# -*- coding: utf-8 -*-
from warnings import warn
import numpy as np
import pandas as pd
import scipy
from ..misc import NeuroKitWarning
from ..signal import signal_filter, signal_resample, signal_timefrequency
from ..signal.signal_power import _signal_power_instant_compute
from ..signal.signal_psd import _signal_psd_welch
from ..stats import standardize
[docs]
def eda_sympathetic(
eda_signal, sampling_rate=1000, frequency_band=[0.045, 0.25], method="posada", show=False
):
"""**Sympathetic Nervous System Index from Electrodermal activity (EDA)**
Derived from Posada-Quintero et al. (2016), who argue that dynamics of the sympathetic component
of EDA signal is represented in the frequency band of 0.045-0.25Hz. Note that the Posada method
requires a signal of a least 64 seconds.
Parameters
----------
eda_signal : Union[list, np.array, pd.Series]
The EDA signal (i.e., a time series) in the form of a vector of values.
sampling_rate : int
The sampling frequency of the signal (in Hz, i.e., samples/second).
frequency_band : list
List indicating the frequency range to compute the the power spectral density in.
Defaults to [0.045, 0.25].
method : str
Can be one of ``"ghiasi"`` or ``"posada"``.
show : bool
If True, will return a plot of the power spectrum of the EDA signal within the specified
frequency band.
See Also
--------
.signal_filter, .signal_power, .signal_psd
Returns
-------
dict
A dictionary containing the EDA sympathetic indexes, accessible by keys
``"EDA_Sympathetic"`` and ``"EDA_SympatheticN"`` (normalized, obtained by dividing EDA_Symp
by total power).
.. codebookadd::
EDA_Sympathetic|Derived from Posada-Quintero et al. (2016), who argue that dynamics of \
the sympathetic component of EDA signal is represented in the frequency band of 0.045-0.25Hz.
EDA_SympatheticN|normalized version of "EDA_Sympathetic" obtained by dividing \
EDA_Sympathetic by total power
Examples
--------
.. ipython:: python
import neurokit2 as nk
eda = nk.data('bio_resting_8min_100hz')['EDA']
@savefig p_eda_sympathetic1.png scale=100%
nk.eda_sympathetic(eda, sampling_rate=100, method='posada', show=True)
@suppress
plt.close()
results = nk.eda_sympathetic(eda, sampling_rate=100, method='ghiasi')
results
References
----------
* Ghiasi, S., Grecol, A., Nardelli, M., Catrambonel, V., Barbieri, R., Scilingo, E., & Valenza,
G. (2018). A New Sympathovagal Balance Index from Electrodermal Activity and Instantaneous
Vagal Dynamics: A Preliminary Cold Pressor Study. 2018 40th Annual International Conference
of the IEEE Engineering in Medicine and Biology Society (EMBC). doi:10.1109/embc.2018.8512932
* Posada-Quintero, H. F., Florian, J. P., Orjuela-Cañón, A. D., Aljama-Corrales, T.,
Charleston-Villalobos, S., & Chon, K. H. (2016). Power spectral density analysis of
electrodermal activity for sympathetic function assessment. Annals of biomedical engineering,
44(10), 3124-3135.
"""
out = {}
if method.lower() in ["ghiasi", "ghiasi2018"]:
out = _eda_sympathetic_ghiasi(
eda_signal, sampling_rate=sampling_rate, frequency_band=frequency_band, show=show
)
elif method.lower() in ["posada", "posada-quintero", "quintero", "posada2016"]:
out = _eda_sympathetic_posada(
eda_signal, sampling_rate=sampling_rate, frequency_band=frequency_band, show=show
)
else:
raise ValueError(
"NeuroKit error: eda_sympathetic(): 'method' should be " "one of 'ghiasi', 'posada'."
)
return out
# =============================================================================
# Methods
# =============================================================================
def _eda_sympathetic_posada(
eda_signal, frequency_band=[0.045, 0.25], sampling_rate=1000, show=True, out={}
):
# This method assumes signal longer than 64 s
if len(eda_signal) <= sampling_rate * 64:
warn(
"The 'posada2016' method requires a signal of length > 60 s. Try with"
+ " `method='ghiasi2018'`. Returning NaN values for now.",
category=NeuroKitWarning,
)
return {"EDA_Sympathetic": np.nan, "EDA_SympatheticN": np.nan}
# Resample the eda signal before calculate the synpathetic index based on Posada (2016)
eda_signal_400hz = signal_resample(
eda_signal, sampling_rate=sampling_rate, desired_sampling_rate=400
)
# 8-th order Chebyshev Type I low-pass filter
sos = scipy.signal.cheby1(8, 1, 0.8, "lowpass", fs=400, output="sos")
eda_signal_filtered = scipy.signal.sosfilt(sos, eda_signal_400hz)
# First step of downsampling
downsampled_1 = scipy.signal.decimate(eda_signal_filtered, q=10, n=8) # Keep every 10th sample
downsampled_2 = scipy.signal.decimate(downsampled_1, q=20, n=8) # Keep every 20th sample
# High pass filter
eda_filtered = signal_filter(
downsampled_2, sampling_rate=2, lowcut=0.01, highcut=None, method="butterworth", order=8
)
nperseg = 128
overlap = nperseg // 2 # 50 % data overlap
# Compute psd
frequency, power = _signal_psd_welch(
eda_filtered, sampling_rate=2, nperseg=nperseg, window_type="blackman", noverlap=overlap
)
psd = pd.DataFrame({"Frequency": frequency, "Power": power})
# Get sympathetic nervous system indexes
eda_symp = _signal_power_instant_compute(psd, (frequency_band[0], frequency_band[1]))
# Compute normalized psd
psd["Power"] /= np.max(psd["Power"])
eda_symp_normalized = _signal_power_instant_compute(psd, (frequency_band[0], frequency_band[1]))
psd_plot = psd.loc[
np.logical_and(psd["Frequency"] >= frequency_band[0], psd["Frequency"] <= frequency_band[1])
]
if show is True:
ax = psd_plot.plot(x="Frequency", y="Power", title="EDA Power Spectral Density (us^2/Hz)")
ax.set(xlabel="Frequency (Hz)", ylabel="Spectrum")
out = {"EDA_Sympathetic": eda_symp, "EDA_SympatheticN": eda_symp_normalized}
return out
def _eda_sympathetic_ghiasi(
eda_signal, sampling_rate=1000, frequency_band=[0.045, 0.25], show=True, out={}
):
min_frequency = frequency_band[0]
max_frequency = frequency_band[1]
# Downsample, normalize, filter
desired_sampling_rate = 50
downsampled = signal_resample(
eda_signal, sampling_rate=sampling_rate, desired_sampling_rate=desired_sampling_rate
)
normalized = standardize(downsampled)
filtered = signal_filter(
normalized,
sampling_rate=desired_sampling_rate,
lowcut=0.01,
highcut=0.5,
method="butterworth",
)
# Divide the signal into segments and obtain the timefrequency representation
overlap = 59 * 50 # overlap of 59s in samples
# TODO: the plot should be improved for this specific case
_, _, bins = signal_timefrequency(
filtered,
sampling_rate=desired_sampling_rate,
min_frequency=min_frequency,
max_frequency=max_frequency,
method="stft",
window=60,
window_type="blackman",
overlap=overlap,
show=show,
)
eda_symp = np.mean(bins)
eda_symp_normalized = eda_symp / np.max(bins)
out = {"EDA_Sympathetic": eda_symp, "EDA_SympatheticN": eda_symp_normalized}
return out
