pebm.ebm package¶
pebm.ebm.Biomarkers¶
- class pebm.ebm.Biomarkers.Biomarkers(signal: numpy.array, fs, fiducials=None, matlab_path: Optional[str] = None)[source]¶
Bases:
object
- Parameters
signal – The ECG signal as a ndarray.
fs – The sampling frequency of the signal.
fiducials – Dictionary that includes indexes for each fiducial point
matlab_path – The indexes of the R- points of the ECG signal – optional input
- intervals()[source]¶
- Returns
for every ‘interval’ biomarker.
Interval duration and segments:
P-waveint: Time interval between P-on and P-off.
PRint: Time interval between the P-on to the QRS-on.
PRseg: Time interval between the P-off to the QRS-on.
PRint2: Time interval between P-peak and R-peak as defined by Mao et al.
QRSint: Time interval between the QRS-on to the QRS-off.
QTint: Time interval between the QRS-on to the T-off.
QTcBint: Corrected QT interval (QTc) using Bazett’s formula.
QTcFriint: QTc using the Fridericia formula.
QTcFraint: QTc using the Framingham formula.
QTcHint: QTc using the Hodges formula.
T-waveint: Time interval between T-on and T-off.
TPseg: Time interval between T-off and P-on.
RRint: Time interval between sequential R-peaks.
Rdep: Time interval betweem Q-on and R-peak.
- waves()[source]¶
- Returns
*waves_b: Dictionary that includes all the row data, for every ‘wave’ biomarker. *waves_statistics: Dictionary that includes the mean, median, min, max, iqr and std, for every ‘wave’ biomarker.
P-wave: Amplitude difference between P-peak and P-off.
T-wave: Amplitude difference between T-peak on and T-off.
R-wave: R-peak amplitude.
P-waveArea: P-wave interval area defined as integral from the P-on to the P-off.
T-waveArea: T-wave interval area defined as integral from the T-on to the T-off.
QRSArea: QRS interval area defined as integral from the QRS-on to the QRS-off.
STseg: Amplitude difference between QRS-off and T-on.
J-point: Amplitude in 40ms after QRS-off as defined by Hollander et al.
pebm.ebm.FiducialPoints¶
- class pebm.ebm.FiducialPoints.FiducialPoints(signal: numpy.array, fs: int)[source]¶
Bases:
object
The purpose of the FiducialPoints class is to calculate the fiducial points :param signal: The ECG signal as a two-dimensional ndarray, when the first dimension is the len of the ecg, and the second is the number of leads. :param fs: The sampling frequency of the signal. :param peaks: The indexes of the R- points of the ECG signal – optional input
- wavedet(matlab_pat: Optional[str] = None, peaks: numpy.array = array([], dtype=float64))[source]¶
The wavedat function uses the matlab algorithm wavedet, compiled for python. The algorithm is described in the following paper: Martinze at el (2004), A wavelet-based ECG delineator: evaluation on standard databases. IEEE Transactions on Biomedical Engineering, 51(4), 570-581.
- Parameters
peaks – Optional input- Annotation of the reference peak detector (Indices of the peaks). If peaks are not given, the peaks are calculated with epltd detector.
matlab_pat – Optional input- required when running on a linux machine.
- Returns
*fiducials: Dictionary that includes indexes for each fiducial point.
- property epltd¶
This function calculates the indexes of the R-peaks with epltd peak detector algorithm. This algorithm were introduced by Pan, Jiapu; Tompkins, Willis J. (March 1985). “A Real-Time QRS Detection Algorithm”. IEEE Transactions on Biomedical Engineering. BME-32 (3): 230–236
- Returns
indexes of the R-peaks in the ECG signal.
- pebm.ebm.FiducialPoints.calculate_jqrs(signal, fs, thr, rp)[source]¶
The function is an Implementation of an energy based qrs detector [1]_. The algorithm is an adaptation of the popular Pan & Tompkins algorithm 2. The function assumes the input ecg is already pre-filtered i.e. bandpass filtered and that the power-line interference was removed. Of note, NaN should be represented by the value -32768 in the ecg (WFDB standard). .. [1] Behar, Joachim, Alistair Johnson, Gari D. Clifford, and Julien Oster.
“A comparison of single channel fetal ECG extraction methods.” Annals of biomedical engineering 42, no. 6 (2014): 1340-1353.
- 2
Pan, Jiapu, and Willis J. Tompkins. “A real-time QRS detection algorithm.” IEEE Trans. Biomed. Eng 32.3 (1985): 230-236.
- Parameters
ecg – vector of ecg signal amplitude (mV)
fs – sampling frequency (Hz)
thr – threshold (nu)
rp – refractory period (sec)
debug – plot results (boolean)
- Returns
qrs_pos: position of the qrs (sample)