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[RTM] FIX: Ensure un-nested lists are not over-flattened #602

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Merged
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Jul 28, 2017
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[RTM] FIX: Ensure un-nested lists are not over-flattened #602

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3 changes: 2 additions & 1 deletion fmriprep/workflows/fieldmap/unwarp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -447,7 +447,8 @@ def init_prepare_epi_wf(ants_nthreads, name="prepare_epi_wf"):
workflow = pe.Workflow(name=name)

def _flatten(l):
return [item for sublist in l for item in sublist]
from niworkflows.nipype.utils.filemanip import filename_to_list
return [item for sublist in l for item in filename_to_list(sublist)]
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Guess I'll just request a review. So the situation is that the input to merge from split is being interpreted as a list of single-character strings.

Given that the output is passed to _flatten before being passed to merge, I believe the correct interpretation is that we get a list with a single element ['/path/to/file']. Expanding that out:

[item for sublist in ['/path/to/file'] for item in sublist]
[item for item in '/path/to/file']
['/', 'p', 'a', 't', 'h', '/', 't', 'o', '/', 'f', 'i', 'l', 'e']

Thus, by using filename_to_list in the inner loop, we get:

[item for sublist in ['/path/to/file'] for item in filename_to_list(sublist)]
[item for item in filename_to_list('/path/to/file')]
[item for item in ['/path/to/file']]
['/path/to/file']

I believe that because this is the output of a MapNode, the original input must always be a list, so there's no concern about l itself being a string. However, we could be more cautious for basically no cost and apply filename_to_list at both the inner and outer loops.


workflow.connect([
(inputnode, split, [('fmaps', 'in_file')]),
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