def test_ecg_fixpeaks():
sampling_rate = 1000
noise = 0.15
ecg = nk.ecg_simulate(duration=120, sampling_rate=sampling_rate,
noise=noise, method="simple", random_state=42)
rpeaks = nk.ecg_findpeaks(ecg)
# Test with iterative artifact correction.
artifacts, rpeaks_corrected = nk.ecg_fixpeaks(rpeaks, iterative=True)
assert np.allclose(rpeaks_corrected["ECG_R_Peaks"].sum(dtype=np.int64),
7383418, atol=1)
assert all(isinstance(x, int) for x in artifacts["ectopic"])
assert all(isinstance(x, int) for x in artifacts["missed"])
assert all(isinstance(x, int) for x in artifacts["extra"])
assert all(isinstance(x, int) for x in artifacts["longshort"])
# Test with non-iterative artifact correction.
artifacts, rpeaks_corrected = nk.ecg_fixpeaks(rpeaks, iterative=False)
assert np.allclose(rpeaks_corrected["ECG_R_Peaks"].sum(dtype=np.int64),
7383418, atol=1)
assert all(isinstance(x, int) for x in artifacts["ectopic"])
assert all(isinstance(x, int) for x in artifacts["missed"])
assert all(isinstance(x, int) for x in artifacts["extra"])
assert all(isinstance(x, int) for x in artifacts["longshort"])
def test_hrv():
ecg = nk.ecg_simulate(duration=60,
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)
columns = [
'HRV_RMSSD', 'HRV_MeanNN', 'HRV_SDNN', 'HRV_SDSD', 'HRV_CVNN',
'HRV_CVSD', 'HRV_MedianNN', 'HRV_MadNN', 'HRV_MCVNN', 'HRV_IQRNN',
'HRV_pNN50', 'HRV_pNN20', 'HRV_TINN', 'HRV_HTI', 'HRV_ULF', 'HRV_VLF',
'HRV_LF', 'HRV_HF', 'HRV_VHF', 'HRV_LFHF', 'HRV_LFn', 'HRV_HFn',
'HRV_LnHF', 'HRV_SD1', 'HRV_SD2', 'HRV_SD1SD2', 'HRV_S', 'HRV_CSI',
'HRV_CVI', 'HRV_CSI_Modified', 'HRV_PIP', 'HRV_IALS', 'HRV_PSS',
'HRV_PAS', 'HRV_GI', 'HRV_SI', 'HRV_AI', 'HRV_PI', 'HRV_C1d',
'HRV_C1a', 'HRV_SD1d', 'HRV_SD1a', 'HRV_C2d', 'HRV_C2a', 'HRV_SD2d',
'HRV_SD2a', 'HRV_Cd', 'HRV_Ca', 'HRV_SDNNd', 'HRV_SDNNa', 'HRV_ApEn',
'HRV_SampEn'
]
assert all(elem in np.array(ecg_hrv.columns.values, dtype=object)
for elem in columns)
def test_ecg_delineate():
sampling_rate = 1000
# test with simulated signals
ecg = nk.ecg_simulate(duration=20, sampling_rate=sampling_rate, random_state=42)
_, rpeaks = nk.ecg_peaks(ecg, sampling_rate=sampling_rate)
number_rpeaks = len(rpeaks["ECG_R_Peaks"])
# Method 1: derivative
_, waves_derivative = nk.ecg_delineate(ecg, rpeaks, sampling_rate=sampling_rate)
assert len(waves_derivative["ECG_P_Peaks"]) == number_rpeaks
assert len(waves_derivative["ECG_Q_Peaks"]) == number_rpeaks
assert len(waves_derivative["ECG_S_Peaks"]) == number_rpeaks
assert len(waves_derivative["ECG_T_Peaks"]) == number_rpeaks
assert len(waves_derivative["ECG_P_Onsets"]) == number_rpeaks
assert len(waves_derivative["ECG_T_Offsets"]) == number_rpeaks
# Method 2: CWT
_, waves_cwt = nk.ecg_delineate(ecg, rpeaks, sampling_rate=sampling_rate, method="cwt")
assert np.allclose(len(waves_cwt["ECG_P_Peaks"]), 22, atol=1)
assert np.allclose(len(waves_cwt["ECG_T_Peaks"]), 22, atol=1)
assert np.allclose(len(waves_cwt["ECG_R_Onsets"]), 23, atol=1)
assert np.allclose(len(waves_cwt["ECG_R_Offsets"]), 23, atol=1)
assert np.allclose(len(waves_cwt["ECG_P_Onsets"]), 22, atol=1)
assert np.allclose(len(waves_cwt["ECG_P_Offsets"]), 22, atol=1)
assert np.allclose(len(waves_cwt["ECG_T_Onsets"]), 22, atol=1)
assert np.allclose(len(waves_cwt["ECG_T_Offsets"]), 22, atol=1)
def test_ecg_clean():
sampling_rate = 1000
noise = 0.05
ecg = nk.ecg_simulate(sampling_rate=sampling_rate, noise=noise)
ecg_cleaned_nk = nk.ecg_clean(ecg, sampling_rate=sampling_rate, method="neurokit")
assert ecg.size == ecg_cleaned_nk.size
# Assert that highpass filter with .5 Hz lowcut was applied.
fft_raw = np.abs(np.fft.rfft(ecg))
fft_nk = np.abs(np.fft.rfft(ecg_cleaned_nk))
freqs = np.fft.rfftfreq(ecg.size, 1 / sampling_rate)
assert np.sum(fft_raw[freqs < 0.5]) > np.sum(fft_nk[freqs < 0.5])
# Comparison to biosppy (https://github.com/PIA-Group/BioSPPy/blob/e65da30f6379852ecb98f8e2e0c9b4b5175416c3/biosppy/signals/ecg.py#L69)
ecg_biosppy = nk.ecg_clean(ecg, sampling_rate=sampling_rate, method="biosppy")
original, _, _ = biosppy.tools.filter_signal(
signal=ecg,
ftype="FIR",
band="bandpass",
order=int(0.3 * sampling_rate),
frequency=[3, 45],
sampling_rate=sampling_rate,
)
assert np.allclose((ecg_biosppy - original).mean(), 0, atol=1e-6)
def test_ecg_rate():
sampling_rate = 1000
noise = 0.15
ecg = nk.ecg_simulate(duration=120,
sampling_rate=sampling_rate,
noise=noise,
random_state=42)
ecg_cleaned_nk = nk.ecg_clean(ecg,
sampling_rate=sampling_rate,
method="neurokit")
signals, info = nk.ecg_peaks(ecg_cleaned_nk, method="neurokit")
# Test without desired length.
rate = nk.ecg_rate(rpeaks=info, sampling_rate=sampling_rate)
assert rate.shape == (info["ECG_R_Peaks"].size, )
assert np.allclose(rate.mean(), 70, atol=2)
# Test with desired length.
test_length = 1200
rate = nk.ecg_rate(rpeaks=info,
sampling_rate=sampling_rate,
desired_length=test_length)
assert rate.shape == (test_length, )
assert np.allclose(rate.mean(), 70, atol=2)
def test_bio_process():
sampling_rate = 1000
# Create data
ecg = nk.ecg_simulate(duration=30, sampling_rate=sampling_rate)
rsp = nk.rsp_simulate(duration=30, sampling_rate=sampling_rate)
eda = nk.eda_simulate(duration=30, sampling_rate=sampling_rate, scr_number=3)
emg = nk.emg_simulate(duration=30, sampling_rate=sampling_rate, burst_number=3)
bio_df, bio_info = nk.bio_process(ecg=ecg,
rsp=rsp,
eda=eda,
emg=emg,
sampling_rate=sampling_rate)
# SCR components
scr = [val for key, val in bio_info.items() if "SCR" in key]
assert all(len(elem) == len(scr[0]) for elem in scr)
assert all(bio_info["SCR_Onsets"] < bio_info["SCR_Peaks"])
assert all(bio_info["SCR_Peaks"] < bio_info["SCR_Recovery"])
# RSP
assert all(bio_info["RSP_Peaks"] > bio_info["RSP_Troughs"])
assert len(bio_info["RSP_Peaks"]) == len(bio_info["RSP_Troughs"])
# EMG
assert all(bio_info["EMG_Offsets"] > bio_info["EMG_Onsets"])
assert len(bio_info["EMG_Offsets"] == len(bio_info["EMG_Onsets"]))
def test_ecg_peaks():
sampling_rate = 1000
noise = 0.15
ecg = nk.ecg_simulate(duration=120,
sampling_rate=sampling_rate,
noise=noise,
random_state=42)
ecg_cleaned_nk = nk.ecg_clean(ecg,
sampling_rate=sampling_rate,
method="neurokit")
# Test without request to correct artifacts.
signals, info = nk.ecg_peaks(ecg_cleaned_nk,
correct_artifacts=False,
method="neurokit")
assert signals.shape == (120000, 1)
assert np.allclose(signals["ECG_R_Peaks"].values.sum(dtype=np.int64),
139,
atol=1)
# Test with request to correct artifacts.
signals, info = nk.ecg_peaks(ecg_cleaned_nk,
correct_artifacts=True,
method="neurokit")
assert signals.shape == (120000, 1)
assert np.allclose(signals["ECG_R_Peaks"].values.sum(dtype=np.int64),
139,
atol=1)
def test_ecg_eventrelated():
ecg, info = nk.ecg_process(nk.ecg_simulate(duration=20))
epochs = nk.epochs_create(ecg,
events=[5000, 10000, 15000],
epochs_start=-0.1,
epochs_end=1.9)
ecg_eventrelated = nk.ecg_eventrelated(epochs)
# Test rate features
assert np.alltrue(
np.array(ecg_eventrelated["ECG_Rate_Min"]) < np.array(
ecg_eventrelated["ECG_Rate_Mean"]))
assert np.alltrue(
np.array(ecg_eventrelated["ECG_Rate_Mean"]) < np.array(
ecg_eventrelated["ECG_Rate_Max"]))
assert len(ecg_eventrelated["Label"]) == 3
assert len(ecg_eventrelated.columns) == 15
assert all(elem in [
"ECG_Rate_Max", "ECG_Rate_Min", "ECG_Rate_Mean", "ECG_Rate_Max_Time",
"ECG_Rate_Min_Time", "ECG_Rate_Trend_Quadratic",
"ECG_Rate_Trend_Linear", "ECG_Rate_Trend_R2", "ECG_Phase_Atrial",
"ECG_Phase_Atrial_Completion", "ECG_Phase_Ventricular",
"ECG_Phase_Ventricular_Completion", 'ECG_Quality_Mean', "Event_Onset",
"Label"
] for elem in np.array(ecg_eventrelated.columns.values, dtype=str))
def test_ecg_plot():
ecg = nk.ecg_simulate(duration=60, heart_rate=70, noise=0.05)
ecg_summary, _ = nk.ecg_process(ecg, sampling_rate=1000, method="neurokit")
# Plot data over samples.
nk.ecg_plot(ecg_summary)
# This will identify the latest figure.
fig = plt.gcf()
assert len(fig.axes) == 2
titles = ["Raw and Cleaned Signal", "Heart Rate"]
for (ax, title) in zip(fig.get_axes(), titles):
assert ax.get_title() == title
assert fig.get_axes()[1].get_xlabel() == "Samples"
np.testing.assert_array_equal(fig.axes[0].get_xticks(), fig.axes[1].get_xticks())
plt.close(fig)
# Plot data over seconds.
nk.ecg_plot(ecg_summary, sampling_rate=1000)
# This will identify the latest figure.
fig = plt.gcf()
assert len(fig.axes) == 3
titles = ["Raw and Cleaned Signal", "Heart Rate", "Individual Heart Beats"]
for (ax, title) in zip(fig.get_axes(), titles):
assert ax.get_title() == title
assert fig.get_axes()[1].get_xlabel() == "Time (seconds)"
np.testing.assert_array_equal(fig.axes[0].get_xticks(), fig.axes[1].get_xticks())
plt.close(fig)
def test_ecg_process():
sampling_rate = 1000
noise = 0.05
ecg = nk.ecg_simulate(sampling_rate=sampling_rate, noise=noise)
signals, info = nk.ecg_process(ecg, sampling_rate=sampling_rate, method="neurokit")
def test_ecg_simulate():
ecg1 = nk.ecg_simulate(duration=20, length=5000, method="simple", noise=0)
assert len(ecg1) == 5000
ecg2 = nk.ecg_simulate(duration=20, length=5000, heart_rate=500)
# pd.DataFrame({"ECG1":ecg1, "ECG2": ecg2}).plot()
# pd.DataFrame({"ECG1":ecg1, "ECG2": ecg2}).hist()
assert len(nk.signal_findpeaks(ecg1, height_min=0.6)["Peaks"]) < len(
nk.signal_findpeaks(ecg2, height_min=0.6)["Peaks"]
)
ecg3 = nk.ecg_simulate(duration=10, length=5000)
# pd.DataFrame({"ECG1":ecg1, "ECG3": ecg3}).plot()
assert len(nk.signal_findpeaks(ecg2, height_min=0.6)["Peaks"]) > len(
nk.signal_findpeaks(ecg3, height_min=0.6)["Peaks"]
)
def load_signal_from_disk(filename=None, sampling_rate=2000):
if filename is None:
ecg = nk.ecg_simulate(
duration=10, sampling_rate=sampling_rate, method="ecgsyn")
else:
filename = (pathlib.Path(__file__) / '../ecg_data' / filename).resolve().as_posix()
ecg = np.array(pd.read_csv(filename))[:, 1]
return ecg, sampling_rate
def test_eeg_add_channel():
raw = mne.io.read_raw_fif(mne.datasets.sample.data_path() +
'/MEG/sample/sample_audvis_raw.fif',
preload=True)
ecg = nk.ecg_simulate(length=170000)
raw = nk.eeg_add_channel(raw, ecg, channel_type="ecg")
df = raw.to_data_frame()
assert len(df.columns) == 377
def test_ecg_eventrelated():
ecg, info = nk.ecg_process(nk.ecg_simulate(duration=20))
epochs = nk.epochs_create(ecg,
events=[5000, 10000, 15000],
epochs_start=-0.1,
epochs_end=1.9)
ecg_eventrelated = nk.ecg_eventrelated(epochs)
# Test rate features
assert np.alltrue(
np.array(ecg_eventrelated["ECG_Rate_Min"]) < np.array(
ecg_eventrelated["ECG_Rate_Mean"]))
assert np.alltrue(
np.array(ecg_eventrelated["ECG_Rate_Mean"]) < np.array(
ecg_eventrelated["ECG_Rate_Max"]))
assert len(ecg_eventrelated["Label"]) == 3
# Test warning on missing columns
with pytest.warns(nk.misc.NeuroKitWarning,
match=r".*does not have an `ECG_Phase_Artrial`.*"):
first_epoch_key = list(epochs.keys())[0]
first_epoch_copy = epochs[first_epoch_key].copy()
del first_epoch_copy["ECG_Phase_Atrial"]
nk.ecg_eventrelated({**epochs, first_epoch_key: first_epoch_copy})
with pytest.warns(nk.misc.NeuroKitWarning,
match=r".*does not have an.*`ECG_Phase_Ventricular`"):
first_epoch_key = list(epochs.keys())[0]
first_epoch_copy = epochs[first_epoch_key].copy()
del first_epoch_copy["ECG_Phase_Ventricular"]
nk.ecg_eventrelated({**epochs, first_epoch_key: first_epoch_copy})
with pytest.warns(nk.misc.NeuroKitWarning,
match=r".*does not have an `ECG_Quality`.*"):
first_epoch_key = list(epochs.keys())[0]
first_epoch_copy = epochs[first_epoch_key].copy()
del first_epoch_copy["ECG_Quality"]
nk.ecg_eventrelated({**epochs, first_epoch_key: first_epoch_copy})
with pytest.warns(nk.misc.NeuroKitWarning,
match=r".*does not have an `ECG_Rate`.*"):
first_epoch_key = list(epochs.keys())[0]
first_epoch_copy = epochs[first_epoch_key].copy()
del first_epoch_copy["ECG_Rate"]
nk.ecg_eventrelated({**epochs, first_epoch_key: first_epoch_copy})
# Test warning on long epochs (eventrelated_utils)
with pytest.warns(nk.misc.NeuroKitWarning,
match=r".*duration of your epochs seems.*"):
first_epoch_key = list(epochs.keys())[0]
first_epoch_copy = epochs[first_epoch_key].copy()
first_epoch_copy.index = range(len(first_epoch_copy))
nk.ecg_eventrelated({**epochs, first_epoch_key: first_epoch_copy})
def simulation(normal_N,abnormal_N, save_params = False):
normal_data = []
normal_params = []
print('Creating normal dataset')
for i in range(normal_N):
ti = np.random.normal(para.mu_t_1, para.sigma_t_1)
ai = np.random.normal(para.mu_a_1, para.sigma_a_1)
bi = np.random.normal(para.mu_b_1, para.sigma_b_1)
hr = np.random.normal(para.mu_hr_1, para.sigma_hr_1)
noise = np.random.uniform(low=para.min_noise_1, high=para.max_noise_1)
ecgs, _ = nk.ecg_simulate(duration=para.duration*2, sampling_rate=para.sampling_rate, noise=noise, Anoise=para.Anoise, heart_rate=hr, gamma=para.gamma, ti=ti, ai=ai, bi=bi)
ecgs = np.array(ecgs)
start_i = np.random.randint(len(ecgs[0])//4, len(ecgs[0])//2)
normal_data.append(ecgs[:,start_i:start_i+para.sampling_rate*para.duration])
normal_params.append({'ti':ti, 'ai':ai, 'bi':bi, 'hr':hr, 'noise':noise, 'gamma': para.gamma})
abnormal_data = []
abnormal_params = []
print('Creating abnormal dataset')
for i in range(abnormal_N):
ti = np.random.normal(para.mu_t_2, para.sigma_t_2)
ai = np.random.normal(para.mu_a_2, para.sigma_a_2)
bi = np.random.normal(para.mu_b_2, para.sigma_b_2)
hr = np.random.normal(para.mu_hr_2, para.sigma_hr_2)
noise = np.random.uniform(low=para.min_noise_2, high=para.max_noise_2)
ecgs, _ = nk.ecg_simulate(duration=para.duration*2, sampling_rate=para.sampling_rate, noise=noise, Anoise=para.Anoise, heart_rate=hr, gamma=para.gamma, ti=ti, ai=ai, bi=bi)
ecgs = np.array(ecgs)
start_i = np.random.randint(len(ecgs[0])//4, len(ecgs[0])//2)
abnormal_data.append(ecgs[:,start_i:start_i+para.sampling_rate*para.duration])
abnormal_params.append({'ti':ti, 'ai':ai, 'bi':bi, 'hr':hr, 'noise':noise, 'gamma': para.gamma})
labels = np.array([0]*len(normal_data) + [1]*len(abnormal_data))
permutation = np.random.permutation(len(labels))
data = np.array(normal_data+abnormal_data)
data_params = np.array(normal_params+abnormal_params)
labels = labels[permutation]
data = data[permutation]
data_params = data_params[permutation]
np.save('sim_ecg_data', data) # save ECG data
np.save('sim_ecg_labels', labels) # save label
if (save_params):
np.save('sim_ecg_params',data_params) # save parameters for each ecg sample (12,2500)
def get_bedmaster_waveforms() -> Dict[str, BedmasterSignal]:
starting_time = int(time())
duration = 8
sample_freq_1 = 240
sample_freq_2 = 120
times = np.arange(starting_time, starting_time + duration, 0.25)
values1 = nk.ecg_simulate(
duration=int(duration / 2),
sampling_rate=sample_freq_1,
)
values2 = nk.ecg_simulate(
duration=int(duration / 2),
sampling_rate=sample_freq_2,
)
values = np.concatenate([values1, values2])
n_samples = np.array([sample_freq_1 * 0.25] * int(duration * 4 / 2) +
[sample_freq_2 * 0.25] * int(duration * 4 / 2), )
# Remove some samples
values = np.delete(values, [10, 11, 250])
n_samples[0] = 58
n_samples[5] = 59
leads = {
lead: BedmasterSignal(
name=lead,
source="waveform",
channel=f"ch{idx}",
value=values,
time=times,
units="mV",
sample_freq=np.array(
[(sample_freq_1, 0), (sample_freq_2, 16)],
dtype="float,int",
),
scale_factor=np.random.uniform() * 5,
time_corr_arr=np.packbits(
np.random.randint(0, 2, 100).astype(np.bool)),
samples_per_ts=n_samples,
)
for idx, lead in enumerate(["i", "ii", "iii", "v", "spo2"])
}
return leads
def test_ecg_hrv():
ecg_slow = nk.ecg_simulate(duration=60, sampling_rate=1000, heart_rate=70, random_state=42)
ecg_fast = nk.ecg_simulate(duration=60, sampling_rate=1000, heart_rate=110, random_state=42)
ecg_slow, _ = nk.ecg_process(ecg_slow, sampling_rate=1000)
ecg_fast, _ = nk.ecg_process(ecg_fast, sampling_rate=1000)
ecg_slow_hrv = nk.ecg_hrv(ecg_slow, sampling_rate=1000)
ecg_fast_hrv = nk.ecg_hrv(ecg_fast, sampling_rate=1000)
assert ecg_fast_hrv["HRV_RMSSD"][0] < ecg_slow_hrv["HRV_RMSSD"][0]
assert ecg_fast_hrv["HRV_MeanNN"][0] < ecg_slow_hrv["HRV_MeanNN"][0]
assert ecg_fast_hrv["HRV_SDNN"][0] < ecg_slow_hrv["HRV_SDNN"][0]
assert ecg_fast_hrv["HRV_CVNN"][0] < ecg_slow_hrv["HRV_CVNN"][0]
assert ecg_fast_hrv["HRV_CVSD"][0] < ecg_slow_hrv["HRV_CVSD"][0]
assert ecg_fast_hrv["HRV_MedianNN"][0] < ecg_slow_hrv["HRV_MedianNN"][0]
assert ecg_fast_hrv["HRV_MadNN"][0] < ecg_slow_hrv["HRV_MadNN"][0]
assert ecg_fast_hrv["HRV_MCVNN"][0] < ecg_slow_hrv["HRV_MCVNN"][0]
assert ecg_fast_hrv["HRV_pNN50"][0] == ecg_slow_hrv["HRV_pNN50"][0]
assert ecg_fast_hrv["HRV_pNN20"][0] < ecg_slow_hrv["HRV_pNN20"][0]
assert ecg_fast_hrv["HRV_TINN"][0] < ecg_slow_hrv["HRV_TINN"][0]
assert ecg_fast_hrv["HRV_HTI"][0] > ecg_slow_hrv["HRV_HTI"][0]
assert ecg_fast_hrv["HRV_ULF"][0] == ecg_slow_hrv["HRV_ULF"][0] == 0
assert all(elem in ['HRV_RMSSD', 'HRV_MeanNN', 'HRV_SDNN', 'HRV_SDSD', 'HRV_CVNN',
'HRV_CVSD', 'HRV_MedianNN', 'HRV_MadNN', 'HRV_MCVNN',
'HRV_pNN50', 'HRV_pNN20', 'HRV_TINN', 'HRV_HTI', 'HRV_ULF',
'HRV_VLF', 'HRV_LF', 'HRV_HF', 'HRV_VHF', 'HRV_LFHF',
'HRV_LFn', 'HRV_HFn', 'HRV_LnHF',
'HRV_SD1', 'HRV_SD2', 'HRV_SD2SD1', 'HRV_CSI', 'HRV_CVI',
'HRV_CSI_Modified', 'HRV_SampEn']
for elem in np.array(ecg_fast_hrv.columns.values, dtype=str))
# Test frequency domain
ecg1 = nk.ecg_simulate(duration=60, sampling_rate=2000, heart_rate=70, random_state=42)
hrv1 = nk.ecg_hrv(nk.ecg_process(ecg1, sampling_rate=2000)[0], sampling_rate=2000)
ecg2 = nk.signal_resample(ecg1, sampling_rate=2000, desired_sampling_rate=500)
hrv2 = nk.ecg_hrv(nk.ecg_process(ecg2, sampling_rate=500)[0], sampling_rate=500)
assert np.allclose(np.mean(hrv1[["HRV_HF", "HRV_LF", "HRV_VLF"]].iloc[0] - hrv2[["HRV_HF", "HRV_LF", "HRV_VLF"]].iloc[0]), 0, atol=1)
def test_ecg_hrv():
ecg_slow = nk.ecg_simulate(duration=60,
sampling_rate=1000,
heart_rate=70,
random_state=42)
ecg_fast = nk.ecg_simulate(duration=60,
sampling_rate=1000,
heart_rate=110,
random_state=42)
ecg_slow, _ = nk.ecg_process(ecg_slow)
ecg_fast, _ = nk.ecg_process(ecg_fast)
ecg_slow_hrv = nk.ecg_hrv(ecg_slow)
ecg_fast_hrv = nk.ecg_hrv(ecg_fast)
assert ecg_fast_hrv["HRV_RMSSD"][0] < ecg_slow_hrv["HRV_RMSSD"][0]
assert ecg_fast_hrv["HRV_MeanNN"][0] < ecg_slow_hrv["HRV_MeanNN"][0]
assert ecg_fast_hrv["HRV_SDNN"][0] < ecg_slow_hrv["HRV_SDNN"][0]
assert ecg_fast_hrv["HRV_CVNN"][0] < ecg_slow_hrv["HRV_CVNN"][0]
assert ecg_fast_hrv["HRV_CVSD"][0] < ecg_slow_hrv["HRV_CVSD"][0]
assert ecg_fast_hrv["HRV_MedianNN"][0] < ecg_slow_hrv["HRV_MedianNN"][0]
assert ecg_fast_hrv["HRV_MadNN"][0] < ecg_slow_hrv["HRV_MadNN"][0]
assert ecg_fast_hrv["HRV_MCVNN"][0] < ecg_slow_hrv["HRV_MCVNN"][0]
assert ecg_fast_hrv["HRV_pNN50"][0] == ecg_slow_hrv["HRV_pNN50"][0]
assert ecg_fast_hrv["HRV_pNN20"][0] < ecg_slow_hrv["HRV_pNN20"][0]
assert ecg_fast_hrv["HRV_TINN"][0] < ecg_slow_hrv["HRV_TINN"][0]
# assert ecg_fast_hrv["HRV_HTI"][0] > ecg_slow_hrv["HRV_HTI"][0]
# assert ecg_fast_hrv["HRV_ULF"][0] == ecg_slow_hrv["HRV_ULF"][0] == 0
# assert ecg_fast_hrv["HRV_VLF"][0] < ecg_slow_hrv["HRV_VLF"][0]
# assert ecg_fast_hrv["HRV_LF"][0] < ecg_slow_hrv["HRV_LF"][0]
# assert ecg_fast_hrv["HRV_HF"][0] < ecg_slow_hrv["HRV_HF"][0]
# assert ecg_fast_hrv["HRV_VHF"][0] > ecg_slow_hrv["HRV_VHF"][0]
assert all(elem in [
'HRV_RMSSD', 'HRV_MeanNN', 'HRV_SDNN', 'HRV_SDSD', 'HRV_CVNN',
'HRV_CVSD', 'HRV_MedianNN', 'HRV_MadNN', 'HRV_MCVNN', 'HRV_pNN50',
'HRV_pNN20', 'HRV_TINN', 'HRV_HTI', 'HRV_ULF', 'HRV_VLF', 'HRV_LF',
'HRV_HF', 'HRV_VHF', 'HRV_LFHF', 'HRV_LFn', 'HRV_HFn', 'HRV_LnHF',
'HRV_SD1', 'HRV_SD2', 'HRV_SD2SD1', 'HRV_CSI', 'HRV_CVI',
'HRV_CSI_Modified', 'HRV_SampEn'
] for elem in np.array(ecg_fast_hrv.columns.values, dtype=str))
def generate(time: int, rate: int):
ecg1 = nk.ecg_simulate(duration=time, sampling_rate= rate, method = "ecgsyn") # duration - ile sekund #sampling rate - ile punktów na sekunde
ecg2 = nk.ecg_simulate(duration=time, sampling_rate= rate, method = "ecgsyn")
ecg3 = nk.ecg_simulate(duration=time, sampling_rate= rate, method="ecgsyn")
ecg4 = nk.ecg_simulate(duration=time, sampling_rate= rate, method="daubechies")
emg1 = nk.emg_simulate(duration=time, sampling_rate= rate, random_state=1, burst_number=3)
emg2 = nk.emg_simulate(duration=time, sampling_rate= rate, random_state=2, burst_number=3)
emg3 = nk.emg_simulate(duration=time, sampling_rate= rate, random_state=3, burst_number=3)
emg4 = nk.emg_simulate(duration=time, sampling_rate= rate, random_state=4, burst_number=3)
# sa jeszcze analogicznie fajne wykresy dla ppg, rsp i eda
nk.signal_plot(ecg1, sampling_rate=rate)
nk.signal_plot(ecg2, sampling_rate=rate)
data = pd.DataFrame({'ecg1': ecg1,
'ecg2': ecg2,
'emg1': emg1,
})
return data
def test_ecg_eventrelated():
ecg, info = nk.ecg_process(nk.ecg_simulate(duration=20))
epochs = nk.epochs_create(ecg, events=[5000, 10000, 15000], epochs_start=-0.1, epochs_end=1.9)
ecg_eventrelated = nk.ecg_eventrelated(epochs)
# Test rate features
assert np.alltrue(np.array(ecg_eventrelated["ECG_Rate_Min"]) < np.array(ecg_eventrelated["ECG_Rate_Mean"]))
assert np.alltrue(np.array(ecg_eventrelated["ECG_Rate_Mean"]) < np.array(ecg_eventrelated["ECG_Rate_Max"]))
assert len(ecg_eventrelated["Label"]) == 3
def test_ecg_process():
sampling_rate = 1000
noise = 0.05
ecg = nk.ecg_simulate(sampling_rate=sampling_rate, noise=noise)
signals, info = nk.ecg_process(ecg,
sampling_rate=sampling_rate,
method="neurokit")
# Only check array dimensions and column names since functions called by
# ecg_process have already been unit tested
assert all(elem in ["ECG_Raw", "ECG_Clean", "ECG_R_Peaks", "ECG_Rate"]
for elem in np.array(signals.columns.values, dtype=str))
def test_bio_process():
sampling_rate = 1000
# Create data
ecg = nk.ecg_simulate(duration=30, sampling_rate=sampling_rate)
rsp = nk.rsp_simulate(duration=30, sampling_rate=sampling_rate)
eda = nk.eda_simulate(duration=30,
sampling_rate=sampling_rate,
scr_number=3)
emg = nk.emg_simulate(duration=30,
sampling_rate=sampling_rate,
burst_number=3)
bio_df, bio_info = nk.bio_process(ecg=ecg,
rsp=rsp,
eda=eda,
emg=emg,
sampling_rate=sampling_rate)
# SCR components
scr = [val for key, val in bio_info.items() if "SCR" in key]
assert all(len(elem) == len(scr[0]) for elem in scr)
assert all(bio_info["SCR_Onsets"] < bio_info["SCR_Peaks"])
assert all(bio_info["SCR_Peaks"] < bio_info["SCR_Recovery"])
# RSP
assert all(bio_info["RSP_Peaks"] > bio_info["RSP_Troughs"])
assert len(bio_info["RSP_Peaks"]) == len(bio_info["RSP_Troughs"])
# EMG
assert all(bio_info["EMG_Offsets"] > bio_info["EMG_Onsets"])
assert len(bio_info["EMG_Offsets"] == len(bio_info["EMG_Onsets"]))
assert all(elem in [
'ECG_Raw', 'ECG_Clean', 'ECG_Rate', 'ECG_Quality', 'ECG_R_Peaks',
"ECG_P_Peaks", "ECG_Q_Peaks", "ECG_S_Peaks", "ECG_T_Peaks",
"ECG_P_Onsets", "ECG_T_Offsets", "ECG_Atrial_Phase",
"ECG_Ventricular_Phase", "ECG_Atrial_PhaseCompletion",
"ECG_Ventricular_PhaseCompletion", 'RSP_Raw', 'RSP_Clean',
'RSP_Amplitude', 'RSP_Rate', 'RSP_Phase', 'RSP_PhaseCompletion',
'RSP_Peaks', 'RSP_Troughs', 'EDA_Raw', 'EDA_Clean', 'EDA_Tonic',
'EDA_Phasic', 'SCR_Onsets', 'SCR_Peaks', 'SCR_Height', 'SCR_Amplitude',
'SCR_RiseTime', 'SCR_Recovery', 'SCR_RecoveryTime', 'EMG_Raw',
'EMG_Clean', 'EMG_Amplitude', 'EMG_Activity', 'EMG_Onsets',
'EMG_Offsets', 'RSA_P2T'
] for elem in np.array(bio_df.columns.values, dtype=str))
def test_ecg_process():
sampling_rate = 1000
noise = 0.05
ecg = nk.ecg_simulate(sampling_rate=sampling_rate, noise=noise)
signals, info = nk.ecg_process(ecg, sampling_rate=sampling_rate,
method="neurokit")
# Only check array dimensions and column names since functions called by
# ecg_process have already been unit tested
assert all(elem in ["ECG_Raw", "ECG_Clean", "ECG_R_Peaks", "ECG_Rate",
'ECG_Quality', "ECG_P_Peaks",
"ECG_Q_Peaks", "ECG_S_Peaks",
"ECG_T_Peaks", "ECG_P_Onsets", "ECG_T_Offsets",
"ECG_Atrial_Phase", "ECG_Ventricular_Phase",
"ECG_Atrial_PhaseCompletion",
"ECG_Ventricular_PhaseCompletion"]
for elem in np.array(signals.columns.values, dtype=str))
def test_hrv():
ecg = nk.ecg_simulate(duration=60,
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 all(elem in [
'HRV_RMSSD', 'HRV_MeanNN', 'HRV_SDNN', 'HRV_SDSD', 'HRV_CVNN',
'HRV_CVSD', 'HRV_MedianNN', 'HRV_MadNN', 'HRV_MCVNN', 'HRV_pNN50',
'HRV_pNN20', 'HRV_TINN', 'HRV_HTI', 'HRV_ULF', 'HRV_VLF', 'HRV_LF',
'HRV_HF', 'HRV_VHF', 'HRV_LFHF', 'HRV_LFn', 'HRV_HFn', 'HRV_LnHF',
'HRV_SD1', 'HRV_SD2', 'HRV_SD2SD1', 'HRV_CSI', 'HRV_CVI',
'HRV_CSI_Modified', 'HRV_SampEn'
] for elem in np.array(ecg_hrv.columns.values, dtype=str))
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_LF"][0])
assert np.isnan(hrv2["HRV_LF"][0])
assert np.isnan(hrv1["HRV_VLF"][0])
assert np.isnan(hrv2["HRV_LF"][0])
import numpy as np
import pandas as pd
import neurokit2 as nk
sampling_rate = 1000
for heartrate in [80]:
# Simulate signal
ecg = nk.ecg_simulate(duration=60,
sampling_rate=sampling_rate,
heartrate=heartrate,
noise=0)
# Segment
_, rpeaks = nk.ecg_peaks(ecg, sampling_rate=sampling_rate)
# _, waves = nk.ecg_delineator(ecg, rpeaks=rpeaks["ECG_R_Peaks"])
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import neurokit2 as nk
# =============================================================================
# Simulate physiological signals
# =============================================================================
# Generate synthetic signals
ecg = nk.ecg_simulate(duration=10, heart_rate=70)
ppg = nk.ppg_simulate(duration=10, heart_rate=70)
rsp = nk.rsp_simulate(duration=10, respiratory_rate=15)
eda = nk.eda_simulate(duration=10, scr_number=3)
emg = nk.emg_simulate(duration=10, burst_number=2)
# Visualise biosignals
data = pd.DataFrame({
"ECG": ecg,
"PPG": ppg,
"RSP": rsp,
"EDA": eda,
"EMG": emg
})
nk.signal_plot(data, subplots=True)
# Save it
data = pd.DataFrame({
"ECG":
nk.ecg_simulate(duration=10, heart_rate=70, noise=0),
"PPG":
def test_ecg_findpeaks():
sampling_rate = 1000
ecg = nk.ecg_simulate(duration=60,
sampling_rate=sampling_rate,
noise=0,
method="simple",
random_state=42)
ecg_cleaned = nk.ecg_clean(ecg,
sampling_rate=sampling_rate,
method="neurokit")
# Test neurokit methodwith show=True
info_nk = nk.ecg_findpeaks(ecg_cleaned, show=True)
assert info_nk["ECG_R_Peaks"].size == 69
# This will identify the latest figure.
fig = plt.gcf()
assert len(fig.axes) == 2
# Test pantompkins1985 method
info_pantom = nk.ecg_findpeaks(nk.ecg_clean(ecg, method="pantompkins1985"),
method="pantompkins1985")
assert info_pantom["ECG_R_Peaks"].size == 70
# Test hamilton2002 method
info_hamilton = nk.ecg_findpeaks(nk.ecg_clean(ecg, method="hamilton2002"),
method="hamilton2002")
assert info_hamilton["ECG_R_Peaks"].size == 69
# Test christov2004 method
info_christov = nk.ecg_findpeaks(ecg_cleaned, method="christov2004")
assert info_christov["ECG_R_Peaks"].size == 273
# Test gamboa2008 method
info_gamboa = nk.ecg_findpeaks(ecg_cleaned, method="gamboa2008")
assert info_gamboa["ECG_R_Peaks"].size == 69
# Test elgendi2010 method
info_elgendi = nk.ecg_findpeaks(nk.ecg_clean(ecg, method="elgendi2010"),
method="elgendi2010")
assert info_elgendi["ECG_R_Peaks"].size == 70
# Test engzeemod2012 method
info_engzeemod = nk.ecg_findpeaks(nk.ecg_clean(ecg,
method="engzeemod2012"),
method="engzeemod2012")
assert info_engzeemod["ECG_R_Peaks"].size == 70
# Test kalidas2017 method
info_kalidas = nk.ecg_findpeaks(nk.ecg_clean(ecg, method="kalidas2017"),
method="kalidas2017")
assert info_kalidas["ECG_R_Peaks"].size == 69
# Test martinez2003 method
ecg = nk.ecg_simulate(duration=60,
sampling_rate=sampling_rate,
noise=0,
random_state=42)
ecg_cleaned = nk.ecg_clean(ecg,
sampling_rate=sampling_rate,
method="neurokit")
info_martinez = nk.ecg_findpeaks(ecg_cleaned, method="martinez2003")
assert np.allclose(info_martinez["ECG_R_Peaks"].size, 69, atol=1)
signaltype =vars(args)["T"]
t = vars(args)["t"]
f = vars(args)["f"]
bpm = vars(args)["b"]
diastolic = vars(args)["D"]
systolic = vars(args)["S"]
respiration = vars(args)["r"]
pespiration = vars(args)["p"]
step = vars(args)["s"]
print(signaltype,t,f,bpm,diastolic,systolic,respiration,pespiration)
ech_array = []
if "po" in signaltype:
#procedure pour generer un pouls
samples_pouls = nk.ecg_simulate(duration=t, sampling_rate=f ,noise=.05, heart_rate=bpm,method="simple")
ech_array = keepOnlyPositive(samples_pouls)
ech_array /= np.max(ech_array,axis=0)/3.3
elif "pr" in signaltype :
index = np.linspace(-9, 9, num= int(f / (bpm/60)))
normal1 = scipy.stats.norm.pdf(index, loc=-2, scale=1)* (systolic/MAX_SYSTOLIQUE)#premier peak systolique
normal2 = scipy.stats.norm.pdf(index, loc=2, scale=1.5)* (diastolic/MAX_DIASTOLIQUE) # deuxieme peak diastolique
samples = 8 * (normal1 + normal2) #facteur 8 seulement pour scaler entre 0 et 3.3
# La valeur en Voltage d'une personne qui a une systolique normal (120), est autour de 2.8 , pour une systolique eleve(140), on est autour de 3.2 , une sytolique basse (100) est autour de 2.3
#la valeur en Voltage d'une personne qui a une diastolique normal (80) est autour de 1.8 , pour une diastolique eleve(90), on est atour de 2.10, une diastolique basse (60) est autour de 1.4
#prolongement du signal de pression selon le temps de signal voulu
for i in range(0,int(t)):
def generate_ecg(time, rate):
ecg = ecg_simulate(duration=time, sampling_rate=rate, method="ecgsyn")
return ecg
