# generate random models
for i in range(n_models):
# create a model randomly from all channels
weights_model = problem.generator(prng, None)
for j, dt in enumerate(dts):
print 'run '+'model: ' + str(i) + ' dt: ' +str(dt)
# change dt
data_newdt = change_dt(dt, problem.data)
problem.simulation_params = extract_simulation_params(data_newdt)
# run simulation
problem.update_cell(weights_model)
currents = [problem.cell.soma.record_from(channel_list[k], 'i'+ion_list[k], pos=.5) for k in range(len(channel_list))]
v_newdt, t_newdt = run_simulation(problem.cell, **problem.simulation_params)
#pl.figure()
#pl.plot(t_newdt, v_newdt)
#pl.show()
# compute parameter
dvdt_newdt = np.concatenate((np.array([(v_newdt[1]-v_newdt[0])/dt]), np.diff(v_newdt)/dt))
i_newdt = data_newdt.i.values
celsius = problem.simulation_params['celsius']
# get currents
candidate = np.ones(len(problem.path_variables)) # gbars should be 1
problem.update_cell(candidate)
os.makedirs(save_dir)
with open(save_dir+'/problem.json', 'w') as f:
json.dump(params, f, indent=4)
with open(save_dir+'/cell.json', 'w') as f:
json.dump(Cell.from_modeldir(params['model_dir']).get_dict(), f, indent=4)
for trial in range(0, n_trials):
# get current traces
v_exp = problem.data.v.values
t_exp = problem.data.t.values
i_exp = problem.data.i.values
dt = t_exp[1] - t_exp[0]
dvdt = np.concatenate((np.array([(v_exp[1]-v_exp[0])/dt]), np.diff(v_exp) / dt))
candidate = np.ones(len(problem.path_variables))
problem.update_cell(candidate)
channel_list = get_channel_list(problem.cell, 'soma')
ion_list = get_ionlist(channel_list)
celsius = problem.simulation_params['celsius']
currents = currents_given_v(v_exp, t_exp, problem.cell.soma, channel_list, ion_list, celsius)
# convert units
dvdt_sc, i_inj_sc, currents_sc, Cm, cell_area = convert_units(problem.cell.soma.L, problem.cell.soma.diam,
problem.cell.soma.cm, dvdt, i_exp,
currents)
# linear regression
weights, residual, y, X = linear_regression(dvdt_sc, i_inj_sc, currents_sc, i_pas=0, Cm=Cm)
#weights, residual, y, X = linear_regression(dvdt_sc, i_inj_sc, currents_sc, i_pas=0, Cm=None, cell_area=cell_area)
