MRG: Add support for reading and writing sufaces to .obj #7824

wmvanvliet · 2020-05-25T15:03:41Z

Add support for exporting FreeSurfer surfaces to .obj files so you can import them in blender.

See also: https://github.com/ezemikulan/blender_freesurfer

Todo:

Implement writing .obj files
Implement reading .obj files
Basic unit tests
Finish unit tests for full coverage
Add tutorial on how to use this to fix Surface inner skull is not completely inside surface outer skull errors
Update what's new

larsoner · 2020-05-25T15:08:34Z

mne/surface.py

+            for v in coords:
+                fid.write('v {} {} {}\n'.format(*v))
+            for f in faces:
+                fid.write('f {} {} {}\n'.format(*(f + 1)))


@wmvanvliet we are allowed to use f-strings now because we require 3.6+

larsoner · 2020-05-25T15:08:55Z

mne/tests/test_surface.py

@@ -244,4 +252,4 @@ def test_normal_orth():
        assert_allclose(ori[2], nn, atol=1e-12)


-run_tests_if_main()
+#run_tests_if_main()


BTW now that we have pytest and it's (much) easier to use, I find these not so helpful. I'd be okay with getting rid of them in the codebase...

Alternatively, is there a good way to run a single test inside a Jupyter console? (I usually need the postmortem debugger)

larsoner · 2020-05-25T17:07:04Z

Alternatively, is there a good way to run a single test inside a Jupyter console? (I usually need the postmortem debugger)

Personally I just do:

pytest mne/tests/test_whatever.py -k test_something --tb=short --pdb

this drops to a (pdb) prompt where you can even do interactive and then have a standard python terminal (with matplotlib interactive, etc.). Not sure if there is a way to get this to be an ipython rather than python terminal, maybe with something like https://cprohm.de/article/ipytest-running-pytest-in-ipython-notebooks.html/ ?

wmvanvliet · 2020-05-26T10:12:18Z

Sphinx-gallery gallery_conf["plot_gallery"] was False, so no examples were executed.

Does that mean that CircleCI is complaining that no examples needed to be build or something?

larsoner · 2020-05-26T13:15:50Z

No, it's a warning about optipng (warnings are treated as errors) that you can safely ignore. It's because your branch is out of date and CircleCI doesn't / can't merge the yaml before executing

larsoner

Looks like it just needs latest.inc update then +1 for merge from me

wmvanvliet · 2020-05-27T05:24:19Z

I'm still working on the "fix my BEM with Blender" tutorial, which I feel should be part of this PR.

wmvanvliet · 2020-06-12T08:57:18Z

Can anyone help me getting the static images (blender screenshots) properly embedded the tutorial text? @larsoner @drammock

larsoner · 2020-06-12T13:27:05Z

I can push a commit to fix the warnings and add a thumbnail (hopefully)

larsoner · 2020-06-12T13:43:33Z

(FYI testing locally with PATTERN=in_blender make html_dev-pattern allows for fairly quick iteration to fix bugs)

Grr... something is wrong with the SG static thumb embedding. I'll probably need to fix that at the SG end, but the syntax here is correct so shouldn't be a blocker for merge

larsoner · 2020-06-12T13:46:12Z

... turns out I just can't spell

mne/surface.py

wmvanvliet · 2020-06-12T14:09:07Z

When CI comes back green, this is ready to merge from my end.

larsoner · 2020-06-12T16:44:50Z

Green other than timeouts that are not your fault that we can ignore

larsoner · 2020-06-12T16:46:09Z

The files are actually kind of big (500 / 700 kB), maybe some suitable JPG compression could be used?

larsoner

Other than the latest.inc tweak LGTM

@ezemikulan do you want to have a look?

doc/changes/latest.inc

wmvanvliet · 2020-06-12T17:10:05Z

Image filesizes are around 100kb now

agramfort · 2020-06-13T12:29:41Z

looks good https://20582-1301584-gh.circle-artifacts.com/0/dev/auto_tutorials/source-modeling/plot_fix_bem_in_blender.html#sphx-glr-auto-tutorials-source-modeling-plot-fix-bem-in-blender-py

agramfort

not sure why CIs complain but it looks good to me

wmvanvliet · 2020-06-13T12:35:42Z

CI's were timing out

ezemikulan · 2020-06-15T09:02:25Z

Hi, sorry for the late reply, looks great to me!

wmvanvliet · 2020-06-15T10:47:42Z

Hi @ezemikulan, thanks! If you can state you full name I can add you properly instead of just your username.

ezemikulan · 2020-06-15T11:37:22Z

It is Ezequiel Mikulan

Thanks again

* upstream/master: (24 commits) WIP: Fix Travis (mne-tools#7906) WIP: Prototype of notebook viz (screencast) (mne-tools#7758) MRG, FIX: Speed up I/O tests, mark some slow (mne-tools#7904) Proper attribution for Blender tutorial (mne-tools#7900) MAINT: Check usage [ci skip] (mne-tools#7902) Allow find_bad_channels_maxwell() to return scores (mne-tools#7845) Warn if NIRx directory structure has been modified from original format (mne-tools#7898) Pin pvyista to 0.24.3 (mne-tools#7899) MRG: Add support for reading and writing sufaces to .obj (mne-tools#7824) Fix _auto_topomap_coords docstring. (mne-tools#7895) MRG, FIX: Ensure Info H5-writeable (mne-tools#7887) Website contents (mne-tools#7889) MRG, ENH: Add mri_resolution="sparse" (mne-tools#7888) MRG, ENH: Allow disabling FXAA (mne-tools#7877) remove "and and" [ci skip] (mne-tools#7882) fix evoked nave → inverse guidance (mne-tools#7881) ENH: Better error messages (mne-tools#7879) FIX : EDF+ Annotation Timestamps missing sub-second accuracy (mne-tools#7875) FIX: Fix get_channel_types (mne-tools#7878) MRG, BUG: Fix combine evokeds (mne-tools#7869) ...

* upstream/master: (23 commits) MAINT: Add mne.surface to docstring tests (mne-tools#7930) MRG: Add smoothing controller to TimeViewer for the notebook backend (mne-tools#7928) MRG: TimeViewer matplotlib figure color (mne-tools#7925) fix typos (mne-tools#7924) MRG, ENH: Add method to project onto max power ori (mne-tools#7883) WIP: Warn if untested NIRX device (mne-tools#7905) MRG, BUG: Fix bug with volume morph and subject_to!="fsaverage" (mne-tools#7896) MRG, MAINT: Clean up use of bool, float, int (mne-tools#7917) ENH: Better error message for incompatible Evoked objects (mne-tools#7910) try to fix nullcontext (mne-tools#7908) WIP: Fix Travis (mne-tools#7906) WIP: Prototype of notebook viz (screencast) (mne-tools#7758) MRG, FIX: Speed up I/O tests, mark some slow (mne-tools#7904) Proper attribution for Blender tutorial (mne-tools#7900) MAINT: Check usage [ci skip] (mne-tools#7902) Allow find_bad_channels_maxwell() to return scores (mne-tools#7845) Warn if NIRx directory structure has been modified from original format (mne-tools#7898) Pin pvyista to 0.24.3 (mne-tools#7899) MRG: Add support for reading and writing sufaces to .obj (mne-tools#7824) Fix _auto_topomap_coords docstring. (mne-tools#7895) ...

larsoner reviewed May 25, 2020

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wmvanvliet force-pushed the surf_to_obj branch from 8920c9d to 0aaadfc Compare May 25, 2020 16:11

wmvanvliet mentioned this pull request May 25, 2020

Make this a tutorial on the official MNE-Python page. ezemikulan/blender_freesurfer#2

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larsoner reviewed May 26, 2020

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wmvanvliet added 3 commits June 12, 2020 10:27

Add support for reading and writing sufaces to .obj

d7143d2

Address comments

6bc5bd6

Make file_format='auto' the default

b35fc99

wmvanvliet force-pushed the surf_to_obj branch from 927fddd to b35fc99 Compare June 12, 2020 07:28

Add Blender tutorial

f410328

wmvanvliet added 2 commits June 12, 2020 15:44

Fixes to doc

8d803d5

Another attempt

0e2086b

FIX: Links

36df94a

FIX: cant spell

780e291

agramfort reviewed Jun 12, 2020

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wmvanvliet added 2 commits June 12, 2020 16:58

Refactor .obj reading code into separate function

a1ea02b

Add entries to whats news

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wmvanvliet changed the title ~~WIP: Add support for reading and writing sufaces to .obj~~ MRG: Add support for reading and writing sufaces to .obj Jun 12, 2020

larsoner approved these changes Jun 12, 2020

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Make images smaller. Change latest.inc

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wmvanvliet added 3 commits June 12, 2020 20:13

Remove erroneous file

0a709bd

typo

a4c5856

Tweaks to blender tutorial

16956d4

agramfort approved these changes Jun 13, 2020

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wmvanvliet merged commit 78bc2a4 into mne-tools:master Jun 13, 2020

wmvanvliet deleted the surf_to_obj branch June 13, 2020 17:13

wmvanvliet mentioned this pull request Jun 15, 2020

Proper attribution for Blender tutorial #7900

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MRG: Add support for reading and writing sufaces to .obj #7824

MRG: Add support for reading and writing sufaces to .obj #7824

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MRG: Add support for reading and writing sufaces to .obj #7824

MRG: Add support for reading and writing sufaces to .obj #7824

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