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cg() got an unexpected keyword argument 'tol' #7896

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KumoLiu opened this issue Jul 2, 2024 · 0 comments · Fixed by #7897
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cg() got an unexpected keyword argument 'tol' #7896

KumoLiu opened this issue Jul 2, 2024 · 0 comments · Fixed by #7897
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KumoLiu commented Jul 2, 2024 

======================================================================
ERROR: test_against_official_code_using_cg (tests.test_ultrasound_confidence_map_transform.TestUltrasoundConfidenceMapTransform)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/MONAI/MONAI/tests/test_ultrasound_confidence_map_transform.py", line 699, in test_against_official_code_using_cg
    output = transform(input_img)
  File "/home/runner/work/MONAI/MONAI/monai/transforms/intensity/array.py", line 2878, in __call__
    conf_map: NdarrayOrTensor = self._compute_conf_map(img_np, mask_np)
  File "/home/runner/work/MONAI/MONAI/monai/data/ultrasound_confidence_map.py", line 381, in __call__
    map_: NDArray = self.confidence_estimation(data, seeds, labels, self.beta, self.gamma)
  File "/home/runner/work/MONAI/MONAI/monai/data/ultrasound_confidence_map.py", line 338, in confidence_estimation
    x = self._solve_linear_system(lap, rhs)
  File "/home/runner/work/MONAI/MONAI/monai/data/ultrasound_confidence_map.py", line 288, in _solve_linear_system
    x, _ = cg(lap, rhs, tol=self.cg_tol, maxiter=self.cg_maxiter, M=m)
TypeError: cg() got an unexpected keyword argument 'tol'
@KumoLiu KumoLiu added the bug Something isn't working label Jul 2, 2024
KumoLiu added a commit to KumoLiu/MONAI that referenced this issue Jul 2, 2024
@KumoLiu
fix Project-MONAI#7896
dffd772 
Signed-off-by: YunLiu <[email protected]>
@KumoLiu KumoLiu mentioned this issue Jul 2, 2024
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ericspod pushed a commit that referenced this issue Jul 6, 2024
@KumoLiu @pre-commit-ci
Fix deprecated argument in 'scipy.sparse.linalg.cg' (#7897)
64ea76d 
Fixes #7896 

### Description

- 'scipy.sparse.linalg.cg' keyword argument `tol` is deprecated in favor
of `rtol` and will be removed in SciPy v1.14.0. Until then, if set, it
will override `rtol`. So update to use `rtol` in `cg`.

- Drop python 3.8 test in packaging and premerge-gpu-test.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: YunLiu <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Fix deprecated argument in 'scipy.sparse.linalg.cg' KumoLiu/MONAI
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