Add "autoreject_local" as new option for preprocessing/ptp_reject
#807
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hoechenberger
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hoechenberger
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hoechenberger
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hoechenberger
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hoechenberger
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Thanks @larsoner |
hoechenberger
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@larsoner I believe the CI error may have to do with mne-tools/mne-python#12156 |
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Tries to fix CI error we get for mne-bids-pipeline: mne-tools/mne-bids-pipeline#807 (comment) This is a followup-fix for mne-tools#12156
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hoechenberger
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| if cfg.reject == "autoreject_local": | ||
| import numpy as np | ||
| import autoreject | ||
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| msg = "Using autoreject to find and repair bad epochs" | ||
| logger.info(**gen_log_kwargs(message=msg)) | ||
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| ar = autoreject.AutoReject( | ||
| n_interpolate=np.array(cfg.autoreject_n_interpolate), | ||
| random_state=cfg.random_state, | ||
| n_jobs=exec_params.n_jobs, | ||
| verbose=False, | ||
| ) | ||
| n_epochs_before_reject = len(epochs) | ||
| epochs, reject_log = ar.fit_transform(epochs, return_log=True) | ||
| n_epochs_after_reject = len(epochs) | ||
| assert ( | ||
| n_epochs_before_reject - n_epochs_after_reject | ||
| == reject_log.bad_epochs.sum() | ||
| ) | ||
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| msg = ( | ||
| f"autoreject marked {reject_log.bad_epochs.sum()} epochs as bad " | ||
| f"(cross-validated n_interpolate limit: {ar.n_interpolate_})" | ||
| ) | ||
| logger.info(**gen_log_kwargs(message=msg)) | ||
| else: | ||
| reject = _get_reject( |
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The diff doesn't look nice here, but I basically just added this new if block and moved the previous code into the else section
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Output looks like this now: I just restarted CI to take advantage of mne-tools/mne-python#12167 |
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We're green! |
hoechenberger
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larsoner
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Nov 3, 2023
Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
…nto autoreject-local
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@larsoner I've addressed your comments |
larsoner
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Nov 3, 2023
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Before merging …
docs/source/changes.md)closes #410
cc @dengemann