[MRG] ENH Current Source Density Feature Add #6910

alexrockhill · 2019-10-04T01:34:27Z

Fixes #4480

Adds a current source density estimate function that converts EEG data using the Laplacian of the sensor data.

doc/test_csd.py

mne/preprocessing/tests/test_ica.py

doc/test_csd.py

agramfort

ok I stopped. Tell me when ready to review

examples/preprocessing/plot_csd.py

mne/preprocessing/_csd.py

codecov · 2019-10-04T16:45:35Z

Codecov Report

Merging #6910 into master will increase coverage by 0.02%.
The diff coverage is 98.7%.

@@            Coverage Diff             @@
##           master    #6910      +/-   ##
==========================================
+ Coverage   89.72%   89.75%   +0.02%     
==========================================
  Files         438      440       +2     
  Lines       77484    77715     +231     
  Branches    12579    12607      +28     
==========================================
+ Hits        69523    69751     +228     
- Misses       5155     5157       +2     
- Partials     2806     2807       +1

alexrockhill · 2019-10-04T17:00:31Z

@sherdim, thanks for the gist, I used it to base the example of off.
https://gist.github.com/sherdim/28b069c8ebca17073f24322e8e721e1f
Would you like your name and email there as an author?

doc/python_reference.rst

examples/preprocessing/plot_csd.py

mne/preprocessing/_csd.py

mne/preprocessing/tests/test_csd.py

alexrockhill · 2019-10-04T19:16:40Z

@agramfort now would be okay to review

mne/preprocessing/_csd.py

mne/preprocessing/tests/test_ica.py

doc/python_reference.rst

mne/preprocessing/_csd.py

mne/preprocessing/tests/test_csd.py

sherdim · 2019-10-05T17:25:34Z

@alexrockhill

Would you like your name and email there as an author?

I do not mind. It is honorable for me

I had to do it myself, but I didn’t. So go ahead!

alexrockhill · 2019-10-05T19:42:37Z

@alexrockhill

Would you like your name and email there as an author?

I do not mind. It is honorable for me

I had to do it myself, but I didn’t. So go ahead!

@sherdim I can add it but I don't know your name and email...

drammock · 2019-10-06T00:42:14Z

These are not timeouts. This is your version of pytest not knowing about the "timeout" mark: E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout Also I noticed you're in the"base" conda env, maybe that's the problem...

…

On October 5, 2019 5:34:50 PM PDT, Alex Rockhill ***@***.***> wrote: Hey I'm getting error when I run "make test" locally but they're all timeout errors. Anyone know how to fix that? (base) Alexs-MacBook-Pro:mne-python alexrockhill$ make test python setup.py build_ext -i running build_ext rm -f .coverage py.test -m 'not ultraslowtest' mne ========================================== test session starts =========================================== platform darwin -- Python 3.6.8, pytest-5.2.0, py-1.8.0, pluggy-0.13.0 rootdir: /Users/alexrockhill/software/mne-python, inifile: setup.cfg plugins: cov-2.7.1, arraydiff-0.3, remotedata-0.3.2, doctestplus-0.4.0, openfiles-0.4.0 collected 1302 items / 20 errors / 1282 selected ================================================= ERRORS ================================================= __________________________ ERROR collecting mne/commands/tests/test_commands.py __________________________ mne/commands/tests/test_commands.py:206: in <module> @pytest.mark.timeout(600) # took ~400 sec on a local test ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html __________________________ ERROR collecting mne/commands/tests/test_commands.py __________________________ mne/commands/tests/test_commands.py:206: in <module> @pytest.mark.timeout(600) # took ~400 sec on a local test ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html _________________ ERROR collecting mne/datasets/sleep_physionet/tests/test_physionet.py __________________ mne/datasets/sleep_physionet/tests/test_physionet.py:62: in <module> @pytest.mark.timeout(60) ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html _________________ ERROR collecting mne/datasets/sleep_physionet/tests/test_physionet.py __________________ mne/datasets/sleep_physionet/tests/test_physionet.py:62: in <module> @pytest.mark.timeout(60) ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ________________________ ERROR collecting mne/forward/tests/test_make_forward.py _________________________ mne/forward/tests/test_make_forward.py:120: in <module> @pytest.mark.timeout(60) # can take longer than 30 sec on Travis ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ________________________ ERROR collecting mne/forward/tests/test_make_forward.py _________________________ mne/forward/tests/test_make_forward.py:120: in <module> @pytest.mark.timeout(60) # can take longer than 30 sec on Travis ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html _____________________ ERROR collecting mne/inverse_sparse/tests/test_mxne_inverse.py _____________________ mne/inverse_sparse/tests/test_mxne_inverse.py:44: in <module> @pytest.mark.timeout(120) # ~30 sec on AppVeyor and Travis Linux ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html _____________________ ERROR collecting mne/inverse_sparse/tests/test_mxne_inverse.py _____________________ mne/inverse_sparse/tests/test_mxne_inverse.py:44: in <module> @pytest.mark.timeout(120) # ~30 sec on AppVeyor and Travis Linux ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ______________________ ERROR collecting mne/inverse_sparse/tests/test_mxne_optim.py ______________________ mne/inverse_sparse/tests/test_mxne_optim.py:158: in <module> @pytest.mark.timeout(60) # ~30 sec on Travis OSX and Linux OpenBLAS ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ______________________ ERROR collecting mne/inverse_sparse/tests/test_mxne_optim.py ______________________ mne/inverse_sparse/tests/test_mxne_optim.py:158: in <module> @pytest.mark.timeout(60) # ~30 sec on Travis OSX and Linux OpenBLAS ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ______________________ ERROR collecting mne/io/artemis123/tests/test_artemis123.py _______________________ mne/io/artemis123/tests/test_artemis123.py:45: in <module> @pytest.mark.timeout(60) # ~25 sec on Travis Linux OpenBLAS ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ______________________ ERROR collecting mne/io/artemis123/tests/test_artemis123.py _______________________ mne/io/artemis123/tests/test_artemis123.py:45: in <module> @pytest.mark.timeout(60) # ~25 sec on Travis Linux OpenBLAS ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html __________________________ ERROR collecting mne/io/eeglab/tests/test_eeglab.py ___________________________ mne/io/eeglab/tests/test_eeglab.py:183: in <module> @pytest.mark.timeout(60) # ~60 sec on Travis OSX ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html __________________________ ERROR collecting mne/io/eeglab/tests/test_eeglab.py ___________________________ mne/io/eeglab/tests/test_eeglab.py:183: in <module> @pytest.mark.timeout(60) # ~60 sec on Travis OSX ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ____________________________ ERROR collecting mne/tests/test_source_space.py _____________________________ mne/tests/test_source_space.py:306: in <module> @pytest.mark.timeout(60) # can be slow on OSX Travis ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ____________________________ ERROR collecting mne/tests/test_source_space.py _____________________________ mne/tests/test_source_space.py:306: in <module> @pytest.mark.timeout(60) # can be slow on OSX Travis ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ___________________________ ERROR collecting mne/utils/tests/test_fetching.py ____________________________ mne/utils/tests/test_fetching.py:9: in <module> @pytest.mark.timeout(60) ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ___________________________ ERROR collecting mne/utils/tests/test_fetching.py ____________________________ mne/utils/tests/test_fetching.py:9: in <module> @pytest.mark.timeout(60) ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html _______________________________ ERROR collecting mne/viz/tests/test_3d.py ________________________________ mne/viz/tests/test_3d.py:425: in <module> @pytest.mark.timeout(60) # can sometimes take > 60 sec ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html _______________________________ ERROR collecting mne/viz/tests/test_3d.py ________________________________ mne/viz/tests/test_3d.py:425: in <module> @pytest.mark.timeout(60) # can sometimes take > 60 sec ../anaconda3/lib/python3.6/site-packages/_pytest/mark/structures.py:324: in __getattr__ PytestUnknownMarkWarning, E pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html ------------- generated xml file: /Users/alexrockhill/software/mne-python/junit-results.xml -------------- ======================================== short test summary info ========================================= FAILED mne/commands/tests/test_commands.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeo... FAILED mne/commands/tests/test_commands.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeo... FAILED mne/datasets/sleep_physionet/tests/test_physionet.py - pytest.PytestUnknownMarkWarning: Unknown ... FAILED mne/datasets/sleep_physionet/tests/test_physionet.py - pytest.PytestUnknownMarkWarning: Unknown ... FAILED mne/forward/tests/test_make_forward.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.ti... FAILED mne/forward/tests/test_make_forward.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.ti... FAILED mne/inverse_sparse/tests/test_mxne_inverse.py - pytest.PytestUnknownMarkWarning: Unknown pytest.... FAILED mne/inverse_sparse/tests/test_mxne_inverse.py - pytest.PytestUnknownMarkWarning: Unknown pytest.... FAILED mne/inverse_sparse/tests/test_mxne_optim.py - pytest.PytestUnknownMarkWarning: Unknown pytest.ma... FAILED mne/inverse_sparse/tests/test_mxne_optim.py - pytest.PytestUnknownMarkWarning: Unknown pytest.ma... FAILED mne/io/artemis123/tests/test_artemis123.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mar... FAILED mne/io/artemis123/tests/test_artemis123.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mar... FAILED mne/io/eeglab/tests/test_eeglab.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeou... FAILED mne/io/eeglab/tests/test_eeglab.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeou... FAILED mne/tests/test_source_space.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - ... FAILED mne/tests/test_source_space.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - ... FAILED mne/utils/tests/test_fetching.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout ... FAILED mne/utils/tests/test_fetching.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout ... FAILED mne/viz/tests/test_3d.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is thi... FAILED mne/viz/tests/test_3d.py - pytest.PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is thi... !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 20 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! =========================================== 20 error in 9.92s ============================================ make: *** [test] Error 2

alexrockhill · 2019-10-06T00:58:12Z

Thanks, I could have figured that out my bad

larsoner · 2019-10-22T13:57:26Z

@alexrockhill somehow you have a bunch of conflicts in unrelated files

alexrockhill · 2019-10-29T01:41:58Z

I'm having some weird issues with tests failing... I'm not sure why files not related to the files being changed for this PR weirdly but I think I fixed that. When I run "make test" most of the tests pass but I get a few errors like

E FileNotFoundError: [Errno 2] No such file or directory: 'mne_compensate_data': 'mne_compensate_data'

/Users/alexrockhill/software/mne-python/mne/preprocessing/_peak_finder.py:45: DocTestFailure

E AssertionError: SNR (worst 2.55) < 3.50 for 18/306 channels (/Users/alexrockhill/mne_data/MNE-testing-data/SSS/test_move_anon_raw.fif)

I'm not sure what these are about. Using a fresh install of the mnedev environment. Here's just the first part of the stack trace:

(mnedev) alexrockhill@Alexs-MacBook-Pro mne-python % make test
python setup.py build_ext -i
running build_ext
rm -f .coverage
py.test -m 'not ultraslowtest' mne
Test session starts (platform: darwin, Python 3.7.4, pytest 5.2.1, pytest-sugar 0.9.2)
rootdir: /Users/alexrockhill/software/mne-python, inifile: setup.cfg
plugins: sugar-0.9.2, timeout-1.3.3, cov-2.7.1, mock-1.10.4
collecting ...
mne/annotations.py s 0%
mne/dipole.py s 0%
mne/epochs.py ss 0%
mne/event.py s✓ 0% ▏
mne/filter.py ✓ 0% ▏

―――――――――――――――――― [doctest] mne.filter.construct_iir_filter ―――――――――――――――――――
103 >>> iir_params = construct_iir_filter(iir_params, 40, 50, 1000, 'low') # doctest:+SKIP
104 >>> print((2 * len(iir_params['sos']), iir_params['padlen'])) # doctest:+SKIP
105 (6, 439)
106
107 Padding and/or filter coefficients can also be manually specified. For
108 a 10-sample moving window with no padding during filtering, for example,
109 one can just do:
110
111 >>> iir_params = dict(b=np.ones((10)), a=[1, 0], padlen=0)
112 >>> iir_params = construct_iir_filter(iir_params, return_copy=False)
Expected nothing
Got:

/Users/alexrockhill/software/mne-python/mne/filter.py:112: DocTestFailure

mne/filter.py ⨯ 1% ▏

――――――――――――――――――――――――― [doctest] mne.filter.detrend ―――――――――――――――――――――――――

cc @jasmainak @larsoner @drammock

agramfort · 2019-10-29T12:24:26Z

@alexrockhill are all the changes here related to this PR?

alexrockhill · 2019-10-29T13:04:51Z

They are or should be now. For some reason there were other files changed but I checked the file change diffs and that should be fixed. Now they are all just the files I had to change for csd

drammock

There are changes to what's new and to _optical_density.py that appear unrelated at first glance. Also maybe the spline stuff? Can you double check?

larsoner · 2019-11-08T19:53:08Z

Tests pass locally now, it was missing a ref_meg=False

alexrockhill · 2019-11-08T21:19:40Z

I saw that it had to do with a false positive meg_ref, I just couldn't figure out at which level (tests, epochs, viz.epochs or viz.utils) so I'm glad you figured it out :)

agramfort

sorry for taking so long to review

mne/preprocessing/_csd.py

examples/preprocessing/plot_eeg_csd.py

examples/preprocessing/plot_csd.py

mne/io/pick.py

agramfort · 2019-11-11T17:47:02Z

mne/io/tests/test_pick.py

-    for t, rules in get_channel_types().items():
+    # go in order from most specific (most rules entries) to least specific
+    channel_types = sorted(
+        get_channel_types().items(), key=lambda x: len(x[1]))[::-1]


I add a comment here to explain this.

examples/preprocessing/plot_eeg_csd.py

@drammock

added some tests WIP CSD MVP example working with example weird cherry-picking error again Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <alexandre.gramfort@m4x.org> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <alexandre.gramfort@m4x.org> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <alexandre.gramfort@m4x.org> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <alexandre.gramfort@m4x.org> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <alexandre.gramfort@m4x.org> typos/small fixes incorporated Eric comments more Eric comments refactoring core comp per Eric realized I did that wrong Eric comments 3 plot fix Fix julian date conversions (mne-tools#6911) * Fix julian date conversions * remove tabs * use UTC and private functions. closes mne-tools#6901 [skip travis][skip azp] (mne-tools#6914) ENH: Add source space SNR estimate (mne-tools#6908) * source-snr-edit * FIX move estimate_snr to be a method * ENH: name change * Make it work * SNR works, now clean up code * fixed unnecessary stc copy, returns stc object * added plot source space SNR tutorial file * updated author names * fixed period for pydocsty and suggested documenation edit * edits suggested from @drammock * made edits suggested by reviewers * made edits suggested by reviewers * N -> n_channels * Fixed formatting of Reference in comment * fixed formatting in doc and in code * fixed snr_stc creation * further minor edits * fixed formatting issues and colormap choice in eg * removed colon after Reference * Corrected SNR calculation to take unwhitened sensor signal b instead of whitened, updated tutorial file * Minor changes to formatting * FIX: transparent * FIX: Rename * FIX? Added dSPM (mne-tools#6913) * Added dSPM * removed term signal covariance * Minor modification of dSPM definition * Corrected according to Mattis suggestions [MRG]: read *.dat electrode position files (mne-tools#6909) * ADD: channels.read_dig_dat() * DOC * DOC * TEST * DOC, __all__ * DOC: intro * DOC * pep & py3.5 compatibility * py3.5 MRG: allow users to annotate epochs with colors (mne-tools#6855) * ENH: copy over diff from autoreject * Make it work * More fixes * More fixes * Make horizontal patch * Cleanup * TST: add tests * Address Eric's comments * Address alex comments * DOC: update whats new * FIX travis + circle * FIX For ICA plot Fix infomax (mne-tools#6921) * fix extended infomax * update whats new * cleaner way, using setdefault DOC: Document authors better [ci skip] FIX: Comments and order umlauts MRG, MAINT: Simplify code for vol ravel (mne-tools#6920) * MAINT: Simplify code for vol ravel * STY: Flake ENH: Convert NIRS raw data to optical density (mne-tools#6827) * Initial framework for fnirs raw to optical density conversion * Add optical density to docs * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> * Import testing * Put optical density docs in preprocessing section * Implement optical density conversion * Fix optical density code style issues * Add plotting of optical density data * Add defaults for optical density plotting * Update mne/preprocessing/optical_density.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> * Handle negative intensities in optical density conversion * Add in -1* that was removed in previous commit * Add tests and fix imports for optical density * Add tests for optical density conversion * Use assert_allclose for testing optical density * Update test_optical_density.py * Update mne/preprocessing/_optical_density.py Co-Authored-By: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Do not operate in place for optical density * Force data to load and modify test to include preload=False condition import fix tidying up weird file conflict errors more unexpected file changes fix weird off target changes doc docstring fixes docstyle reformatted plots changes formatting fix Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> Update examples/preprocessing/plot_csd.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> Update mne/preprocessing/tests/test_csd.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <larson.eric.d@gmail.com> halfway through Eric suggested changes getting on plane WIP Eric comments almost done testing fixes updated fif constants csd formatting small change references

…ork for csd

alexrockhill · 2019-11-12T16:58:21Z

@agramfort I'm not sure if there was a versioning issue but there weren't any evo in the last one, they had all been changed to evoked... not sure what happened there. Anyway, I did as you suggested, and it should be good to go now.

examples/preprocessing/plot_csd.py

agramfort

we've never been so close ! thx for your patience and energy @alexrockhill !

examples/preprocessing/plot_eeg_csd.py

agramfort · 2019-11-12T21:16:48Z

mne/io/edf/tests/test_edf.py

    """Test stim_channel."""
-    TYPE_LUT = {v[0]: k for k, v in _KIND_DICT.items()}
+    # This is fragile for EEG/EEG-CSD, so just omit csd
+    TYPE_LUT = {v[0]: k for k, v in _KIND_DICT.items() if k != 'csd'}


having to change something outside seems like a code smell. @larsoner any thought? why is this needed?

agramfort · 2019-11-12T21:17:44Z

mne/io/tests/test_pick.py

-    for t, rules in get_channel_types().items():
+    # go in order from most specific (most rules entries) to least specific
+    channel_types = sorted(
+        get_channel_types().items(), key=lambda x: len(x[1]))[::-1]


what specific means in this context was not clear to me.

mne/preprocessing/_csd.py

agramfort · 2019-11-13T07:19:46Z

thx heaps @alexrockhill for leading this effort !

alexrockhill force-pushed the csd branch from ebf9c0b to c32e6f3 Compare October 4, 2019 04:22