Python tools for annotated electrocardiogram (aECG) files

Abstract

This python package provides basic functionality to read and index annotated electrocardiogram (aECG) files in HL7 aECG (XML) format. See the TUTORIAL for a quick introduction to examples of use.

See LICENSE and DISCLAIMER at the bottom of this document.

Installing the software

These instructions assume you already have python 3.7.7 or conda installed in your system. The use of a virtual environment is recommended.

Setting up a virtual environment (optional)

Python venv

Setup a virtual environment. In this example, we create the aecgvenv environment in ~/code/virtenvs

cd ~/code/virtenvs
python -m venv aecgvenv

Next, activate the virtual environment

source ~/code/virtenvs/aecgvenv/bin/activate

And upgrade pip to the most recent version

pip install --upgrade pip

Conda (Anaconda)

Launch anaconda prompt/console (from start menu or from anaconda navigator) from the base environment. In this example, we create the aecgvenv environment using the path command line option of conda.

Go to your project directory and create a new environment by typing:

conda create -p aecgvenv

Next, activate the conda environment

conda activate .\aecgvenv

Next, install python 3.7.7 in the conda environment

conda install python==3.7.7

Installing from the source

First, clone the aecg-python repository from https://github.com/FDA/aecg-python or get a copy of the source code as a tar ball.
Change to the directory where you have cloned or downloaded the source code

cd ~/code/aecg-python

Install aecg-python in editable mode so you can both use it and make changes to its source code when developing other tools that use aecg-python. Installing with pip will also install aecg-python dependencies. If you do not plan to do development or debugging, then you can omit the -e flag.

pip install -e .

Run unit tests using pytest (optional)

pytest -v

Development and deployment tips

How to build the package for distribution from the source code

To create a source and wheels distributions by typing python setup.py sdist bdist_wheel in the command line.

How to generate a local copy of the documentation

Additional requirements

pip install sphinx sphinx-autobuild sphinx-autodoc-typehints mock autodoc myst-parser

Once you have installed the additional packages listed above and assuming you have a copy of the source code in ~/code/aecg-python, you can generate a local html version of the documentation from the command line as follows:

cd ~/code/aecg-python/docs
make html

License

This code is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal Public Domain Dedication. This example is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See DISCLAIMER section below, the COPYING file in the root directory of this project and https://creativecommons.org/publicdomain/zero/1.0/ for more details.

Disclaimer

FDA assumes no responsibility whatsoever for use by other parties of the Software, its source code, documentation or compiled executables, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. Further, FDA makes no representations that the use of the Software will not infringe any patent or proprietary rights of third parties. The use of this code in no way implies endorsement by the FDA or confers any advantage in regulatory decisions.

FDA / aecg-python