Introduction to Matlab & Data Analysis

Lecture 1: Introduction

Lecture time:

Sunday 9:00 11:00 Wolfson

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

Eran Eden, Weizmann 2008

Team members

Lecturers:

Natalie Kalev-Kronik kalev001@umn.edu Yuval Hart Maya Geva

Tutors:

Yuval Hart Maya Geva Anat Tzimmer

Exercise checkers:
Anat Tzimmer Ariel Gispan

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% Final Project

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

Tips / formalities

Signing up for tutorials

Levine 101 (#1) Sunday 09:00 11:00 (#2) Wednesday 9:00 11:00 Starts Nov 9, 2011. Choose either.

HW assistance at the computer room

Once a week in Levine 101 Wednesday 11:00-13:00 (Starts Nov 16, 2011)

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 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.

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
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 73 10 3 8 21 21 4 21 21 10 18 8 10 2 21 21 21 45 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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Matlabs main disadvantage

Its 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 inside the current directory

The command window

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
o

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'); % Record the movie for j = 1:20 surf(sin(2*pi*j/20)*Z,Z) F(j) = getframe; end % Play the movie twenty times movie(F,20)
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-5

2 0 -2 y -3 -2 -1 x 0 1 2

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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

The Matlab Building Blocks - Variables, Arrays and Matrices

Topic #2:

Eran Eden, Weizmann 2008

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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 illegal identifiers: 007bond #time ba-baluba if while
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Examples of Legal identifiers: time day_of_the_week bond007 findWord

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
Chars
c

Numbers
100 0.3

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

Example:

27000

variable

>> salary = 9000; >> new_salary = salary * 3; >> disp(new_salary); 27000

Library functions

If we update salary, new_salary will NOT be updated automatically

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Variables

Another example:

The Matlab Console price_bamba = 3

price_bamba = 3

What happens if you omit the ; ?

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Variables

Another example:

The Matlab Console price_bamba = 3

price_bamba = 3 n_bamba = 2; What happens when we add the ; ?

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Variables

Another example:
= = = = 3 2; 5 3;

The Matlab Console price_bamba = 3 price_bisly = 5

price_bamba n_bamba price_bisly n_bisly

total_price = 21
n_bamba = 5

total_price = 21

How can we fix it?

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

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: 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

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 >> b = 10.56 b = 10.5600 >> class(b) ans = double >> c = 'Bush' c = Bush >> class(c) ans = char >> d = true d = 1 >> 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 2
1 0 1 1 1 0 0 0

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0 0 0 0 1 0 0 0

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1 0 0 0 1 0 0 0

1 0 0 0 1 1 0 0

>> b = 'B' b = B 1

%char requires 2 bytes Memory allocation and release is done automatically in Matlab

2
1 0 1 1 1 0 0 0

1 0 0 0 1 1 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

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Special variables

ans pi inf

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

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Special variables

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

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

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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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