[BUG] nibabel 5.3.0 breaks dcmmeta.py

[bpinsard]

Seems like changes here nipy/nibabel#1336 broke dcmstack dcmmeta.make_empty (FYI: @effigies ), which in turns causes heudiconv to fail too @yarikoptic as can be seen in recent PRs ( eg. nipy/heudiconv#791 ).

As dcmstack do not seem to pin specific version of nibabel as reqs, any fresh install is likely to trigger that bug.

    @classmethod
    def make_empty(klass, shape, affine, reorient_transform=None,
                   slice_dim=None):
        '''Make an empty DcmMetaExtension.
    
        Parameters
        ----------
        shape : tuple
            The shape of the data associated with this extension.
    
        affine : array
            The RAS affine for the data associated with this extension.
    
        reorient_transform : array
            The transformation matrix representing any reorientation of the
            data array.
    
        slice_dim : int
            The index of the slice dimension for the data associated with this
            extension
    
        Returns
        -------
        result : DcmMetaExtension
            An empty DcmMetaExtension with the required values set to the
            given arguments.
    
        '''
        result = klass(dcm_meta_ecode, '{}')
>       result._content['global'] = OrderedDict()
E       TypeError: 'str' object does not support item assignment

[effigies]

I think if you use self.get_content() instead of self._content throughout this class, then you should be able to continue as you were. I didn't really expect people to depend on the underscored variable and aimed to keep the public functions constant.

I could also cut a bug-fix release where I switch ._content back to the unmangled object and use some other private variable to refer to the byte serialization.

[effigies]

@bpinsard Could you try patching in nipy/nibabel#1378 and seeing if that resolves your issue?

[bpinsard]

All dcmstack tests are green with nibabel from that branch.

[bpinsard]

heudiconv tests are back to green too.