def test_nterms_methods(method, center_data, fit_mean, errors, nterms, normalization, data): t, y, dy = data frequency = 0.8 + 0.01 * np.arange(40) if errors == 'none': dy = None elif errors == 'partial': dy = dy[0] elif errors == 'full': pass else: raise ValueError(f"Unrecognized error type: '{errors}'") ls = LombScargle(t, y, dy, center_data=center_data, fit_mean=fit_mean, nterms=nterms, normalization=normalization) if nterms == 0 and not fit_mean: with pytest.raises(ValueError) as err: ls.power(frequency, method=method) assert 'nterms' in str(err.value) and 'bias' in str(err.value) else: P_expected = ls.power(frequency) # don't use fast fft approximations here kwds = {} if 'fast' in method: kwds['method_kwds'] = dict(use_fft=False) P_method = ls.power(frequency, method=method, **kwds) assert_allclose(P_expected, P_method, rtol=1E-7, atol=1E-25)
def test_nterms_methods(method, center_data, fit_mean, errors, nterms, normalization, data): t, y, dy = data frequency = 0.8 + 0.01 * np.arange(40) if errors == 'none': dy = None elif errors == 'partial': dy = dy[0] elif errors == 'full': pass else: raise ValueError("Unrecognized error type: '{0}'".format(errors)) ls = LombScargle(t, y, dy, center_data=center_data, fit_mean=fit_mean, nterms=nterms, normalization=normalization) if nterms == 0 and not fit_mean: with pytest.raises(ValueError) as err: ls.power(frequency, method=method) assert 'nterms' in str(err.value) and 'bias' in str(err.value) else: P_expected = ls.power(frequency) # don't use fast fft approximations here kwds = {} if 'fast' in method: kwds['method_kwds'] = dict(use_fft=False) P_method = ls.power(frequency, method=method, **kwds) assert_allclose(P_expected, P_method, rtol=1E-7, atol=1E-25)
def test_all_methods(data, method, center_data, fit_mean, errors, with_units, normalization): if method == 'scipy' and (fit_mean or errors != 'none'): return t, y, dy = data frequency = 0.8 + 0.01 * np.arange(40) if with_units: t = t * units.day y = y * units.mag dy = dy * units.mag frequency = frequency / t.unit if errors == 'none': dy = None elif errors == 'partial': dy = dy[0] elif errors == 'full': pass else: raise ValueError("Unrecognized error type: '{0}'".format(errors)) kwds = {} ls = LombScargle(t, y, dy, center_data=center_data, fit_mean=fit_mean, normalization=normalization) P_expected = ls.power(frequency) # don't use the fft approximation here; we'll test this elsewhere if method in FAST_METHODS: kwds['method_kwds'] = dict(use_fft=False) P_method = ls.power(frequency, method=method, **kwds) if with_units: if normalization == 'psd' and errors == 'none': assert P_method.unit == y.unit**2 else: assert P_method.unit == units.dimensionless_unscaled else: assert not hasattr(P_method, 'unit') assert_quantity_allclose(P_expected, P_method)
def test_all_methods(data, method, center_data, fit_mean, errors, with_units, normalization): if method == 'scipy' and (fit_mean or errors != 'none'): return t, y, dy = data frequency = 0.8 + 0.01 * np.arange(40) if with_units: t = t * u.day y = y * u.mag dy = dy * u.mag frequency = frequency / t.unit if errors == 'none': dy = None elif errors == 'partial': dy = dy[0] elif errors == 'full': pass else: raise ValueError("Unrecognized error type: '{0}'".format(errors)) kwds = {} ls = LombScargle(t, y, dy, center_data=center_data, fit_mean=fit_mean, normalization=normalization) P_expected = ls.power(frequency) # don't use the fft approximation here; we'll test this elsewhere if method in FAST_METHODS: kwds['method_kwds'] = dict(use_fft=False) P_method = ls.power(frequency, method=method, **kwds) if with_units: if normalization == 'psd' and errors == 'none': assert P_method.unit == y.unit ** 2 else: assert P_method.unit == u.dimensionless_unscaled else: assert not hasattr(P_method, 'unit') assert_quantity_allclose(P_expected, P_method)
def test_autopower(data): t, y, dy = data ls = LombScargle(t, y, dy) kwargs = dict(samples_per_peak=6, nyquist_factor=2, minimum_frequency=2, maximum_frequency=None) freq1 = ls.autofrequency(**kwargs) power1 = ls.power(freq1) freq2, power2 = ls.autopower(**kwargs) assert_allclose(freq1, freq2) assert_allclose(power1, power2)
def test_autopower(data): t, y, dy = data ls = LombScargle(t, y, dy) kwargs = dict(samples_per_peak=6, nyquist_factor=2, minimum_frequency=2, maximum_frequency=None) freq1 = ls.autofrequency(**kwargs) power1 = ls.power(freq1) freq2, power2 = ls.autopower(**kwargs) assert_allclose(freq1, freq2) assert_allclose(power1, power2)
def test_fast_approximations(method, center_data, fit_mean, errors, nterms, data): t, y, dy = data frequency = 0.8 + 0.01 * np.arange(40) if errors == 'none': dy = None elif errors == 'partial': dy = dy[0] elif errors == 'full': pass else: raise ValueError("Unrecognized error type: '{0}'".format(errors)) ls = LombScargle(t, y, dy, center_data=center_data, fit_mean=fit_mean, nterms=nterms, normalization='standard') # use only standard normalization because we compare via absolute tolerance kwds = dict(method=method) if method == 'fast' and nterms != 1: with pytest.raises(ValueError) as err: ls.power(frequency, **kwds) assert 'nterms' in str(err.value) elif nterms == 0 and not fit_mean: with pytest.raises(ValueError) as err: ls.power(frequency, **kwds) assert 'nterms' in str(err.value) and 'bias' in str(err.value) else: P_fast = ls.power(frequency, **kwds) kwds['method_kwds'] = dict(use_fft=False) P_slow = ls.power(frequency, **kwds) assert_allclose(P_fast, P_slow, atol=0.008)
def test_fast_approximations(method, center_data, fit_mean, errors, nterms, data): t, y, dy = data frequency = 0.8 + 0.01 * np.arange(40) if errors == 'none': dy = None elif errors == 'partial': dy = dy[0] elif errors == 'full': pass else: raise ValueError("Unrecognized error type: '{0}'".format(errors)) ls = LombScargle(t, y, dy, center_data=center_data, fit_mean=fit_mean, nterms=nterms, normalization='standard') # use only standard normalization because we compare via absolute tolerance kwds = dict(method=method) if method == 'fast' and nterms != 1: with pytest.raises(ValueError) as err: ls.power(frequency, **kwds) assert 'nterms' in str(err.value) elif nterms == 0 and not fit_mean: with pytest.raises(ValueError) as err: ls.power(frequency, **kwds) assert 'nterms' in str(err.value) and 'bias' in str(err.value) else: P_fast = ls.power(frequency, **kwds) kwds['method_kwds'] = dict(use_fft=False) P_slow = ls.power(frequency, **kwds) assert_allclose(P_fast, P_slow, atol=0.008)
def test_absolute_times(data, timedelta): # Make sure that we handle absolute times correctly. We also check that # TimeDelta works properly when timedelta is True. # The example data uses relative times t, y, dy = data # FIXME: There seems to be a numerical stability issue in that if we run # the algorithm with the same values but offset in time, the transit_time # is not offset by a fixed amount. To avoid this issue in this test, we # make sure the first time is also the smallest so that internally the # values of the relative time should be the same. t[0] = 0. # Add units t = t * u.day y = y * u.mag dy = dy * u.mag # We now construct a set of absolute times but keeping the rest the same start = Time('2019-05-04T12:34:56') trel = TimeDelta(t) if timedelta else t t = trel + start # and we set up two instances of LombScargle, one with absolute and one # with relative times. ls1 = LombScargle(t, y, dy) ls2 = LombScargle(trel, y, dy) kwargs = dict(samples_per_peak=6, nyquist_factor=2, minimum_frequency=2 / u.day, maximum_frequency=None) freq1 = ls1.autofrequency(**kwargs) freq2 = ls2.autofrequency(**kwargs) assert_quantity_allclose(freq1, freq2) power1 = ls1.power(freq1) power2 = ls2.power(freq2) assert_quantity_allclose(power1, power2) freq1, power1 = ls1.autopower(**kwargs) freq2, power2 = ls2.autopower(**kwargs) assert_quantity_allclose(freq1, freq2) assert_quantity_allclose(power1, power2) model1 = ls1.model(t, 2 / u.day) model2 = ls2.model(trel, 2 / u.day) assert_quantity_allclose(model1, model2) # Check model validation with pytest.raises(TypeError) as exc: ls1.model(trel, 2 / u.day) assert exc.value.args[0] == ('t was provided as a relative time but the ' 'LombScargle class was initialized with ' 'absolute times.') with pytest.raises(TypeError) as exc: ls2.model(t, 2 / u.day) assert exc.value.args[0] == ('t was provided as an absolute time but the ' 'LombScargle class was initialized with ' 'relative times.') # Check design matrix design1 = ls1.design_matrix(2 / u.day, t=t) design2 = ls2.design_matrix(2 / u.day, t=trel) assert_quantity_allclose(design1, design2) # Check design matrix validation with pytest.raises(TypeError) as exc: ls1.design_matrix(2 / u.day, t=trel) assert exc.value.args[0] == ('t was provided as a relative time but the ' 'LombScargle class was initialized with ' 'absolute times.') with pytest.raises(TypeError) as exc: ls2.design_matrix(2 / u.day, t=t) assert exc.value.args[0] == ('t was provided as an absolute time but the ' 'LombScargle class was initialized with ' 'relative times.')
def test_absolute_times(data, timedelta): # Make sure that we handle absolute times correctly. We also check that # TimeDelta works properly when timedelta is True. # The example data uses relative times t, y, dy = data # FIXME: There seems to be a numerical stability issue in that if we run # the algorithm with the same values but offset in time, the transit_time # is not offset by a fixed amount. To avoid this issue in this test, we # make sure the first time is also the smallest so that internally the # values of the relative time should be the same. t[0] = 0. # Add units t = t * u.day y = y * u.mag dy = dy * u.mag # We now construct a set of absolute times but keeping the rest the same start = Time('2019-05-04T12:34:56') trel = TimeDelta(t) if timedelta else t t = trel + start # and we set up two instances of LombScargle, one with absolute and one # with relative times. ls1 = LombScargle(t, y, dy) ls2 = LombScargle(trel, y, dy) kwargs = dict(samples_per_peak=6, nyquist_factor=2, minimum_frequency=2 / u.day, maximum_frequency=None) freq1 = ls1.autofrequency(**kwargs) freq2 = ls2.autofrequency(**kwargs) assert_quantity_allclose(freq1, freq2) power1 = ls1.power(freq1) power2 = ls2.power(freq2) assert_quantity_allclose(power1, power2) freq1, power1 = ls1.autopower(**kwargs) freq2, power2 = ls2.autopower(**kwargs) assert_quantity_allclose(freq1, freq2) assert_quantity_allclose(power1, power2) model1 = ls1.model(t, 2 / u.day) model2 = ls2.model(trel, 2 / u.day) assert_quantity_allclose(model1, model2) # Check model validation with pytest.raises(TypeError) as exc: ls1.model(trel, 2 / u.day) assert exc.value.args[0] == ('t was provided as a relative time but the ' 'LombScargle class was initialized with ' 'absolute times.') with pytest.raises(TypeError) as exc: ls2.model(t, 2 / u.day) assert exc.value.args[0] == ('t was provided as an absolute time but the ' 'LombScargle class was initialized with ' 'relative times.') # Check design matrix design1 = ls1.design_matrix(2 / u.day, t=t) design2 = ls2.design_matrix(2 / u.day, t=trel) assert_quantity_allclose(design1, design2) # Check design matrix validation with pytest.raises(TypeError) as exc: ls1.design_matrix(2 / u.day, t=trel) assert exc.value.args[0] == ('t was provided as a relative time but the ' 'LombScargle class was initialized with ' 'absolute times.') with pytest.raises(TypeError) as exc: ls2.design_matrix(2 / u.day, t=t) assert exc.value.args[0] == ('t was provided as an absolute time but the ' 'LombScargle class was initialized with ' 'relative times.')