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WaveForm DataBase Toolbox for MATLAB and Octave
Ikaro Silva1
1Laboratory for Computational PhysiologyMassachusetts Institute of Technology
February 25, 2014
Ikaro Silva (MIT) WaveForm DataBase Toolbox for MATLAB and Octave February 25, 2014 1 / 37
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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Origins of MATLAB and OctaveMATLAB
MATrix LABoratory ( MATLAB ).
Developed by Cleve Moler in the 1970s.
Purpose: teach matrix theory at University of New Mexico.
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Origins of MATLAB and OctaveOctave
Octave is an open source (GPL) project that is similar to MATLAB
Developed by John W. Eaton in 1988 for chemical reactor designcourse
Named after his professor, Octave Levenspiel
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What is MATLAB/Octave ?Characteristics of the language
Scripting language (not strongly typed), biased towards high precisionnumerical computations:
x=1 (defaults to 64 bit double)
Integrated development environment with debugger & compiler
Heavy use of linear algebra libraries
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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What are the advantages of using MATLAB/Octave ?Outline
Language syntax and libraries suitable for applying signal processingand linear algebra techniques
Graphics
Highly portable and very well documented
Strong user community
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What are the advantages of using MATLAB/Octave ?Language syntax and libraries
Very concise and intuitive syntax for developing linear algebra andsignal processing algorithms:
y= Axx= A\y
Libraries for filter design, wavelets, control systems, neural networks,image processing, statistics ... etc
Ideal for quickly developing, testing, and cross validating
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What are the advantages of using MATLAB/Octave ?Graphics
Easy to use and well documented graphics library
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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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 )
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MATLAB/Octave User CommunityTIOBE Index : Ranked 14th
Increasing trend in user base
Ahead of: PL/SQL, Scala, Lisp, and R
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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WFDB Toolbox for MATLAB/Octave DescribedDescription
MATLAB/Octave/Java functions for accessing and processingphysiologic signals in the formats used by PhysioBank databases
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WFDB Toolbox for MATLAB/Octave DescribedContributors
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, BlaMerela, Benjamin Moody, George Moody, Shamin Nemati, Bryann Tripp,Daniel J. Scott, Ikaro Silva, Gabriel Squillace
www.against-the-grain.com
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WFDB Toolbox for MATLAB/Octave DescribedGeneral Information
Beta release 0.9.6.1 (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
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How is the WFDB Toolbox is built?
Let’s take a look inside
www.vintageprintable.com
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How is the WFDB Toolbox is built?Structure of the WFDB Toolbox
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How is the WFDB Toolbox is built?Example
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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InstallationWeb install
www.physionet.org/physiotools/matlab/wfdb-app-matlab/
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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Exploring the toolboxDemo
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Exploring the toolboxTable of Contents
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Exploring the toolboxTable of Contents
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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MATLAB DocGeneral Toolbox Info
>>doc
%Browse to -> Supplemental Software
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MATLAB DocFunction list help
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Outline
1 MATLAB, Octave, and the WFDB ToolboxOrigins of MATLAB and OctaveWhat are the advantages of using MATLAB/Octave ?User communityWhat is the WFDB Toolbox for MATLAB/Octave?
2 Getting StartedInstallationExploring the toolboxGetting helpPhysioNet Tools (Alpha)
3 Future work
4 Getting involved
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Exploring data basesPrinting database list
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Exploring data basesDatabase list webview
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Exploring data basesPrinting & Downloading signals
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Calling LightWaveDisplaying data in LightWave (Alpha!)
>>wfdbtool(’challenge/2013/set-a/a01’,[],[],1);
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Future WorkNear Horizon
Adding unit testing, documentation, tutorial
Improving JVM performance and memory efficiency
Testing on MATLAB 2014a, Octave 3.8, WFDB 10.5.23, and Java 1.8
Dropping support to MATLAB 2013a and Java 1.6
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Future WorkLong 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 ?
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In conclusionWays to get involved
Use the toolbox and submit open-source code to PhysioNet
Join the community:www.physionet.org/physiotools/matlab/wfdb-app-matlab/
Report any bugs, fixes, and enhancement requests:[email protected]
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