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

The package is available on PyPI, and conda, with the latest source code available on gitlab.

Installation using PyPI

To install the package from PyPI, run:

pip install ecgprocess

This installs the latest stable release along with its dependencies.

Installation using conda

A Conda package is maintained in my personal Conda channel. To install from this channel, run:

conda install afschmidt::ecgprocess

Installation using gitlab

If you require the latest updates, potentially not yet formally released, you can install the package directly from GitLab.

First, clone the repository and move into its root directory:

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

Install the dependencies:

# 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:

make install

Development

For development work, install the package in editable mode with Git commit hooks configured:

make install-dev

This command installs the package in editable mode and configures Git commit hooks, allowing you to run git pull to update the repository or switch branches without reinstalling.

Alternatively, you can install manually:

python -m pip install -e .
python .setup_git_hooks.py

Git Hooks Configuration

When setting up a development environment, the setup-hooks command configures Git hooks to enforce conventional commit message formatting and spell check using codespell.

To view the commit message format requirements, run:

./.githooks/commit-msg -help

For frequent use, add this function to your shell configuration (~/.bashrc or ~/.zshrc):

commit-format-help() {
    local git_root
    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
    
    if [ -z "$git_root" ]; then
        echo "Error: Not inside a git repository"
        return 1
    fi
    
    local hook_path="$git_root/.githooks/commit-msg"
    
    if [ ! -f "$hook_path" ]; then
        echo "Error: commit-msg hook not found"
        return 1
    fi
    
    "$hook_path" --help
}

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.