[MRG] Coregistration-GUI: use *.mff as digitization source #8790
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larsoner
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larsoner
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I like the idea of supporting formats other than FIF! I think we can probably make it general to all formats rather than just extending to EGI that should take about the same number of lines. I think that there are other formats (e.g., CTF) that would immediately benefit. Feel free to pytest.mark.parametrize over these files in a test to see if you want.
mne/gui/_file_traits.py
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| if self.file: | ||
| if not self.file: | ||
| return | ||
| elif self.file.endswith('.mff'): |
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I would make the pattern self.file.endswith('.fif') or self.file.endswith('.fif.gz'): and in that case use return read_info(...), else use return read_raw(...).info. This should make it work with any reader that supports digitization
larsoner
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larsoner
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Other than one small idea for more DRY code and needing to wait for the EGI PR then a rebase/merge here, LGTM! Also don't forget to update doc/changes/latest.inc
mne/gui/_file_traits.py
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| for d in info['dig']: | ||
| if d['kind'] == FIFF.FIFFV_POINT_CARDINAL: | ||
| has_point[d['ident']] = True | ||
| if not all(has_point.values()): |
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It seems like this whole section could be simplified, DRY'd, and have fewer missed coverage lines with something like:
missing = [key for key in ('LPA', 'Nasion', 'RPA') if not
has_point[getattr(FIFF, f'FIFFV_POINT_{key.upper()}']
if missing:
points = _fiducial_coords(info['dig'])
if len(points == 3):
_append_fiducials(info['dig'], *points.T)
else:
error(...)
self.reset_traits(['file'])
return
christianbrodbeck
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I added tests for MFF and CTF, are there other formats that contain digitizer info? |
christianbrodbeck
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CI failures look unrelated, thanks @christianbrodbeck ! |
* upstream/main: MRG, ENH: Add warning about bad whitener conditioning (mne-tools#8805) MRG, MAINT: Deprecated param and pytest-qt (mne-tools#8808) fix mne.viz.plot_topomap with some missing grad in a pair (mne-tools#8817) [MRG] Coregistration-GUI: use *.mff as digitization source (mne-tools#8790) FIX: Path [MRG] ENH EGI MFF reader: populate info['dig'] (mne-tools#8789) MRG: Improve Brain UX (mne-tools#8792) FIX missing Axes3D import in viz._3d._plot_mpl_stc (mne-tools#8811) Better error message if configured download folder doesn't exist (mne-tools#8809) MRG, ENH: Add support for other formats to browse_raw (mne-tools#8807) MRG, BUG: Allow depth > 1 (mne-tools#8804)
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Depends on #8789.
This adds the capability to use
*.mfffiles directly as digitization source to the coregistration GUI. I started on it for verifying the result of #8789, but it could be a useful feature since it obviates the need to convert to FIFF before doing coregistration. The screen-shot istest_egi.mff.