# Licensed under a 3-clause BSD style license - see LICENSE.rst # pylint: disable=invalid-name from contextlib import nullcontext import numpy as np import pytest from numpy.testing import assert_allclose, assert_array_equal, assert_array_less from astropy import units as u from astropy.coordinates import Angle from astropy.modeling import InputParameterError, fitting, models from astropy.utils.compat.optional_deps import HAS_SCIPY from astropy.utils.exceptions import AstropyDeprecationWarning, AstropyUserWarning fitters = [ fitting.LevMarLSQFitter, fitting.TRFLSQFitter, fitting.LMLSQFitter, fitting.DogBoxLSQFitter, ] fitters_bounds = [ fitting.LevMarLSQFitter, fitting.TRFLSQFitter, fitting.DogBoxLSQFitter, ] def test_sigma_constant(): """ Test that the GAUSSIAN_SIGMA_TO_FWHM constant matches the gaussian_sigma_to_fwhm constant in astropy.stats. We define it manually in astropy.modeling to avoid importing from astropy.stats. """ from astropy.modeling.functional_models import GAUSSIAN_SIGMA_TO_FWHM from astropy.stats.funcs import gaussian_sigma_to_fwhm assert gaussian_sigma_to_fwhm == GAUSSIAN_SIGMA_TO_FWHM def test_Trapezoid1D(): """Regression test for https://github.com/astropy/astropy/issues/1721""" model = models.Trapezoid1D(amplitude=4.2, x_0=2.0, width=1.0, slope=3) xx = np.linspace(0, 4, 8) yy = model(xx) yy_ref = [0.0, 1.41428571, 3.12857143, 4.2, 4.2, 3.12857143, 1.41428571, 0.0] assert_allclose(yy, yy_ref, rtol=0, atol=1e-6) def test_Gaussian1D(): model = models.Gaussian1D(4.2, 1.7, stddev=5.1) x = np.mgrid[0:5] g = model(x) g_ref = [3.97302977, 4.16062403, 4.19273985, 4.06574509, 3.79389376] assert_allclose(g, g_ref, rtol=0, atol=1e-6) assert_allclose(model.fwhm, 12.009582229657841) def test_Gaussian2D(): """ Test rotated elliptical Gaussian2D model. https://github.com/astropy/astropy/pull/2038 """ model = models.Gaussian2D( 4.2, 1.7, 3.1, x_stddev=5.1, y_stddev=3.3, theta=np.pi / 6.0 ) y, x = np.mgrid[0:5, 0:5] g = model(x, y) g_ref = [ [3.01907812, 2.99051889, 2.81271552, 2.5119566, 2.13012709], [3.55982239, 3.6086023, 3.4734158, 3.17454575, 2.75494838], [3.88059142, 4.0257528, 3.96554926, 3.70908389, 3.29410187], [3.91095768, 4.15212857, 4.18567526, 4.00652015, 3.64146544], [3.6440466, 3.95922417, 4.08454159, 4.00113878, 3.72161094], ] assert_allclose(g, g_ref, rtol=0, atol=1e-6) assert_allclose( [model.x_fwhm, model.y_fwhm], [12.009582229657841, 7.7709061486021325] ) def test_Gaussian2DCovariance(): """ Test rotated elliptical Gaussian2D model when cov_matrix is input. https://github.com/astropy/astropy/pull/2199 """ cov_matrix = [[49.0, -16.0], [-16.0, 9.0]] model = models.Gaussian2D(17.0, 2.0, 2.5, cov_matrix=cov_matrix) y, x = np.mgrid[0:5, 0:5] g = model(x, y) g_ref = [ [4.3744505, 5.8413977, 7.42988694, 9.00160175, 10.38794269], [8.83290201, 10.81772851, 12.61946384, 14.02225593, 14.84113227], [13.68528889, 15.37184621, 16.44637743, 16.76048705, 16.26953638], [16.26953638, 16.76048705, 16.44637743, 15.37184621, 13.68528889], [14.84113227, 14.02225593, 12.61946384, 10.81772851, 8.83290201], ] assert_allclose(g, g_ref, rtol=0, atol=1e-6) # Test bad cov_matrix shape cov_matrix = [[49.0, 3.14, -16.0], [3.14, -16.0, 9.0], [-16, 27, 3.14]] MESSAGE = r"Covariance matrix must be 2x2" with pytest.raises(ValueError, match=MESSAGE): models.Gaussian2D(17.0, 2.0, 2.5, cov_matrix=cov_matrix) def test_Gaussian2DRotation(): amplitude = 42 x_mean, y_mean = 0, 0 x_stddev, y_stddev = 2, 3 theta = Angle(10, "deg") pars = dict( amplitude=amplitude, x_mean=x_mean, y_mean=y_mean, x_stddev=x_stddev, y_stddev=y_stddev, ) rotation = models.Rotation2D(angle=theta.degree) point1 = (x_mean + 2 * x_stddev, y_mean + 2 * y_stddev) point2 = rotation(*point1) g1 = models.Gaussian2D(theta=0, **pars) g2 = models.Gaussian2D(theta=theta.radian, **pars) value1 = g1(*point1) value2 = g2(*point2) assert_allclose(value1, value2) def test_Gaussian2D_invalid_inputs(): x_stddev = 5.1 y_stddev = 3.3 theta = 10 cov_matrix = [[49.0, -16.0], [-16.0, 9.0]] # first make sure the valid ones are OK models.Gaussian2D() models.Gaussian2D(x_stddev=x_stddev, y_stddev=y_stddev, theta=theta) models.Gaussian2D(x_stddev=None, y_stddev=y_stddev, theta=theta) models.Gaussian2D(x_stddev=x_stddev, y_stddev=None, theta=theta) models.Gaussian2D(x_stddev=x_stddev, y_stddev=y_stddev, theta=None) models.Gaussian2D(cov_matrix=cov_matrix) MESSAGE = r"Cannot specify both cov_matrix and x/y_stddev/theta" with pytest.raises(InputParameterError, match=MESSAGE): models.Gaussian2D(x_stddev=0, cov_matrix=cov_matrix) with pytest.raises(InputParameterError, match=MESSAGE): models.Gaussian2D(y_stddev=0, cov_matrix=cov_matrix) with pytest.raises(InputParameterError, match=MESSAGE): models.Gaussian2D(theta=0, cov_matrix=cov_matrix) def test_Gaussian2D_theta(): theta = Angle(90, "deg") model1 = models.Gaussian2D(1, 25, 25, 15, 5, theta=theta) theta2 = np.pi / 2.0 model2 = models.Gaussian2D(1, 25, 25, 15, 5, theta=theta2) assert model1.theta.quantity.to("radian").value == model2.theta.value assert model1.bounding_box == model2.bounding_box assert model1(619.42, 31.314) == model2(619.42, 31.314) @pytest.mark.parametrize("gamma", (10, -10)) def test_moffat_fwhm(gamma): ans = 34.641016151377542 kwargs = {"gamma": gamma, "alpha": 0.5} m1 = models.Moffat1D(**kwargs) m2 = models.Moffat2D(**kwargs) assert_allclose([m1.fwhm, m2.fwhm], ans) assert_array_less(0, [m1.fwhm, m2.fwhm]) def test_RedshiftScaleFactor(): """Like ``test_ScaleModel()``.""" # Scale by a scalar m = models.RedshiftScaleFactor(0.4) assert m(0) == 0 assert_array_equal(m([1, 2]), [1.4, 2.8]) assert_allclose(m.inverse(m([1, 2])), [1, 2]) # Scale by a list m = models.RedshiftScaleFactor([-0.5, 0, 0.5], n_models=3) assert_array_equal(m(0), 0) assert_array_equal(m([1, 2], model_set_axis=False), [[0.5, 1], [1, 2], [1.5, 3]]) assert_allclose( m.inverse(m([1, 2], model_set_axis=False)), [[1, 2], [1, 2], [1, 2]] ) def test_RedshiftScaleFactor_inverse(): m = models.RedshiftScaleFactor(1.2345) assert_allclose(m.inverse(m(6.789)), 6.789) def test_RedshiftScaleFactor_inverse_bounding_box(): model = models.RedshiftScaleFactor(2) model.bounding_box = (1, 5) assert model.bounding_box == (1, 5) inverse_model = model.inverse assert inverse_model.bounding_box == (3, 15) assert_allclose( inverse_model(model(4, with_bounding_box=True), with_bounding_box=True), 4 ) @pytest.mark.skipif(not HAS_SCIPY, reason="requires scipy") def test_RedshiftScaleFactor_model_levmar_fit(): """Test fitting RedshiftScaleFactor model with LevMarLSQFitter.""" init_model = models.RedshiftScaleFactor() x = np.arange(10) y = 2.7174 * x fitter = fitting.LevMarLSQFitter() fitted_model = fitter(init_model, x, y) assert_allclose(fitted_model.parameters, [1.7174]) def test_Ellipse2D(): """Test Ellipse2D model.""" amplitude = 7.5 x0, y0 = 15, 15 theta = Angle(45, "deg") em = models.Ellipse2D(amplitude, x0, y0, 7, 3, theta.radian) y, x = np.mgrid[0:30, 0:30] e = em(x, y) assert np.all(e[e > 0] == amplitude) assert e[y0, x0] == amplitude rotation = models.Rotation2D(angle=theta.degree) point1 = [2, 0] # Rotation2D center is (0, 0) point2 = rotation(*point1) point1 = np.array(point1) + [x0, y0] point2 = np.array(point2) + [x0, y0] e1 = models.Ellipse2D(amplitude, x0, y0, 7, 3, theta=0.0) e2 = models.Ellipse2D(amplitude, x0, y0, 7, 3, theta=theta.radian) assert e1(*point1) == e2(*point2) def test_Ellipse2D_circular(): """Test that circular Ellipse2D agrees with Disk2D [3736].""" amplitude = 7.5 radius = 10 size = (radius * 2) + 1 y, x = np.mgrid[0:size, 0:size] ellipse = models.Ellipse2D(amplitude, radius, radius, radius, radius, theta=0)(x, y) disk = models.Disk2D(amplitude, radius, radius, radius)(x, y) assert np.all(ellipse == disk) def test_Ellipse2D_theta(): theta = Angle(90, "deg") model1 = models.Ellipse2D(1, 25, 25, 15, 5, theta=theta) theta2 = np.pi / 2.0 model2 = models.Ellipse2D(1, 25, 25, 15, 5, theta=theta2) assert model1.theta.quantity.to("radian").value == model2.theta.value assert model1.bounding_box == model2.bounding_box assert model1(619.42, 31.314) == model2(619.42, 31.314) def test_Scale_inverse(): m = models.Scale(1.2345) assert_allclose(m.inverse(m(6.789)), 6.789) def test_Scale_inverse_bounding_box(): model = models.Scale(2) model.bounding_box = (1, 5) assert model.bounding_box == (1, 5) inverse_model = model.inverse assert inverse_model.bounding_box == (2, 10) assert ( inverse_model(model(4, with_bounding_box=True), with_bounding_box=True) == 4.0 ) def test_Multiply_inverse(): m = models.Multiply(1.2345) assert_allclose(m.inverse(m(6.789)), 6.789) def test_Multiply_inverse_bounding_box(): model = models.Multiply(2) model.bounding_box = (1, 5) assert model.bounding_box == (1, 5) inverse_model = model.inverse assert inverse_model.bounding_box == (2, 10) assert ( inverse_model(model(4, with_bounding_box=True), with_bounding_box=True) == 4.0 ) def test_Shift_inverse(): m = models.Shift(1.2345) assert_allclose(m.inverse(m(6.789)), 6.789) def test_Shift_inverse_bounding_box(): model = models.Shift(10) model.bounding_box = (1, 5) assert model.bounding_box == (1, 5) inverse_model = model.inverse assert inverse_model.bounding_box == (11, 15) assert ( inverse_model(model(4, with_bounding_box=True), with_bounding_box=True) == 4.0 ) @pytest.mark.skipif(not HAS_SCIPY, reason="requires scipy") @pytest.mark.parametrize("fitter", fitters) def test_Shift_model_levmar_fit(fitter): """Test fitting Shift model with LevMarLSQFitter (issue #6103).""" fitter = fitter() init_model = models.Shift() x = np.arange(10) y = x + 0.1 with pytest.warns(AstropyUserWarning, match="Model is linear in parameters"): fitted_model = fitter(init_model, x, y) assert_allclose(fitted_model.parameters, [0.1], atol=1e-15) def test_Shift_model_set_linear_fit(): """Test linear fitting of Shift model (issue #6103).""" init_model = models.Shift(offset=[0, 0], n_models=2) x = np.arange(10) yy = np.array([x + 0.1, x - 0.2]) fitter = fitting.LinearLSQFitter() fitted_model = fitter(init_model, x, yy) assert_allclose(fitted_model.parameters, [0.1, -0.2], atol=1e-15) @pytest.mark.parametrize("Model", (models.Scale, models.Multiply)) def test_Scale_model_set_linear_fit(Model): """Test linear fitting of Scale model (#6103).""" init_model = Model(factor=[0, 0], n_models=2) x = np.arange(-3, 7) yy = np.array([1.15 * x, 0.96 * x]) fitter = fitting.LinearLSQFitter() fitted_model = fitter(init_model, x, yy) assert_allclose(fitted_model.parameters, [1.15, 0.96], atol=1e-15) @pytest.mark.parametrize("Model", (models.Scale, models.Multiply)) def test_Scale_model_evaluate_without_units(Model): m = Model(factor=4 * u.m) kwargs = {"x": 3 * u.m, "y": 7 * u.m} mnu = m.without_units_for_data(**kwargs) x = np.linspace(-1, 1, 100) assert_allclose(mnu(x), 4 * x) # https://github.com/astropy/astropy/issues/6178 def test_Ring2D_rout(): # Test with none of r_in, r_out, width specified m = models.Ring2D(amplitude=1, x_0=1, y_0=1) assert m.amplitude.value == 1 assert m.x_0.value == 1 assert m.y_0.value == 1 assert m.r_in.value == 1 assert m.width.value == 1 # Test with r_in specified only m = models.Ring2D(amplitude=1, x_0=1, y_0=1, r_in=4) assert m.amplitude.value == 1 assert m.x_0.value == 1 assert m.y_0.value == 1 assert m.r_in.value == 4 assert m.width.value == 1 # Test with r_out specified only m = models.Ring2D(amplitude=1, x_0=1, y_0=1, r_out=7) assert m.amplitude.value == 1 assert m.x_0.value == 1 assert m.y_0.value == 1 assert m.r_in.value == 1 assert m.width.value == 6 # Error when r_out is too small for default r_in MESSAGE = r"r_in=.* and width=.* must both be >=0" with pytest.raises(InputParameterError, match=MESSAGE): models.Ring2D(amplitude=1, x_0=1, y_0=1, r_out=0.5) # Test with width specified only m = models.Ring2D(amplitude=1, x_0=1, y_0=1, width=11) assert m.amplitude.value == 1 assert m.x_0.value == 1 assert m.y_0.value == 1 assert m.r_in.value == 1 assert m.width.value == 11 # Test with r_in and r_out specified only m = models.Ring2D(amplitude=1, x_0=1, y_0=1, r_in=2, r_out=5) assert m.amplitude.value == 1 assert m.x_0.value == 1 assert m.y_0.value == 1 assert m.r_in.value == 2 assert m.width.value == 3 # Error when r_out is smaller than r_in with pytest.raises(InputParameterError, match=MESSAGE): models.Ring2D(amplitude=1, x_0=1, y_0=1, r_out=1, r_in=4) # Test with r_in and width specified only m = models.Ring2D(amplitude=1, x_0=1, y_0=1, r_in=2, width=4) assert m.amplitude.value == 1 assert m.x_0.value == 1 assert m.y_0.value == 1 assert m.r_in.value == 2 assert m.width.value == 4 # Test with r_out and width specified only m = models.Ring2D(amplitude=1, x_0=1, y_0=1, r_out=12, width=7) assert m.amplitude.value == 1 assert m.x_0.value == 1 assert m.y_0.value == 1 assert m.r_in.value == 5 assert m.width.value == 7 # Error when width is larger than r_out with pytest.raises(InputParameterError, match=MESSAGE): models.Ring2D(amplitude=1, x_0=1, y_0=1, r_out=1, width=4) # Test with r_in, r_out, and width all specified m = models.Ring2D(amplitude=1, x_0=1, y_0=1, r_in=3, r_out=11, width=8) assert m.amplitude.value == 1 assert m.x_0.value == 1 assert m.y_0.value == 1 assert m.r_in.value == 3 assert m.width.value == 8 # error when specifying all MESSAGE = r"Width must be r_out - r_in" with pytest.raises(InputParameterError, match=MESSAGE): models.Ring2D(amplitude=1, x_0=1, y_0=1, r_in=3, r_out=11, width=7) @pytest.mark.skipif(not HAS_SCIPY, reason="requires scipy") @pytest.mark.parametrize("fitter", fitters) def test_Voigt1D(fitter): fitter = fitter() voi = models.Voigt1D(amplitude_L=-0.5, x_0=1.0, fwhm_L=5.0, fwhm_G=5.0) xarr = np.linspace(-5.0, 5.0, num=40) yarr = voi(xarr) voi_init = models.Voigt1D(amplitude_L=-1.0, x_0=1.0, fwhm_L=5.0, fwhm_G=5.0) voi_fit = fitter(voi_init, xarr, yarr) assert_allclose(voi_fit.param_sets, voi.param_sets) # Invalid method MESSAGE = r"Not a valid method for Voigt1D Faddeeva function: test" with pytest.raises(ValueError, match=MESSAGE): models.Voigt1D(method="test") @pytest.mark.skipif(not HAS_SCIPY, reason="requires scipy") @pytest.mark.parametrize("algorithm", ("humlicek2", "wofz")) def test_Voigt1D_norm(algorithm): """Test integral of normalized Voigt profile.""" from scipy.integrate import quad if algorithm == "humlicek2": ctx = pytest.warns( AstropyDeprecationWarning, match=r"humlicek2 has been deprecated since .*" ) atol = 1e-8 else: ctx = nullcontext() atol = 1e-14 def voigt(algorithm): return models.Voigt1D( amplitude_L=1.0 / np.pi, x_0=0.0, fwhm_L=2.0, fwhm_G=1.5, method=algorithm ) with ctx: voi = models.Voigt1D( amplitude_L=1.0 / np.pi, x_0=0.0, fwhm_L=2.0, fwhm_G=1.5, method=algorithm ) assert_allclose(quad(voi, -np.inf, np.inf)[0], 1.0, atol=atol) @pytest.mark.skipif(not HAS_SCIPY, reason="requires scipy") @pytest.mark.parametrize("doppler", (1.0e-3, 1.0e-2, 0.1, 0.5, 1.0, 2.5, 5.0, 10)) @pytest.mark.filterwarnings(r"ignore:humlicek2 has been deprecated since .*") def test_Voigt1D_hum2(doppler): """ Verify accuracy of Voigt profile in Humlicek approximation to Faddeeva.cc (SciPy). """ x = np.linspace(-20, 20, 400001) voi_w = models.Voigt1D( amplitude_L=2.0 / np.pi, fwhm_L=1.0, fwhm_G=doppler, method="wofz" ) vf_w = voi_w(x) dvda_w = voi_w.fit_deriv( x, x_0=0, amplitude_L=2.0 / np.pi, fwhm_L=1.0, fwhm_G=doppler ) voi_h = models.Voigt1D( amplitude_L=2.0 / np.pi, fwhm_L=1.0, fwhm_G=doppler, method="humlicek2" ) vf_h = voi_h(x) dvda_h = voi_h.fit_deriv( x, x_0=0, amplitude_L=2.0 / np.pi, fwhm_L=1.0, fwhm_G=doppler ) assert_allclose(vf_h, vf_w, rtol=1e-7 * (2 + 1 / np.sqrt(doppler))) assert_allclose(dvda_h, dvda_w, rtol=1e-9, atol=1e-7 * (1 + 30 / doppler)) @pytest.mark.filterwarnings(r"ignore:humlicek2 has been deprecated since .*") def test_Voigt1D_method(): """Test Voigt1D default method""" voi = models.Voigt1D(method="humlicek2") assert voi.method == "_hum2zpf16c" voi = models.Voigt1D() if HAS_SCIPY: assert voi.method == "wofz" voi = models.Voigt1D(method="wofz") assert voi.method == "wofz" voi = models.Voigt1D(method="scipy") assert voi.method == "wofz" else: assert voi.method == "_hum2zpf16c" @pytest.mark.skipif(not HAS_SCIPY, reason="requires scipy") @pytest.mark.parametrize("fitter", fitters_bounds) def test_KingProjectedAnalytic1D_fit(fitter): fitter = fitter() km = models.KingProjectedAnalytic1D(amplitude=1, r_core=1, r_tide=2) xarr = np.linspace(0.1, 2, 10) yarr = km(xarr) km_init = models.KingProjectedAnalytic1D(amplitude=1, r_core=1, r_tide=1) km_fit = fitter(km_init, xarr, yarr) assert_allclose(km_fit.param_sets, km.param_sets) assert_allclose(km_fit.concentration, 0.30102999566398136) @pytest.mark.parametrize("model", [models.Exponential1D(), models.Logarithmic1D()]) def test_ExponentialAndLogarithmic1D_fit(model): xarr = np.linspace(0.1, 10.0, 200) assert_allclose(xarr, model.inverse(model(xarr))) @pytest.mark.parametrize("model", [models.Exponential1D(), models.Logarithmic1D()]) def test_ExponentialAndLogarithmic_set_tau(model): MESSAGE = r"0 is not an allowed value for tau" with pytest.raises(ValueError, match=MESSAGE): model.tau = 0 def test_Linear1D_inverse(): model = models.Linear1D(slope=4, intercept=-12) inverse = model.inverse assert inverse.slope == 1 / 4 assert inverse.intercept == 3 @pytest.mark.parametrize( "trig", [ (models.Sine1D, [-0.25, 0.25]), (models.ArcSine1D, [-0.25, 0.25]), (models.Cosine1D, [0, 0.5]), (models.ArcCosine1D, [0, 0.5]), (models.Tangent1D, [-0.25, 0.25]), (models.ArcTangent1D, [-0.25, 0.25]), ], ) def test_trig_inverse(trig): mdl = trig[0]() lower, upper = trig[1] x = np.arange(lower, upper, 0.01) assert_allclose(mdl.inverse(mdl(x)), x, atol=1e-10) assert_allclose(mdl(mdl.inverse(x)), x, atol=1e-10) @pytest.mark.skipif(not HAS_SCIPY, reason="requires scipy") def test_Sersic2D_theta(): theta = Angle(90, "deg") model1 = models.Sersic2D(1, 5, 4, 25, 25, 0.5, theta=theta) theta2 = np.pi / 2.0 model2 = models.Sersic2D(1, 5, 4, 25, 25, 0.5, theta=theta2) assert model1.theta.quantity.to("radian").value == model2.theta.value assert model1(619.42, 31.314) == model2(619.42, 31.314)