Fix infomax #6921
Merged
Fix infomax #6921
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Member
|
+1 for merge and backport once CIs are happy |
agramfort
approved these changes
Oct 5, 2019
mne/preprocessing/ica.py
Outdated
Comment on lines
362
to
363
| ext = fit_params.get('extended', False) | ||
| fit_params.update({'extended': ext}) |
Member
There was a problem hiding this comment.
Could use a single line
fit_params.setdefault('extended', False)
Member
Author
There was a problem hiding this comment.
ooh, that is nicer. Thanks.
Codecov Report
@@ Coverage Diff @@
## master #6921 +/- ##
==========================================
+ Coverage 89.66% 89.66% +<.01%
==========================================
Files 426 426
Lines 76336 76332 -4
Branches 12438 12436 -2
==========================================
- Hits 68447 68445 -2
Misses 5114 5114
+ Partials 2775 2773 -2 |
christianbrodbeck
approved these changes
Oct 5, 2019
agramfort
pushed a commit
that referenced
this pull request
Oct 5, 2019
* fix extended infomax * update whats new * cleaner way, using setdefault
Member
|
back ported to 0.19 branch |
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 6, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 28, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 29, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 29, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 29, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 29, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 29, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 29, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 29, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 29, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Oct 31, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Nov 1, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Nov 4, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Nov 4, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Nov 8, 2019
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
alexrockhill
pushed a commit
to alexrockhill/mne-python
that referenced
this pull request
Nov 12, 2019
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
agramfort
pushed a commit
that referenced
this pull request
Nov 13, 2019
* 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
closes #6919