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-rw-r--r--pyspike/cython/cython_distances.pyx91
1 files changed, 57 insertions, 34 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])
generated by cgit v1.2.3 (git 2.39.1) at 2024-04-19 23:16:58 +0000