def create_heart_beat_dataset(path, name, group, save_dfile=None):
X = load_signal(path=path, name=name, group=group) # 1 record per row
rpeaks = load_signal(path=path, name='rpeaks', group=group)
signal_to_segment = X['signal'][0,:].T
heart_beat, rpeaks = ecg.extract_heartbeats(
signal=signal_to_segment,
rpeaks=rpeaks['signal'], sampling_rate=1000.0,
before=0.2, after=0.4
)
return heart_beat, rpeaks
def extract_beats(data_path):
data = loadmat("./ECGTestData/ECGTestData/" + data_path)['data'].T # II导
data = data[1:, :] # 去除第一行index
beats_matrix = []
logging.info("--------------------------------------------------")
logging.info("载入信号-%s, 长度 = %d " % (data_path, len(data[0])))
min_beats = math.inf
for i in DAOLIAN:
signal = data[i]
fs = 500 # 信号采样率 500 Hz
# logging.info("调用 hamilton_segmenter 进行R波检测 ...")
# tic = time.time()
rpeaks = ecg.hamilton_segmenter(signal, sampling_rate=fs)
# toc = time.time()
# logging.info("完成. 用时: %f 秒. " % (toc - tic))
rpeaks = rpeaks[0]
# heart_rate = 60 / (np.mean(np.diff(rpeaks)) / fs)
# np.diff 计算相邻R峰之间的距离分别有多少个采样点，np.mean求平均后，除以采样率，
# 将单位转化为秒，然后计算60秒内可以有多少个RR间期作为心率
# logging.info("平均心率: %.3f / 分钟." % (heart_rate))
win_before = 0.2
win_after = 0.4
# logging.info("根据R波位置截取心拍, 心拍前窗口：%.3f 秒 ~ 心拍后窗口：%.3f 秒 ..." % (win_before, win_after)) # rpeak全部落在100处
# tic = time.time()
beats, rpeaks_beats = ecg.extract_heartbeats(signal, rpeaks, fs,
win_before, win_after)
# toc = time.time()
# logging.info("完成. 用时: %f 秒." % (toc - tic))
# logging.info("共截取到 %d 个心拍, 每个心拍长度为 %d 个采样点" % (beats.shape[0], beats.shape[1]))
# plt.figure()
# plt.grid(True)
# for i in range(beats.shape[0]):
# plt.plot(beats[i])
# plt.title(data_path)
# plt.show()
beats_matrix.append(beats)
if len(beats) < min_beats:
min_beats = len(beats)
test_data = []
for i in range(min_beats):
tdata = []
for j in range(len(DAOLIAN)):
rbeats = denoise(beats_matrix[j][i])
tdata.append(rbeats)
test_data.append(tdata)
test_data = np.array(test_data).flatten().reshape(-1, 300 * len(DAOLIAN),
1)
return test_data
def segment_beat(X, tgrid, alg="christov-aligned", grid_len=100, detrend=True):
#X = preproc_raw_multi_lead(X, tgrid)
if alg == "christov":
samp_rate = 1. / (tgrid[1]-tgrid[0])
rpeaks = becg.christov_segmenter(X[0], samp_rate)
bmat = np.dstack([
becg.extract_heartbeats(Xr, rpeaks=rpeaks['rpeaks'],
sampling_rate=samp_rate, before=.3, after=.4)['templates']
for Xr in X
])
return bmat
elif alg == "christov-aligned":
# first detect R peaks (using preprocessed first lead)
samp_rate = 1. / (tgrid[1]-tgrid[0])
Xfix = preproc_raw(X[0], tgrid)[0]
rpeaks = becg.christov_segmenter(Xfix, samp_rate)
# then extract irregularly lengthed beats and resample
if detrend:
Xdet = detrend_raw_multi_lead(X, tgrid)
else:
Xdet = X
# actually extract beats
bmat, lens = extract_irregular_beats(Xdet,
rpeaks=rpeaks['rpeaks'], grid_len=grid_len)
return bmat, lens
elif alg == "gen-conv":
raise NotImplementedError
fit_dict = bcm.fit(X, tgrid, global_params, verbose=True)
edbest = fit_dict['elbo_best']
beat_starts = bcm.segment_sparse_zgrid(
edbest['pzgrid'], tgrid, edbest['filter_time'])
dt = tgrid[1] - tgrid[0]
beat_width = np.int(edbest['filter_time'] / dt)
beat_idx = np.array([ np.where(bs < tgrid)[0][0] for bs in beat_starts])
templates = [ X[bi:(bi+beat_width)] for bi in beat_idx]
lens = np.array([ len(t) for t in templates ])
too_short = lens != np.max(lens)
templates = np.row_stack([templates[i] for ts in too_short if not ts])
return templates
def GetRawSamplesFromSignals(dataSignals, sampleRate):
allRawSamples = []
for signal in dataSignals:
label = signal[0] # Get the label value
signal = signal[1:] # Getting rid of the label value
rPeaks = ecg.christov_segmenter(signal=signal,
sampling_rate=sampleRate)
extractions = ecg.extract_heartbeats(signal=signal,
rpeaks=rPeaks[0],
sampling_rate=sampleRate,
before=0.2,
after=0.4)
heartbeats = extractions['templates']
for heartbeat in heartbeats:
heartbeat = np.insert(heartbeat, 0, label)
allRawSamples.append(heartbeat)
return allRawSamples
def segmentation(data, label=None):
inputs, labels = [], []
for sap_id in range(len(data)):
data_ref = denoise(copy.copy(data[sap_id][:, 9]))
r_peaks = ecg.hamilton_segmenter(data_ref, 500).as_dict()['rpeaks']
beats = np.hstack([
ecg.extract_heartbeats(signal=denoise(
copy.copy(data[sap_id][:, dao_id])),
rpeaks=r_peaks,
sampling_rate=500,
before=0.2,
after=0.4)["templates"]
for dao_id in [1, 3, 6, 9]
])
inputs.append(beats)
if label: labels.append(np.full(beats.shape[0], label[sap_id]))
# if label: labels.append(label[sap_id])
if not label:
return np.array(inputs, dtype=object)
else:
return np.vstack(inputs), np.hstack(labels)
def calculate_features(signal): sampling_rate = 400 ts, signal, rpeaks, templates_ts, templates, heart_rate_ts, heart_rates = ecg.ecg(signal=signal, sampling_rate=sampling_rate, show=False) rpeaks = ecg.hamilton_segmenter(signal=signal, sampling_rate=sampling_rate)[0] heartbeat_templates, heartbeat_rpeaks = ecg.extract_heartbeats(signal=signal, rpeaks=rpeaks, sampling_rate=sampling_rate) rpeaks_diff = np.diff(rpeaks) rpeaks_diff_diff = np.diff(rpeaks_diff) heartbeat_rpeaks_diff = np.diff(heartbeat_rpeaks) feature = "" mean_amplitude = np.mean(signal) std_amplitude = np.std(signal) max_amplitude = np.amax(signal) min_amplitude = np.amin(signal) median_amplitude = np.median(signal) feature = feature + str(mean_amplitude) + "," + str(std_amplitude) + "," + str(max_amplitude) + "," + str(min_amplitude) + "," + str(median_amplitude) mean_rpeaks_diff = np.mean(rpeaks_diff) std_rpeaks_diff = np.std(rpeaks_diff) median_rpeaks_diff = np.median(rpeaks_diff) feature = feature + "," + str(mean_rpeaks_diff) + "," + str(std_rpeaks_diff) + "," + str(median_rpeaks_diff) mean_rpeaks_diff_diff = np.mean(rpeaks_diff_diff) std_rpeaks_diff_diff = np.std(rpeaks_diff_diff) median_rpeaks_diff_diff = np.median(rpeaks_diff_diff) feature = feature + "," + str(mean_rpeaks_diff_diff) + "," + str(std_rpeaks_diff_diff) + "," + str(median_rpeaks_diff_diff) heartbeat_length = len(heartbeat_templates) mean_heart_rate = np.mean(heart_rates) if len(heart_rates) > 0 else 0.0 std_heart_rate = np.std(heart_rates) if len(heart_rates) > 0 else 0.0 median_heart_rate = np.median(heart_rates) if len(heart_rates) > 0 else 0.0 feature = feature + "," + str(heartbeat_length) + "," + str(mean_heart_rate) + "," + str(std_heart_rate) + "," + str(median_heart_rate) mean_heartbeat_rpeaks_diff = np.mean(heartbeat_rpeaks_diff) std_heartbeat_rpeaks_diff = np.std(heartbeat_rpeaks_diff) median_heartbeat_rpeaks_diff = np.median(heartbeat_rpeaks_diff) feature = feature + "," + str(mean_heartbeat_rpeaks_diff) + "," + str(std_heartbeat_rpeaks_diff) + "," + str(median_heartbeat_rpeaks_diff) return feature
def test_extract_beats(data_path):
signal, mdata = load_txt(data_path)
logging.info("--------------------------------------------------")
logging.info("载入信号-%s, 长度 = %d " % (data_path, len(signal)))
fs = 360 # 信号采样率 360 Hz
logging.info("调用 hamilton_segmenter 进行R波检测 ...")
tic = time.time()
rpeaks = ecg.hamilton_segmenter(signal, sampling_rate=fs)
toc = time.time()
logging.info("完成. 用时: %f 秒. " % (toc - tic))
rpeaks = rpeaks[0]
heart_rate = 60 / (np.mean(np.diff(rpeaks)) / fs)
# np.diff 计算相邻R峰之间的距离分别有多少个采样点，np.mean求平均后，除以采样率，
# 将单位转化为秒，然后计算60秒内可以有多少个RR间期作为心率
logging.info("平均心率: %.3f / 分钟." % (heart_rate))
win_before = 0.2
win_after = 0.4
logging.info("根据R波位置截取心拍, 心拍前窗口：%.3f 秒 ~ 心拍后窗口：%.3f 秒 ..." \
% (win_before, win_after))
tic = time.time()
beats, rpeaks_beats = ecg.extract_heartbeats(signal, rpeaks, fs,
win_before, win_after)
toc = time.time()
logging.info("完成. 用时: %f 秒." % (toc - tic))
logging.info("共截取到 %d 个心拍, 每个心拍长度为 %d 个采样点" % \
(beats.shape[0], beats.shape[1]))
plt.figure()
plt.grid(True)
for i in range(beats.shape[0]):
plt.plot(beats[i])
plt.title(data_path)
plt.show()
return
import numpy as np
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import biosppy.signals.ecg as ecg
signal = np.load('one_hb.npy')
print('shape of signal: ', signal.shape)
ts, filtered, rpeaks, templates_ts, templates, heart_rate_ts, heart_rate = ecg.ecg(
signal, sampling_rate=300, show=False)
templates, rpeaks_ = ecg.extract_heartbeats(filtered,
rpeaks=rpeaks,
sampling_rate=300)
print('shape templates: ', templates.shape)
np.save('one_templates', templates)
def extract_features(ts):
"""Extract features from individual patient
Arguments
---------
ts: time series of interest
Returns
-------
"""
"""
1. R-R interval:
-what is the average interval between peaks?
-how much variation is there in this measure?
-max/min value
"""
# Peak detection: perhaps take it from .ecg function?
rpeak0=ecg.hamilton_segmenter(signal=ts,\
sampling_rate=300)[0]
# Interval lengths
l_RRint = []
for a in range(len(rpeak0)):
if (a > 0):
l_RRint.append(rpeak0[a] - rpeak0[a - 1])
# Some "robust" extreme values statistics (no max or min)
RRint_10, RRint_90 = np.percentile(l_RRint, q=[0.1, 0.9])
RRint_mean = np.mean(l_RRint)
RRint_sd = np.std(l_RRint)
"""
2. R amplitude (difference between value at peak
minus baseline -not "valley"-):
-what is the average R amplitude?
-how much variation is there in this measure?
-max/min value
NOTE: YOU CANNOT USE THE INDEXING OF THE R-PEAKS TO FIND THE
VALUE OF THE Y! First impression: use ecg.ecg and work with
the filtered series (here indeces seem to match)
Idea: work with index of filtered series. For baseline
take an average of the first and last 20 values of the series
"""
filtered_ts = ecg.ecg(ts, sampling_rate=300, show=False)
hb, hb_peaks= ecg.extract_heartbeats(signal=filtered_ts["filtered"], \
rpeaks= rpeak0, sampling_rate=300.0)
# if all(hb[1]==rpeak0):
# hb=hb[0]
#else:
# print "Error"
# Finding value at R-peak
R_max_value = filtered_ts["filtered"][hb_peaks]
# Computing baseline
ts_baselines = []
for a_hb in hb:
ts_baselines.append((sum(a_hb[0:20])+ \
sum(a_hb[(len(a_hb)-20):(len(a_hb)-1)]))/40.)
# R_max -baseline
R_amplitude = []
for hb_nr in range(len(hb)):
R_amplitude.append(R_max_value[hb_nr] - ts_baselines[hb_nr])
Rampl_10, Rampl_90 = np.percentile(R_amplitude, q=[0.1, 0.9])
Rampl_mean = np.mean(R_amplitude)
Rampl_sd = np.std(R_amplitude)
"""
3. Q and S (latter optional) amplitude
(difference between value at min before R
minus baseline):
Idea: Examinate the HB. Find out: what is a reasonal nr of
steps to look before the R peak to find Q? Baseline (see above)
- 25 time steps before R-peak to find Q value (the same for S)
--> Note, since the R-peak is sometimes identified at the very
beginning of the series, we need the window to be relative
to where this index is choice: look at indeces
int(2./3*R_index):R_index
"""
Q_vals = []
Q_amplitude = []
S_vals = []
S_amplitude = []
for hb_nr in range(len(hb)):
# Q stats
R_index = np.where(hb[hb_nr] == R_max_value[hb_nr])[0][0]
Q_min = min(hb[hb_nr][int(2. / 3 * R_index):R_index])
Q_vals.append(Q_min)
Q_amplitude.append(ts_baselines[hb_nr] - Q_min)
# S stats
S_min = min(hb[hb_nr][R_index:(R_index + 25)])
S_vals.append(S_min)
S_amplitude.append(ts_baselines[hb_nr] - S_min)
# Remark: some values are completely off due to clear errors in the
# peak detction algorithm (e.g. heartbeat 34 in 19th individual)
Qampl_10, Qampl_90 = np.percentile(Q_amplitude, q=[0.1, 0.9])
Qampl_mean = np.mean(Q_amplitude)
Qampl_sd = np.std(Q_amplitude)
Sampl_10, Sampl_90 = np.percentile(S_amplitude, q=[0.1, 0.9])
Sampl_mean = np.mean(S_amplitude)
Sampl_sd = np.std(S_amplitude)
"""
4. QRS duration:
Idea: we have the index of Q_min and that of S_min. Difference between the two
APPROXIMATES this feature (the way I understand it, I should measure how
long it takes, once we have left the "baseline" to fall into the Q-in, to
come back to the baseline after the S min)
"""
QRS_time = []
for hb_nr in range(len(hb)):
Q_index = np.where(hb[hb_nr] == Q_vals[hb_nr])[0][0]
S_index = np.where(hb[hb_nr] == S_vals[hb_nr])[0][0]
QRS_time.append(S_index - Q_index)
QRSts_10, QRSts_90 = np.percentile(QRS_time, q=[0.1, 0.9])
QRSts_mean = np.mean(QRS_time)
QRSts_sd = np.std(QRS_time)
"""
5. Hearth rate variability
Idea: extract from the .ecg function
"""
hr_ts = filtered_ts[
"heart_rate"] # For subjet 2719 no heart rate is computed! Weird...
if len(hr_ts) == 0:
HR_10, HR_90, HR_mean, HR_sd = [None] * 4
else:
HR_10, HR_90 = np.percentile(hr_ts, q=[0.1, 0.9])
HR_mean = np.mean(hr_ts)
HR_sd = np.std(hr_ts)
"""
5. Wavelet energy
Idea: don't understand what this is or how to obtain it
"""
return RRint_mean, RRint_sd, RRint_10, RRint_90, \
Rampl_mean, Rampl_sd, Rampl_10, Rampl_90, \
Qampl_mean, Qampl_sd, Qampl_10, Qampl_90, \
Sampl_mean, Sampl_sd, Sampl_10, Sampl_90, \
QRSts_mean, QRSts_sd, QRSts_10, QRSts_90, \
HR_mean, HR_sd, HR_10, HR_90
avg_earliness = 0
for idx, raw_testing_ecg in tqdm(enumerate(raw_testing_data)):
start = time.time()
peaks = ecg.christov_segmenter(signal=raw_testing_ecg[:, 0], sampling_rate = 500)[0]
if(len(peaks)<=1):
la_peaks = ecg.christov_segmenter(signal=raw_testing_ecg[peaks[0]+500:, 0],
sampling_rate = 500)[0]
peaks = [(x+500) for x in la_peaks]
hb = ecg.extract_heartbeats(signal=raw_testing_ecg,
rpeaks=peaks,
sampling_rate=500,
before=1,
after=1)
rpeak_list = hb[1]
raw_testing_ecg_corresponding_label = raw_testing_label[idx]
input_snippet = np.array([hb[0]])
predictions, t = model(input_snippet)
end = time.time()
run_time += (end - start)
data_train = pd.read_csv('Dropbox/MK/ETH MSc Statistics/Machine Learning/Advanced Machine Learning/exercises/project/task3/X_train.csv')
del data_train['id']
rpeaks_init = []
for i in range(0,data_train.shape[0]):
rpeaks_init.append(bse.engzee_segmenter(signal=data_train.iloc[i,:].values, sampling_rate=300))
rpeaks_corrected = []
for i in range(0,data_train.shape[0]):
rpeaks_corrected.append(bse.correct_rpeaks(signal=data_train.iloc[i,:].values, rpeaks=rpeaks_init[i][0], sampling_rate=300, tol=0.05))
heartbeats = []
for i in range(0,data_train.shape[0]):
heartbeats.append(bse.extract_heartbeats(signal=data_train.iloc[i,:].values, rpeaks=rpeaks_corrected[i][0], sampling_rate=300, before=0.2, after=0.4)
)
R_peaks = []
for i in range(0,data_train.shape[0]):
R = []
for j in range(0,len(heartbeats[i][1])):
R.append(heartbeats[i][1][j])
R_peaks.append(np.array(R))
df = pd.DataFrame(R_peaks)
df.to_csv('R_train.csv', index=True, header=False)
lst = []
for i in range(0,data_train.shape[0]):
def feature_extraction(sample, sampling_rate=300):
# Normalize raw signal
signal = ecg.st.normalize(sample)['signal']
# ensure numpy
signal = np.array(signal)
sampling_rate = float(sampling_rate)
# filter signal
order = int(0.3 * sampling_rate)
filtered, _, _ = ecg.st.filter_signal(signal=signal,
ftype='FIR',
band='bandpass',
order=order,
frequency=[5, 15],
sampling_rate=sampling_rate)
# segment
rpeaks, = ecg.hamilton_segmenter(signal=filtered,
sampling_rate=sampling_rate)
# correct R-peak locations
rpeaks, = ecg.correct_rpeaks(signal=filtered,
rpeaks=rpeaks,
sampling_rate=sampling_rate,
tol=0.05)
templates, rpeaks = ecg.extract_heartbeats(signal=filtered,
rpeaks=rpeaks,
sampling_rate=sampling_rate,
before=0.2,
after=0.4)
# get time vectors
length = len(signal)
T = (length - 1) / sampling_rate
ts = np.linspace(0, T, length, endpoint=False)
# Extract time domain measures
rpeaks_time = ts[rpeaks]
rr_intervals = extract_rr_intervals(rpeaks_time)
rr_diffs = extract_rr_diffs(rr_intervals)
bpm = get_bpm(rr_intervals)
ibi = np.mean(rr_intervals)
sdnn = np.std(rr_intervals)
sdsd = np.std(rr_diffs)
rmssd = np.sqrt(np.mean(rr_diffs**2))
nn20 = np.sum([rr_diffs > 0.02]) / len(rr_diffs)
nn50 = np.sum([rr_diffs > 0.05]) / len(rr_diffs)
# QRS
qpeaks = find_q_point(filtered, rpeaks)
speaks = find_s_point(filtered, rpeaks)
# Extract wavelet power
power_spectrum = ecg.st.power_spectrum(filtered, 300)
frequency = [power_spectrum['freqs'][0], power_spectrum['freqs'][-1]]
wavelet_energie = ecg.st.band_power(power_spectrum['freqs'],
power_spectrum['power'],
frequency)['avg_power']
# Amplitudes
qamplitudes = filtered[qpeaks]
ramplitudes = filtered[rpeaks]
samplitudes = filtered[speaks]
# QRS duration
qrs_duration = ts[speaks] - ts[qpeaks]
qrs_duration_diffs = extract_rr_diffs(qrs_duration)
iqrs = np.mean(qrs_duration)
sdqrs = np.std(qrs_duration)
sdqrsdiffs = np.std(qrs_duration_diffs)
rmssqrsdiffs = np.sqrt(np.mean(qrs_duration_diffs**2))
extracted_features = [
bpm, ibi, sdnn, sdsd, rmssd, nn20, nn50, wavelet_energie, iqrs, sdqrs,
sdqrsdiffs, rmssqrsdiffs,
np.median(qamplitudes),
np.min(qamplitudes),
np.max(qamplitudes),
np.median(ramplitudes),
np.min(ramplitudes),
np.max(ramplitudes),
np.median(samplitudes),
np.min(samplitudes),
np.max(samplitudes)
]
return extracted_features
def run_algo(algorithm: str, sig: numpy.ndarray,
freq_sampling: int) -> List[int]:
"""
run a qrs detector on a signal
:param algorithm: name of the qrs detector to use
:type algorithm: str
:param sig: values of the sampled signal to study
:type sig: ndarray
:param freq_sampling: value of sampling frequency of the signal
:type freq_sampling: int
:return: localisations of qrs detections
:rtype: list(int)
"""
detectors = Detectors(freq_sampling)
if algorithm == 'Pan-Tompkins-ecg-detector':
qrs_detections = detectors.pan_tompkins_detector(sig)
elif algorithm == 'Hamilton-ecg-detector':
qrs_detections = detectors.hamilton_detector(sig)
elif algorithm == 'Christov-ecg-detector':
qrs_detections = detectors.christov_detector(sig)
elif algorithm == 'Engelse-Zeelenberg-ecg-detector':
qrs_detections = detectors.engzee_detector(sig)
elif algorithm == 'SWT-ecg-detector':
qrs_detections = detectors.swt_detector(sig)
elif algorithm == 'Matched-filter-ecg-detector' and freq_sampling == 360:
qrs_detections = detectors.matched_filter_detector(
sig, 'templates/template_360hz.csv')
elif algorithm == 'Matched-filter-ecg-detector' and freq_sampling == 250:
qrs_detections = detectors.matched_filter_detector(
sig, 'templates/template_250hz.csv')
elif algorithm == 'Two-average-ecg-detector':
qrs_detections = detectors.two_average_detector(sig)
elif algorithm == 'Hamilton-biosppy':
qrs_detections = bsp_ecg.ecg(signal=sig,
sampling_rate=freq_sampling,
show=False)[2]
elif algorithm == 'Christov-biosppy':
order = int(0.3 * freq_sampling)
filtered, _, _ = bsp_tools.filter_signal(signal=sig,
ftype='FIR',
band='bandpass',
order=order,
frequency=[3, 45],
sampling_rate=freq_sampling)
rpeaks, = bsp_ecg.christov_segmenter(signal=filtered,
sampling_rate=freq_sampling)
rpeaks, = bsp_ecg.correct_rpeaks(signal=filtered,
rpeaks=rpeaks,
sampling_rate=freq_sampling,
tol=0.05)
_, qrs_detections = bsp_ecg.extract_heartbeats(
signal=filtered,
rpeaks=rpeaks,
sampling_rate=freq_sampling,
before=0.2,
after=0.4)
elif algorithm == 'Engelse-Zeelenberg-biosppy':
order = int(0.3 * freq_sampling)
filtered, _, _ = bsp_tools.filter_signal(signal=sig,
ftype='FIR',
band='bandpass',
order=order,
frequency=[3, 45],
sampling_rate=freq_sampling)
rpeaks, = bsp_ecg.engzee_segmenter(signal=filtered,
sampling_rate=freq_sampling)
rpeaks, = bsp_ecg.correct_rpeaks(signal=filtered,
rpeaks=rpeaks,
sampling_rate=freq_sampling,
tol=0.05)
_, qrs_detections = bsp_ecg.extract_heartbeats(
signal=filtered,
rpeaks=rpeaks,
sampling_rate=freq_sampling,
before=0.2,
after=0.4)
elif algorithm == 'Gamboa-biosppy':
order = int(0.3 * freq_sampling)
filtered, _, _ = bsp_tools.filter_signal(signal=sig,
ftype='FIR',
band='bandpass',
order=order,
frequency=[3, 45],
sampling_rate=freq_sampling)
rpeaks, = bsp_ecg.gamboa_segmenter(signal=filtered,
sampling_rate=freq_sampling)
rpeaks, = bsp_ecg.correct_rpeaks(signal=filtered,
rpeaks=rpeaks,
sampling_rate=freq_sampling,
tol=0.05)
_, qrs_detections = bsp_ecg.extract_heartbeats(
signal=filtered,
rpeaks=rpeaks,
sampling_rate=freq_sampling,
before=0.2,
after=0.4)
elif algorithm == 'mne-ecg':
qrs_detections = mne_ecg.qrs_detector(freq_sampling, sig)
elif algorithm == 'heartpy':
rol_mean = rolling_mean(sig, windowsize=0.75, sample_rate=100.0)
qrs_detections = hp_pkdetection.detect_peaks(
sig, rol_mean, ma_perc=20, sample_rate=100.0)['peaklist']
elif algorithm == 'gqrs-wfdb':
qrs_detections = processing.qrs.gqrs_detect(sig=sig, fs=freq_sampling)
elif algorithm == 'xqrs-wfdb':
qrs_detections = processing.xqrs_detect(sig=sig, fs=freq_sampling)
else:
raise ValueError(
f'Sorry... unknown algorithm. Please check the list {algorithms_list}'
)
cast_qrs_detections = [int(element) for element in qrs_detections]
return cast_qrs_detections
def heartbeats(f):
signal, fs = filtrar_ler(f)
x, ts, filtered, rpeaks, templates_ts, templates, heart_rate_ts, heart_rate = returning_all(f)
out = ecg.extract_heartbeats(signal=signal, rpeaks=rpeaks, sampling_rate=fs, before=0.2, after=0.4)
return f, out
