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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.
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.
2016-03-24+function for saving spike trains to txt filesMario Mulansky
save_spike_trains_to_txt allows to save spike train data into txt files which can then be loaded via load_spike_trains_from_txt again.
2015-12-14removed directionality from __init__ and setup.pyMario Mulansky
2015-12-14py3: absolute_importIgor Gnatenko
Signed-off-by: Igor Gnatenko <i.gnatenko.brain@gmail.com>
2015-08-12new spike delay asymmetry measuresMario Mulansky
added first version of spike delay asymmetry functions. still incomplete and untested.
2015-07-07add disable_backend_warning propertyMario Mulansky
Users can now disable the warning messages produced when the cython backend is not available by writing spk.disable_backend_warning = True in the beginning
2015-04-30addresses #5 - added __version__ propertyMario Mulansky
2015-04-24further adjustments in spike syncMario 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.
2015-02-03first version of psth profileMario Mulansky
2015-02-03copyright, docsMario Mulansky
2015-02-03split distance.py into 3 separate modulesMario Mulansky
2015-01-28each function class in separate source fileMario Mulansky
2015-01-20added spike sync matrixMario Mulansky
2015-01-19renamed IntervalSequence -> DiscreteFunction, cython implementation of addMario Mulansky
2015-01-19final version for spike syncMario Mulansky
2014-12-26spike syncMario Mulansky
2014-12-12+spike synchronization, python impl onlyMario Mulansky
2014-11-21added spike generation functionMario Mulansky
2014-10-16added spike_matrix, refactoring dist matrix functsMario Mulansky
2014-10-16changed function names distance -> profiles,Mario Mulansky
added distance functions
2014-10-15+average_profile functionMario Mulansky
2014-10-13changed to BSD licenseMario Mulansky
2014-10-10added License note in headersMario Mulansky
2014-10-10added load_txt function, some restructuringMario Mulansky
2014-10-02+isi distance matrix with examplesMario Mulansky
2014-09-29+ multivariate distancesMario Mulansky
2014-09-26+ add_auxiliary_spikes function incl testMario Mulansky
2014-09-18add spike-distance, PWL function (probably buggy)Mario Mulansky
2014-09-15+merge_spike_trainsMario Mulansky
2014-09-15isi distance and basic exampleMario Mulansky
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