Make the RandCropByLabelClassesd warning only show when ratio for a missing class is set to nonzero #7594
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…ng class is not set to 0 (#7602) Fixes #7594 ### Description Only warn users that the ratio of a missing class is set to 0, when it wasn't already set to 0 by the user, in `generate_label_classes_crop_centers`, function being used by `RandCropByLabelClasses` transform. ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`.⚠️ See notes - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`.⚠️ See notes - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. ### Notes regarding tests Some tests were failing, see details: <details> ====================================================================== ERROR: test_cuda_0_2_batches_1_dimensions_1_channels_2_classes_2_mixtures (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 288, in test_cuda gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/networks/layers/gmm.py", line 44, in __init__ self.compiled_extension = load_module( File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_1_2_1_Linux_3_10_12_22_12_1' ====================================================================== ERROR: test_cuda_1_1_batches_1_dimensions_5_channels_2_classes_1_mixtures (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 288, in test_cuda gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/networks/layers/gmm.py", line 44, in __init__ self.compiled_extension = load_module( File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_5_2_1_Linux_3_10_12_22_12_1' ====================================================================== ERROR: test_cuda_2_1_batches_2_dimensions_2_channels_4_classes_4_mixtures (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 288, in test_cuda gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/networks/layers/gmm.py", line 44, in __init__ self.compiled_extension = load_module( File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_2_4_1_Linux_3_10_12_22_12_1' ====================================================================== ERROR: test_cuda_3_1_batches_3_dimensions_1_channels_2_classes_1_mixtures (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 288, in test_cuda gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/networks/layers/gmm.py", line 44, in __init__ self.compiled_extension = load_module( File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_1_2_1_Linux_3_10_12_22_12_1_v1' ====================================================================== ERROR: test_load (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 311, in test_load load_module("gmm", {"CHANNEL_COUNT": 2, "MIXTURE_COUNT": 2, "MIXTURE_SIZE": 3}, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_2_2_3_Linux_3_10_12_22_12_1' ====================================================================== ERROR: test_spacing_35 (tests.test_spacing.TestSpacingCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_spacing.py", line 289, in test_spacing res: MetaTensor = tr(**call_param) # type: ignore File "/home/szabolcslorincz/MONAI/monai/transforms/spatial/array.py", line 525, in __call__ data_array = self.sp_resample( File "/home/szabolcslorincz/MONAI/monai/transforms/spatial/array.py", line 223, in __call__ return spatial_resample( File "/home/szabolcslorincz/MONAI/monai/transforms/spatial/functional.py", line 178, in spatial_resample img = affine_xform(img.unsqueeze(0), theta=xform.to(img), spatial_size=spatial_size).squeeze(0) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl return self._call_impl(*args, **kwargs) File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl return forward_call(*args, **kwargs) File "/home/szabolcslorincz/MONAI/monai/networks/layers/spatial_transforms.py", line 584, in forward grid = nn.functional.affine_grid(theta=theta[:, :sr], size=list(dst_size), align_corners=self.align_corners) File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/nn/functional.py", line 4418, in affine_grid return torch.affine_grid_generator(theta, size, align_corners) torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 840.00 MiB. GPU 0 has a total capacity of 8.00 GiB of which 0 bytes is free. Including non-PyTorch memory, this process has 17179869184.00 GiB memory in use. Of the allocated memory 6.47 GiB is allocated by PyTorch, and 156.63 MiB is reserved by PyTorch but unallocated. If reserved but unallocated memory is large try setting PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True to avoid fragmentation. See documentation for Memory Management (https://pytorch.org/docs/stable/notes/cuda.html#environment-variables) ====================================================================== FAIL: test_seg_res_net_1_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 108, in test_seg_res_net onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 233543 / 1451520 (16.1%) Greatest absolute difference: 0.0014852285385131836 at index (0, 19, 12, 13, 22) (up to 0.0001 allowed) Greatest relative difference: 589.0405883789062 at index (0, 32, 21, 16, 15) (up to 0.001 allowed) ====================================================================== FAIL: test_unet_4_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 57, in test_unet onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 6705 / 49152 (13.6%) Greatest absolute difference: 0.0015408992767333984 at index (11, 0, 21, 27) (up to 0.0001 allowed) Greatest relative difference: 51.80112838745117 at index (14, 0, 25, 19) (up to 0.001 allowed) ====================================================================== FAIL: test_unet_5_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 57, in test_unet onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 6218 / 49152 (12.7%) Greatest absolute difference: 0.0015670061111450195 at index (2, 0, 23, 14) (up to 0.0001 allowed) Greatest relative difference: 7.987473964691162 at index (8, 0, 27, 8) (up to 0.001 allowed) ====================================================================== FAIL: test_unet_6_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 57, in test_unet onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 6743 / 49152 (13.7%) Greatest absolute difference: 0.0015552043914794922 at index (1, 1, 9, 11) (up to 0.0001 allowed) Greatest relative difference: 2.0317020416259766 at index (11, 0, 19, 21) (up to 0.001 allowed) ====================================================================== FAIL: test_unet_7_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 57, in test_unet onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 6823 / 49152 (13.9%) Greatest absolute difference: 0.0018431544303894043 at index (10, 0, 9, 19) (up to 0.0001 allowed) Greatest relative difference: 4.297887325286865 at index (13, 0, 12, 13) (up to 0.001 allowed) ====================================================================== FAIL: test_shape_2 (tests.test_multi_scale.TestMultiScale) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_multi_scale.py", line 59, in test_shape np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, rtol=1e-5) File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/numpy/testing/_private/utils.py", line 1504, in assert_allclose assert_array_compare(compare, actual, desired, err_msg=str(err_msg), File "/usr/lib/python3.10/contextlib.py", line 79, in inner return func(*args, **kwds) File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/numpy/testing/_private/utils.py", line 797, in assert_array_compare raise AssertionError(msg) AssertionError: Not equal to tolerance rtol=1e-05, atol=0 Mismatched elements: 1 / 1 (100%) Max absolute difference: 0. Max relative difference: 0. x: array(0.715212, dtype=float32) y: array(0.715228) ---------------------------------------------------------------------- Ran 14392 tests in 2252.916s FAILED (failures=6, errors=6, skipped=450) --------- Signed-off-by: Szabolcs Botond Lorincz Molnar <szabolcs.lorincz@mvision.ai> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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Is your feature request related to a problem? Please describe.
Warnings such as
no available indices of class 1 to crop, set the crop ratio of this class to zero.appear even when ratios is already set to 0 for the missing class 1.Describe the solution you'd like
I would suggest that if ratio for a class is already 0 set by the user, then such warnings should not be printed.
I would like to see something similar:
Describe alternatives you've considered
Suppressing such warnings could be an option too, but I think the other option would be friendlier.
Additional context
Found slightly related issue and PR: #6094 #6121 , but it's not completely the same.
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