Switch to kernel for local CAR#4454
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alejoe91 merged 13 commits intoSpikeInterface:mainfrom Mar 19, 2026
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backup reference for local reference when local channels too few; knn can be more robust than local as it ensures the # of reference channels
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alejoe91
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Mar 18, 2026
| assert np.allclose(traces[:, 0], rec_local_cmr.get_traces()[:, 0] + np.median(traces[:, [2, 3]], axis=1), atol=0.01) | ||
| assert np.allclose(traces[:, 1], rec_local_cmr.get_traces()[:, 1] + np.median(traces[:, [3]], axis=1), atol=0.01) | ||
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| # TODO: fix this!!! |
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It's fixed, I was missing a transpose in the code :P
alejoe91
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Mar 19, 2026
src/spikeinterface/preprocessing/tests/test_common_reference.py
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| warnings.warn( | ||
| "Using a local median reference can be very computationally intensive. Consider using a local " | ||
| "average reference instead or pre-computing the local median reference and using the 'single' " | ||
| "reference option." | ||
| ) |
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I find this warning a bit annoying, since you can't turn it off if you use local + median. I also don't understand the second part of the warning. It sounds like I can pre-compute the reference and pass it? Can I??
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Yeah the second part doesn't make sense. Shoudl I just remove it?
chrishalcrow
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Mar 19, 2026
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This looks good to me and is working about x10 faster locally (loading big traces on the GUI). Thanks!
Just mild complaints about warnings ;)
alejoe91
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Mar 19, 2026
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Following up on #4412
Added a "kernel" mode for local CAR: when computing the common average referencing, we can simply pre-compute a kernel with 1/local_neighbors for each channel and use it in the
get_traceswith a simple dot product, skipping an inefficient channel loop.This makes the
get_tracesx10 faster (added a skipped test to test locally):