File: test_builtin_models.py

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"""Tests for built-in models."""

import inspect

import numpy as np
from numpy.testing import assert_allclose
import pytest
from scipy.optimize import fsolve

from lmfit import lineshapes, models
from lmfit.models import GaussianModel


def check_height_fwhm(x, y, lineshape, model):
    """Check height and fwhm parameters."""
    pars = model.guess(y, x=x)
    out = model.fit(y, pars, x=x)

    # account for functions whose centers are not mu
    mu = out.params['center'].value
    if lineshape is lineshapes.lognormal:
        cen = np.exp(mu - out.params['sigma']**2)
    elif lineshape is lineshapes.pearson4:
        cen = out.params['position']
    else:
        cen = mu

    # get arguments for lineshape
    sig = inspect.signature(lineshape)
    args = {key: out.best_values[key] for key in sig.parameters.keys()
            if key != 'x'}

    # output format for assertion errors
    fmt = ("Program calculated values and real values do not match!\n"
           "{:^20s}{:^20s}{:^20s}{:^20s}\n"
           "{:^20s}{:^20f}{:^20f}{:^20f}")

    if 'height' in out.params:
        height_pro = out.params['height'].value
        height_act = lineshape(cen, **args)
        diff = height_act - height_pro

        assert abs(diff) < 0.001, fmt.format(model._name, 'Actual', 'program',
                                             'Difference', 'Height',
                                             height_act, height_pro, diff)

        if 'fwhm' in out.params:
            fwhm_pro = out.params['fwhm'].value
            func = lambda x: lineshape(x, **args) - 0.5*height_act
            ret = fsolve(func, [cen - fwhm_pro/4, cen + fwhm_pro/2])
            fwhm_act = ret[1] - ret[0]
            diff = fwhm_act - fwhm_pro

            assert abs(diff) < 0.5, fmt.format(model._name, 'Actual',
                                               'program', 'Difference',
                                               'FWHM', fwhm_act, fwhm_pro,
                                               diff)


def test_height_fwhm_calculation(peakdata):
    """Test for correctness of height and FWHM calculation."""
    # mu = 0
    # variance = 1.0
    # sigma = np.sqrt(variance)
    # x = np.linspace(mu - 20*sigma, mu + 20*sigma, 100.0)
    # y = norm.pdf(x, mu, 1)
    x = peakdata[0]
    y = peakdata[1]
    check_height_fwhm(x, y, lineshapes.voigt, models.VoigtModel())
    check_height_fwhm(x, y, lineshapes.pvoigt, models.PseudoVoigtModel())
    check_height_fwhm(x, y, lineshapes.pearson4, models.Pearson4Model())
    check_height_fwhm(x, y, lineshapes.pearson7, models.Pearson7Model())
    check_height_fwhm(x, y, lineshapes.moffat, models.MoffatModel())
    check_height_fwhm(x, y, lineshapes.students_t, models.StudentsTModel())
    check_height_fwhm(x, y, lineshapes.breit_wigner, models.BreitWignerModel())
    check_height_fwhm(x, y, lineshapes.damped_oscillator,
                      models.DampedOscillatorModel())
    check_height_fwhm(x, y, lineshapes.dho,
                      models.DampedHarmonicOscillatorModel())
    check_height_fwhm(x, y, lineshapes.expgaussian,
                      models.ExponentialGaussianModel())
    check_height_fwhm(x, y, lineshapes.skewed_gaussian,
                      models.SkewedGaussianModel())
    check_height_fwhm(x, y, lineshapes.doniach, models.DoniachModel())
    # this test fails after allowing 'center' to be negative (see PR #645)
    # it's a bit strange to fit a LognormalModel to a Voigt-like lineshape
    # anyway, so adisable the test for now
    # x = x-9  # Lognormal will only fit peaks with centers < 1
    # check_height_fwhm(x, y, lineshapes.lognormal, models.LognormalModel())


def test_height_and_fwhm_expression_evalution_in_builtin_models():
    """Assert models do not throw an ZeroDivisionError."""
    mod = models.GaussianModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9)
    params.update_constraints()

    mod = models.LorentzianModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9)
    params.update_constraints()

    mod = models.SplitLorentzianModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, sigma_r=1.0)
    params.update_constraints()

    mod = models.VoigtModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, gamma=1.0)
    params.update_constraints()

    mod = models.PseudoVoigtModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, fraction=0.5)
    params.update_constraints()

    mod = models.MoffatModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, beta=0.0)
    params.update_constraints()

    mod = models.Pearson4Model()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, expon=1.0, skew=5.0)
    params.update_constraints()

    mod = models.Pearson7Model()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, expon=1.0)
    params.update_constraints()

    mod = models.StudentsTModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9)
    params.update_constraints()

    mod = models.BreitWignerModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, q=0.0)
    params.update_constraints()

    mod = models.LognormalModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9)
    params.update_constraints()

    mod = models.DampedOscillatorModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9)
    params.update_constraints()

    mod = models.DampedHarmonicOscillatorModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, gamma=0.0)
    params.update_constraints()

    mod = models.ExponentialGaussianModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, gamma=0.0)
    params.update_constraints()

    mod = models.SkewedGaussianModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, gamma=0.0)
    params.update_constraints()

    mod = models.SkewedVoigtModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, gamma=0.0,
                             skew=0.0)
    params.update_constraints()

    mod = models.DoniachModel()
    params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, gamma=0.0)
    params.update_constraints()

    mod = models.StepModel()
    for f in ('linear', 'arctan', 'erf', 'logistic'):
        params = mod.make_params(amplitude=1.0, center=0.0, sigma=0.9, form=f)
        params.update_constraints()

    mod = models.RectangleModel()
    for f in ('linear', 'arctan', 'erf', 'logistic'):
        params = mod.make_params(amplitude=1.0, center1=0.0, sigma1=0.0,
                                 center2=0.0, sigma2=0.0, form=f)
        params.update_constraints()

    mod = models.Gaussian2dModel()
    params = mod.make_params(amplitude=1.0, centerx=0.0, sigmax=0.9,
                             centery=0.0, sigmay=0.9)
    params.update_constraints()


def test_guess_modelparams():
    """Tests for the 'guess' function of built-in models."""
    x = np.linspace(-10, 10, 501)

    mod = models.ConstantModel()
    y = 6.0 + x*0.005
    pars = mod.guess(y)
    assert_allclose(pars['c'].value, 6.0, rtol=0.01)

    mod = models.ComplexConstantModel(prefix='f_')
    y = 6.0 + x*0.005 + (4.0 - 0.02*x)*1j
    pars = mod.guess(y)
    assert_allclose(pars['f_re'].value, 6.0, rtol=0.01)
    assert_allclose(pars['f_im'].value, 4.0, rtol=0.01)

    mod = models.QuadraticModel(prefix='g_')
    y = -0.2 + 3.0*x + 0.005*x**2
    pars = mod.guess(y, x=x)
    assert_allclose(pars['g_a'].value, 0.005, rtol=0.01)
    assert_allclose(pars['g_b'].value, 3.0, rtol=0.01)
    assert_allclose(pars['g_c'].value, -0.2, rtol=0.01)

    mod = models.PolynomialModel(4, prefix='g_')
    y = -0.2 + 3.0*x + 0.005*x**2 - 3.3e-6*x**3 + 1.e-9*x**4
    pars = mod.guess(y, x=x)
    assert_allclose(pars['g_c0'].value, -0.2, rtol=0.01)
    assert_allclose(pars['g_c1'].value, 3.0, rtol=0.01)
    assert_allclose(pars['g_c2'].value, 0.005, rtol=0.1)
    assert_allclose(pars['g_c3'].value, -3.3e-6, rtol=0.1)
    assert_allclose(pars['g_c4'].value, 1.e-9, rtol=0.1)

    mod = models.GaussianModel(prefix='g_')
    y = lineshapes.gaussian(x, amplitude=2.2, center=0.25, sigma=1.3)
    y += np.random.normal(size=len(x), scale=0.004)
    pars = mod.guess(y, x=x)
    assert_allclose(pars['g_amplitude'].value, 3, rtol=2)
    assert_allclose(pars['g_center'].value, 0.25, rtol=1)
    assert_allclose(pars['g_sigma'].value, 1.3, rtol=1)

    mod = models.LorentzianModel(prefix='l_')
    pars = mod.guess(y, x=x)
    assert_allclose(pars['l_amplitude'].value, 3, rtol=2)
    assert_allclose(pars['l_center'].value, 0.25, rtol=1)
    assert_allclose(pars['l_sigma'].value, 1.3, rtol=1)

    mod = models.Pearson4Model(prefix='g_')
    pars = mod.guess(y, x=x)
    assert_allclose(pars['g_amplitude'].value, 3, rtol=2)
    assert_allclose(pars['g_center'].value, 0.25, rtol=1)
    assert_allclose(pars['g_sigma'].value, 1.3, rtol=1)

    mod = models.SplitLorentzianModel(prefix='s_')
    pars = mod.guess(y, x=x)
    assert_allclose(pars['s_amplitude'].value, 3, rtol=2)
    assert_allclose(pars['s_center'].value, 0.25, rtol=1)
    assert_allclose(pars['s_sigma'].value, 1.3, rtol=1)
    assert_allclose(pars['s_sigma_r'].value, 1.3, rtol=1)

    mod = models.VoigtModel(prefix='l_')
    pars = mod.guess(y, x=x)
    assert_allclose(pars['l_amplitude'].value, 3, rtol=2)
    assert_allclose(pars['l_center'].value, 0.25, rtol=1)
    assert_allclose(pars['l_sigma'].value, 1.3, rtol=1)

    mod = models.SkewedVoigtModel(prefix='l_')
    pars = mod.guess(y, x=x)
    assert_allclose(pars['l_amplitude'].value, 3, rtol=2)
    assert_allclose(pars['l_center'].value, 0.25, rtol=1)
    assert_allclose(pars['l_sigma'].value, 1.3, rtol=1)


def test_splitlorentzian_prefix():
    """Regression test for SplitLorentzian model (see GH #566)."""
    mod1 = models.SplitLorentzianModel()
    par1 = mod1.make_params(amplitude=1.0, center=0.0, sigma=0.9, sigma_r=1.3)
    par1.update_constraints()

    mod2 = models.SplitLorentzianModel(prefix='prefix_')
    par2 = mod2.make_params(amplitude=1.0, center=0.0, sigma=0.9, sigma_r=1.3)
    par2.update_constraints()


def test_guess_from_peak():
    """Regression test for guess_from_peak function (see GH #627)."""
    x = np.linspace(-5, 5)
    amplitude = 0.8
    center = 1.7
    sigma = 0.3
    y = lineshapes.lorentzian(x, amplitude=amplitude, center=center, sigma=sigma)

    model = models.LorentzianModel()
    guess_increasing_x = model.guess(y, x=x)
    guess_decreasing_x = model.guess(y[::-1], x=x[::-1])

    assert guess_increasing_x == guess_decreasing_x

    for param, value in zip(['amplitude', 'center', 'sigma'],
                            [amplitude, center, sigma]):
        assert np.abs((guess_increasing_x[param].value - value)/value) < 0.5


def test_guess_from_peak2d():
    """Regression test for guess_from_peak2d function (see GH #627)."""
    x = np.linspace(-5, 5)
    y = np.linspace(-5, 5)
    amplitude = 0.8
    centerx = 1.7
    sigmax = 0.3
    centery = 1.3
    sigmay = 0.2
    z = lineshapes.gaussian2d(x, y, amplitude=amplitude,
                              centerx=centerx, sigmax=sigmax,
                              centery=centery, sigmay=sigmay)

    model = models.Gaussian2dModel()
    guess_increasing_x = model.guess(z, x=x, y=y)
    guess_decreasing_x = model.guess(z[::-1], x=x[::-1], y=y[::-1])

    assert guess_increasing_x == guess_decreasing_x

    for param, value in zip(['centerx', 'centery'], [centerx, centery]):
        assert np.abs((guess_increasing_x[param].value - value)/value) < 0.5


def test_guess_requires_x():
    """Regression test for GH #747."""
    x = np.arange(100)
    y = np.exp(-(x-50)**2/(2*10**2))

    mod = GaussianModel()
    msg = r"guess\(\) missing 1 required positional argument: 'x'"
    with pytest.raises(TypeError, match=msg):
        mod.guess(y)