def test_model_io():
# get example data
data = np.genfromtxt('./data/exampleData.csv', delimiter=',')
frequencies = data[:, 0]
Z = data[:, 1] + 1j * data[:, 2]
randles = CustomCircuit(initial_guess=[.01, .005, .1, .005, .1, .001, 200],
circuit='R_0-p(R_1,C_1)-p(R_1,C_1)-W_1/W_2')
randles.fit(frequencies, Z)
print(randles)
model_export(randles, './test_io.json')
randles2 = model_import('./test_io.json')
print(randles2)
assert randles == randles2
def test_CustomCircuit():
initial_guess = [.01, .005, .1, .005, .1, .001, 200]
custom_string = 'R0-p(R1,C1)-p(R2,C2)-W1'
custom_circuit = CustomCircuit(initial_guess=initial_guess,
circuit=custom_string)
# check get_param_names()
print(custom_circuit.get_param_names())
assert custom_circuit.get_param_names() == \
['R0', 'R1', 'C1', 'R2', 'C2', 'W1_0', 'W1_1']
# check _is_fit()
assert not custom_circuit._is_fit()
initial_guess = [.01, .005, .1]
custom_string = 'R_0-p(R_1,C_1)'
custom_circuit = CustomCircuit(initial_guess=initial_guess,
circuit=custom_string,
name='Test')
line = '\n-------------------------------\n'
assert str(custom_circuit) == line + \
'Circuit: Test\n' + \
'Circuit string: R_0-p(R_1,C_1)\n' + \
'Fit: False\n' + line + \
'Initial guesses:\n' + \
'\tR_0 = 1.00e-02\n' + \
'\tR_1 = 5.00e-03\n' + \
'\tC_1 = 1.00e-01\n'
# check that it rejects improper inputs
# enforcing the length of initial_guess
try:
initial_guess = [.01, .005, .1, .005, .1, .001, 200]
custom_string = 'R_0-p(R_1,E_1/E_2)-p(R_1,C_1)-W_1/W_2'
custom_circuit = CustomCircuit(initial_guess=initial_guess,
circuit=custom_string)
except (AssertionError):
pass
else:
raise Exception('unhandled error occurred')
return
def test_CustomCircuit():
initial_guess = [.01, .005, .1, .005, .1, .001, 200]
custom_string = 'R0-p(R1,C1)-p(R2,C2)-W1'
custom_circuit = CustomCircuit(initial_guess=initial_guess,
circuit=custom_string)
# check get_param_names()
full_names, all_units = custom_circuit.get_param_names()
assert full_names == ['R0', 'R1', 'C1', 'R2', 'C2', 'W1_0', 'W1_1']
assert all_units == ['Ohm', 'Ohm', 'F', 'Ohm', 'F', 'Ohm', 'sec']
# check _is_fit()
assert not custom_circuit._is_fit()
initial_guess = [.01, .005, .1]
custom_string = 'R0-p(R1,C1)'
custom_circuit = CustomCircuit(initial_guess=initial_guess,
circuit=custom_string,
name='Test')
assert str(custom_circuit) == \
'\nName: Test\n' + \
'Circuit string: R0-p(R1,C1)\n' + \
'Fit: False\n' + \
'\nInitial guesses:\n' + \
' R0 = 1.00e-02 [Ohm]\n' + \
' R1 = 5.00e-03 [Ohm]\n' + \
' C1 = 1.00e-01 [F]\n'
# check that it rejects improper inputs
# enforcing the length of initial_guess
try:
initial_guess = [.01, .005, .1, .005, .1, .001, 200]
custom_string = 'R0-p(R1,E1)-p(R1,C1)-W1'
custom_circuit = CustomCircuit(initial_guess=initial_guess,
circuit=custom_string)
except (AssertionError):
pass
else:
raise Exception('unhandled error occurred')
return
def get_fitting_data(data, model, guess):
if model == "randles":
circuit = Randles(initial_guess=guess)
else:
# circuit = Randles(initial_guess=[.01, .005, .1, .001, 200])
circuit = CustomCircuit(initial_guess=guess,
circuit=model)
columns = ['freq/Hz', 'Re(Z)/Ohm', '-Im(Z)/Ohm']
frequencies = data["freq/Hz"].values
Z = data['Re(Z)/Ohm'].values - 1j * data['-Im(Z)/Ohm'].values
instance_of_impedance_lib = circuit.fit(frequencies, Z)
print(instance_of_impedance_lib)
param_names = instance_of_impedance_lib.get_param_names()
param_values = instance_of_impedance_lib.parameters_
param_error = instance_of_impedance_lib.conf_
# f_pred = np.logspace(5, -2)
circuit_fit = circuit.predict(frequencies)
return circuit_fit, param_names, param_values, param_error
if n == 000:
break
if n != 0:
# READ EXPERIM ENT
data = np.genfromtxt('Impedance -' + str(n) + '.z',
skip_header=123,
delimiter='')
data = data[:52]
frequencies = data[:, 0]
Z = data[:, 4] + 1j * data[:, 5]
frequencies = frequencies[np.imag(Z) < 0]
Z = Z[np.imag(Z) < 0]
############## FIG. B
circuitB = 'R0-p(E, R1-p(C1,R2,W1))'
initial_guessB = [1, 1, 1, 1000, 1, 100, 1, 1]
circuitB = CustomCircuit(circuitB, initial_guess=initial_guessB)
circuitB.fit(frequencies, Z)
circuitB.parameters_
print("Схема Б", circuitB)
P = [
-1 * n,
m.log10(circuitB.parameters_[3]),
m.log10(circuitB.parameters_[4]),
m.log10(circuitB.parameters_[5])
]
# ФИТТИНГ
Z_fitB = circuitB.predict(frequencies)
# Погрешность
res_meas_real = (Z - circuitB.predict(frequencies)).real / np.abs(Z)
res_meas_imag = (Z - circuitB.predict(frequencies)).imag / np.abs(Z)
# ploting
#while measuring the EIS we do not want flow
actions.pump_off()
time.sleep(2)
eis_exp = actions.eis(start_freq, end_freq, points, blockd=blockd)
Zreal, Zimag, Zfreq = eis_exp['data']
Z = np.array(Zreal) + 1j * np.array(Zimag)
frequencies = np.array(Zfreq)
#do both a randles and custom fit and check which one works better
randles = Randles(initial_guess=[.01, .005, .1, .001, 200])
RRC = CustomCircuit(circuit='R0-p(R1,C1)',
initial_guess=[
np.percentile(Z.real, 5),
np.percentile(Z.real, 95), 10**-5
])
#fit them
res_randles = randles.fit(frequencies, Z)
res_rrc = RRC.fit(frequencies, Z)
exp_results[sno] = {
'pulse_params': {
'centers': centers,
'pots': pots,
'widths': widths
},
'eis_params': {
'start_freq': start_freq,
del connection
pstat.SetCell(GamryCOM.CellOff)
pstat.Close()
import matplotlib.pyplot as plt
plt.scatter(np.array(Zreal),-np.array(Zimag),c=np.log(Zfreq))
plt.colorbar()
plt.axis('equal')
plt.show()
from impedance.circuits import CustomCircuit
frequencies = np.array(Zfreq)
Z = np.array(Zreal)+1j*np.array(Zimag)
circuit = 'R0-p(R1,C1)'
guess = [np.min(Z.real),np.max(Z.real),10**-6]
circuit_mod = CustomCircuit(circuit,initial_guess=guess)
circuit_mod.fit(frequencies, Z)
Z_fit = circuit_mod.predict(frequencies)
import matplotlib.pyplot as plt
from impedance.plotting import plot_nyquist
fig, ax = plt.subplots()
plot_nyquist(ax, frequencies, Z, fmt='o')
plot_nyquist(ax, frequencies, Z_fit, fmt='-')
plt.legend(['Data', 'Fit'])
plt.show()