[ENH] Add interface to SPM realign_unwarp #2635

qtabs · 2018-07-10T13:41:19Z

Adds am interface to SPM's realing & unwarp function.

mgxd

Hi @qtabs , thank you for the contribution! I left a couple comments + suggestions to get past the CI errors you're encountering - if you have any questions let me know!

EDIT: can you also run make specs and add the new autotest?

mgxd · 2018-07-10T14:51:44Z

nipype/interfaces/spm/preprocess.py

@@ -437,6 +437,251 @@ def _list_outputs(self):
        return outputs


+class RealignUnwarpInputSpec(SPMCommandInputSpec):
+    in_files = InputMultiPath(


InputMultiPath is in the process of replaced by InputMultiObject, let's use that instead

mgxd · 2018-07-10T14:56:39Z

nipype/interfaces/spm/preprocess.py

@@ -437,6 +437,251 @@ def _list_outputs(self):
        return outputs


+class RealignUnwarpInputSpec(SPMCommandInputSpec):
+    in_files = InputMultiPath(
+        traits.Either(traits.List(File(exists=True)),


and you could use ImageFileSPM for image files

nipype/nipype/interfaces/spm/base.py

Line 599 in 7ea4f1b

class ImageFileSPM(ImageFile):

instead of File, since it will not allow compressed niftis as well

mgxd · 2018-07-10T15:04:39Z

nipype/interfaces/spm/preprocess.py

+    Examples
+    --------
+
+    >>> import nipype.interfaces.spm as spm


you'll have to add RealignUnwarp to

nipype/nipype/interfaces/spm/__init__.py

Lines 8 to 10 in 7ea4f1b

from .preprocess import (FieldMap, SliceTiming, Realign, Coregister, Normalize,

Normalize12, Segment, Smooth, NewSegment, DARTEL,

DARTELNorm2MNI, CreateWarped, VBMSegment)

in order to import this way

mgxd · 2018-07-10T15:12:33Z

nipype/interfaces/spm/preprocess.py

+    >>> import nipype.interfaces.spm as spm
+    >>> realignUnwarp = spm.RealignUnwarp()
+    >>> realignUnwarp.inputs.in_files = ['func-run01.nii', func-run02.nii']
+    >>> realignUnwarp.inputs.phase_map = 'phasemap.vdm'


IIRC, these files must exist to satisfy the traits requirements - we have quite a bit included in the repo already, but for the sake of interface clarity if you cannot reuse any existing files, feel free to add necessary (empty) files

effigies · 2018-07-24T00:44:44Z

Hi @qtabs, do you have time to finish this up this week?

qtabs · 2018-07-27T12:14:23Z

Thanks a lot for the help! :) I'm sorry I didn't reply any earlier, I left for vacation right after the request and couldn't check my mailbox until now. I'll try to implement your suggestions and run the tests again next week :).

effigies · 2018-08-06T13:35:03Z

Hi @qtabs. Please let us know if you need anything from us. Just a heads up that we'll try to release on August 27, so it'd be great to have this within the next two weeks (by August 20).

…e to InputMultiObject

…into addSPMrealingUnwarp

codecov-io · 2018-08-10T15:17:31Z

Codecov Report

❗ No coverage uploaded for pull request base (master@297a24c). Click here to learn what that means.
The diff coverage is 48.75%.

@@           Coverage Diff            @@
##             master   #2635   +/-   ##
========================================
  Coverage          ?   66.5%           
========================================
  Files             ?     340           
  Lines             ?   43140           
  Branches          ?    5348           
========================================
  Hits              ?   28691           
  Misses            ?   13679           
  Partials          ?     770

Flag	Coverage Δ
#smoketests	`48.7% <48.75%> (?)`
#unittests	`64.6% <48.75%> (?)`

Impacted Files	Coverage Δ
nipype/interfaces/spm/__init__.py	`100% <100%> (ø)`
nipype/interfaces/spm/preprocess.py	`52.56% <48.1%> (ø)`

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qtabs · 2018-08-10T15:58:41Z

Hi guys! I tried to fix the problems you hinted above but I still get some errors. I think (sorry, it's my first time dealing with automated tests!) the tests are failing to load the new module:

597     >>> realignUnwarp = spm.RealignUnwarp()
UNEXPECTED EXCEPTION: AttributeError("'module' object has no attribute 'RealignUnwarp'",)

but I have added RealignUnwarp to __init__.py as suggested by @mgxd, I'm not sure what's what I'm missing! O:)

Thanks a lot for your help!

effigies · 2018-08-10T17:38:53Z

597     >>> realignUnwarp = spm.RealignUnwarp()
UNEXPECTED EXCEPTION: AttributeError("'module' object has no attribute 'RealignUnwarp'",)

I'm not seeing this issue in the logs. I am seeing:

NameError: name 'InputMultiObject' is not defined

Which just means you need to import InputMultiObject at the top of the file, or revert to InputMultiPath.

You should also merge master to fix the BIDSDataGrabber issue.

effigies · 2018-08-10T18:57:51Z

Merged master for you. If this passes it'll make it into 1.1.2 (we need to do an emergency release). If not, we'll push it off to 1.1.3 next month.

For reference I did the following:

Add your repository as a qtabs remote and the main repository as upstream.

git remote add upstream [email protected]:nipy/nipype.git
git remote add qtabs [email protected]:qtabs/nipype.git

(You wouldn't need to add your own.)

Update all remotes to the latest state:

git fetch --all

Check out your branch, merge upstream/master and push:

git checkout add addSPMrealingUnwarp
git merge upstream/master
git push

qtabs · 2018-08-10T19:00:36Z

Thanks a lot @effigies! I'm trying my best but I'm still quite new to all this stuff, sorry for my noobie incompetence! O:)

effigies · 2018-08-10T19:07:55Z

No worries. I'd usually try to be a little more helpful and give newbies a chance to practice, but with a shortened release window, I figured we could squeeze this one in. I hope you keep your eyes out for some more practice opportunities. :-)

effigies · 2018-08-10T19:18:47Z

Well, the latest failures aren't related to this PR. I'm fixing them in #2679.

qtabs · 2018-08-10T19:21:07Z

Thanks a lot! :) Please let me know if there's anything else from here causing problems!

qtabs and others added 3 commits June 15, 2018 16:18

BF - added SPM realign_unwarp function to SPM-preprocessing

d6b6786

BF - added SPM realign_unwarp function to SPM-preprocessing

6d0895f

remove accidental linebreak

4037d39

mgxd reviewed Jul 10, 2018

View reviewed changes

effigies changed the title ~~[ENH] Add interface to SPM realing_unwarp~~ [ENH] Add interface to SPM realign_unwarp Jul 23, 2018

effigies added this to the 1.1.2 milestone Jul 27, 2018

qtabs added 2 commits August 10, 2018 17:06

added vdm file, changed File to ImageFileSPM and updated InputMuliFil…

f1ed66b

…e to InputMultiObject

Merge branch 'addSPMrealingUnwarp' of https://github.com/qtabs/nipype …

9303025

…into addSPMrealingUnwarp

changed example filename from functional1.nii to functional2.nii

b61c1d7

importing InputMultiObject

a4c4de5

effigies modified the milestones: 1.1.2, 1.1.3 Aug 10, 2018

Merge remote-tracking branch 'upstream/master' into HEAD

3f6c5d2

Merge remote-tracking branch 'upstream/master' into addSPMrealingUnwarp

1b12a27

effigies merged commit fdb3227 into nipy:master Aug 10, 2018

effigies modified the milestones: 1.1.3, 1.1.2 Aug 10, 2018

	from .preprocess import (FieldMap, SliceTiming, Realign, Coregister, Normalize,
	Normalize12, Segment, Smooth, NewSegment, DARTEL,
	DARTELNorm2MNI, CreateWarped, VBMSegment)

[ENH] Add interface to SPM realign_unwarp #2635

[ENH] Add interface to SPM realign_unwarp #2635

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