ENH: Add copy() method to ArrayProxy

[effigies]

Small addition to ArrayProxy class to allow copying. Used in #1090, but not central to it.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (41e6dad) 92.24% compared to head (1c1845f) 92.24%.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1255   +/-   ##
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  Coverage   92.24%   92.24%           
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  Files          99       99           
  Lines       12452    12460    +8     
  Branches     2560     2561    +1     
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+ Hits        11486    11494    +8     
  Misses        643      643           
  Partials      323      323           

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[effigies]

@pauldmccarthy This is bound to interact with indexed gzip. If you have time for a quick read-through, I would appreciate your thoughts.

[pauldmccarthy]

Hi @effigies, apologies for the delay - I missed this mention.

On the surface, I think this looks fine. In the typical case where an ArrayProxy is created with a file path, and keep_file_open=True (rules 2 and 4 in the _should_keep_file_open docs), the two ArrayProxy instances will create independent ImageOpener instances and in turn independent IndexedGzipFile instances, so they will have nothing to do with each other.

In the less common case where an ArrayProxy is created with an IndexedGzipFile instance (rules 1 and 3 in the _should_keep_file_open docs), I think your lock sharing logic is a good idea.

If you like, you could add another (very rudimentary) test with something like this:

def test_copy_with_indexed_gzip_handle():

    import nibabel as nib

    indexed_gzip = pytest.importorskip('indexed_gzip')

    with InTemporaryDirectory():

        # ~24MB
        spec = ((50, 50, 50, 50), np.float32, 352, 1, 0)
        data = np.arange(np.prod(spec[0]), dtype=np.float32).reshape(spec[0])
        nib.Nifti1Image(data, np.eye(4)).to_filename('image.nii.gz')

        with indexed_gzip.IndexedGzipFile('image.nii.gz') as gzf:
            ap1 = nib.arrayproxy.ArrayProxy(gzf, spec)
            ap2 = ap1.copy()
            assert ap1.file_like is gzf
            assert ap2.file_like is gzf
            assert (ap1[ 0,  0,  0, :] == ap2[ 0,  0,  0, :]).all()
            assert (ap1[-1, -1, -1, :] == ap2[-1, -1, -1, :]).all()

[effigies]

Thanks for the review and test! If you think of a more strenuous test or something we can do upstream, happy to discuss more.

[effigies]

Test failure unrelated.