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tests_hrv.py
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tests_hrv.py
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import numpy as np
import pandas as pd
import pytest
import neurokit2 as nk
from neurokit2 import misc
def test_hrv_time():
ecg_slow = nk.ecg_simulate(duration=60, sampling_rate=1000, heart_rate=60, random_state=42)
ecg_fast = nk.ecg_simulate(duration=60, sampling_rate=1000, heart_rate=150, random_state=42)
_, peaks_slow = nk.ecg_process(ecg_slow, sampling_rate=1000)
_, peaks_fast = nk.ecg_process(ecg_fast, sampling_rate=1000)
hrv_slow = nk.hrv_time(peaks_slow, sampling_rate=1000)
hrv_fast = nk.hrv_time(peaks_fast, sampling_rate=1000)
assert np.all(hrv_fast["HRV_RMSSD"] < hrv_slow["HRV_RMSSD"])
assert np.all(hrv_fast["HRV_MeanNN"] < hrv_slow["HRV_MeanNN"])
assert np.all(hrv_fast["HRV_SDNN"] < hrv_slow["HRV_SDNN"])
assert np.all(hrv_fast["HRV_CVNN"] < hrv_slow["HRV_CVNN"])
assert np.all(hrv_fast["HRV_CVSD"] < hrv_slow["HRV_CVSD"])
assert np.all(hrv_fast["HRV_MedianNN"] < hrv_slow["HRV_MedianNN"])
assert np.all(hrv_fast["HRV_MadNN"] < hrv_slow["HRV_MadNN"])
assert np.all(hrv_fast["HRV_MCVNN"] < hrv_slow["HRV_MCVNN"])
assert np.all(hrv_fast["HRV_pNN50"] == hrv_slow["HRV_pNN50"])
assert np.all(hrv_fast["HRV_pNN20"] < hrv_slow["HRV_pNN20"])
assert np.all(hrv_fast["HRV_TINN"] < hrv_slow["HRV_TINN"])
assert np.all(hrv_fast["HRV_HTI"] != hrv_slow["HRV_HTI"])
def test_hrv_frequency():
# Test frequency domain
ecg1 = nk.ecg_simulate(duration=60, sampling_rate=2000, heart_rate=70, random_state=42)
_, peaks1 = nk.ecg_process(ecg1, sampling_rate=2000)
hrv1 = nk.hrv_frequency(peaks1, sampling_rate=2000)
ecg2 = nk.signal_resample(ecg1, sampling_rate=2000, desired_sampling_rate=500)
_, peaks2 = nk.ecg_process(ecg2, sampling_rate=500)
hrv2 = nk.hrv_frequency(peaks2, sampling_rate=500)
assert np.allclose(hrv1["HRV_HF"] - hrv2["HRV_HF"], 0, atol=1.5)
assert np.isnan(hrv1["HRV_ULF"][0])
assert np.isnan(hrv1["HRV_VLF"][0])
assert np.isnan(hrv2["HRV_ULF"][0])
assert np.isnan(hrv2["HRV_VLF"][0])
def test_hrv():
ecg = nk.ecg_simulate(duration=120, sampling_rate=1000, heart_rate=110, random_state=42)
_, peaks = nk.ecg_process(ecg, sampling_rate=1000)
ecg_hrv = nk.hrv(peaks, sampling_rate=1000)
assert np.isclose(ecg_hrv["HRV_RMSSD"].values[0], 3.526, atol=0.1)
def test_rri_input_hrv():
ecg = nk.ecg_simulate(duration=120, sampling_rate=1000, heart_rate=110, random_state=42)
_, peaks = nk.ecg_process(ecg, sampling_rate=1000)
peaks = peaks["ECG_R_Peaks"]
rri = np.diff(peaks).astype(float)
rri_time = peaks[1:] / 1000
rri[3:5] = [np.nan, np.nan]
ecg_hrv = nk.hrv({"RRI": rri, "RRI_Time": rri_time})
assert np.isclose(ecg_hrv["HRV_RMSSD"].values[0], 3.526, atol=0.2)
@pytest.mark.parametrize("detrend", ["polynomial", "loess"])
def test_hrv_detrended_rri(detrend):
ecg = nk.ecg_simulate(duration=120, sampling_rate=1000, heart_rate=110, random_state=42)
_, peaks = nk.ecg_process(ecg, sampling_rate=1000)
peaks = peaks["ECG_R_Peaks"]
rri = np.diff(peaks).astype(float)
rri_time = peaks[1:] / 1000
rri_processed, rri_processed_time, _ = nk.intervals_process(
rri, intervals_time=rri_time, interpolate=False, interpolation_rate=None, detrend=detrend
)
ecg_hrv = nk.hrv({"RRI": rri_processed, "RRI_Time": rri_processed_time})
assert np.isclose(
ecg_hrv["HRV_RMSSD"].values[0],
np.sqrt(np.mean(np.square(np.diff(rri_processed)))),
atol=0.1,
)
@pytest.mark.parametrize("interpolation_rate", ["from_mean_rri", 1, 4, 100])
def test_hrv_interpolated_rri(interpolation_rate):
ecg = nk.ecg_simulate(duration=120, sampling_rate=1000, heart_rate=110, random_state=42)
_, peaks = nk.ecg_process(ecg, sampling_rate=1000)
peaks = peaks["ECG_R_Peaks"]
rri = np.diff(peaks).astype(float)
rri_time = peaks[1:] / 1000
if interpolation_rate == "from_mean_rri":
interpolation_rate = 1000 / np.mean(rri)
rri_processed, rri_processed_time, _ = nk.intervals_process(
rri, intervals_time=rri_time, interpolate=True, interpolation_rate=interpolation_rate
)
ecg_hrv = nk.hrv({"RRI": rri_processed, "RRI_Time": rri_processed_time})
assert np.isclose(
ecg_hrv["HRV_RMSSD"].values[0],
np.sqrt(np.mean(np.square(np.diff(rri_processed)))),
atol=0.1,
)
def test_hrv_missing():
random_state = 42
rng = misc.check_random_state(random_state)
# Download data
data = nk.data("bio_resting_5min_100hz")
sampling_rate = 100
ecg = data["ECG"]
_, peaks = nk.ecg_process(ecg, sampling_rate=sampling_rate)
peaks = peaks["ECG_R_Peaks"]
rri = np.diff(peaks / sampling_rate).astype(float) * 1000
rri_time = peaks[1:] / sampling_rate
# remove some intervals and their corresponding timestamps
missing = rng.choice(len(rri), size=int(len(rri) / 5))
rri_missing = rri[np.array([i for i in range(len(rri)) if i not in missing])]
rri_time_missing = rri_time[np.array([i for i in range(len(rri_time)) if i not in missing])]
orig_hrv = nk.hrv_time(peaks, sampling_rate=sampling_rate)
miss_only_rri_hrv = nk.hrv_time({"RRI": rri_missing})
# by providing the timestamps corresponding to each interval
# we should be able to better estimate the original RMSSD
# before some intervals were removed
# (at least for this example signal)
miss_rri_time_hrv = nk.hrv_time({"RRI": rri_missing, "RRI_Time": rri_time_missing})
abs_diff_only_rri = np.mean(
np.abs(np.diff([orig_hrv["HRV_RMSSD"].values[0], miss_only_rri_hrv["HRV_RMSSD"].values[0]]))
)
abs_diff_rri_time = np.mean(
np.abs(np.diff([orig_hrv["HRV_RMSSD"].values[0], miss_rri_time_hrv["HRV_RMSSD"].values[0]]))
)
assert abs_diff_only_rri > abs_diff_rri_time
def test_hrv_rsa():
data = nk.data("bio_eventrelated_100hz")
ecg_signals, info = nk.ecg_process(data["ECG"], sampling_rate=100)
rsp_signals, _ = nk.rsp_process(data["RSP"], sampling_rate=100)
rsa_feature_columns = [
"RSA_P2T_Mean",
"RSA_P2T_Mean_log",
"RSA_P2T_SD",
"RSA_P2T_NoRSA",
"RSA_PorgesBohrer",
"RSA_Gates_Mean",
"RSA_Gates_Mean_log",
"RSA_Gates_SD",
]
rsa_features = nk.hrv_rsa(
ecg_signals, rsp_signals, rpeaks=info, sampling_rate=100, continuous=False
)
assert all(key in rsa_feature_columns for key in rsa_features.keys())
# Test simulate RSP signal warning
with pytest.warns(misc.NeuroKitWarning, match=r"RSP signal not found. For this.*"):
nk.hrv_rsa(ecg_signals, rpeaks=info, sampling_rate=100, continuous=False)
with pytest.warns(misc.NeuroKitWarning, match=r"RSP signal not found. For this time.*"):
nk.hrv_rsa(ecg_signals, pd.DataFrame(), rpeaks=info, sampling_rate=100, continuous=False)
# Test missing rsp onsets/centers
with pytest.warns(misc.NeuroKitWarning, match=r"Couldn't find rsp cycles onsets and centers.*"):
rsp_signals["RSP_Peaks"] = 0
_ = nk.hrv_rsa(ecg_signals, rsp_signals, rpeaks=info, sampling_rate=100, continuous=False)
def test_hrv_nonlinear_fragmentation():
# https://github.com/neuropsychology/NeuroKit/issues/344
from neurokit2.hrv.hrv_nonlinear import _hrv_nonlinear_fragmentation
edge_rri = np.array([888.0, 1262.0, 1290.0, 1274.0, 1300.0, 1244.0, 1266.0])
test_out = {}
_hrv_nonlinear_fragmentation(edge_rri, out=test_out)
assert test_out == {
"IALS": 0.8333333333333334,
"PAS": 1.0,
"PIP": 0.5714285714285714,
"PSS": 1.0,
}