Python utils.sum_squared函数代码示例

def test_notch_filters():
    """Test notch filters."""
    # let's use an ugly, prime sfreq for fun
    sfreq = 487.0
    sig_len_secs = 20
    t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
    freqs = np.arange(60, 241, 60)

    # make a "signal"
    a = rng.randn(int(sig_len_secs * sfreq))
    orig_power = np.sqrt(np.mean(a ** 2))
    # make line noise
    a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)

    # only allow None line_freqs with 'spectrum_fit' mode
    assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
    assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
    methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
    filter_lengths = ['auto', 'auto', 'auto', 8192, 'auto']
    line_freqs = [None, freqs, freqs, freqs, freqs]
    tols = [2, 1, 1, 1]
    for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
        with catch_logging() as log_file:
            with warnings.catch_warnings(record=True):
                b = notch_filter(a, sfreq, lf, fl, method=meth, verbose=True)
        if lf is None:
            out = log_file.getvalue().split('\n')[:-1]
            if len(out) != 2 and len(out) != 3:  # force_serial: len(out) == 3
                raise ValueError('Detected frequencies not logged properly')
            out = np.fromstring(out[-1], sep=', ')
            assert_array_almost_equal(out, freqs)
        new_power = np.sqrt(sum_squared(b) / b.size)
        assert_almost_equal(new_power, orig_power, tol)

def test_notch_filters():
    """Test notch filters
    """
    # let's use an ugly, prime sfreq for fun
    sfreq = 487.0
    sig_len_secs = 20
    t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
    freqs = np.arange(60, 241, 60)

    # make a "signal"
    rng = np.random.RandomState(0)
    a = rng.randn(int(sig_len_secs * sfreq))
    orig_power = np.sqrt(np.mean(a ** 2))
    # make line noise
    a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)

    # only allow None line_freqs with 'spectrum_fit' mode
    assert_raises(ValueError, notch_filter, a, sfreq, None, "fft")
    assert_raises(ValueError, notch_filter, a, sfreq, None, "iir")
    methods = ["spectrum_fit", "spectrum_fit", "fft", "fft", "iir"]
    filter_lengths = [None, None, None, 8192, None]
    line_freqs = [None, freqs, freqs, freqs, freqs]
    tols = [2, 1, 1, 1]
    for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
        with catch_logging() as log_file:
            b = notch_filter(a, sfreq, lf, filter_length=fl, method=meth, verbose="INFO")

        if lf is None:
            out = log_file.getvalue().split("\n")[:-1]
            if len(out) != 2:
                raise ValueError("Detected frequencies not logged properly")
            out = np.fromstring(out[1], sep=", ")
            assert_array_almost_equal(out, freqs)
        new_power = np.sqrt(sum_squared(b) / b.size)
        assert_almost_equal(new_power, orig_power, tol)

def test_csd_multitaper():
    """Test computing cross-spectral density using multitapers."""
    epochs = _generate_coherence_data()
    sfreq = epochs.info['sfreq']
    _test_fourier_multitaper_parameters(epochs, csd_multitaper,
                                        csd_array_multitaper)

    # Compute CSDs using various parameters
    times = [(None, None), (1, 9)]
    as_arrays = [False, True]
    adaptives = [False, True]
    parameters = product(times, as_arrays, adaptives)
    for (tmin, tmax), as_array, adaptive in parameters:
        if as_array:
            csd = csd_array_multitaper(epochs.get_data(), sfreq, epochs.tmin,
                                       adaptive=adaptive, fmin=9, fmax=23,
                                       tmin=tmin, tmax=tmax,
                                       ch_names=epochs.ch_names)
        else:
            csd = csd_multitaper(epochs, adaptive=adaptive, fmin=9, fmax=23,
                                 tmin=tmin, tmax=tmax)
        if tmin is None and tmax is None:
            assert csd.tmin == 0 and csd.tmax == 9.98
        else:
            assert csd.tmin == tmin and csd.tmax == tmax
        csd = csd.mean([9.9, 14.9, 21.9], [10.1, 15.1, 22.1])
        _test_csd_matrix(csd)

    # Test equivalence with PSD
    psd, psd_freqs = psd_multitaper(epochs, fmin=1e-3,
                                    normalization='full')  # omit DC
    csd = csd_multitaper(epochs)
    assert_allclose(psd_freqs, csd.frequencies)
    csd = np.array([np.diag(csd.get_data(index=ii))
                    for ii in range(len(csd))]).T
    assert_allclose(psd[0], csd)

    # For the next test, generate a simple sine wave with a known power
    times = np.arange(20 * sfreq) / sfreq  # 20 seconds of signal
    signal = np.sin(2 * np.pi * 10 * times)[None, None, :]  # 10 Hz wave
    signal_power_per_sample = sum_squared(signal) / len(times)

    # Power per sample should not depend on time window length
    for tmax in [12, 18]:
        t_mask = (times <= tmax)
        n_samples = sum(t_mask)
        n_fft = len(times)

        # Power per sample should not depend on number of tapers
        for n_tapers in [1, 2, 5]:
            bandwidth = sfreq / float(n_samples) * (n_tapers + 1)
            csd_mt = csd_array_multitaper(signal, sfreq, tmax=tmax,
                                          bandwidth=bandwidth,
                                          n_fft=n_fft).sum().get_data()
            mt_power_per_sample = np.abs(csd_mt[0, 0]) * sfreq / n_fft
            assert abs(signal_power_per_sample - mt_power_per_sample) < 0.001

def test_csd_on_artificial_data():
    """Test computing CSD on artificial data. """
    # Ignore deprecation warnings for this test
    epochs = _generate_simple_data()
    sfreq = epochs.info['sfreq']

    # Computing signal power in the time domain
    signal_power = sum_squared(epochs._data)
    signal_power_per_sample = signal_power / len(epochs.times)

    # Computing signal power in the frequency domain
    with warnings.catch_warnings(record=True):  # deprecation
        csd_mt = csd_array(epochs._data, sfreq, mode='multitaper').get_data()
        csd_fourier = csd_array(epochs._data, sfreq, mode='fourier').get_data()

    fourier_power = np.abs(csd_fourier[0, 0]) * sfreq
    mt_power = np.abs(csd_mt[0, 0]) * sfreq
    assert abs(fourier_power - signal_power) <= 0.5
    assert abs(mt_power - signal_power) <= 1

    # Power per sample should not depend on time window length
    for tmax in [0.2, 0.8]:
        tslice = np.where(epochs.times <= tmax)[0]

        for add_n_fft in [0, 30]:
            t_mask = (epochs.times >= 0) & (epochs.times <= tmax)
            n_samples = sum(t_mask)
            n_fft = n_samples + add_n_fft

            with warnings.catch_warnings(record=True):  # deprecation
                csd_fourier = csd_array(epochs._data[:, :, tslice], sfreq,
                                        mode='fourier', fmin=0, fmax=np.inf,
                                        n_fft=n_fft).get_data()

            first_samp = csd_fourier[0, 0]
            fourier_power_per_sample = np.abs(first_samp) * sfreq / n_fft
            assert abs(signal_power_per_sample -
                       fourier_power_per_sample) < 0.003
        # Power per sample should not depend on number of tapers
        for n_tapers in [1, 2, 5]:
            mt_bandwidth = sfreq / float(n_samples) * (n_tapers + 1)
            with warnings.catch_warnings(record=True):  # deprecation
                csd_mt = csd_array(
                    epochs._data[:, :, tslice], sfreq,
                    mt_bandwidth=mt_bandwidth, n_fft=n_fft
                ).get_data()
            mt_power_per_sample = np.abs(csd_mt[0, 0]) * sfreq / n_fft
            # The estimate of power gets worse for small time windows when more
            # tapers are used
            if n_tapers == 5 and tmax == 0.2:
                delta = 0.05
            else:
                delta = 0.004
            assert abs(signal_power_per_sample -
                       mt_power_per_sample) < delta

def test_csd_on_artificial_data():
    """Test computing CSD on artificial data. """
    epochs = _get_data(mode='sin')
    sfreq = epochs.info['sfreq']

    # Computing signal power in the time domain
    signal_power = sum_squared(epochs._data)
    signal_power_per_sample = signal_power / len(epochs.times)

    # Computing signal power in the frequency domain
    data_csd_mt, freqs_mt = csd_array(epochs._data, sfreq,
                                      mode='multitaper')
    data_csd_fourier, freqs_fft = csd_array(epochs._data, sfreq,
                                            mode='fourier')

    fourier_power = np.abs(data_csd_fourier[0, 0]) * sfreq
    mt_power = np.abs(data_csd_mt[0, 0]) * sfreq
    assert_true(abs(fourier_power - signal_power) <= 0.5)
    assert_true(abs(mt_power - signal_power) <= 1)

    # Power per sample should not depend on time window length
    for tmax in [0.2, 0.8]:
        tslice = np.where(epochs.times <= tmax)[0]

        for add_n_fft in [0, 30]:
            t_mask = (epochs.times >= 0) & (epochs.times <= tmax)
            n_samples = sum(t_mask)
            n_fft = n_samples + add_n_fft

            data_csd_fourier, _ = csd_array(epochs._data[:, :, tslice],
                                            sfreq, mode='fourier',
                                            fmin=0, fmax=np.inf, n_fft=n_fft)

            first_samp = data_csd_fourier[0, 0]
            fourier_power_per_sample = np.abs(first_samp) * sfreq / n_fft
            assert_true(abs(signal_power_per_sample -
                            fourier_power_per_sample) < 0.003)
        # Power per sample should not depend on number of tapers
        for n_tapers in [1, 2, 5]:
            for add_n_fft in [0, 30]:
                mt_bandwidth = sfreq / float(n_samples) * (n_tapers + 1)
                data_csd_mt, _ = csd_array(epochs._data[:, :, tslice],
                                           sfreq, mt_bandwidth=mt_bandwidth,
                                           n_fft=n_fft)
                mt_power_per_sample = np.abs(data_csd_mt[0, 0]) *\
                    sfreq / n_fft
                # The estimate of power gets worse for small time windows when
                # more tapers are used
                if n_tapers == 5 and tmax == 0.2:
                    delta = 0.05
                else:
                    delta = 0.004
                assert_true(abs(signal_power_per_sample -
                                mt_power_per_sample) < delta)

def test_compute_epochs_csd_on_artificial_data():
    """Test computing CSD on artificial data
    """
    epochs, epochs_sin = _get_data()
    sfreq = epochs_sin.info['sfreq']

    # Computing signal power in the time domain
    signal_power = sum_squared(epochs_sin._data)
    signal_power_per_sample = signal_power / len(epochs_sin.times)

    # Computing signal power in the frequency domain
    data_csd_fourier = compute_epochs_csd(epochs_sin, mode='fourier')
    data_csd_mt = compute_epochs_csd(epochs_sin, mode='multitaper')
    fourier_power = np.abs(data_csd_fourier.data[0, 0]) * sfreq
    mt_power = np.abs(data_csd_mt.data[0, 0]) * sfreq
    assert_almost_equal(fourier_power, signal_power, delta=0.5)
    assert_almost_equal(mt_power, signal_power, delta=1)

    # Power per sample should not depend on time window length
    for tmax in [0.2, 0.4, 0.6, 0.8]:
        for add_n_fft in [30, 0, 30]:
            t_mask = (epochs_sin.times >= 0) & (epochs_sin.times <= tmax)
            n_samples = sum(t_mask)
            n_fft = n_samples + add_n_fft

            data_csd_fourier = compute_epochs_csd(epochs_sin, mode='fourier',
                                                  tmin=None, tmax=tmax, fmin=0,
                                                  fmax=np.inf, n_fft=n_fft)
            fourier_power_per_sample = np.abs(data_csd_fourier.data[0, 0]) *\
                sfreq / data_csd_fourier.n_fft
            assert_almost_equal(signal_power_per_sample,
                                fourier_power_per_sample, delta=0.003)

        # Power per sample should not depend on number of tapers
        for n_tapers in [1, 2, 3, 5]:
            for add_n_fft in [30, 0, 30]:
                mt_bandwidth = sfreq / float(n_samples) * (n_tapers + 1)
                data_csd_mt = compute_epochs_csd(epochs_sin, mode='multitaper',
                                                 tmin=None, tmax=tmax, fmin=0,
                                                 fmax=np.inf,
                                                 mt_bandwidth=mt_bandwidth,
                                                 n_fft=n_fft)
                mt_power_per_sample = np.abs(data_csd_mt.data[0, 0]) *\
                    sfreq / data_csd_mt.n_fft
                # The estimate of power gets worse for small time windows when
                # more tapers are used
                if n_tapers == 5 and tmax == 0.2:
                    delta = 0.05
                else:
                    delta = 0.004
                assert_almost_equal(signal_power_per_sample,
                                    mt_power_per_sample, delta=delta)

def test_csd_fourier():
    """Test computing cross-spectral density using short-term Fourier."""
    epochs = _generate_coherence_data()
    sfreq = epochs.info['sfreq']
    _test_fourier_multitaper_parameters(epochs, csd_fourier, csd_array_fourier)

    # Compute CSDs using various parameters
    times = [(None, None), (1, 9)]
    as_arrays = [False, True]
    parameters = product(times, as_arrays)
    for (tmin, tmax), as_array in parameters:
        if as_array:
            csd = csd_array_fourier(epochs.get_data(), sfreq, epochs.tmin,
                                    fmin=9, fmax=23, tmin=tmin, tmax=tmax,
                                    ch_names=epochs.ch_names)
        else:
            csd = csd_fourier(epochs, fmin=9, fmax=23, tmin=tmin, tmax=tmax)

        if tmin is None and tmax is None:
            assert csd.tmin == 0 and csd.tmax == 9.98
        else:
            assert csd.tmin == tmin and csd.tmax == tmax
        csd = csd.mean([9.9, 14.9, 21.9], [10.1, 15.1, 22.1])
        _test_csd_matrix(csd)

    # For the next test, generate a simple sine wave with a known power
    times = np.arange(20 * sfreq) / sfreq  # 20 seconds of signal
    signal = np.sin(2 * np.pi * 10 * times)[None, None, :]  # 10 Hz wave
    signal_power_per_sample = sum_squared(signal) / len(times)

    # Power per sample should not depend on time window length
    for tmax in [12, 18]:
        t_mask = (times <= tmax)
        n_samples = sum(t_mask)

        # Power per sample should not depend on number of FFT points
        for add_n_fft in [0, 30]:
            n_fft = n_samples + add_n_fft
            csd = csd_array_fourier(signal, sfreq, tmax=tmax,
                                    n_fft=n_fft).sum().get_data()
            first_samp = csd[0, 0]
            fourier_power_per_sample = np.abs(first_samp) * sfreq / n_fft
            assert abs(signal_power_per_sample -
                       fourier_power_per_sample) < 0.001

def test_notch_filters():
    """Test notch filters
    """
    tempdir = _TempDir()
    log_file = op.join(tempdir, 'temp_log.txt')
    # let's use an ugly, prime sfreq for fun
    sfreq = 487.0
    sig_len_secs = 20
    t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
    freqs = np.arange(60, 241, 60)

    # make a "signal"
    rng = np.random.RandomState(0)
    a = rng.randn(int(sig_len_secs * sfreq))
    orig_power = np.sqrt(np.mean(a ** 2))
    # make line noise
    a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)

    # only allow None line_freqs with 'spectrum_fit' mode
    assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
    assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
    methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
    filter_lengths = [None, None, None, 8192, None]
    line_freqs = [None, freqs, freqs, freqs, freqs]
    tols = [2, 1, 1, 1]
    for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
        if lf is None:
            set_log_file(log_file, overwrite=True)

        b = notch_filter(a, sfreq, lf, filter_length=fl, method=meth,
                         verbose='INFO')

        if lf is None:
            set_log_file()
            with open(log_file) as fid:
                out = fid.readlines()
            if len(out) != 2:
                raise ValueError('Detected frequencies not logged properly')
            out = np.fromstring(out[1], sep=', ')
            assert_array_almost_equal(out, freqs)
        new_power = np.sqrt(sum_squared(b) / b.size)
        assert_almost_equal(new_power, orig_power, tol)

def test_sum_squared():
    """Test optimized sum of squares."""
    X = np.random.RandomState(0).randint(0, 50, (3, 3))
    assert_equal(np.sum(X ** 2), sum_squared(X))