pyerrors/tests/fits_test.py

158 lines
5 KiB
Python

import autograd.numpy as np
import math
import scipy.optimize
from scipy.odr import ODR, Model, RealData
from scipy.linalg import cholesky
from scipy.stats import norm
import pyerrors as pe
import pytest
np.random.seed(0)
def test_least_squares():
dim = 10 + int(30 * np.random.rand())
x = np.arange(dim)
y = 2 * np.exp(-0.06 * x) + np.random.normal(0.0, 0.15, dim)
yerr = 0.1 + 0.1 * np.random.rand(dim)
oy = []
for i, item in enumerate(x):
oy.append(pe.pseudo_Obs(y[i], yerr[i], str(i)))
def f(x, a, b):
return a * np.exp(-b * x)
popt, pcov = scipy.optimize.curve_fit(f, x, y, sigma=[o.dvalue for o in oy], absolute_sigma=True)
def func(a, x):
y = a[0] * np.exp(-a[1] * x)
return y
out = pe.least_squares(x, oy, func)
beta = out.fit_parameters
for i in range(2):
beta[i].gamma_method(S=1.0)
assert math.isclose(beta[i].value, popt[i], abs_tol=1e-5)
assert math.isclose(pcov[i, i], beta[i].dvalue ** 2, abs_tol=1e-3)
assert math.isclose(pe.covariance(beta[0], beta[1]), pcov[0, 1], abs_tol=1e-3)
pe.Obs.e_tag_global = 0
chi2_pyerrors = np.sum(((f(x, *[o.value for o in beta]) - y) / yerr) ** 2) / (len(x) - 2)
chi2_scipy = np.sum(((f(x, *popt) - y) / yerr) ** 2) / (len(x) - 2)
assert math.isclose(chi2_pyerrors, chi2_scipy, abs_tol=1e-10)
out = pe.least_squares(x, oy, func, const_par=[beta[1]])
assert((out.fit_parameters[0] - beta[0]).is_zero)
assert((out.fit_parameters[1] - beta[1]).is_zero)
num_samples = 400
N = 10
x = norm.rvs(size=(N, num_samples))
r = np.zeros((N, N))
for i in range(N):
for j in range(N):
r[i, j] = np.exp(-0.1 * np.fabs(i - j))
errl = np.sqrt([3.4, 2.5, 3.6, 2.8, 4.2, 4.7, 4.9, 5.1, 3.2, 4.2])
errl *= 4
for i in range(N):
for j in range(N):
r[i, j] *= errl[i] * errl[j]
c = cholesky(r, lower=True)
y = np.dot(c, x)
x = np.arange(N)
for linear in [True, False]:
data = []
for i in range(N):
if linear:
data.append(pe.Obs([[i + 1 + o for o in y[i]]], ['ens']))
else:
data.append(pe.Obs([[np.exp(-(i + 1)) + np.exp(-(i + 1)) * o for o in y[i]]], ['ens']))
[o.gamma_method() for o in data]
if linear:
def fitf(p, x):
return p[1] + p[0] * x
else:
def fitf(p, x):
return p[1] * np.exp(-p[0] * x)
fitp = pe.least_squares(x, data, fitf, expected_chisquare=True)
fitpc = pe.least_squares(x, data, fitf, correlated_fit=True)
for i in range(2):
assert((fitp[i] - fitpc[i]).is_zero_within_error)
def test_total_least_squares():
dim = 10 + int(30 * np.random.rand())
x = np.arange(dim) + np.random.normal(0.0, 0.15, dim)
xerr = 0.1 + 0.1 * np.random.rand(dim)
y = 2 * np.exp(-0.06 * x) + np.random.normal(0.0, 0.15, dim)
yerr = 0.1 + 0.1 * np.random.rand(dim)
ox = []
for i, item in enumerate(x):
ox.append(pe.pseudo_Obs(x[i], xerr[i], str(i)))
oy = []
for i, item in enumerate(x):
oy.append(pe.pseudo_Obs(y[i], yerr[i], str(i)))
def f(x, a, b):
return a * np.exp(-b * x)
def func(a, x):
y = a[0] * np.exp(-a[1] * x)
return y
data = RealData([o.value for o in ox], [o.value for o in oy], sx=[o.dvalue for o in ox], sy=[o.dvalue for o in oy])
model = Model(func)
odr = ODR(data, model, [0, 0], partol=np.finfo(np.float64).eps)
odr.set_job(fit_type=0, deriv=1)
output = odr.run()
out = pe.total_least_squares(ox, oy, func)
beta = out.fit_parameters
pe.Obs.e_tag_global = 5
for i in range(2):
beta[i].gamma_method(e_tag=5, S=1.0)
assert math.isclose(beta[i].value, output.beta[i], rel_tol=1e-5)
assert math.isclose(output.cov_beta[i, i], beta[i].dvalue ** 2, rel_tol=2.5e-1), str(output.cov_beta[i, i]) + ' ' + str(beta[i].dvalue ** 2)
assert math.isclose(pe.covariance(beta[0], beta[1]), output.cov_beta[0, 1], rel_tol=2.5e-1)
out = pe.total_least_squares(ox, oy, func, const_par=[beta[1]])
assert((out.fit_parameters[0] - beta[0]).is_zero)
assert((out.fit_parameters[1] - beta[1]).is_zero)
pe.Obs.e_tag_global = 0
def test_odr_derivatives():
x = []
y = []
x_err = 0.01
y_err = 0.01
for n in np.arange(1, 9, 2):
loc_xvalue = n + np.random.normal(0.0, x_err)
x.append(pe.pseudo_Obs(loc_xvalue, x_err, str(n)))
y.append(pe.pseudo_Obs((lambda x: x ** 2 - 1)(loc_xvalue) +
np.random.normal(0.0, y_err), y_err, str(n)))
def func(a, x):
return a[0] + a[1] * x ** 2
out = pe.total_least_squares(x, y, func)
fit1 = out.fit_parameters
with pytest.warns(DeprecationWarning):
tfit = pe.fits.fit_general(x, y, func, base_step=0.1, step_ratio=1.1, num_steps=20)
assert np.abs(np.max(np.array(list(fit1[1].deltas.values()))
- np.array(list(tfit[1].deltas.values())))) < 10e-8