diff options
Diffstat (limited to 'pyspike/spike_distance.py')
| -rw-r--r-- | pyspike/spike_distance.py | 58 |
1 files changed, 29 insertions, 29 deletions
diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py index 8d03d70..cc620d4 100644 --- a/pyspike/spike_distance.py +++ b/pyspike/spike_distance.py @@ -1,11 +1,6 @@ -""" - -Module containing several functions to compute SPIKE profiles and distances - -Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> - -Distributed under the BSD License -""" +# Module containing several functions to compute SPIKE profiles and distances +# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> +# Distributed under the BSD License from pyspike import PieceWiseLinFunc from pyspike.generic import _generic_profile_multi, _generic_distance_matrix @@ -15,16 +10,16 @@ from pyspike.generic import _generic_profile_multi, _generic_distance_matrix # spike_profile ############################################################ 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. + """ 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:`pyspike.SpikeTrain` + :type spike_train1: :class:`.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` + :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 @@ -56,15 +51,15 @@ Falling back to slow python backend.") # spike_distance ############################################################ 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): + """ 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:: S = \int_{T_0}^{T_1} S_{spike}(t) dt. + .. math:: D_S = \int_{T_0}^{T_1} S(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. @@ -81,15 +76,17 @@ def spike_distance(spike_train1, spike_train2, interval=None): 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:`S_spike(t) = 2/((N(N-1)) sum_{<i,j>} S_{spike}^{i, j}`, + + .. math:: <S(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} S^{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 indices: list or None - :returns: The averaged spike profile :math:`<S_{spike}>(t)` - :rtype: :class:`pyspike.function.PieceWiseLinFunc` + :returns: The averaged spike profile :math:`<S>(t)` + :rtype: :class:`.PieceWiseLinFunc` """ average_dist, M = _generic_profile_multi(spike_trains, spike_profile, @@ -104,17 +101,20 @@ def spike_profile_multi(spike_trains, indices=None): 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: - S_{spike} = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{spike}^{i, j} dt + + .. math:: D_S = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>} + S^{i, j} dt + 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 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 spike distance S. + :returns: The averaged multi-variate spike distance :math:`D_S`. :rtype: double """ return spike_profile_multi(spike_trains, indices).avrg(interval) @@ -126,7 +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 :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 @@ -134,7 +134,7 @@ def spike_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 spike distances - :math:`S_{ij}` + :math:`D_S^{ij}` :rtype: np.array """ return _generic_distance_matrix(spike_trains, spike_distance, |