Inital commit to add niftyfit interfaces

[byvernault]

Dear nipype team,

We are ready to add niftyfit to nipype. I copied all the interfaces we generated for this package as well as the test.

I tested it with python 2 and python 3. It's working on my computer.

Let me know if you see anything not compatible or that I should change in the code.

Kind Regards,

Ben

[codecov-io]

Codecov Report

Merging #1910 into master will increase coverage by 0.04%.
The diff coverage is 77.53%.

@@            Coverage Diff            @@
##           master   #1910      +/-   ##
=========================================
+ Coverage   72.15%   72.2%   +0.04%     
=========================================
  Files        1117    1130      +13     
  Lines       56456   56918     +462     
  Branches     8112    8140      +28     
=========================================
+ Hits        40736   41095     +359     
- Misses      14443   14539      +96     
- Partials     1277    1284       +7

Flag	Coverage Δ
#smoketests	72.2% <77.53%> (+0.04%)	⬆️
#unittests	69.78% <77.53%> (+0.06%)	⬆️

Impacted Files	Coverage Δ
nipype/interfaces/niftyseg/em.py	92.3% <ø> (ø)	⬆️
nipype/interfaces/niftyreg/reg.py	86.36% <ø> (ø)	⬆️
nipype/interfaces/niftyseg/patchmatch.py	100% <ø> (ø)	⬆️
nipype/interfaces/niftyseg/maths.py	78.88% <ø> (ø)	⬆️
nipype/interfaces/niftyseg/stats.py	63.82% <ø> (ø)	⬆️
nipype/interfaces/niftyseg/lesions.py	100% <ø> (ø)	⬆️
nipype/interfaces/niftyseg/label_fusion.py	57.46% <ø> (ø)	⬆️
nipype/interfaces/niftyreg/regutils.py	84% <ø> (ø)	⬆️
nipype/interfaces/setup.py	6.45% <0%> (-0.22%)	⬇️
nipype/interfaces/niftyfit/qt1.py	100% <100%> (ø)
... and 25 more

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[oesteban]

Hi @byvernault all the tests seem to be passing in our settings as well. I also went through the code quickly and overall it looks really good.

We are right now in a Nipype workshop for this week so we may not find time for the deep review this deserves, but I'm sure we can get this merged over the next two weeks.

Thanks a lot, this is a really valuable contribution and I'm sure it will expose Nifty- tools to a good bunch of new users.

[byvernault]

Hi,

I think we are finally good with this branch to add niftyfit interface to nipype.

Let me know if you have any question.

Kind Regards,
Ben

[byvernault]

Hi guys,

Thank you for pulling niftyreg and niftyseg request to nipype.
I extended the few changes you recommended for niftryseg into niftyfit.

Let me know if you think there is other changes to do.

Thanks for all your help.

Kind Regards,
Ben

P.S: BTW, do you have an idea when is the next nipype release?

[satra]

@byvernault -re: release, i'm hoping tomorrow.

[byvernault]

@satra Great :).

Do you think you will have time to add niftyfit before the release?

Cheers,
Ben

[satra]

@byvernault - i ran into an issue with doc building - the ones already pulled in are giving a bunch of errors. i believe they are all from the docstrings, so i'm replacing this

    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
    For Documentation, see:
        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation

with

    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
    `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_

you'll need a few more tools to build the docs: sphinx, pydotplus. and then do make html > doc.txt 2>&1 and look for ERROR in doc.txt

[byvernault]

Oops. Ok, I will check that for niftyfit (as well as niftyreg/niftyseg) and fix those issues.

Sorry.

[byvernault]

@satra , when I build the doc, It finishes without issue on the build:

copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 2768 warnings.

Build finished. The HTML pages are in _build/html.
Build HTML and API finished.

When I load the index.html and I look at niftyseg.patchmatch, I can see the docsting fine, the only thing is that I am missing a ending line after the first url.

What kind of error do you have? I am probably doing something wrong.
I am running 'make html > doc_error.txt 2>&1' from the folder nipype/doc.

Cheers,

[satra]

@byvernault - do cat doc.txt | grep ERROR.

i pushed the changes for master here: #1997

[byvernault]

Got it. I see the errors. I will edit niftyseg files to fix them in this branch. Is that fine?

I don't see any for niftyfit and niftyreg.

Do you?

[byvernault]

@satra I think I fixed all the docstring for niftyseg and I didn't see any for the other packages.

WDYT?

[satra]

@byvernault - #1997 fixes the issues with niftyseg - so you should be able to remove those from here. once that PR gets merged, i would suggest merging with master, running make check-before-commit and then updating this.

doesn't look like i'll be able to cut a release tonight. so sometime over the weekend.

[satra]

@byvernault - if you could merge master and resolve the conflicts that would be great. i think you could replace niftiseg files with the one from master.

[byvernault]

Sorry, I committed from another computer and I changed the author after the commit. I though I did change it for the commit but apparently not.

I'm still the author of it. I will try to edit this.

Thanks @satra for your help.

Kind Regards,
Ben