def save (name_trace, trace):
name = 'I_Gen_'+name_trace+'_'+str(time_step/ms)+'_ev'+str(int(eval_time/second))
head = 't (s)\t'
series_list = [duration_time_series[0:eval_points]]
for i,ix in enumerate(plot_indices):
head = head + plot_labels[i]+'\t'
series_list += [trace[ix]]
save_plot_list(name, head, series_list)
print("Written data in: ", name)
return
def fitfunc_verbose(indv, save_traces = False):
trace = get_trace(indv)
norm_trace = norm_trace_avg_unitary_2points(trace,s1,e1,s2,e2)
fwd_trace=(trace[:, eval_start:n_points])
bkw_trace=(trace[:, n_points+eval_start:2*n_points])
norm_f_trace = (norm_trace[:, eval_start:n_points])
norm_b_trace = (norm_trace[:, n_points+eval_start:2*n_points])
# plots
plot_labels = ['AS', 'DA', 'VA', 'DB', 'VB']
plot_indices = [0,2,4,10,6]
for j in plot_indices:
plot(eval_time_series, fwd_trace[j], label = 'v_'+labels[j])
xlabel('Time (s)')
ylabel('V')
title('Forward traces')
legend(loc='upper right')
show()
for j in plot_indices:
plot(eval_time_series, norm_f_trace[j], label = 'v_'+labels[j])
xlabel('Time (s)')
ylabel('dV')
title('Norm Forward traces')
legend(loc='upper right')
show()
for j in plot_indices:
plot(eval_time_series, bkw_trace[j], label = 'v_'+labels[j])
xlabel('Time (s)')
ylabel('V')
title('Backward traces')
legend(loc='upper right')
show()
for j in plot_indices:
plot(eval_time_series, norm_b_trace[j], label = 'v_'+labels[j])
xlabel('Time (s)')
ylabel('dV')
title('Norm Backward traces')
legend(loc='upper right')
show()
#only for final testing fw+bkw+fw
# for j in plot_indices:
# plot(arange(3*n_points)*time_step ,trace[j], label = 'v_'+labels[j])
# xlabel('Time (s)')
# ylabel('V')
# title('Full traces (forward + backward)')
# legend(loc='upper right')
# show()
# for j in plot_indices:
# plot(arange(3*n_points-transient_points)*time_step ,norm_trace[j][:], label = 'v_'+labels[j])
# xlabel('Time (s)')
# ylabel('V')
# title('Full traces norm (forward + backward)')
# legend(loc='upper right')
# show()
print('fitness normalized')
print('f1=', f1(norm_f_trace, norm_b_trace, time_step/second, eval_time/second))
print('f2=', f2(norm_f_trace, norm_b_trace, time_step/second, eval_time/second))
print('f3=', f3(norm_f_trace, norm_b_trace))
print('f3_mod=', f3_mod(norm_f_trace, norm_b_trace))
f = fitness(norm_f_trace, norm_b_trace, time_step/second)
print('f=', f)
print('fitness not normalized')
print('f1=', f1(fwd_trace, bkw_trace, time_step/second, eval_time/second))
print('f2=', f2(fwd_trace, bkw_trace, time_step/second, eval_time/second))
print('f3=', f3(fwd_trace, bkw_trace))
print('f3_mod=', f3_mod(fwd_trace, bkw_trace))
f = fitness(fwd_trace, bkw_trace, time_step/second)
print('f=', f)
if (save_traces):
def save (name_trace, trace):
name = 'I_Gen_'+name_trace+'_'+str(time_step/ms)+'_ev'+str(int(eval_time/second))
head = 't (s)\t'
series_list = [duration_time_series[0:eval_points]]
for i,ix in enumerate(plot_indices):
head = head + plot_labels[i]+'\t'
series_list += [trace[ix]]
save_plot_list(name, head, series_list)
print("Written data in: ", name)
return
names = ['norm_Ftrace','F_trace','norm_Btrace','B_trace']
traces = [norm_f_trace, fwd_trace, norm_b_trace, bkw_trace]
for i in range(0,4):
save(names[i],traces[i])
name = 'I_Gen_'+'Full_trace_'+str(time_step/ms)+'_dur'+str(int(3*duration/second))
head = 't (s)\t'
series_list = [arange(3*n_points)*time_step]
for i,ix in enumerate(plot_indices):
head = head + plot_labels[i]+'\t'
series_list += [trace[ix]]
save_plot_list(name, head, series_list)
print("Written data in: ", name)
name = 'I_Gen_'+'Full_trace_norm_'+str(time_step/ms)+'_dur'+str(int(3*duration/second))
head = 't (s)\t'
series_list = [arange(3*n_points)*time_step]
for i,ix in enumerate(plot_indices):
head = head + plot_labels[i]+'\t'
series_list += [norm_trace[ix]]
save_plot_list(name, head, series_list)
print("Written data in: ", name)
return f
# plt.plot(eval_time_series, a2, label = 'a2')
# plt.xlabel('Time (s)')
# plt.ylabel('a')
# plt.legend(loc='upper right')
# plt.title(ablation_type+' ablations')
# plt.show()
# plt.plot(a1, a2)
# plt.xlabel('a1')
# plt.ylabel('a2')
# plt.show()
# see decomposition of all fwd indices
# plot_traces_color(loco_indices, norm_v_traces, eval_time_series, loco_colors,'norm loco traces with '+ablation_type+' ablated')
#
sys.exit()
name = 'K_ABL_a1_a2_h' + str(
t_step * 1000) + '_I' + str(I_max) + '_ev' + str(t_eval)
head = 't (s)\tI (pA)'
series_list = [duration_time_series[0:eval_points], I_shape[0:eval_points]]
for ab in abl_runs:
head = head + '\t a1' + ab + '\t a2' + ab
series_list += [abl_runs[ab]['a1'], abl_runs[ab]['a2']]
save_plot_list(name, head, series_list)
print("Written data in: ", name)