ENH: Re-enable spm.Realign to take lists of lists of files

[effigies]

Fixes #2406. Essentially reverts #2375, but using InputMultiPath instead of Either.

Changes proposed in this pull request

• Re-enables spm.Realign to take lists of lists, using nested InputMultiPaths.

[effigies]

Before working on these tests, is there a semantic difference between [['in_fileA.nii', 'in_fileB.nii']] and [['in_fileA.nii'], ['in_fileB.nii']], and which would be the correct interpretation of ['in_fileA.nii', 'in_fileB.nii']?

[effigies]

@mgxd @djarecka I'm undoing your consensus here, so I'd appreciate your input.

@satra Looks like you initially implemented support for a series of 3D files for Realign, so you might understand better than us the best way to go about this.

[djarecka]

@effigies - i will take a look later today, but i'm still not sure how my changes could be responsible for issue with ver 0.13... but will read more about the issue.

[mgxd]

I'm also not sure how this would affect version 0.13 - however I would prefer the interface to work as intended and raise a cryptic error message rather than vice-versa. perhaps we should also add an additional realign test that handles a list of lists as input?

[satra]

this was the original formulation:

nipype/nipype/interfaces/spm/preprocess.py

Line 122 in 8946bca

in_files = InputMultiPath(traits.Either(traits.List(

so as a first pass we could switch back to this.

in terms of tests we would really have to check this against the matlab file that's created, so that would be a little involved.

[effigies]

Okay, I'll just revert #2375 for now, rather than try to be fancy and concise with nested InputMultiPaths.

[satra]

there are a few things here:

1. the error message that comes from InputMultiPath is correct, but doesn't reflect the ImageFileSPM error, so that should be a fix in InputMultiPath, not the SPM interface.
2. SPM accepts a list of list of 3d nifti files where each inner list corresponds to a run. while most people use 4D files these days, the support from SPM should not be revoked.
3. nesting InputMultiPath would be fine, if that works properly. i'm not sure that works fine. someone should check.

[effigies]

1. Sounds good.
2. Agreed.
3. I guess the failing test builds suggest that it's at least not working exactly as before, so it would likely break workflows, even if the behavior is still supported.

[effigies]

Just to clarify:

• self.inner_traits() is always True for a traits.List (default value: (traits.Any(),))
• isinstance(value, list) is always True at this point in the short-circuit
• bool(value) is always True, or we would have returned Undefined already

These changes aren't really related to the rest of the PR, but I thought I would be modifying code in here at first, so factoring the inner_trait local variable led to this.

[djarecka]

@effigies what if value = []?

[djarecka]

ok, sorry, it would return undefined in l.331

[effigies]

New error message:

In [1]: from nipype.interfaces import spm

In [2]: realign = spm.Realign()

In [3]: realign.inputs.in_files = ['test.nii.gz', 'test.img']
---------------------------------------------------------------------------
TraitError                                Traceback (most recent call last)
<ipython-input-3-b45a253e48c2> in <module>()
----> 1 realign.inputs.in_files = [['test.nii.gz', 'test.img']]

/data/cjmarkie/Projects/nipype/nipype/interfaces/base/traits_extension.py in validate(self, object, name, value)
    345             newvalue = [value]
    346 
--> 347         value = super(MultiPath, self).validate(object, name, newvalue)
    348         # try:
    349         # except TraitError as excp:

~/.anaconda3/lib/python3.6/site-packages/traits/trait_types.py in validate(self, object, name, value)
   2334                 return value
   2335 
-> 2336             return TraitListObject( self, object, name, value )
   2337 
   2338         self.error( object, name, value )

~/.anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py in __init__(self, trait, object, name, value)
   2311             except TraitError as excp:
   2312                 excp.set_prefix( 'Each element of the' )
-> 2313                 raise excp
   2314 
   2315         self.len_error( len( value ) )

~/.anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py in __init__(self, trait, object, name, value)
   2303                 validate = trait.item_trait.handler.validate
   2304                 if validate is not None:
-> 2305                     value = [ validate( object, name, val ) for val in value ]
   2306 
   2307                 list.__setitem__(self, slice(0, 0), value )

~/.anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py in <listcomp>(.0)
   2303                 validate = trait.item_trait.handler.validate
   2304                 if validate is not None:
-> 2305                     value = [ validate( object, name, val ) for val in value ]
   2306 
   2307                 list.__setitem__(self, slice(0, 0), value )

~/.anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py in validate(self, object, name, value)
   1981             except TraitError:
   1982                pass
-> 1983         return self.slow_validate( object, name, value )
   1984 
   1985     def slow_validate ( self, object, name, value ):

~/.anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py in slow_validate(self, object, name, value)
   1989             except TraitError:
   1990                pass
-> 1991         self.error( object, name, value )
   1992 
   1993     def full_info ( self, object, name, value ):

~/.anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py in error(self, object, name, value)
    170         """
    171         raise TraitError( object, name, self.full_info( object, name, value ),
--> 172                           value )
    173 
    174     def full_info ( self, object, name, value ):

TraitError: Each element of the 'in_files' trait of a RealignInputSpec instance must be a list of
items which are an existing, uncompressed file (valid extensions: [.img, .nii, .hdr]) or an existing,
uncompressed file (valid extensions: [.img, .nii, .hdr]), but a value of 'test.nii.gz' <class 'str'> was
specified.

[effigies]

Last change I think makes the grammar a little smoother.

TraitError: Each element of the 'in_files' trait of a RealignInputSpec instance must be an
existing, uncompressed file (valid extensions: [.hdr, .img, .nii]) or a list of items which
are an existing, uncompressed file (valid extensions: [.hdr, .img, .nii]), but a value of
'test.nii.gz' <class 'str'> was specified.

[djarecka]

lgtm