diff options
Diffstat (limited to 'pyspike/spike_distance.py')
| -rw-r--r-- | pyspike/spike_distance.py | 37 |
1 files changed, 21 insertions, 16 deletions
diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py index f721c86..8d03d70 100644 --- a/pyspike/spike_distance.py +++ b/pyspike/spike_distance.py @@ -14,23 +14,23 @@ from pyspike.generic import _generic_profile_multi, _generic_distance_matrix ############################################################ # spike_profile ############################################################ -def spike_profile(spikes1, spikes2): +def spike_profile(spike_train1, spike_train2): """ Computes the spike-distance profile S_spike(t) of the two given spike trains. Returns the profile as a PieceWiseLinFunc object. The S_spike - values are defined positive S_spike(t)>=0. 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. + values are defined positive S_spike(t)>=0. - :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` :returns: The spike-distance profile :math:`S_{spike}(t)`. :rtype: :class:`pyspike.function.PieceWiseLinFunc` """ - # check for auxiliary spikes - first and last spikes should be identical - assert spikes1[0] == spikes2[0], \ + # 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 spikes1[-1] == spikes2[-1], \ + assert spike_train1.t_end == spike_train2.t_end, \ "Given spike trains seems not to have auxiliary spikes!" # cython implementation @@ -45,21 +45,26 @@ Falling back to slow python backend.") from cython.python_backend import spike_distance_python \ as spike_distance_impl - times, y_starts, y_ends = spike_distance_impl(spikes1, spikes2) + times, y_starts, y_ends = spike_distance_impl(spike_train1.spikes, + spike_train2.spikes, + spike_train1.t_start, + spike_train1.t_end) return PieceWiseLinFunc(times, y_starts, y_ends) ############################################################ # spike_distance ############################################################ -def spike_distance(spikes1, spikes2, interval=None): +def spike_distance(spike_train1, spike_train2, interval=None): """ Computes the spike-distance S of the given spike trains. The spike-distance is the integral over the isi distance profile S_spike(t): .. math:: S = \int_{T_0}^{T_1} S_{spike}(t) dt. - :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. :type interval: Pair of floats or None. @@ -67,7 +72,7 @@ def spike_distance(spikes1, spikes2, interval=None): :rtype: double """ - return spike_profile(spikes1, spikes2).avrg(interval) + return spike_profile(spike_train1, spike_train2).avrg(interval) ############################################################ @@ -102,7 +107,7 @@ def spike_distance_multi(spike_trains, indices=None, interval=None): S_{spike} = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{spike}^{i, j} dt where the sum goes over all pairs <i,j> - :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 @@ -121,7 +126,7 @@ def spike_distance_multi(spike_trains, indices=None, interval=None): 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 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 |