From bec2529367f1bdd5dac6d6fbaec560a30feec3c7 Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Mon, 11 May 2015 17:41:08 +0200 Subject: treatment of empty spike trains in spike sync --- pyspike/cython/cython_distances.pyx | 13 +++++++++---- pyspike/cython/cython_profiles.pyx | 9 +++++---- pyspike/cython/python_backend.py | 2 +- 3 files changed, 15 insertions(+), 9 deletions(-) (limited to 'pyspike/cython') diff --git a/pyspike/cython/cython_distances.pyx b/pyspike/cython/cython_distances.pyx index bf90638..16780f2 100644 --- a/pyspike/cython/cython_distances.pyx +++ b/pyspike/cython/cython_distances.pyx @@ -333,8 +333,8 @@ def spike_distance_cython(double[:] t1, double[:] t2, # get_tau ############################################################ cdef inline double get_tau(double[:] spikes1, double[:] spikes2, - int i, int j, double max_tau): - cdef double m = 1E100 # some huge number + int i, int j, double interval, double max_tau): + cdef double m = interval # use interval length as initial tau cdef int N1 = spikes1.shape[0]-1 # len(spikes1)-1 cdef int N2 = spikes2.shape[0]-1 # len(spikes2)-1 if i < N1 and i > -1: @@ -363,12 +363,13 @@ def coincidence_value_cython(double[:] spikes1, double[:] spikes2, cdef int j = -1 cdef double coinc = 0.0 cdef double mp = 0.0 + cdef double interval = t_end - t_start cdef double tau while i + j < N1 + N2 - 2: if (i < N1-1) and (j == N2-1 or spikes1[i+1] < spikes2[j+1]): i += 1 mp += 1 - tau = get_tau(spikes1, spikes2, i, j, max_tau) + tau = get_tau(spikes1, spikes2, i, j, interval, max_tau) if j > -1 and spikes1[i]-spikes2[j] < tau: # coincidence between the current spike and the previous spike # both get marked with 1 @@ -376,7 +377,7 @@ def coincidence_value_cython(double[:] spikes1, double[:] spikes2, elif (j < N2-1) and (i == N1-1 or spikes1[i+1] > spikes2[j+1]): j += 1 mp += 1 - tau = get_tau(spikes1, spikes2, i, j, max_tau) + tau = get_tau(spikes1, spikes2, i, j, interval, max_tau) if i > -1 and spikes2[j]-spikes1[i] < tau: # coincidence between the current spike and the previous spike # both get marked with 1 @@ -389,4 +390,8 @@ def coincidence_value_cython(double[:] spikes1, double[:] spikes2, mp += 2 coinc += 2 + if coinc == 0 and mp == 0: + # empty spike trains -> set mp to one to avoid 0/0 + mp = 1 + return coinc, mp diff --git a/pyspike/cython/cython_profiles.pyx b/pyspike/cython/cython_profiles.pyx index 3690091..d937a02 100644 --- a/pyspike/cython/cython_profiles.pyx +++ b/pyspike/cython/cython_profiles.pyx @@ -345,8 +345,8 @@ def spike_profile_cython(double[:] t1, double[:] t2, # get_tau ############################################################ cdef inline double get_tau(double[:] spikes1, double[:] spikes2, - int i, int j, double max_tau): - cdef double m = 1E100 # some huge number + int i, int j, double interval, double max_tau): + cdef double m = interval # use interval as initial tau cdef int N1 = spikes1.shape[0]-1 # len(spikes1)-1 cdef int N2 = spikes2.shape[0]-1 # len(spikes2)-1 if i < N1 and i > -1: @@ -377,12 +377,13 @@ def coincidence_profile_cython(double[:] spikes1, double[:] spikes2, cdef double[:] st = np.zeros(N1 + N2 + 2) # spike times cdef double[:] c = np.zeros(N1 + N2 + 2) # coincidences cdef double[:] mp = np.ones(N1 + N2 + 2) # multiplicity + cdef double interval = t_end - t_start cdef double tau while i + j < N1 + N2 - 2: if (i < N1-1) and (j == N2-1 or spikes1[i+1] < spikes2[j+1]): i += 1 n += 1 - tau = get_tau(spikes1, spikes2, i, j, max_tau) + tau = get_tau(spikes1, spikes2, i, j, interval, max_tau) st[n] = spikes1[i] if j > -1 and spikes1[i]-spikes2[j] < tau: # coincidence between the current spike and the previous spike @@ -392,7 +393,7 @@ def coincidence_profile_cython(double[:] spikes1, double[:] spikes2, elif (j < N2-1) and (i == N1-1 or spikes1[i+1] > spikes2[j+1]): j += 1 n += 1 - tau = get_tau(spikes1, spikes2, i, j, max_tau) + tau = get_tau(spikes1, spikes2, i, j, interval, max_tau) st[n] = spikes2[j] if i > -1 and spikes2[j]-spikes1[i] < tau: # coincidence between the current spike and the previous spike diff --git a/pyspike/cython/python_backend.py b/pyspike/cython/python_backend.py index 1fd8c42..830dc69 100644 --- a/pyspike/cython/python_backend.py +++ b/pyspike/cython/python_backend.py @@ -340,7 +340,7 @@ def cumulative_sync_python(spikes1, spikes2): def coincidence_python(spikes1, spikes2, t_start, t_end, max_tau): def get_tau(spikes1, spikes2, i, j, max_tau): - m = 1E100 # some huge number + m = t_end - t_start # use interval as initial tau if i < len(spikes1)-1 and i > -1: m = min(m, spikes1[i+1]-spikes1[i]) if j < len(spikes2)-1 and j > -1: -- cgit v1.2.3