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""" spikes.py
Module containing several function to load and transform spike trains
Copyright 2014, Mario Mulansky <mario.mulansky@gmx.net>
"""
import numpy as np
############################################################
# spike_train_from_string
############################################################
def spike_train_from_string(s, sep=' '):
""" Converts a string of times into an array of spike times.
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)
############################################################
# merge_spike_trains
############################################################
def merge_spike_trains(spike_trains):
""" Merges a number of spike trains into a single spike train.
Params:
- spike_trains: list of arrays of spike times
Returns:
- array with the merged spike times
"""
# get the lengths of the spike trains
lens = np.array([len(st) for st in spike_trains])
merged_spikes = np.empty(np.sum(lens))
index = 0 # the index for merged_spikes
indices = np.zeros_like(lens) # indices of the spike trains
index_list = np.arange(len(indices)) # indices of indices of spike trains
# that have not yet reached the end
# list of the possible events in the spike trains
vals = [spike_trains[i][indices[i]] for i in index_list]
while len(index_list) > 0:
i = np.argmin(vals) # the next spike is the minimum
merged_spikes[index] = vals[i] # put it to the merged spike train
i = index_list[i]
index += 1 # next index of merged spike train
indices[i] += 1 # next index for the chosen spike train
if indices[i] >= lens[i]: # remove spike train index if ended
index_list = index_list[index_list != i]
vals = [spike_trains[i][indices[i]] for i in index_list]
return merged_spikes
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