ENH: Convert NIRS raw data to optical density #6827
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larsoner
reviewed
Sep 26, 2019
Codecov Report
@@ Coverage Diff @@
## master #6827 +/- ##
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- Coverage 89.67% 89.66% -0.01%
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Files 427 428 +1
Lines 76317 76389 +72
Branches 12439 12440 +1
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+ Hits 68439 68498 +59
- Misses 5099 5116 +17
+ Partials 2779 2775 -4 |
larsoner
reviewed
Sep 27, 2019
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Thanks @larsoner, now I need to actually write the code 😆 |
rob-luke
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@rob-luke it would be really great to have a tutorial using a public dataset like we have sample for MEG/EEG. It would help a lot to document this new code |
@agramfort thanks for the suggestion. I haven’t been able to find a relevant dataset online, so I’ve been recording my own to upload when complete (but I’ll keep looking in the meantime). |
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The best set I have been able to find is this but the file are in the old format (version 14.1) whereas the reader in MNE currently only supports files with version 15.2. I would like to support 15.1 too, but that will take a bit of a rewrite, version 14 is too far back for me. |
I actually think this is the best option because we can make sure it has everything you need to show all functionality. We can upload it to the MNE-Python OSF account if you want. |
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larsoner
reviewed
Oct 2, 2019
rob-luke
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I have uploaded a small jupyter notebook to show that this approach gives a similar value to a MATLAB implementation https://github.com/rob-luke/mne-fnirs-demo/blob/master/OpticalDensity_Validation.ipynb I uploaded the data to the repo too, so the result should be reproducible. I will update once I have recorded a proper data set. I need to add some more tests, then this PR should be ready to go. |
larsoner
reviewed
Oct 3, 2019
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FYI master currently has a docstyle bug, will fix momentarily |
larsoner
reviewed
Oct 4, 2019
Co-Authored-By: Eric Larson <[email protected]>
Co-Authored-By: Eric Larson <[email protected]>
Co-Authored-By: Eric Larson <[email protected]>
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That failure is not your fault, it's spurious and happens from time to time. I'll open a separate PR to fix it. I've restarted it in the meantime |
larsoner
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agramfort
reviewed
Oct 4, 2019
Co-Authored-By: Alexandre Gramfort <[email protected]>
larsoner
reviewed
Oct 5, 2019
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Thanks @rob-luke! |
alexrockhill
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Do not operate in place for optical density * Force data to load and modify test to include preload=False condition
agramfort
reviewed
Oct 6, 2019
| from ..utils import _validate_type, warn | ||
| from ..io.pick import _picks_to_idx | ||
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| import numpy as np |
There was a problem hiding this comment.
numpy should have been imported before mne stuff
| # not occur. If they do it is likely due to hardware or movement issues. | ||
| # Set all negative values to abs(x), this also has the benefit of ensuring | ||
| # that the means are all greater than zero for the division below. | ||
| if len(np.where(raw._data[picks] <= 0)[0]) > 0: |
There was a problem hiding this comment.
if np.any(raw._data[picks] <= 0):
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| import pytest as pytest | ||
| import numpy as np | ||
| from numpy.testing import assert_allclose |
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same remark. Imports should be from more general packages to local ones
Merged
alexrockhill
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Do not operate in place for optical density * Force data to load and modify test to include preload=False condition
alexrockhill
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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
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that referenced
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/tests/test_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> halfway through Eric suggested changes getting on plane WIP Eric comments almost done testing fixes
alexrockhill
pushed a commit
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/tests/test_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/tests/test_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> halfway through Eric suggested changes getting on plane WIP Eric comments almost done testing fixes updated fif constants csd formatting small change references
alexrockhill
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/tests/test_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/tests/test_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/tests/test_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> 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
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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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Alexandre Gramfort <[email protected]> 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 <[email protected]> * Update mne/preprocessing/tests/test_optical_density.py Co-Authored-By: Eric Larson <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Update examples/preprocessing/plot_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/tests/test_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> Update mne/preprocessing/_csd.py Co-Authored-By: Eric Larson <[email protected]> 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
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What does this implement/fix?
This PR adds the ability to convert raw fnirs data (see #6674) to optical density (see description)