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Enh/adaptive kernel #462

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Enh/adaptive kernel #462

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@essink essink commented Mar 14, 2022

This pull request arose from #461

While investigating the issue, it seemed reasonable to restructure the code, such that intermediate results are easily accessible. A look into the originating package AdaptiveKDE showed, that the existing elephant code of estimating one fixed optimal kernel bandwidth (sskernel) could be easily extended cover the adaptive case (ssvkernel).

To avoid code duplications both cases were integrated into a class called KernelBandwidth.

(See original publication Shimazaki, H. & Shinomoto, S. Kernel bandwidth optimization in spike rate estimation. J Comput Neurosci 29, 171–182 (2010). for details)

Open TODOs:

  • Preliminary testing suggests that the code reproduces the results of AdaptiveKDE and the optimal_kernel_bandwidth function. But there is definitely need to check this systematically!
  • proper integration into the elephant.statistics.instantaneous_rate function
  • naming of the functions and variables was a bit ad-hoc and could be improved with a bit of thinking
  • remove old code

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Hello @essink! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

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@Moritz-Alexander-Kern Moritz-Alexander-Kern mentioned this pull request Mar 15, 2022
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@Moritz-Alexander-Kern Moritz-Alexander-Kern added this to the v0.12.0 milestone Mar 31, 2022
@Moritz-Alexander-Kern Moritz-Alexander-Kern linked an issue Apr 4, 2022 that may be closed by this pull request
[Bug] optimal_kernel_bandwidth yields extremely large kernel widths #461
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@Moritz-Alexander-Kern Moritz-Alexander-Kern modified the milestones: v0.12.0, v0.13.0 Dec 5, 2022
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Moritz-Alexander-Kern commented Dec 5, 2022 •
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todo

@Moritz-Alexander-Kern Moritz-Alexander-Kern added the enhancement Editing an existing module, improving something label Dec 5, 2022
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coveralls commented Dec 7, 2022 •
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Coverage Status

Coverage: 86.325% (-0.09%) from 86.418% when pulling cdbd26d on INM-6:enh/adaptive_kernel into 471bf0f on NeuralEnsemble:master.

@Moritz-Alexander-Kern Moritz-Alexander-Kern removed this from the v0.13.0 milestone Apr 24, 2023
@Moritz-Alexander-Kern Moritz-Alexander-Kern self-requested a review May 26, 2023 09:17
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Stale, feel free to reopen if this project is continued.

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[Bug] optimal_kernel_bandwidth yields extremely large kernel widths
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