WIP: STC baseline correction #8452
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mne/tests/test_source_estimate.py
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| times = stc.times | ||
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| for baseline in baselines: |
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I would do
| for baseline in baselines: | |
| for (start, stop) in baselines: |
mne/tests/test_source_estimate.py
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| # test on different source estimates | ||
| stcs = [] | ||
| stcs.append(read_source_estimate(fname_stc)) | ||
| stcs.append(read_source_estimate(fname_vol, 'sample')) |
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| stcs.append(read_source_estimate(fname_vol, 'sample')) | |
| stcs = [read_source_estimate(fname_stc), read_source_estimate(fname_vol, 'sample')] |
mne/tests/test_source_estimate.py
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| if baseline[1] is None: | ||
| t1 = stc.times[-1] | ||
| else: | ||
| t1 = baseline[1] |
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I would do t1 = baseline or stc.times[-1]
mne/tests/test_source_estimate.py
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| else: | ||
| t1 = baseline[1] | ||
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| # indec for baseline interval (include boundary latencies) |
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| # indec for baseline interval (include boundary latencies) | |
| # index for baseline interval (include boundary latencies) |
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@jona-sassenhagen Thanks a lot - I hope I managed to implement all your suggestions. I cannot make sense of the following build_docs complaints: /home/circleci/project/mne/source_estimate.py:docstring of mne.MixedSourceEstimate.apply_baseline:31: WARNING: Explicit markup ends without a blank line; unexpected unindent. |
Merge branch 'master' into stc_baseline_correction
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I don't think the remaining errors have anything to do with me - please let me know. |
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I restarted Azure and it's green now. |
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@olafhauk You need to mark this PR as ready for review so it can be merged |
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@jona-sassenhagen Merge if you're happy |
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was missing a what's new entry... @olafhauk can you make a PR to get credit for this work? |
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Reference issue
#8232
What does this implement/fix?
Baseline-correction for source estimates is recommended/necessary for some processing steps. For example, for unsigned source estimates, differences in noise levels may result in differences in intensities (e.g. for conditions with very different numbers of trials). This can be compenstated for by baseline-correction.
I will add a method appy_baseline() to source_estimate.py, analogous to evoked.py. I will add documentation to highlight the caveats of baseline correction for source estimates.
Additional information
Any additional information you think is important.