vital_sqi.common package¶
Submodules¶
vital_sqi.common.generate_template module¶
Generating templates of ECG and PPG complexes
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vital_sqi.common.generate_template.
ecg_dynamic_template
(width, sfecg=256, N=256, Anoise=0, hrmean=60, hrstd=1, lfhfratio=0.5, sfint=512, ti=array([- 70, - 15, 0, 15, 100]), ai=array([1.2, - 5., 30., - 7.5, 0.75]), bi=array([0.25, 0.1, 0.1, 0.1, 0.4]))[source]¶ EXPOSE :param width: :param sfecg: :param N: :param Anoise: :param hrmean: :param hrstd: :param lfhfratio: :param sfint: :param ti: :param ai: :param bi: :return:
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vital_sqi.common.generate_template.
interp
(ys, mul)[source]¶ handy func :param ys: :param mul: :return:
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vital_sqi.common.generate_template.
ordinary_differential_equation
(t, x_equations, rr=None, sfint=None, ti=None, ai=None, bi=None)[source]¶ handy :param t: :param x_equations: :param rr: :param sfint: :param ti: :param ai: :param bi: :return:
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vital_sqi.common.generate_template.
ppg_absolute_dual_skewness_template
(width, e_1=1, w_1=2.5, e_2=3, w_2=3, a=4)[source]¶ EXPOSE Generate a PPG template by using 2 skewness distribution. :param width: the sample size of the generated waveform :param e_1: the epsilon location of the first skew distribution :param w_1: the scale of the first skew distribution :param e_2: the epsilon location of the second skew distribution :param w_2: the scale of the second skew distribution :param a: the order :return: a 1-D numpy array of PPG waveform having diastolic peak at the high position
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vital_sqi.common.generate_template.
ppg_dual_double_frequency_template
(width)[source]¶ EXPOSE Generate a PPG template by using 2 sine waveforms. The first waveform double the second waveform frequency :param width: the sample size of the generated waveform :return: a 1-D numpy array of PPG waveform having diastolic peak at the low position
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vital_sqi.common.generate_template.
ppg_nonlinear_dynamic_system_template
(width)[source]¶ EXPOSE :param width: :return:
vital_sqi.common.rpeak_detection module¶
R peak detection approaches for PPG and ECG
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class
vital_sqi.common.rpeak_detection.
PeakDetector
(wave_type='ppg', fs=100)[source]¶ Bases:
object
Various peak detection approaches getting from the paper Systolic Peak Detection in Acceleration Photoplethysmograms Measured from Emergency Responders in Tropical Conditions
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detect_peak_trough_adaptive_threshold
(s, adaptive_size=0.75, overlap=0, sliding=1)[source]¶ - Parameters
s –
adaptive_size –
overlap – overlapping ratio
- Returns
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detect_peak_trough_clusterer
(s, clusterer='kmean', **kwargs)[source]¶ handy Method 1: using clustering technique
- Parameters
s – The input signals
method – param kwargs:
**kwargs –
- Returns
tuple of 1-D numpy array the first array is the peak list and the second array is the troughs list
- Return type
type
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detect_peak_trough_count_orig
(s)[source]¶ handy Method 2: using local extreme technique with threshold
- Parameters
s – Input signal
- Returns
tuple of 1-D numpy array the first array is the peak list and the second array is the troughs list
- Return type
type
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detect_peak_trough_moving_average_threshold
(s)[source]¶ handy Method 4 (examine second derivative)
- Parameters
s – return:
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detect_peak_trough_slope_sum
(s)[source]¶ handy Method 3: analyze the slope sum to get local extreme
- Parameters
s – return:
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ecg_detector
(s, detector_type='pan_tompkins')[source]¶ Expose
ECG peak detector from the github https://github.com/berndporr/py-ecg-detectors
- Parameters
s – Input signal
fs – The signal frequency. Default is ‘256 Hz’
detector_type –
‘hamilton’: Open Source ECG Analysis Software Documentation, E.P.Limited, 2002.
’christov’:Real time electrocardiogram QRS detection using combined adaptive threshold
’engzee’: A single scan algorithm for QRS detection and feature extraction
’swt’: Real-time QRS detector using Stationary Wavelet Transform for Automated ECG Analysis. Uses the Pan and Tompkins thresolding.
’mva’: Frequency Bands Effects on QRS Detection.
’mtemp’:
’pan_tompkins’: A Real-Time QRS Detection Algorithm
Default = ‘pan_tompkins’
- Returns
an array of 1-D numpy array represent the peak list
- Return type
type
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matched_filter_detector
(unfiltered_ecg)[source]¶ handy FIR matched filter using template of QRS complex. Template provided in generate_template file
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ppg_detector
(s, detector_type=1, clusterer='kmean', preprocess=True, cubing=False)[source]¶ Expose
PPG peak detector from the paper Systolic Peak Detection in Acceleration Photoplethysmograms Measured from Emergency Responders in Tropical Conditions
- Parameters
s – the input signal
detector_type –
clusterer –
- Returns
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