MincHeader.get_xyzt_units()

[jennydaman]

The headers of MINC files have information which specifies the volume units (almost always mm). This PR exposes the data via MincHeader.get_xyzt_units(), which is homologous to Nifti1Header.get_xyzt_units(). But I don't work with 4D MINC so the 't' unit is simply "unknown".

I'm thinking that it would be nice to have get_xyzt_units() part of the header interface.

This PR is kind of a draft? It works, though my intention is to open a discussion and perhaps support get_xyzt_units() for other file formats too.

[pep8speaks]

Hello @jennydaman, 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 2022-04-01 19:46:07 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 79.31034% with 6 lines in your changes missing coverage. Please review.

Project coverage is 95.27%. Comparing base (e9ed337) to head (ca61800).

Files with missing lines	Patch %	Lines
nibabel/minc1.py	81.25%	1 Missing and 2 partials ⚠️
nibabel/minc2.py	57.14%	1 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1098      +/-   ##
==========================================
- Coverage   95.37%   95.27%   -0.11%     
==========================================
  Files         207      207              
  Lines       29652    29679      +27     
  Branches     3017     3021       +4     
==========================================
- Hits        28282    28277       -5     
- Misses        933      953      +20     
- Partials      437      449      +12     

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[jennydaman]

Possibly convergent work: #567

[jennydaman]

@effigies PTAL or close?

[effigies]

Sorry, what does PTAL mean?

[jennydaman]

Please Take A Look (which you just did)

[effigies]

I assume you're seeing (in the CI output):

  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
  nibabel/tests/test_image_api.py:234: in validate_data_interface
      img = imaker()
  nibabel/tests/test_image_api.py:608: in <lambda>
      yield lambda: self.loader(img_params['fname']), img_params
  nibabel/dataobj_images.py:504: in from_filename
      return klass.from_file_map(file_map, mmap=mmap, keep_file_open=keep_file_open)
  nibabel/minc1.py:353: in from_file_map
      units = minc_file.get_units()
  nibabel/minc1.py:117: in get_units
      return tuple(d.units.decode('utf-8') for d in self._dims)
  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
  
  .0 = <list_iterator object at 0x7f929c3f3700>
  
  >   return tuple(d.units.decode('utf-8') for d in self._dims)
  E   AttributeError: 'netcdf_variable' object has no attribute 'units'

[jennydaman]

Whoops. Looks like too much has changed in the past 2 years and this PR isn't going to work anymore.

Could we continue the conversation in #1116? If we decide get_xyzt_units is a desirable feature to have, I can look into how to support it for MINC.