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""" distances.py
Module containing several functions to compute spike distances
Copyright 2014, Mario Mulansky <mario.mulansky@gmx.net>
"""
import numpy as np
from pyspike import PieceWiseConstFunc
def isi_distance(spikes1, spikes2, T_end, T_start=0.0):
""" Computes the instantaneous isi-distance S_isi (t) of the two given spike
trains.
Args:
- spikes1, spikes2: ordered arrays of spike times.
- T_end: end time of the observation interval.
- T_start: begin of the observation interval (default=0.0).
Returns:
- PieceWiseConstFunc describing the isi-distance.
"""
# add spikes at the beginning and end of the interval
s1 = np.empty(len(spikes1)+2)
s1[0] = T_start
s1[-1] = T_end
s1[1:-1] = spikes1
s2 = np.empty(len(spikes2)+2)
s2[0] = T_start
s2[-1] = T_end
s2[1:-1] = spikes2
# compute the interspike interval
nu1 = s1[1:]-s1[:-1]
nu2 = s2[1:]-s2[:-1]
# compute the isi-distance
spike_events = np.empty(len(nu1)+len(nu2))
spike_events[0] = T_start
spike_events[-1] = T_end
# the values have one entry less - the number of intervals between events
isi_values = np.empty(len(spike_events)-1)
# add the distance of the first events
# isi_values[0] = nu1[0]/nu2[0] - 1.0 if nu1[0] <= nu2[0] \
# else 1.0 - nu2[0]/nu1[0]
isi_values[0] = (nu1[0]-nu2[0])/max(nu1[0],nu2[0])
index1 = 0
index2 = 0
index = 1
while True:
# check which spike is next - from s1 or s2
if s1[index1+1] <= s2[index2+1]:
index1 += 1
if index1 >= len(nu1):
break
spike_events[index] = s1[index1]
else:
index2 += 1
if index2 >= len(nu2):
break
spike_events[index] = s2[index2]
# compute the corresponding isi-distance
isi_values[index] = (nu1[index1]-nu2[index2]) / \
max(nu1[index1], nu2[index2])
index += 1
return PieceWiseConstFunc(spike_events, isi_values)
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