MRG, FIX: Fixes for BEM contours #7763
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Reported as fixing orientations for @christian-oreilly here, so this one should be good to go |
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thanks for cleaning my mess @larsoner :) |
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Decided to take care of the deduplication here, it was't so bad actually. On
And on this PR it looks like
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Going to push one more fix to adjust the
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Style failure is just the one from #7767 |
agramfort
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May 12, 2020
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thx @larsoner |
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May 19, 2020
* upstream/master: (74 commits) FIX: Correct a bug in find_bads_eog (mne-tools#7797) [MRG] split_naming='bids' changes from _part-%d to _split-%d (mne-tools#7794) MRG, MAINT, DOC: Remove spyder (mne-tools#7796) MAINT: fixes for linkcheck (mne-tools#7762) [WIP] Update ieeg data example for ECoG (mne-tools#7768) fix examples/tutorials [circle full] (mne-tools#7786) MAINT: Clean up VTK and add to pre on Azure (mne-tools#7780) ENH: Add matplotlib animation support [skip travis] (mne-tools#7783) MRG, API: change out_type default in permutation_cluster_(1samp_)test (mne-tools#7781) DOC: docstring fixes (mne-tools#7777) MRG, ENH: Add tol_kind option (mne-tools#7736) MRG, DOC: Notes about info (mne-tools#7772) ENH: Speed up NIRx read without preload (mne-tools#7759) Minor plot_raw aes improvement (mne-tools#7770) MRG, FIX: Fixes for BEM contours (mne-tools#7763) MRG, STY: Fix E741 (mne-tools#7767) MRG, ENH - Plot optodes in plot_alignment for fNIRS channels (mne-tools#7747) FIX: Update NIH support [skip travis] (mne-tools#7766) MAINT: Bump tol for gamma map test (mne-tools#7764) MRG, FIX: Fix MRI orientations (mne-tools#7725) ...
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Should fix the bug mentioned in #7725. @christian-oreilly can you try it with your out-of-standard-ori MRI? I don't have any to test with but in principle I think this should work...
This PR also:
show_orientations=False)mne.viz._3d._plot_mri_contoursthat we should really refactor with themne.viz.misc._plot_mri_contours-- the function names match and there is a lot of similar code so it's unfortunate that we ended up with two copies, presumably due to @agramfort 6 years ago accidentally making two copies in 5c1d64b :)slices=Nonefrom:masterwe correctly avoid the last but not the first and unevenly sample in between, we now evenly sample from near-to-first to near-to-last instead by making 14 points evenly spaced between first and last slice (inclusive) and then excluding the first and last of those 14 to obtain 12.On master for
plot_forward.pywe get:And on this PR:
Note that there is a left-to-right flip here. On
masterthe subject's left was shown on the right (radiological convention, probably not intentional) and this PR sets it to the more standard (for us at least) neurological convention of having the subject's left on the left. You can tell this by the fact that in the image from this PR, slice 177 (bottom left) has the pill on the right, and then the last slice is flipped left-right relative to themasterplots.