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"""
Fit Specifying a Function to Compute the Jacobian
=================================================
Specifying an analytical function to calculate the Jacobian can speed-up the
fitting procedure.
"""
import matplotlib.pyplot as plt
import numpy as np
from lmfit import Minimizer, Parameters
def func(pars, x, data=None):
a, b, c = pars['a'], pars['b'], pars['c']
model = a * np.exp(-b*x) + c
if data is None:
return model
return model - data
def dfunc(pars, x, data=None):
a, b = pars['a'], pars['b']
v = np.exp(-b*x)
return np.array([v, -a*x*v, np.ones(len(x))])
def f(var, x):
return var[0] * np.exp(-var[1]*x) + var[2]
params = Parameters()
params.add('a', value=10)
params.add('b', value=10)
params.add('c', value=10)
a, b, c = 2.5, 1.3, 0.8
x = np.linspace(0, 4, 50)
y = f([a, b, c], x)
np.random.seed(2021)
data = y + 0.15*np.random.normal(size=x.size)
###############################################################################
# Fit without analytic derivative:
min1 = Minimizer(func, params, fcn_args=(x,), fcn_kws={'data': data})
out1 = min1.leastsq()
fit1 = func(out1.params, x)
###############################################################################
# Fit with analytic derivative:
min2 = Minimizer(func, params, fcn_args=(x,), fcn_kws={'data': data})
out2 = min2.leastsq(Dfun=dfunc, col_deriv=1)
fit2 = func(out2.params, x)
###############################################################################
# Comparison of fit to exponential decay with/without analytical derivatives
# to model = a*exp(-b*x) + c:
print(f'"true" parameters are: a = {a:.3f}, b = {b:.3f}, c = {c:.3f}\n\n'
'|=========================================\n'
'| Statistic/Parameter | Without | With |\n'
'|-----------------------------------------\n'
f'| N Function Calls | {out1.nfev:d} | {out2.nfev:d} |\n'
f'| Chi-square | {out1.chisqr:.4f} | {out2.chisqr:.4f} |\n'
f"| a | {out1.params['a'].value:.4f} | {out2.params['a'].value:.4f} |\n"
f"| b | {out1.params['b'].value:.4f} | {out2.params['b'].value:.4f} |\n"
f"| c | {out1.params['c'].value:.4f} | {out2.params['c'].value:.4f} |\n"
'------------------------------------------')
###############################################################################
# and the best-fit to the synthetic data (with added noise) is the same for
# both methods:
plt.plot(x, data, 'o', label='data')
plt.plot(x, fit1, label='with analytical derivative')
plt.plot(x, fit2, '--', label='without analytical derivative')
plt.legend()
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