diff options
Diffstat (limited to 'pyspike/cython/cython_profiles.pyx')
| -rw-r--r-- | pyspike/cython/cython_profiles.pyx | 61 |
1 files changed, 41 insertions, 20 deletions
diff --git a/pyspike/cython/cython_profiles.pyx b/pyspike/cython/cython_profiles.pyx index f9893eb..f08de6e 100644 --- a/pyspike/cython/cython_profiles.pyx +++ b/pyspike/cython/cython_profiles.pyx @@ -181,6 +181,8 @@ def spike_profile_cython(double[:] t1, double[:] t2, cdef double[:] spike_events cdef double[:] y_starts cdef double[:] y_ends + cdef double[:] t_aux1 = np.empty(2) + cdef double[:] t_aux2 = np.empty(2) cdef int N1, N2, index1, index2, index cdef double t_p1, t_f1, t_p2, t_f2, dt_p1, dt_p2, dt_f1, dt_f2 @@ -189,6 +191,10 @@ def spike_profile_cython(double[:] t1, double[:] t2, N1 = len(t1) N2 = len(t2) + # we can assume at least two spikes per spike train + assert N1 > 1 + assert N2 > 1 + spike_events = np.empty(N1+N2+2) y_starts = np.empty(len(spike_events)-1) @@ -196,19 +202,27 @@ def spike_profile_cython(double[:] t1, double[:] t2, with nogil: # release the interpreter to allow multithreading spike_events[0] = t_start - t_p1 = t_start - t_p2 = t_start + # t_p1 = t_start + # t_p2 = t_start + # auxiliary spikes for edge correction - consistent with first/last ISI + t_aux1[0] = fmin(t_start, t1[0]-(t1[1]-t1[0])) + t_aux1[1] = fmax(t_end, t1[N1-1]+(t1[N1-1]-t1[N1-2])) + t_aux2[0] = fmin(t_start, t2[0]-(t2[1]-t2[0])) + t_aux2[1] = fmax(t_end, t2[N2-1]+(t2[N2-1]-t2[N2-2])) + t_p1 = t_start if (t1[0] == t_start) else t_aux1[0] + t_p2 = t_start if (t2[0] == t_start) else t_aux2[0] if t1[0] > t_start: # dt_p1 = t2[0]-t_start t_f1 = t1[0] - dt_f1 = get_min_dist_cython(t_f1, t2, N2, 0, t_start, t_end) + dt_f1 = get_min_dist_cython(t_f1, t2, N2, 0, t_aux2[0], t_aux2[1]) isi1 = fmax(t_f1-t_start, t1[1]-t1[0]) dt_p1 = dt_f1 - s1 = dt_p1*(t_f1-t_start)/isi1 + # s1 = dt_p1*(t_f1-t_start)/isi1 + s1 = dt_p1 index1 = -1 else: t_f1 = t1[1] - dt_f1 = get_min_dist_cython(t_f1, t2, N2, 0, t_start, t_end) + dt_f1 = get_min_dist_cython(t_f1, t2, N2, 0, t_aux2[0], t_aux2[1]) dt_p1 = 0.0 isi1 = t1[1]-t1[0] s1 = dt_p1 @@ -216,14 +230,15 @@ def spike_profile_cython(double[:] t1, double[:] t2, if t2[0] > t_start: # dt_p1 = t2[0]-t_start t_f2 = t2[0] - dt_f2 = get_min_dist_cython(t_f2, t1, N1, 0, t_start, t_end) + dt_f2 = get_min_dist_cython(t_f2, t1, N1, 0, t_aux1[0], t_aux1[1]) dt_p2 = dt_f2 isi2 = fmax(t_f2-t_start, t2[1]-t2[0]) - s2 = dt_p2*(t_f2-t_start)/isi2 + # s2 = dt_p2*(t_f2-t_start)/isi2 + s2 = dt_p2 index2 = -1 else: t_f2 = t2[1] - dt_f2 = get_min_dist_cython(t_f2, t1, N1, 0, t_start, t_end) + dt_f2 = get_min_dist_cython(t_f2, t1, N1, 0, t_aux1[0], t_aux1[1]) dt_p2 = 0.0 isi2 = t2[1]-t2[0] s2 = dt_p2 @@ -245,7 +260,7 @@ def spike_profile_cython(double[:] t1, double[:] t2, if index1 < N1-1: t_f1 = t1[index1+1] else: - t_f1 = t_end + t_f1 = t_aux1[1] spike_events[index] = t_p1 s2 = (dt_p2*(t_f2-t_p1) + dt_f2*(t_p1-t_p2)) / isi2 y_ends[index-1] = (s1*isi2 + s2*isi1)/isi_avrg_cython(isi1, @@ -253,14 +268,16 @@ def spike_profile_cython(double[:] t1, double[:] t2, # now the next interval start value if index1 < N1-1: dt_f1 = get_min_dist_cython(t_f1, t2, N2, index2, - t_start, t_end) + t_aux2[0], t_aux2[1]) isi1 = t_f1-t_p1 s1 = dt_p1 else: dt_f1 = dt_p1 isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) # s1 needs adjustment due to change of isi1 - s1 = dt_p1*(t_end-t1[N1-1])/isi1 + # s1 = dt_p1*(t_end-t1[N1-1])/isi1 + # Eero's correction: no adjustment + s1 = dt_p1 # s2 is the same as above, thus we can compute y2 immediately y_starts[index] = (s1*isi2 + s2*isi1)/isi_avrg_cython(isi1, isi2) @@ -275,7 +292,7 @@ def spike_profile_cython(double[:] t1, double[:] t2, if index2 < N2-1: t_f2 = t2[index2+1] else: - t_f2 = t_end + t_f2 = t_aux2[1] spike_events[index] = t_p2 s1 = (dt_p1*(t_f1-t_p2) + dt_f1*(t_p2-t_p1)) / isi1 y_ends[index-1] = (s1*isi2 + s2*isi1) / isi_avrg_cython(isi1, @@ -283,14 +300,16 @@ def spike_profile_cython(double[:] t1, double[:] t2, # now the next interval start value if index2 < N2-1: dt_f2 = get_min_dist_cython(t_f2, t1, N1, index1, - t_start, t_end) + t_aux1[0], t_aux1[1]) isi2 = t_f2-t_p2 s2 = dt_p2 else: dt_f2 = dt_p2 isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) # s2 needs adjustment due to change of isi2 - s2 = dt_p2*(t_end-t2[N2-1])/isi2 + # s2 = dt_p2*(t_end-t2[N2-1])/isi2 + # Eero's correction: no adjustment + s2 = dt_p2 # s2 is the same as above, thus we can compute y2 immediately y_starts[index] = (s1*isi2 + s2*isi1)/isi_avrg_cython(isi1, isi2) else: # t_f1 == t_f2 - generate only one event @@ -306,19 +325,19 @@ def spike_profile_cython(double[:] t1, double[:] t2, if index1 < N1-1: t_f1 = t1[index1+1] dt_f1 = get_min_dist_cython(t_f1, t2, N2, index2, - t_start, t_end) + t_aux2[0], t_aux2[1]) isi1 = t_f1 - t_p1 else: - t_f1 = t_end + t_f1 = t_aux1[1] dt_f1 = dt_p1 isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) if index2 < N2-1: t_f2 = t2[index2+1] dt_f2 = get_min_dist_cython(t_f2, t1, N1, index1, - t_start, t_end) + t_aux1[0], t_aux1[1]) isi2 = t_f2 - t_p2 else: - t_f2 = t_end + t_f2 = t_aux2[1] dt_f2 = dt_p2 isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) index += 1 @@ -330,8 +349,10 @@ def spike_profile_cython(double[:] t1, double[:] t2, # the ending value of the last interval isi1 = max(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) isi2 = max(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) - s1 = dt_f1*(t_end-t1[N1-1])/isi1 - s2 = dt_f2*(t_end-t2[N2-1])/isi2 + # s1 = dt_f1*(t_end-t1[N1-1])/isi1 + # s2 = dt_f2*(t_end-t2[N2-1])/isi2 + s1 = dt_f1 + s2 = dt_f2 y_ends[index-1] = (s1*isi2 + s2*isi1) / isi_avrg_cython(isi1, isi2) # end nogil |