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Diffstat (limited to 'pyspike/spike_distance.py')
| -rw-r--r-- | pyspike/spike_distance.py | 231 |
1 files changed, 231 insertions, 0 deletions
diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py new file mode 100644 index 0000000..0fd86c1 --- /dev/null +++ b/pyspike/spike_distance.py @@ -0,0 +1,231 @@ +# 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 __future__ import absolute_import + +import pyspike +from pyspike import PieceWiseLinFunc +from pyspike.generic import _generic_profile_multi, _generic_distance_multi, \ + _generic_distance_matrix + + +############################################################ +# spike_profile +############################################################ +def spike_profile(*args, **kwargs): + """ Computes the spike-distance profile :math:`S(t)` of the given + spike trains. Returns the profile as a PieceWiseConstLin object. The + SPIKE-values are defined positive :math:`S(t)>=0`. + + Valid call structures:: + + spike_profile(st1, st2) # returns the bi-variate profile + spike_profile(st1, st2, st3) # multi-variate profile of 3 spike trains + + spike_trains = [st1, st2, st3, st4] # list of spike trains + spike_profile(spike_trains) # profile of the list of spike trains + spike_profile(spike_trains, indices=[0, 1]) # use only the spike trains + # given by the indices + + The multivariate spike-distance profile is defined as the average of all + pairs of spike-trains: + + .. math:: <S(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} S^{i, j}`, + + where the sum goes over all pairs <i,j> + + :returns: The spike-distance profile :math:`S(t)` + :rtype: :class:`.PieceWiseConstLin` + """ + if len(args) == 1: + return spike_profile_multi(args[0], **kwargs) + elif len(args) == 2: + return spike_profile_bi(args[0], args[1]) + else: + return spike_profile_multi(args) + + +############################################################ +# spike_profile_bi +############################################################ +def spike_profile_bi(spike_train1, spike_train2): + """ Specific function to compute a bivariate SPIKE-profile. This is a + deprecated function and should not be called directly. Use + :func:`.spike_profile` to compute SPIKE-profiles. + + :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: + if not(pyspike.disable_backend_warning): + 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_profile_multi +############################################################ +def spike_profile_multi(spike_trains, indices=None): + """ Specific function to compute a multivariate SPIKE-profile. This is a + deprecated function and should not be called directly. Use + :func:`.spike_profile` to compute SPIKE-profiles. + + :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>(t)` + :rtype: :class:`.PieceWiseLinFunc` + + """ + average_dist, M = _generic_profile_multi(spike_trains, spike_profile_bi, + indices) + average_dist.mul_scalar(1.0/M) # normalize + return average_dist + + +############################################################ +# spike_distance +############################################################ +def spike_distance(*args, **kwargs): + """ Computes the SPIKE-distance :math:`D_S` of the given spike trains. The + spike-distance is the integral over the spike distance profile + :math:`D(t)`: + + .. math:: D_S = \\int_{T_0}^{T_1} S(t) dt. + + + Valid call structures:: + + spike_distance(st1, st2) # returns the bi-variate distance + spike_distance(st1, st2, st3) # multi-variate distance of 3 spike trains + + spike_trains = [st1, st2, st3, st4] # list of spike trains + spike_distance(spike_trains) # distance of the list of spike trains + spike_distance(spike_trains, indices=[0, 1]) # use only the spike trains + # given by the indices + + In the multivariate case, the spike distance is given as the integral over + the multivariate profile, that is the average profile of all spike train + pairs: + + .. math:: D_S = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>} + S^{i, j} dt + + :returns: The spike-distance :math:`D_S`. + :rtype: double + """ + + if len(args) == 1: + return spike_distance_multi(args[0], **kwargs) + elif len(args) == 2: + return spike_distance_bi(args[0], args[1], **kwargs) + else: + return spike_distance_multi(args, **kwargs) + + +############################################################ +# spike_distance_bi +############################################################ +def spike_distance_bi(spike_train1, spike_train2, interval=None): + """ Specific function to compute a bivariate SPIKE-distance. This is a + deprecated function and should not be called directly. Use + :func:`.spike_distance` to compute SPIKE-distances. + + :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_bi(spike_train1, spike_train2).avrg(interval) + else: + # some specific interval is provided: compute the whole profile + return spike_profile_bi(spike_train1, spike_train2).avrg(interval) + + +############################################################ +# spike_distance_multi +############################################################ +def spike_distance_multi(spike_trains, indices=None, interval=None): + """ Specific function to compute a multivariate SPIKE-distance. This is a + deprecated function and should not be called directly. Use + :func:`.spike_distance` to compute SPIKE-distances. + + :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_bi, 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_bi, + indices, interval) |