diff options
Diffstat (limited to 'pyspike/spike_sync.py')
| -rw-r--r-- | pyspike/spike_sync.py | 79 |
1 files changed, 65 insertions, 14 deletions
diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py index 9d2e363..40d98d2 100644 --- a/pyspike/spike_sync.py +++ b/pyspike/spike_sync.py @@ -3,6 +3,7 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License +import numpy as np from functools import partial from pyspike import DiscreteFunc from pyspike.generic import _generic_profile_multi, _generic_distance_matrix @@ -29,35 +30,68 @@ def spike_sync_profile(spike_train1, spike_train2, max_tau=None): """ # 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!" + "Given spike trains are not defined on the same interval!" assert spike_train1.t_end == spike_train2.t_end, \ - "Given spike trains seems not to have auxiliary spikes!" + "Given spike trains are not defined on the same interval!" # cython implementation try: - from cython.cython_distance import coincidence_cython \ - as coincidence_impl + from cython.cython_profiles import coincidence_profile_cython \ + as coincidence_profile_impl except ImportError: print("Warning: spike_distance_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 coincidence_python \ - as coincidence_impl + as coincidence_profile_impl if max_tau is None: max_tau = 0.0 - times, coincidences, multiplicity = coincidence_impl(spike_train1.spikes, - spike_train2.spikes, - spike_train1.t_start, - spike_train1.t_end, - max_tau) + times, coincidences, multiplicity \ + = coincidence_profile_impl(spike_train1.spikes, spike_train2.spikes, + spike_train1.t_start, spike_train1.t_end, + max_tau) return DiscreteFunc(times, coincidences, multiplicity) ############################################################ +# _spike_sync_values +############################################################ +def _spike_sync_values(spike_train1, spike_train2, interval, max_tau): + """" Internal function. Computes the summed coincidences and multiplicity + for spike synchronization of the two given spike trains. + + Do not call this function directly, use `spike_sync` or `spike_sync_multi` + instead. + """ + if interval is None: + # distance over the whole interval is requested: use specific function + # for optimal performance + try: + from cython.cython_distances import coincidence_value_cython \ + as coincidence_value_impl + if max_tau is None: + max_tau = 0.0 + c, mp = coincidence_value_impl(spike_train1.spikes, + spike_train2.spikes, + spike_train1.t_start, + spike_train1.t_end, + max_tau) + return c, mp + except ImportError: + # Cython backend not available: fall back to profile averaging + return spike_sync_profile(spike_train1, spike_train2, + max_tau).integral(interval) + else: + # some specific interval is provided: use profile + return spike_sync_profile(spike_train1, spike_train2, + max_tau).integral(interval) + + +############################################################ # spike_sync ############################################################ def spike_sync(spike_train1, spike_train2, interval=None, max_tau=None): @@ -80,8 +114,8 @@ def spike_sync(spike_train1, spike_train2, interval=None, max_tau=None): :rtype: `double` """ - return spike_sync_profile(spike_train1, spike_train2, - max_tau).avrg(interval) + c, mp = _spike_sync_values(spike_train1, spike_train2, interval, max_tau) + return 1.0*c/mp ############################################################ @@ -131,8 +165,25 @@ def spike_sync_multi(spike_trains, indices=None, interval=None, max_tau=None): :rtype: double """ - return spike_sync_profile_multi(spike_trains, indices, - max_tau).avrg(interval) + if indices is None: + indices = np.arange(len(spike_trains)) + indices = np.array(indices) + # check validity of indices + assert (indices < len(spike_trains)).all() and (indices >= 0).all(), \ + "Invalid index list." + # generate a list of possible index pairs + pairs = [(indices[i], j) for i in range(len(indices)) + for j in indices[i+1:]] + + coincidence = 0.0 + mp = 0.0 + for (i, j) in pairs: + c, m = _spike_sync_values(spike_trains[i], spike_trains[j], + interval, max_tau) + coincidence += c + mp += m + + return coincidence/mp ############################################################ |