Paragraph Spacing

setlength{parskip}{7pt}

This goes in the preamble of the document (after the document class stuff, but before the begin document line).

Removing Page Numbers

thispagestyle{empty}

This gets rid of page numbers for that particular page, but the numbering sequence continues on the next page.

Adding Unnumbered Sections into the TOC

section*{Introduction}
addcontentsline{toc}{section}{Introduction}

By default, unnumbered sections do not appear in the table of contents and therefore they must be added manually.

Defining a New Style with fancyhdr

fancypagestyle{plain}{%
fancyhf{}}% clear all header and footer fields

New style definitions should go before the very last curly brace.

Unnumbered Sections Not Working with leftmark and rightmark

section*{Introductionmarkboth{Introduction}{}}

For some reason, unnumbered sections don’t play nice with fancyhdr and don’t get treated as real sections when the leftmark and rightmark commands are used.  By using markboth, it fixes the problem.  Now my headers show the correct section name.

Bulleted List

begin{itemize}
item Here is a bullet.
item Here is another bullet.
end{itemize}

Numbered List

begin{enumerate}
item Here is item one.
item Here is item two.
end{enumerate}

Referencing Sections by Name

section{MyFirstSection} label{marker}
section{MySecondSection}
In section~nameref{marker} we defined...

Requires the hyperref package!  Put the line below in the preamble.

usepackage{hyperref}

Linking to a Website

href{http://www.example.com}{Link}

Umlauts

"{o}

That gives an o with an umlaut.  Just replace the letter to get an umlaut on a different character.

• Introduction
• Motivation
• Newton’s Method
• Steepest Descent Method
• Limitation
• Sources

Introduction

In many sciences, the problem of non-linear optimization appears quite often.  What happens if they’re non-linear?  Sometimes, the system of equations remains easy to solve even given non-linearity, but other times, the possibility of solving the problem analytically may not exist if the algebra gets too complicated.  The solution lies in using numerical methods (approximations).  Here, I present two common methods: Newton’s Method, and the Steepest Descent Method. 

Each method has its own limitations and the choice of which method to use depends on the problem.  These methods involve using iterative computation in order to reach a solution.  Luckily, computers can prove useful in providing solutions very quickly due to its quick processing power for numerical computation.

In order to understand some of the concepts and terms used in this article, the reader has knowledge in multivariable calculus.  Also, equations in picture form made the line spacing look funny, so I’m going to do my best write the equations as text.  I should also point out that I couldn’t write the vector arrow on top of the variables in text form so vectors are written in bold.

Motivation

In calculus, the idea of optimization involves taking the derivative of the function and equating it to zero.  In multivariable calculus, the same idea applies except, we set all the partial derivatives to zero and solve the system.

So in general, if we are given a function:

ƒ(x), where x = [x₁, x₂, … x_n]^T

The maximum or minimum can be found by taking a partial derivative with respect to the vector x.  This gives the following equations:

∂ƒ/dx₁ = 0

∂ƒ/dx₂ = 0

…

∂ƒ/dx_n = 0

A short-hand way of expressing the above equations is by using the gradient vector, giving∇ƒ(x) = 0.  By definition, the gradient is defined by:

∇ƒ(x) = [∂ƒ/dx₁, ∂ƒ/dx₂, … , ∂ƒ/dx_n].

An analytical solution is not always possible, hence the motivation for approximating the solution using numerical methods.

Newton’s Method

In general, this method is written below.  Explanation of each step will follow.

1. Given the equations to solve, derive equations for the approximating line or plane, depending on whether the problem is 2D, 3D, nD, etc.
2. Using the linearized equations, solve the system of equations
3. Using the results from step 2, generate new equations for a new approximating line or plane, and repeat step 2.

This method also involves starting with a guess, denoted by a variable with a subscript of 0.  A guess is required, because this is the starting point for this method.  Using this guess, each successive solution should converge (more on that later).

Step 1

In order to solve the equations ∇ƒ(x) = 0 (see Motivation for more information), we can apply multivariate Newton’s method to approximate the solution.  Like the single-variate (two-dimensional) version, a linear approximation is required.  However, instead of having an approximation in the form of a line, the approximation is a plane instead.

2D (line): ƒ(x) ≈ ƒ(x₀) + ƒ’(x₀)(x – x₀)

3D (plane): ƒ(x, y) ≈ ƒ(x₀, y₀) + ƒ_x(x₀, y₀)(x – x₀) + ƒ_y(x₀, y₀)(y – y₀)

nD (nD plane): ƒ(x) ≈ ƒ(x₀) + ∇ƒ(x₀)(x – x₀)

Since we are trying to optimize, we have the partial derivatives of the function we are trying to optimize, but in order to apply Newton’s Method, we need a linear approximation of the partial derivatives.  This means that in order to approximate the partial derivatives, we need to take another derivative in order to get the slopes of the approximating planes.  If that description didn’t make sense, try the following.  For an equation with two independent variables, there will be two equations for the partial derivatives, one for x and one for y.  Taking partial derivatives from each of those equations again will give the slopes of the plane that approximate the first partial derivative.  So if we have two independent variables, we end up getting four equations: ƒ_xx, ƒ_xy,ƒ_yy, and ƒ_yx (ƒ_xy and ƒ_yx should be the same).  In general, for n partial derivatives, we would have n² equations if we took another set of derivatives.  The approximations for both of the partial derivatives would be:

ƒ_x(x, y) ≈ ƒ_x(x₀, y₀) + ƒ_xx(x₀, y₀)(x – x₀) + ƒ_xy(x₀, y₀)(y – y₀)

ƒ_y(x, y) ≈ ƒ_y(x₀, y₀) + ƒ_yy(x₀, y₀)(x – x₀) + ƒ_yx(x₀, y₀)(y – y₀)

Plug in the values for the second derivatives, and the values from the initial guess (the x y values and what function value you get using those values).

Step 2

Although the equations generated from step 1 is yet another system of equations, the main difference is that the equations from step 1 are linear.  This means that the system can be solved analytically.  Solve for the solution of the system using row reduction methods, or other methods.  The solution from solving the system will be the values used for the next iteration and will replace the guessed values.  The solution may or may not be close to the actual solution.  More iterations need to be done to see if the answer changes with each iteration.  Usually if the guess is really far away, then it takes a lot of iterations to get it really close.  However, sometimes, a bad guess may cause the solution to diverge, meaning that the solution will be further and further off.

Step 3

Generate new equations for the approximating planes using the solution from step 2.  Using these equations, go back to step 2 and solve it again.  This method is super tedious if done on paper.  Matlab can help, but then again, Matlab can do the entire approximation with just a few commands, but not everyone has access to it unfortunately.

Hopefully after a few iterations, the solution stops changing.  When that happens, you can substitute the final solution back into the original equation to see if it works!

Steepest Descent Method

Here is the general method:

1. Find the direction of the maximum or minimum directional derivative
2. Follow it until a maximum or minimum is reached

Newton’s Method is sufficient in a lot of cases, but sometimes it may be too hard to go beyond first derivatives.  This main idea of this method is to use the first derivative and follow the direction in which the function gets larger/smaller.  A fundamental concept used in this method is the directional derivative.  Since in 3D (or higher dimensions), we are not restricted to movement along the x axis.  This means we could move in any random direction, and in each direction the rate of change is going to be different.  To calculate the max or min, we need to calculate where the directional derivative is largest or smallest.  Just like a boulder rolling down the steepest slope on the hill.

Starting with a guess, we can find out the value of the function at the point and the direction to travel in.  Take a step in that direction and see how the value of the function changed.  Keep doing that until a max or min is reached.

Step 1

The definition of the directional derivative is the dot product of the gradient and the unit vector specifying the direction.  Here is the definition of the directional derivative:

D_uƒ = ∇ƒ(x)·u

Since the definition involves a dot product, it is true that if the two vectors are orthogonal, the resulting dot product is zero.  The direction that this derivative is in is called the level direction.  But if the two vectors are parallel, we get the highest value of the directional derivative.  For a vector that is parallel in the same direction, the directional derivative will be a maximum, but if the vector is antiparallel (parallel but both pointing opposite ways), the directional derivative will be a minimum.

Since the maximum value of the directional derivative is parallel to the gradient, we can calculate the unit vector of the gradient and use it as the unit vector u.  In order to get the minimum, simply flip the direction of the vector by multiplying it by –1.

u = ∇ƒ(x)/|∇ƒ(x)|

Although not necessarily required, substituting this value into the definition of the directional derivative, and doing some simplification with algebra, the maximum and minimum directional derivative is given by:

Max D_uƒ = |∇ƒ(x)|

Min D_uƒ = -|∇ƒ(x)|

Using the initial guess, calculate the direction of to travel in at that point.

Step 2

Knowing the direction to travel choose a desired step size “h”.  This means that if the equation will be traversed in a particular direction, we need to know exactly how far to go.  Choosing smaller step sizes gives better computational accuracy but increases computation time.

To get to the maximum, use the direction for the maximum directional derivative.  To get the minimum, use the direction for the smallest directional derivative.

Starting with a guess, calculate the function value at that point.  Then take a step in the direction given by Step 1 using the step size.  The variable “u” here is a component of the unit vector

x_n+1 = x_n + u_xh

y_n+1 = y_n + u_yh

At this new value, calculate the function value again.  Keep repeating this until the maximum or minimum is reached.

Limitation

The approximation is generally only as good as the initial guess.  Sometimes, a bad guess can lead to a solution that never converges.  In that case, a different value must be used in order to find a converging solution.  For example, if we have a fourth order polynomial function, a local extreme will exist.  As x approaches –∞ or ∞, y will do the same.  If I use the steepest descent and give a bad guess, my solution will go to ∞ instead of the local extreme.

Sources

1. Calculus by Gilbert Strang
2. Applied Regression Analysis by Norman Draper and Harry Smith

As with the first day of most things, it almost always involves an introduction of some sort.  After I walked the huge hike to work, I arrived at about 8:00, thirty minutes ahead early than the scheduled time.  I guess I gave myself too much extra time.

Once the meeting got started, all the interns each got their paperwork sorted out.  Since most people there came from other parts of the European Union, their paperwork seemed to be much simpler.  After they sorted out the paperwork, they issued me my employee badge.

Afterward, I met other members of my department and one of the PhD students introduced me to their MEMS research project.  Seeing that I knew next to nothing about this field of research, I will most likely need to do lots of background reading.

For lunch, employees don’t bring their own lunch.  Many visit the cafeteria, or canteen as they call it, to buy food.  Since I am an intern, I get discounts on lunch.  For a 2.80 euro meal with pasta, salad and soup, it only cost me 1.10 euro.  What an amazing deal.  That is even cheaper than me buying all the ingredients and cooking it myself.  Looks like I will have to stuff my face during lunch so I don’t have to bother cooking that much! Yes I am quite lazy when it comes to cooking.

I spent the rest of the day reading some Wikipedia articles on manufacturing processes in MEMS and attending to some introductory business, like obtaining my time card, and going through computer safety rules.  Reading those Wiki articles already seemed kind of overwhelming since technical articles on Wiki are almost always written for an expert to read.  But luckily, on my way out, I found the logbook from the previous intern, which should be extremely helpful.

Generally, communication with serial ports involves these steps (in no particular order):

• Searching for serial ports
• Connecting to the serial port
• Starting the input output streams
• Adding an event listener to listen for incoming data
• Disconnecting from the serial port
• Sending Data
• Receiving Data

I wrote an example program that includes all of those steps in it and are each in their own separate method within the class, but first I will go through my hardware set up.

Hardware Setup

My current hardware setup is as follows:

• PC connected to an XBee
• Arduino connected to an XBee

User input is given from the PC through the a Java GUI that contains code for serial communication, which is the code presented here.

The Arduino is responsible for reading this data.  This set up is pretty much using my computer as a remote control for whatever device is on the Arduino end.  It could be a motor control, on-off switch, etc.

Existing Code

The purpose of this post is to discuss serial programming in Java, and not GUI’s.  However, I did create a GUI for testing purposes.  See the Code Downloads section for the actual files.

Above is the picture of the GUI complete with the buttons that I use to interact with the program.  I also added key bindings which I can use to control the throttle.

When the program is first started, none of the GUI elements will work except for the combo box and the connect button.  Once a successful connection is made the controls are enabled.  This is done through the use of the setConnected(true) and the toggleControls() methods shown in the example code that follows.

Imports

The imports i used for this program were as follows:

import gnu.io.*;
import java.awt.Color;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.TooManyListenersException;

Depending on the Java IDE it might already know to tell you to use these imports except for the first one.  That first import is specific to RXTX, and all its library methods/classes are in there.

Class Declaration

The code here reads:

public class Communicator implements SerialPortEventListener

I named my class Communicator, but the name is really up to the programmer.  The name pretty much reflects its intended use.

The class should also implement the SerialPortEventListener class.  This is a class in RXTX and is required in order to receive incoming data.

On some IDE’s this may generate a public void method called serialEvent().  This method will be defined later.

Class Variables and Constants

Below are the variables and constants that I defined in my class.  What the variables are for is in the comments but a more detailed explanation will follow.

    //passed from main GUI
    GUI window = null;

    //for containing the ports that will be found
    private Enumeration ports = null;
    //map the port names to CommPortIdentifiers
    private HashMap portMap = new HashMap();

    //this is the object that contains the opened port
    private CommPortIdentifier selectedPortIdentifier = null;

I could have easily put the variable definitions in the constructor but it wouldn’t change anything.

The GUI object is another class that I wrote separate from this one that contains all the GUI elements.  The GUI class extends javax.swing.JFrame.

The HashMap is for mapping each of the ports’ names to the actual object. What that means is that I can associate (put() method) the name of a serial port, say a string that says COM1, to an object in the code.  Later, I can access the name COM1 from the HashMap by using the get() method and it will return the object that it was associated with previously.

The CommPortIdentifiers object is needed to gather the list of ports that are available for connection. by using its getPortIdentifiers() method.

The SerialPort object is for storing the data for the port once a successful connection is made.

The InputStream and OutputStream is the object that is required for sending and receiving data.

The Boolean variable bConnected is just a flag that I use for enabling and disabling elements on the GUI.

The constant TIMEOUT is a number required when opening the port so that it knows how long to try for before stopping.

The constants for the ASCII values are some values that I use to send through the output stream that act as delimiters for data.

The string logText is basically what the comment says.  When stuff happens in the program, the program stores a string in this variable and it will be appended to a text area in the GUI.

Searching for Available Serial Ports

The method below is for searching for available serial ports on the computer.  Code adapted from Discovering Available Comm Ports from the Reference Material.

    //search for all the serial ports
    //pre style="font-size: 11px;": none
    //post: adds all the found ports to a combo box on the GUI
    void searchForPorts()
    {
        ports = CommPortIdentifier.getPortIdentifiers();

        <span style="color: blue;">while (ports.hasMoreElements())
        {
            CommPortIdentifier curPort = (CommPortIdentifier)ports.nextElement();

            //get only serial ports
            <span style="color: blue;">if (curPort.getPortType() == CommPortIdentifier.PORT_SERIAL)
            {
                window.cboxPorts.addItem(curPort.getName());
                portMap.put(curPort.getName(), curPort);
            }
        }
    }

The method getPortIdentifiers() returns an Enumeration of all the comm ports on the computer.  The code can iterate through each element inside the Enumeration and determine whether or not it is a serial port.  The method getPortType() can identify what kind of port it is.  If it is a serial port, then the code will add its name to a combo box in the GUI (so that users can pick what port to connect to).  The serial port that is found should also be mapped to the HashMap so we can identify the object later.  This is helpful because the names listed in the combo box are the actual names of the object (COM1, COM2, etc), and so we can use these names to identify the actual object they are tied to.

Connecting to the Serial Port

The method below is for connecting to the serial port once they have been found (see previous section).  See How to Open A Serial Port in the Reference Material for more information.

    //connect to the selected port in the combo box
    //ports are already found by using the searchForPorts
    //method
    //post: the connected comm port is stored in commPort, otherwise,
    //an exception is generated
    public void connect()
    {
        String selectedPort = (String)window.cboxPorts.getSelectedItem();
        selectedPortIdentifier = (CommPortIdentifier)portMap.get(selectedPort);

        CommPort commPort = null;

        try
        {
            //the method below returns an object of type CommPort
            commPort = selectedPortIdentifier.open("TigerControlPanel", TIMEOUT);
            //the CommPort object can be casted to a SerialPort object
            serialPort = (SerialPort)commPort;

            //for controlling GUI elements
            setConnected(true);

            //logging
            logText = selectedPort + " opened successfully.";
            window.txtLog.setForeground(Color.black);
            window.txtLog.append(logText + "n");

            //CODE ON SETTING BAUD RATE ETC OMITTED
            //XBEE PAIR ASSUMED TO HAVE SAME SETTINGS ALREADY

            //enables the controls on the GUI if a successful connection is made
            window.keybindingController.toggleControls();
        }
        catch (PortInUseException e)
        {
            logText = selectedPort + " is in use. (" + e.toString() + ")";

            window.txtLog.setForeground(Color.RED);
            window.txtLog.append(logText + "n");
        }
        catch (Exception e)
        {
            logText = "Failed to open " + selectedPort + "(" + e.toString() + ")";
            window.txtLog.append(logText + "n");
            window.txtLog.setForeground(Color.RED);
        }
    }

Using the HashMap we can retrieve the CommPortIdentifier object from the string that was mapped earlier.  This is achieved through the HashMap’s get() method.  The object must also be casted as a CommPortIdentifier because the get() method has a return type of Object.

The setConnected method just changes a boolean flag so that the program can store whether or not it is connected to a serial port or not.

The CommPort must also be initialized because the port object will be stored here once a successful connection is made.

The main method of interest here is the open() method.  This instructs the program to open the port, and this method will return the object for the opened port, which I store in in the previously initialized CommPort object.  I then cast this object as a SerialPort and store it as well.  This is helpful for accessing the methods and variables specific to the SerialPort class.

It should also be noted that the open() method requires the use of a try-catch block.  So applying that, I catch two different exceptions.  The PortInUseException is what the name says.  If the port is in use, then this exception is thrown.  The next catch block is just for the generic exceptions that occur.  I never came across that during testing, nor do I know how to replicate that.

I neglected to include any code for setting the baud rate and other settings on the XBee’s (see Hardware Configuration), because I already set those parameters previously using X-CTU (more on setting up XBee’s here).

Initializing the Input and Output Streams

This method is pretty short and is pretty straightforward to read.

    //open the input and output streams
    //pre style="font-size: 11px;": an open port
    //post: initialized input and output streams for use to communicate data
    public boolean initIOStream()
    {
        //return value for whether opening the streams is successful or not
        boolean successful = false;

        try {
            //
            input = serialPort.getInputStream();
            output = serialPort.getOutputStream();
            writeData(0, 0);

            successful = true;
            return successful;
        }
        catch (IOException e) {
            logText = "I/O Streams failed to open. (" + e.toString() + ")";
            window.txtLog.setForeground(Color.red);
            window.txtLog.append(logText + "n");
            return successful;
        }
    }

The streams are initialized by returning the input and output streams of the open serial port.  In order for the serial port object to not be null, it must store the object for the open serial port.

The getInputStream() and getOutputStream() methods both require a try-catch block.  The important exception to catch here is the IOException to signify whether the streams failed to open or not.  For more information see How to Open A Serial Port in the Reference Material.

I also call a method called writeData(0, 0).  This is the method that encapsulates the code required to write serial data.  More on that later.  Right now it is just used to set variables on the microcontroller side to zero.

Setting Up Event Listeners to Read Data

Once the port is open, the serial port must know whenever there is data to be read.  This approach is event driven rather than by polling.  When the event is hit, a special block of code will run.  This is advantageous to polling because polling requires constantly asking if data is available.  The code for the event driven approach is below.  See Event Based Two Way Communication for more information.

    //starts the event listener that knows whenever data is available to be read
    //pre style="font-size: 11px;": an open serial port
    //post: an event listener for the serial port that knows when data is received
    public void initListener()
    {
        try
        {
            serialPort.addEventListener(this);
            serialPort.notifyOnDataAvailable(true);
        }
        catch (TooManyListenersException e)
        {
            logText = "Too many listeners. (" + e.toString() + ")";
            window.txtLog.setForeground(Color.red);
            window.txtLog.append(logText + "n");
        }
    }

The code here is pretty much the whole reason why this class implements SerialPortEventListener.  The parameter for adding the event listener is just the object itself.  The base class has a method called serialEvent(event) that should be overridden before the event code will work.  Overriding that method defines what happens when the event is hit.

The method addEventListener(this) is the event that is always checking for SerialEvents.  It isn’t really important to know what the events actually are, just that the one we’re interested in is the one that tells us whenever data is received.  Adding the event listener is complemented by the method notifyOnDataAvailable(true), which definitely helps us achieve what I mentioned previously.

This code requires a try-catch box.  The exception here is that there may be too many event listeners.  I only use one in the code, so this exception should never be hit.

Disconnecting from the Serial Port

Once all the communication is completed, the serial port must be disconnected.  In some instances, some ports stay stuck open, which isn’t exactly a good thing.

    //disconnect the serial port
    //pre style="font-size: 11px;": an open serial port
    //post: closed serial port
    public void disconnect()
    {
        //close the serial port
        try
        {
            writeData(0, 0);

            serialPort.removeEventListener();
            serialPort.close();
            input.close();
            output.close();
            setConnected(false);
            window.keybindingController.toggleControls();

            logText = "Disconnected.";
            window.txtLog.setForeground(Color.red);
            window.txtLog.append(logText + "n");
        }
        catch (Exception e)
        {
            logText = "Failed to close " + serialPort.getName()
                              + "(" + e.toString() + ")";
            window.txtLog.setForeground(Color.red);
            window.txtLog.append(logText + "n");
        }
    }

The code here requires a try-catch block so there it is.  The exception to catch here is pretty generic.

Before closing the port, I reset the data on the microcontroller.  That step is optional depending on the application.  For example, if the value sent to the microcontroller is controlling the speed of a motor, I’d want the motor to turn off if I turn off the remote control.

The event listener should be removed as it is no longer needed.

The method to close the port is the close() method.

The input and output streams should also be closed via the same method as above.

See How to Close A Serial Port in the Reference section for more information.

Reading Data – The serialEvent Method

This is a follow-up to the section on preparing to Read Data.  It has information on how to process the data that the program reads.

    //what happens when data is received
    //pre style="font-size: 11px;": serial event is triggered
    //post: processing on the data it reads
    public void serialEvent(SerialPortEvent evt) {
        if (evt.getEventType() == SerialPortEvent.DATA_AVAILABLE)
        {
            try
            {
                byte singleData = (byte)input.read();

                if (singleData != NEW_LINE_ASCII)
                {
                    logText = new String(new byte[] {singleData});
                    window.txtLog.append(logText);
                }
                else
                {
                    window.txtLog.append("n");
                }
            }
            catch (Exception e)
            {
                logText = "Failed to read data. (" + e.toString() + ")";
                window.txtLog.setForeground(Color.red);
                window.txtLog.append(logText + "n");
            }
        }
    }

Since we only want to read data if it exists, we test the condition in the if statement above.  This could be redundant because we wouldn’t be in this method if the event never got triggered.

Reading the data requires a try-catch block.  The read() method returns an integer, but the value in it is actually a byte value so this is casted to a byte, in which I store in a variable called singleData.  When I was testing this code before, I noticed that the data being read would always have random new line characters in it, and I never knew why this happened.  I never wrote any new line characters.  Since I don’t want these, I add an if condition saying that if it encounters that, don’t display that data on the screen.

Java also has a nice way of converting bytes to a string.  A byte array can be used as a parameter when initializing a string, which is what I’ve done when I assign a value to logText.

The exception here is just the usual generic one.

Writing Data

Here is the method for writing data.  In my application, I am writing two integers sequentially to my microcontroller.  Data that is sent to the MCU can be used for such things such as controlling motor speeds, which is what I am trying to do here.  I hope to use the data sent do control the PWM duty cycle of the motor for speed control.

    //method that can be called to send data
    //pre style="font-size: 11px;": open serial port
    //post: data sent to the other device
    public void writeData(int leftThrottle, int rightThrottle)
    {
        try
        {
            output.write(leftThrottle);
            output.flush();
            //this is a delimiter for the data
            output.write(DASH_ASCII);
            output.flush();

            output.write(rightThrottle);
            output.flush();
            //will be read as a byte so it is a space key
            output.write(SPACE_ASCII);
            output.flush();
        }
        catch (Exception e)
        {
            logText = "Failed to write data. (" + e.toString() + ")";
            window.txtLog.setForeground(Color.red);
            window.txtLog.append(logText + "n");
        }
    }

The write() method here requires a try-catch block just like many of the other methods used for serial communication.  Using the output stream, I call that method to write an integer value.  I also write a dash and a space to separate the actual data being read.  See the ASCII Table for the values of what these characters should be.  This helps me differentiate the sets of data that is sent back and forth.  The dash separates the two integers being sent and the space separates the entire set.  On the Arduino end, four called to read() can separate the data without mixing things up.  Example of that later.

Putting All the Java Code Together

Once all these methods are setup, they need to be called somewhere in the program so we can put them to use.  When the program starts, the code for searching for serial ports will run so that it can populate the combo box on the GUI.  The GUI buttons also need to be disabled to reflect the fact they should be disabled when there is no connection to a port.  When the connect button is pressed, the input and output streams are started and the event listener is added.  The code for that is shown below.

        private void btnConnectActionPerformed(java.awt.event.ActionEvent evt) {
            communicator.connect();
            if (communicator.getConnected() == true)
            {
                if (communicator.initIOStream() == true)
                {
                    communicator.initListener();
                }
            }
        }

The if statement is needed such that the code will not run if a successful connection was not made.  This is the precondition for the initIOStream() and the initLIstener() methods.

When the user decides to disconnect from the serial port, the user only needs to call the disconnect() method when the disconnect button is pressed.

The up/down arrows on my GUI are set to write data to the serial port when they are pressed.  When data is written to the Arduino, the MCU will send the data back to the Java program, which will signal the event listener to display that data back to the screen.

Arduino Code

The Arduino code is pretty straight forward.  There are just a few calls to the read() method.

Update 6 May 2012: the syntax for the Arduino code has updated since the writing of this article.  Apparently, the lines

Serial.print(separator, BYTE);
Serial.print(space, BYTE);

are no longer valid and have since been replaced by the following:

Serial.write(byte(separator));
Serial.write(byte(space));

The code below hasn’t been edited with this change, but basically the code required for writing a byte value through serial communication has changed.

// this is where we will put our data
int left = 0;
int right = 0;
byte space = 0;
byte separator = 0;

void setup(){
  // Start up our serial port, we configured our XBEE devices for 38400 bps. 
  Serial.begin(9200);
}

void loop(){
  // handle serial data, if any
  if (Serial.available() >= 4){
    left = Serial.read();
    separator = Serial.read();
    right = Serial.read();
    space = Serial.read();
    Serial.flush();

    Serial.print(left);
    Serial.print(separator, BYTE);
    Serial.print(right);
    Serial.print(space, BYTE);
    Serial.print("n");
  }
}

I first declare four variables to reflect the fact that I’m writing four different variables to the serial port.

In the loop method, I added a condition which will check whether there are four pieces of data available before reading them.  This again reflects the fact I’m writing four values.

The four variables initially declared store the values in the order that they are written, and then are just printed to the screen.

The print() method is able to convert the byte value to an actual character by adding a second parameter called BYTE.  The left and right variables don’t need it because the values written were integers to begin with, however, the dash and space characters were written as ASCII values.

For more information about Arduino and Java, and Arduino’s Serial library, please refer to those in the Reference Section.

Code Downloads

Here are the code downloads for the GUI, key bindings and the serial communication.  WordPress doesn’t allow uploads of zip or java files so I uploaded it all to Megaupload.

Link to download: http://www.mediafire.com/?z2l26ncypmzn20z

Other Examples

There are also other sites I looked at which had example code for serial port communication in Java.  The sites are Programming Serial and Parallel Ports and Serial Port Access Using RXTX in Java, which are both in the Reference section.

Reference Material

Below are a bunch of links to reference sites that I used to find some of the information written here.  I mostly referred to bits and pieces of each article to understand the serial code and to come up with the example I present here.  The list is in the order that I referenced them.

Discovering Available Comm Ports

http://rxtx.qbang.org/wiki/index.php/Discovering_available_comm_ports

The code on this page is pretty specific to the title of this heading, and the code is pretty easy to follow.

How to Open A Serial Port

http://embeddedfreak.wordpress.com/2008/08/08/how-to-open-serial-port-using-rxtx/

This page provides a very concise and detailed explanation on what each line of code does in order to get a serial port open.  Definitely work a look if you’re trying to understand the code.

Event Based Two Way Communication

http://rxtx.qbang.org/wiki/index.php/Event_Based_Two_Way_Communication

This page has example code on how to connect to a serial port and how to interact with it.  The code here uses events, rather than polling, to send data back and forth, which means that whenever data is received, the event code is triggered.

How to Close A Serial Port

http://embeddedfreak.wordpress.com/2008/08/08/how-to-close-serial-port-in-rxtx/

This article is written by the same author who wrote the article on how to open serial ports.  Good example code here.

ASCII Table

http://www.asciitable.com/

Having the ASCII Table is quite handy for serial data because data being sent and written are bytes, so being able to know what byte values correspond to what character really helps.

Arduino and Java

http://www.arduino.cc/playground/Interfacing/Java

This article discusses how to use the serial port communication with Java and Arduino, which is exactly what I am after.  It has example code on pretty much the entire process of serial port communication, but it may be too much to read since there is little explanation about the code.

Arduino Serial Class

http://arduino.cc/en/Reference/Serial

A good reference for Arduino’s Serial class methods.  Also has example code to look at.

Programming Serial and Parallel Ports

This article provides a brief introduction to programming serial ports and has information on the steps required to talk to the serial port.  However, the code examples in there may be hard to follow for someone new to serial programming.

Serial Port Access Using RXTX in Java

http://gomultidomain.blogspot.com/2008/06/serial-port-access-using-rxtx-in-java.html

This page also has complete code for serial communication in Java, but what I was looking for here was how to use the write method to send serial data from Java.