How to use the biosppy.plotting function in biosppy

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github PIA-Group / BioSPPy / biosppy / signals / eeg.py View on Github external
gamma = out['gamma']

    # PLF features
    _, plf_pairs, plf = get_plf_features(signal=filtered,
                                         sampling_rate=sampling_rate,
                                         size=0.25,
                                         overlap=0.5)

    # get time vectors
    length = len(signal)
    T = (length - 1) / sampling_rate
    ts = np.linspace(0, T, length, endpoint=True)

    # plot
    if show:
        plotting.plot_eeg(ts=ts,
                          raw=signal,
                          filtered=filtered,
                          labels=labels,
                          features_ts=ts_feat,
                          theta=theta,
                          alpha_low=alpha_low,
                          alpha_high=alpha_high,
                          beta=beta,
                          gamma=gamma,
                          plf_pairs=plf_pairs,
                          plf=plf,
                          path=None,
                          show=True)

    # output
    args = (ts, filtered, ts_feat, theta, alpha_low, alpha_high, beta, gamma,
github PIA-Group / BioSPPy / biosppy / signals / emg.py View on Github external
band='highpass',
                                      order=4,
                                      frequency=100,
                                      sampling_rate=sampling_rate)

    # find onsets
    onsets, = find_onsets(signal=filtered, sampling_rate=sampling_rate)

    # get time vectors
    length = len(signal)
    T = (length - 1) / sampling_rate
    ts = np.linspace(0, T, length, endpoint=True)

    # plot
    if show:
        plotting.plot_emg(ts=ts,
                          sampling_rate=1000.,
                          raw=signal,
                          filtered=filtered,
                          processed=None,
                          onsets=onsets,
                          path=None,
                          show=True)

    # output
    args = (ts, filtered, onsets)
    names = ('ts', 'filtered', 'onsets')

    return utils.ReturnTuple(args, names)
github PIA-Group / BioSPPy / biosppy / biometrics.py View on Github external
id_res = np.array(id_res)
            results[subject] = {'authentication': auth_res,
                                'identification': id_res,
                                }

        # assess classification results
        assess, = assess_classification(results, thresholds)

        # output
        args = (results, assess)
        names = ('classification', 'assessment')
        out = utils.ReturnTuple(args, names)

        if show:
            # plot
            plotting.plot_biometrics(assess, self.EER_IDX, show=True)

        return out
github PIA-Group / BioSPPy / biosppy / signals / ecg.py View on Github external
# compute heart rate
    hr_idx, hr = st.get_heart_rate(beats=rpeaks,
                                   sampling_rate=sampling_rate,
                                   smooth=True,
                                   size=3)

    # get time vectors
    length = len(signal)
    T = (length - 1) / sampling_rate
    ts = np.linspace(0, T, length, endpoint=True)
    ts_hr = ts[hr_idx]
    ts_tmpl = np.linspace(-0.2, 0.4, templates.shape[1], endpoint=False)

    # plot
    if show:
        plotting.plot_ecg(ts=ts,
                          raw=signal,
                          filtered=filtered,
                          rpeaks=rpeaks,
                          templates_ts=ts_tmpl,
                          templates=templates,
                          heart_rate_ts=ts_hr,
                          heart_rate=hr,
                          path=None,
                          show=True)

    # output
    args = (ts, filtered, rpeaks, ts_tmpl, templates, ts_hr, hr)
    names = ('ts', 'filtered', 'rpeaks', 'templates_ts', 'templates',
             'heart_rate_ts', 'heart_rate')

    return utils.ReturnTuple(args, names)
github PIA-Group / BioSPPy / biosppy / signals / resp.py View on Github external
# smooth with moving average
        size = 3
        rate, _ = st.smoother(signal=rate,
                              kernel='boxcar',
                              size=size,
                              mirror=True)

    # get time vectors
    length = len(signal)
    T = (length - 1) / sampling_rate
    ts = np.linspace(0, T, length, endpoint=True)
    ts_rate = ts[rate_idx]

    # plot
    if show:
        plotting.plot_resp(ts=ts,
                           raw=signal,
                           filtered=filtered,
                           zeros=zeros,
                           resp_rate_ts=ts_rate,
                           resp_rate=rate,
                           path=None,
                           show=True)

    # output
    args = (ts, filtered, zeros, ts_rate, rate)
    names = ('ts', 'filtered', 'zeros', 'resp_rate_ts', 'resp_rate')

    return utils.ReturnTuple(args, names)
github PIA-Group / BioSPPy / biosppy / signals / eda.py View on Github external
size=sm_size,
                              mirror=True)

    # get SCR info
    onsets, peaks, amps = kbk_scr(signal=filtered,
                                  sampling_rate=sampling_rate,
                                  min_amplitude=min_amplitude)

    # get time vectors
    length = len(signal)
    T = (length - 1) / sampling_rate
    ts = np.linspace(0, T, length, endpoint=True)

    # plot
    if show:
        plotting.plot_eda(ts=ts,
                          raw=signal,
                          filtered=filtered,
                          onsets=onsets,
                          peaks=peaks,
                          amplitudes=amps,
                          path=None,
                          show=True)

    # output
    args = (ts, filtered, onsets, peaks, amps)
    names = ('ts', 'filtered', 'onsets', 'peaks', 'amplitudes')

    return utils.ReturnTuple(args, names)
github PIA-Group / BioSPPy / biosppy / signals / bvp.py View on Github external
# compute heart rate
    hr_idx, hr = st.get_heart_rate(beats=onsets,
                                   sampling_rate=sampling_rate,
                                   smooth=True,
                                   size=3)

    # get time vectors
    length = len(signal)
    T = (length - 1) / sampling_rate
    ts = np.linspace(0, T, length, endpoint=False)
    ts_hr = ts[hr_idx]

    # plot
    if show:
        plotting.plot_bvp(ts=ts,
                          raw=signal,
                          filtered=filtered,
                          onsets=onsets,
                          heart_rate_ts=ts_hr,
                          heart_rate=hr,
                          path=None,
                          show=True)

    # output
    args = (ts, filtered, onsets, ts_hr, hr)
    names = ('ts', 'filtered', 'onsets', 'heart_rate_ts', 'heart_rate')

    return utils.ReturnTuple(args, names)