ENH: generate_label_classes_crop_centers: warn only if ratio of missing class is not set to 0 #7602
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ng class is not set to 0
…[email protected]> I, Szabolcs Botond Lorincz Molnar <[email protected]>, hereby add my Signed-off-by to this commit: 58d69c0 Signed-off-by: Szabolcs Botond Lorincz Molnar <[email protected]>
KumoLiu
reviewed
Apr 1, 2024
|
/build |
KumoLiu
approved these changes
Apr 2, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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 byRandCropByLabelClassestransform.Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.Notes regarding tests
Some tests were failing, see details:
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)