The WFDB Toolbox for MATLAB and Octave is a collection of functions for reading, writing, and processing physiologic signals and time series in the formats used by PhysioBank databases (among others). The Toolbox is compatible with 64-bit MATLAB and GNU Octave on GNU/Linux, Mac OS X, and MS-Windows.
When using any of these functions in your work, please look at the help for that function to see how to cite the original publication and authors.
In addition, please cite the following references in any publication that make use of this toolbox:
For questions, see the FAQ; if your question is not
answered there, or for contributions and feedback, please post at our community forum:
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
Sources for the current version of the Toolbox are available
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).
- 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:
- Open MATLAB or Octave.
- Go into the directory where you wish to install the Toolbox:
- Type (or copy and paste) the following commands into the MATLAB or Octave
[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
To read and plot an ECG signal from one of PhysioBank's data collections, try these commands:
[sig, Fs, tm] = rdsamp('mitdb/100', 1); plot(tm, sig);
If these tests do not run successfully, please see the Toolbox FAQ for troubleshooting hints.
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.
|ann2rr||[source]||Extract a list of intervals from an annotation file|
|bxb||[source]||ANSI/AAMI-standard beat-by-beat annotation comparator|
|dfa||[source]||Detrended Fluctuation Analysis|
|corrint||[source]||Correlation Integral Analysis|
|ecgpuwave||[source]||Estimation of QRS and P waves from ECG signals|
|edr||[source]||Derives a respiration signal from an ECG signal|
|gqrs||[source]||Estimation of QRS from ECG signals|
|lomb||[source]||Estimates power spectrum using the Lomb periodogram method|
|mat2wfdb||[source]||Writes a MATLAB variable into a WDFB record file|
|mrgann||[source]||Merge annotation files|
|msentropy||[source]||Multi scale entropy estimation|
|pbsearch||[source]||Search PhysioBank from MALTAB's browser for records with specific features|
|physionetdb||[source]||Get information about all of PhysioNet's available databases and signals|
|rdann||[source]||Read annotation files for WFDB records|
|rdmat||[source]||Read signal stored in a MAT file, converting it to physical units.|
|rdmimic2wave||[source]||Searches MIMIC II matched waveform records within a clinical time range|
|rdsamp||[source]||Read signal files of WFDB records|
|snip||[source]||Copy an excerpt of a WFDB record|
|sortann||[source]||Rearrange annotations in canonical order|
|sqrs||[source]||Finds the QRS complexes of a WFDB ECG record signal|
|sumann||[source]||Summarize the contents of a WFDB annotation file|
|surrogate||[source]||Generates amplitude adjusted phase shuffled surrogate time series|
|tach||[source]||Calculates instantaneous heart rate of a WFDB ECG record signal|
|visgraph||[source]||Visibility Graph Analysis|
|wabp||[source]||Arterial blood pressure (ABP) pulse detector|
|wfdb||[source]||Prints this help information of the Toolbox|
|wfdb2mat||[source]||Converts a *.dat record file into a MATLAB *.mat file.|
|wfdbexec||[source]||Executes a system call to any installed native WFDB command.|
|wfdbdemo||[source]||Demonstration of the WFDB App Toolbox|
|wfdbdesc||[source]||Return signal information for about a WFDB record|
|wfdbdownload||[source]||Download a WFDB record to the local cache|
|wfdbloadlib||[source]||Loads WFDB Library and returns toolbox version and configuration.|
|wfdbRecordViewer||[source]||GUI for visualizing and analyzing WFDB records and annotations.|
|wfdbtest||[source]||Tests installation of the Toolbox|
|wfdbtime||[source]||Converts sample index to WFDB Time based on WFDB record information|
|woody||[source]||Performs Woody average (averaging with alignment)|
|wqrs||[source]||Finds the QRS complexes of a WFDB ECG record signal|
|wrann||[source]||Writes annotations for WFDB records into annotation files|
|wrsamp||[source]||Writes signal data into WFDB-compatible records|
|xform||[source]||Copy an excerpt of a WFDB record|
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.
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:
Gari D. Clifford
Daniel J. Scott
Previous releases of the WFDB Toolbox for MATLAB and Octave can be found here.
If you would like help understanding, using, or downloading content, please see our Frequently Asked Questions.
If you have any comments, feedback, or particular questions regarding this page, please send them to the webmaster.
Comments and issues can also be raised on PhysioNet's GitHub page.
Updated Wednesday, 31 October 2018 at 16:11 EDT