diff options
Diffstat (limited to 'pyspike/isi_distance.py')
| -rw-r--r-- | pyspike/isi_distance.py | 59 |
1 files changed, 29 insertions, 30 deletions
diff --git a/pyspike/isi_distance.py b/pyspike/isi_distance.py index cb8ef54..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 @@ -15,16 +10,16 @@ from pyspike.generic import _generic_profile_multi, _generic_distance_matrix # isi_profile ############################################################ def isi_profile(spike_train1, spike_train2): - """ 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. + """ 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:`pyspike.SpikeTrain` + :type spike_train1: :class:`.SpikeTrain` :param spike_train2: Second spike train. - :type spike_train2: :class:`pyspike.SpikeTrain` - :returns: The isi-distance profile :math:`S_{isi}(t)` - :rtype: :class:`pyspike.function.PieceWiseConstFunc` + :type spike_train2: :class:`.SpikeTrain` + :returns: The isi-distance profile :math:`I(t)` + :rtype: :class:`.PieceWiseConstFunc` """ # check whether the spike trains are defined for the same interval @@ -54,20 +49,20 @@ Falling back to slow python backend.") # isi_distance ############################################################ def isi_distance(spike_train1, spike_train2, interval=None): - """ Computes the isi-distance I of the given spike trains. The + """ 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 spike_train1: First spike train. - :type spike_train1: :class:`pyspike.SpikeTrain` + :type spike_train1: :class:`.SpikeTrain` :param spike_train2: Second spike train. - :type spike_train2: :class:`pyspike.SpikeTrain` + :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(spike_train1, spike_train2).avrg(interval) @@ -79,15 +74,17 @@ def isi_distance(spike_train1, spike_train2, 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 :class:`pyspike.SpikeTrain` + :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) @@ -101,16 +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) @@ -122,7 +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 :class:`pyspike.SpikeTrain` + :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 @@ -130,7 +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, |