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Reading freesurfer stats files correctly #1152
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there was a problem with reading the stats files
A couple thoughts:
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Why a class with only static methods? I think flat functions would make more sense and be consistent with this module.
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Is it possible to do what you want with plain numpy? Pandas is a very heavy dependency that we are unlikely to make an installation requirement.
The code has been revised regard to your comments
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@ ## master #1152 +/- ## ========================================== - Coverage 95.36% 95.33% -0.03% ========================================== Files 207 207 Lines 29680 29694 +14 Branches 4992 4996 +4 ========================================== + Hits 28305 28310 +5 - Misses 935 944 +9 Partials 440 440 ☔ View full report in Codecov by Sentry. |
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Thanks for this. I've made a couple comments.
A larger question is whether this is intended to be for any stats files in FreeSurfer, or just the ones generated by mris_anatomical_stats? We might want to do some detecting of the kind of stats in order to correctly build a dtype. I imagine a column header -> dtype lookup table would not be too difficult to construct.
What do you think?
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If we're going to have example code, it needs to run. We could drop an example file in nibabel/tests/data/ and access it with
from nibabel.testing import test_data stats_a2009 = read_stats_file(test_data(fname='lh.aparc.a2009s.stats'))
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
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You're no longer returning column names. I think you can use numpy.lib.recfunctions.join_by to do what you want.
I would also use the following pattern for doctests:
.. testsetup:: >>> import os >>> from nibabel.testing import get_test_data >>> cwd = os.getcwd() >>> os.chdir(get_test_data()) >>> stats_a2009 = read_stats_file_both_hemispheres(r'lh.aparc.a2009s.stats') .. testcleanup:: >>> os.chdir(cwd)
@simkarwin Sorry about the long radio silence. Any interest in finishing this up?
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