diff options
Diffstat (limited to 'pyspike')
| -rw-r--r-- | pyspike/isi_distance.py | 54 | ||||
| -rw-r--r-- | pyspike/spike_distance.py | 47 | ||||
| -rw-r--r-- | pyspike/spike_sync.py | 36 |
3 files changed, 77 insertions, 60 deletions
diff --git a/pyspike/isi_distance.py b/pyspike/isi_distance.py index 122e11d..e91dce2 100644 --- a/pyspike/isi_distance.py +++ b/pyspike/isi_distance.py @@ -20,14 +20,22 @@ def isi_profile(*args, **kwargs): Valid call structures:: - isi_profile(st1, st2) # returns the bi-variate profile + isi_profile(st1, st2) # returns the bi-variate profile isi_profile(st1, st2, st3) # multi-variate profile of 3 spike trains spike_trains = [st1, st2, st3, st4] # list of spike trains - isi_profile(spike_trains) # profile of the list of spike trains + isi_profile(spike_trains) # profile of the list of spike trains isi_profile(spike_trains, indices=[0, 1]) # use only the spike trains # given by the indices + The multivariate ISI distance profile for a set of spike trains is defined + as the average ISI-profile of all pairs of spike-trains: + + .. math:: <I(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j}, + + where the sum goes over all pairs <i,j> + + :returns: The isi-distance profile :math:`I(t)` :rtype: :class:`.PieceWiseConstFunc` """ @@ -43,10 +51,9 @@ def isi_profile(*args, **kwargs): # isi_profile_bi ############################################################ def isi_profile_bi(spike_train1, spike_train2): - """ Bi-variate ISI-profile. - Computes the isi-distance profile :math:`I(t)` of the two given - spike trains. Returns the profile as a PieceWiseConstFunc object. - See :func:`.isi_profile`. + """ Specific function to compute a bivariate ISI-profile. This is a + deprecated function and should not be called directly. Use + :func:`.isi_profile` to compute ISI-profiles. :param spike_train1: First spike train. :type spike_train1: :class:`.SpikeTrain` @@ -85,12 +92,10 @@ Falling back to slow python backend.") # isi_profile_multi ############################################################ 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: + """ Specific function to compute the multivariate ISI-profile for a set of + spike trains. This is a deprecated function and should not be called + directly. Use :func:`.isi_profile` to compute ISI-profiles. - .. 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:`.SpikeTrain` :param indices: list of indices defining which spike trains to use, @@ -115,6 +120,14 @@ def isi_distance(*args, **kwargs): .. math:: D_I = \\int_{T_0}^{T_1} I(t) dt. + In the multivariate case it is the integral over the multivariate + ISI-profile, i.e. the average profile over all spike train pairs: + + .. 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> + + Valid call structures:: @@ -139,14 +152,12 @@ def isi_distance(*args, **kwargs): ############################################################ -# isi_distance_bi +# _isi_distance_bi ############################################################ def isi_distance_bi(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:`I(t)`: - - .. math:: D_I = \\int_{T_0}^{T_1} I(t) dt. + """ Specific function to compute the bivariate ISI-distance. + This is a deprecated function and should not be called directly. Use + :func:`.isi_distance` to compute ISI-distances. :param spike_train1: First spike train. :type spike_train1: :class:`.SpikeTrain` @@ -181,12 +192,9 @@ def isi_distance_bi(spike_train1, spike_train2, interval=None): # isi_distance_multi ############################################################ 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: - - .. 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> + """ Specific function to compute the multivariate ISI-distance. + This is a deprecfated function and should not be called directly. Use + :func:`.isi_distance` to compute ISI-distances. :param spike_trains: list of :class:`.SpikeTrain` :param indices: list of indices defining which spike trains to use, diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py index 7acb959..0fd86c1 100644 --- a/pyspike/spike_distance.py +++ b/pyspike/spike_distance.py @@ -28,6 +28,13 @@ def spike_profile(*args, **kwargs): 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` """ @@ -43,9 +50,9 @@ def spike_profile(*args, **kwargs): # spike_profile_bi ############################################################ def spike_profile_bi(spike_train1, spike_train2): - """ 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`. + """ 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` @@ -86,12 +93,9 @@ Falling back to slow python backend.") # spike_profile_multi ############################################################ 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(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} S^{i, j}`, - - where the sum goes over all pairs <i,j> + """ 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, @@ -128,6 +132,13 @@ def spike_distance(*args, **kwargs): 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 """ @@ -144,11 +155,9 @@ def spike_distance(*args, **kwargs): # spike_distance_bi ############################################################ def spike_distance_bi(spike_train1, spike_train2, interval=None): - """ Computes the spike-distance :math:`D_S` of the given spike trains. The - spike-distance is the integral over the spike distance profile - :math:`S(t)`: - - .. math:: D_S = \int_{T_0}^{T_1} S(t) dt. + """ 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` @@ -183,13 +192,9 @@ def spike_distance_bi(spike_train1, spike_train2, interval=None): # spike_distance_multi ############################################################ 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: - - .. 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> + """ 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, diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py index ccb09d9..617dd86 100644 --- a/pyspike/spike_sync.py +++ b/pyspike/spike_sync.py @@ -34,6 +34,11 @@ def spike_sync_profile(*args, **kwargs): spike_sync_profile(sts, indices=[0, 1]) # use only the spike trains # given by the indices + In the multivariate case, the profile is defined as the number of + coincidences for each spike in the set of spike trains divided by the + number of spike trains pairs involving the spike train of containing this + spike, which is the number of spike trains minus one (N-1). + :returns: The spike-sync profile :math:`S_{sync}(t)`. :rtype: :class:`pyspike.function.DiscreteFunction` """ @@ -49,10 +54,9 @@ def spike_sync_profile(*args, **kwargs): # spike_sync_profile_bi ############################################################ def spike_sync_profile_bi(spike_train1, spike_train2, max_tau=None): - """ Computes the spike-synchronization profile S_sync(t) of the two given - spike trains. Returns the profile as a DiscreteFunction object. The S_sync - values are either 1 or 0, indicating the presence or absence of a - coincidence. + """ Specific function to compute a bivariate SPIKE-Sync-profile. This is a + deprecated function and should not be called directly. Use + :func:`.spike_sync_profile` to compute SPIKE-Sync-profiles. :param spike_train1: First spike train. :type spike_train1: :class:`pyspike.SpikeTrain` @@ -98,11 +102,9 @@ Falling back to slow python backend.") # spike_sync_profile_multi ############################################################ def spike_sync_profile_multi(spike_trains, indices=None, max_tau=None): - """ Computes the multi-variate spike synchronization profile for a set of - spike trains. For each spike in the set of spike trains, the multi-variate - profile is defined as the number of coincidences divided by the number of - spike trains pairs involving the spike train of containing this spike, - which is the number of spike trains minus one (N-1). + """ Specific function to compute a multivariate SPIKE-Sync-profile. + This is a deprecated function and should not be called directly. Use + :func:`.spike_sync_profile` to compute SPIKE-Sync-profiles. :param spike_trains: list of :class:`pyspike.SpikeTrain` :param indices: list of indices defining which spike trains to use, @@ -176,6 +178,9 @@ def spike_sync(*args, **kwargs): spike_sync(spike_trains, indices=[0, 1]) # use only the spike trains # given by the indices + The multivariate SPIKE-Sync is again defined as the overall ratio of all + coincidence values divided by the total number of spikes. + :returns: The spike synchronization value. :rtype: `double` """ @@ -192,11 +197,9 @@ def spike_sync(*args, **kwargs): # spike_sync_bi ############################################################ def spike_sync_bi(spike_train1, spike_train2, interval=None, max_tau=None): - """ Computes the spike synchronization value SYNC of the given spike - trains. The spike synchronization value is the computed as the total number - of coincidences divided by the total number of spikes: - - .. math:: SYNC = \sum_n C_n / N. + """ Specific function to compute a bivariate SPIKE-Sync value. + This is a deprecated function and should not be called directly. Use + :func:`.spike_sync` to compute SPIKE-Sync values. :param spike_train1: First spike train. :type spike_train1: :class:`pyspike.SpikeTrain` @@ -219,8 +222,9 @@ def spike_sync_bi(spike_train1, spike_train2, interval=None, max_tau=None): # spike_sync_multi ############################################################ def spike_sync_multi(spike_trains, indices=None, interval=None, max_tau=None): - """ Computes the multi-variate spike synchronization value for a set of - spike trains. + """ Specific function to compute a multivariate SPIKE-Sync value. + This is a deprecated function and should not be called directly. Use + :func:`.spike_sync` to compute SPIKE-Sync values. :param spike_trains: list of :class:`pyspike.SpikeTrain` :param indices: list of indices defining which spike trains to use, |