# Module containing several functions to compute SPIKE profiles and distances # Copyright 2014-2015, Mario Mulansky # Distributed under the BSD License from pyspike import PieceWiseLinFunc from pyspike.generic import _generic_profile_multi, _generic_distance_multi, \ _generic_distance_matrix ############################################################ # spike_profile ############################################################ def spike_profile(spike_train1, spike_train2): """ Computes the spike-distance profile :math:`S(t)` of the two given spike trains. Returns the profile as a PieceWiseLinFunc object. The SPIKE-values are defined positive :math:`S(t)>=0`. :param spike_train1: First spike train. :type spike_train1: :class:`.SpikeTrain` :param spike_train2: Second spike train. :type spike_train2: :class:`.SpikeTrain` :returns: The spike-distance profile :math:`S(t)`. :rtype: :class:`.PieceWiseLinFunc` """ # check whether the spike trains are defined for the same interval assert spike_train1.t_start == spike_train2.t_start, \ "Given spike trains are not defined on the same interval!" assert spike_train1.t_end == spike_train2.t_end, \ "Given spike trains are not defined on the same interval!" # cython implementation try: from cython.cython_profiles import spike_profile_cython \ as spike_profile_impl except ImportError: print("Warning: spike_profile_cython not found. Make sure that \ PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \ Falling back to slow python backend.") # use python backend from cython.python_backend import spike_distance_python \ as spike_profile_impl times, y_starts, y_ends = spike_profile_impl( spike_train1.get_spikes_non_empty(), spike_train2.get_spikes_non_empty(), spike_train1.t_start, spike_train1.t_end) return PieceWiseLinFunc(times, y_starts, y_ends) ############################################################ # spike_distance ############################################################ def spike_distance(spike_train1, spike_train2, interval=None): """ Computes the spike-distance :math:`D_S` of the given spike trains. The spike-distance is the integral over the isi distance profile :math:`S(t)`: .. math:: D_S = \int_{T_0}^{T_1} S(t) dt. :param spike_train1: First spike train. :type spike_train1: :class:`.SpikeTrain` :param spike_train2: Second spike train. :type spike_train2: :class:`.SpikeTrain` :param interval: averaging interval given as a pair of floats (T0, T1), if None the average over the whole function is computed. :type interval: Pair of floats or None. :returns: The spike-distance. :rtype: double """ if interval is None: # distance over the whole interval is requested: use specific function # for optimal performance try: from cython.cython_distances import spike_distance_cython \ as spike_distance_impl return spike_distance_impl(spike_train1.get_spikes_non_empty(), spike_train2.get_spikes_non_empty(), spike_train1.t_start, spike_train1.t_end) except ImportError: # Cython backend not available: fall back to average profile return spike_profile(spike_train1, spike_train2).avrg(interval) else: # some specific interval is provided: compute the whole profile return spike_profile(spike_train1, spike_train2).avrg(interval) ############################################################ # spike_profile_multi ############################################################ def spike_profile_multi(spike_trains, indices=None): """ Computes the multi-variate spike distance profile for a set of spike trains. That is the average spike-distance of all pairs of spike-trains: .. math:: = \\frac{2}{N(N-1)} \\sum_{} S^{i, j}`, where the sum goes over all pairs :param spike_trains: list of :class:`.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 :returns: The averaged spike profile :math:`(t)` :rtype: :class:`.PieceWiseLinFunc` """ average_dist, M = _generic_profile_multi(spike_trains, spike_profile, indices) average_dist.mul_scalar(1.0/M) # normalize return average_dist ############################################################ # spike_distance_multi ############################################################ def spike_distance_multi(spike_trains, indices=None, interval=None): """ Computes the multi-variate spike distance for a set of spike trains. That is the time average of the multi-variate spike profile: .. math:: D_S = \\int_0^T \\frac{2}{N(N-1)} \\sum_{} S^{i, j} dt where the sum goes over all pairs :param spike_trains: list of :class:`.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 interval: averaging interval given as a pair of floats, if None the average over the whole function is computed. :type interval: Pair of floats or None. :returns: The averaged multi-variate spike distance :math:`D_S`. :rtype: double """ return _generic_distance_multi(spike_trains, spike_distance, indices, interval) ############################################################ # spike_distance_matrix ############################################################ def spike_distance_matrix(spike_trains, indices=None, interval=None): """ Computes the time averaged spike-distance of all pairs of spike-trains. :param spike_trains: list of :class:`.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 interval: averaging interval given as a pair of floats, if None the average over the whole function is computed. :type interval: Pair of floats or None. :returns: 2D array with the pair wise time average spike distances :math:`D_S^{ij}` :rtype: np.array """ return _generic_distance_matrix(spike_trains, spike_distance, indices, interval)