def test_lomb_scargle_regular_multi_freq():
"""Test Lomb-Scargle model features on regularly-sampled periodic data with
multiple frequencies, each with a single harmonic. Estimated parameters
should be very accurate in this case.
"""
frequencies = WAVE_FREQS
amplitudes = np.zeros((len(frequencies),4))
amplitudes[:,0] = [4,2,1]
phase = 0.1
times, values, errors = regular_periodic(frequencies, amplitudes, phase)
all_lomb = generate_features(times, values, errors, LOMB_SCARGLE_FEATS)
for i, frequency in enumerate(frequencies):
npt.assert_allclose(frequency,
all_lomb['freq{}_freq'.format(i+1)])
for (i,j), amplitude in np.ndenumerate(amplitudes):
npt.assert_allclose(amplitude,
all_lomb['freq{}_amplitude{}'.format(i+1,j+1)],
rtol=5e-2, atol=5e-2)
for i in [2,3]:
npt.assert_allclose(amplitudes[i-1,0] / amplitudes[0,0],
all_lomb['freq_amplitude_ratio_{}1'.format(i)], atol=2e-2)
npt.assert_array_less(10., all_lomb['freq1_signif'])
def test_lomb_scargle_regular_multi_freq():
"""Test Lomb-Scargle model features on regularly-sampled periodic data with
multiple frequencies, each with a single harmonic. Estimated parameters
should be very accurate in this case.
"""
frequencies = WAVE_FREQS
amplitudes = np.zeros((len(frequencies), 4))
amplitudes[:, 0] = [4, 2, 1]
phase = 0.1
times, values, errors = regular_periodic(frequencies, amplitudes, phase)
all_lomb = generate_features(times, values, errors, LOMB_SCARGLE_FEATS)
for i, frequency in enumerate(frequencies):
npt.assert_allclose(frequency, all_lomb['freq{}_freq'.format(i + 1)])
for (i, j), amplitude in np.ndenumerate(amplitudes):
npt.assert_allclose(amplitude,
all_lomb['freq{}_amplitude{}'.format(i + 1,
j + 1)],
rtol=5e-2,
atol=5e-2)
for i in [2, 3]:
npt.assert_allclose(amplitudes[i - 1, 0] / amplitudes[0, 0],
all_lomb['freq_amplitude_ratio_{}1'.format(i)],
atol=2e-2)
npt.assert_array_less(10., all_lomb['freq1_signif'])
def test_lomb_scargle_regular_single_freq():
"""Test Lomb-Scargle model features on regularly-sampled periodic data with
one frequency/multiple harmonics. Estimated parameters should be very
accurate in this case.
"""
frequencies = np.hstack((WAVE_FREQS[0], np.zeros(len(WAVE_FREQS)-1)))
amplitudes = np.zeros((len(frequencies),4))
amplitudes[0,:] = [8,4,2,1]
phase = 0.1
times, values, errors = regular_periodic(frequencies, amplitudes, phase)
all_lomb = generate_features(times, values, errors, LOMB_SCARGLE_FEATS)
# Only test the first (true) frequency; the rest correspond to noise
npt.assert_allclose(all_lomb['freq1_freq'], frequencies[0])
# Hard-coded value from previous solution
npt.assert_allclose(0.001996007984, all_lomb['freq1_lambda'], rtol=1e-7)
for (i,j), amplitude in np.ndenumerate(amplitudes):
npt.assert_allclose(amplitude,
all_lomb['freq{}_amplitude{}'.format(i+1,j+1)], rtol=1e-2,
atol=1e-2)
# Only test the first (true) frequency; the rest correspond to noise
for j in range(1, amplitudes.shape[1]):
npt.assert_allclose(phase*j*(-1**j),
all_lomb['freq1_rel_phase{}'.format(j+1)], rtol=1e-2, atol=1e-2)
# Frequency ratio not relevant since there is only; only test amplitude/signif
for i in [2,3]:
npt.assert_allclose(0., all_lomb['freq_amplitude_ratio_{}1'.format(i)], atol=1e-3)
npt.assert_array_less(10., all_lomb['freq1_signif'])
# Only one frequency, so this should explain basically all the variance
npt.assert_allclose(0., all_lomb['freq_varrat'], atol=5e-3)
# Exactly periodic, so the same minima/maxima should reoccur
npt.assert_allclose(0., all_lomb['freq_model_max_delta_mags'], atol=1e-6)
npt.assert_allclose(0., all_lomb['freq_model_min_delta_mags'], atol=1e-6)
# Linear trend should be zero since the signal is exactly sinusoidal
npt.assert_allclose(0., all_lomb['linear_trend'], atol=1e-4)
folded_times = times % 1./(frequencies[0]/2.)
sort_indices = np.argsort(folded_times)
folded_times = folded_times[sort_indices]
folded_values = values[sort_indices]
# Residuals from doubling period should be much higher
npt.assert_array_less(10., all_lomb['medperc90_2p_p'])
# Slopes should be the same for {un,}folded data; use unfolded for stability
slopes = np.diff(values) / np.diff(times)
npt.assert_allclose(np.percentile(slopes,10),
all_lomb['fold2P_slope_10percentile'], rtol=1e-2)
npt.assert_allclose(np.percentile(slopes,90),
all_lomb['fold2P_slope_90percentile'], rtol=1e-2)
def test_lomb_scargle_fast_regular():
"""Test gatspy's fast Lomb-Scargle period estimate on regularly-sampled
periodic data.
Note: this model fits only a single sinusoid with no additional harmonics,
so we use only 1 frequency and 1 amplitude to generate test data.
"""
frequencies = np.array([4])
amplitudes = np.array([[1]])
phase = 0.1
times, values, errors = regular_periodic(frequencies, amplitudes, phase)
f = generate_features(times, values, errors, ['period_fast'])
npt.assert_allclose(f['period_fast'], 1. / frequencies[0], rtol=5e-4)
def test_lomb_scargle_fast_regular():
"""Test gatspy's fast Lomb-Scargle period estimate on regularly-sampled
periodic data.
Note: this model fits only a single sinusoid with no additional harmonics,
so we use only 1 frequency and 1 amplitude to generate test data.
"""
frequencies = np.array([4])
amplitudes = np.array([[1]])
phase = 0.1
times, values, errors = regular_periodic(frequencies, amplitudes, phase)
f = generate_features(times, values, errors, ['period_fast'])
npt.assert_allclose(f['period_fast'], 1. / frequencies[0], rtol=5e-4)
def test_lomb_scargle_linear_trend():
frequencies = np.hstack((WAVE_FREQS[0], np.zeros(len(WAVE_FREQS)-1)))
amplitudes = np.zeros((len(WAVE_FREQS),4))
amplitudes[0,:] = [8,4,2,1]
phase = 0.1
slope = 0.5
# Estimated trend should be almost exact for noiseless data
times, values, errors = regular_periodic(frequencies, amplitudes, phase)
values += slope * times
all_lomb = generate_features(times, values, errors, LOMB_SCARGLE_FEATS)
npt.assert_allclose(slope, all_lomb['linear_trend'], rtol=1e-3)
# Should still be close to true trend when noise is present
times, values, errors = irregular_periodic(frequencies, amplitudes, phase)
values += slope * times
values += np.random.normal(scale=1e-3, size=len(times))
all_lomb = generate_features(times, values, errors, LOMB_SCARGLE_FEATS)
npt.assert_allclose(slope, all_lomb['linear_trend'], rtol=1e-1)
def test_lomb_scargle_linear_trend():
frequencies = np.hstack((WAVE_FREQS[0], np.zeros(len(WAVE_FREQS) - 1)))
amplitudes = np.zeros((len(WAVE_FREQS), 4))
amplitudes[0, :] = [8, 4, 2, 1]
phase = 0.1
slope = 0.5
# Estimated trend should be almost exact for noiseless data
times, values, errors = regular_periodic(frequencies, amplitudes, phase)
values += slope * times
all_lomb = generate_features(times, values, errors, LOMB_SCARGLE_FEATS)
npt.assert_allclose(slope, all_lomb['linear_trend'], rtol=1e-3)
# Should still be close to true trend when noise is present
times, values, errors = irregular_periodic(frequencies, amplitudes, phase)
values += slope * times
values += np.random.normal(scale=1e-3, size=len(times))
all_lomb = generate_features(times, values, errors, LOMB_SCARGLE_FEATS)
npt.assert_allclose(slope, all_lomb['linear_trend'], rtol=1e-1)
def test_lomb_scargle_regular_single_freq():
"""Test Lomb-Scargle model features on regularly-sampled periodic data with
one frequency/multiple harmonics. Estimated parameters should be very
accurate in this case.
"""
frequencies = np.hstack((WAVE_FREQS[0], np.zeros(len(WAVE_FREQS) - 1)))
amplitudes = np.zeros((len(frequencies), 4))
amplitudes[0, :] = [8, 4, 2, 1]
phase = 0.1
times, values, errors = regular_periodic(frequencies, amplitudes, phase)
all_lomb = generate_features(times, values, errors, LOMB_SCARGLE_FEATS)
# Only test the first (true) frequency; the rest correspond to noise
npt.assert_allclose(all_lomb['freq1_freq'], frequencies[0])
# Hard-coded value from previous solution
npt.assert_allclose(0.001996007984, all_lomb['freq1_lambda'], rtol=1e-7)
for (i, j), amplitude in np.ndenumerate(amplitudes):
npt.assert_allclose(amplitude,
all_lomb['freq{}_amplitude{}'.format(i + 1,
j + 1)],
rtol=1e-2,
atol=1e-2)
# Only test the first (true) frequency; the rest correspond to noise
for j in range(1, amplitudes.shape[1]):
npt.assert_allclose(phase * j * (-1**j),
all_lomb['freq1_rel_phase{}'.format(j + 1)],
rtol=1e-2,
atol=1e-2)
# Frequency ratio not relevant since there is only; only test amplitude/signif
for i in [2, 3]:
npt.assert_allclose(0.,
all_lomb['freq_amplitude_ratio_{}1'.format(i)],
atol=1e-3)
npt.assert_array_less(10., all_lomb['freq1_signif'])
# Only one frequency, so this should explain basically all the variance
npt.assert_allclose(0., all_lomb['freq_varrat'], atol=5e-3)
# Exactly periodic, so the same minima/maxima should reoccur
npt.assert_allclose(0., all_lomb['freq_model_max_delta_mags'], atol=1e-6)
npt.assert_allclose(0., all_lomb['freq_model_min_delta_mags'], atol=1e-6)
# Linear trend should be zero since the signal is exactly sinusoidal
npt.assert_allclose(0., all_lomb['linear_trend'], atol=1e-4)
folded_times = times % 1. / (frequencies[0] / 2.)
sort_indices = np.argsort(folded_times)
folded_times = folded_times[sort_indices]
folded_values = values[sort_indices]
# Residuals from doubling period should be much higher
npt.assert_array_less(10., all_lomb['medperc90_2p_p'])
# Slopes should be the same for {un,}folded data; use unfolded for stability
slopes = np.diff(values) / np.diff(times)
npt.assert_allclose(np.percentile(slopes, 10),
all_lomb['fold2P_slope_10percentile'],
rtol=1e-2)
npt.assert_allclose(np.percentile(slopes, 90),
all_lomb['fold2P_slope_90percentile'],
rtol=1e-2)