[WIP] Major refactor of input/output specs and autonaming #1240
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oesteban
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oesteban
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| '--outformat is set to spline the format will be a (4D) file of spline ' | ||
| 'coefficients.')) | ||
| out_file = File( | ||
| argstr='--out=%s', position=-1, name_source=['in_file'], name_template='%s_coeffs.nii', keep_extension=True, |
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why are we forcing the output to be nifti here?
|
please rebase/merge master - we have fixed the CircleCI tests |
…ipype into enh/NameSourceInBaseInterface
oesteban
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| @@ -665,14 +534,122 @@ def _run_interface(self, runtime): | |||
| nrows.append(mc_in.shape[0]) | |||
| matrix = self._get_spm_submatrix(spmmat, sessidx, rows) | |||
| self._stimcorr_core(motparamlist[i], intensityfiles[i], | |||
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Codacy only found this?? Then it's useless! :P
Seriously, this is still very preliminary. I am coding with the pylint on, so I also address these issues. I'll let you know when this is ready.
BTW, with this refactoring, we get rid of the infamous _list_outputs :)
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Make name_source available at BaseInterface level
This PR enables the functionality of name_source for any interface derived from BaseInterface. Previously, it only worked for CommandLine interfaces.
There's some previous discussion about this issue here #573.
And we started working on this from here #1234.
I have moved the old
_filename_from_sourceinCommandLinetoBaseInterface, with the new name of_resolve_namesource.The
run()method andcmdlineinCommandLinecall a wrapper to that function named_update_autonames. This must be done AFTER mandatory inputs are checked.Regarding outputs, I set the output values in
aggregate_outputs. I'm not 100% sure this is a good call though.TODO list
_list_outputsnipype.algorithms.misc.Gunzip)nipype.algorithms.misc.ModifyAffine)nipype.algorithms.misc.Matlab2CSV)List of interfaces that should be updated when this PR works