diff options
Diffstat (limited to 'pyspike/cython')
| -rw-r--r-- | pyspike/cython/cython_distances.pyx | 91 | ||||
| -rw-r--r-- | pyspike/cython/cython_profiles.pyx | 67 | ||||
| -rw-r--r-- | pyspike/cython/python_backend.py | 63 |
3 files changed, 128 insertions, 93 deletions
diff --git a/pyspike/cython/cython_distances.pyx b/pyspike/cython/cython_distances.pyx index 41baa60..7dc9cb9 100644 --- a/pyspike/cython/cython_distances.pyx +++ b/pyspike/cython/cython_distances.pyx @@ -55,20 +55,27 @@ def isi_distance_cython(double[:] s1, double[:] s2, N2 = len(s2) # first interspike interval - check if a spike exists at the start time + # and also account for spike trains with single spikes if s1[0] > t_start: - # edge correction - nu1 = fmax(s1[0]-t_start, s1[1]-s1[0]) + # edge correction for the first interspike interval: + # take the maximum of the distance from the beginning to the first + # spike and the interval between the first two spikes. + # if there is only one spike, take the its distance to the beginning + nu1 = fmax(s1[0]-t_start, s1[1]-s1[0]) if N1 > 1 else s1[0]-t_start index1 = -1 else: - nu1 = s1[1]-s1[0] + # if the first spike is exactly at the start, take the distance + # to the next spike. If this is the only spike, take the distance to + # the end. + nu1 = s1[1]-s1[0] if N1 > 1 else t_end-s1[0] index1 = 0 if s2[0] > t_start: - # edge correction - nu2 = fmax(s2[0]-t_start, s2[1]-s2[0]) + # edge correction as above + nu2 = fmax(s2[0]-t_start, s2[1]-s2[0]) if N2 > 1 else s2[0]-t_start index2 = -1 else: - nu2 = s2[1]-s2[0] + nu2 = s2[1]-s2[0] if N2 > 1 else t_end-s2[0] index2 = 0 last_t = t_start @@ -86,8 +93,12 @@ def isi_distance_cython(double[:] s1, double[:] s2, if index1 < N1-1: nu1 = s1[index1+1]-s1[index1] else: - # edge correction - nu1 = fmax(t_end-s1[index1], nu1) + # edge correction for the last ISI: + # take the max of the distance of the last + # spike to the end and the previous ISI. If there was only + # one spike, always take the distance to the end. + nu1 = fmax(t_end-s1[index1], nu1) if N1 > 1 \ + else t_end-s1[index1] elif (index2 < N2-1) and ((index1 == N1-1) or (s1[index1+1] > s2[index2+1])): index2 += 1 @@ -95,8 +106,9 @@ def isi_distance_cython(double[:] s1, double[:] s2, if index2 < N2-1: nu2 = s2[index2+1]-s2[index2] else: - # edge correction - nu2 = fmax(t_end-s2[index2], nu2) + # edge correction for the end as above + nu2 = fmax(t_end-s2[index2], nu2) if N2 > 1 \ + else t_end-s2[index2] else: # s1[index1+1] == s2[index2+1] index1 += 1 index2 += 1 @@ -104,13 +116,15 @@ def isi_distance_cython(double[:] s1, double[:] s2, if index1 < N1-1: nu1 = s1[index1+1]-s1[index1] else: - # edge correction - nu1 = fmax(t_end-s1[index1], nu1) + # edge correction for the end as above + nu1 = fmax(t_end-s1[index1], nu1) if N1 > 1 \ + else t_end-s1[index1] if index2 < N2-1: nu2 = s2[index2+1]-s2[index2] else: - # edge correction - nu2 = fmax(t_end-s2[index2], nu2) + # edge correction for the end as above + nu2 = fmax(t_end-s2[index2], nu2) if N2 > 1 \ + else t_end-s2[index2] # compute the corresponding isi-distance isi_value += curr_isi * (curr_t - last_t) curr_isi = fabs(nu1 - nu2) / fmax(nu1, nu2) @@ -184,31 +198,35 @@ def spike_distance_cython(double[:] t1, double[:] t2, N1 = len(t1) N2 = len(t2) + # we can assume at least one spikes per spike train + assert N1 > 0 + assert N2 > 0 + + with nogil: # release the interpreter to allow multithreading t_last = 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_aux1[0] = fmin(t_start, 2*t1[0]-t1[1]) if N1 > 1 else t_start + t_aux1[1] = fmax(t_end, 2*t1[N1-1]-t1[N1-2]) if N1 > 1 else t_end + t_aux2[0] = fmin(t_start, 2*t2[0]-t2[1]) if N2 > 1 else t_start + t_aux2[1] = fmax(t_end, 2*t2[N2-1]+-t2[N2-2]) if N2 > 1 else t_end + # print "aux spikes %.15f, %.15f ; %.15f, %.15f" % (t_aux1[0], t_aux1[1], t_aux2[0], t_aux2[1]) 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_aux2[0], t_aux2[1]) - isi1 = fmax(t_f1-t_start, t1[1]-t1[0]) + isi1 = fmax(t_f1-t_start, t1[1]-t1[0]) if N1 > 1 else t_f1-t_start dt_p1 = dt_f1 # s1 = dt_p1*(t_f1-t_start)/isi1 s1 = dt_p1 index1 = -1 - else: - t_f1 = t1[1] + else: # t1[0] == t_start + t_f1 = t1[1] if N1 > 1 else 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] + dt_p1 = get_min_dist_cython(t_p1, t2, N2, 0, t_aux2[0], t_aux2[1]) + isi1 = t_f1-t1[0] s1 = dt_p1 index1 = 0 if t2[0] > t_start: @@ -216,15 +234,16 @@ def spike_distance_cython(double[:] t1, double[:] t2, t_f2 = t2[0] 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]) + isi2 = fmax(t_f2-t_start, t2[1]-t2[0]) if N2 > 1 else t_f2-t_start # s2 = dt_p2*(t_f2-t_start)/isi2 s2 = dt_p2 index2 = -1 - else: - t_f2 = t2[1] + else: # t2[0] == t_start + t_f2 = t2[1] if N2 > 1 else 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] + # dt_p2 = t_start-t_p1 # 0.0 + dt_p2 = get_min_dist_cython(t_p2, t1, N1, 0, t_aux1[0], t_aux1[1]) + isi2 = t_f2-t2[0] s2 = dt_p2 index2 = 0 @@ -259,7 +278,8 @@ def spike_distance_cython(double[:] t1, double[:] t2, s1 = dt_p1 else: dt_f1 = dt_p1 - isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) + isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) if N1 > 1 \ + else t_end-t1[N1-1] # s1 needs adjustment due to change of isi1 # s1 = dt_p1*(t_end-t1[N1-1])/isi1 # Eero's correction: no adjustment @@ -292,7 +312,8 @@ def spike_distance_cython(double[:] t1, double[:] t2, s2 = dt_p2 else: dt_f2 = dt_p2 - isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) + isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) if N2 > 1 \ + else t_end-t2[N2-1] # s2 needs adjustment due to change of isi2 # s2 = dt_p2*(t_end-t2[N2-1])/isi2 # Eero's correction: no adjustment @@ -318,7 +339,8 @@ def spike_distance_cython(double[:] t1, double[:] t2, else: t_f1 = t_aux1[1] dt_f1 = dt_p1 - isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) + isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) if N1 > 1 \ + else t_end-t1[N1-1] if index2 < N2-1: t_f2 = t2[index2+1] dt_f2 = get_min_dist_cython(t_f2, t1, N1, index1, @@ -327,7 +349,8 @@ def spike_distance_cython(double[:] t1, double[:] t2, else: t_f2 = t_aux2[1] dt_f2 = dt_p2 - isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) + isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) if N2 > 1 \ + else t_end-t2[N2-1] index += 1 t_last = t_curr # isi1 = max(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) diff --git a/pyspike/cython/cython_profiles.pyx b/pyspike/cython/cython_profiles.pyx index f08de6e..4a42cdb 100644 --- a/pyspike/cython/cython_profiles.pyx +++ b/pyspike/cython/cython_profiles.pyx @@ -63,18 +63,18 @@ def isi_profile_cython(double[:] s1, double[:] s2, # first interspike interval - check if a spike exists at the start time if s1[0] > t_start: # edge correction - nu1 = fmax(s1[0]-t_start, s1[1]-s1[0]) + nu1 = fmax(s1[0]-t_start, s1[1]-s1[0]) if N1 > 1 else s1[0]-t_start index1 = -1 else: - nu1 = s1[1]-s1[0] + nu1 = s1[1]-s1[0] if N1 > 1 else t_end-s1[0] index1 = 0 if s2[0] > t_start: # edge correction - nu2 = fmax(s2[0]-t_start, s2[1]-s2[0]) + nu2 = fmax(s2[0]-t_start, s2[1]-s2[0]) if N2 > 1 else s2[0]-t_start index2 = -1 else: - nu2 = s2[1]-s2[0] + nu2 = s2[1]-s2[0] if N2 > 1 else t_end-s2[0] index2 = 0 isi_values[0] = fabs(nu1-nu2)/fmax(nu1, nu2) @@ -92,7 +92,8 @@ def isi_profile_cython(double[:] s1, double[:] s2, nu1 = s1[index1+1]-s1[index1] else: # edge correction - nu1 = fmax(t_end-s1[index1], nu1) + nu1 = fmax(t_end-s1[index1], nu1) if N1 > 1 \ + else t_end-s1[index1] elif (index2 < N2-1) and ((index1 == N1-1) or (s1[index1+1] > s2[index2+1])): index2 += 1 @@ -101,7 +102,8 @@ def isi_profile_cython(double[:] s1, double[:] s2, nu2 = s2[index2+1]-s2[index2] else: # edge correction - nu2 = fmax(t_end-s2[index2], nu2) + nu2 = fmax(t_end-s2[index2], nu2) if N2 > 1 \ + else t_end-s2[index2] else: # s1[index1+1] == s2[index2+1] index1 += 1 index2 += 1 @@ -110,12 +112,14 @@ def isi_profile_cython(double[:] s1, double[:] s2, nu1 = s1[index1+1]-s1[index1] else: # edge correction - nu1 = fmax(t_end-s1[index1], nu1) + nu1 = fmax(t_end-s1[index1], nu1) if N1 > 1 \ + else t_end-s1[index1] if index2 < N2-1: nu2 = s2[index2+1]-s2[index2] else: # edge correction - nu2 = fmax(t_end-s2[index2], nu2) + nu2 = fmax(t_end-s2[index2], nu2) if N2 > 1 \ + else t_end-s2[index2] # compute the corresponding isi-distance isi_values[index] = fabs(nu1 - nu2) / fmax(nu1, nu2) index += 1 @@ -191,9 +195,9 @@ 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 + # we can assume at least one spikes per spike train + assert N1 > 0 + assert N2 > 0 spike_events = np.empty(N1+N2+2) @@ -205,26 +209,26 @@ def spike_profile_cython(double[:] t1, double[:] t2, # 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_aux1[0] = fmin(t_start, 2*t1[0]-t1[1]) if N1 > 1 else t_start + t_aux1[1] = fmax(t_end, 2*t1[N1-1]-t1[N1-2]) if N1 > 1 else t_end + t_aux2[0] = fmin(t_start, 2*t2[0]-t2[1]) if N2 > 1 else t_start + t_aux2[1] = fmax(t_end, 2*t2[N2-1]-t2[N2-2]) if N2 > 1 else t_end 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_aux2[0], t_aux2[1]) - isi1 = fmax(t_f1-t_start, t1[1]-t1[0]) + isi1 = fmax(t_f1-t_start, t1[1]-t1[0]) if N1 > 1 else t_f1-t_start dt_p1 = dt_f1 # s1 = dt_p1*(t_f1-t_start)/isi1 s1 = dt_p1 index1 = -1 else: - t_f1 = t1[1] + t_f1 = t1[1] if N1 > 1 else 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] + dt_p1 = get_min_dist_cython(t_p1, t2, N2, 0, t_aux2[0], t_aux2[1]) + isi1 = t_f1-t1[0] s1 = dt_p1 index1 = 0 if t2[0] > t_start: @@ -232,15 +236,15 @@ def spike_profile_cython(double[:] t1, double[:] t2, t_f2 = t2[0] 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]) + isi2 = fmax(t_f2-t_start, t2[1]-t2[0]) if N2 > 1 else t_f2-t_start # s2 = dt_p2*(t_f2-t_start)/isi2 s2 = dt_p2 index2 = -1 else: - t_f2 = t2[1] + t_f2 = t2[1] if N2 > 1 else 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] + dt_p2 = get_min_dist_cython(t_p2, t1, N1, 0, t_aux1[0], t_aux1[1]) + isi2 = t_f2-t2[0] s2 = dt_p2 index2 = 0 @@ -273,7 +277,8 @@ def spike_profile_cython(double[:] t1, double[:] t2, s1 = dt_p1 else: dt_f1 = dt_p1 - isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) + isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) if N1 > 1 \ + else t_end-t1[N1-1] # s1 needs adjustment due to change of isi1 # s1 = dt_p1*(t_end-t1[N1-1])/isi1 # Eero's correction: no adjustment @@ -305,7 +310,8 @@ def spike_profile_cython(double[:] t1, double[:] t2, s2 = dt_p2 else: dt_f2 = dt_p2 - isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) + isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) if N2 > 1 \ + else t_end-t2[N2-1] # s2 needs adjustment due to change of isi2 # s2 = dt_p2*(t_end-t2[N2-1])/isi2 # Eero's correction: no adjustment @@ -330,7 +336,8 @@ def spike_profile_cython(double[:] t1, double[:] t2, else: t_f1 = t_aux1[1] dt_f1 = dt_p1 - isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) + isi1 = fmax(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) if N1 > 1 \ + else t_end-t1[N1-1] if index2 < N2-1: t_f2 = t2[index2+1] dt_f2 = get_min_dist_cython(t_f2, t1, N1, index1, @@ -339,18 +346,14 @@ def spike_profile_cython(double[:] t1, double[:] t2, else: t_f2 = t_aux2[1] dt_f2 = dt_p2 - isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) + isi2 = fmax(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) if N2 > 1 \ + else t_end-t2[N2-1] index += 1 # the last event is the interval end if spike_events[index-1] == t_end: index -= 1 else: spike_events[index] = t_end - # 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 s2 = dt_f2 y_ends[index-1] = (s1*isi2 + s2*isi1) / isi_avrg_cython(isi1, isi2) diff --git a/pyspike/cython/python_backend.py b/pyspike/cython/python_backend.py index a5f7ae4..a1e3a65 100644 --- a/pyspike/cython/python_backend.py +++ b/pyspike/cython/python_backend.py @@ -28,17 +28,17 @@ def isi_distance_python(s1, s2, t_start, t_end): isi_values = np.empty(len(spike_events) - 1) if s1[0] > t_start: # edge correction - nu1 = max(s1[0] - t_start, s1[1] - s1[0]) + nu1 = max(s1[0] - t_start, s1[1] - s1[0]) if N1 > 1 else s1[0]-t_start index1 = -1 else: - nu1 = s1[1] - s1[0] + nu1 = s1[1] - s1[0] if N1 > 1 else t_end-s1[0] index1 = 0 if s2[0] > t_start: # edge correction - nu2 = max(s2[0] - t_start, s2[1] - s2[0]) + nu2 = max(s2[0] - t_start, s2[1] - s2[0]) if N2 > 1 else s2[0]-t_start index2 = -1 else: - nu2 = s2[1] - s2[0] + nu2 = s2[1] - s2[0] if N2 > 1 else t_end-s2[0] index2 = 0 isi_values[0] = abs(nu1 - nu2) / max(nu1, nu2) @@ -52,7 +52,8 @@ def isi_distance_python(s1, s2, t_start, t_end): nu1 = s1[index1+1]-s1[index1] else: # edge correction - nu1 = max(t_end-s1[N1-1], s1[N1-1]-s1[N1-2]) + nu1 = max(t_end-s1[N1-1], s1[N1-1]-s1[N1-2]) if N1 > 1 \ + else t_end-s1[N1-1] elif (index2 < N2-1) and (index1 == N1-1 or s1[index1+1] > s2[index2+1]): @@ -62,7 +63,8 @@ def isi_distance_python(s1, s2, t_start, t_end): nu2 = s2[index2+1]-s2[index2] else: # edge correction - nu2 = max(t_end-s2[N2-1], s2[N2-1]-s2[N2-2]) + nu2 = max(t_end-s2[N2-1], s2[N2-1]-s2[N2-2]) if N2 > 1 \ + else t_end-s2[N2-1] else: # s1[index1 + 1] == s2[index2 + 1] index1 += 1 @@ -72,12 +74,14 @@ def isi_distance_python(s1, s2, t_start, t_end): nu1 = s1[index1+1]-s1[index1] else: # edge correction - nu1 = max(t_end-s1[N1-1], s1[N1-1]-s1[N1-2]) + nu1 = max(t_end-s1[N1-1], s1[N1-1]-s1[N1-2]) if N1 > 1 \ + else t_end-s1[N1-1] if index2 < N2-1: nu2 = s2[index2+1]-s2[index2] else: # edge correction - nu2 = max(t_end-s2[N2-1], s2[N2-1]-s2[N2-2]) + nu2 = max(t_end-s2[N2-1], s2[N2-1]-s2[N2-2]) if N2 > 1 \ + else t_end-s2[N2-1] # compute the corresponding isi-distance isi_values[index] = abs(nu1 - nu2) / \ max(nu1, nu2) @@ -146,27 +150,30 @@ def spike_distance_python(spikes1, spikes2, t_start, t_end): t_aux1 = np.zeros(2) t_aux2 = np.zeros(2) - t_aux1[0] = min(t_start, t1[0]-(t1[1]-t1[0])) - t_aux1[1] = max(t_end, t1[N1-1]+(t1[N1-1]-t1[N1-2])) - t_aux2[0] = min(t_start, t2[0]-(t2[1]-t2[0])) - t_aux2[1] = max(t_end, t2[N2-1]+(t2[N2-1]-t2[N2-2])) + t_aux1[0] = min(t_start, t1[0]-(t1[1]-t1[0])) if N1 > 1 else t_start + t_aux1[1] = max(t_end, t1[N1-1]+(t1[N1-1]-t1[N1-2])) if N1 > 1 else t_end + t_aux2[0] = min(t_start, t2[0]-(t2[1]-t2[0])) if N2 > 1 else t_start + t_aux2[1] = max(t_end, t2[N2-1]+(t2[N2-1]-t2[N2-2])) if N2 > 1 else t_end 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] + # print "t_aux1", t_aux1, ", t_aux2:", t_aux2 + spike_events[0] = t_start if t1[0] > t_start: t_f1 = t1[0] dt_f1 = get_min_dist(t_f1, t2, 0, t_aux2[0], t_aux2[1]) dt_p1 = dt_f1 - isi1 = max(t_f1-t_start, t1[1]-t1[0]) + isi1 = max(t_f1-t_start, t1[1]-t1[0]) if N1 > 1 else t_f1-t_start # s1 = dt_p1*(t_f1-t_start)/isi1 s1 = dt_p1 index1 = -1 else: - dt_p1 = 0.0 - t_f1 = t1[1] + # dt_p1 = t_start-t_p2 + t_f1 = t1[1] if N1 > 1 else t_end + dt_p1 = get_min_dist(t_p1, t2, 0, t_aux2[0], t_aux2[1]) dt_f1 = get_min_dist(t_f1, t2, 0, t_aux2[0], t_aux2[1]) - isi1 = t1[1]-t1[0] + isi1 = t_f1-t1[0] s1 = dt_p1 index1 = 0 if t2[0] > t_start: @@ -174,15 +181,15 @@ def spike_distance_python(spikes1, spikes2, t_start, t_end): t_f2 = t2[0] dt_f2 = get_min_dist(t_f2, t1, 0, t_aux1[0], t_aux1[1]) dt_p2 = dt_f2 - isi2 = max(t_f2-t_start, t2[1]-t2[0]) + isi2 = max(t_f2-t_start, t2[1]-t2[0]) if N2 > 1 else t_f2-t_start # s2 = dt_p2*(t_f2-t_start)/isi2 s2 = dt_p2 index2 = -1 else: - dt_p2 = 0.0 - t_f2 = t2[1] + t_f2 = t2[1] if N2 > 1 else t_end + dt_p2 = get_min_dist(t_p2, t1, 0, t_aux1[0], t_aux1[1]) dt_f2 = get_min_dist(t_f2, t1, 0, t_aux1[0], t_aux1[1]) - isi2 = t2[1]-t2[0] + isi2 = t_f2-t2[0] s2 = dt_p2 index2 = 0 @@ -213,7 +220,8 @@ def spike_distance_python(spikes1, spikes2, t_start, t_end): s1 = dt_p1 else: dt_f1 = dt_p1 - isi1 = max(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) + isi1 = max(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) if N1 > 1 \ + else t_end-t1[N1-1] # s1 needs adjustment due to change of isi1 # s1 = dt_p1*(t_end-t1[N1-1])/isi1 # Eero's correction: no adjustment @@ -242,7 +250,8 @@ def spike_distance_python(spikes1, spikes2, t_start, t_end): s2 = dt_p2 else: dt_f2 = dt_p2 - isi2 = max(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) + isi2 = max(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) if N2 > 1 \ + else t_end-t2[N2-1] # s2 needs adjustment due to change of isi2 # s2 = dt_p2*(t_end-t2[N2-1])/isi2 # Eero's adjustment: no correction @@ -266,7 +275,8 @@ def spike_distance_python(spikes1, spikes2, t_start, t_end): else: t_f1 = t_aux1[1] dt_f1 = dt_p1 - isi1 = max(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) + isi1 = max(t_end-t1[N1-1], t1[N1-1]-t1[N1-2]) if N1 > 1 \ + else t_end-t1[N1-1] if index2 < N2-1: t_f2 = t2[index2+1] dt_f2 = get_min_dist(t_f2, t1, index1, t_aux1[0], t_aux1[1]) @@ -274,16 +284,15 @@ def spike_distance_python(spikes1, spikes2, t_start, t_end): else: t_f2 = t_aux2[1] dt_f2 = dt_p2 - isi2 = max(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) + isi2 = max(t_end-t2[N2-1], t2[N2-1]-t2[N2-2]) if N2 > 1 \ + else t_end-t2[N2-1] index += 1 + # the last event is the interval end if spike_events[index-1] == t_end: index -= 1 else: spike_events[index] = t_end - # 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 y_ends[index-1] = (s1*isi2 + s2*isi1) / (0.5*(isi1+isi2)**2) |