Introduction to Matlab

& Data Analysis

Lecture 1: Introduction

Lecture time:
Thursday 11:00 – 13:00

Course website: http://www.weizmann.ac.il/midrasha/courses/MatlabIntro/

Eran Eden, Weizmann 2008 © 1

Team members
 Lecturers:
 Natalie Kalev-Kronik [email protected]
 Eran Eden
 Maya Geva

 Tutors:
 Yuval Hart
 Maya Geva

 Exercise checkers:
 Yuval Dorfan
 Anat Tzimmer

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Tips / formalities
 Course website
http://www.weizmann.ac.il/midrasha/courses/MatlabIntro

 The website contains

 Course material: Lectures + tutorials + other Matlab resources
 HW and solutions
 News

 Where can I do the HW?

 On any pc computer at Weizmann (installation of Matlab will be discussed in the
first tutorial)
 In the tutorial class

 Grade
 HWs 60% + 40% ( Exam)

 Course references
 Official course book: Mastering Matlab 7, Hanselman & Littlefield
 Matlab built in tutorial and references

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Tips / formalities
 Signing up for tutorials

(#1) Wed 11:00 – 12:00

(#2) Wed 12:00 – 13:00
(#3) Wed 13:00 – 14:00

 HW assistance at the computer room

Once a week in Levine 101

Tuesday 8-9 am

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Course overview
 Introduction to Matlab
Maya Geva:
 Matlab building blocks: 1D 2D and 3D  Image Processing toolbox
arrays

 Simple data analysis and graphics

 Signal processing tollbox, curvefitting toolbox
Eran Eden
 Control and boolean logic  The Bioinformatics Toolbox
 Unsupervised learning using Statistics
 Loops Toolbox
 Supervised learning & the Artificial Neural
 Functions and program design network Toolbox
 Cells, structures and Files

 Simple algorithms and complexity

 Debugger

 GUI toolbox

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For whom is the course intended?

• For student with no or little experience of Matlab- first two thirds of

the course.
• For students familiar with Matlab who want to expand their knowledge
using Matlab toolboxes- especially last four weeks.

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What is the course about?

(1) Programming in Matlab

(2) Tackling data analysis problems with Matlab

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What is the course about?
Example #1 of a data analysis problem

CAGCATATTTGAAGCCGGGCCCACACACAATTGGGGAACGGATCCCCGCGGCCTCCCGGCA
GACCCCGTCCGGCACGACGACGAAGAAGGGGAGGATGAAGTCGAATTTGAAGCGGATGAAG
GATGAGGAGAGTGACGAAGAAGAGGACGAAGACGACGAGGTCCTTGACGAGGAAGTGAACT
ATTGAATTTGAAGCTTATTCCATCTCAGATAATGATTATGACGGAATTAAGAAATTACTAG
CAGCAGCTTTTCCTAAAGGCTCCTGTGAACACTGCAGAACTAACAGATCTCTTAATTCATA
CAGAACCATATTGGAAGTGTGAATTTGAAGCTTAAGCAAACAAATGTTTCAGAAGACAGCG
ATGATGATGATGCAGATGAAGATGAAATTTTTGGTTTCATAAGCCTTTTAAATTTAACTGA
AAGAAAGGTACCCAGTGTGCTGAACAAATTAAAGAGTTGGTATTTGAAGCGGGTGAGAAGA
ACTGTAAAGAATTTGAAGCGGCAGCTGGACAAGCTTTTAAATGACACCACCAAGCCTGTGG
GCTTTCTCCTAAGTGAAAGATTCATTAATGTCCCTCCTCAGATTGCTCTGCCCATGCACCA
GCAGCTTCAGAAAGAATTTGAAGCAATTTGAAGCCTAGTATTTGAAGCTTCTACCTTCTGA
GACCCCGTCCGGCACGACGACGAAGAAGGGGAGGATGAAGTCGAGGATGAAGACGAAGATC
GATGAGGAGAGTGACGAAGAAGAGGATTTGAAGCACGAAGACGACGAGGTCCTTGACGAGG
AAGTGAATATTGAATTTGAAGCTTATTCCATCTCAGATAATGATTATGACGGAATTAAGAA
ATTACTGCAGCAATTTGAAGCAAAGGCTCCTGTGAACACTGCAGATTTGAAGCAACTAACA
ATTCAACAGAACCATATTGGAAGTGTGATTAAGCAAACAAATGTTTCAGAAGACAGCGATG
ATGATGATGCATTTGAAGCAGATGAAGATGAAATTTTTGGTTTCATAAGCCTTTTAAATTT
CTAATAAGCCATGTGGGAAGTGCTCTTTCTACCTTATTTGAAGCACACCATTTGTGGAAGA
ATTACTGCAGCAATTTGAAGCAAAGGCTCCTGTGAACACTGCAGATTTGAAGCAACTAACA

8
What is the course about?
Example #1 of a data analysis problem

CAGCATATTTGAAGCCGGGCCCACACACAATTGGGGAACGGATCCCCGCGGCCTCCCGGCA
GACCCCGTCCGGCACGACGACGAAGAAGGGGAGGATGAAGTCGAATTTGAAGCGGATGAAG
GATGAGGAGAGTGACGAAGAAGAGGACGAAGACGACGAGGTCCTTGACGAGGAAGTGAACT
ATTGAATTTGAAGCTTATTCCATCTCAGATAATGATTATGACGGAATTAAGAAATTACTAG
CAGCAGCTTTTCCTAAAGGCTCCTGTGAACACTGCAGAACTAACAGATCTCTTAATTCATA
CAGAACCATATTGGAAGTGTGAATTTGAAGCTTAAGCAAACAAATGTTTCAGAAGACAGCG
ATGATGATGATGCAGATGAAGATGAAATTTTTGGTTTCATAAGCCTTTTAAATTTAACTGA
AAGAAAGGTACCCAGTGTGCTGAACAAATTAAAGAGTTGGTATTTGAAGCGGGTGAGAAGA
ACTGTAAAGAATTTGAAGCGGCAGCTGGACAAGCTTTTAAATGACACCACCAAGCCTGTGG
GCTTTCTCCTAAGTGAAAGATTCATTAATGTCCCTCCTCAGATTGCTCTGCCCATGCACCA
GCAGCTTCAGAAAGAATTTGAAGCAATTTGAAGCCTAGTATTTGAAGCTTCTACCTTCTGA
GACCCCGTCCGGCACGACGACGAAGAAGGGGAGGATGAAGTCGAGGATGAAGACGAAGATC
GATGAGGAGAGTGACGAAGAAGAGGATTTGAAGCACGAAGACGACGAGGTCCTTGACGAGG
AAGTGAATATTGAATTTGAAGCTTATTCCATCTCAGATAATGATTATGACGGAATTAAGAA
ATTACTGCAGCAATTTGAAGCAAAGGCTCCTGTGAACACTGCAGATTTGAAGCAACTAACA
ATTCAACAGAACCATATTGGAAGTGTGATTAAGCAAACAAATGTTTCAGAAGACAGCGATG
ATGATGATGCATTTGAAGCAGATGAAGATGAAATTTTTGGTTTCATAAGCCTTTTAAATTT
CTAATAAGCCATGTGGGAAGTGCTCTTTCTACCTTATTTGAAGCACACCATTTGTGGAAGA
ATTACTGCAGCAATTTGAAGCAAAGGCTCCTGTGAACACTGCAGATTTGAAGCAACTAACA

9
What is the course about?
Example #2 of a data analysis problem

10 21 10 21
73 21 18 21
10 4 8 21
3 21 10 45
8 21 2 21

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What is the course about?
Examples #3-4 of data analysis problems

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What is the course about?

(1) Programming in Matlab

(2) Tackling data analysis problems with Matlab

(3) Learn how to learn Matlab by yourself

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Why Matlab?
 Easy to learn

 Easy to debug

 Great tool for scientific work

 Exploring your data
 Visualizing your data

 Many useful “toolboxes”

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Matlab’s main disadvantage…

 It’s slower than other programming

languages.
 (unless you use the compiler)…

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Background - computers
Output

Input
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Background - hardware

CPU Memory

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Background - software
High level languages
Examples: C, C++, C#, Java, Pascal, Perl, Lisp, Matlab

Low level language

Example: Assembly

Machine language
Example: 0111010101111101…
Another important player:
The operating system

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The Matlab environment
First we need to Open Matlab

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The Matlab environment
Opening/saving a file

Changing current directory

Prompt / Command line

Files and Directories

The command window
inside the current
directory

workspace

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Matlab can be used as a calculator

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Our first command
Writing a command in the command line

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Our first script (M-file)
(1) Writing the script (2) Saving the script

Comments start
with a %
(3) Defining script name (4) Running the script

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Making errors…

This command does NOT

exist in Matlab! Pressing here will bring you to
the line in the script where the
error occurred

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Another script…
Making sophisticated graphics and animation in Matlab is easy.
We will learn how to do this in two lectures
Peaks

Z = peaks; surf(Z);
axis tight
set(gca,'nextplot','replacechildren');
5
% Record the movie
for j = 1:20
surf(sin(2*pi*j/20)*Z,Z) 0
F(j) = getframe;
end
-5
% Play the movie twenty times
movie(F,20) 2
3
2
0 1
0
-2 -1
-2
y -3
x

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Help!!!
 help
 doc
 Example: doc disp
 Google

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Matlab toolboxes

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Introduction to Matlab
& Data Analysis

Topic #2:
The Matlab Building Blocks - Variables,
Arrays and Matrices

Eran Eden, Weizmann 2008 © 27

identifiers
 Identifiers are all the words that build up the program
 An identifier is a sequence of letters, digits and underscores “_”
 Maximal length of identifiers is 63 characters
 Can’t start with a digit
 Can’t be a reserved word

Examples of Legal Examples of illegal

identifiers: identifiers:

 time  007bond
 day_of_the_week  #time
 bond007  ba-baluba
 findWord  if
 while

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An overview of the main players in
a program
Identifiers

Reserved Library Constants Variables User defined

words functions functions

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Reserved words (keywords)
 Words that are part of the Matlab language
 There are 17 reserved words:

 for  if
 function
 elseif
 otherwise
 try
 continue
 break
 global
 end
 while
 return  case
 switch  else
 catch  persistent

 Do NOT try to redefine their meaning!

 Don NOT try to redefine their library function names either!

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Constants
 The value of a constant is fixed and does not change
throughout the program

Numbers Chars
100 ‘c’
0.3
Strings
Arrays ‘I like to eat sushi’
[12345] ‘1 + 2’

Matrices
[5 3
4 2]
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Variables
 Why do we need variables?
Computer memory

salary
9000

constant
new_salary
 Example:
27000
>> salary = 9000;
>> new_salary = salary * 3;
>> disp(new_salary);
variable
27000

Library functions
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Variables
 Another example: The Matlab Console

price_bamba =
price_bamba = 3 3

What happens if you omit the ‘;’ ?

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Variables
 Another example: The Matlab Console

price_bamba =
price_bamba = 3 3
n_bamba = 2;

What happens when we add the ‘;’ ?

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Variables
The Matlab Console
 Another example:
price_bamba =
price_bamba = 3 3
n_bamba = 2; price_bisly =
price_bisly = 5 5
n_bisly = 3; total_price =
21

n_bamba =
5

total_price =
21

total_price = price_bamba * n_bamba + price_bisly * n_bisly

n_bamba = 5
total_price
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Variables

 Tip #1: Give your variable meaningful names.

a = 9000
b = 100
are a bad choice for naming variables that store your working hours
and salary!

A more meaningful choice of names would

salary = 9000;
hours = 5;

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Variables

 Tip #2: Don’t make variable names too long

salary_I_got_for_my_work_at_the_gasoline_station = 9000;

salary_I_got_for_my_work_in_the_bakery = salary_I_got_for_my_work_at_the_gasoline_station * 3;

disp(salary_I_got_for_my_work_in_the_bakery);

Very bad choice of variable name!!!

 When should I use capital letters ?

 Tip #3: Whatever you do - be consistent.

37
Variables Types
 Each variable has a type

 Why do we need variable types?

 Different types of variable store different types of data

>> a = 10
a = Returns the type
10 of a variable

>> class(a)
ans = The default variable type
double in Matlab is double
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Variables Types
 Each variable has a type

 Why do we need variable types?

 Different types of variable store different types of data

>> a = 10 >> b = 10.56 >> c = 'Bush' >> d = true

a = b = c = d =
10 10.5600 Bush 1

>> class(a) >> class(b) >> class(c) >> class(d)

ans = ans = ans = ans =
double double char logical
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Variables Types
 Different variable types require different memory allocations

>> a = 10.4 %double requires 8 bytes

a =
10.4
1 2 3 8
 How many bytes are required to store this variable: c = 'Bush' ?
1 0 0 0 1 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 … 1 0 0 0 1 0 0 0

>> b = 'B' %char requires 2 bytes

b =
B Memory allocation and
release is done
1 2 automatically in Matlab

1 0 0 0 1 1 0 0 1 0 1 1 1 0 0 0

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Computer precision limitations
 How much is:
>> 0.42 + 0.08 - 0.5
ans =
0

 How much is:

>> 0.42 - 0.5 + 0.08
ans =
-1.3878e-017

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Special variables
>> 4 * 5
 ans ans =
20

>> ans + 1
ans =
21

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Special variables
>> 2 * inf
ans =
 ans Inf

 pi >> 1 / 0
Warning: Divide by zero.
 inf ans =
Inf

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Special variables
>> 0 / 0
Warning: Divide by zero.
 ans ans =
NaN
 pi
 inf >> NaN + 1
ans =
 NaN NaN
 In the tutorial you’ll see more…

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Summary
 Matlab is a high level language

 Matlab working environment

 Variables & variable types + how to use

them

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