MATLAB_Class_1

Report
Introduction to MATLAB and
MATLAB Programming
#1
Outline
• Who are we and why are we here? (to
paraphrase James Stockdale, 1992)
• Who am I and how did I get here?
• Who are you and why are you here?
• MATLAB
• Started programming (BASIC) in 1981
• Started imaging algorithm and software
development (Pascal) in 1983
• Cambridge Instruments Quantimet 900
– 1 MB memory
– Booted from 8” floppy disk
– $100,000
• BCC ASET (1983), AA (1986)
– BASIC, Pascal, FORTRAN, x86 Assembler
• TSU BSEE (1986)
• NCSU MSEE (1988)
– MATLAB
– C/C++
– APL, ProLog
• NCSU PhD (1996)
3D ICUS
• 3D Intracoronary Ultrasound
• Lumen and medial-adventitial boundary
estimation
3D Imaging Geometry
 xw 
y 
~
X   w
 zw 
 
1
zw
xw
yw
v
u
u 
~
x   v 
1 
C
u
v
u
~
x   v 
 1 
C
TIPS
Surgical Planning
MRA Vessel Extraction
Objectives
• Develop a basic working knowledge of
MATLAB (notation, syntax, built-in functions)
• Learn to use the command line (MATLAB as a
calculator)
• Learn to develop scripts and functions
• Learn basic programming skills
• Learn to use the debugger to troubleshoot
scripts and functions
Objectives
• Generate 2D and 3D data plots
• Read, write, and manipulate numeric data
(e.g. text files, binary files, Excel)
• Read, write, manipulate, and display image
data
• Learn the basics of linear algebra
• Learn about the FFT and complex variables
What is MATLAB?
• MATLAB - Matrix Laboratory
• What is a matrix?
– Fundamental data type in MATLAB
– An image
• What is an image?
– A rectangular array of numbers
– A point in a high-dimensional space
– A representation of a system of equations
What is MATLAB?
• What is a matrix?
n
m
n
m
– A linear mapping from R to R (or C to C )**
• What’s a linear mapping?
• Lines map to lines. Origin maps to the origin.
– A collection of vectors
– What is a vector?
» Magnitude and direction (velocity, force, etc.)
» An n-tuple of numbers
What is MATLAB?
• History
– Netlib (netlib.org)
• Large software library written in FORTRAN (FORmula
TRANslator)
– Cleve Moler (EISPACK, LINPACK, cofounder of
MathWorks)
• Computing environment for technical
computation, visualization, design, simulation,
and implementation in a wide range of
application areas.
Common MATLAB Applications
• Numerical Methods
– Linear algebraic equations
– Roots and optimization
– Curve fitting
– Integration and differentiation
– Differential equations
• MATLAB toolboxes
– Statistics, optimization, image processing,
computer vision, bioinformatics, …
Why MATLAB?
• Pros:
– Easy to start using MATLAB with little or no prior
programming experience
– Relatively easy to learn
– Can be used as a calculator or as a programming
language
– Can be used to test simple algorithms (command
line or scripts) prior to coding in a higher-level
language
Why MATLAB?
• Pros:
– MATLAB has a large library of optimized, robust
mathematical functions
– MATLAB has a large collection of very powerful
toolboxes (e.g. image processing, statistics)
– Easy to produce 2D and 3D graphs
Why Not MATLAB?
• Cons:
– Cost associated with ease of use
• Interpreted language
• Slow (10-100x) compared to some other programming
languages (e.g. C, C++, FORTRAN, Pascal)
• May be too slow to solve large problems
– Fairly expensive (free alternatives available)
– Designed for scientific computing
• Not always the best solution for other applications
2-by-2 System of Equations
• Can solve graphically
• Can add/subtract equations
x y 4
x y 0
2x  4
2y  4
x2
y 2
2-by-2 System of Equations
• Can solve with the cross or outer product
– cross ()
 1  1   4 
2
2
     
 
1  1  4  2   
     
 
2
  4   0    2 
 1 
n-by-n System of Equations
• What about higher dimensions?
• Cross product only works in 3D.
• Harder (impossible?) to visualize.
– Circuit analysis example
• Graph theory (non-planar) and linear algebra
• 6-by-6 system of equations
Matrix Operations
• The entry (or element) in row i and row j of a
matrix, A, is denoted by aij
• The entry in row i of a vector (i.e. matrix with
only one column) v is denoted by vi.
 a11

A  a 21

 a 31
a12
a13
a 22
a 23
a 32
a 33
a14 

a 24

a 34 
 v1 
 
v2


v 
 v3 
 
 v4 
Matrix Operations
• Two matrices are equal if:
– They are the same size
– All corresponding entries are equal
• Two matrices can be added together if they
have the same size (i.e. the same number of
rows and columns)
C = A+B
c ij  a ij  bij
Matrix Operations
• Multiplication by a scalar
 a11
cA  c 
 a 21
a12   ca11
 
a 22   ca 21
ca12 

ca 22 
• Matrix-vector multiplication
n
b  Ax
bi   a ij x j
j 1
– If A is m-by-n and x is n-by-1, b is m-by-1.
Matrix Operations
• Matrix-vector multiplication
Ax = b
 a11

a
 21
 a 31
a12
a13
a 22
a 23
a 32
a 33
 x1 
a14     a11 x1  a12 x 2  a13 x 3  a14 x 4   b1 
  x2  
  
a 24
 a 21 x1  a 22 x 2  a 23 x 3  a 24 x 4  b 2
 x  
  
3
a 34     a 31 x1  a 32 x 2  a 33 x 3  a 34 x 4   b3 
 x4 
Matrix Operations
• Matrix-matrix multiplication
n
C  AB
c ij   a ik b kj
k 1
– If A is m-by-r and B is r-by-n, C is m-by-n.
Matrix Operations
• Matrix-matrix multiplication
– To find cij (i.e. the element of C in row i and
column j) multiply corresponding entries in row i
of A and column j of B, and add them together.
C  AB
 a11

 a 21
a12   b11

a 22   b 21
b12   a11b11  a12 b 21
 
b 22   a 21b12  a 22 b 21
a11b12  a12 b 22   c11

a 21b12  a 22 b 22   c 21
c12 

c 22 
Matrix Operations
AB BA
A + B + C  = A + B  + C
A BC  =  AB C
A B + C  = AB + AC
B + C  A
= BA + CA
AB  BA
Matrix Operations
• Zero matrix
– A matrix where each element is 0
– zeros()
0

0
04  
0

0
0
0
0
0
0
0
0
0
0

0

0

0
Matrix Operations
• Identity matrix
– Square (i.e. m=n)
– Diagonal entries equal to 1; all others are 0.
– Multiplication by the identity matrix doesn’t
change the matrix
– eye()
1 0 0 0


0

I4 
0

0
1
0
0
1
0
0


0

0

1
Row Reduction
• Elementary row operations
– Multiply a row by a scalar.
– Add a scalar multiple of one row to another.
– Exchange two rows.
• Solve Ax=b
– Row reduction with augmented matrix
 a11

a
 21
 a 31
a12
a13
a 22
a 23
a 32
a 33
b1 
1


b2  0


 0
b3 
0
0
1
0
0
1
x1 

x2

x 3 
2-by-2 cont’d
• Back to 2-by-2 example
– Rewrite as a matrix equation
x y 4
x y 0
1

1
1  x   4 
    
 1  y   0 
– Form an augmented matrix
1

1
1
1
4

0
2-by-2 cont’d
• Solve by row reduction
– Make left side look like an identity matrix using
only elementary row operations
1

1
1

0
1
1
1
2
4

0
4

4 
1 1

0 1
4

2
1

0
2

2
0
1
Rank
• r=rank(A)
• Number of leading 1’s in the row-reduced
matrix
• From previous example, rank(A)=2
1

1
1
1
4
1
 
0
0
0
1
2

2
Matrix Inverse
• Matrix inverse
– A must be square and full rank
– If a matrix can be found such that AB=In, then B is
called the inverse of A.
2-by-2 cont’d
• Computing the inverse
A
1

1
1

0
I    I
1
1
1
0
1

0
0

1
1
1
2
1
1 1

0 1
-1
A 
1
0.5
0
0.5
1
0.5
0

1
0

 0.5 
0.5 

 0.5 
1
x A b
 0.5

 0.5
0.5   4   2 
    
 0.5   0   2 
Matrix Inverse
-1
• If A is n-by-n and rank(A)=n, then A exists.
– Implies there is a solution for every b
• b is in the range of A
– inv()
• If A and B are both invertible,
1
A 
1
 AB 
 A
1
1
B A
1
2-by-2 cont’d
• Inconsistent (no solution)
– n=2, Rank=1
– Inverse doesn’t exist
x y 4
x y 5
1

1
1

0
1  x   4 
    
1  y   5 
1
0
4

1
2-by-2 cont’d
• Consistent (infinite solutions)
– n=2, Rank=1
– Inverse doesn’t exist
x y 4
2x  2 y  8
1

2
1  x   4 
    
2   y  8 
1

0
1
0
4

0
Matrix Transpose
• Transpose (‘ in MATLAB)
– Swap rows and columns
B  A
T
A 
T
bij  a ji
1

3

 5
 A
A  B  A + B
T
 cA 
T
2
1

4
 

2
6 
T
3
4
5

6
T
 AB 
T
T
 cA
T
B A
T
T
T
Scalar Product
• Also called inner or dot product
– Vectors must have the same length (size)
– Multiply corresponding elements and add
n
uv =
uv
i
i 1
i
 u 1 v1  u 2 v 2 
 u nvn
Scalar Product
• Inner (dot) product
 u1 
 
u = u2
 
 u 3 
 v1 
 
v  v2
 
 v 3 
u v  u 1 v1  u 2 v 2  u 3 v 3
T
– Also written as:
uv  u v  u
T
v cos  

Scalar Product
• Properties
u  v  v u
u v  w   u  v  u w
k  u  v    ku   v  u   kv 
vv  0
vv  0  v = 0
Norms
• Vector norms
– 1-norm
n
x
1


xi
i 1
– 2-norm (Euclidean norm or length)
n
x
2


xi 
2
T
x x
i 1
– Infinity-norm
x

 m ax  x1 , x 2 ,
, xn

Norms
• Matrix Norm
– 1-norm (column sum)
m
A
1
 m ax  a ij
1 j  n
i 1
– 2-norm – later
n
– Infinity norm (row sum)
– Frobenius norm
A

 m ax  a ij
1 i  m
m
A
F

j 1
n

i 1
j 1
2
a ij
Norms
• Vector norm properties
x 0
x 0 x0
x   x
x+y  x  y
• Matrix norm properties
A 0
A   A
A+B  A  B
AB  A
B
Vector Product
• Also called the cross product
– 3D only
u 2 v 3 - u 3 v 2 


u  v  u 3 v1 - u1v 3


 u 1 v 2 - u 2 v 1 
Vector Product
• Properties
u  v   u  v 
uv  w  u v  u w
u  v   w  u  w    v  w 
k  u  v    ku   v  u   kv 
u0  0u  0
uu  0
Unit Vectors
• Unit vector
v
uˆ 
v
uˆ  1
• Projections
T
w 
u v
v
2
v
Noise
• Always present
• Quantization noise
• Finite word length (data type differences (intn,
uintn, float, double)
– Catastrophic cancellation
• Electronic noise, photon noise, etc.
• When is it a problem? Depends on the problem.
• Be aware of effects of noise!
Ill-Conditioning
x  2y  4
2 x  3.999 y  7.999
1

2
 x  4 
   

3.999   y   7.999 
2
Ill-Conditioning
• Results are sensitive to noise
• Loss of precision
• cond() – condition number
x  2 y  4.001
2 x  3.999 y  7.998
1.001 x  2.001 y  4
2.001 x  3.998 y  7.999
Ill-Conditioning
• Trefethen least-squares ill-conditioned
example (14th-order polynomial fit)
• Solution by different methods
– \ - matrix divide
– inv() – matrix inverse
– LU() – LU decomposition
– QR() – QR decomposition
– SVD() – Singular value decomposition
MATLAB Workspace
•
•
•
•
•
Using MATLAB as a calculator
Command window
Command history
Current directory
Workspace
MATLAB Workspace
•
•
•
•
Help browser
diary()
Saving/loading the workspace
Quitting MATLAB
Variables, Assignments, and
Keywords
• Datatypes - scalars, vectors ([1, 2, 3, 4], [1:4]),
matrices ([m,n], [1, 2; 3, 4]), uintn, intn,
double, char, structs, cells, classes
• Vector – magnitude and direction, n-tuple
n
m
n
m)
• Matrix – mapping from R to R (or C to C ,
collection of vectors, representation of an
image, representation of a system of
equations
Variables, Assignments, and
Keywords
•
•
•
•
Entering variables, vectors and matrices
Incrementation and overwriting of variables
Recalling expressions and making corrections
Addressing vector and matrix elements
– v(m:n), v(m:step:n), v([1 3 5 2 4 6])
– A(:,j), A(i,:), A(i,j:end)
Matrix Properties
•
•
•
•
•
•
•
•
•
size(), length()
Manipulating vectors and matrices
reshape(), transpose operator(‘)
Transpose algebra
Inverse algebra
Row/column vectors
Matrices from vectors
Semicolons – index generator
Vector and matrix norms (1, 2, infinity, Frobenius)
Special Matrices
• Square, symmetric, skew-symmetric, diagonal,
identity, upper/lower triangular, banded or
Toeplitz, circulant, Vandermonde
• eye(), zeros(), ones(), diag(), toeplitz(), rand(),
randn(), etc.
Notation and Operators
•
•
•
•
Colon notation
Indexing
Conformance
Expressions, operators (normal and elementwise), and operator precedence (+, -, *, /, ^, :,
;, ,, …, %, ‘, =, (), [], .+, .-, .*, ./, .^, .\, .’, < <=, >,
>=, ==, ~=, &, |, &&, ||)
• Operator Precedence
Built-In Functions
• cd, clc, clear, clear x, dir, pwd, exist, type, who,
which
• linspace
• disp, length, ndims, numel, size
• cross, diag, dot, end, kron, max, min, prod,
reshape, sort, sum, size
• det, inv, linsolve, lu, norm, null, orth, rank, rref,
trace
• cond – condition number and loss of precision
Operators
• Calculations with vectors and matrices (+, -, *,
^, .*, .^)
• Operators and element-wise operators
• Solving linear systems (inv, LU, QR, SVD,
normal equations, pseudo-inverse)
• Inconsistent
• Consistent, full rank
• Consistent, rank-deficient
Operators
•
•
•
•
Least squares fitting
Robust fitting
Matrix inverse
Matrix functions (det, diag, eig, inv, norm,
rank)
Special Variables
• ans, eps, i, j, NaN, pi, Inf, and –Inf
Programming
• Writing your own functions (implies input and output
arguments, variables in local workspace)
• Functions
– [output_argument_list]=function
function_name(input_argument_list)
• Scripts (implies no input or output arguments,
variables in global workspace)
– Variables in the global workspace may be overwritten
– Script execution can be affected by variables in the global
workspace
– Advisable to use functions for large and/or complicated
applications
Programming cont’d
•
•
•
•
•
•
•
•
•
Comments (%)
Recursion
Pretty print
Operation types
Sequential (commands executed in order)
Conditional (if-then-else, switch-case)
Iterative (for loops, do loops)
Structured programing
Reusable code
Programming - Flow Control
• Looping
– for-end
– Indexing (also reverse indexing)
– while-end
– break
– continue
– return
Programming - Flow Control
• Conditional statements
– if-elseif-else-end
– Relational operators (>, <, >=, <=, ==, ~=, &, |, ~)
– Boolean algebra (truth tables, Karnaugh maps,
DeMorgan’s Law)
– bitor, bitand, bitxor, xor, and, or, not
– switch-case-end
Debugging
•
•
•
•
•
•
•
•
•
•
Breakpoints
Conditional breakpoints
Step into
Step over
Return
Examining variables
dbquit
disp()
End debugging from menu
Function keys
Help System
• Help command
• Product Help
Editor
• Editor window
• Pretty print (smart indent, ctrl-i)
• Comments - % (ctrl-r, ctrl-t)
I/O – Plotting and Graphics
•
•
•
•
•
2D/3D Plots
Plotting points and lines
plot(), plot3(), surf(), mesh()
Line color and style (color, linestyle)
Marker color and style
General I/O
•
•
•
•
•
To/from screen and files
Binary and text file I/O
format (format long, format short, etc.)
Numerical format
load, save, fopen, fscanf, fprintf, sprintf, fclose
Image I/O
•
•
•
•
imread, imwrite, imshow, imagesc, colormap
Image types
Image manipulation
Image display (imshow, imscale)
Fourier
•
•
•
•
•
•
•
Complex variables
Complex algebra
Complex exponential
Fourier series
Fourier transform
Fast Fourier transform
Sampling
GUI Development
• Event-driven programming
• Design and implementation
Matrix Decompositions
• LU, Cholesky, QR, SVD
• Condition number, accuracy, FLOPS
Equation Solving
•
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•
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Matrix division
inv(), \, /
Pseudo-inverse
LU decomposition
QR decomposition
SVD
Operation counts versus robustness
Least-Squares
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Normal equations
Pseudo-inverse solution
Ill-conditioning
SVD solution
Camera calibration
3D measurement
Eigenvalues
• eig()
Performance
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Vectorization
Preallocation of variables
Timing (tic, toc)
Profiler
Toolbox Overview
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Signal Processing
Image Processing
Statistics
Optimization
Parallel Processing
Image Processing and Image Analysis
• Morphology
• Filtering
• Convolution

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