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-rw-r--r--pyspike/cython/cython_profiles.pyx110
1 files changed, 67 insertions, 43 deletions
diff --git a/pyspike/cython/cython_profiles.pyx b/pyspike/cython/cython_profiles.pyx
index 4663f2e..aa24db4 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
@@ -181,6 +185,8 @@ 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 +195,10 @@ def spike_profile_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
+
spike_events = np.empty(N1+N2+2)
y_starts = np.empty(len(spike_events)-1)
@@ -196,36 +206,45 @@ 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, 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_start, t_end)
- isi1 = fmax(t_f1-t_start, t1[1]-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]) if N1 > 1 else t_f1-t_start
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_p1 = 0.0
- isi1 = t1[1]-t1[0]
+ 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 = 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:
# 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
+ 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]
- dt_f2 = get_min_dist_cython(t_f2, t1, N1, 0, t_start, t_end)
- dt_p2 = 0.0
- isi2 = t2[1]-t2[0]
+ 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 = 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
@@ -245,7 +264,7 @@ 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 +272,17 @@ 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])
+ 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
+ # 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 +297,7 @@ 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 +305,17 @@ 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])
+ 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
+ # 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
@@ -306,32 +331,31 @@ 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])
+ 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,
- 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])
+ 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)
# end nogil
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-30 22:45:55 +0000