py-neuromodulation 0.0.3__py3-none-any.whl → 0.0.4__py3-none-any.whl

tests/test_osc_features.py

@@ -1,424 +0,0 @@
-import numpy as np
-import pytest
-
-from py_neuromodulation import nm_oscillatory, nm_settings
-
-
-def setup_osc_settings(
-    osc_feature_name: str,
-    osc_feature_setting: str,
-    windowlength_ms: int,
-    log_transform: bool,
-):
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.reset_settings(settings)
-    settings[osc_feature_name] = True
-    settings[osc_feature_setting]["windowlength_ms"] = windowlength_ms
-    settings[osc_feature_setting]["log_transform"] = log_transform
-
-    return settings
-
-
-def test_fft_wrong_logtransform_param_init():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="fft",
-        osc_feature_setting="fft_settings",
-        windowlength_ms=1000,
-        log_transform="123",
-    )
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "beta": [10, 20]}
-
-    with pytest.raises(Exception) as e_info:
-        nm_oscillatory.FFT.test_settings(settings, ch_names, sfreq)
-
-
-def test_fft_wrong_frequencyband_range_init():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="fft",
-        osc_feature_setting="fft_settings",
-        windowlength_ms=1000,
-        log_transform="123",
-    )
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "broadband": [10, 600]}
-
-    with pytest.raises(Exception):
-        nm_oscillatory.FFT.test_settings(settings, ch_names, sfreq)
-
-
-def test_fft_zero_data():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="fft",
-        osc_feature_setting="fft_settings",
-        windowlength_ms=1000,
-        log_transform=False,
-    )
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "beta": [10, 20]}
-    fft_obj = nm_oscillatory.FFT(settings, ch_names, sfreq)
-    fft_obj.test_settings(settings, ch_names, sfreq)
-
-    data = np.ones([len(ch_names), sfreq])
-    features_out = fft_obj.calc_feature(data, {})
-
-    for f in features_out.keys():
-        if "psd_0" not in f:
-            assert np.isclose(features_out[f], 0, atol=1e-6)
-
-
-def test_fft_random_data():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="fft",
-        osc_feature_setting="fft_settings",
-        windowlength_ms=1000,
-        log_transform=False,
-    )
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "beta": [10, 20]}
-    fft_obj = nm_oscillatory.FFT(settings, ch_names, sfreq)
-    fft_obj.test_settings(settings, ch_names, sfreq)
-
-    data = np.random.random([len(ch_names), sfreq])
-    features_out = fft_obj.calc_feature(data, {})
-
-    for f in features_out.keys():
-        assert features_out[f] != 0
-
-
-def test_fft_beta_osc():
-    ch_names = [
-        "ch1",
-    ]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="fft",
-        osc_feature_setting="fft_settings",
-        windowlength_ms=1000,
-        log_transform=False,
-    )
-
-    settings["frequency_ranges_hz"] = {
-        "theta": [4, 8],
-        "beta": [10, 28],
-        "gamma": [50, 60],
-    }
-
-    fft_obj = nm_oscillatory.FFT(settings, ch_names, sfreq)
-    fft_obj.test_settings(settings, ch_names, sfreq)
-
-    time_duration = 1
-
-    time_points = np.arange(0, time_duration, 1 / sfreq)
-    beta_freq = 20
-
-    beta_wave = np.sin(2 * np.pi * beta_freq * time_points)
-
-    np.random.seed(0)
-    data = np.random.random([len(ch_names), sfreq]) + beta_wave
-
-    features_out = fft_obj.calc_feature(data, {})
-
-    assert (
-        features_out["ch1_fft_beta_mean"] > features_out["ch1_fft_theta_mean"]
-        and features_out["ch1_fft_beta_mean"]
-        > features_out["ch1_fft_gamma_mean"]
-    )
-
-
-def test_stft_wrong_logtransform_param_init():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="stft",
-        osc_feature_setting="stft_settings",
-        windowlength_ms=1000,
-        log_transform="123",
-    )
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "beta": [10, 20]}
-
-    with pytest.raises(Exception) as e_info:
-        nm_oscillatory.STFT.test_settings(settings, ch_names, sfreq)
-
-
-def test_stft_wrong_frequencyband_range_init():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="stft",
-        osc_feature_setting="stft_settings",
-        windowlength_ms=1000,
-        log_transform="123",
-    )
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "broadband": [10, 600]}
-
-    with pytest.raises(Exception):
-        nm_oscillatory.STFT.test_settings(settings, ch_names, sfreq)
-
-
-def test_stft_beta_osc():
-    ch_names = [
-        "ch1",
-    ]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="stft",
-        osc_feature_setting="stft_settings",
-        windowlength_ms=1000,
-        log_transform=True,
-    )
-
-    settings["frequency_ranges_hz"] = {
-        "theta": [4, 8],
-        "beta": [10, 28],
-        "gamma": [50, 60],
-    }
-
-    stft_obj = nm_oscillatory.STFT(settings, ch_names, sfreq)
-    stft_obj.test_settings(settings, ch_names, sfreq)
-
-    time_duration = 1
-
-    time_points = np.arange(0, time_duration, 1 / sfreq)
-    beta_freq = 20
-
-    beta_wave = np.sin(2 * np.pi * beta_freq * time_points)
-
-    np.random.seed(0)
-    data = np.random.random([len(ch_names), sfreq]) + beta_wave
-
-    features_out = stft_obj.calc_feature(data, {})
-
-    assert (
-        features_out["ch1_stft_beta_mean"] > features_out["ch1_stft_theta_mean"]
-        and features_out["ch1_stft_beta_mean"]
-        > features_out["ch1_stft_gamma_mean"]
-    )
-
-
-def test_welch_beta_osc():
-    ch_names = [
-        "ch1",
-    ]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="welch",
-        osc_feature_setting="welch_settings",
-        windowlength_ms=1000,
-        log_transform=True,
-    )
-
-    settings["frequency_ranges_hz"] = {
-        "theta": [4, 8],
-        "beta": [10, 28],
-        "gamma": [50, 60],
-    }
-
-    stft_obj = nm_oscillatory.Welch(settings, ch_names, sfreq)
-    stft_obj.test_settings(settings, ch_names, sfreq)
-
-    time_duration = 1
-
-    time_points = np.arange(0, time_duration, 1 / sfreq)
-    beta_freq = 20
-
-    beta_wave = np.sin(2 * np.pi * beta_freq * time_points)
-
-    np.random.seed(0)
-    data = np.random.random([len(ch_names), sfreq]) + beta_wave
-
-    features_out = stft_obj.calc_feature(data, {})
-
-    assert (
-        features_out["ch1_welch_beta_mean"]
-        > features_out["ch1_welch_theta_mean"]
-        and features_out["ch1_welch_beta_mean"]
-        > features_out["ch1_welch_gamma_mean"]
-    )
-
-
-def test_bp_wrong_logtransform_param_init():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="bandpass_filter",
-        osc_feature_setting="bandpass_filter_settings",
-        windowlength_ms=1000,
-        log_transform="123",
-    )
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "beta": [10, 20]}
-
-    with pytest.raises(Exception) as e_info:
-        nm_oscillatory.BandPower.test_settings(settings, ch_names, sfreq)
-
-
-def test_bp_wrong_frequencyband_range_init():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="bandpass_filter",
-        osc_feature_setting="bandpass_filter_settings",
-        windowlength_ms=1000,
-        log_transform="123",
-    )
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "broadband": [10, 600]}
-
-    with pytest.raises(Exception):
-        nm_oscillatory.BandPower.test_settings(settings, ch_names, sfreq)
-
-
-def test_bp_non_defined_fband():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="bandpass_filter",
-        osc_feature_setting="bandpass_filter_settings",
-        windowlength_ms=1000,
-        log_transform=True,
-    )
-
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "broadband": [10, 600]}
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["theta"] = 1000
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["beta"] = 300
-
-    with pytest.raises(Exception):
-        nm_oscillatory.BandPower.test_settings(settings, ch_names, sfreq)
-
-
-def test_bp_segment_length_fb_exceeds_segment_length_features():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = setup_osc_settings(
-        osc_feature_name="bandpass_filter",
-        osc_feature_setting="bandpass_filter_settings",
-        windowlength_ms=1000,
-        log_transform=True,
-    )
-
-    settings["segment_length_features_ms"] = 500
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "broadband": [10, 600]}
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["theta"] = 1000
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["beta"] = 300
-
-    with pytest.raises(Exception):
-        nm_oscillatory.BandPower.test_settings(settings, ch_names, sfreq)
-
-
-def test_bp_zero_data():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.reset_settings(settings)
-    settings["features"]["bandpass_filter"] = True
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["theta"] = 1000
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["beta"] = 300
-
-    settings["bandpass_filter_settings"]["log_transform"] = False
-    settings["bandpass_filter_settings"]["kalman_filter"] = False
-    settings["bandpass_filter_settings"]["bandpower_features"][
-        "activity"
-    ] = True
-
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "beta": [10, 20]}
-    stft_obj = nm_oscillatory.BandPower(settings, ch_names, sfreq)
-    stft_obj.test_settings(settings, ch_names, sfreq)
-
-    data = np.zeros([len(ch_names), sfreq])
-    features_out = stft_obj.calc_feature(data, {})
-
-    for f in features_out.keys():
-        assert pytest.approx(0, 0.01) == features_out[f]
-
-
-def test_bp_random_data():
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-    sfreq = 1000
-
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.reset_settings(settings)
-    settings["frequency_ranges_hz"] = {"theta": [4, 8], "beta": [10, 30]}
-    settings["features"]["bandpass_filter"] = True
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["theta"] = 1000
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["beta"] = 300
-
-    settings["bandpass_filter_settings"]["log_transform"] = False
-    settings["bandpass_filter_settings"]["kalman_filter"] = False
-    settings["bandpass_filter_settings"]["bandpower_features"][
-        "activity"
-    ] = True
-
-    stft_obj = nm_oscillatory.BandPower(settings, ch_names, sfreq)
-    stft_obj.test_settings(settings, ch_names, sfreq)
-
-    np.random.seed(0)
-    data = np.random.random([len(ch_names), sfreq])
-    features_out = stft_obj.calc_feature(data, {})
-
-    for f in features_out.keys():
-        assert pytest.approx(0, 0.01) != features_out[f]
-
-
-def test_bp_beta_osc():
-    ch_names = [
-        "ch1",
-    ]
-    sfreq = 1000
-
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.reset_settings(settings)
-    settings["frequency_ranges_hz"] = {
-        "theta": [4, 8],
-        "beta": [10, 30],
-        "gamma": [50, 60],
-    }
-
-    settings["features"]["bandpass_filter"] = True
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["theta"] = 1000
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["beta"] = 300
-    settings["bandpass_filter_settings"]["segment_lengths_ms"]["gamma"] = 100
-
-    settings["bandpass_filter_settings"]["log_transform"] = False
-    settings["bandpass_filter_settings"]["kalman_filter"] = False
-    settings["bandpass_filter_settings"]["bandpower_features"][
-        "activity"
-    ] = True
-
-    bp_obj = nm_oscillatory.BandPower(settings, ch_names, sfreq)
-    bp_obj.test_settings(settings, ch_names, sfreq)
-
-    time_duration = 1
-
-    time_points = np.arange(0, time_duration, 1 / sfreq)
-    beta_freq = 20
-
-    beta_wave = np.sin(2 * np.pi * beta_freq * time_points)
-
-    np.random.seed(0)
-    data = np.random.random([len(ch_names), sfreq]) + beta_wave
-
-    features_out = bp_obj.calc_feature(data, {})
-
-    assert (
-        features_out["ch1_bandpass_activity_beta"]
-        > features_out["ch1_bandpass_activity_theta"]
-        and features_out["ch1_bandpass_activity_beta"]
-        > features_out["ch1_bandpass_activity_gamma"]
-    )

tests/test_preprocessing_filter.py

@@ -1,151 +0,0 @@
-import numpy as np
-from scipy import signal
-
-from py_neuromodulation import nm_settings
-from py_neuromodulation.nm_filter_preprocessing import PreprocessingFilter
-
-
-def test_preprocessing_within_pipeline(setup_default_stream_fast_compute):
-
-    data, stream = setup_default_stream_fast_compute
-
-    stream.settings["preprocessing"].append("preprocessing_filter")
-
-    stream.settings["preprocessing_filter"]["bandstop_filter"] = True
-    stream.settings["preprocessing_filter"]["bandpass_filter"] = True
-    stream.settings["preprocessing_filter"]["lowpass_filter"] = True
-    stream.settings["preprocessing_filter"]["highpass_filter"] = True
-
-    stream.sfreq
-
-    try:
-        _ = stream.run(data[:, : int(stream.sfreq * 2)])
-    except Exception as e:
-        assert False, f"Error in pipeline including preprocess filtering : {e}"
-
-
-def test_preprocessing_filter_lowpass():
-
-    data_batch = np.random.random([1, 1000])
-
-    settings = nm_settings.get_default_settings()
-    settings["preprocessing"] = settings["preprocessing"].append(
-        "preprocessing_filter"
-    )
-    settings["preprocessing_filter"]["lowpass_filter"] = True
-    settings["preprocessing_filter"]["highpass_filter"] = False
-    settings["preprocessing_filter"]["bandpass_filter"] = False
-    settings["preprocessing_filter"]["bandstop_filter"] = False
-
-    settings["preprocessing_filter"]["lowpass_filter_settings"][
-        "frequency_cutoff_hz"
-    ] = 100
-
-    sfreq = 1000
-
-    preprocessing_filter = PreprocessingFilter(settings, sfreq)
-    data_filtered = preprocessing_filter.process(data_batch)
-
-    # compute a scipy signal welch to check if the filter worked
-    f, Pxx = signal.welch(data_batch, fs=sfreq, nperseg=1000)
-    f, Pxx_f = signal.welch(data_filtered, fs=sfreq, nperseg=1000)
-
-    # check if the power in the frequency range of the lowpass filter is reduced
-    assert np.mean(Pxx_f[0, 100:500]) < np.mean(Pxx[0, 100:500])
-
-
-def test_preprocessing_filter_highpass():
-
-    data_batch = np.random.random([1, 1000])
-
-    settings = nm_settings.get_default_settings()
-    settings["preprocessing"] = settings["preprocessing"].append(
-        "preprocessing_filter"
-    )
-    settings["preprocessing_filter"]["highpass_filter"] = True
-    settings["preprocessing_filter"]["lowpass_filter"] = False
-    settings["preprocessing_filter"]["bandpass_filter"] = False
-    settings["preprocessing_filter"]["bandstop_filter"] = False
-
-    settings["preprocessing_filter"]["highpass_filter_settings"][
-        "frequency_cutoff_hz"
-    ] = 100
-
-    sfreq = 1000
-
-    preprocessing_filter = PreprocessingFilter(settings, sfreq)
-    data_filtered = preprocessing_filter.process(data_batch)
-
-    # compute a scipy signal welch to check if the filter worked
-    f, Pxx = signal.welch(data_batch, fs=sfreq, nperseg=1000)
-    f, Pxx_f = signal.welch(data_filtered, fs=sfreq, nperseg=1000)
-
-    # check if the power in the frequency range of the highpass filter is reduced
-    assert np.mean(Pxx_f[0, 0:100]) < np.mean(Pxx[0, 0:100])
-
-
-def test_preprocessing_filter_bandstop():
-
-    data_batch = np.random.random([1, 1000])
-
-    settings = nm_settings.get_default_settings()
-    settings["preprocessing"] = settings["preprocessing"].append(
-        "preprocessing_filter"
-    )
-    settings["preprocessing_filter"]["bandstop_filter"] = True
-    settings["preprocessing_filter"]["bandpass_filter"] = False
-    settings["preprocessing_filter"]["lowpass_filter"] = False
-    settings["preprocessing_filter"]["highpass_filter"] = False
-
-    settings["preprocessing_filter"]["bandstop_filter_settings"][
-        "frequency_low_hz"
-    ] = 100
-    settings["preprocessing_filter"]["bandstop_filter_settings"][
-        "frequency_high_hz"
-    ] = 160
-
-    sfreq = 1000
-
-    preprocessing_filter = PreprocessingFilter(settings, sfreq)
-    data_filtered = preprocessing_filter.process(data_batch)
-
-    # compute a scipy signal welch to check if the filter worked
-    f, Pxx = signal.welch(data_batch, fs=sfreq, nperseg=1000)
-    f, Pxx_f = signal.welch(data_filtered, fs=sfreq, nperseg=1000)
-
-    # check if the power in the frequency range of the bandstop filter is reduced
-    assert np.mean(Pxx_f[0, 100:160]) < np.mean(Pxx[0, 100:160])
-
-
-def test_preprocessing_filter_bandpass():
-
-    data_batch = np.random.random([1, 1000])
-
-    settings = nm_settings.get_default_settings()
-    settings["preprocessing"] = settings["preprocessing"].append(
-        "preprocessing_filter"
-    )
-    settings["preprocessing_filter"]["bandstop_filter"] = False
-    settings["preprocessing_filter"]["bandpass_filter"] = True
-    settings["preprocessing_filter"]["lowpass_filter"] = False
-    settings["preprocessing_filter"]["highpass_filter"] = False
-
-    settings["preprocessing_filter"]["bandpass_filter_settings"][
-        "frequency_low_hz"
-    ] = 100
-    settings["preprocessing_filter"]["bandpass_filter_settings"][
-        "frequency_high_hz"
-    ] = 160
-
-    sfreq = 1000
-
-    preprocessing_filter = PreprocessingFilter(settings, sfreq)
-    data_filtered = preprocessing_filter.process(data_batch)
-
-    # compute a scipy signal welch to check if the filter worked
-    f, Pxx = signal.welch(data_batch, fs=sfreq, nperseg=1000)
-    f, Pxx_f = signal.welch(data_filtered, fs=sfreq, nperseg=1000)
-
-    # check if the power in the frequency range of the bandpass filter is reduced
-    assert np.mean(Pxx_f[0, 0:100]) < np.mean(Pxx[0, 0:100])
-    assert np.mean(Pxx_f[0, 160:500]) < np.mean(Pxx[0, 160:500])