diff options
Diffstat (limited to 'pyspike/isi_distance.py')
| -rw-r--r-- | pyspike/isi_distance.py | 82 |
1 files changed, 42 insertions, 40 deletions
diff --git a/pyspike/isi_distance.py b/pyspike/isi_distance.py index c2ef8e8..aeab0df 100644 --- a/pyspike/isi_distance.py +++ b/pyspike/isi_distance.py @@ -1,11 +1,6 @@ -""" - -Module containing several functions to compute the ISI profiles and distances - -Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> - -Distributed under the BSD License -""" +# Module containing several functions to compute the ISI profiles and distances +# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> +# Distributed under the BSD License from pyspike import PieceWiseConstFunc from pyspike.generic import _generic_profile_multi, _generic_distance_matrix @@ -14,23 +9,23 @@ from pyspike.generic import _generic_profile_multi, _generic_distance_matrix ############################################################ # isi_profile ############################################################ -def isi_profile(spikes1, spikes2): - """ Computes the isi-distance profile :math:`S_{isi}(t)` of the two given - spike trains. Retruns the profile as a PieceWiseConstFunc object. The S_isi - values are defined positive S_isi(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. - - :param spikes1: ordered array of spike times with auxiliary spikes. - :param spikes2: ordered array of spike times with auxiliary spikes. - :returns: The isi-distance profile :math:`S_{isi}(t)` - :rtype: :class:`pyspike.function.PieceWiseConstFunc` +def isi_profile(spike_train1, spike_train2): + """ Computes the isi-distance profile :math:`I(t)` of the two given + spike trains. Retruns the profile as a PieceWiseConstFunc object. The + ISI-values are defined positive :math:`I(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 isi-distance profile :math:`I(t)` + :rtype: :class:`.PieceWiseConstFunc` """ - # 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!" # load cython implementation @@ -45,29 +40,32 @@ Falling back to slow python backend.") from cython.python_backend import isi_distance_python \ as isi_distance_impl - times, values = isi_distance_impl(spikes1, spikes2) + times, values = isi_distance_impl(spike_train1.spikes, spike_train2.spikes, + spike_train1.t_start, spike_train1.t_end) return PieceWiseConstFunc(times, values) ############################################################ # isi_distance ############################################################ -def isi_distance(spikes1, spikes2, interval=None): - """ Computes the isi-distance I of the given spike trains. The +def isi_distance(spike_train1, spike_train2, interval=None): + """ Computes the ISI-distance :math:`D_I` of the given spike trains. The isi-distance is the integral over the isi distance profile - :math:`S_{isi}(t)`: + :math:`I(t)`: - .. math:: I = \int_{T_0}^{T_1} S_{isi}(t) dt. + .. math:: D_I = \\int_{T_0}^{T_1} I(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:`.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 isi-distance I. + :returns: The isi-distance :math:`D_I`. :rtype: double """ - return isi_profile(spikes1, spikes2).avrg(interval) + return isi_profile(spike_train1, spike_train2).avrg(interval) ############################################################ @@ -76,15 +74,17 @@ def isi_distance(spikes1, spikes2, interval=None): def isi_profile_multi(spike_trains, indices=None): """ computes the multi-variate isi distance profile for a set of spike trains. That is the average isi-distance of all pairs of spike-trains: - S_isi(t) = 2/((N(N-1)) sum_{<i,j>} S_{isi}^{i,j}, + + .. math:: <I(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j}, + where the sum goes over all pairs <i,j> - :param spike_trains: list 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 state: list or None - :returns: The averaged isi profile :math:`<S_{isi}>(t)` - :rtype: :class:`pyspike.function.PieceWiseConstFunc` + :returns: The averaged isi profile :math:`<I(t)>` + :rtype: :class:`.PieceWiseConstFunc` """ average_dist, M = _generic_profile_multi(spike_trains, isi_profile, indices) @@ -98,16 +98,18 @@ def isi_profile_multi(spike_trains, indices=None): def isi_distance_multi(spike_trains, indices=None, interval=None): """ computes the multi-variate isi-distance for a set of spike-trains. That is the time average of the multi-variate spike profile: - I = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{isi}^{i,j}, + + .. math:: D_I = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j}, + where the sum goes over all pairs <i,j> - :param spike_trains: list 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) :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 time-averaged isi distance :math:`I` + :returns: The time-averaged multivariate ISI distance :math:`D_I` :rtype: double """ return isi_profile_multi(spike_trains, indices).avrg(interval) @@ -119,7 +121,7 @@ def isi_distance_multi(spike_trains, indices=None, interval=None): def isi_distance_matrix(spike_trains, indices=None, interval=None): """ Computes the time averaged isi-distance of all pairs of spike-trains. - :param spike_trains: list 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 @@ -127,7 +129,7 @@ def isi_distance_matrix(spike_trains, indices=None, interval=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 isi distances - :math:`I_{ij}` + :math:`D_{I}^{ij}` :rtype: np.array """ return _generic_distance_matrix(spike_trains, isi_distance, |