Scientific Computation and

Programming

PYTHON, R, MATLAB, FREEMAT

 What is Python?

 A programming language with strong similarities to

PERL (Practical Extraction and Report Language),
but with powerful typing and object oriented
features.
 Commonly used for producing HTML (HyperText Markup
Language) content on websites. Great for text files.
 Useful built-in types (lists, dictionaries).
 Clean syntax, powerful extensions.
 Why Python?

 Natural Language ToolKit

 Ease of use; interpreter
 The scientist‟s need:
- Get data (simulation, experiment control)
- Manipulate and process data
- Visualize results (to understand what we are
doing)
- Communicate results: produce figures for reports
or publications, write presentations
 Advantages of python

 Very rich scientific computing libraries (a bit less

than Matlab, though)
 Well thought out language, allowing to write very
readable and well structured code: we “code what we
think”.
 Many libraries for other tasks than scientific
computing (web server management, serial port
access, etc.)
 Free and open-source software, widely spread, with a
vibrant community
 Drawbacks of Python

 less pleasant development environment than, for

example, Matlab. (More geek-oriented).
 Not all the algorithms that can be found in more
specialized software or toolboxes.
 Python Readings

Things to read through

 “Dive into Python” (Chapters 2 to 4)
http://diveintopython.org/
 Python 101 – Beginning Python
http://www.rexx.com/~dkuhlman/python_101/python_101.htm
l
Things to refer to
 The Official Python Tutorial
http://www.python.org/doc/current/tut/tut.html
 The Python Quick Reference
http://rgruet.free.fr/PQR2.3.html
 R

 A programming environment for data analysis and

graphics
 Software for Statistical Data Analysis
 R is a software that provides a programming
environment for doing statistical data analysis. This
software was written by Robert Gentleman and Ross
Ihaka and the name of the software bear the name of
the creators. R can be effectively used for data
storage, data analysis and a variety of graphing
functions. R is distributed free and it is an open
source software.
 The ‘R’ Environment

 R is an integrated suite of software facilities for data

manipulation, calculation and graphical display.
 an effective data handling and storage facility
 a suite of operators for calculations on arrays, in particular
matrices
 a large, coherent, integrated collection of intermediate tools
for data analysis
 graphical facilities for data analysis and display either directly
at the computer or on hardcopy
 a well developed, simple and effective programming language
(called „S‟) which includes
 conditionals, loops, user defined recursive functions and input
and output facilities. (Indeed
 most of the system supplied functions are themselves written
in the S language.)
R Window
 Scalars, Vectors and Matrices

 Like in many other programs, R

organizes numbers in scalars (a
single number { 0-dimensional),
vectors (a row of numbers, also
called arrays {1-dimensional) and
matrices (like a table { 2-
dimensional).
Strengths and Weaknesses of R

 Strengths
 Free and Open Source

 Strong User Community

 Highly extensible, flexible

 Implementation of high end statistical

methods
 Flexible graphics and intelligent defaults

 Weakness
 Steep learning curve

 Slow for large datasets

 Matlab
 Matlab is basically a high level language which has
many specialized toolboxes for making things easier
for us
 How high?
Matlab

High Level
Languages such as
C, Pascal etc.

Assembly
 What is MATLAB?

 High level language for technical computing

 Stands for MATrix LABoratory
 Everything is a matrix - easy to do linear algebra

 MATLAB is a powerful, general-purpose

system or environment for doing
mathematics, scientific and engineering
calculations.
 The MATLAB System

 Development Environment

 Mathematical Function Library

 MATLAB language

 Application Programming
Language
 Matlab Screen
 Command Window
 type commands

 Current Directory
 View folders and m-files

 Workspace
 View program variables

 Double click on a variable

to see it in the Array Editor

 Command History
 view past commands

 save a whole session

using diary
 Arrays, Vectors, and Matrices

 Array :
 A collection of data elements
arranged in rows and columns
 Vector:
 A one-dimensional array (single >> A=[1:9] row or column?
row or single column of data
elements) >> B=[1:9]‟ column vector

 Matrix :
>> C=[1:3; 4:6; 7:9]
 A two-dimensional array (more
than one row and/or column of
C=
data elements) 1 2 3
4 5 6
7 8 9
 Variables
 No need for types. i.e.,

int a;
double b;
float c;

 All variables are created with double precision unless

specified and they are matrices.
Example:
>>x=5;
>>x1=2;

 After these statements, the variables are 1x1 matrices

with double precision
 Display Facilities
0.7

 plot(.) 0.6

0.5

0.4

Example: 0.3

>>x=linspace(0,4*pi,100); 0.2

>>y=sin(x); 0.1

>>plot(y)
0

-0.1
>>plot(x,y) -0.2

-0.3
0 10 20 30 40 50 60 70 80 90 100

 stem(.)
0.7

0.6

0.5

0.4

Example:
0.3

0.2
>>stem(y) 0.1

>>stem(x,y) 0

-0.1

-0.2

-0.3
0 10 20 30 40 50 60 70 80 90 100
 Display Facilities

 title(.)

>>title(‘This is the sinus function’)

This is the sinus function
1

0.8

0.6

 xlabel(.) 0.4

0.2

sin(x)
0

-0.2
>>xlabel(‘x (secs)’) -0.4

-0.6

 ylabel(.) -0.8

-1
0 10 20 30 40 50 60 70 80 90 100
x (secs)

>>ylabel(‘sin(x)’)
 MATLAB WORKSHOP

WORKSHOP
WebPages

www.csee.wvu.edu/~jalali
 Advantages of MATLAB

 This is a powerful and versatile simulation software,

very popular in industry and academia
 due to its exibility in allowing direct programming
and linking to FORTRAN and C routines, the
package has grown immensely, with many added
routines to allow numerical simulations of nonlinear
systems as well.
 Drawbacks_MATLAB

 Its size and relative complexity; it takes some time to

become familiar with its language and become
familiar with several of the main routines needed for
basic simulations.
 Equations must be handled in certain form and
sequence, requiring the user to be familiar with the
phenomena being analyzed, making it somewhat
complex for inexperienced users
 Good comprehension of numerical analysis, linear
algebra and linear systems is required, which makes
it somewhat inappropriate for learners or beginners
 Freemat

 FreeMat is an open software package that provides

all the basic functions of MATLAB
 It lacks the sophisticated toolboxes provided by the
MATLAB, but it works perfectly if you use basic
functions
Freemat Window
 Freemat Info

 FreeMat is a numerical computational package designed

to be compatible with other numerical packages such as
Matlab and Octave. The supported operating systems for
FreeMat include Windows, Linux, and Mac OS X. Samit
Basu created this program with the hope of constructing
a free numerical computational package that is Matlab
friendly. The web page of FreeMat at www.freemat.org.
states that some of features for FreeMat include
eigenvalue and singular value decompositions, 2D/3D
plotting, parallel processing with MPI, handle-based
graphics, function pointers, etc. To download FreeMat,
go to http: //sourceforge.net/projects/freemat.