MRG: allow users to annotate epochs with colors #6855

jasmainak · 2019-10-01T04:33:51Z

just started by copying over changes from autoreject. Will iterate tomorrow

mne/viz/epochs.py

codecov · 2019-10-03T02:23:39Z

Codecov Report

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jasmainak · 2019-10-03T03:36:50Z

okay, this now works in conjunction with this PR on autoreject: https://github.com/autoreject/autoreject/pull/155/files

next step is tests

mne/viz/epochs.py

mne/viz/tests/test_epochs.py

jasmainak · 2019-10-04T18:46:17Z

comments addressed

agramfort · 2019-10-04T18:53:48Z

mne/viz/epochs.py

        .. versionadded:: 0.18.0
    %(show_scrollbars)s
+    color : list of list, shape (n_epochs, n_channels) | None
+        Colors to use for individual epochs. If None, use default colors


Suggested change

Colors to use for individual epochs. If None, use default colors

Colors to use for individual epochs. If None, use default colors.

agramfort · 2019-10-04T18:55:17Z

mne/viz/tests/test_epochs.py

+    epochs.plot(color=color)
+    with pytest.raises(TypeError, match='must be an instance of'):
+        epochs.plot(color='r')
+    with pytest.raises(ValueError, match='color must be list'):


Suggested change

with pytest.raises(ValueError, match='color must be list'):

with pytest.raises(ValueError, match='must be list of len'):

drammock · 2019-10-04T19:06:48Z

@jasmainak would be great to have a demo of this functionality in one of the examples / tutorials.

agramfort

1+ to illustrate this in an tutorial. For example at the bottom of the https://mne.tools/stable/auto_tutorials/epochs/plot_visualize_epochs.html#sphx-glr-auto-tutorials-epochs-plot-visualize-epochs-py

mne/viz/epochs.py

jasmainak · 2019-10-04T19:30:01Z

@drammock we agreed with @larsoner that for now we don't expose this in a tutorial or example. The main purpose of this PR is to fix autoreject which fails now with the latest MNE release.

If we want to expose this in a tutorial, the correct approach would be to allow also a flat list, not just a nested list of list as it's more complicated to demo in an example. Then you would have to implement broadcasting and the code begins to get more complicated. Probably not worth the effort and future complexity in maintaining the code

agramfort

please just add a tiny entry in API section of latest.inc and we're good !

jasmainak · 2019-10-05T17:34:14Z

CIs are happy

agramfort · 2019-10-05T19:11:11Z

Thx @jasmainak

@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

* 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

@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

jasmainak mentioned this pull request Oct 1, 2019

Fix epochs plotter autoreject/autoreject#155

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larsoner reviewed Oct 2, 2019

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mne/viz/epochs.py Outdated Show resolved Hide resolved

jasmainak changed the title ~~ENH: copy over diff from autoreject~~ WIP: allow users to annotate epochs with colors Oct 3, 2019

jasmainak force-pushed the color_epochs_plot branch from 188cf1c to ce327a9 Compare October 3, 2019 03:33

jasmainak marked this pull request as ready for review October 3, 2019 03:34

larsoner reviewed Oct 4, 2019

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jasmainak added 7 commits October 4, 2019 13:29

ENH: copy over diff from autoreject

132fd36

Make it work

696d1a7

More fixes

d04106a

More fixes

7ced661

Make horizontal patch

3fdd14c

Cleanup

d563d98

TST: add tests

484cd58

jasmainak force-pushed the color_epochs_plot branch from b041572 to 1492c75 Compare October 4, 2019 17:39

jasmainak changed the title ~~WIP: allow users to annotate epochs with colors~~ MRG: allow users to annotate epochs with colors Oct 4, 2019

agramfort reviewed Oct 4, 2019

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jasmainak force-pushed the color_epochs_plot branch 2 times, most recently from c4f1eb9 to fbaee4c Compare October 4, 2019 19:09

agramfort reviewed Oct 4, 2019

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Address Eric's comments

63ebb21

jasmainak force-pushed the color_epochs_plot branch from fbaee4c to 63ebb21 Compare October 4, 2019 19:21

Address alex comments

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DOC: update whats new

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jasmainak changed the title ~~MRG: allow users to annotate epochs with colors~~ WIP: allow users to annotate epochs with colors Oct 5, 2019

FIX travis + circle

c8b81df

jasmainak changed the title ~~WIP: allow users to annotate epochs with colors~~ MRG: allow users to annotate epochs with colors Oct 5, 2019

FIX For ICA plot

8ce9b4f

agramfort merged commit b42a91c into mne-tools:master Oct 5, 2019

jasmainak mentioned this pull request Oct 5, 2019

ENH: Add epochs_color argument to epochs.plot #6923

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	Colors to use for individual epochs. If None, use default colors
	Colors to use for individual epochs. If None, use default colors.

	with pytest.raises(ValueError, match='color must be list'):
	with pytest.raises(ValueError, match='must be list of len'):

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MRG: allow users to annotate epochs with colors #6855

MRG: allow users to annotate epochs with colors #6855

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