIntensityd(keys="image")]) def _test_dataset(dataset): self.assertEqual(len(dataset), int(MEDNIST_FULL_DATASET_LENGTH * dataset.test_frac)) diff --git a/tests/test_rotated.py b/tests/test_rotated.py index 43b5a68f61..799ab198e9 100644 --- a/tests/test_rotated.py +++ b/tests/test_rotated.py @@ -17,6 +17,7 @@ import torch from parameterized import parameterized +from monai.data import MetaTensor from monai.transforms import Rotated from tests.utils import TEST_NDARRAYS, NumpyImageTestCase2D, NumpyImageTestCase3D @@ -65,6 +66,8 @@ def test_correct_results(self, im_type, angle, keep_size, mode, padding_mode, al self.segn[0, 0], -np.rad2deg(angle), (0, 1), not keep_size, order=0, mode=_mode, prefilter=False ) expected = np.stack(expected).astype(int) + if isinstance(rotated["seg"][0], MetaTensor): + rotated["seg"][0] = rotated["seg"][0].as_tensor() # pytorch 1.7 compatible self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 30) From f939c538e9d23c9afb09ecd9d5054dcfeee9c825 Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Thu, 12 May 2022 09:03:59 +0100 Subject: [PATCH 2/6] temp test Signed-off-by: Wenqi Li --- .github/workflows/cron.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml index 99977457d0..5dda4fbee7 100644 --- a/.github/workflows/cron.yml +++ b/.github/workflows/cron.yml @@ -8,6 +8,7 @@ on: push: branches: - feature-tests-metatensor + pull_request: jobs: cron-gpu: From 791df7afa13d81fa582d3163c0cd6ff5f5eb24dd Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Thu, 12 May 2022 10:03:14 +0100 Subject: [PATCH 3/6] fixes rotated test Signed-off-by: Wenqi Li --- tests/test_rotated.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/test_rotated.py b/tests/test_rotated.py index 799ab198e9..201b2f2cd7 100644 --- a/tests/test_rotated.py +++ b/tests/test_rotated.py @@ -99,6 +99,8 @@ def test_correct_results(self, im_type, angle, keep_size, mode, padding_mode, al self.segn[0, 0], np.rad2deg(angle), (0, 2), not keep_size, order=0, mode=_mode, prefilter=False ) expected = np.stack(expected).astype(int) + if isinstance(rotated["seg"][0], MetaTensor): + rotated["seg"][0] = rotated["seg"][0].as_tensor() # pytorch 1.7 compatible self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 160) @@ -130,6 +132,8 @@ def test_correct_results(self, im_type, angle, keep_size, mode, padding_mode, al self.segn[0, 0], -np.rad2deg(angle), (0, 1), not keep_size, order=0, mode=_mode, prefilter=False ) expected = np.stack(expected).astype(int) + if isinstance(rotated["seg"][0], MetaTensor): + rotated["seg"][0] = rotated["seg"][0].as_tensor() # pytorch 1.7 compatible self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 160) From a541c9f1331d1a946a336a9c1ae103f08464fdf2 Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Thu, 12 May 2022 10:06:43 +0100 Subject: [PATCH 4/6] mednist dataset fix Signed-off-by: Wenqi Li --- tests/test_mednistdataset.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_mednistdataset.py b/tests/test_mednistdataset.py index c4ac7fa30d..87a0d6a2ec 100644 --- a/tests/test_mednistdataset.py +++ b/tests/test_mednistdataset.py @@ -52,7 +52,7 @@ def _test_dataset(dataset): data = MedNISTDataset(root_dir=testing_dir, transform=transform, section="test", download=False, seed=42) _test_dataset(data) self.assertEqual(data[0]["class_name"], "AbdomenCT") - self.assertEqual(data[0]["label"].cpu().item(), 0) + self.assertEqual(data[0]["label"], 0) shutil.rmtree(os.path.join(testing_dir, "MedNIST")) try: MedNISTDataset(root_dir=testing_dir, transform=transform, section="test", download=False) From 90c4bd0c52fe64a1cd1e8576b8dba2474bb74187 Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Thu, 12 May 2022 06:36:29 -0400 Subject: [PATCH 5/6] fixes Signed-off-by: Wenqi Li --- tests/test_rotated.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/test_rotated.py b/tests/test_rotated.py index 201b2f2cd7..24ed82b84d 100644 --- a/tests/test_rotated.py +++ b/tests/test_rotated.py @@ -66,8 +66,8 @@ def test_correct_results(self, im_type, angle, keep_size, mode, padding_mode, al self.segn[0, 0], -np.rad2deg(angle), (0, 1), not keep_size, order=0, mode=_mode, prefilter=False ) expected = np.stack(expected).astype(int) - if isinstance(rotated["seg"][0], MetaTensor): - rotated["seg"][0] = rotated["seg"][0].as_tensor() # pytorch 1.7 compatible + if isinstance(rotated["seg"], MetaTensor): + rotated["seg"] = rotated["seg"].as_tensor() # pytorch 1.7 compatible self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 30) @@ -99,8 +99,8 @@ def test_correct_results(self, im_type, angle, keep_size, mode, padding_mode, al self.segn[0, 0], np.rad2deg(angle), (0, 2), not keep_size, order=0, mode=_mode, prefilter=False ) expected = np.stack(expected).astype(int) - if isinstance(rotated["seg"][0], MetaTensor): - rotated["seg"][0] = rotated["seg"][0].as_tensor() # pytorch 1.7 compatible + if isinstance(rotated["seg"], MetaTensor): + rotated["seg"] = rotated["seg"].as_tensor() # pytorch 1.7 compatible self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 160) @@ -132,8 +132,8 @@ def test_correct_results(self, im_type, angle, keep_size, mode, padding_mode, al self.segn[0, 0], -np.rad2deg(angle), (0, 1), not keep_size, order=0, mode=_mode, prefilter=False ) expected = np.stack(expected).astype(int) - if isinstance(rotated["seg"][0], MetaTensor): - rotated["seg"][0] = rotated["seg"][0].as_tensor() # pytorch 1.7 compatible + if isinstance(rotated["seg"], MetaTensor): + rotated["seg"] = rotated["seg"].as_tensor() # pytorch 1.7 compatible self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 160) From c805baf1005d75e0defadde13bebb9dc6b236871 Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Thu, 12 May 2022 15:49:21 +0100 Subject: [PATCH 6/6] remove temp tests Signed-off-by: Wenqi Li --- .github/workflows/cron.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml index 5dda4fbee7..5b4e2f7285 100644 --- a/.github/workflows/cron.yml +++ b/.github/workflows/cron.yml @@ -7,8 +7,7 @@ on: workflow_dispatch: push: branches: - - feature-tests-metatensor - pull_request: + - feature/MetaTensor jobs: cron-gpu: