settings

class stream.settings.NMSettings(*args, sampling_rate_features_hz: Annotated[float, Gt(gt=0)] = 10, segment_length_features_ms: Annotated[float, Gt(gt=0)] = 1000, frequency_ranges_hz: dict[str, FrequencyRange] = {'HFA': FrequencyRange(frequency_low_hz=200.0, frequency_high_hz=400.0), 'alpha': FrequencyRange(frequency_low_hz=8.0, frequency_high_hz=12.0), 'high_beta': FrequencyRange(frequency_low_hz=20.0, frequency_high_hz=35.0), 'high_gamma': FrequencyRange(frequency_low_hz=90.0, frequency_high_hz=200.0), 'low_beta': FrequencyRange(frequency_low_hz=13.0, frequency_high_hz=20.0), 'low_gamma': FrequencyRange(frequency_low_hz=60.0, frequency_high_hz=80.0), 'theta': FrequencyRange(frequency_low_hz=4.0, frequency_high_hz=8.0)}, preprocessing: list[Literal['preprocessing_filter', 'notch_filter', 'raw_resampling', 're_referencing', 'raw_normalization']] = ['raw_resampling', 'notch_filter', 're_referencing'], raw_resampling_settings: ResamplerSettings = ResamplerSettings(resample_freq_hz=1000), preprocessing_filter: FilterSettings = FilterSettings(bandstop_filter=True, bandpass_filter=True, lowpass_filter=True, highpass_filter=True, bandstop_filter_settings=FrequencyRange(frequency_low_hz=100.0, frequency_high_hz=160.0), bandpass_filter_settings=FrequencyRange(frequency_low_hz=2.0, frequency_high_hz=200.0), lowpass_filter_cutoff_hz=200, highpass_filter_cutoff_hz=3), raw_normalization_settings: NormalizationSettings = NormalizationSettings(normalization_time_s=30, normalization_method='zscore', clip=3), postprocessing: PostprocessingSettings = PostprocessingSettings(feature_normalization=True, project_cortex=False, project_subcortex=False), feature_normalization_settings: FeatureNormalizationSettings = FeatureNormalizationSettings(normalization_time_s=30, normalization_method='zscore', clip=3, normalize_psd=False), project_cortex_settings: ProjectionSettings = ProjectionSettings(max_dist_mm=20.0), project_subcortex_settings: ProjectionSettings = ProjectionSettings(max_dist_mm=5.0), features: FeatureSelector = FeatureSelector(raw_hjorth=True, return_raw=True, bandpass_filter=False, stft=False, fft=True, welch=True, sharpwave_analysis=True, fooof=False, nolds=False, coherence=False, bursts=True, linelength=True, mne_connectivity=False, bispectrum=False), fft_settings: OscillatorySettings = OscillatorySettings(windowlength_ms=1000, log_transform=True, features=OscillatoryFeatures(mean=True, median=False, std=False, max=False), return_spectrum=True), welch_settings: OscillatorySettings = OscillatorySettings(windowlength_ms=1000, log_transform=True, features=OscillatoryFeatures(mean=True, median=False, std=False, max=False), return_spectrum=True), stft_settings: OscillatorySettings = OscillatorySettings(windowlength_ms=1000, log_transform=True, features=OscillatoryFeatures(mean=True, median=False, std=False, max=False), return_spectrum=True), bandpass_filter_settings: BandPowerSettings = BandPowerSettings(segment_lengths_ms={'theta': 1000, 'alpha': 500, 'low beta': 333, 'high beta': 333, 'low gamma': 100, 'high gamma': 100, 'HFA': 100}, bandpower_features=BandpowerFeatures(activity=True, mobility=False, complexity=False), log_transform=True, kalman_filter=False), kalman_filter_settings: KalmanSettings = KalmanSettings(Tp=0.1, sigma_w=0.7, sigma_v=1.0, frequency_bands=['theta', 'alpha', 'low_beta', 'high_beta', 'low_gamma', 'high_gamma', 'HFA']), bursts_settings: BurstsSettings = BurstsSettings(threshold=75, time_duration_s=30, frequency_bands=['low_beta', 'high_beta', 'low_gamma'], burst_features=BurstFeatures(duration=True, amplitude=True, burst_rate_per_s=True, in_burst=True)), sharpwave_analysis_settings: SharpwaveSettings = SharpwaveSettings(sharpwave_features=SharpwaveFeatures(peak_left=False, peak_right=False, num_peaks=False, trough=False, width=False, prominence=True, interval=True, decay_time=False, rise_time=False, sharpness=True, rise_steepness=False, decay_steepness=False, slope_ratio=False), filter_ranges_hz=[FrequencyRange(frequency_low_hz=5.0, frequency_high_hz=80.0), FrequencyRange(frequency_low_hz=5.0, frequency_high_hz=30.0)], detect_troughs=PeakDetectionSettings(estimate=True, distance_troughs_ms=10, distance_peaks_ms=5), detect_peaks=PeakDetectionSettings(estimate=True, distance_troughs_ms=10, distance_peaks_ms=5), estimator=SharpwaveEstimators(mean=['interval'], median=[], max=['prominence', 'sharpness'], min=[], var=[]), apply_estimator_between_peaks_and_troughs=True), mne_connectivity_settings: MNEConnectivitySettings = MNEConnectivitySettings(method='plv', mode='multitaper', channels=[]), coherence_settings: CoherenceSettings = CoherenceSettings(features=CoherenceFeatures(mean_fband=True, max_fband=True, max_allfbands=True), method=CoherenceMethods(coh=True, icoh=True), channels=[], nperseg=256, frequency_bands=['high_beta']), fooof_settings: FooofSettings = FooofSettings(aperiodic=FooofAperiodicSettings(exponent=True, offset=True, knee=True), periodic=FooofPeriodicSettings(center_frequency=False, band_width=False, height_over_ap=False), windowlength_ms=800, peak_width_limits=FrequencyRange(frequency_low_hz=0.5, frequency_high_hz=12.0), max_n_peaks=3, min_peak_height=0, peak_threshold=2, freq_range_hz=FrequencyRange(frequency_low_hz=2.0, frequency_high_hz=40.0), knee=True), nolds_features: NoldsSettings = NoldsSettings(raw=True, frequency_bands=['low_beta'], features=NoldsFeatures(sample_entropy=False, correlation_dimension=False, lyapunov_exponent=True, hurst_exponent=False, detrended_fluctuation_analysis=False)), bispectrum_settings: BispectraSettings = BispectraSettings(f1s=FrequencyRange(frequency_low_hz=5.0, frequency_high_hz=35.0), f2s=FrequencyRange(frequency_low_hz=5.0, frequency_high_hz=35.0), compute_features_for_whole_fband_range=True, frequency_bands=['theta', 'alpha', 'low_beta', 'high_beta'], components=BispectraComponents(absolute=True, real=True, imag=True, phase=True), bispectrum_features=BispectraFeatures(mean=True, sum=True, var=True)), **kwargs)

static from_file(PATH: str | PathLike) → NMSettings

Load settings from file or a directory.

Parameters:

PATH (_PathLike) – Path to settings file or to directory containing settings file, or path to experiment including experiment prefix (e.g. /path/to/exp/exp_prefix[_SETTINGS.json]). Supported file types are .json and .yaml

Raises:

ValueError – when file format is not supported.

Returns:

PyNM settings object

Return type:

NMSettings

model_config: ClassVar[ConfigDict] = {'extra': 'allow', 'validate_assignment': False}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].