DeprecationWarning: get_data() is deprecated in favor of get_fdata()

[tashrifbillah]

/software/rocky9/tract_querier/scripts/tract_querier:138: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  img = labels_nii.get_data()
Calculating labels and crossings
/software/rocky9/tract_querier/scripts/tract_querier:173: DeprecationWarning: get_affine method is deprecated.
Please use the ``img.affine`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  affine_ijk_2_ras = labels_nii.get_affine()

@demianw , I can do some work on nibabel upgrade if you want. But the primary bottleneck is going to be your use of trackvis. Nibabel 5 no longer supports it: MIC-DKFZ/TractSeg#248 (comment). Do you have any idea to overcome this bottleneck?

Here are where you use trackvis:

tract_querier/tractography/__init__.py:from .trackvis import tractography_from_trackvis_file, tractography_to_trackvis_file
tract_querier/tractography/__init__.py:    'tractography_from_trackvis_file', 'tractography_to_trackvis_file',
tract_querier/tractography/__init__.py:        return tractography_from_trackvis_file(filename)
tract_querier/tractography/__init__.py:        return tractography_to_trackvis_file(filename, tractography, **kwargs)
tract_querier/tractography/tests/test_tractography.py:    tractography_from_trackvis_file, tractography_to_trackvis_file,
tract_querier/tractography/tests/test_tractography.py:    tractography_to_trackvis_file(
tract_querier/tractography/tests/test_tractography.py:    new_tractography = tractography_from_trackvis_file(fname)
tract_querier/tractography/trackvis.py:from nibabel import trackvis
tract_querier/tractography/trackvis.py:def tractography_to_trackvis_file(filename, tractography, affine=None, image_dimensions=None):
tract_querier/tractography/trackvis.py:    trk_header = trackvis.empty_header()
tract_querier/tractography/trackvis.py:    trackvis.aff_to_hdr(affine, trk_header, True, True)
tract_querier/tractography/trackvis.py:        raise ValueError("Image dimensions needed to save a trackvis file")
tract_querier/tractography/trackvis.py:                "Scalar data %s ignored as trackvis "
tract_querier/tractography/trackvis.py:    trackvis.write(filename, trk_tracts, trk_header, points_space='rasmm')
tract_querier/tractography/trackvis.py:def tractography_from_trackvis_file(filename):
tract_querier/tractography/trackvis.py:    tracts_and_data, header = trackvis.read(filename, points_space='rasmm')

[tashrifbillah]

I pushed up my deprecation avoiding changes here:
https://github.com/pnlbwh/tract_querier/commits/patch-1/