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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
2016-06-18Merge 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.
2016-03-24quick fix in format stringMario Mulansky
2016-03-24add empty spike trains when loading from txtMario Mulansky
treatment of empty lines was incorrect. now empty spike trains are created from empty lines in the txt file if parameter ignore_empty_lines=False is given.
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.
2016-03-09deprecated old multivariate functionsMario Mulansky
with the new interface, the previous functions for computing multivariate profiles and distances are obsolete. This is now noted in the docs.
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".
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.
2015-12-18removed print outs from python backendMario 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
2015-12-14removed directionality from __init__ and setup.pyMario Mulansky
2015-12-14remove directionality from developMario Mulansky
directionality development happens in separate branch.
2015-12-14python backend updated for new edge correctionMario Mulansky
Eero's improved edge correction now also implemented in the python backend.
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.
2015-12-14py3: 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>
2015-12-14py3: absolute_importIgor Gnatenko
Signed-off-by: Igor Gnatenko <i.gnatenko.brain@gmail.com>
2015-08-17add python backend for directionalityMario Mulansky
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
2015-08-13more directionality functionsMario Mulansky
+ spike delay asymmetry profile + spike delay dual profile
2015-08-12new spike delay asymmetry measuresMario Mulansky
added first version of spike delay asymmetry functions. still incomplete and untested.
2015-08-11Merge branch 'ImmanuelSamuel-master' into developMario Mulansky
fixes #11
2015-08-10Added more //ImmanuelSamuel
2015-08-10Used // instead of type conversionImmanuelSamuel
2015-08-10Syntax correctionImmanuelSamuel
2015-08-10Indices for matrix slicing needs to be integersImmanuelSamuel
Dividing the indices by 2 gives a float which cannot be used for slicing the matrix. Changed the type of the indices to integer to ensure that matrix slicing does not return error.
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
2015-06-24fixed typoMario Mulansky
2015-06-12implement __getitem__ and __len__ for SpikeTrainMario Mulansky
This allows to use SpikeTrain objects to be used in many applications as if they were arrays with spike times.
2015-05-18Merge branch 'master' into developMario Mulansky
Conflicts: setup.py
2015-05-18cosmeticsMario 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
2015-05-11treatment of empty spike trains in spike distanceMario Mulansky
2015-05-11treatment of empty spike trains in isi functionsMario Mulansky
2015-05-11performance improvement for spike syncMario Mulansky
Additional cython implementation for overall spike sync values. It is not necessary to compute the profile anymore if only the spike sync value is required. 3x performance gain.
2015-05-08introduce backend for distance functionMario Mulansky
isi- and spike distances over complete intervals are now computed without obtaining the profile first. This gives more than x2 performance improvements.
2015-05-08renamed cython_distance module -> cython_profilesMario Mulansky
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