New feature for removing heart artifacts from EEG or ESG data using a Principal Component Analysis - Optimal Basis Sets (PCA-OBS) algorithm #13037
Conversation
This file contains 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
Updating master with most recent package features
feat: add initial source code
for more information, see https://pre-commit.ci
…e size of indentation tree
…ove more unused variables and imports, add some types
…et data from, how we call functions, how we assert outputs
Update PCA OBS fork with most recent changes in main MNE repo
…ogging to use mne logger instead of prints, add wrapper method in front of private _pca_obs method to handle parallel processing
… to have consistent patterns
Sounds good! Thanks for the feedback. Removed conditional return in d170c39 |
* upstream/main: [DOC] extend documentation for add_channels (mne-tools#13051) Add `combine_tfr` to API (mne-tools#13054) Add `combine_spectrum()` function and allow `grand_average()` to support `Spectrum` data (mne-tools#13058) BUG: Fix bug with helium anon (mne-tools#13056) [ENH] Add option to store and return TFR taper weights (mne-tools#12910)
drammock
requested changes
Jan 16, 2025
Fix typo Co-authored-by: Daniel McCloy <[email protected]>
add punctuation Co-authored-by: Daniel McCloy <[email protected]>
Co-authored-by: Daniel McCloy <[email protected]>
drammock
approved these changes
Jan 17, 2025
|
pip-pre will fail until #13069 lands, which contains a fix |
|
Marking for merge-when-green, thanks in advance @emma-bailey @steinnhauser ! |
|
🎉 Congrats on merging your first pull request! 🥳 Looking forward to seeing more from you in the future! 💪 |
qian-chu
pushed a commit
to qian-chu/mne-python
that referenced
this pull request
Jan 20, 2025
… Principal Component Analysis - Optimal Basis Sets (PCA-OBS) algorithm (mne-tools#13037) Co-authored-by: Emma Bailey <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Steinn Magnusson <[email protected]> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: emma-bailey <[email protected]> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]>
larsoner
added a commit
to larsoner/mne-python
that referenced
this pull request
Jan 24, 2025
* upstream/main: (57 commits) Allow lasso selection sensors in a plot_evoked_topo (mne-tools#12071) MAINT: Fix doc build (mne-tools#13076) BUG: Improve sklearn compliance (mne-tools#13065) [pre-commit.ci] pre-commit autoupdate (mne-tools#13073) MAINT: Add Numba to 3.13 test (mne-tools#13075) Bump autofix-ci/action from ff86a557419858bb967097bfc916833f5647fa8c to 551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef in the actions group (mne-tools#13071) [BUG] Correct annotation onset for exportation to EDF and EEGLAB (mne-tools#12656) New feature for removing heart artifacts from EEG or ESG data using a Principal Component Analysis - Optimal Basis Sets (PCA-OBS) algorithm (mne-tools#13037) [BUG] Fix taper weighting in computation of TFR multitaper power (mne-tools#13067) [FIX] Reading an EDF with preload=False and mixed frequency (mne-tools#13069) Fix evoked topomap colorbars, closes mne-tools#13050 (mne-tools#13063) [pre-commit.ci] pre-commit autoupdate (mne-tools#13060) BUG: Fix bug with interval calculation (mne-tools#13062) [DOC] extend documentation for add_channels (mne-tools#13051) Add `combine_tfr` to API (mne-tools#13054) Add `combine_spectrum()` function and allow `grand_average()` to support `Spectrum` data (mne-tools#13058) BUG: Fix bug with helium anon (mne-tools#13056) [ENH] Add option to store and return TFR taper weights (mne-tools#12910) BUG: viz plot window's 'title' argument showed no effect. (mne-tools#12828) MAINT: Ensure limited set of tests are skipped (mne-tools#13053) ...
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
What does this implement/fix?
Our PR implements the PCA-OBS algorithm for removal of heart-artefacts from EEG or ESG datasets. The PCA-OBS algorithm was originally designed to remove the ballistocardiographic artefact in simultaneous EEG-fMRI. Here, it has been adapted to remove the delay between the detected R-peak and the ballistocardiographic artefact such that the algorithm can be applied to remove the cardiac artefact in EEG (electroencephalogrpahy) and ESG (electrospinography) data.
Positive and negative tests have been implemented for the feature, and we have also included an example script which is implemented using data from
openneuro(dataset ID:ds004388).Authors:
Emma Bailey [email protected]
Steinn Hauser Magnusson [email protected]