ECG Processing and Feature Extraction

This package performs ECG processing on custom datasets followed by feature extraction.

1. R-Peak Detection - Detect R-peaks in 12-lead ecgs using Neurokit2 tool.
2. ECG Delineation - to detect P/QRS/T onset/peak/offset.
3. Feature Extraction - Compute baseline features such as heart rate and ecg-related intervals (PR interval, QT interval, etc.)

Workflow

• Load ECG data from a specified dataset.
• Perform cleaning and preprocessing of ECG signals.
• Detect R-peaks and delineate ECG signals into their physiological components.
• Extract features from the cleaned ECG data.
• Save the extracted features and annotations to output files.

Installation

1. Clone the repository:

   git@github.com:dieterich-lab/ecg_processing.git
   cd ecg_processing
   

2. Install the package:

   pip install -r requirements.txt
   

3. To run the script:

   python main.py
   

Configuration

Edit the config.json file to specify dataset paths and output directories.

Data Loader and Formats

Currently, the pipeline is tested with 3 different datasets i.e. Mediconnect, UK Biobank and MIMIC-IV ECGs. The data loader script for each of these datasets is available under data_loader/ directory.

Now, to use your own dataset, create a data loader under the same directory,

Expected Output

1. A NumPy array of ECG signals (signal_array) with shape (n_samples, n_leads, n_timepoints).
2. The sample frequency (samp_freq).
3. A predefined list of channel sequences (CHANNELS_SEQ).

Extracted ECG Features

Features	Description	Data Type	Units
p_peaks	Amplitude of the P-wave	Float64	mV
p_onsets	Time at the onset of the P-wave	object	msec
p_offsets	Time at the offset of the P-wave	object	msec
q_peaks	Amplitude of the Q-wave	Float64	mV
r_onsets	Time at the onset of the R-wave	object	msec
r_offsets	Time at the offset of the R-wave	object	msec
s_peaks	Amplitude of the S-wave	Float64	mV
t_peaks	Amplitude of the T-wave	Float64	mV
t_onsets	Time at the onset of the T-wave	object	msec
t_offsets	Time at the offset of the T-wave	object	msec
heart_rate	Number of contractions of the heart per minute	Float64	bpm
r_peaks	Amplitude of the R-wave	object	mV
pr_interval	Time between onset of P-wave to onset of R-wave	Float64	msec
qrs_complex	Time between onset of Q-wave to offset of S-wave	Float64	msec
qt_interval	Time between onset of Q-wave to offset of T-wave	Float64	msec
rr_interval	Time between successive R-waves	Float64	msec
st_segment	Time between offset of S-wave to onset of T-wave	Float64	msec