Skip to content

BUG: fixed wrong space directions interpretation in nrrd reader #8091

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
KumoLiu merged 1 commit into from
Sep 18, 2024
Merged

BUG: fixed wrong space directions interpretation in nrrd reader #8091

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion monai/data/image_reader.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1359,7 +1359,7 @@ def _get_affine(self, header: dict) -> np.ndarray:
x, y = direction.shape
affine_diam = min(x, y) + 1
affine: np.ndarray = np.eye(affine_diam)
affine[:x, :y] = direction
affine[:x, :y] = direction.T
affine[: (affine_diam - 1), -1] = origin # len origin is always affine_diam - 1
return affine

Expand Down
8 changes: 6 additions & 2 deletions tests/test_nrrd_reader.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,8 @@
"dimension": 4,
"space": "left-posterior-superior",
"sizes": [3, 4, 4, 1],
"space directions": [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]],
"space origin": [0.0, 0.0, 0.0],
"space directions": [[0.7, 0.0, 0.0], [0.0, 0.0, -0.8], [0.0, 0.9, 0.0]],
"space origin": [1.0, 5.0, 20.0],
},
]

Expand Down Expand Up @@ -110,6 +110,10 @@ def test_read_with_header(self, data_shape, filename, expected_shape, dtype, ref
np.testing.assert_allclose(image_array, test_image)
self.assertIsInstance(image_header, dict)
self.assertTupleEqual(tuple(image_header["spatial_shape"]), expected_shape)
np.testing.assert_allclose(
image_header["affine"],
np.array([[-0.7, 0.0, 0.0, -1.0], [0.0, 0.0, -0.9, -5.0], [0.0, -0.8, 0.0, 20.0], [0.0, 0.0, 0.0, 1.0]]),
)

@parameterized.expand([TEST_CASE_8])
def test_read_with_header_index_order_c(self, data_shape, filename, expected_shape, dtype, reference_header):
Expand Down