Cleanup Warnings

[garrettwrong]

Some of our numerical tools have had major releases and are now triggering some more warnings. I've captured current warnings for 3.10 on caf below.

========================================================= warnings summary ==========================================================
tests/test_FBbasis3D.py: 4 warnings
tests/test_FBbasis2D.py: 70 warnings
tests/test_FLEbasis2D.py: 18 warnings
tests/test_FFBbasis2D.py: 52 warnings
tests/test_FFBbasis3D.py: 4 warnings
tests/test_covar2d_denoiser.py: 664 warnings
tests/test_steerable_bases_2d.py: 10 warnings
tests/test_FPSWFbasis2D.py: 1 warning
tests/test_PSWFbasis2D.py: 1 warning
  /scratch/gbwright/Projects/ASPIRE-Python.np2/src/aspire/basis/basis.py:583: DeprecationWarning: '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`.
    v[isample], info = cg(operator, b, tol=tol, atol=atol)

tests/test_image.py::test_corrupt_mrc_load
  /scratch/gbwright/miniconda3/envs/np2_310/lib/python3.10/site-packages/numpy/core/_methods.py:176: RuntimeWarning: overflow encountered in multiply
    x = um.multiply(x, x, out=x)

tests/test_mean_estimator.py: 24 warnings
tests/test_mean_estimator_boosting.py: 12 warnings
tests/test_weighted_mean_estimator.py: 24 warnings
tests/test_array_image_source.py: 2 warnings
  /scratch/gbwright/Projects/ASPIRE-Python.np2/src/aspire/reconstruction/mean.py:248: DeprecationWarning: '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`.
    x, info = cg(

tests/test_fourier_correlation.py: 32 warnings
tests/test_micrograph_source.py: 8 warnings
tests/test_image.py: 1 warning
tests/test_simulation.py: 3 warnings
  /scratch/gbwright/Projects/ASPIRE-Python.np2/tests/test_utils.py:403: MatplotlibDeprecationWarning: Auto-close()ing of figures upon backend switching is deprecated since 3.8 and will be removed in 3.10.  To suppress this warning, explicitly call plt.close('all') first.
    matplotlib.use(backend)

tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float32'>]
  /scratch/gbwright/Projects/ASPIRE-Python.np2/src/aspire/utils/resolution_estimation.py:380: UserWarning: No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
    plt.legend(title=f"Method: {self.method}")

tests/test_orient_symmetric.py: 192 warnings
  /scratch/gbwright/Projects/ASPIRE-Python.np2/tests/test_orient_symmetric.py:195: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    dist[i] = Rotation.angle_dist(estimate, Rii_gt)

tests/test_orient_symmetric.py: 2970 warnings
  /scratch/gbwright/Projects/ASPIRE-Python.np2/tests/test_orient_symmetric.py:641: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    clmatrix_gt[idx, i, j] = CLSymmetryC3C4.cl_angles_to_ind(

tests/test_orient_symmetric.py: 2970 warnings
  /scratch/gbwright/Projects/ASPIRE-Python.np2/tests/test_orient_symmetric.py:644: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    clmatrix_gt[idx, j, i] = CLSymmetryC3C4.cl_angles_to_ind(

tests/test_covar2d_denoiser.py: 15 warnings
  /scratch/gbwright/Projects/ASPIRE-Python.np2/src/aspire/basis/steerable.py:524: UserWarning: BlkDiagMatrix.from_dense truncating values exceeding 0.001
    filt = BlkDiagMatrix.from_dense(

tests/test_orient_symmetric.py: 1932 warnings
  /scratch/gbwright/Projects/ASPIRE-Python.np2/tests/test_orient_symmetric.py:158: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    dist[s] = np.minimum(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

Most of these look straightforward. After they're completed, should scan 3.9 and 3.11 as well. At this time my 3.8 only reports the internal BlkDiagMatrix.from_dense warning.

[j-c-c]

Going to work on these warnings. Here is the current list from 3.8 - 3.10.

Warnings from 3.8

tests/test_sinogram.py: 12 warnings
  /scratch/jc5485/miniconda3/envs/warnings_3.8/lib/python3.8/site-packages/skimage/transform/radon_transform.py:75: UserWarning: Radon transform: image must be zero outside the reconstruction circle
    warn('Radon transform: image must be zero outside the '

tests/test_covar2d_denoiser.py: 15 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.8/src/aspire/basis/steerable.py:524: UserWarning: BlkDiagMatrix.from_dense truncating values exceeding 0.001
    filt = BlkDiagMatrix.from_dense(

Warnings from 3.9

tests/test_FFBbasis2D.py: 52 warnings
tests/test_FBbasis2D.py: 70 warnings
tests/test_FFBbasis3D.py: 4 warnings
tests/test_FLEbasis2D.py: 18 warnings
tests/test_FBbasis3D.py: 4 warnings
tests/test_covar2d_denoiser.py: 664 warnings
tests/test_mean_estimator.py: 24 warnings
tests/test_mean_estimator_boosting.py: 11 warnings
tests/test_steerable_bases_2d.py: 10 warnings
tests/test_FPSWFbasis2D.py: 1 warning
tests/test_PSWFbasis2D.py: 1 warning
tests/test_weighted_mean_estimator.py: 24 warnings
tests/test_array_image_source.py: 2 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/numeric/scipy.py:17: DeprecationWarning: 'scipy.sparse.linalg.cg' keyword argu
ment `tol` is deprecated in favor of `rtol` and will be removed in SciPy v1.14.0. Until then, if set, it will override `rtol`.
    return scipy.sparse.linalg.cg(*args, **kwargs)

tests/test_fourier_correlation.py: 32 warnings
tests/test_image.py: 1 warning
tests/test_micrograph_source.py: 8 warnings
tests/test_simulation.py: 3 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_utils.py:403: MatplotlibDeprecationWarning: Auto-close()ing of figures upon ba
ckend switching is deprecated since 3.8 and will be removed in 3.10.  To suppress this warning, explicitly call plt.close('all') first.
    matplotlib.use(backend)

tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float32'>]
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/utils/resolution_estimation.py:380: UserWarning: No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
    plt.legend(title=f"Method: {self.method}")

tests/test_micrograph_source.py::test_rectangular_micrograph_source_files
  /scratch/jc5485/miniconda3/envs/warnings_3.9/lib/python3.9/site-packages/mrcfile/mrcobject.py:626: RuntimeWarning: Data array contains NaN values
    warnings.warn("Data array contains NaN values", RuntimeWarning)

tests/test_sinogram.py: 60 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/image/image.py:243: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.
    return aspire.sinogram.Sinogram(xp.asnumpy(image_rt))

tests/test_sinogram.py: 20 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/sinogram/sinogram.py:62: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.
    return self.__class__(self._data[key])

tests/test_sinogram.py: 22 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/sinogram/sinogram.py:90: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.
    return self.__class__(self._data.reshape(*shape, *self._data.shape[-2:]))

tests/test_sinogram.py: 12 warnings
  /scratch/jc5485/miniconda3/envs/warnings_3.9/lib/python3.9/site-packages/skimage/transform/radon_transform.py:74: UserWarning: Radon transform: image must be zero outside the reconstruction circle
    warn(

tests/test_covar2d_denoiser.py: 15 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/basis/steerable.py:524: UserWarning: BlkDiagMatrix.from_dense truncating values exceeding 0.001
    filt = BlkDiagMatrix.from_dense(

tests/test_orient_symmetric.py: 2970 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_orient_symmetric.py:641: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    clmatrix_gt[idx, i, j] = CLSymmetryC3C4.cl_angles_to_ind(   

tests/test_orient_symmetric.py: 2970 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_orient_symmetric.py:644: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    clmatrix_gt[idx, j, i] = CLSymmetryC3C4.cl_angles_to_ind(   

tests/test_orient_symmetric.py: 1932 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_orient_symmetric.py:158: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    dist[s] = np.minimum(

tests/test_orient_symmetric.py: 192 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_orient_symmetric.py:195: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    dist[i] = Rotation.angle_dist(estimate, Rii_gt)

Warnings from 3.10

tests/test_fourier_correlation.py: 32 warnings
tests/test_image.py: 1 warning
tests/test_micrograph_source.py: 8 warnings
tests/test_simulation.py: 3 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_utils.py:403: MatplotlibDeprecationWarning: Auto-close()ing of figures upon backend switching is deprecated since 3.8 and will be removed in 3.10.  To suppress this warning, explicitly call plt.close('all') first.
    matplotlib.use(backend)

tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float32'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float64'>]
tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float32'>]
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/utils/resolution_estimation.py:380: UserWarning: No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
    plt.legend(title=f"Method: {self.method}")

tests/test_sinogram.py: 60 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/image/image.py:243: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.
    return aspire.sinogram.Sinogram(xp.asnumpy(image_rt))

tests/test_sinogram.py: 20 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/sinogram/sinogram.py:62: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.
    return self.__class__(self._data[key])

tests/test_sinogram.py: 22 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/sinogram/sinogram.py:90: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.
    return self.__class__(self._data.reshape(*shape, *self._data.shape[-2:]))

tests/test_sinogram.py: 12 warnings
  /scratch/jc5485/miniconda3/envs/warnings_3.10/lib/python3.10/site-packages/skimage/transform/radon_transform.py:74: UserWarning: Radon transform: image must be zero outside the reconstruction circle
    warn(

tests/test_covar2d_denoiser.py: 15 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/basis/steerable.py:524: UserWarning: BlkDiagMatrix.from_dense truncating values exceeding 0.001
    filt = BlkDiagMatrix.from_dense(

tests/test_orient_symmetric.py: 1932 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_orient_symmetric.py:158: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    dist[s] = np.minimum(

tests/test_orient_symmetric.py: 192 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_orient_symmetric.py:195: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    dist[i] = Rotation.angle_dist(estimate, Rii_gt)

tests/test_orient_symmetric.py: 2970 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_orient_symmetric.py:641: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    clmatrix_gt[idx, i, j] = CLSymmetryC3C4.cl_angles_to_ind(

tests/test_orient_symmetric.py: 2970 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_orient_symmetric.py:644: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    clmatrix_gt[idx, j, i] = CLSymmetryC3C4.cl_angles_to_ind(

[j-c-c]

Closed by #1170