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

*intervals_b: Dictionary that includes all the row data, for the intervals and segments biomarkers. *intervals_statistics: Dictionary that includes the mean, median, min, max, iqr and std,

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.

isECG()[source]
calculate_isECG(fiducials)[source]

pebm.ebm.fecgyn_tgen

pebm.ebm.fecgyn_tgen.fecgyn_tgen(ecg, qrs, fs)[source]

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.

xqrs()[source]
jqrs()[source]
pebm.ebm.FiducialPoints.calculate_xqrs(signal, fs)[source]
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)

pebm.ebm.IntervalsDuration

pebm.ebm.IntervalsDuration.compute_int(freq, features_dict, factor=1000)[source]
pebm.ebm.IntervalsDuration.compute_QTc(QT, RR, factor=1000)[source]
pebm.ebm.IntervalsDuration.extract_intervals_duration(fs, features_dict, factor=1000)[source]

pebm.ebm.Preprocessing

pebm.ebm.Statistics

pebm.ebm.Statistics.statistics(data_dict)[source]

pebm.ebm.WavesCharacteristics

pebm.ebm.WavesCharacteristics.compute_amp(ecg, features_dict)[source]
pebm.ebm.WavesCharacteristics.compute_area(ecg, freq, features_dict, factor=1000)[source]
pebm.ebm.WavesCharacteristics.extract_waves_characteristics(ecg, freq, features_dict)[source]

Module contents