ENH: Add interface for fslorient #2955
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Pasted it above 'Reorient2Std'.
| out_file = File(desc = "out file", exists = True) | ||
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| 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
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| class FslOrientInputSpec(FSLCommandInputSpec): | ||
| in_file = File(exists=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.
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Hi @felixsc1, I wonder if you have some time to address @TheChymera's suggestions? I've also made a couple.
| @@ -1700,7 +1700,28 @@ def _gen_filename(self, name): | |||
| return self._list_outputs()['out_file'] | |||
| return None | |||
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| 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)
| 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) |
| 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.
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Hi @felixsc1, we're aiming for a release in the next week or so, if you'd like to try to get this in by then. Please let us know if you need any help. |
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Hi @felixsc1, sorry to do this to you, but we just merged some pretty huge changes. Could you re-apply these changes on the latest Please let me know if you need any help or clarifications. |
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This pull request is "orphaned," which means it has been deemed to be abandoned by its original author. Orphaned pull requests have not been rejected, and we hope that if a user sees one that will meet their needs with a little work, that they will fork it and open a new pull request (or, in the case of the original author, reopen the original PR). We ask that all adopted PRs be updated to merge or rebase the current master. If you would like to adopt a PR and need help getting started, any of a number of contributors will be happy to help. |
Summary
Simple interface for fslorient.
Input arguments:
Acknowledgment