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update integration tests metatensor #4262

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merged 6 commits into from
May 12, 2022
Merged

update integration tests metatensor #4262

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4865672
temp tests
wyli May 12, 2022
f939c53
temp test
wyli May 12, 2022
791df7a
fixes rotated test
wyli May 12, 2022
a541c9f
mednist dataset fix
wyli May 12, 2022
90c4bd0
fixes
wyli May 12, 2022
c805baf
remove temp tests
wyli May 12, 2022
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9 changes: 2 additions & 7 deletions tests/test_cross_validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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


Expand All @@ -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"])

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9 changes: 2 additions & 7 deletions tests/test_decathlondataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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


Expand All @@ -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):
Expand Down
13 changes: 3 additions & 10 deletions tests/test_mednistdataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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))
Expand All @@ -59,7 +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)
Expand Down
7 changes: 7 additions & 0 deletions tests/test_rotated.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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"], MetaTensor):
rotated["seg"] = rotated["seg"].as_tensor() # pytorch 1.7 compatible
self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 30)


Expand Down Expand Up @@ -96,6 +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"], MetaTensor):
rotated["seg"] = rotated["seg"].as_tensor() # pytorch 1.7 compatible
self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 160)


Expand Down Expand Up @@ -127,6 +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"], MetaTensor):
rotated["seg"] = rotated["seg"].as_tensor() # pytorch 1.7 compatible
self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 160)


Expand Down