An ECG processing module

version: 1.1.0

This repository host a mixture of function dealing with processing electrocardiogram (ECG) data, and preparing these data for analysis. The processing functions are intended for user defined parametrisation (using user supplied configuration files cnf) about the data which should be extracted, covering signal data such as waveforms or median beats, as well as metadata relevant for downstream QC or as tabular information.

The module implements a basic application programming interface, mapping ECG data from distinct file types (e.g. XML or DICOM) to class attributes providing a fixed interface for downstream analysis and interrogation.

The documentation for ECGProcess can be found here.

Installation

At present, the repository is undergoing development and no packages exist yet on PyPy or in Conda. Therefore it is recommended that it is installed in either of the two ways listed below. First, clone this repository and then cd to the root of the repository.

git clone git@gitlab.com:SchmidtAF/ECGProcess.git
cd ECGProcess

Installation using conda dependencies

A conda environment is provided in a yaml file in the directory ./resources/conda/envs/. A new conda environment called ecgprocess can be built using the command:

# From the root of the repository
conda env create --file ./resources/conda/envs/conda_create.yaml

To add to an existing environment use:

# From the root of the repository
conda env update --file ./resources/conda/envs/conda_update.yaml

Next the package can be installed:

python -m pip install .

Or for an editable (developer) install run the command below from the root of the repository. The difference with this is that you can just to a git pull to update repository, or switch branches without re-installing:

python -m pip install -e .

Installation not using any conda dependencies

If you are not using conda in any way then install the dependencies via pip and install repository as an editable install also via pip:

Install dependencies:

python -m pip install --upgrade -r requirements.txt

Then to install repository you can either do:

python -m pip install .

Or for an editable (developer) install run the command below from the root of the repository. The difference with this is that you can just to a git pull to update repository, or switch branches without re-installing:

python -m pip install -e .

Next steps...

After installation you might wish to try the pytest to confirm everything is in working order.

# From the root of the repository
pytest tests

Usage

Please have a look at the examples in resources for some possible recipes.