[ENH] added slice_encoding_direction input to TShift

[fliem]

Summary

Fixes #2752

List of changes proposed in this PR (pull-request)

• adds slice_encoding_direction input to TShift
• if slice_encoding_direction == k-, reverse slice_timing

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[fliem]

@effigies is there a simple way to add a test for that?

[effigies]

To test, I would add to the docstring:

     ## EXISTING
     When the ``slice_timing`` input is used, the ``timing_file`` output is populated,
     in this case with the generated file.
 
     >>> tshift._list_outputs()['timing_file']  # doctest: +ELLIPSIS
    '.../slice_timing.1D'
    ## NEW
    >>> np.loadtxt(tshift._list_outputs()['timing_file'])[:5]
    [0.0, 0.4, 0.8, 1.2, 1.6]

    If ``slice_encoding_direction`` is set to ``'k-'``, the slice timing is reversed:

    >>> tshift.slice_encoding_direction = 'k-'
    >>> tshift.cmdline
    '3dTshift -prefix functional_tshift -tpattern @slice_timing.1D -TR 2.5s -tzero 0.0 functional.nii'
    >>> np.loadtxt(tshift._list_outputs()['timing_file'])[:5]
    [15.6, 15.2, 14.8, 14.4, 14.0]

Seem reasonable?

[codecov-io]

Codecov Report

Merging #2753 into master will decrease coverage by 3.41%.
The diff coverage is 60%.

@@            Coverage Diff             @@
##           master    #2753      +/-   ##
==========================================
- Coverage   67.44%   64.03%   -3.42%     
==========================================
  Files         340      338       -2     
  Lines       43164    43117      -47     
  Branches     5351     5349       -2     
==========================================
- Hits        29110    27608    -1502     
- Misses      13355    14430    +1075     
- Partials      699     1079     +380

Flag	Coverage Δ
#smoketests	?
#unittests	64.03% <60%> (-0.78%)	⬇️

Impacted Files	Coverage Δ
nipype/interfaces/afni/preprocess.py	80.66% <60%> (-0.74%)	⬇️
nipype/interfaces/nilearn.py	40% <0%> (-56.67%)	⬇️
nipype/utils/spm_docs.py	25.92% <0%> (-44.45%)	⬇️
nipype/interfaces/freesurfer/base.py	49.59% <0%> (-30.9%)	⬇️
nipype/utils/logger.py	59.7% <0%> (-29.86%)	⬇️
nipype/algorithms/rapidart.py	35.39% <0%> (-29.21%)	⬇️
nipype/interfaces/spm/base.py	58.41% <0%> (-29.05%)	⬇️
nipype/utils/provenance.py	55.73% <0%> (-28.99%)	⬇️
nipype/interfaces/fsl/model.py	55.26% <0%> (-25.35%)	⬇️
nipype/testing/fixtures.py	77.33% <0%> (-21.34%)	⬇️
... and 46 more

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[fliem]

That all sounds reasonable. If there should be any other changes, I can take a look in a couple of days.

[effigies]

This LGTM. If it passes the Travis tests for Python < 3.7, I'll merge. Thanks!