""" spikefn.py - parsing spikes from the file written by the sim
Copyright (C) 2013 Shane Lee and Stephanie Jones
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
"""
import numpy as np
import os
import fileio as fio
# returns lists of spiketimes for each cell of the simulation
def spikes_from_file(fspikes, gid_dict):
src_list = []
src_extinput_list = []
src_unique_list = []
# fill in 2 lists from the keys
for key in gid_dict:
if key.startswith('L2_') or key.startswith('L5_'):
src_list.append(key)
elif key == 'extinput':
src_extinput_list.append(key)
else:
src_unique_list.append(key)
# check to see if there are spikes in here, otherwise return an empty array
if os.stat(fspikes).st_size:
s = np.loadtxt(open(fspikes, 'rb'))
else:
s = np.array([], dtype='float64')
# sorted here
s_sorted = {}
for t, gid_float in s[:]:
gid = int(gid_float)
if gid not in s_sorted:
s_sorted[gid] = []
s_sorted[gid].append(t)
gids = [gid for gid in s_sorted]
gids.sort()
s_by_type = {}
for key in src_list:
if key not in s_by_type:
s_by_type[key] = []
for gid in gid_dict[key]:
if gid in s_sorted:
s_sorted[gid].sort()
s_by_type[key].append(np.array(s_sorted[gid]))
else:
s_by_type[key].append(np.array([]))
return s_by_type
if __name__ == '__main__':
f = 'data/gammaweak/data.pkl'
fspk = 'data/gammaweak/spikes.txt'
x = fio.pkl_load(f)
s = spikes_from_file(fspk, x['gid_dict'])