How to use the biosppy.signals.ecg function in biosppy

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github Tomatenbiss / HRVAnalysisInNoisySignals / main.py View on Github external
import matplotlib.pyplot as plt
from scipy.stats.stats import pearsonr
from astropy.stats import LombScargle

#Getting the data
f = open("sampleDataEcgEda.txt", "r")
dataEcg = []

for line in f:
	lineValues = line.split(",")
	dataEcg.append(float(lineValues[1]))



#Perform QRS detection
ecgOut = ecg.ecg(signal=dataEcg, sampling_rate=1000., show=False)

#Calculate RR Tachogram
rPeaks = ecgOut[2]
rrTachogram = []
prevPeak = rPeaks[0]
for peak in rPeaks[1:(len(rPeaks))]:
	rrTachogram.append(peak - prevPeak)
	prevPeak = peak


#Calculate median heartbeat template
templatesForCorrCoef = ecgOut[4]
templates = templatesForCorrCoef
medianTemplate = [x / len(templates) for x in [sum(x) for x in zip(*templates)]]

#Calculate correlation coeffcients
github Aiwiscal / ECG-ML-DL-Algorithm-Python / rpeak_seg_simple_v1.0.py View on Github external
#    然后使用说明文档中的参数名(这里是rpeaks)作为key取值。
    rpeaks_indices_2 = rpeaks_indices_2["rpeaks"]
    logging.info("完成. 结果类型为 " + str(type(rpeaks_indices_2)))

    # 检验两种方法得到的结果是否相同:
    check_sum = np.sum(rpeaks_indices_1 == rpeaks_indices_2)
    if check_sum == len(rpeaks_indices_1):
        logging.info("两种取值方式结果相同 ... ")
    else:
        logging.info("两种取值方式结果不同,退出 ...")
        sys.exit(1)

    # 与 christov_segmenter 接口一致的还有 hamilton_segmenter
    logging.info("调用接口一致的 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_indices_3 = rpeaks.as_dict()["rpeaks"]
    # 绘波形图和R波位置
    num_plot_samples = 3600
    logging.info("绘制波形图和检测的R波位置 ...")
    sig_plot = signal[:num_plot_samples]
    rpeaks_plot_1 = rpeaks_indices_1[rpeaks_indices_1 <= num_plot_samples]
    plt.figure()
    plt.plot(sig_plot, "g", label="ECG")
    plt.grid(True)
    plt.plot(rpeaks_plot_1, sig_plot[rpeaks_plot_1], "ro", label="christov_segmenter")
    rpeaks_plot_3 = rpeaks_indices_3[rpeaks_indices_3 <= num_plot_samples]
    plt.plot(rpeaks_plot_3, sig_plot[rpeaks_plot_3], "b^", label="hamilton_segmenter")
    plt.legend()
    plt.title(data_path)
github Seb-Good / deepecg / deepecg / training / data / ecg.py View on Github external
def _get_rpeaks(self):
        """Hamilton-Tompkins r-peak detection."""
        # Get BioSPPy ecg object
        ecg_object = ecg.ecg(signal=self.waveform, sampling_rate=self.fs, show=False)

        return ecg_object['rpeaks']
github Seb-Good / deepecg / deepecg / training / utils / plotting / class_activation_map_template.py View on Github external
ax1.tick_params(labelbottom='off')
    ax1.yaxis.set_tick_params(labelsize=16)

    # Plot CAM
    ax2.plot(time_series_filt_ts, cam_filt, '-k', lw=1.5)

    # Axes labels
    ax2.set_xlabel('Time, seconds', fontsize=22)
    ax2.set_ylabel('Class Activation Map', fontsize=22)
    ax2.set_xlim([0, time_series_filt_ts.max()])
    ax2.set_ylim([cam_filt.min()-0.05, cam_filt.max()+0.05])
    ax2.xaxis.set_tick_params(labelsize=16)
    ax2.yaxis.set_tick_params(labelsize=16)

    # Get ecg object
    ecg_object = ecg.ecg(time_series_filt, sampling_rate=fs, show=False)

    # Get waveform templates
    templates, _ = _get_templates(time_series_filt, ecg_object['rpeaks'], 0.4, 0.6, fs)

    cam_filt, _, _ = filter_signal(signal=cam_filt,
                                   ftype='FIR',
                                   band='bandpass',
                                   order=int(0.3 * fs),
                                   frequency=[3, 100],
                                   sampling_rate=fs)

    # Get cam templates
    cam_templates, _ = _get_templates(cam_filt, ecg_object['rpeaks'], 0.4, 0.6, fs)

    templates_ts = np.linspace(-250, 400, templates.shape[0], endpoint=False)
github Seb-Good / ecg-features / features / feature_extractor.py View on Github external
def _preprocess_signal(self, signal_raw, filter_bandwidth, normalize, polarity_check,
                           template_before, template_after):

        # Filter signal
        signal_filtered = self._apply_filter(signal_raw, filter_bandwidth)

        # Get BioSPPy ECG object
        ecg_object = ecg.ecg(signal=signal_raw, sampling_rate=self.fs, show=False)

        # Get BioSPPy output
        ts = ecg_object['ts']          # Signal time array
        rpeaks = ecg_object['rpeaks']  # rpeak indices

        # Get templates and template time array
        templates, rpeaks = self._extract_templates(signal_filtered, rpeaks, template_before, template_after)
        templates_ts = np.linspace(-template_before, template_after, templates.shape[1], endpoint=False)

        # Polarity check
        signal_raw, signal_filtered, templates = self._check_waveform_polarity(polarity_check=polarity_check,
                                                                               signal_raw=signal_raw,
                                                                               signal_filtered=signal_filtered,
                                                                               templates=templates)
        # Normalize waveform
        signal_raw, signal_filtered, templates = self._normalize_waveform_amplitude(normalize=normalize,
github Tomatenbiss / HRVAnalysisInNoisySignals / mainNew.py View on Github external
def plotEcgSignal(file=f, delimiter="", positionInCsvFile=2):
	return ecg.ecg(signal=getEcgDataFromFile(), sampling_rate=1000., show=True)