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Reverse ITK spatial shape #1045

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Merged
wyli merged 11 commits into from
Sep 17, 2020
Merged

Reverse ITK spatial shape #1045

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59ba32d
Merge pull request #86 from Project-MONAI/master
Nic-Ma Jul 17, 2020
10e95c4
Merge pull request #136 from Project-MONAI/master
Nic-Ma Sep 8, 2020
3b9280b
Merge pull request #137 from Project-MONAI/master
Nic-Ma Sep 8, 2020
8f679cc
Merge pull request #138 from Project-MONAI/master
Nic-Ma Sep 10, 2020
b430bac
Merge pull request #139 from Project-MONAI/master
Nic-Ma Sep 11, 2020
468a6bf
Merge pull request #140 from Project-MONAI/master
Nic-Ma Sep 14, 2020
9e476ca
Merge pull request #141 from Project-MONAI/master
Nic-Ma Sep 16, 2020
08da9df
[DLMED] update itk spatial shape
Nic-Ma Sep 16, 2020
fdbdb21
Merge branch 'master' into update-itk-spatial-shape
wyli Sep 17, 2020
f3a5c23
update test case
wyli Sep 17, 2020
3808b22
[MONAI] python code formatting
monai-bot Sep 17, 2020
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4 changes: 3 additions & 1 deletion monai/data/image_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -227,7 +227,9 @@ def _get_spatial_shape(self, img) -> Sequence:
img: a ITK image object loaded from a image file.

"""
return list(itk.size(img))
shape = list(itk.size(img))
shape.reverse()
return shape

def _get_array_data(self, img) -> np.ndarray:
"""
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4 changes: 2 additions & 2 deletions tests/test_load_image.py
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Expand Up @@ -128,6 +128,7 @@ def test_itk_dicom_series_reader(self, input_param, filenames, expected_shape):
),
),
self.assertTupleEqual(result.shape, expected_shape)
self.assertTupleEqual(tuple(header["spatial_shape"]), expected_shape)

def test_load_png(self):
spatial_size = (256, 256)
Expand All @@ -144,7 +145,6 @@ def test_load_png(self):

def test_register(self):
spatial_size = (32, 64, 128)
expected_shape = (128, 64, 32)
test_image = np.random.rand(*spatial_size)
with tempfile.TemporaryDirectory() as tempdir:
filename = os.path.join(tempdir, "test_image.nii.gz")
Expand All @@ -154,7 +154,7 @@ def test_register(self):
loader = LoadImage(image_only=False)
loader.register(ITKReader())
result, header = loader(filename)
self.assertTupleEqual(tuple(header["spatial_shape"]), expected_shape)
self.assertTupleEqual(tuple(header["spatial_shape"]), spatial_size)
self.assertTupleEqual(result.shape, spatial_size)

def test_kwargs(self):
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3 changes: 1 addition & 2 deletions tests/test_load_imaged.py
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Expand Up @@ -42,7 +42,6 @@ def test_shape(self, input_param, expected_shape):

def test_register(self):
spatial_size = (32, 64, 128)
expected_shape = (128, 64, 32)
test_image = np.random.rand(*spatial_size)
with tempfile.TemporaryDirectory() as tempdir:
filename = os.path.join(tempdir, "test_image.nii.gz")
Expand All @@ -52,7 +51,7 @@ def test_register(self):
loader = LoadImaged(keys="img")
loader.register(ITKReader())
result = loader({"img": filename})
self.assertTupleEqual(tuple(result["img_meta_dict"]["spatial_shape"]), expected_shape)
self.assertTupleEqual(tuple(result["img_meta_dict"]["spatial_shape"]), spatial_size)
self.assertTupleEqual(result["img"].shape, spatial_size)


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