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ENH: Add a Bandpass filter interface under algorithms.filters #2915

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oesteban
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Upranks the bandpass_filter implementation that we had within the example workflows to a fully fledged Nipype Interface.

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codecov-io commented Apr 10, 2019

Codecov Report

Merging #2915 into master will decrease coverage by 3.39%.
The diff coverage is 34.04%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master    #2915     +/-   ##
=========================================
- Coverage   67.57%   64.17%   -3.4%     
=========================================
  Files         343      342      -1     
  Lines       43645    43637      -8     
  Branches     5428     5430      +2     
=========================================
- Hits        29494    28005   -1489     
- Misses      13447    14552   +1105     
- Partials      704     1080    +376
Flag Coverage Δ
#smoketests ?
#unittests 64.17% <34.04%> (-0.84%) ⬇️
Impacted Files Coverage Δ
nipype/algorithms/filters.py 34.04% <34.04%> (ø)
nipype/interfaces/nilearn.py 40% <0%> (-56.67%) ⬇️
nipype/utils/spm_docs.py 25.92% <0%> (-44.45%) ⬇️
nipype/interfaces/freesurfer/base.py 50% <0%> (-30.51%) ⬇️
nipype/utils/logger.py 59.7% <0%> (-29.86%) ⬇️
nipype/algorithms/rapidart.py 35% <0%> (-29.42%) ⬇️
nipype/interfaces/spm/base.py 58.08% <0%> (-29.05%) ⬇️
nipype/utils/provenance.py 55.73% <0%> (-28.35%) ⬇️
nipype/interfaces/fsl/model.py 55.26% <0%> (-25.35%) ⬇️
nipype/testing/fixtures.py 77.33% <0%> (-21.34%) ⬇️
... and 45 more

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@oesteban
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Thumbs up?

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satra commented Apr 17, 2019

@oesteban - this looks good.

could we add a real test to this perhaps generating a random (white noise) nifti timeseries file and filtering it with this code in _bandpass_filter?

also could we add a pointer to the discussion on neurostars (or at least the wording about ringing artifacts with this method)?

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will do

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Seems reasonable. Couple comments.

Parameters
----------
files : str
4D NIfTI file
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Necessarily NIfTI?

the default of 0 sets low pass cutoff to Nyquist
freq_hi : float
cutoff frequency for the high pass filter (in Hz)
the default of 0 sets high pass cutoff to 0
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This seems wrong...

@effigies effigies added this to the 1.2.3 milestone Sep 9, 2019
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@oesteban You're going to need to merge/rebase master to fix the Docker builds.

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@oesteban Do you want to try to finish this up with Satra's suggestions this weekend, or just push off to another release?

@oesteban oesteban modified the milestones: 1.2.3, 1.3.0 Sep 20, 2019
@effigies effigies modified the milestones: 1.3.0, 1.4.0 Nov 11, 2019
@effigies effigies modified the milestones: 1.4.0, 1.5.0 Dec 14, 2019
@effigies effigies mentioned this pull request Feb 23, 2020
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@effigies effigies removed this from the 1.5.0 milestone Feb 23, 2020
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This pull request is "orphaned," which means it has been deemed to be abandoned by its original author. Orphaned pull requests have not been rejected, and we hope that if a user sees one that will meet their needs with a little work, that they will fork it and open a new pull request (or, in the case of the original author, reopen the original PR).

We ask that all adopted PRs be updated to merge or rebase the current master. If you would like to adopt a PR and need help getting started, any of a number of contributors will be happy to help.

@effigies effigies closed this Feb 23, 2020
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4 participants