Make peak detection (locally_exclussive, matched_filtering) faster and more accurate. #4341
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Great, this is cool, looking forward to try it out ! But what about the matched filtering ? |
samuelgarcia
changed the title
| templates=None, | ||
| peak_sign="neg", | ||
| exclude_sweep_ms=0.1, | ||
| exclude_sweep_ms=0.8, |
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You're using 0.8 for all the internal sorters, but 1.0 for the defaults in detect_peaks. Is this deliberate?
| # if inside spatial zone ... | ||
| if abs(samples_inds[i] - samples_inds[j]) <= exclude_sweep_size: | ||
| # ...and if inside tempral zone ... | ||
| value_i = abs(traces[samples_inds[i], chan_inds[i]]) / abs_thresholds[chan_inds[i]] |
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So here, the abs_threshold is proportional to the noise on the channel. What's the advantage of using the noise normalised value? Is this to avoid peaks on very noisy channels?
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This avoid that a peak is eliminated even if the snr is higher.
It was not the case before. This is a marjor change in this PR when the noise_levels is different over channel.
I think this is more correct
| if peak_sign == "both": | ||
| peak_mask_pos = peak_mask.copy() | ||
| if samples_inds[i] - exclude_sweep_size > samples_inds[j]: | ||
| next_start = j |
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| next_start = j | |
| next_start = j+1 |
shave off those nanoseconds ;)
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not sure. why ?
The following j will do it if nessecary.
4 participants
After playing a bit with the rust language, and trying to reimplement the peak detection algo using "locally_exclussive"
I discover that the actual impelmentation could be fasten a lot (at least 3X faster on my machine).
"matched_filtering" has also beeb changed in this PR.
Also the new implementation is is more accurate for corener cases :
Also I change the
exclude_sweep_ms=0.1at many place in the code this was a bad value by default it has to be half on the peak waveforms or a bit more.