Enh/adaptive kernel

[essink]

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

[pep8speaks]

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

• In the file elephant/statistics.py:

Line 1495:1: W293 blank line contains whitespace Line 1498:1: W293 blank line contains whitespace Line 1501:1: E302 expected 2 blank lines, found 1 Line 1504:1: W293 blank line contains whitespace Line 1519:1: E302 expected 2 blank lines, found 1 Line 1523:80: E501 line too long (81 > 79 characters) Line 1533:80: E501 line too long (88 > 79 characters) Line 1534:54: W291 trailing whitespace Line 1569:1: E302 expected 2 blank lines, found 1 Line 1590:1: E302 expected 2 blank lines, found 1 Line 1593:1: E302 expected 2 blank lines, found 1 Line 1765:1: E302 expected 2 blank lines, found 1 Line 1799:1: W293 blank line contains whitespace Line 1801:53: W291 trailing whitespace Line 1802:46: E127 continuation line over-indented for visual indent Line 1804:1: W293 blank line contains whitespace Line 1811:1: W293 blank line contains whitespace Line 1834:80: E501 line too long (83 > 79 characters) Line 1835:80: E501 line too long (83 > 79 characters) Line 1842:80: E501 line too long (88 > 79 characters) Line 1843:44: E128 continuation line under-indented for visual indent Line 1851:80: E501 line too long (88 > 79 characters) Line 1852:44: E128 continuation line under-indented for visual indent Line 1864:1: W293 blank line contains whitespace Line 1866:5: E303 too many blank lines (2) Line 1886:80: E501 line too long (85 > 79 characters) Line 1892:80: E501 line too long (82 > 79 characters) Line 1909:1: E302 expected 2 blank lines, found 1 Line 1910:75: W291 trailing whitespace Line 1911:65: W291 trailing whitespace Line 1912:80: E501 line too long (81 > 79 characters) Line 1913:27: E251 unexpected spaces around keyword / parameter equals Line 1913:29: E251 unexpected spaces around keyword / parameter equals Line 1917:41: W291 trailing whitespace Line 1925:1: W293 blank line contains whitespace Line 1939:80: E501 line too long (91 > 79 characters) Line 1940:37: E128 continuation line under-indented for visual indent Line 1940:80: E501 line too long (83 > 79 characters) Line 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79 characters) Line 2170:80: E501 line too long (89 > 79 characters) Line 2171:1: W293 blank line contains whitespace Line 2174:1: W293 blank line contains whitespace Line 2178:1: W293 blank line contains whitespace Line 2179:54: W291 trailing whitespace Line 2183:1: W293 blank line contains whitespace Line 2186:52: W291 trailing whitespace Line 2189:80: W291 trailing whitespace Line 2190:52: W291 trailing whitespace Line 2192:80: E501 line too long (101 > 79 characters) Line 2199:80: E501 line too long (87 > 79 characters) Line 2200:60: W291 trailing whitespace Line 2210:80: E501 line too long (87 > 79 characters) Line 2211:60: W291 trailing whitespace Line 2216:64: W291 trailing whitespace Line 2220:1: W293 blank line contains whitespace Line 2221:80: E501 line too long (81 > 79 characters) Line 2223:80: E501 line too long (84 > 79 characters) Line 2224:1: W293 blank line contains whitespace Line 2229:1: W293 blank line contains whitespace Line 2231:1: W293 blank line contains 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[Moritz-Alexander-Kern]

todo

• [ ] create unittests (check against authors' implementation, see: https://github.com/shimazaki/AdaptiveKDE)
• [ ] restructure code (?)
• [ ] refactor based on development guidelines (parameter names, docstrings)

[coveralls]

Coverage: 86.325% (-0.09%) from 86.418% when pulling cdbd26d907937b003c9c7a51a37c88cbd2052935 on INM-6:enh/adaptive_kernel into 471bf0f1b04e6faa821020a31722c520853ddec2 on NeuralEnsemble:master.

[Moritz-Alexander-Kern]

Stale, feel free to reopen if this project is continued.