ENH: Add "element" containers and make dicom wrappers compatible

[moloney]

Add two main types: ElemDict and ElemList. Each can only store
objects with an attribute value. Standard lookups with
__getitem__ and get return just this value attribute. To
access the underlying object, a get_elem method is provided.

Also updated the DICOM wrappers to provide a get_elem method that
returns the full DICOM element rather than just the value. Added a
__iter__ method that returns the available DICOM keys.

[moloney]

This is a bite-sized chunk from #290. The goal is to provide a nice standard way to access meta data structures, especially once they become nested. So instead of having to do something like:

meta['key1'].value['key2'].value[0].value

we can do:

meta['key1']['key2'][0]

If you need to access the full "element" you can use the get_elem method. The dicomwrappers classes were lacking this ability and so I added a get_elem method that returns the full pydicom DataElement object. I also added a __iter__ method that produces the available DICOM keywords for the data set. It may also make sense to add some other dict-like methods, I am thinking at least keys.

[moloney]

I think we should make meta data access on the DICOM wrappers the same as meta data access on other Nibabel image classes. Are we okay with making the image classes dict-like for meta data access? If not, we should figure out what we want and implement it for the DICOM wrappers as well.

For the other image classes things are a bit more complicated as there is also the existing "header" attribute which contains some meta data. I guess we could make it so that nii.header['dim_info'] is the same as nii['header']['dim_info']?

[matthew-brett]

Single first line (docstring standard - also makes auto-generated docs look nicer).

[nibotmi]

☔ The latest upstream changes (presumably #439) made this pull request unmergeable. Please resolve the merge conflicts.

[pep8speaks]

Hello @moloney, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, pip install flake8 and then run flake8 nibabel.

Comment last updated at 2020-03-23 22:17:20 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 83.06452% with 21 lines in your changes missing coverage. Please review.

Project coverage is 91.62%. Comparing base (65d5fc6) to head (bd21464).
Report is 1219 commits behind head on master.

Files with missing lines	Patch %	Lines
nibabel/elemcont.py	82.90%	13 Missing and 7 partials ⚠️
nibabel/nicom/dicomwrappers.py	85.71%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #416      +/-   ##
==========================================
- Coverage   91.70%   91.62%   -0.09%     
==========================================
  Files          96       97       +1     
  Lines       12311    12435     +124     
  Branches     2173     2208      +35     
==========================================
+ Hits        11290    11393     +103     
- Misses        684      698      +14     
- Partials      337      344       +7     

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[effigies]

@moloney Thanks for rebasing this against master.

@matthew-brett Do you have the time to resume reviewing this (and/or #417, #419)?

[effigies]

Please feel free to reopen with a fresh PR.

[matthew-brett]

I can't this week, but if you can wait until middle of next, I can review.