Ensure Reorient2Std output is compressed or uncompressed as per output_type trait.

nipype_fixed_reorient2std.py

#!/usr/bin/env python

"""
Ensure Reorient2Std output is compressed or uncompressed as per output_type trait.

Notes
-----
Works around possible fslreorient2std bug: https://github.com/nipy/nipype/issues/1683
"""

import logging
import os

from nipype.interfaces.fsl import Reorient2Std

iflogger = logging.getLogger('interface')

class FixedReorient2Std(Reorient2Std):
    def _run_wrapper(self, runtime):
        runtime = super(FixedReorient2Std, self)._run_wrapper(runtime)

        # The absence of the output file is a sign that the input may have been oriented and
        # the requested output type differs from that of the actually generated output file:
        out_file = self._list_outputs()['out_file']
        if not os.path.exists(out_file):
            # Input oriented and uncompressed, but compressed output requested:
            if self._output_type == 'NIFTI_GZ' and os.path.exists(os.path.splitext(out_file)[0]):
                iflogger.debug('explicitly compressing %s' % os.path.splitext(out_file)[0])
                os.system('gzip %s' % os.path.splitext(out_file)[0])

            # Input oriented and compressed, but uncompressed output requested:
            elif self._output_type == 'NIFTI' and os.path.exists(out_file+'.gz'):
                iflogger.debug('explicitly uncompressing %s' % (out_file+'.gz'))
                os.system('gunzip %s' % (out_file+'.gz'))
        
        return runtime

if __name__ == '__main__':

    # To test, obtain MNI152_T1_2mm.nii.gz from FSL distro or some other source,
    # uncompress with gunzip -k, and rename the uncompressed and compressed files to
    # oriented1.nii and oriented2.nii.gz.
    
    # This should still generate a compressed file ..
    r = FixedReorient2Std(in_file='oriented1.nii', output_type='NIFTI_GZ')
    r.run()

    # .. and this should generate an uncompressed file:
    r = FixedReorient2Std(in_file='oriented2.nii.gz', output_type='NIFTI')
    r.run()