Introduction to Matlab

& Data Analysis

Lecture 1: Introduction

Lecture time:

Wednesday 11:00 13:00

Wolfson Hall

Eran Eden, Weizmann 2008

Team members

Lecturers:

Natalie Kalev-Kronik kalev001@umn.edu

Yuval Hart
Maya Geva

Tutors:

Maya Geva
Anat Tzimmer
Yuval Hart

Exercise checkers:

Gil Farkash

Tips / formalities

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

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

Course material: Lectures + tutorials + other Matlab resources

HW and solutions
News

HWs 60% + 40% Final Project

Course references

Official course book: Mastering Matlab 7, Hanselman & Littlefield

Matlab built-in tutorial and references
3

Tips / formalities

Signing up for tutorials

Levine 101
(#1) Sunday 14:00-16:00
(#2) Tuesday 9:00-11:00
(#3) Tuesday 14:00-16:00

HW assistance at the computer room

Once a week in Levine 101
Tuesday 11:00-12:00

Course overview

Introduction to Matlab

Matlab building blocks: 1D 2D and 3D

arrays

Simple data analysis and graphics

Control and boolean logic

Loops

Functions and program design

Cells, structures and Files

Simple algorithms and complexity

Debugger

GUI toolbox

Producing publication quality graphs (Maya Geva)

Solving ODEs for a living:

Math modeling of cancer treatment (Natalie)

Protein production (Prof. Nir Friedman)

TBD (Yuval Hart)

For whom is the course intended?

For students with no or little experience of Matlab- first two thirds of
the course.
Please note that the workload is heavy and each assignment may take
a few hours.
Submit HW with a study partner.
Some overlap or unsynchronized material may occur (lecture, tutorial,
HW).

What is the course about?

(1) Programming in Matlab

(2) Tackling data analysis problems with Matlab

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

What is the course about?

Example #1 of a data analysis problem
Identifying repeating motifs
CAGCATATTTGAAGCCGGGCCCACACACAATTGGGGAACGGATCCCCGCGGCCTCCCGGCA
GACCCCGTCCGGCACGACGACGAAGAAGGGGAGGATGAAGTCGAATTTGAAGCGGATGAAG
GATGAGGAGAGTGACGAAGAAGAGGACGAAGACGACGAGGTCCTTGACGAGGAAGTGAACT
ATTGAATTTGAAGCTTATTCCATCTCAGATAATGATTATGACGGAATTAAGAAATTACTAG
CAGCAGCTTTTCCTAAAGGCTCCTGTGAACACTGCAGAACTAACAGATCTCTTAATTCATA
CAGAACCATATTGGAAGTGTGAATTTGAAGCTTAAGCAAACAAATGTTTCAGAAGACAGCG
ATGATGATGATGCAGATGAAGATGAAATTTTTGGTTTCATAAGCCTTTTAAATTTAACTGA
AAGAAAGGTACCCAGTGTGCTGAACAAATTAAAGAGTTGGTATTTGAAGCGGGTGAGAAGA
ACTGTAAAGAATTTGAAGCGGCAGCTGGACAAGCTTTTAAATGACACCACCAAGCCTGTGG
GCTTTCTCCTAAGTGAAAGATTCATTAATGTCCCTCCTCAGATTGCTCTGCCCATGCACCA
GCAGCTTCAGAAAGAATTTGAAGCAATTTGAAGCCTAGTATTTGAAGCTTCTACCTTCTGA
GACCCCGTCCGGCACGACGACGAAGAAGGGGAGGATGAAGTCGAGGATGAAGACGAAGATC
GATGAGGAGAGTGACGAAGAAGAGGATTTGAAGCACGAAGACGACGAGGTCCTTGACGAGG
AAGTGAATATTGAATTTGAAGCTTATTCCATCTCAGATAATGATTATGACGGAATTAAGAA
ATTACTGCAGCAATTTGAAGCAAAGGCTCCTGTGAACACTGCAGATTTGAAGCAACTAACA
ATTCAACAGAACCATATTGGAAGTGTGATTAAGCAAACAAATGTTTCAGAAGACAGCGATG
ATGATGATGCATTTGAAGCAGATGAAGATGAAATTTTTGGTTTCATAAGCCTTTTAAATTT
CTAATAAGCCATGTGGGAAGTGCTCTTTCTACCTTATTTGAAGCACACCATTTGTGGAAGA
ATTACTGCAGCAATTTGAAGCAAAGGCTCCTGTGAACACTGCAGATTTGAAGCAACTAACA

What is the course about?

Example #2 of a data analysis problem
10

21

10

21

73

21

18

21

10

21

21

10

45

21

21

Image processing
10

What is the course about?

Examples #3-4 of data analysis problems
Signal
processing

11

What is the course about?

(1) Programming in Matlab

(2) Tackling data analysis problems with Matlab

(3) Learn how to learn Matlab by yourself

12

Why Matlab?

Easy to learn

Easy to debug

Great tool for scientific work

Exploring your data

Visualizing your data

Many useful toolboxes

13

Matlabs main disadvantage

Its slower than other programming

languages.

(unless you use the compiler)

14

Background - computers
Output

Processing unit

Input
15

Background - hardware
CPU

Memory

16

Background - hardware
CPU

Memory

A central processing unit (CPU), also referred to as a

central processor unit, is the hardware within a computer
that carries out the instructions of a computer program by
performing the basic arithmetical, logical, and input/output
operations of the system. (Wikipedia).

In computing, memory refers to the physical devices used

to store programs (sequences of instructions) or data (e.g.
program state information) on a temporary or permanent
basis for use in a computer or other digital electronic device.
(Wikipedia).

Not to be confused with the hard disk which is used to store data.

17

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

19

The Matlab environment

Opening/saving a file

Changing current directory

Prompt / Command line

Files and Directories

inside the current
directory

The command window

workspace
20

Matlab can be used as a calculator

21

Our first command

Writing a command in the command line

22

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

23

Making errors

This command does NOT

exist in Matlab!

Pressing here will bring you to

the line in the script where the
error occurred

24

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');
% Record the movie
for j = 1:20
surf(sin(2*pi*j/20)*Z,Z)
F(j) = getframe;
end

-5

% Play the movie twenty times

movie(F,20)

2
0
-2
y

-3

-2

-1

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Help!!!

help
doc

Example: doc disp

Google

26

Matlab toolboxes

27

Introduction to Matlab
& Data Analysis

Topic #2:

The Matlab Building Blocks - Variables,

Arrays and Matrices

Eran Eden, Weizmann 2008

28

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
Cant start with a digit
Cant be a reserved word

Examples of Legal
identifiers:

time
day_of_the_week
bond007
findWord

Examples of illegal
identifiers:

007bond
#time
ba-baluba
if
while
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An overview of the main players in

a program
Identifiers

Reserved
words

Library
functions

Constants

Variables

User defined
functions

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Reserved words (keywords)

Words that are part of the Matlab language

There are 17 reserved words:

for
function
otherwise
try
break
end
return
switch
catch

if
elseif
continue
global
while
case
else
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
100
0.3

Chars
c

Strings
Arrays
[12345]

I like to eat sushi

1 + 2

Matrices
[5 3
4 2]
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Variables

Why do we need variables?

Computer memory
salary
9000

constant
new_salary

variable

27000

Example:

>> salary = 9000;

>> new_salary = salary * 3;
>> disp(new_salary);
27000
Library functions

If we update salary,
new_salary will NOT
be updated
automatically
33

Variables

Another example:

price_bamba = 3

The Matlab Console

price_bamba =
3

What happens if you omit the ; ?

34

Variables

Another example:

price_bamba = 3
n_bamba
= 2;

The Matlab Console

price_bamba =
3

What happens when we add the ; ?

35

Variables

The Matlab Console

Another example:

price_bamba
n_bamba
price_bisly
n_bisly

=
=
=
=

3
2;
5
3;

price_bamba =
3
price_bisly =
5

total_price =
21
n_bamba =
5

total_price =
21

How can
we fix it?

36

Redefine total_price
total_price = price_bamba * n_bamba + price_bisly * n_bisly
n_bamba
= 5
total_price

Variables

Tip #1: Give your variables 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: Dont 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.

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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
a =
10
>> class(a)
ans =
double

Returns the type

of a variable
The default variable type
in Matlab is double
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Variables Types

Double

Double-precision floating-point format is a

computer number format that occupies 8 bytes
(64 bits) in computer memory and represents a
wide dynamic range of values by using floating
point. (Wikipedia).

Allows representation of very large numbers (size of a galaxy) to

very small numbers (subatomic particles).

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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
a =
10

>> b = 10.56
b =
10.5600

>> c = 'Bush'
c =
Bush

>> d = true
d =
1

>> class(a)
ans =
double

>> class(b)
ans =
double

>> class(c)
ans =
char

>> class(d)
ans =
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

1 0 0 0 1 1 0 0

>> b = 'B'
b =
B

1 0 1 1 1 0 0 0

0 0 0 0 1 0 0 0

1 0 0 0 1 0 0 0

%char requires 2 bytes

1
1 0 0 0 1 1 0 0

Memory allocation and

release is done
automatically in Matlab

1 0 1 1 1 0 0 0

How many bytes are required to store this variable: c = 'Bush' ?

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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

ans

>> 4 * 5
ans =
20
>> ans + 1
ans =
21

44

Special variables

ans
pi
inf

>> 2 * inf
ans =
Inf
>> 1 / 0
Warning: Divide by zero.
ans =
Inf

45

Special variables

>> 0 / 0
Warning: Divide by zero.
ans =
NaN

ans
pi
>> NaN + 1
inf
ans =
NaN
NaN
In the tutorial youll see more

46

Summary

Matlab is a high level language

Matlab working environment

Variables & variable types + how to use

them

47

Floating point

From Wikipedia, the free encyclopedia.

In computing, floating point describes a method of representing an
approximation of a real number in a way that can support a wide range
of values. The numbers are, in general, represented approximately to a
fixed number of significant digits (the mantissa) and scaled using an
exponent. The base for the scaling is normally 2, 10 or 16. The typical
number that can be represented exactly is of the form:
Significant digits baseexponentThe idea of floating-point representation
over intrinsically integer fixed-point numbers, which consist purely of
significand, is that expanding it with the exponent component achieves
greater range. For instance, to represent large values, e.g. distances
between galaxies, there is no need to keep all 39 decimal places down
to femtometre-resolution (employed in particle physics).

48

Floating point (continued)

Assuming that the best resolution is in light years, only the 9 most
significant decimal digits matter, whereas the remaining 30 digits carry
pure noise, and thus can be safely dropped. This represents a savings
of 100 bits of computer data storage. Instead of these 100 bits, much
fewer are used to represent the scale (the exponent), e.g. 8 bits or 2
decimal digits. Given that one number can encode both astronomic and
subatomic distances with the same nine digits of accuracy, but because
a 9-digit number is 100 times less accurate than the 11 digits reserved
for scale, this is considered a trade-off exchanging range for precision.
The example of using scaling to extend the dynamic range reveals
another contrast with fixed-point numbers: Floating-point values are
not uniformly spaced. Small values, close to zero, can be represented
with much higher resolution (e.g. one femtometre) than large ones
because a greater scale (e.g. light years) must be selected for
encoding significantly larger values.[1] That is, floating-point numbers
cannot represent point coordinates with atomic accuracy at galactic
distances, only close to the origin.

49

Floating point

The term floating point refers to the fact that a number's radix point
(decimal point, or, more commonly in computers, binary point) can
"float"; that is, it can be placed anywhere relative to the significant
digits of the number. This position is indicated as the exponent
component in the internal representation, and floating point can thus
be thought of as a computer realization of scientific notation.

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