From 33ebd0ade8c82740d6bed7a87675e7192aa17617 Mon Sep 17 00:00:00 2001 From: UGBOMEH OGOCHUKWU WILLIAMS Date: Thu, 9 Apr 2026 12:14:16 +0100 Subject: [PATCH 1/2] Fix #8775: handle torch.Tensor input in compute_shape_offset np.array(spatial_shape) fails with PyTorch >= 2.9 when spatial_shape is a torch.Tensor, because PyTorch removed the non-tuple sequence indexing protocol from tensors in that release. Wrapping with tuple() first routes through __iter__, yielding scalar 0-d tensors that NumPy can consume via the scalar protocol. This makes the function compatible with torch.Tensor, np.ndarray, and plain sequence inputs alike. The caller in monai/transforms/spatial/functional.py (line 115) already passes a torch.Tensor, so this is a real-world breakage on PyTorch 2.9. Signed-off-by: UGBOMEH OGOCHUKWU WILLIAMS --- monai/data/utils.py | 2 +- tests/data/utils/test_compute_shape_offset.py | 49 +++++++++++++++++++ 2 files changed, 50 insertions(+), 1 deletion(-) create mode 100644 tests/data/utils/test_compute_shape_offset.py diff --git a/monai/data/utils.py b/monai/data/utils.py index 4e5a3bd7f6..d548ed7248 100644 --- a/monai/data/utils.py +++ b/monai/data/utils.py @@ -881,7 +881,7 @@ def compute_shape_offset( Default is False, using option 1 to compute the shape and offset. """ - shape = np.array(spatial_shape, copy=True, dtype=float) + shape = np.array(tuple(spatial_shape), copy=True, dtype=float) sr = len(shape) in_affine_ = convert_data_type(to_affine_nd(sr, in_affine), np.ndarray)[0] out_affine_ = convert_data_type(to_affine_nd(sr, out_affine), np.ndarray)[0] diff --git a/tests/data/utils/test_compute_shape_offset.py b/tests/data/utils/test_compute_shape_offset.py new file mode 100644 index 0000000000..4c63e9aca3 --- /dev/null +++ b/tests/data/utils/test_compute_shape_offset.py @@ -0,0 +1,49 @@ +# Copyright (c) MONAI Consortium +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# http://www.apache.org/licenses/LICENSE-2.0 +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from __future__ import annotations + +import unittest + +import numpy as np +import torch + +from monai.data.utils import compute_shape_offset + + +class TestComputeShapeOffset(unittest.TestCase): + + def setUp(self): + self.affine = np.eye(4) + + def test_numpy_array_input(self): + shape = np.array([64, 64, 64]) + out_shape, offset = compute_shape_offset(shape, self.affine, self.affine) + self.assertEqual(len(out_shape), 3) + + def test_list_input(self): + shape = [64, 64, 64] + out_shape, offset = compute_shape_offset(shape, self.affine, self.affine) + self.assertEqual(len(out_shape), 3) + + def test_torch_tensor_input(self): + shape = torch.tensor([64, 64, 64]) + out_shape, offset = compute_shape_offset(shape, self.affine, self.affine) + self.assertEqual(len(out_shape), 3) + + def test_identity_affines_preserve_shape(self): + shape = torch.tensor([32, 48, 16]) + out_shape, offset = compute_shape_offset(shape, self.affine, self.affine) + np.testing.assert_allclose(np.array(out_shape, dtype=float), shape.numpy().astype(float), atol=1e-5) + + +if __name__ == "__main__": + unittest.main() From dfdb87d8d79cf90cfacf5cfc7096e3d84374ba9c Mon Sep 17 00:00:00 2001 From: UGBOMEH OGOCHUKWU WILLIAMS Date: Thu, 9 Apr 2026 15:45:29 +0100 Subject: [PATCH 2/2] Address review feedback on #8812: add docstrings and fix unused variable - Add Google-style docstrings to class and all test methods to satisfy docstring coverage CI check (was 16.67%, needed 80%) - Replace unused `offset` variable with `_` in four test cases (RUF059) Signed-off-by: UGBOMEH OGOCHUKWU WILLIAMS --- tests/data/utils/test_compute_shape_offset.py | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/tests/data/utils/test_compute_shape_offset.py b/tests/data/utils/test_compute_shape_offset.py index 4c63e9aca3..d2dbd124f5 100644 --- a/tests/data/utils/test_compute_shape_offset.py +++ b/tests/data/utils/test_compute_shape_offset.py @@ -20,28 +20,39 @@ class TestComputeShapeOffset(unittest.TestCase): + """Unit tests for :func:`monai.data.utils.compute_shape_offset`.""" def setUp(self): + """Set up a 4x4 identity affine used across all test cases.""" self.affine = np.eye(4) def test_numpy_array_input(self): + """Verify compute_shape_offset accepts a numpy array as spatial_shape.""" shape = np.array([64, 64, 64]) - out_shape, offset = compute_shape_offset(shape, self.affine, self.affine) + out_shape, _ = compute_shape_offset(shape, self.affine, self.affine) self.assertEqual(len(out_shape), 3) def test_list_input(self): + """Verify compute_shape_offset accepts a plain list as spatial_shape.""" shape = [64, 64, 64] - out_shape, offset = compute_shape_offset(shape, self.affine, self.affine) + out_shape, _ = compute_shape_offset(shape, self.affine, self.affine) self.assertEqual(len(out_shape), 3) def test_torch_tensor_input(self): + """Verify compute_shape_offset accepts a torch.Tensor as spatial_shape. + + This path broke in PyTorch >= 2.9 because np.array() relied on the + non-tuple sequence indexing protocol that PyTorch removed. Wrapping with + tuple() fixes it. + """ shape = torch.tensor([64, 64, 64]) - out_shape, offset = compute_shape_offset(shape, self.affine, self.affine) + out_shape, _ = compute_shape_offset(shape, self.affine, self.affine) self.assertEqual(len(out_shape), 3) def test_identity_affines_preserve_shape(self): + """Verify that identity in/out affines produce an output shape matching the input.""" shape = torch.tensor([32, 48, 16]) - out_shape, offset = compute_shape_offset(shape, self.affine, self.affine) + out_shape, _ = compute_shape_offset(shape, self.affine, self.affine) np.testing.assert_allclose(np.array(out_shape, dtype=float), shape.numpy().astype(float), atol=1e-5)