FIX: Reuse _gen_filename logic in ants.LaplacianThickness

[yarikoptic]

Without this fix it

• looks for the wrong file whenever output_name is not provided (Closes genfile'ed output name "is not remembered" to be used later (in self.aggregate_outputs)? #2733)
• keeps looking for the wrong file even if name is provided

[effigies]

Any chance of a test?

[yarikoptic]

oh, there are real tests for the interfaces? ;) what would be the best example to follow?

[oesteban]

Can't we just use name_source for this?

 class LaplacianThicknessInputSpec(ANTSCommandInputSpec):
     input_wm = File(
         argstr='%s',
         mandatory=True,
         copyfile=True,
         desc='white matter segmentation image',
         position=1)
     input_gm = File(
         argstr='%s',
         mandatory=True,
         copyfile=True,
         desc='gray matter segmentation image',
         position=2)
     output_image = File(
         desc='name of output file',
         argstr='%s',
         position=3,
         name_source=['input_wm'],
         name_template='%s_thickness',
         keep_extension=True,
         hash_files=False)
     smooth_param = traits.Float(argstr='smoothparam=%d', desc='', position=4)
     prior_thickness = traits.Float(
         argstr='priorthickval=%d', desc='', position=5)
     dT = traits.Float(argstr='dT=%d', desc='', position=6)
     sulcus_prior = traits.Bool(argstr='use-sulcus-prior', desc='', position=7)
     opt_tolerance = traits.Float(
         argstr='optional-laplacian-tolerance=%d', desc='', position=8)
 
 
 class LaplacianThicknessOutputSpec(TraitedSpec):
     output_image = File(exists=True, desc='Cortical thickness')
 
 
 class LaplacianThickness(ANTSCommand):
     """Calculates the cortical thickness from an anatomical image
 
     Examples
     --------
 
     >>> from nipype.interfaces.ants import LaplacianThickness
     >>> cort_thick = LaplacianThickness()
     >>> cort_thick.inputs.input_wm = 'white_matter.nii.gz'
     >>> cort_thick.inputs.input_gm = 'gray_matter.nii.gz'
     >>> cort_thick.cmdline
     'LaplacianThickness white_matter.nii.gz gray_matter.nii.gz white_matter_thickness.nii.gz'

     >>> cort_thick.inputs.output_image = 'output_thickness.nii.gz'
     >>> cort_thick.cmdline
     'LaplacianThickness white_matter.nii.gz gray_matter.nii.gz output_thickness.nii.gz'
 
     """
 
     _cmd = 'LaplacianThickness'
     input_spec = LaplacianThicknessInputSpec
     output_spec = LaplacianThicknessOutputSpec

(and both _gen_filename and _list_outputs definitions can go away). We would need to re-generate specs (make spec).

EDITED: added a doctest (hopefully to cover @effigies' request)

[effigies]

👍 to @oesteban's suggestion, including doctest. Consistency with the post-run outputs should already be tested in a more generic context (hopefully with a cheap interface).

[yarikoptic]

Guys, I am not sure if I am to do anything, or may be this could get merged and then altogether or instead be replaced with @oesteban 's version?

[oesteban]

I'm happy with whatever you prefer. Or if you want me to push to this branch. I just would like to see that we abandon gen_filename and genfile at some point in time 👍

[effigies]

@oesteban We can move to name_source in a separate PR.