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Diffstat (limited to 'pyspike/distances.py')
-rw-r--r-- | pyspike/distances.py | 75 |
1 files changed, 75 insertions, 0 deletions
diff --git a/pyspike/distances.py b/pyspike/distances.py new file mode 100644 index 0000000..d9790dc --- /dev/null +++ b/pyspike/distances.py @@ -0,0 +1,75 @@ +""" distances.py + +Module containing several function to compute spike distances + +Copyright 2014, Mario Mulansky <mario.mulansky@gmx.net> +""" + +import numpy as np + +from pyspike import PieceWiseConstFunc + +def spike_train_from_string(s, sep=' '): + """ Converts a string of times into a SpikeTrain object. + Params: + - s: the string with (ordered) spike times + - sep: The separator between the time numbers. + Returns: + - array of spike times + """ + return np.fromstring(s, sep=sep) + +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) |