def main(dbfile):
"""Run the script given a bigrun file"""
# Get the db
db = tables.openFile(dbfile)
simulations = hm.get_first_level_groups(db.root)
# Sort simulations according to `rate` and `strength`
ind_rate_strength = get_ind_rate_strength(simulations)
n_rate = len(set([i[0] for i in ind_rate_strength]))
# Selected simus are input like "1,2 1,5 2,10"
selected_simus = raw_input("Simulations #").split(' ')
selected_simus = [get_1d_ind_simu(s, n_rate) for s in selected_simus]
# Plot the histogram for each selected simulation
for i_sim in selected_simus:
histogram_peaks(simulations[i_sim])
plt.show()
db.close()
def main(dbfile):
"""Run the script given the HDF5 filename"""
# Get the simulations
db = tables.openFile(dbfile)
simus = hm.get_first_level_groups(db.root)
# Define some function to get specific result values
def get_strength(simu):
return hm.get_group_attr(simu, ('paramset', '_v_attrs', 'Common', 'inter_conn_strength', 0, 1))
def get_mps(simu):
return hm.get_group_attr(simu, ('results', '_v_attrs', 'MPS', 'whole'))
def get_sts(simu):
return hm.get_group_attr(simu, ('results', '_v_attrs', 'STS', 'whole'))
def get_fftmax(simu):
return hm.get_group_attr(simu, ('results', '_v_attrs', 'FFTMAX', 'mean'))
def get_peakdist(simu):
peakdist = hm.get_group_attr(simu, ('results', '_v_attrs', 'peak_distances'))
peakdist_means = utils.get_dict_values(peakdist, 2, "mean")
peakdist_disps = utils.get_dict_values(peakdist, 2, "disp")
return peakdist_means, peakdist_disps
def get_peakdist_mean(simu):
means, _ = get_peakdist(simu)
return np.mean(means), np.std(means)
def get_peakdist_mean_mean(simu):
mean, _ = get_peakdist_mean(simu)
return mean
def get_peakdist_mean_disp(simu):
_, disp = get_peakdist_mean(simu)
return disp
def get_peakdist_disp(simu):
_, disps = get_peakdist(simu)
return np.mean(disps), np.std(disps)
def get_peakdist_disp_mean(simu):
mean, _ = get_peakdist_disp(simu)
return mean
def get_peakdist_disp_disp(simu):
_, disp = get_peakdist_disp(simu)
return disp
def get_spiking_rate(simu):
spikes_it = hm.get_group_attr(simu, ('results', 'spikes_it')).read()
nspikes = spikes_it.shape[1]
nneurons = hm.get_group_attr(simu, ('paramset', '_v_attrs', 'Common', 'N_mitral'))
simu_length = hm.get_group_attr(simu, ('paramset', '_v_attrs', 'Common', 'simu_length'))
return nspikes/float(simu_length)/nneurons
get_indexes = (get_strength, get_mps, get_sts, get_fftmax,
get_peakdist_mean_mean, get_peakdist_mean_disp,
get_peakdist_disp_mean, get_peakdist_disp_disp,
get_spiking_rate)
index_names = ("strength", "MPS", "STS", "FFTMAX",
"Peak Dist mean (mean)", "Peak Dist mean (disp)",
"Peak Dist disp (mean)", "Peak Dist disp (disp)",
"Spiking rate")
# Get simulation indexes for each simulation
res_indexes = np.ndarray((len(simus), len(get_indexes)))
for i_simu, simu in enumerate(simus):
for i_index, get_index in enumerate(get_indexes):
res_indexes[i_simu, i_index] = get_index(simu)
# Sort index array on `strength` index
indsort = res_indexes[:, 0].argsort()
res_indexes = res_indexes[indsort, :]
# Sort simulations accordingly
sorted_simulations = []
for sorted_index in indsort:
sorted_simulations.append(simus[sorted_index])
# Plot the res_indexes against interconnection strength
plt.ion()
plt.figure()
# Plot standard indexes
data = {1: "MPS (whole)",
2: "STS (whole)",
3: "FFTMAX (mean) (Hz)",
8: "Spiking rate (spikes/sec/neuron)"}
for iplot in data:
plt.plot(res_indexes[:, 0], res_indexes[:, iplot], '.', label=data[iplot])
# Plot peak dist index
plt.errorbar(res_indexes[:, 0], res_indexes[:, 4], yerr=res_indexes[:, 5],
fmt=".", label="Peak Dist (mean)")
plt.errorbar(res_indexes[:, 0], res_indexes[:, 6], yerr=res_indexes[:, 7],
fmt=".", label="Peak Dist (disp)")
# Add some plot information
plt.xlabel("Interconnection strength")
plt.legend()
plt.show()
# Get simulations to plot
psimu = raw_input("Plot simulation #")
while psimu != "":
simu = sorted_simulations[int(psimu)]
for index_name, index_fun in zip(index_names, get_indexes):
print index_name, index_fun(simu)
print "\n"
hm.plot_simulation(simu)
psimu = raw_input("Plot simulation #")
db.close()