WFDB Toolbox for MATLAB and Octave

The WFDB Toolbox for MATLAB and Octave is a set of Java and m-code wrapper functions, which make system calls to WFDB Software Package and other PhysioToolkit applications.

Using the WFDB Toolbox, MATLAB and Octave users have access to over 50 PhysioBank databases (over 3 TB of physiologic signals including ECG, EEG, EMG, fetal ECG, PLETH (PPG), ABP, respiration, and more). Additionally, most of these databases are also accompanied by metadata such as expert annotations of physiologically relevant events in WFDB annotation files. These can include, for example, cardiologists' beat and rhythm annotations of ECGs, or sleep experts' hypnograms (sleep stage annotations) of polysomnograms. All of these physiologic signals and annotations can be read on demand from the PhysioNet web server and its mirrors using the toolbox functions, or from local copies if you choose to download them. This feature allows your code to analyze the wide range of physiologic signals available from PhysioBank without the need to download entire records and to store them locally.

The Toolbox is open-source (distributed under the GNU GPL.) Sources for the current version of the Toolbox are available here (signature). For development snapshots, see the project repository on GitHub. Note that to simplify installation, the Toolbox is distributed with precompiled native executables used by some of its functions. Sources for all of the native executables used in this toolbox can be obtained from PhysioNet (see the individual help files).

Quick Start

Prerequisites:

• 64-bit GNU/Linux, Mac OS X 10.9, or MS-Windows
  Other platforms may also work, but are not supported by the PhysioNet team, and will require compiling the Toolbox from source.
• MATLAB R2014a or later, with a working Java Virtual Machine (JVM) that supports Java 1.7 or later; or GNU Octave 3.8.1 or later with the Java package.

The WFDB Toolbox for MATLAB includes and uses its own copies of the compiled WFDB library and many of the WFDB applications. This means that separate shared libraries and executable applications are components of the toolbox for each supported platform (operating system and CPU). Installing the WFDB Toolbox for MATLAB does not interfere with any separate installation of the WFDB Software Package.

To install or update a previous installation of this Toolbox:

1. Open MATLAB or Octave.
2. Go into the directory where you wish to install the Toolbox:

   cd directoryname
   

3. Type (or copy and paste) the following commands into the MATLAB or Octave window:

   
   [old_path]=which('rdsamp'); if(~isempty(old_path)) rmpath(old_path(1:end-8)); end
   wfdb_url='https://physionet.org/physiotools/matlab/wfdb-app-matlab/wfdb-app-toolbox-0-10-0.zip';
   [filestr,status] = urlwrite(wfdb_url,'wfdb-app-toolbox-0-10-0.zip');
   unzip('wfdb-app-toolbox-0-10-0.zip');
   cd mcode
   addpath(pwd)
   savepath
   
   

Test the Toolbox:

For a demonstration of the toolbox, run

wfdbdemo

To read and plot an ECG signal from one of PhysioBank's data collections, try these commands:

[tm,sig]=rdsamp('mitdb/100',1);
plot(tm,sig);

If these tests do not run successfully, please see the Toolbox FAQ for troubleshooting hints.

Toolbox functions

The toolbox's wrapper functions provide MATLAB and Octave interfaces to some of the most useful stand-alone (command-line) WFDB applications, which are more fully documented here. Many, but not all, of the features of the stand-alone applications are accessible via toolbox wrappers that have the same names as the stand-alone applications; use MATLAB's or Octave's help function to discover which features are available and how to use them. The toolbox's wfdbexec.html allows access to all features of any of the installed WFDB stand-alone applications, including any that are inaccessible via the other wrappers.

Click on the name of any of the toolbox functions in the list below to view its help file (also visible within MATLAB or Octave using the standard help function), or on the adjacent [source] link to view its source m-code.

Frequently Asked Questions

Please make sure you check our list of frequently asked questions before contacting us! For the list of frequently asked questions, see our FAQ.

Acknowledgments

The current WFDB Toolbox for MATLAB and Octave (also known as the WFDB App Toolbox) was created by Ikaro Silva in 2012. The previous WFDB-SWIG Toolbox for MATLAB was created by Michael Craig in 2009. Original contributors of open source native code that is available at PhysioNet are credited in their respective MATLAB wrappers. In addition, the following people contributed to the development or testing of the MATLAB wrappers and the JVM interface:

Previous Releases

Previous releases of the WFDB Toolbox for MATLAB and Octave can be found here.