Java for Digital Signal Processing

In a Nut Shell
(Draft: February 1, 2007)
Jarmo T. Alander
University of Vaasa, Finland
Department of Electrical Engineering and Automation
Java for
Digital Signal Processing
(AUTO1030 course)
Spring 2007
int[] A = {1,2,1};
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This document can be found in the Web at
ftp://ftp.uwasa.fi/cs/AUTO/AUTO1030/JavaDSPprinter.pdf
as this printer friendly hand-out version, or at
ftp://ftp.uwasa.fi/cs/AUTO/AUTO1030/JavaDSP.pdf
as a slide show. All comments are warmly welcome.
ftp://ftp.uwasa.fi/cs/AUTO/AUTO1030/DSP.java
contains the Java source code used in this document.
c 2006, 2007 Jarmo T. Alander. These are the revised (February 1, 2007) web notes of a lecture of Java usage for DSP.
1
Java & DSP CONTENTS
Contents
1 Introduction 4
1.1 Project group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2 Why Programming and DSP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 Why Java . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4 Why not DSP assembler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.5 Why not Matlab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.6 Why mathematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.7 Why image processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.8 Why in English . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.9 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.10 Examples of signal processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2 Numerics 6
2.1 Arithmetic operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2 Division and multiplication by 2
n
can be done efciently . . . . . . . . . . . . . . . . . . 6
3 Methods 7
3.1 Methods and classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.2 Example 1: constant vector or signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.3 Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3.4 Constant vector by Java . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.5 Example 2: Moving average . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.6 Method as a black box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.7 Example 3: combining methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.8 Example 4: derivative1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.9 Example 5: method add . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.10 Example 6: FIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.11 Example N (long): NIRS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.12 Sqrt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.13 S/N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4 Classes 19
4.1 DSP class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.2 Example class DSP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.3 Graphical representation: container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
5 Image Processing 23
6 Hyperimage processing 24
6.1 What is hyperimage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
7 Conclusions and Future 25
7.1 Future . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
7.2 Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
7.3 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
A Solutions to problems 27
A.1 Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
A.2 Useful links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2
Java & DSP CONTENTS
Trademarks
Java is a registered trademark of Sun Microsystems, Inc.
This document was typeset by the author using Leslie Lamports L
A
T
E
X(http://www.latex-project.org/)
extension of Donald Knuths T
E
Xtypesetting systemand Beamer (http://latex-beamer.sourceforge.net/)
extension of L
A
T
E
X for slides.
3
Java & DSP 1 INTRODUCTION
1 Introduction
Abstract
This is a draft for a tutorial for Java programming for solving basic signal processing problems. The
goal of this tutorial is to help students to learn how to use computer programming as a tool to design
and implement signal processing methods. This tutorial contains basics of Java syntax and semantics,
examples of DSP problems solved by Java, and references to further reading.
Keywords: digital signal processing, image processing, Java, object-oriented programming,
1.1 Project group
Persons more or less inuenced this tutorial include
Prof. Jarmo Alander: rst draft
DI Janne Koljonen: Java examples (Virtual Keeper)
Econ. Olli Snellman: Java multimedia programming
DI Petri Vlisuo: Java examples
Dr. Timo Mantere: Java examples and testing
BSc Olli Kanniainen: Java examples.
The idea and need to write this tutorial emerged from the difculties encountered by the students to
solve exercises using programming approach essential in modern engineering design and creativity.
Programming is like eating an elephantdo it piece by piece.
1.2 Why Programming and DSP
Signals is digital format are suitable only for digital electronics and computer processing, the latter of
which is more exible and also the main processing type. This means that most signal processing is done
by computer programs in computers and embedded systems like mobile phones, CD-players, and digital
cameras. Before microprocessors, signal processing was done by analog electronics.
1.3 Why Java
The high level programming language Java is gaining more and more popularity as a tool for programming
large software systems for smaller and smaller devices. It is a general purpose programming language also
suitable for signal processing. In this tutorial we will only take some parts of the language, and leave the
rest for the main programming studies.
Java programmers do it more modularly,
1.4 Why not DSP assembler
Signal processing is done much with special DSP processors having special tailored commands to do nu-
merical calculations. Java was preferred here because it can be used also in very many other applications,
contrary to DSP programming, which is not used much outside the DSP community.
1.5 Why not Matlab
This programming introduction to DSP could also have been done using Matlab. However, Java is a general
purpose language useful also in more general setting of automation software and beyond. Hence program-
ming skills in Java are more useful for anybody not intending to concentrate only on DSP.
4
Java & DSP 1 INTRODUCTION
1.6 Why mathematics
Digital signal processing is based on mathematical methods and notations, most of which are easy
1
to
implement using any programming language. These mathematical concepts include real and complex
arithmetics, basic functions, iteration, vectors, and matrices. We will look these by a few simple examples
taken from DSP.
1.7 Why image processing
Vision is perhaps the most important sense:
it makes human-computer interaction natural.
it has endless number of applications, and
it is in a rapid development phase due to computing and digital electronics.
More and more tasks are aided by graphical user-interfaces with extremely high quality image features. In
these kinds of applications Java is a good choise for a programming language.
Information as images are often excellent for human interpretation and consultations. The human eye,
even if being in very many ways an excellent device, has some weak points that can be quite easily assisted
by a modern computer system. The weaknesses include:
Limited contrast resolution, which can be often adjusted by rather simple scaling algorithms.
Lack of absolute image memory makes it difcult to monitor slow processes like tumour growth or
tensile testing []. A computer can memorise precisely image information as long as needed. There
are also rather simple algorithms to compare images, display the differences, and to calculate the
amount of differences. [?]
Hence we will use quite many image processing examples in what follows.
1.8 Why in English
These notes are written in English so that both Finnish and foreign students can use these notes.
1.9 Motivation
Before going into details of Java and DSP, a word of motivation: Remember, that programming skills are
highly esteemed in labour market. About half (50%) of industrial productivity is due to ITC development,
and that is based on programming new applications.
2
1.10 Examples of signal processing
The following list gives an example of signal processing applications done by our group.
Under construction ...
1
This is really true.
2
The rest is due to all the other engineering branches altogether, hence what ever you develop, half of it should be ICT, on the
average.
5
Java & DSP 2 NUMERICS
2 Numerics
The basic numerical types in Java are shown in table 1. As can be seen the integer type is long enough for
any basic signal processing, where ADC signals are processed. Typically ADC signals contain only 8 to 16,
sometimes even 24, signicant bits. In what follows we are mainly using integers (int 32bits) to represent
signal values and integer arrays (int[]) to represent signal sequences like time series.
Table 1: Numerical types in Java.
type size range
byte 1 byte (8 bits) -128 ... 127
short 2 bytes (16 bits) -32 768 ... 32 767
int 4 bytes (32 bits) -2 147 483 648 ... 2 147 483 647
long 8 bytes (64 bits) -2
63
... 2
63
1
float 4 bytes (32 bits) 3.410
38
about 7 decimal positions
double 8 bytes (64 bits) 1.710
308
about 15 decimal positions
2.1 Arithmetic operations
Evaluating a formula in oating point arithmetics is sensitive to the execution order of the operations. Here
some advice:
Always sum in increasing order. Otherwise precision may be lost in oating point scaling.
Avoid subtraction of nearly equal values. Again the oating point scaling is the potential reason of
loss of precision.
Division of zero is always a headache for a programmer of numerical software. Test before division
that the denominator is not too small (0).
Using integers instead of oating point values we can avoid some problems, while unfortunately geting
some integer dependent problems like imprecise function values. A decent compromise is xed point
numbers that use integers to represent decimal numbers of given decimal places. In practise we can e.g.
compute by values 100 times larger than the real ones (from ADC etc) and output values with decimal point
between the second and third less signicant digit positions.
2.2 Division and multiplication by 2
n
can be done efciently
In case we have division (or multiplication) of a binary coded integer by 2
n
the fastest way to do it is just to
shift the integer n steps right:
i/8 is equivalent to i3.
The -operator shifts the bits of the rst operand to the right by the amount given as the second operand
(here 3; 2
3
= 8). The reverse -operator can be used when multiplication by 2
n
is needed:
16*i is equivalent to i4.
6
Java & DSP 3 METHODS
3 Methods
In what follows we will briey introduce the most important concepts and constructions of Java -language
in the framework of introductory signal processing application. We will not be extremely purist with respect
to Java denitions. When in doubt, please make experiments with our Java interpreter or consult the Java
tutorials by the Sun Microsystems (http://java.sun.com/docs/books/tutorial/) or still better do
both.
Allways remember the KISS principle: Keep It Simple Stupid.
3.1 Methods and classes
Subroutines, functions, and procedures are all called methods in Java. Here we will collect a set of methods
to a subroutine package, called class in Java language terminology.
Before looking classes more carefully, we start by writing a few methods and by that way learn basic
constructions of Java.
3.2 Example 1: constant vector or signal
Our rst method will create a vector of n integer items all set to a given constant c:
public static int[] constant(int n, int c) //
/** create an n item constant vector = c*/ // comment
{ // create a constant vector
int[] R = new int[n]; // reserve space
for(int i=0; i<n; i++) // n rounds
R[i] = c; // just do it
return R; // ready
} // end of constant
The program symbols have the following meanings:
/** */ Text within /* */ and after // is comment that is skipped by the compiler/interpreter. Extra
* is used here for automatic documentation (the method listing in appendix XX is done using these
comments). Comments are very important for the human reader. Always comment your code when
coding, afterwards you may have forgotten the great ideas the code is based on.
public We allow this method to be used quite freely. Later we will protect some methods that can be
dangerous in wrong hands.
static This method can be used without an object. We use class only to collect subroutines and
functions together as a package.
int[] This method is a function returning an integer vector value. We can call this method in formulas
where vectors i.e. integer arrays are needed. Brackets [] after an array are essential and every
pair corresponds to one dimension or index. Here we have one pair of brackets so that the array is
one-dimensional. An array symbol without brackets is valid and means the whole array, when we
pass an array as a parameter.
constant is the name of this method. The parenthesis () after the method name and surrounding the
parameters are essential: All methods have parentheses whether or not they have any parameters.
Unlike in many languages, we can have several methods with identical names, if and only if they
differ by the number and/or types of their parameters. This is called overloading the name of a
function. A similar naming systems is also used in C++, where in addition the operators may be
overloaded.
int n Declaration of parameter n of type integer. All parameters, and variables must have type, which
is given by a type declaration. Parameters are separated by a comma , and like local variables they
are not available outside the method denition.
7
Java & DSP 3 METHODS
int c parameter c of type integer.
int[] R = new int[n]; allocation of space (creation of an object) for the result. When returning a
non-scalar value we have to reserve memory space (new) for it. Operator = is an assignment of the
created vector to variable R (or actually a link to the memory).
for(int i=0; i<n; i++) a for-loop from i=0, 1, 2, ... until i=n-1. This is the famous C-
language for-loop, where in addition to C, you can also dene the loop index int i, which is only
visible within the loop. A good programming practise is to avoid using non-local index variables.
R[i]=c; constant integer value c is assigned as the ith item of vector R. This is the core of our rst
method: using the for-loop the vector R to be returned is lled with contant integer values c. Observe
that = is an assignment of value, not comparison for equality, which is the operator ==. A
common mistake in C/C++ or Java is the confusion between the assignment = and comparison ==
-operators.
return R; The value of this method (R) is returned. return should be the last command to be executed
in a method returning a value as the by-product of calling the method. It is a jump back to where
this method was called and R is put to stack for further processing, if this method was called from
an expression. Stack is used in the evaluation of expressions. It is not necessary to use the returned
value, if there is no reason to do that.
We can now use our constant() method to create constant integer vectors:
int[] ZeroVector = constant(3,0);
which creates a vector:
{0, 0, 0}
Observe, that in the method call we do not have any types, only colons separating the parameters.
3.3 Errors
The following code line contains several errors:
constant(1.5) = int OneVector,
1.5 Method constant should have two parameters, instead of one (1.5), which is actually a oating
point number.
int The type of method constant is an integer array (int[]), which is not the same as an integer (int).
= The assingment is from right to left, while all expressions are evaluated primarily from left to right,
depending on parenthesis and priorities of operators. The order must be due to historical reasons,
only.
, Every command ends at semicolon ;, not comma ,, or full stop ., or any other character.
The errorless code is as follows:
int[] OneVector = constant(1,5);
which creates the vector {1,1,1,1,1} and assignes it to a variable called OneVector.
In practise the computer, actually the Java interpreter, will tell you that something is wrong in similar
situations. However, sometimes the computer is not so good at guessing what you might have tried to say
to it.
Little by little you will understand the computer/compiler/interpreter betterthe reverse is not true.
8
Java & DSP 3 METHODS
3.4 Constant vector by Java
In Java we can also write directly constant initialisation vectors:
int[] ZeroVector = {0, 0, 0};
Which one is better depends on the situation: tiny vectors are usually easier to write explicitly than program
while it is best to program longer vectors. Writing constant(10000,999999) will save a lot, lot, ... of
boring and errorprone typing.
Exercise 3.1 Implement the delta function:
i, j
= 1, when i = j, and
i, j
= 0, when i = j, outputting an
integer array of given length (parameter n).
Observe, that due to maintenance reasons it is usually good to avoid scattering constants other than 0
and 1 around the program code. Use symbolic constants instead.
3.5 Example 2: Moving average
Our second example will be a method that evaluates a moving average of a given time series x[] using
moving window of width 2n+1:
public static int[] moving(int[] x, int n) // COMMENTS:
/** average of x using window size 2x+1 */ // comment
{ // moving average of window 2n+1
if (n<0) return x; // check n
// in case of invalid n do nothing (return x)
int W = 2*n+1; // window size
int N = x.length; // length of x
int[] R = new int[N]; // reserve space for result
for(int i=n; i<(N-n); i++) // scan x
{ //
int S = x[i], I = i-1, J = i+1; // window centre
for (int j=0; j<n; j++) // scan half window
{ //
S += x[I-]+x[J++]; // sum in window
} //
R[i] = S/W; // the average
} //
return R; // ready!
} // end of moving average
Some comments on method moving():
if(n<0) return x; Parameter value n is checked: if it is invalid (<0) then nothing is done i.e. x is
returned unchanged. Observe that x is not automatically returned but must be returned explicitly.
int W = 2*n+1; An odd window size is assumed to have a middle element.
int N = x.length; Size of x retrieved by the length attribute of a class/object integer array. All Java
arrays are objects of an array class (or its subclass) and have several methods and attributes inluding
length of obvious semantics.
for(int i=n; i<(N-n); i++) The n outermost items are left unchanged: i = n, n+1, ..., N-n-1.
int S = x[i], I = i-1, J = i+1; Integer variables S, I, and J are dened and assigned. Observe
the colon , between the variables instead of semicolon ;, which ends the integer denition list. This
is a short hand notation of int S=x[i]; int I=i-1; int J=i+1;, which is a short hand notation
of int S; S = x[i]; int I; I = i-1; int J; J = i+1;. This is a nice example of how there
are often many ways of doing things in coding.
9
Java & DSP 3 METHODS
S += x[I-]+x[J++]; Operators - and ++ are shorthand notations for expressions I = I-1 and J = J+1.
This notation is inhereted from C-language, and used where utmost efciency is needed. Namely they
are often found as machine level commands (increment or decrement by 1). Similarly S+=x is a short
hand notation for S=S+x also this is usually translated into an efcient special machine code command
(the contents of the accumulator register is increased by x).
Summing is done starting from the center of the window and proceeding towards the ends of the
window.
R[i] = S/W; In a nished program every division should be checked to be valid. W should not be zero,
which is true because W=2*n+1= 0, for n IN.
3.6 Method as a black box
In order to clarify Java concepts we use some simple graphics like rectangular boxes and other similar
constructions. The methods constant and moving are shown in gure 1. Parameters are represented by
arrows pointing to the left side of the method box, while the type returned by the method is shown by an
arrow pointing outwards from the right side of the method box. The types of the parameters and the output
are shown above or under the arrows.
The term black box means that the observer i.e. the one who is using a method does not know the details
of its implementation inside the black box. It is enough to know the interface, the parameter and output
types, and what the method should do.
The details of the method could not interest less the observerthe details are left just for the programmer
of the method.
constant
-
int[]
-
int
-
int
int[] constant(int,int)
moving
-
int[]
-
int[]
-
int
int[] moving(int[],int)
Figure 1: Box representation of the denition of the methods constant and moving.
3.7 Example 3: combining methods
In this example we will combine our two methods into a simple signal ltering example. Our task is to
apply the moving average lter to a constant time series to see what really happens.
Let the constant time series be ten (10) times one (1) and the window size of the moving average lter
W= 22+1 = 5.
Our codeline is shown in the graphical representation of gure 2.
int[] S1 = moving(constant(1, 10), 2);
int[]
constant
-
-
n=10
-
c=1 r r r r r r r r r r
moving
-
-
-
n=2
r r
r r r r r r
r r
S1
Figure 2: Box representation of command int[] S1 = moving(constant(10,1),2).
Exercise 3.2 Take a moving average of the output of a delta function method of the exercise 3.1.
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Java & DSP 3 METHODS
3.8 Example 4: derivative1
Our next method called derivative1 will estimate the derivative of a time series by taking the difference
between the consecutive items of the time series.
public static int[] derivative1(int[] x) //
/** the 1st derivative of series x */ //
{ // derivative by difference xi - xi+1
int N = x.length; // length of x
int[] R = new int[N]; // reserve space for result
for(int i=1; i<N; i++) // scan x
{ //
R[i] = x[i]-x[i-1]; // the difference
} //
return R; // ready!
} // end of derivative1
derivative1 applied to the output of our previous example is shown in gure 3.
S1 S2
derivative1
- -
int[] S2 = derivative1(S1);
r r
r r r r r r
r r r
r
r r r r r
r
r r
Figure 3: Application of method derivative1 to the output of our previous example.
Exercise 3.3 Implement a method to evaluate the given nth derivative. Apply it to the output of a delta
function method.
3.9 Example 5: method add
Our next method called add will sum two time series.
public static int[] add(int[] s1, int[] s2) //
/** sum series s1 and s2 */ // add time series s1 and s2
{ //
// assume s1 and s2 are of equal size
int N = s1.length; // length of s1
int[] R = new int[N]; // reserve space for result
for(int i=0; i<N; i++) // scan s1 and s2
{ //
R[i] = s1[i]+s2[i]; // the sum
} //
return R; // ready!
} // end of add
add applied to the input and output of our previous example is shown in gure 4.
3.10 Example 6: FIR
Finally we will look what a simple 1-dimensional FIR lter looks like in Java. Observe that in the solution
arithmetics is done between integers. Only one division is done per point.
Observe also that the input is multiplied by 10 before ltering by method mult.
public static int[] FIR(int[] x, int[] a) //
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Java & DSP 3 METHODS
int[] S4 = derivative1(add(S1,S2));
S1
S2
S1+S2
S4
r r
r r r r r r
r r
r
r
r r r r r
r
r r
add
-
-
-
r
r
r r r r r
r
r r
derivative1
- -
r
r
r r r r
r
r
r r
Figure 4: Application of method derivative1 to the added output of our previous examples.
/** FIR filter of x using coeff a */ // FIR lter; coeff a
{ //
int N = x.length; // length of x
int M = a.length; // length of a
int[] R = new int[N]; // reserve space for result
int W=0; //
for(int i=0; i<M; i++) //
W+=a[i]; // sum a for division
for(int i=M-1; i<N; i++) // scan x
{ //
int S = 0; // sum=0
for (int j=0; j<M; j++) // scan a
{ // sum
S += x[i-j]*a[j]; // the convolution
} //
R[i] = S/W; // only one division
} //
return R; // ready!
} // end of FIR
int[] A = {1,2,1};
int[] S5 = FIR(mult(10,S3),A);
S3
A={1,2,1}
S5
10*
FIR
-
-
-
r
r
r r r r r
r
r r
r
r
r r r
r r
r
r r
Figure 5: Application of method FIR using coefcients {1,2,1} to the time series 10S3 of our previous
example.
Exercise 3.4 Implement the above FIR method by using a method called mult, which multiplies a time-
series with a given constant k.
Exercise 3.5 Implement a method returning a random time series. Use FIR to lter a random time series.
Exercise 3.6 How could you implement a method doing unsharp masking using a FIR method?
3.11 Example N (long): NIRS
As a more realistic signal processing example we will next process some measured near-infrared spectra
(NIRS).
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Java & DSP 3 METHODS
Figure 6 below shows a typical NIR spectrum of human skin taken for clinical research purposes. You can
nd more information on this medical application of signal processing from the web address below:
More information from:
ftp://ftp.uwasa.fi/cs/report05-4/TTIprinter.pdf or
ftp://ftp.uwasa.fi/cs/report05-4/TTI.pdf
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Figure 6: A NIR spectrum of human skin (spectrum A)
There should be some small details in the spectrum, peaks and valleys, that are of interest to the clinician
for diagnostic purposes. In order to nd them we try to lter away the background by derivating the
spectrum by our derivative1 method. The result is shown in gure 7.
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Figure 7: The rst derivative of NIR spectrum A using derivative1 method.
Our derivative1 method is not good in suppressing noise. According to theory a better method should
be e.g. der101. The result of applying der101 to our example spectrum is shown in gure 8.
Exercise 3.7 Method der101 estimates the derivative of a series x by formula x[i] = x[i+1]-x[i-1].
Implement method der101 returning the derivative series.
The peaks and valleys in NIRS vary much in size. The basic properties of peaks and valleys are their
location and height. The peak location gives the wavelength, which is further inversely proportional to
the energy difference between the vibrational states of the molecule, which further give information on
the physics and chemistry of the object measured. In our example case the peaks correspond to certain
13
Java & DSP 3 METHODS
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Figure 8: The rst derivative of NIR spectrum A using der101 method.
molecules or parts of molecules and their interactions that strongly absorb certain NIR wavelengths. The
peak height is proportional to the concentration of the given molecule.
Geometrically in the rst derivative spectrum the peak or valley location i.e. the highest or lowest point
correspond to points where the derivative signal crosses zero.
The third important property of peak or valley is its width. There are several ways to dene width, how-
ever. Here we will approximate the width by the distance between the peak and valley of the corresponding
second derivative signal at the peak or valley.
In order to evaluate the basic properties of peaks and valleys we need methods to evaluate derivatives
and peak locations. The easies way of implementing the second derivative is to apply the rst derivative
twice, like:
int[] D1 = der101(S);
int[] D2 = der101(D1);
The fourth important peak/valley property is its area, which can be estimated once the local background
is estimated.
The details of spectra vary much. Hence, the values of derivatives also vary much. This complicates
the graphical display of derivatives. The dynamics of derivation can be suppressed by a logarithm or root
function for graphical display. Figure ?? shows the results of applying square root function (method Sqrt)
to the output of our der101 derivation method. Similarly gure 9 shows the derivative of another skin
spectrum done by applying der101 and square root dampening.
3.12 Sqrt
Method Sqrt compressing signal dynamics for graphical display is as follows:
public static int[] Sqrt(int[] x, double a) //
/** square root of abs x scaled by a */ // sign(x) a sqrt(|x|)
{ //
int N = x.length; // length of x
int[] R = new int[N]; // reserve space for result
for(int i=0; i<N; i++) // scan x
{ //
double r = Math.abs((double) x[i]); // convert abs(x) to double
R[i] = (int)(a*Math.sqrt(r)); // sqrt
if (x[i]<0) R[i] = -R[i]; // sign of x
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Java & DSP 3 METHODS
} //
return R; // ready!
} // end of special sqrt
Observe, that the x values are rst converted into double precision because the mathematical methods
assume that parameter type.
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Figure 9: Square root of the derivative of the above NIR spectrum using der101 method for spectrum A
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Figure 10: Noise range for spectrum A compressed with Sqrt.
The effect of derivation on noise level is demonstrated in gure 12 where der101 is used twice to
estimate the second derivative, The coefcients of the FIR lter are
AveD = {4, 5, 6, 7, 8, 9, 10, 9, 8, 7, 6, 5, 4}.
We can easily get worse results by applying derivative1 twice without any smoothing as can be seen in
gure 12.
The strength of signal processing can be seen clearly in gure ??, where the second derivatives of
several spectra are shown. While even the details of the rst derivative are practically impossible to detect
15
Java & DSP 3 METHODS
with the naked eye on the original spectra, it is much more difcult to detect the details of the second
derivative. And indeed, the second derivative seems to contain details that the different spectra i.e. different
measurements on different persons share. Most of the details would drown without this kind of simple
signal preprosessing.
If the information is therejust persuade it with DSP.
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Figure 11: The fourth (upper), third (middle; upmost FIR ltered only once) and second derivative (bottom)
using (der101) for spectrumB, C, D, and E, and FIR average ltering between derivations compressed with
Sqrt.
3.13 S/N
Once we have the estimate of noise amplitude A
n
we can draw the signal to noise ratio dened to be
S/N = 20log
10
(A
s
/A
n
)[dB],
where A
s
is the estimated amplitude of the signal and A
n
is the, also estimated, amplitude of noise. Here we
estimate the noise amplitude by the expected local deviation of the rst derivative signal (g. 13(upper)),
while the signal is here the original raw signal. In gure 13(lower) you can see the signal to noise ratio over
spectrum A. As can be seen the signal to noise ratio steadily increases until the middle of the frequency
range is reached, after which the peaks of the original signal dominate the S/N behavior. Observe, that the
peaks are actually valleys and thus contain much noise. This is so because we are actually processing the
inverse of the measured spectra.
16
Java & DSP 3 METHODS
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Figure 12: The second derivative using (derivative1) twice for spectrum A without smoothing com-
pressed with Sqrt.
6
0
10
S/N[dB]
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Figure 13: The noise amplitude A
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10
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for spectrum A.
17
Java & DSP 3 METHODS
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Figure 14: Example spectra.
18
Java & DSP 4 CLASSES
4 Classes
A Java class is an aggregation of attributes (variables) and methods (functions). In addition we can create
new copies of class variables. In Java, and in general in other object-oriented langueges, these copies in
computers memory are called objects.
4.1 DSP class
The simplest class contains only methods and can be seen as a method or subroutine package, where some
of the methods may call other methods in the same class.
4.2 Example class DSP
The following class called DSP was used in our rst method examples.
public class DSP //
{ //
public static int[] constant(int n, int c) //
/** ... */ // create a constant vector
{ //
int[] R = new int[n]; // reserve space
for(int i=0; i<n; i++) // n rounds
R[i] = c; // just do it
return R; // ready
} // end of constant
. //
. // some methods here ...
. //
public static void testDSP(int n) // method testing
/** ... */ //
{ //
int[] S1 = moving(constant(n,1),2); // these were used in our examples
int[] S2 = derivative1(S1); // these were used in our examples
int[] S3 = add(S1,S2); // these were used in our examples
int[] S4 = derivative1(S3); // these were used in our examples
int[] A = 1,2,1; // these were used in our examples
int[] S5 = FIR(mult(3,S3),A); // these were used in our examples
seriesForVerb("S5",S5); // these were used in our examples
} //
public static void main(String[] args) //
/** ... */ // the main method
{ //
testDSP(10); // do some testing
} //
} // end of class DSP
Some comments on this DSP class:
public class DSP This is a publicly usable class named DSP.
void testDSP This is a method used to test (call) other methods. (Not all details are shown here) This is
not a function but a subroutine, because it does not return any value (void).
seriesForVerb was used to output the given parameter array for graphical representation. (also for other
arrays, but not shown here)
The complete source code can be found at URL: ....
19
Java & DSP 4 CLASSES
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Figure 15: Derivatives of example spectra of gure 14.
20
Java & DSP 4 CLASSES
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Figure 16: Second derivatives of example spectra of gure 14. Smoothed by FIR average lter B between
derivations.
21
Java & DSP 4 CLASSES
4.3 Graphical representation: container
Because the most important function of a class is to be a container holding all methods and attributes
together, we will use an oval shaped container as the symbol of a class and object of a class:
_
`

DSP
add()
-
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_
`

DSP
fun()
-
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-
?
6
a1 a2
Figure 17: Method add of class DSP using no attributes of DSP. Another method fun updating attribute a1
and reading another attribute a2 of class DSP.
Still working on this subject ... hold on, please.
22
Java & DSP 5 IMAGE PROCESSING
5 Image Processing
In this section we will see how basic image processing methods can be implemented in Java. An image is
typically represented by a two-dimensional integer array:
int[][] Image = new int[1024][1024];
reserves space for a 10241024 pixel one color (grey tone) image.
For processing an image array we need two loops like this:
public static int[][] Ifun(int[][] Image) //
/** ... */ // an image processing function
{ //
int N = Image.length; // height of Image
int M = Image[0].length; // width of Image
int[][] R = new int[N][M]; // space for result
for(int i=0; i<N; i++) // outer loop
{ // outer loop
for(int j=0; j<M; j++) // inner loop
{ // inner loop
. // do pixel processing
. // do pixel processing
. // do pixel processing
R[i][j] = Image[i][j] ... // update result image
} // inner loop
} // outer loop
return R; // return result
} // end Ifun
The graphical representation of Ifun is shown in gure 18.
_
`

DSP
Ifun
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int[][]
-
int[][]
Figure 18: An image processing method Ifun of class DSP.
Still working on this subject ... hold on, please.
23
Java & DSP 6 HYPERIMAGE PROCESSING
6 Hyperimage processing
6.1 What is hyperimage
The by far most common image types are grey tone and color images. It is also possible to increase the
number of colors in a color image far beyond the three necessary for visible color images as well as going
beyond visible light to ultraviolet and infrared even beyond. Figure 19 shows schematically the relation
between pixel, image, and hyperimage.
_
`

Hyperimage
Processing
6
?
_
`

Image Processing
6
?
_
`

Chemometrics
(Spectroscopy)
image[][]
(photo)
6
?
pixel[]
(spectrum)
hyperimage[][][]
-
6
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66
melanoma
??
ulcers

a
Figure 19: Pixel, image, and hyperimage
Still working on this subject ... hold on, please.
24
Java & DSP 7 CONCLUSIONS AND FUTURE
7 Conclusions and Future
7.1 Future
The anticipated future activities could include signal processing Java package, exercises, some of which
interactive, graphical tools for demonstrating the above, and graphical tools for teaching programming in
Java.
7.2 Acknowledgements
Mr. P. Vlisuo is acknowledged for introducing Beamer slide processing.
7.3 Further reading
Arto Wikla, "Ohjelmoinnin perusteet Java-kielell [Principles of Programming using Java Language]", Ota-
DATA, Espoo, 1999.
25
Java & DSP 7 CONCLUSIONS AND FUTURE
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Figure 20: Comparison of spectra of gure 14
26
Java & DSP A SOLUTIONS TO PROBLEMS
A Solutions to problems
Not any yet, sorryplease supply some.
A.1 Abbreviations
ADC Analog Digital Converter
CAD Computer Aided Design
DI Diplomi-Insinri (MSc eng.)
DSP Digital Signal Processing
FIR Finite Impulse Response (lter)
HCI Human-Computer Interface
NIR Near-InfraRed
NIRS NIR Spectroscopy
A.2 Useful links
Our homepage:
http://www.uwasa.fi/TAU
AUTO1030 homepage:
http://www.uwasa.fi/TAU/AUTO1030
27
Java & DSP A SOLUTIONS TO PROBLEMS
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Figure 21: Comparison of the rst derivative of spectra of gure 14 to the bottommost derivative of the
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28
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Figure 22: Comparison of spectra of gure 14
29
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Figure 23: Comparison of the rst derivative of spectra of gure 14 to the bottommost derivative of the
spectrum.
30
Java & DSP A SOLUTIONS TO PROBLEMS
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Figure 24: Comparison of spectra of gure 14
31
Java & DSP A SOLUTIONS TO PROBLEMS
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Figure 25: Comparison of the rst derivative of spectra of gure 14 to the bottommost derivative of the
spectrum.
32