Chapter 2

Matlab Tutorial

What is MATLAB?
both a computing environment and a language initially developed as an easy interface to LAPACK: Linear Algebra Package

(FORTRAN libraries) MATrix LABoratory Written in C. For matrix computations, it calls C/Fortran libraries == Fast Matlab + "Toolboxes"
Symbolic Math Toolbox: mathematical manipulation of symbols Partial Differential Equation Toolbox: tools for solving PDEs in 2-D Statistics Toolbox: statistical data analysis Image processing toolbox: visualization and image analysis Bioinformatics toolbox: computational molecular biology Compiler: application development many many more. http://www.mathworks.com

Why Matlab?
The Good:
Fast development times no compiling, easy debugging accessible syntax and language constructs in-house graphics capabilities tons of basic "libraries" or functions available many more complicated "toolboxes" can be added

The Bad:
small coding mistakes can result in slow code loops are extremely computationally intensive language is limited: no templates, classes etc.

The Ugly:
proprietary (but the language format is open) expensive the open source substitue, Octave, is not fully compatible
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How to Matlab?
Lukes 4 big ideas: Let Matlab help you Everything is a matrix tri-development: interactive, scripting, functions (next time) visualize

Let Matlab Help You

>> help >> doc >> lookfor Actually read the error messages

Everything is a Matrix
>> a = [1 2 3 4 5] >> b = some string >> whos >> a(3) >> b(3) >> length(a) >> length(b)

Exercise #1

Exercise #1

do not use loops consider n = 100, 1000, 10000 can be done in 4 lines:

Exercise #1

Exercise #2
Ruffed Grouse: Primary upland game bird of central/northern Wisconsin

Wisconsin DNR data: grouse.dat

1964 1.14 1965 1.02 1966 0.94 . .

First Column: year Second Column: Average number of "drums" per stop (overlap starting at year

1994. Line 34) Plot the data. Are there any trends?

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Exercise #2

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Today: Programming Basics

Three things to keep in mind about Matlab when programming: everything is linear script versus function vectorize vectorize vectorize

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Interpreter vs. Scripts vs. Function

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Interpreter vs. Scripts vs. Function

Interpreter: quick access good for developing ideas good for accessing data in the workspace poor performance and editing/debugging capabilities Script good test bed: all info in the workspace fast, linear poor profiling/optimization Functions can be optimized and cached doesnt fill up the workspace with memory that you have to manage, but... pass by value (ouch!) reuseable code
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Functions
save in functionname.m can have 0, n, or variable number of inputs can have 0, n, or variable number of outputs use return; to leave a function early use inline(...) to define without another file variables not "passed in" are local: only available within

the function scope use global varname; to declare a variable that is visible through all functions

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More on functions:
use eval to call a function from a string varnargin: variable number of argument inputs nargin: number of argument inputs varnargout: variable number of argument outputs nargout: number of argument outputs

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break versus return

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Vectorize!

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More vectorization: Memory

Preallocate memory: set size of the matrix beforehand: A=zeros(n) this allocates a chunk of memory at ones instead of multiple times on the fly

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Hany Vectorized Functions

all(X): true if all elements are nonzero any(X): true if any elements are nonzero is*: checks for *: isnan, isfinite, isinf, isempty, isnumeric find: finds subset satisfying conditions

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Visualizing Data

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Advice on programming
use disp pause spy surf whos profile and semicolons to

help debug and visualize your code. Matlabs in-house debugger often not enough vectorize when you can avoid loops when you can modularize your code...this will take practice

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Advice on "good" code write-ups

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An excercise

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Any Question??

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