From 34bd30415dd93a2425ce566627e24ee9483ada3e Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Thu, 20 Sep 2018 10:49:42 -0700 Subject: Spike Order support (#39) * reorganized directionality module * further refactoring of directionality * completed python directionality backend * added SPIKE-Sync based filtering new function filter_by_spike_sync removes spikes that have a multi-variate Spike Sync value below some threshold not yet fully tested, python backend missing. * spike sync filtering, cython sim ann Added function for filtering out events based on a threshold for the spike sync values. Usefull for focusing on synchronous events during directionality analysis. Also added cython version of simulated annealing for performance. * added coincidence single profile to python backend missing function in python backend added, identified and fixed a bug in the implementation as well * updated test case to new spike sync behavior * python3 fixes * another python3 fix * reorganized directionality module * further refactoring of directionality * completed python directionality backend * added SPIKE-Sync based filtering new function filter_by_spike_sync removes spikes that have a multi-variate Spike Sync value below some threshold not yet fully tested, python backend missing. * spike sync filtering, cython sim ann Added function for filtering out events based on a threshold for the spike sync values. Usefull for focusing on synchronous events during directionality analysis. Also added cython version of simulated annealing for performance. * added coincidence single profile to python backend missing function in python backend added, identified and fixed a bug in the implementation as well * updated test case to new spike sync behavior * python3 fixes * another python3 fix * Fix absolute imports in directionality measures * remove commented code * Add directionality to docs, bump version * Clean up directionality module, add doxy. * Remove debug print from tests * Fix bug in calling Python backend * Fix incorrect integrals in PieceWiseConstFunc (#36) * Add (some currently failing) tests for PieceWiseConstFunc.integral * Fix implementation of PieceWiseConstFunc.integral Just by adding a special condition for when we are only taking an integral "between" two edges of a PieceWiseConstFunc All tests now pass. Fixes #33. * Add PieceWiseConstFunc.integral tests for ValueError * Add testing bounds of integral * Raise ValueError in function implementation * Fix incorrect integrals in PieceWiseLinFunc (#38) Integrals of piece-wise linear functions were incorrect if the requested interval lies completely between two support points. This has been fixed, and a unit test exercising this behavior was added. Fixes #38 * Add Spike Order example and Tutorial section Adds an example computing spike order profile and the optimal spike train order. Also adds a section on spike train order to the tutorial. --- Readme.rst | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) (limited to 'Readme.rst') diff --git a/Readme.rst b/Readme.rst index 0422dad..74b014b 100644 --- a/Readme.rst +++ b/Readme.rst @@ -31,19 +31,14 @@ Additionally, depending on the used methods: ISI-distance [1], SPIKE-distance [2 Important Changelog ----------------------------- +With version 0.6.0, the spike directionality and spike train order function have been added. + With version 0.5.0, the interfaces have been unified and the specific functions for multivariate computations have become deprecated. With version 0.2.0, the :code:`SpikeTrain` class has been introduced to represent spike trains. This is a breaking change in the function interfaces. Hence, programs written for older versions of PySpike (0.1.x) will not run with newer versions. - -Upcoming Functionality -------------------------- - -In an upcoming release, new functionality for analyzing Synfire patterns based on the new measures SPIKE-Order and Spike-Train-Order method will become part of the PySpike library. -The new measures and algorithms are described in `this preprint `_. - Requirements and Installation ----------------------------- -- cgit v1.2.3