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2018-09-20Spike Order support (#39)0.6.0Mario Mulansky
* 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.
2018-02-04Make merge_spike_trains work with empty spike trains, and fasterJonathan Jouty
1. Fixes https://github.com/mariomulansky/PySpike/issues/30 2. Code is faster 3. Add test case
2016-06-18added missing data files for testsMario Mulansky
2016-06-18Merge branch 'import_time_series' into developMario Mulansky
Conflicts: pyspike/__init__.py resolved
2016-06-18added function to import time seriesMario Mulansky
new function import_spike_trains_from_time_series that loads spike trains from time series.
2016-03-24bugfix for Python 3 (xrange->range)Mario Mulansky
2016-03-24added test for save spike train functionalityMario Mulansky
2016-02-03fixed spike-sync bugMario Mulansky
fixed ugly bugs in code for computing multi-variate spike sync profile and multi-variate spike sync value.
2016-02-02new generic interface for spike_sync functionsMario Mulansky
Similar to the isi and spike distance functions, also the spike sync functions now support the new generic interface.
2016-01-31generic interface for spike distance/profileMario Mulansky
spike_profile and spike_distance now have a generic interface that allows to compute bi-variate and multi-variate results with the same function.
2016-01-31generalized interface to isi profile and distanceMario Mulansky
isi profile and distance functionc an now compute bi-variate and multi-variate results. Therefore, it can be called with different "overloads".
2016-01-28+numeric test of profilesMario Mulansky
2015-12-22moved extensive random spike test to test/numericMario Mulansky
2015-12-22changed edge correction for single spikesMario Mulansky
Spike trains with single spikes now only get auxiliary spikes at the edges for the SPIKE distance instead of real spikes before.
2015-12-19python3 print function in new regression testMario Mulansky
2015-12-18bugfix for edge correctionMario Mulansky
fixed bug within new edge correction (auxiliary spike was ignored in some cases) added regression test with 10000 random spike train sets
2015-12-14remove directionality from developMario Mulansky
directionality development happens in separate branch.
2015-12-14Merge branch 'develop' of github.com:mariomulansky/PySpike into developMario Mulansky
2015-12-14improved edge correction for spike distanceMario Mulansky
Improvement following Eeros suggestions to use auxiliary spike at the edges consistently with the corresponding corrected ISI intervals.
2015-12-14tests: allow to run out-of-treeIgor Gnatenko
Signed-off-by: Igor Gnatenko <i.gnatenko.brain@gmail.com>
2015-12-14py3: divisionIgor Gnatenko
Signed-off-by: Igor Gnatenko <i.gnatenko.brain@gmail.com>
2015-12-14py3: xrange() -> range()Igor Gnatenko
Signed-off-by: Igor Gnatenko <i.gnatenko.brain@gmail.com>
2015-08-17major renaming of spike train order functionsMario Mulansky
2015-08-17first unit tests for directionalityMario Mulansky
2015-08-17fix for #14Mario Mulansky
test case and fix for Issue #14. Spike-Sync function now correctly deal with empty intervals as well.
2015-08-17fix #15Mario Mulansky
add test case and fix for Issue #15 closes #15
2015-08-11add regression #11 test caseMario Mulansky
2015-05-17return correct values at exact spike timesMario Mulansky
pwc and pwl function object return the average of the left and right limit as function value at the exact spike times.
2015-05-13pwc function now returns intermediate value at exact spike timesMario Mulansky
2015-05-12+functions to obtain values of the pwc/pwl profileMario Mulansky
Added __call__ operators to PieceWiseConst and PieceWiseLin class for obtaining function values at certain points in time.
2015-05-11bugfix: spike_sync=1 for empty spike trainsMario Mulansky
2015-05-11treatment of empty spike trains in spike syncMario Mulansky
2015-05-11updated copyright yearMario Mulansky
2015-05-11treatment of empty spike trains in spike distanceMario Mulansky
2015-05-11treatment of empty spike trains in isi functionsMario Mulansky
2015-05-07performance improvementsMario Mulansky
use recursive approach to compute average profile for average multivariate distances, dont compute average multivariate profile, but average distances directly.
2015-04-28edge correction for the ISI-distanceMario Mulansky
2015-04-24bugfixes for spike distanceMario Mulansky
2015-04-24renamed interval -> edges in load functionsMario Mulansky
2015-04-24removed auxiliary_spike test, all tests passMario Mulansky
2015-04-24distance tests now pass with new spike trainsMario Mulansky
2015-04-24further adjustments in spike syncMario Mulansky
2015-04-24changed spike sync implementation to SpikeTrainMario Mulansky
2015-04-24changed spike distance to use new SpikeTrain classMario Mulansky
2015-04-22added SpikeTrain class, changed isi_distanceMario Mulansky
spike trains are now represented as SpikeTrain objects consisting of the spike times and the interval edges. The implementation of the ISI-distance has been modified accordingly. The SPIKE-distance and SPIKE-Synchronization are still to be done.
2015-04-02added max_tau to spike_sync functionsMario Mulansky
2015-01-28each function class in separate source fileMario Mulansky
2015-01-22better test for subsets of spike train listsMario Mulansky
added another test case to check if the computation of the multi-variate distance is correct if only a subset of the given spike trains is to be considered.
2015-01-22test mutlivariate with subset of spike trainsMario Mulansky
2015-01-20added spike sync matrixMario Mulansky
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