diff options
Diffstat (limited to 'pyspike/directionality/spike_delay_asymmetry.py')
| -rw-r--r-- | pyspike/directionality/spike_delay_asymmetry.py | 55 |
1 files changed, 53 insertions, 2 deletions
diff --git a/pyspike/directionality/spike_delay_asymmetry.py b/pyspike/directionality/spike_delay_asymmetry.py index 7d59601..0676f6d 100644 --- a/pyspike/directionality/spike_delay_asymmetry.py +++ b/pyspike/directionality/spike_delay_asymmetry.py @@ -147,6 +147,57 @@ def spike_delay_asymmetry_matrix(spike_trains, indices=None, ############################################################ +# spike_delay_asymmetry_full +############################################################ +def spike_delay_asymmetry_full(spike_trains, indices=None, + interval=None, max_tau=None): + """ Computes the spike train symmetry value for each spike in each spike + train. + """ + 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." + # list of arrays for reulting asymmetry values + asymmetry_list = [np.zeros_like(st.spikes) for st in spike_trains] + # generate a list of possible index pairs + pairs = [(indices[i], j) for i in range(len(indices)) + for j in indices[i+1:]] + + # cython implementation + try: + from cython.cython_directionality import \ + spike_delay_dual_profile_cython as \ + sda_dual_profile_impl + except ImportError: + raise NotImplementedError() +# if not(pyspike.disable_backend_warning): +# 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_profile_impl + + if max_tau is None: + max_tau = 0.0 + + for i, j in pairs: + a1, a2 = sda_dual_profile_impl(spike_trains[i].spikes, + spike_trains[j].spikes, + spike_trains[i].t_start, + spike_trains[i].t_end, + max_tau) + asymmetry_list[i] += a1 + asymmetry_list[j] += a2 + for a in asymmetry_list: + a /= len(spike_trains)-1 + return asymmetry_list + + +############################################################ # optimal_asymmetry_order_from_D ############################################################ def optimal_asymmetry_order_from_D(D, full_output=False): @@ -188,7 +239,7 @@ def optimal_asymmetry_order_from_D(D, full_output=False): ############################################################ -# _optimal_asymmetry_order +# optimal_asymmetry_order ############################################################ def optimal_asymmetry_order(spike_trains, indices=None, interval=None, max_tau=None, full_output=False): @@ -203,7 +254,7 @@ def optimal_asymmetry_order(spike_trains, indices=None, interval=None, ############################################################ # reorder_asymmetry_matrix ############################################################ -def reorder_asymmetry_matrix(D, p): +def permutate_asymmetry_matrix(D, p): N = len(D) D_p = np.empty_like(D) for n in xrange(N): |