ENH: Add eSSS #762
ENH: Add eSSS #762
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@drammock could be a good one for you to review and merge since it's pretty straightforward in terms of how to add something! |
| # Now take everything from the bids_path_in and overwrite the parameters | ||
| subject = bids_path_in.subject # noqa: F841 | ||
| session = bids_path_in.session # noqa: F841 | ||
| run = bids_path_in.run | ||
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This fixes a logging bug where it used to look like this:
[20:05:28] │ ⏳️ preprocessing/_03_maxfilter sub-01 Saving report: /home/larsoner/mne_data/derivatives/mne-bids-pipeline/ds003392/sub-01/meg/sub-01_task-localizer_report.html
[20:05:28] │ ⏳️ preprocessing/_03_maxfilter sub-emptyroom ses-19111211 run-noise Loading reference run: None.
instead of this:
[20:12:13] │ ⏳️ preprocessing/_03_maxfilter sub-01 Saving report: /home/larsoner/mne_data/derivatives/mne-bids-pipeline/ds003392/sub-01/meg/sub-01_task-localizer_report.html
[20:12:13] │ ⏳️ preprocessing/_03_maxfilter sub-01 run-noise Loading reference run: None.
The logging of which file/step we're on makes more sense now I think, and is also consistent with how _01_data_quality and _04_frequency_filter were already logging:
[20:11:40] │ ⏳️ preprocessing/_01_data_quality sub-01 Saving report: /home/larsoner/mne_data/derivatives/mne-bids-pipeline/ds003392/sub-01/meg/sub-01_task-localizer_report.html
[20:11:40] │ ⏳️ preprocessing/_01_data_quality sub-01 run-noise Finding flat channels and noisy channels using Maxwell filtering.
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[20:12:37] │ ⏳️ preprocessing/_04_frequency_filter sub-01 Saving report: /home/larsoner/mne_data/derivatives/mne-bids-pipeline/ds003392/sub-01/meg/sub-01_task-localizer_report.html
[20:12:38] │ ⏳️ preprocessing/_04_frequency_filter sub-01 run-noise Reading empty-room recording: sub-01_task-noise_proc-sss_raw.fif
| import gc | ||
| from typing import Optional | ||
| from types import SimpleNamespace | ||
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| import numpy as np | ||
| import mne | ||
| from mne.utils import _pl |
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of all the cases of using a private function outside its package, this is quite possibly the most innocuous. But still I feel it's my duty to say that if we're going to use _pl outside of MNE-Python then we should make it public.
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And this too:
mne_bids_pipeline/_config_import.py:from mne.utils import _check_option, _validate_type
but I can at least replicate the _pl here to avoid that one. Maybe check_option and validate_type should be public at some point... but I've always been annoyed their signatures don't have the name/val in the same order, so making them public feels dissatisfying :(
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Okay got rid of _pl and made #766 to mention _check_option and _validate_type
| run, task = None, "noise" | ||
| in_key = f"raw_task-{task}_run-{run}" | ||
| bids_path_in = in_files.pop(in_key) | ||
| bids_path_bads_in = in_files.pop(f"{in_key}-bads", None) # noqa |
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this is F841 (assigned but never used): why not assign to underscore? I see the commented-out TODO below but don't really understand it.
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Because eventually we should use this (with the given variable filename) but we have an unaddressed bug. So to me it helps to have the variable name we should be using here, and it commented out (with that same name) below to at least establish the link (which you did implicitly already, even if you didn't understand the "why aren't we actually using it" part!)
* upstream/main: ENH: More compact logging (mne-tools#764)
* upstream/main: ENH: Add eSSS (mne-tools#762)
Before merging …
docs/source/changes.md)Might not be 100% working yet but I think it's close