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fixes distortion fig interpolation order #3156

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Merged
wyli merged 4 commits into from
Oct 20, 2021
Merged

fixes distortion fig interpolation order #3156

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97f4737
update based on comments
wyli Oct 20, 2021
5f0660e
fixes unit tests
wyli Oct 20, 2021
8241b12
skip downloading when quick testing
wyli Oct 20, 2021
18333db
formmatting
wyli Oct 20, 2021
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4 changes: 1 addition & 3 deletions monai/transforms/croppad/array.py
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Original file line number Diff line number Diff line change
Expand Up @@ -397,9 +397,7 @@ def __init__(
data=roi_center, output_type=torch.Tensor, dtype=torch.int16, wrap_sequence=True
)
roi_size, *_ = convert_to_dst_type(src=roi_size, dst=roi_center, wrap_sequence=True)
roi_start_torch = maximum(
roi_center - floor_divide(roi_size, 2), torch.zeros_like(roi_center) # type: ignore
)
roi_start_torch = maximum(roi_center - floor_divide(roi_size, 2), torch.zeros_like(roi_center)) # type: ignore
roi_end_torch = maximum(roi_start_torch + roi_size, roi_start_torch)
else:
if roi_start is None or roi_end is None:
Expand Down
14 changes: 6 additions & 8 deletions monai/transforms/utils_create_transform_ims.py
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Original file line number Diff line number Diff line change
Expand Up @@ -520,13 +520,7 @@ def create_transform_im(
create_transform_im(RandKSpaceSpikeNoise, dict(prob=1, intensity_range=(10, 13)), data)
create_transform_im(
RandKSpaceSpikeNoised,
dict(
keys=CommonKeys.IMAGE,
global_prob=1,
prob=1,
common_sampling=True,
intensity_ranges={CommonKeys.IMAGE: (13, 15)},
),
dict(keys=CommonKeys.IMAGE, global_prob=1, prob=1, common_sampling=True, intensity_range=(13, 15)),
data,
)
create_transform_im(GibbsNoise, dict(alpha=0.8), data)
Expand Down Expand Up @@ -677,4 +671,8 @@ def create_transform_im(
KeepLargestConnectedComponentd, dict(keys=CommonKeys.LABEL, applied_labels=1), data_binary, is_post=True, ndim=2
)
create_transform_im(RandGridDistortion, dict(num_cells=3, prob=1.0, distort_limit=(-0.1, 0.1)), data)
create_transform_im(RandGridDistortiond, dict(keys=keys, num_cells=5, prob=1.0, distort_limit=(-0.1, 0.1)), data)
create_transform_im(
RandGridDistortiond,
dict(keys=keys, num_cells=4, prob=1.0, distort_limit=(-0.2, 0.2), mode=["bilinear", "nearest"]),
data,
)
4 changes: 2 additions & 2 deletions tests/test_rotated.py
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Expand Up @@ -92,7 +92,7 @@ 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)
self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 130)
self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 160)


class TestRotated3DXY(NumpyImageTestCase3D):
Expand Down Expand Up @@ -121,7 +121,7 @@ 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)
self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 130)
self.assertLessEqual(np.count_nonzero(expected != rotated["seg"][0]), 160)


if __name__ == "__main__":
Expand Down
4 changes: 3 additions & 1 deletion tests/test_transchex.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@

from monai.networks import eval_mode
from monai.networks.nets.transchex import Transchex
from tests.utils import skip_if_quick

TEST_CASE_TRANSCHEX = []
for drop_out in [0.4]:
Expand All @@ -42,7 +43,8 @@
TEST_CASE_TRANSCHEX.append(test_case)


class TestPatchEmbeddingBlock(unittest.TestCase):
@skip_if_quick
class TestTranschex(unittest.TestCase):
@parameterized.expand(TEST_CASE_TRANSCHEX)
def test_shape(self, input_param, expected_shape):
net = Transchex(**input_param)
Expand Down