ENH: add interface for MRTrix3's dwidenoise

[mvdoc]

Changes proposed in this pull request

• Adds interface for dwidenoise

[mvdoc]

Apparently there's a timeout kicking in when downloading the test data

curl: (7) Failed to connect to storage.googleapis.com port 443: Connection timed out

[effigies]

I'm seeing similar problems for pip installations. Possibly Circle is getting rate-limited by some recent web server release (I've been able to navigate to the timing-out locations manually). Hopefully it's a temporary condition.

[mvdoc]

@effigies do you want me to push a commit to start the ci testing?

[effigies]

Sure. Maybe just merge master, to avoid having a pointless commit?

[codecov-io]

Codecov Report

Merging #2568 into master will increase coverage by 0.55%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #2568      +/-   ##
==========================================
+ Coverage   67.13%   67.69%   +0.55%     
==========================================
  Files         333      335       +2     
  Lines       42547    42822     +275     
  Branches     5266     5351      +85     
==========================================
+ Hits        28566    28990     +424     
+ Misses      13279    13153     -126     
+ Partials      702      679      -23

Flag	Coverage Δ
#smoketests	50.7% <ø> (ø)	⬆️
#unittests	65.18% <100%> (+0.7%)	⬆️

Impacted Files	Coverage Δ
nipype/interfaces/mrtrix3/preprocess.py	79.61% <100%> (+2.41%)	⬆️
nipype/interfaces/mrtrix3/__init__.py	100% <100%> (ø)	⬆️
nipype/interfaces/fsl/utils.py	70.62% <0%> (ø)	⬆️
nipype/algorithms/icc.py	59.21% <0%> (ø)	⬆️
nipype/utils/docparse.py	53.04% <0%> (ø)	⬆️
nipype/interfaces/mixins/__init__.py	100% <0%> (ø)
nipype/interfaces/mixins/reporting.py	48.57% <0%> (ø)
nipype/interfaces/fsl/model.py	80.61% <0%> (+0.18%)	⬆️
nipype/interfaces/afni/preprocess.py	81.5% <0%> (+0.24%)	⬆️
... and 29 more

---

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[mvdoc]

Seems it's failing still for timeout, but for another reason:

180511-00:41:51,523 workflow INFO:
         [Node] Finished "level1.datasink".
180511-00:41:53,304 workflow DEBUG:
         Progress: 52 jobs, 50/2/0 (done/running/ready), 2/0 (pending_tasks/waiting).
180511-00:41:53,304 workflow INFO:
         [Job 45] Completed (level1.datasink).
180511-00:41:53,307 workflow DEBUG:
         Tasks currently running: 1. Pending: 1.
180511-00:41:53,308 workflow INFO:
         [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 6.37/6.57, Free processors: 1/2.
                     Currently running:
                       * level1.report
180511-00:41:55,306 workflow DEBUG:
         Progress: 52 jobs, 51/1/0 (done/running/ready), 1/0 (pending_tasks/waiting).
180511-00:41:55,306 workflow DEBUG:
         Tasks currently running: 1. Pending: 1.
Too long with no output (exceeded 1h0m0s)

[effigies]

This happens with that test, sometimes. I think it's related to #2548.

[effigies]

Looks good. A couple minor suggestions.

[effigies]

We don't generally set mandatory=True or exists=False.

[effigies]

Sorry, I meant mandatory=False. I fixed the change here.

[effigies]

Consider using the following:

out_file = File(
    name_template='%s_denoised',
    name_source='in_file', 
    keep_extension=True,
    argstr="%s",
    position=-1,
    desc="the output denoised DWI image")

This will also auto-fill out_file in the output spec, so you can drop _list_outputs.

[effigies]

@mvdoc Just a bump. Do you have a couple minutes to finish this one up?

[mvdoc]

Yes absolutely. Will finish up over the weekend.

…

On Fri, May 18, 2018 at 10:44 AM Chris Markiewicz ***@***.***> wrote: @mvdoc <https://github.com/mvdoc> Just a bump. Do you have a couple minutes to finish this one up? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2568 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF3ZmrQV8PTzvprPaHyTp4pmNek-bh6gks5tzt5dgaJpZM4T1WVO> .

-- Matteo Visconti di Oleggio Castello Ph.D. Candidate in Cognitive Neuroscience Dartmouth College +1 (603) 646-8665 mvdoc.me || github.com/mvdoc || linkedin.com/in/matteovisconti