ENH: Add source space SNR estimate #6908

klankinen · 2019-10-03T20:57:05Z

estimate_snr was moved from class BaseSourceEstimate to class SourceEstimate, as it currently works properly only for fixed orientation
a quick check for fixed/free orientation and warning was also added (see if all the values for etc are > 0)
G used in calculating b_k2 should not be whitened, otherwise it gives wrong results. This was corrected by taking first output from _prepare_forward function instead of the third one. The correct G to be used is G = G['sol']['data']
tutorial was updated with examples of MEG-EEG, EEG and MEG according to the reference article

Fixes #1453

…of whitened, updated tutorial file

mne/source_estimate.py

tutorials/source-modeling/plot_source_space_SNR.py

mne/source_estimate.py

codecov · 2019-10-04T14:57:24Z

Codecov Report

Merging #6908 into master will decrease coverage by 0.01%.
The diff coverage is 12.5%.

@@            Coverage Diff             @@
##           master    #6908      +/-   ##
==========================================
- Coverage   89.67%   89.66%   -0.02%     
==========================================
  Files         426      426              
  Lines       76294    76336      +42     
  Branches    12436    12438       +2     
==========================================
+ Hits        68417    68445      +28     
- Misses       5102     5116      +14     
  Partials     2775     2775

larsoner · 2019-10-04T16:42:55Z

@klankinen I'll push a small commit with some tweaks then this should be good to go

larsoner · 2019-10-04T17:19:13Z

https://16029-1301584-gh.circle-artifacts.com/0/dev/auto_examples/inverse/plot_source_space_SNR.html

jasmainak

LGTM can merge if CIs are happy

larsoner · 2019-10-04T20:12:15Z

Whoops, should have asked for latest.inc update. @klankinen @padmasundaram can you give me a URL you want me to add to names.inc and I'll make a quick push to master?

jasmainak · 2019-10-05T18:03:06Z

I also realized that there is no test ...

agramfort · 2019-10-05T19:13:25Z

Naughty @larsoner !

larsoner · 2019-10-05T20:43:08Z

Whoops! I'll make a follow-up PR Monday

@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

@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

@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

@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

@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

@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

@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

@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

@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

@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

@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

@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

@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

@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

@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

@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

@drammock

* CSD with working example and tests 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 (#6911) * Fix julian date conversions * remove tabs * use UTC and private functions. closes #6901 [skip travis][skip azp] (#6914) ENH: Add source space SNR estimate (#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 (#6913) * Added dSPM * removed term signal covariance * Minor modification of dSPM definition * Corrected according to Mattis suggestions [MRG]: read *.dat electrode position files (#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 (#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 (#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 (#6920) * MAINT: Simplify code for vol ravel * STY: Flake ENH: Convert NIRS raw data to optical density (#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 * improve tests, dropped bad channels from data for consistency * could have totally messed a bunch of stuff up, but got the units to work for csd * clarified check test; all zeros or any non-finite fail * added test for pick, fixed meas_info * changed formatting * BUG: Clean up picking and related functions * FIX: Plotting order * FIX: Cruft * FIX: Cleanups from review * small doc change * FIX: ref_meg * AG suggestions * pare down on examples * messed everything up, fixing it * Last AG suggestions

padmasundaram and others added 20 commits October 1, 2019 14:43

source-snr-edit

244e2cc

FIX move estimate_snr to be a method

908e7b9

ENH: name change

f9fb26b

Make it work

d954ae4

SNR works, now clean up code

aef9f00

fixed unnecessary stc copy, returns stc object

a013fe7

added plot source space SNR tutorial file

3b4a93d

updated author names

a80c567

fixed period for pydocsty and suggested documenation edit

5ad490f

edits suggested from @drammock

9bf444e

made edits suggested by reviewers

6e3106b

made edits suggested by reviewers

04012cf

N -> n_channels

3213d2b

Fixed formatting of Reference in comment

3efeba9

fixed formatting in doc and in code

beac772

fixed snr_stc creation

60c1fd0

further minor edits

dbcff92

fixed formatting issues and colormap choice in eg

66fdd89

removed colon after Reference

39b64fb

Corrected SNR calculation to take unwhitened sensor signal b instead …

48a7c70

…of whitened, updated tutorial file

larsoner changed the title ~~Snr 1453~~ ENH: Add source space SNR estimate Oct 3, 2019

larsoner mentioned this pull request Oct 3, 2019

ENH: Add source space SNR estimate #6886

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Minor changes to formatting

7cd0057

FIX: transparent

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larsoner force-pushed the SNR_1453 branch from bd555d1 to fb2655f Compare October 4, 2019 16:55

FIX: Rename

40c4713

FIX?

8c65e2e

jasmainak approved these changes Oct 4, 2019

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larsoner merged commit 341a078 into mne-tools:master Oct 4, 2019

larsoner mentioned this pull request Oct 8, 2019

MRG, FIX: Add tests for estimate_snr #6928

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ENH: Add source space SNR estimate #6908

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