Additional option to flatten TMS artifact #6915
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@@ Coverage Diff @@
## master #6915 +/- ##
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+ Coverage 89.55% 89.65% +0.1%
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Files 430 430
Lines 76952 76985 +33
Branches 12549 12552 +3
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+ Hits 68915 69023 +108
+ Misses 5215 5149 -66
+ Partials 2822 2813 -9 |
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@fmamashli can you update what's new after addressing my small comment? |
I checked if the mean during baseline is equal to the data from the TMS artifact time interval. I only checked one sample. I think that should be fine. |
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CIs are failing |
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Don't forget to update the |
What is Cls? |
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The status icons toward the bottom of this PR page. For example from a few commits ago, Travis CI was unhappy: |
Co-Authored-By: Mainak Jas <[email protected]>
Co-Authored-By: Mainak Jas <[email protected]>
Co-Authored-By: Mainak Jas <[email protected]>
Co-Authored-By: Mainak Jas <[email protected]>
Co-Authored-By: Mainak Jas <[email protected]>
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mne/preprocessing/stim.py
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| @@ -55,10 +63,13 @@ def fix_stim_artifact(inst, events=None, event_id=None, tmin=0., | |||
| Start time of the interpolation window in seconds. | |||
| tmax : float | |||
| End time of the interpolation window in seconds. | |||
| mode : 'linear' | 'window' | |||
| baseline: None or tuple of length 2 | |||
| When mode = 'constant', baseline is required | |||
mne/preprocessing/stim.py
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| s_start = int(np.ceil(inst.info['sfreq'] * tmin)) | ||
| s_end = int(np.ceil(inst.info['sfreq'] * tmax)) | ||
| if mode == "constant" and baseline is None: | ||
| raise ValueError('Please provide the baseline for mode="constant"') |
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use the function _check_baseline to make sure that base_t1 and base_t2 provided by the user are good
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It's a bit more complicated than this because this function can also operate on raw instances.
Given this I'm just going to make it take a tuple of length 2 containing floats only, a follow-up PR could make it support None for Epochs if it makes sense. But in the meantime I don't mind the extra explicitness!
* upstream/main: (3619 commits) MAINT: Update code credit [ci skip] (mne-tools#13029) MAINT: Credit [ci skip] Add `raw.rescale` (mne-tools#13018) MAINT: Automerge for bot PRs (mne-tools#13015) MAINT: Also update fsaverage in sample (mne-tools#13009) Revert "[ENH] Add fig.mne container for colorbar (mne-tools#13019)" [ENH] Add fig.mne container for colorbar (mne-tools#13019) BUG: Better Wayland and open-source 3D support (mne-tools#13012) DEP: Support Python 3.13 (mne-tools#13021) MAINT: Audit CIs using zizmor (mne-tools#13011) [BUG] Fix simple documentation bug (mne-tools#13020) [pre-commit.ci] pre-commit autoupdate (mne-tools#13017) [pre-commit.ci] pre-commit autoupdate (mne-tools#13001) expose transform_to_head in API docs (mne-tools#13010) Fix cnt response (mne-tools#13007) ENH: Add round-trip channel name saving (mne-tools#13003) update governance (mne-tools#12896) pin selenium and stop filtering its warning (mne-tools#13000) DOC: fix return value doc of inst.get_montage() (mne-tools#12995) remove some ._filenames uses in favor of .filenames (mne-tools#12996) ...
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Merged with |
larsoner
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drammock,
agramfort and
dengemann
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OpenNeuro is having a bad day so I'm going to manually merge |
Co-authored-by: Mainak Jas <[email protected]> Co-authored-by: Eric Larson <[email protected]>
Reference issue
I added 'constant' mode to the fix_stim_artifact which uses the baseline to flatten the TMS pulse artifact.
What does this implement/fix?
It provides smoother signal relative to the 'linear' and 'window' mode.