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Add computation of smoothed firing rates for spike trains #189

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merged 4 commits into from
Feb 9, 2020

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jpgill86
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@jpgill86 jpgill86 commented Feb 9, 2020

This is a major new feature used when lazy loading is off lazy=False.

Smoothed firing rates may be computed via spike train convolution, stored as annotations of the SpikeTrain objects, and plotted in the GUI. Users may specify a convolution kernel from the elephant package, or use the CausalAlphaKernel provided by neurotic.

See the documentation for details: https://neurotic.readthedocs.io/en/latest/metadata.html#firing-rates

The old behavior would issue a warning when a negative firing rate was detected. Because of machine precision errors, this warning was almost always issued. This change removes the warning and instead clips the values, so that negative firing rates are replaced with zero.
@jpgill86 jpgill86 added the enhancement New feature or request label Feb 9, 2020
@jpgill86 jpgill86 added this to the 1.4.0 milestone Feb 9, 2020
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Coverage Status

Coverage decreased (-3.7%) to 51.983% when pulling f727f2c on firing-rates into 070d209 on master.

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coveralls commented Feb 9, 2020

Coverage Status

Coverage decreased (-3.7%) to 51.984% when pulling f727f2c on firing-rates into 070d209 on master.

@jpgill86 jpgill86 merged commit a14a901 into master Feb 9, 2020
@jpgill86 jpgill86 deleted the firing-rates branch February 9, 2020 03:08
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