diff options
Diffstat (limited to 'pyspike/spike_sync.py')
| -rw-r--r-- | pyspike/spike_sync.py | 73 |
1 files changed, 41 insertions, 32 deletions
diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py index e12ebb8..9d2e363 100644 --- a/pyspike/spike_sync.py +++ b/pyspike/spike_sync.py @@ -1,12 +1,7 @@ -""" - -Module containing several functions to compute SPIKE-Synchronization profiles -and distances - -Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> - -Distributed under the BSD License -""" +# Module containing several functions to compute SPIKE-Synchronization profiles +# and distances +# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> +# Distributed under the BSD License from functools import partial from pyspike import DiscreteFunc @@ -16,22 +11,27 @@ from pyspike.generic import _generic_profile_multi, _generic_distance_matrix ############################################################ # spike_sync_profile ############################################################ -def spike_sync_profile(spikes1, spikes2, max_tau=None): +def spike_sync_profile(spike_train1, spike_train2, max_tau=None): """ Computes the spike-synchronization profile S_sync(t) of the two given spike trains. Returns the profile as a DiscreteFunction object. The S_sync values are either 1 or 0, indicating the presence or absence of a - coincidence. The spike trains are expected to have auxiliary spikes at the - beginning and end of the interval. Use the function add_auxiliary_spikes to - add those spikes to the spike train. + coincidence. - :param spikes1: ordered array of spike times with auxiliary spikes. - :param spikes2: ordered array of spike times with auxiliary spikes. + :param spike_train1: First spike train. + :type spike_train1: :class:`pyspike.SpikeTrain` + :param spike_train2: Second spike train. + :type spike_train2: :class:`pyspike.SpikeTrain` :param max_tau: Maximum coincidence window size. If 0 or `None`, the - coincidence window has no upper bound. + coincidence window has no upper bound. :returns: The spike-distance profile :math:`S_{sync}(t)`. :rtype: :class:`pyspike.function.DiscreteFunction` """ + # check whether the spike trains are defined for the same interval + assert spike_train1.t_start == spike_train2.t_start, \ + "Given spike trains seems not to have auxiliary spikes!" + assert spike_train1.t_end == spike_train2.t_end, \ + "Given spike trains seems not to have auxiliary spikes!" # cython implementation try: @@ -48,7 +48,10 @@ Falling back to slow python backend.") if max_tau is None: max_tau = 0.0 - times, coincidences, multiplicity = coincidence_impl(spikes1, spikes2, + times, coincidences, multiplicity = coincidence_impl(spike_train1.spikes, + spike_train2.spikes, + spike_train1.t_start, + spike_train1.t_end, max_tau) return DiscreteFunc(times, coincidences, multiplicity) @@ -57,24 +60,28 @@ Falling back to slow python backend.") ############################################################ # spike_sync ############################################################ -def spike_sync(spikes1, spikes2, interval=None, max_tau=None): +def spike_sync(spike_train1, spike_train2, interval=None, max_tau=None): """ Computes the spike synchronization value SYNC of the given spike trains. The spike synchronization value is the computed as the total number of coincidences divided by the total number of spikes: .. math:: SYNC = \sum_n C_n / N. - :param spikes1: ordered array of spike times with auxiliary spikes. - :param spikes2: ordered array of spike times with auxiliary spikes. + :param spike_train1: First spike train. + :type spike_train1: :class:`pyspike.SpikeTrain` + :param spike_train2: Second spike train. + :type spike_train2: :class:`pyspike.SpikeTrain` :param interval: averaging interval given as a pair of floats (T0, T1), - if None the average over the whole function is computed. + if `None` the average over the whole function is computed. :type interval: Pair of floats or None. :param max_tau: Maximum coincidence window size. If 0 or `None`, the - coincidence window has no upper bound. + coincidence window has no upper bound. :returns: The spike synchronization value. - :rtype: double + :rtype: `double` + """ - return spike_sync_profile(spikes1, spikes2, max_tau).avrg(interval) + return spike_sync_profile(spike_train1, spike_train2, + max_tau).avrg(interval) ############################################################ @@ -87,21 +94,21 @@ def spike_sync_profile_multi(spike_trains, indices=None, max_tau=None): spike trains pairs involving the spike train of containing this spike, which is the number of spike trains minus one (N-1). - :param spike_trains: list of spike trains + :param spike_trains: list of :class:`pyspike.SpikeTrain` :param indices: list of indices defining which spike trains to use, if None all given spike trains are used (default=None) :type indices: list or None :param max_tau: Maximum coincidence window size. If 0 or `None`, the - coincidence window has no upper bound. + coincidence window has no upper bound. :returns: The multi-variate spike sync profile :math:`<S_{sync}>(t)` :rtype: :class:`pyspike.function.DiscreteFunction` """ prof_func = partial(spike_sync_profile, max_tau=max_tau) - average_dist, M = _generic_profile_multi(spike_trains, prof_func, + average_prof, M = _generic_profile_multi(spike_trains, prof_func, indices) # average_dist.mul_scalar(1.0/M) # no normalization here! - return average_dist + return average_prof ############################################################ @@ -111,7 +118,7 @@ def spike_sync_multi(spike_trains, indices=None, interval=None, max_tau=None): """ Computes the multi-variate spike synchronization value for a set of spike trains. - :param spike_trains: list of spike trains + :param spike_trains: list of :class:`pyspike.SpikeTrain` :param indices: list of indices defining which spike trains to use, if None all given spike trains are used (default=None) :type indices: list or None @@ -119,9 +126,10 @@ def spike_sync_multi(spike_trains, indices=None, interval=None, max_tau=None): the average over the whole function is computed. :type interval: Pair of floats or None. :param max_tau: Maximum coincidence window size. If 0 or `None`, the - coincidence window has no upper bound. + coincidence window has no upper bound. :returns: The multi-variate spike synchronization value SYNC. :rtype: double + """ return spike_sync_profile_multi(spike_trains, indices, max_tau).avrg(interval) @@ -134,7 +142,7 @@ def spike_sync_matrix(spike_trains, indices=None, interval=None, max_tau=None): """ Computes the overall spike-synchronization value of all pairs of spike-trains. - :param spike_trains: list of spike trains + :param spike_trains: list of :class:`pyspike.SpikeTrain` :param indices: list of indices defining which spike trains to use, if None all given spike trains are used (default=None) :type indices: list or None @@ -142,10 +150,11 @@ def spike_sync_matrix(spike_trains, indices=None, interval=None, max_tau=None): the average over the whole function is computed. :type interval: Pair of floats or None. :param max_tau: Maximum coincidence window size. If 0 or `None`, the - coincidence window has no upper bound. + coincidence window has no upper bound. :returns: 2D array with the pair wise time spike synchronization values :math:`SYNC_{ij}` :rtype: np.array + """ dist_func = partial(spike_sync, max_tau=max_tau) return _generic_distance_matrix(spike_trains, dist_func, |