def single_run(filter, spk_src, bg_src, params):
import evaluate as eval
sp_win = params['sp_win']
spadd_win = params['sp_add_win']
pow_frac = params['pow_frac']
f_filter = params['f_filter']
type = params['sp_type']
thresh = params['thresh']
feats = params['features']
contacts = params['contacts']
n_pts = params['n_pts']
sp, stim, spt_real = eval.mix_cellbg(filter, spk_src, bg_src,
spadd_win, pow_frac)
sp = eval.filter_data(sp, f_filter)
spt, clust_idx, n_missing = eval.spike_clusters(sp, spt_real,
stim,
thresh,
type, sp_win)
features = eval.calc_features(sp, spt, sp_win, feats, contacts)
uni_metric = eval.univariate_metric(eval.mutual_information,
features, clust_idx)
multi_metric = eval.k_nearest(features, clust_idx, n_pts=n_pts)
n_total = len(spt_real['data'])
result_dict= {"cell" : spk_src,
"electrode" : bg_src,
"spikes_total" : n_total,
"spikes_missed" : n_missing,
"mutual_information" : uni_metric,
"k_nearest" : multi_metric}
result_dict.update(params)
import socket
#from sim_manager import get_version
result_dict['host'] = socket.gethostname()
#result_dict['dependencies'] ={'evaluate': get_version(eval),
# 'spike_sort': get_version(eval.sort)}
return result_dict
from spike_analysis import basic
import evaluate as eval
spike_src = "/Gollum/s44gollum07/el3/cell1"
background_src = "/Gollum/s44gollum01/el4"
sp_win = [-2, 2]
pow_frac = 5
out_dataset = "/TestSubject/sSession01/el1"
if __name__ == "__main__":
in_filter = filters.BakerlabFilter("../data/gollum.inf")
out_filter = filters.PyTablesFilter("simulated.h5")
sp_sim, stim_bg, spt_sim = eval.mix_cellbg(in_filter, spike_src,
background_src,
sp_win, pow_frac)
#export
out_filter.write_spt(spt_sim, out_dataset+"/cell1_orig",
overwrite=True)
out_filter.write_spt(stim_bg,out_dataset+ "stim",
overwrite=True)
out_filter.write_sp(sp_sim, out_dataset+"/raw",
overwrite=True)
#plotting
print "Total spikes: ", len(spt_sim['data'])
raw_bg, _ = eval.read_data(in_filter, background_src)
basic.plotPSTH(spt_sim['data'], stim_bg['data'], win=[0,300])
plt.figure()
plt.plot(raw_bg['data'][0,:25E3])
