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I’ve written in the past about my fear of being in the shower. One thing my therapist suggested last week was to take some small steps to work on overcoming those fears. Those of you who have done any sort of cognitive-behavioral therapy or taken a psychology class on therapy techniques or learning and behavior (a la Skinner or Pavlov) will probably recognize the term “systematic desensitization“.

The basic idea behind systematic desensitization is first to teach the client effective relaxation technique and then have him/her use those techniques when confronting an object or situation that elicits fear. So, in essence, you retrain the mind to not get anxious or scared when confronting an anxiety provoking stimulus.

I’ve pretty much got the relaxation techniques down. I’ve pretty good at the deep breathing and I have a quick and dirty version of progressive relaxation.

My therapist’s suggestion was to run the shower and stick my arm in it. Eh… I’m not much on getting wet when I don’t have to. Plus, it would probably elicit too many questions from my grandmother and brother as to why the shower is on for extremely short periods of time. And as I don’t really feel comfortable with talking to them about this stuff, the fewer the questions the better.

So I came up with my own version (yippee me for being pro-active). I decided that every time I went to the bathroom, I would step into the shower fully clothed and leaving the shower door open (as I tend to start feeling a bit claustrophobic when the door is closed). As I get ready, I take about five deep breathes. Then I step in. As I’m in there, I tell myself what the date is to reinforce in my mind that this is the present and I tell myself that there is nothing in the shower that will hurt me. All the while making sure I’m breathing. I’m one of those people who seems to forget to breathe when I start getting extremely anxious.

Last week when I started this, I could barely make it ten seconds before I started to freak out. Now, I can make it for roughly a minute. My goal is to make it up to five minutes. Then I’m going to start back at a few seconds with my shirt removed. Work myself back up to about five minutes. And then start again with both my shirt and pants removed working my way back up to the five minute mark. Then start again with the water running and actually taking mini showers. I figure by the time I actually get to this point my brother will have moved out of the house and gone back to college. I can work on it while my grandmother is napping.

So that’s the plan. I don’t know how well it’s going to work.

I think this weekend I’m going to go to Bath and Body Works with my best friend and smell some bath stuff and shampoos. I’ll need the moral support. I doubt that I’ll actually buy anything, but it’s just one more small step.

These are simplified instructions for setting up Eclipse using the source tree.See eclipse.htmfor instructions about how to set up Eclipse using the Subversion version control system.Subversion allows you to get updates from the Ptolemy development tree. The instructions here provide access to a static source code tree, suchas what is shipped with the Ptolemy II release.

These instructions assume you are using Eclipse Helios under Windows or Mac OS X.Other ways of setting up and building Ptolemy II are described on thePtolemy II install page.

Contents of this page:

Set up Eclipse for Ptolemy II

• Eclipse is unaware of the version control aspects of the project.

Install Eclipse

1. Download the latest version of Eclipse fromhttp://www.eclipse.org.
   In October, 2010, we chose Eclipse for RCP and RAP Developers, which is 190Mb.The Eclipse for RCP and RAP Developers version includes theplug-in development environment (PDE), which is needed by the backtrackfacility, which is an optional part of Ptolemy II that allows models torestore their old state. If the version of Eclipse that you installdoes not have the PDE, then there will be build errors, which can be fixed byexcluding ptolemy/backtrack/ from the build.

   Eclipse is available as both 32-bit and 64-bit binaries. Decidingwhich one to download can be complex.

   The basic idea is that to use a 64-bit version of Eclipse, you musthave a 64-bit JVM and an operating system that will support 64-bitapplications. When in doubt, choose the 32-bit version of Eclipse,it is more likely to work than the 64-bit version.

   See below for details.

   32-bit or 64-bit?

   • (Linux): Run uname -a. If the result contains x64, you are running a 64-bit version of Linux and would select the 64-bit version of Eclipse.. Also, try java -version. Below is a run on a 64-bit Linux machine:
   • (Mac OS X):Under Mac OS X 10.5 and 10.6, the default JVM is 1.6, which is 64-bit. However,Java 1.6.0_20 does not work well. The issue is thatthe following stack trace appears:The bug happens when running from Eclipse or from the command line.The bug requires UI interactions such as mouse movement or clicking.The bug is probably a threading bug and may only show up on multi-coremachines. The downside is that when the bug occurs, the debuggingsession in Eclipse may become non-responsive.

     For further information, see:http://lists.apple.com/archives/java-dev/2010/May/msg00140.html.
     So, at this time, we are recommending the 32-bit version with Java 1.5.
     Download eclipse-rcp-helios-SR1-macosx-cocoa.tar.gz uncompress it and move eclipse/ into /Applications, which will create /Applications/eclipse/Eclipse.app.
     Firefox Mac OS X Details:

     1. Firefox will download the file into a directory, which may be /Downloads
     2. Double click on eclipse-rcp-helios-SR1-macosx-cocoa.tar.gz which will create the eclipse directory.
     3. Drag the eclipse directory to your Applications directory.
     
     The next step on the Mac is to force Eclipse to use Java 1.5 by editing eclipse.ini.
     1. In the Finder, go to /Applications/eclipse, find the Eclipse executable and right click (Control + click) and choose 'Show Package Contents'.
     2. Browse to Contents/MacOS and double click on eclipse.ini, which will open up the file in TextEdit
     3. Edit the file and insert -vm /System/Library/Frameworks/JavaVM.framework/Versions/1.5/Home/bin/java
        before the -vmargs line.
     4. Save the file and exit TextEdit.
     For details about eclipse.ini, see http://wiki.eclipse.org/Eclipse.ini
     When you start up Eclipse, if you want to verify which version of Java you are running
     • (Mac OS X): EclipseAbout EclipseInstallation DetailsConfiguration.
       For Java 1.5, the java.class.version property should be 49.0.
       For a 64-bit JVM, the java.vm.name property might have the string 64 in it.
   • (Windows): Determine whether you are running a 32-bit or 64-bit version of the OS.
     • Windows 7 or Vista: 'Start', then right click on'Computer', then click on 'Properties'. Under System, youshould see the system type. The 64-bit version of Windows 7 willsay '64-bit Operating System'. Seehttp://windows.microsoft.com/en-US/windows7/32-bit-and-64-bit-Windows-frequently-asked-questions.for details.
     • Windows XP: 'Start', then right click on 'My Computer',and then click on 'Properties'. Under 'System', if you see 'x64Edition', then you are running a 64-bit version of Windows. If 'x64Edition' is not listed, then you are running a 32-bit version of Windows.
     
     After determining whether to download the 32-bit or 64-bit versionof Eclipse, download the file and unzip the download file into anappropriate place, such as C:Program Files, which willcreate C:Program Fileseclipseeclipse.exe.
     If eclipseeclipse.exe is not created, then it couldbe that the security policy on your machine is preventing the creationof .exe files. If this is the case, then try rightclicking on the zip file, select 'Properties' and then at the bottom,hit 'Unblock' and then 'Apply'. Or try runningunzip from the command line.
2. (All Platforms): Finish the installation by double clickingon /Applications/eclipse/Eclipse.app or eclipse/eclipse.exe.
   The first time this is run it will complete the installation process.
   • (Windows): If Eclipse fails to start with the message 'Windows cannot access the specified device, path or file. You may not have the appropriate permissions to access the item', then it may be necessary to make eclipse.exe and a dll executable:
     If you get the message 'The Eclipse executable launcher was unable to locate its companion shared library', then run the following commandin the eclipse directory.
     After the first run, normal start-up will occur whenever it is started.

Eclipse Preferences for Ptolemy II

Eclipse has the notion of a workspace, which is a collection ofone or more projects. Ptolemy II is a project.
When the 'Workspace Launcher' window comes up, either stick with the defaultor choose a new directory. Note that the projects can be located outsideof the workspace directory. One caveat is that Eclipse will not permitthe project directory to be a parent of the workspace directory, so placing theworkspace in a subdirectory such as the default location is best.
Click 'OK' to create the workspace and open Eclipse.
Below is the Workspace Launcher Window:

The default configuration of Eclipse has some difficulties with Ptolemy II,so a few changes are necessary.

1. (Optional): Shortcuts and Memory Size
   • (Mac OS X): In Applications/eclipse, drag the Eclipse.app icon to the Finder Dock on the edge of your screen. This will give you fast access to starting Eclipse.
     There is usually no need to set the memory size for Eclipse under Mac OS X. By default, it is set to 512 megabytes. For details about setting the memory size, see: Eclipse Workbench User Guide/Tasks/Running Eclipse.
   • (Windows): In Windows, create a shortcut to eclipse.exe by going to the directory where Eclipse is installed, right clicking on eclipse.exe and selecting Create Shortcut.
     To add Eclipse to the start menu, right click on the shortcut and select Pin to Start Menu
     There is usually no need to set the memory size for Eclipse. By default, it is set to 512 megabytes in the eclipse.ini file.
2. Eclipse requires some customization to build Ptolemy IIand to keep the Ptolemy II coding style.In the steps below, weoutline changes to be made in the Eclipse Preferences window.
   Under Windows the Eclipse Preferences windowis invoked via WindowPreferences.
   Under Mac OS X the Eclipse Preferences windowis invoked via EclipsePreferences.
   For each of thechanges, hit Apply. When all the changes are done, hitOK, which will close the Eclipse Preferences Window.in the preferences window
   (Mac OS X: EclipsePreferences)
   (Windows: WindowPreferences)
3. Go to JavaCode StyleFormatter and click New
4. In the 'New Profile' Window, for the Profile name, enter 'Ptolemy II' Under 'Initialize settings with the following profile', select 'Java Conventions [built-in]' (We use Java Conventions over the 'Eclipse' setting because the Eclipse style uses tabs.) Then hit OK
5. Under the 'Indentation' tab, change the Tab policy to 'Spaces only'.
6. Under the 'New Lines' tab, select 'at end of file'
7. Under the 'Comments' tab,
   unselect 'Enable Javadoc comment formatting'
   unselect 'Enable block comment formatting', otherwise the block comments that have <pre> ... <pre> get changed.
   unselect 'Enable line comment formatting', otherwise the headers for public methods etc. get changed.
8. Click OK.
9. In the Preferences Window, click Apply.

Ptolemy II 8.0 uses some features of Java 1.5, which is also known as Java 5.0.In particular, ptolemy/actor/ptalon uses generics,which require Java 1.5 (aka Java 5.0) or later.

However, the Ptolemy II development trunk that includes changes afterPtolemy II 8.0 uses some features of Java 1.6 (aka Java 6.0).In particular, ptdb to uses javax.swing.GroupLayout. which requires Java 1.6 (also known as 6.0) or later.

• (Mac OS X): It is best to set Eclipse to use Java 1.5 or 5.0or later source code compliance.
• (Windows): It is best to set Eclipse to use Java 1.6 or 6.0or later source code compliance.

1. While still in the preferences window
   (Mac OS X: EclipsePreferences)
   (Windows: WindowPreferences)
   expand JavaCompiler
2. Make sure that Set 'Compiler compliance level':
   • (Mac OS X): '1.5' or '5.0'
   • (Windows): '1.6' or '6.0'
   Note that Java 1.5 is the same as Java 5.0 and Java 1.6 is the same as Java 6.0. What we don't wantis '1.4' or '4.0'. If you plan on using the the Ptolemy II developmenttree after Ptolemy II 8.0. then you don't want '1.5' or '5.0'.
3. Click Apply.

Eclipse has very good compiler error/warning. One of thewarnings complains if a Serializable class does not haveserialVersionUID declared. Since this warning is only usefulif you are tightly managing serialization, we turn it off:

1. While still in the preferences window
   (Mac OS X: EclipsePreferences)
   (Windows: WindowPreferences)
   Expand JavaCompilerErrors/Warning
2. Under 'Potential programming problems', change 'Serializable class without serialVersionUID' to 'Ignore'
3. Under 'Generic Types', change 'Unchecked generic type operation' to 'Ignore'.
4. Under 'Generic Types', change 'Usage of a raw type' to 'Ignore'.
5. Click Apply. If you are prompted for a full rebuild, click Yes.

(Windows:) The PtDoc Doclet in $PTII/doc/doclets/PtDoclet.javarequires tools.jar, which is only in the Java DevelopmentKit (JDK), not the Java Runtime Environment (JRE). So, be sure that aJDK is selected for building, not a JRE.
While still in the preferences window:
(Mac OS X: EclipsePreferences)
(Windows: WindowPreferences)

1. Select JavaInstalled JREs
   (Mac OS X): select JVM 1.5.0.
   (Windows): select JVM 1.6.0.
2. Verify that the checked line corresponds with a JDK, nota JRE.

(Windows): While in the 'Installed JREs' window, under Java 1.6,tools.jar must be added the external jars:

1. Select the default JRE EditAdd External Jars.
2. Browse to the path of your JDK for example c:Program FilesJava JDK1.6.0_22lib
3. Hit Open, select tools.jar and then finish.

Click OK in the Preferences window to apply all of the above changes.

Setting up Eclipse to manage your Ptolemy II development environment

Eclipse will manage your ptII code tree as a project calledthe ptII project.

1. Download a ptII source tree fromhttp://ptolemy.eecs.berkeley.edu/ptolemyII/ptIIlatest
   The Windows and Mac OS X installers include the source, or you mayinstall a separate source-only download.
2. Eclipse uses the .classpath file to set paths and exclude files. There are two choices:
   1. In the Ptolemy II source tree, copy .classpath.default to .classpath. This choice is the simpler choice, but might exclude optional third party packages.
   2. Run ./configure. This choice is more complex, especially for Windows users. However, this choice will include optional third party software that is already installed on your machine.
   Choose one of the options below

   A. Copy .classpath to .classpath.default

   • (Mac OS X): Unfortunately, by default the Mac OS X Finder hides files whose names begin with a period, such as .classpath. One solution is to follow the instructions from: http://www.macworld.com/article/51830/2006/07/showallfinder.html:
     1. Start up the Terminal application, which may be found as /Utilities/Terminal.app. Enter:
     2. Restart the Finder by holding down the Option key, then clicking and holding on the Finder icon in the Dock. Then, select 'Relaunch'. Or, log out and log back in again.
     3. Start up the Terminal application, which may be found as /Utilities/Terminal.app
     4. In the Terminal, change to the directory where the Ptolemy II source code was installed. For example:
     5. Copy the files:
   • (Windows):
     1. Find the Ptolemy II source distribution, which by default would be c:PtolemyptII8.0.1.
     2. Right click on .classpath and select delete.
     3. Right click on .classpath.default, select copy.
     4. Select paste and paste a copy of the file.
     5. Right click on the copy, select rename and rename the file to .classpath.default.

   OR

   B. Run ./configure

   Ptolemy II includes a number of packages that rely on software that you may or may not have installed, such as MATLAB, the rxtx package (for serial port connections), joystick support, Java Advanced Imaging (JAI), the Java Media Framework (JMF), and Java 3D. If you wish to use or extend these features, you will need to perform a few extra steps. These steps require execution of a script called configureThe procedure below will modify the .classpath file that is provided in the version control repository to customize it for the software that you have installed.
   • (Mac OS X): Using the Terminal to run configure
     1. Start up the Terminal application, which may be found as /Utilities/Terminal.app
     2. In the Terminal, change to the directory where the Ptolemy II source code was installed. For example:
     3. Set $PTII to the location of the source tree:
     4. Make configure executable.
   • (Windows): Install Cygwin and run configure Unfortunately Windows does not ship with Unix shell commands like make. The workaround is to install Cygwin, see http://ptolemy.eecs.berkeley.edu/ptolemyII/ptIIlatest/cygwin.htm
     1. Start up the Cygwin Bash shell: StartRunCygwin
     2. Change to the directory where the Ptolemy II source code was installed. For example: Note that if there are spaces in the path name to the directory where your Ptolemy installation is located, then you should use double quotes around the path: cd 'c:/Documents and Settings/yourLogin/workspace/ptII'
     3. Set $PTII to the location of the Ptolemy II source tree: Again, if there are spaces in the path, use double quotes: export PTII='c:/Documents and Settings/yourLogin/workspace/ptII'
     4. Run: This will create $PTII/.classpath
3. If Eclipse is not running, start up Eclipse
4. In Eclipse, do FileNewProject.
5. In the 'New Project' window, select 'Java' > 'Java project', Click Next.
6. In the 'New Java Project' window:
In 'Project Name', enter any project name, ptII is a common choice.
Uncheck 'Use default location' and browse to the location of the source tree.
(Mac OS X): For example, browse to /Applications/Ptolemy/ptII8.0.1
Press 'Next'. There might be a delay as Eclipse scans your ptII tree.
Below is the New Java Project window: Warning: If the 'Setting Build Paths' window comes up with a message 'The output folder has changed. Do you want to remove all generated resources from the old location ptII/bin', then the problem is that the .classpath file was not found. It is best if you exit Eclipse, create the .classpath file and redo the above steps.
7. In the 'New Java Project' window, select 'Allow output folders for source folder', then click 'Finish'
Below is the second New Java Project window:
8. When asked if you want to shift to the Java perspective, click on Yes.
9. The workspace will take a few minutes to build.

Running Ptolemy II

1. In the Run menu, select 'Run Configurations...'.
2. In the resulting dialog, select 'Java Application' and click 'New'.
3. In the dialog, fill in the boxes as follows:
   • Name: Vergil
   • Project: ptII
   • Main class: ptolemy.vergil.VergilApplication
4. Press the Run button.

The Ptolemy II welcome window should appear.

You may now wish to read the Using Vergiltutorial.

Simple Debugging Session

1. Locate ptolemy/vergil/VergilApplication in the Explorer anddouble click. Place a breakpoint on the first line of main()by using RunAdd/Remove Breakpoint
2. Tell Eclipse which class to run with RunRun.On the Maintab, select the Ptolemy II package and enterptolemy.vergil.VergilApplication as Main class.
3. Press the Run button
4. To debug, quit Vergil, and place a breakpoint in, say, the fire() methodof ptolemy.domains.ct.kernel.CTBaseIntegrator. Then RunDebug, andas above. Open the Lorenz CT demo from the Quick Tour and run it.

Troubleshooting

Preferences

If you have already used Eclipse and you would like to start over withnew projects and preferences, remove the workspace directory in theEclipse directory. The workspace directory will onlyappear if you have already run Eclipse. Note that removing theworkspace directory will cause Eclipse to 'forget'about any projects that you may have set up

Build Error: Assert cannot be resolved

If, when building, the Problem tab shows 'Assert cannot be resolved',then the problem is that Junit is not being found.

Rebuilding Briefly flashes a window

If you have problems where clicking on build briefly flashes upa window, look in $PTII/.classpath for and emptyexclusion that looks like

If you have problems with the classpath, look in the workspace/.metadata/log file that is inthe directory where eclipse is installed. For more informationabout the .metadata directory, seebelow.

Eclipse takes a long time to start up

If Eclipse takes a long time to start up, then the problem could be a problem in your .metadata file.

Sisyphus (austincaskie) Mac Os Update

Basically, when eclipse starts up, it might try to updateH:/workspace/.metadata. The solution is covered inhttp://www.eclipse.org/documentation/html/plugins/org.eclipse.platform.doc.user/doc/tasks/running_eclipse.htm:The way I figured this out was by running Norton Antivirus anddoing View -> File System Realtime Scan Statistics and then I noticed that my machine was updating H:/workspace/.metadata

Sisyphus (austincaskie) Mac Os Download

I think I introduced the problem by clicking on the Eclipse.exebinary and selecting Pin to Start Menu. My solution was to remove theEclipse bogus entry in the start menu and then create a shortcut,change Start in property and then pin that shortcut to my start menu.