How to use the biosppy.signals function in biosppy

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github PGomes92 / pyhrv / pyhrv / tools.py View on Github external
------
	TypeError
		If no input data for 'nni', 'rpeaks' or 'signal' is provided

	Notes
	-----
	..	NN intervals are derived from the ECG signal if 'signal' is provided.
	.. 	If both 'nni' and 'rpeaks' are provided, 'rpeaks' will be chosen over the 'nn' and the 'nni' data will be computed
		from the 'rpeaks'.
	..	If both 'nni' and 'signal' are provided, 'nni' will be chosen over 'signal'.
	..	If both 'rpeaks' and 'signal' are provided, 'rpeaks' will be chosen over 'signal'.

	"""
	# Check input
	if signal is not None:
		rpeaks = biosppy.signals.ecg.ecg(signal=signal, sampling_rate=sampling_rate, show=False)[2]
	elif nni is None and rpeaks is None:
		raise TypeError('No input data provided. Please specify input data.')

	# Get NNI series
	nni = check_input(nni, rpeaks)

	# Time vector back to ms
	t = np.cumsum(nni) / 1000.

	# Configure interval of visualized signal
	interval = check_interval(interval, limits=[0, t[-1]], default=[0, 10])

	# Prepare figure
	if figsize is None:
		figsize = (12, 4)
	fig = plt.figure(figsize=figsize)
github PGomes92 / pyhrv / pyhrv / frequency_domain.py View on Github external
t = np.cumsum(nn)
	t -= t[0]

	# Compute PSD according to the Lomb-Scargle method
	# Specify frequency grid
	frequencies = np.linspace(0, 0.41, nfft)
	# Compute angular frequencies
	a_frequencies = np.asarray(2 * np.pi / frequencies)
	powers = np.asarray(lombscargle(t, nn, a_frequencies, normalize=True))

	# Fix power = inf at f=0
	powers[0] = 2

	# Apply moving average filter
	if ma_size is not None:
		powers = biosppy.signals.tools.smoother(powers, size=ma_size)['signal']

	# Define metadata
	meta = utils.ReturnTuple((nfft, ma_size, ), ('lomb_nfft', 'lomb_ma'))

	if mode not in ['normal', 'dev', 'devplot']:
		warnings.warn("Unknown mode '%s'. Will proceed with 'normal' mode." % mode, stacklevel=2)
		mode = 'normal'

	# Normal Mode:
	# Returns frequency parameters, PSD plot figure and no frequency & power series/arrays
	if mode == 'normal':
		# ms^2 to s^2
		powers = powers * 10 ** 6

		# Compute frequency parameters
		params, freq_i = _compute_parameters('lomb', frequencies, powers, fbands)
github neuropsychology / NeuroKit.py / neurokit / bio / bio_ecg.py View on Github external
# Frequency Domain Features
        # ==========================
        freq_bands = {
          "ULF": [0.0001, 0.0033],
          "VLF": [0.0033, 0.04],
          "LF": [0.04, 0.15],
          "HF": [0.15, 0.40],
          "VHF": [0.4, 0.5]}


        # Frequency-Domain Power over time
        freq_powers = {}
        for band in freq_bands:
            freqs = freq_bands[band]
            # Filter to keep only the band of interest
            filtered, sampling_rate, params = biosppy.signals.tools.filter_signal(signal=RRi, ftype='butter', band='bandpass', order=1, frequency=freqs, sampling_rate=sampling_rate)
            # Apply Hilbert transform
            amplitude, phase = biosppy.signals.tools.analytic_signal(filtered)
            # Extract Amplitude of Envelope (power)
            freq_powers["ECG_HRV_" + band] = amplitude

        freq_powers = pd.DataFrame.from_dict(freq_powers)
        freq_powers.index = hrv["df"].index
        hrv["df"] = pd.concat([hrv["df"], freq_powers], axis=1)


        # Compute Power Spectral Density (PSD) using multitaper method
        power, freq = mne.time_frequency.psd_array_multitaper(RRi, sfreq=sampling_rate, fmin=0, fmax=0.5,  adaptive=False, normalization='length')

        def power_in_band(power, freq, band):
            power =  np.trapz(y=power[(freq >= band[0]) & (freq < band[1])], x=freq[(freq >= band[0]) & (freq < band[1])])
            return(power)
github PGomes92 / pyhrv / pyhrv / hrv.py View on Github external
in the successive segment N+1. In this case, use the 'overlap' parameter to select if the first element of the
		segment should be dropped or not:
		..	If True: overlap allowed, returns all NNI but the cumulative sum of the NNI in a segment can be greater
			than the specified duration.
		..	If False: no overlap allowed, first NNI will be dropped and the cumulative sum of the NNI in a segment
			will always be < specified duration.

	Raises
	------
	TypeError
		If no input data for 'signal', 'nn' and 'rpeaks' provided.

	"""
	# Check input
	if signal is not None:
		signal, rpeaks = biosppy.signals.ecg.ecg(signal=signal, sampling_rate=sampling_rate, show=False)[1:3]
	elif nni is None and rpeaks is None:
		raise TypeError('No input data provided. Please specify input data.')

	nn = tools.check_input(nni, rpeaks)

	version = utils.ReturnTuple(('v.' + pyhrv.__version__, ), ('version', ))

	# COMPUTE TIME DOMAIN PARAMETERS
	# Check for kwargs for the 'kwargs_time'
	if kwargs_time is not None:
		if type(kwargs_time) is not dict:
			raise TypeError("Expected , got %s: 'kwargs_time' must be a dictionary containing "
							"parameters (keys) and values for the 'time_domain()' function." % type(kwargs_time))

		# Supported kwargs
		available_kwargs = ['threshold', 'binsize', 'plot']
github neuropsychology / NeuroKit.py / neurokit / bio / bio_rsp.py View on Github external
- Dominique Makowski (https://github.com/DominiqueMakowski)

    *Dependencies*

    - biosppy
    - numpy
    - pandas

    *See Also*

    - BioSPPY: https://github.com/PIA-Group/BioSPPy
    """
    processed_rsp = {"df": pd.DataFrame({"RSP_Raw": np.array(rsp)})}

    biosppy_rsp = dict(biosppy.signals.resp.resp(rsp, sampling_rate=sampling_rate, show=False))
    processed_rsp["df"]["RSP_Filtered"] = biosppy_rsp["filtered"]


#   RSP Rate
#   ============
    rsp_rate = biosppy_rsp["resp_rate"]*60  # Get RSP rate value (in cycles per minute)
    rsp_times = biosppy_rsp["resp_rate_ts"]   # the time (in sec) of each rsp rate value
    rsp_times = np.round(rsp_times*sampling_rate).astype(int)  # Convert to timepoints
    try:
        rsp_rate = interpolate(rsp_rate, rsp_times, sampling_rate)  # Interpolation using 3rd order spline
        processed_rsp["df"]["RSP_Rate"] = rsp_rate
    except TypeError:
        print("NeuroKit Warning: rsp_process(): Sequence too short to compute respiratory rate.")
        processed_rsp["df"]["RSP_Rate"] = np.nan

github neuropsychology / NeuroKit.py / neurokit / bio / bio_ecg.py View on Github external
freq_bands = {
          "ULF": [0.0001, 0.0033],
          "VLF": [0.0033, 0.04],
          "LF": [0.04, 0.15],
          "HF": [0.15, 0.40],
          "VHF": [0.4, 0.5]}


        # Frequency-Domain Power over time
        freq_powers = {}
        for band in freq_bands:
            freqs = freq_bands[band]
            # Filter to keep only the band of interest
            filtered, sampling_rate, params = biosppy.signals.tools.filter_signal(signal=RRi, ftype='butter', band='bandpass', order=1, frequency=freqs, sampling_rate=sampling_rate)
            # Apply Hilbert transform
            amplitude, phase = biosppy.signals.tools.analytic_signal(filtered)
            # Extract Amplitude of Envelope (power)
            freq_powers["ECG_HRV_" + band] = amplitude

        freq_powers = pd.DataFrame.from_dict(freq_powers)
        freq_powers.index = hrv["df"].index
        hrv["df"] = pd.concat([hrv["df"], freq_powers], axis=1)


        # Compute Power Spectral Density (PSD) using multitaper method
        power, freq = mne.time_frequency.psd_array_multitaper(RRi, sfreq=sampling_rate, fmin=0, fmax=0.5,  adaptive=False, normalization='length')

        def power_in_band(power, freq, band):
            power =  np.trapz(y=power[(freq >= band[0]) & (freq < band[1])], x=freq[(freq >= band[0]) & (freq < band[1])])
            return(power)

        # Extract Power according to frequency bands
github neuropsychology / NeuroKit.py / neurokit / bio / bio_eda.py View on Github external
- Greco et al. (2015): http://ieeexplore.ieee.org/abstract/document/7229284/?reload=true

    """

    eda_df = pd.DataFrame({"EDA_Raw": np.array(eda)})

    # Convex optimization
    if use_cvxEDA is True:
        try:
            eda = cvxeda(eda, sampling_rate=sampling_rate)
            eda_df["EDA_Phasic"] = eda
        except:
            print("NeuroKit Warning: couln't apply cvxEDA on EDA signal. Using normal.")

    # Compute several features using biosppy
    biosppy_eda = dict(biosppy.signals.eda.eda(eda, sampling_rate=sampling_rate, show=False))

    eda_df["EDA_Filtered"] = biosppy_eda["filtered"]

    # Store SCR onsets
    scr_onsets = np.array([np.nan]*len(eda))
    scr_onsets[biosppy_eda['onsets']] = 1
    eda_df["SCR_Onsets"] = scr_onsets

    # Store SCR peaks and amplitudes
    scr_peaks = np.array([np.nan]*len(eda))
    peak_index = 0
    for index in range(len(scr_peaks)):
        try:
            if index == biosppy_eda["peaks"][peak_index]:
                scr_peaks[index] = biosppy_eda['amplitudes'][peak_index]
                peak_index += 1
github PGomes92 / pyhrv / pyhrv / tools.py View on Github external
ax.yaxis.grid(which='minor', color='salmon', lw=0.3)
	ax.set_yticks(y_major)
	ax.yaxis.grid(which='major', color='r', lw=0.7)

	# Add legend
	unit = '' if unit == '-' else unit
	text_ = 'Division (x): %is\nDivision (y): %.1f%s' % (n, (np.abs(y_major[1] - y_major[0])), unit)
	ax.text(0.88, 0.85, text_, transform=ax.transAxes, fontsize=9,
		bbox=dict(boxstyle='round', facecolor='white', alpha=0.9))

	# Plot ECG signal
	ax.plot(t, signal, 'r')
	fig_ecg.tight_layout()

	# Plot r-peaks
	rps = biosppy.signals.ecg.ecg(signal=signal, sampling_rate=sampling_rate, show=False)[2]
	p = [float(signal[x]) for x in rps]
	r = t[rps]
	if rpeaks:
		ax.plot(r, p, 'g*', alpha=0.7)

	# Add title
	if title is not None:
		ax.set_title('ECG Signal - %s' % str(title))
	else:
		ax.set_title('ECG Signal')

	# Show plot
	if show:
		plt.show()

	# Output