cvxEDA

This program implements the cvxEDA algorithm for the analysis of electrodermal activity (EDA) using methods of convex optimization, described in:

See:

A Greco, G Valenza, A Lanata, EP Scilingo, and L Citi
"cvxEDA: a Convex Optimization Approach to Electrodermal Activity Processing"
IEEE Transactions on Biomedical Engineering, 2015
DOI: 10.1109/TBME.2015.2474131

It is based on a model which describes EDA as the sum of three terms: the phasic component, the tonic component, and an additive white Gaussian noise term incorporating model prediction errors as well as measurement errors and artifacts. This model is physiologically inspired and fully explains EDA through a rigorous methodology based on Bayesian statistics, mathematical convex optimization and sparsity.

The algorithm was evaluated in three different experimental sessions (see paper) to test its robustness to noise, its ability to separate and identify stimulus inputs, and its capability of properly describing the activity of the autonomic nervous system in response to strong affective stimulation.

Python Implementation

To use the software with Python, simply import the cvxEDA module located in the src/ folder, then call the cvxEDA function. Type help(cvxEDA) from the python shell for help on the function's syntax and input/output arguments.

The software does not come with a GUI. Assuming 'y' is a numpy vector with the recorded EDA signal sampled at 25 Hz, the following example performs the cvxEDA analysis (with default parameters) and plots the results:

import cvxEDA
yn = (y - y.mean()) / y.std()
Fs = 25.
cvxeda_results: dict = cvxEDA.cvxEDA(yn, 1./Fs)
[r, p, t, l, d, e, obj] = cvxeda_results.values()
import pylab as pl
tm = pl.arange(1., len(y)+1.) / Fs
pl.hold(True)
pl.plot(tm, yn)
pl.plot(tm, r)
pl.plot(tm, p)
pl.plot(tm, t)
pl.show()

The code reported here has been edited by me (Leonardo) for the purpose of having a pip in installable repository. Indeed, the idea is to be able to run pip install git@github.com:LeonardoAlchieri/cvxEDA.git and be done with it.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

If you use this program in support of published research, please include a citation of the reference above. If you use this code in a software package, please explicitly inform the end users of this copyright notice and ask them to cite the reference above in their published research.

TODOs

Implement pip installable
Remove matlab implementation
Publish the package on pip (?)
Setup some pytests