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ENH: Add interface for fslorient #2955

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ENH: Add interface for fslorient #2955

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21 changes: 21 additions & 0 deletions nipype/interfaces/fsl/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1700,7 +1700,28 @@ def _gen_filename(self, name):
return self._list_outputs()['out_file']
return None


class FslOrientInputSpec(FSLCommandInputSpec):
in_file = File(exists=True, desc='input file', argstr='%s', position=2, mandatory=True)
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I would suggest adding copyfile=True, since this tool modifies the input file. This will only have an effect in workflows/nodes. (See https://nipype.readthedocs.io/en/latest/devel/interface_specs.html)

Suggested change
in_file = File(exists=True, desc='input file', argstr='%s', position=2, mandatory=True)
in_file = File(exists=True,
copyfile=True,
desc='input file',
argstr='%s',
position=2,
mandatory=True)

main_option = traits.Str(desc='main option', argstr='-%s', position=0, mandatory=True)
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Since this command takes a specific (and historically very stable) set of main options, it would be best to enumerate them. The current interface attempt available in SAMRI demonstrates how.

code = traits.Int(argstr='%d', desc='code for setsformcode', position=1)


class FslOrientOutputSpec(TraitedSpec):
out_file = File(desc = "out file", exists = True)


class FslOrient(FSLCommand):
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Please add a minimal usage example analogous to that seen in other interfaces in this module:

nipype/nipype/interfaces/fsl/utils.py

Line 220 in e722d61

Examples

_cmd = 'fslorient'
input_spec = FslOrientInputSpec
output_spec = FslOrientOutputSpec

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.in_file)
return outputs
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These three lines are over-indented.



class Reorient2StdInputSpec(FSLCommandInputSpec):
in_file = File(exists=True, mandatory=True, argstr="%s")
out_file = File(genfile=True, hash_files=False, argstr="%s")
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