WaveForm DataBase Toolbox for MATLAB and Octave
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1 WaveForm DataBase Toolbox for MATLAB and Octave Ikaro Silva 1 1 Laboratory for Computational Physiology Massachusetts Institute of Technology February 25, 2014 Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
2 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
3 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
4 Origins of MATLAB and Octave MATLAB MATrix LABoratory ( MATLAB ). Developed by Cleve Moler in the 1970s. Purpose: teach matrix theory at University of New Mexico. Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
5 Origins of MATLAB and Octave Octave Octave is an open source (GPL) project that is similar to MATLAB Developed by John W. Eaton in 1988 for chemical reactor design course Named after his professor, Octave Levenspiel Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
6 What is MATLAB/Octave? Characteristics of the language Scripting language (not strongly typed), biased towards high precision numerical computations: x=1 (defaults to 64 bit double) Integrated development environment with debugger & compiler Heavy use of linear algebra libraries Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
7 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
8 What are the advantages of using MATLAB/Octave? Outline Language syntax and libraries suitable for applying signal processing and linear algebra techniques Graphics Highly portable and very well documented Strong user community Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
9 What are the advantages of using MATLAB/Octave? Language syntax and libraries Very concise and intuitive syntax for developing linear algebra and signal processing algorithms: y= Ax x= A\y Libraries for filter design, wavelets, control systems, neural networks, image processing, statistics... etc Ideal for quickly developing, testing, and cross validating Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
10 What are the advantages of using MATLAB/Octave? Graphics Easy to use and well documented graphics library Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
11 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
12 MATLAB/Octave User Community Used by students, researchers, government, and industry Academic textbooks (Over 5k books in Amazon) Active forum, magazine, developer blogs, and code repository (MATLAB Central) Ranked 14th most popular programming language ( tiobe.com ) Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
13 MATLAB/Octave User Community TIOBE Index : Ranked 14th Increasing trend in user base Ahead of: PL/SQL, Scala, Lisp, and R Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
14 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
15 WFDB Toolbox for MATLAB/Octave Described Description MATLAB/Octave/Java functions for accessing and processing physiologic signals in the formats used by PhysioBank databases Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
16 WFDB Toolbox for MATLAB/Octave Described Contributors Contributors: Sahar Alkhairy, Fernando Andreotti, Joachim Behar, Thomas Brennan, Eudald Bogatell, Gari D. Clifford, Michael Craig, Mohammad Ghassemi, Li-wei Lehman, Erina Katsumata, Sara Mariani, Louis Mayaud, Bla Merela, Benjamin Moody, George Moody, Shamin Nemati, Bryann Tripp, Daniel J. Scott, Ikaro Silva, Gabriel Squillace Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
17 WFDB Toolbox for MATLAB/Octave Described General Information Beta release (February 10, 2014) 31 M-functions Provides access to over 3 TB of physiological signals Interface to LightWave (annotation visualization tool) Multicore processing at JVM level (alpha) Unit tested on 64-bit Windows, Mac, and Linux Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
18 How is the WFDB Toolbox is built? Let s take a look inside Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
19 How is the WFDB Toolbox is built? Structure of the WFDB Toolbox Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
20 How is the WFDB Toolbox is built? Example Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
21 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
22 Installation Web install Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
23 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
24 Exploring the toolbox Demo Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
25 Exploring the toolbox Table of Contents Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
26 Exploring the toolbox Table of Contents Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
27 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
28 MATLAB Doc General Toolbox Info >>doc %Browse to -> Supplemental Software Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
29 MATLAB Doc Function list help Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
30 Outline 1 MATLAB, Octave, and the WFDB Toolbox Origins of MATLAB and Octave What are the advantages of using MATLAB/Octave? User community What is the WFDB Toolbox for MATLAB/Octave? 2 Getting Started Installation Exploring the toolbox Getting help PhysioNet Tools (Alpha) 3 Future work 4 Getting involved Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
31 Exploring data bases Printing database list Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
32 Exploring data bases Database list webview Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
33 Exploring data bases Printing & Downloading signals Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
34 Calling LightWave Displaying data in LightWave (Alpha!) >>wfdbtool( challenge/2013/set-a/a01,[],[],1); Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
35 Future Work Near Horizon Adding unit testing, documentation, tutorial Improving JVM performance and memory efficiency Testing on MATLAB 2014a, Octave 3.8, WFDB , and Java 1.8 Dropping support to MATLAB 2013a and Java 1.6 Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
36 Future Work Long term development Read/write user annotation from LightWave Upload & download data from PhysioNetWorks Have a parallel and distributed computing framework using Hadoop Document and release Java API Suggestions? Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
37 In conclusion Ways to get involved Use the toolbox and submit open-source code to PhysioNet Join the community: Report any bugs, fixes, and enhancement requests: Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, / 37
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