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jist:DevTutorial

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Note: This page is currently under construction.

1 Installing the Software
- 1.1 Downloading Development Programs
  - 1.1.1 Java Preferences and MIPAV
  - 1.1.2 Download and Install Eclipse
- 1.2 Creating Accounts
  - 1.2.1 Create a NITRC Account
  - 1.2.2 Create a JIST Account
2 Adding the Code
- 2.1 Preparing Software Environment
3 Editing Modules

Installing the Software

Before installing, see the JIST Prerequisites.

Downloading Development Programs

Java Preferences and MIPAV

BEFORE YOU START: See the JIST Tutorial on MIPAV installation / Getting Started: JIST Prerequisites
In particular, the prerequisites include:
- Uninstall any previous versions.
- Prepare your Java Preferences to make sure that you're using Java 1.6 or higher.
- Even if you already have MIPAV already installed, make sure that you have the version of MIPAV that is most compatible with JIST.

Download and Install Eclipse

Go to the Eclipse web site: [http://www.eclipse.org]
Click [Download Eclipse].
Choose [Eclipse IDE for Java Developers].
Click the download button or choose a mirror site.
1. For a Mac, it just downloads the archived file.
2. Unzipping this archived file creates a new folder named [eclipse].
3. You can move the [eclipse] folder to the [Applications] folder
Run the installer and follow the on-screen instructions for installation
Workspace Launcher: Set the folder wherever you'd like the Workspace to be
1. For example: /Documents/workspace

Creating Accounts

Create a NITRC Account

Notes: NITRC = The Neuroimaging Informatics Tools and Resources Clearinghouse

NITRC website: http://www.nitrc.org/
Under [Participate], click on [Register as a NITRC user]
NITRC will send you a verification email.
To further access your NITRC account: http://www.nitrc.org/account/login.php Select the appropriate timezone.
Once you're logged in, you can see your account on the main toolbar, by clicking [My NITRC]

Create a JIST Account

Notes: JIST = Java Image Science Toolkit

JIST website: http://www.nitrc.org/projects/jist/
Under [Member Info], click on [Request to Join Development Team]
List whether you're willing to "be a reference."
Under [Associations], click on [JIST Resources for Algorithm Development]: http://www.nitrc.org/projects/jhumipavplugins/
Under [Member Info], click on [Request to Join Development Team]
Wait for requests to be validated.

Adding the Code

Preparing Software Environment

Set Up Paths for CVS Repositories

Open Eclipse. Eclipse will ask you which folder to store your work in; the default for this is under "Documents/workspace." If you ever need to clear over, check out the repositories again, etc, then you can just create a new folder (e.g., "Workspace2"), and you can start from scratch.
Our first task is to tell eclipse where the CVS repositories are located. Eclipse has a window dedicated to managing CVS repositories, but it may not appear. To show this window follow these steps:
- Click "Window -> Show View -> Other" as shown below. (Figure P-1)
- Choose the CVS folder, highlight CVS Repositories and click Ok. (Figure P-2)
- Now the CVS Repositories Window should be open.

Figure P-1: Window -> Show View -> Other

Figure P-2: CVS Repositories

Add the CVS Repositories

Now we will add the repositories containing the JIST plugin code and supporting JIST infrastructure code.
First we will add the JIST infrastructure code.
Right click in the "CVS Repository" window and select New -> Repository location. (Figure P-3)
This brings up the "Add new CVS Repository" window. We will be adding several repositories to run JIST. (Figure P-4)

Figure P-3: New -> Repository Location

Enter the following information:

Host: www.nitrc.org

Repostitory Path: /cvsroot/jist

User: <Your Nitrc User name>

Password: <Nothing - you will be prompted> or <Your Nitrc Password>

Connection type: extssh

Alternatively if you do not have a Nitrc user name, you can download the code anonymously using the following username / password

User: jhuuser

Password: jhuuser

Click "Finish." You should see that a repository has been added in Eclipse.

Figure P-4: Add New CVS Repository Window

Other CVS trees:
- There's one other CVS tree that you should have access to. This JHU MIPAV Plugins code is also on Nitrc and contains algorithm and plugin code that has been released as open source. The information for this repository is:

Host: www.nitrc.org

Repostitory Path: /cvsroot/jhumipavplugins

User: <Your Nitrc User name>

Password: <Nothing - you will be prompted> or <Your Nitrc Password>

Connection type: extssh

Figure P-5: Alternate Window for JHUMipavPlugins

Download the Code and Create Java Projects

Now that we have the repositories, we can download the source code for JIST and the algorithms built using its infrastructure. In eclipse, this is done by creating a "Java Project" from the CVS repository with the following steps:

Choose the repository location you want to download code from, and navigate to the appropriate folder. Right click on the folder and choose "Check out as."
- For the JIST repository (www.nitrc.org:/cvsroot/jist), check out from "HEAD/JIST"

Figure D-1: Check Out As...

For the NITRC plugins repository (www.nitrc.org:/cvsroot/jhumipavplugins), check out from "HEAD/JIST-CVS/"

Figure D-2: Alternate Check Out As... for JHUMipavPlugins

Choose "Check out as a project configured using the New Project Wizard" and click Next.

Figure D-3: Check Out As Project using New Project Wizard

Choose the Head tag from the list of directories. Click "Finish".

Figure D-4: Choose Head Tag

Select "Java Project" from the menu. Click "Next." (Figure D-4)

Figure D-5: Select Java Project

Name your project according to the name of the repository (e.g., "JIST" or "JIST Base Code" for the base code associated with /jist, and maybe "JHUMipavPlugins" or "JIST Plugins" for the NITRC plugins associated with /jhumipavplugins).
- Be sure that "JavaSE-1.6" is selected as the "Execution Environment".
- Also choose "Create Separate Folders for Source and Class Files" if it is not selected
- Click "Finish" when you are done

Figure D-6: Name Project and Configure Project Settings

Wait for the code to download... You can click "Run in Background" if you wish.

Figure D-7: Check Out Progress Window

You now have a new Java Project! After adding both repositories, you'll be able to see these projects in the "Package Explorer" Window.

Figure D-3: Created Projects

Specify Dependencies and Add Libraries

After the above steps, all of the JIST and algorithm source code should be in your workspace. However, these will have compilation errors, since they depend on third-party libraries as well as each other. So, the next step is to specify these dependencies for each project.

The JIST infrastructure code, which correlates with "/cvsroot/jist", is at the "top" of the hierarchy, so we'll deal with this first.

To edit the Project's Build Path, click on the project in the workspace on the left, then select Build Path -> Configure Build Path.

Figure L-1: Configure Build Path...

The first thing that we need to add is the MIPAV class folder. Click "Add Class Folder."

Figure L-2: Add Class Folder

Click "Create New Folder."

Figure L-3: Create New Folder

Select "Advanced." Check "Link to folder in the file system." Type in or browse to the directory where MIPAV is installed. Click "OK"

Figure L-4: Add MIPAV Directory

The "MIPAV" folder will now show up in the "Add Class Folder" window. Click "OK" to return to the build path window.

Figure L-5: Add MIPAV Class Folder

Next, we add the MIPAV libraries. From the Build Path Screen click "Add JARs".

Figure L-6: Click Add JARs

Navigate to the MIPAV folder which was just created under the JIST project. Select all the jars in the "mipav/lib" folder, and click "OK" to add them to the Build Path.
- (Note: You can select a subset of the jars, click "OK", then repeat the process to add more JARs.)

Figure L-7: Add JARs from mipav/lib

Finally, we need to add other third-party libraries. These can be added to the classpath in the same way we added the MIPAV JARs.
- From the Build Path Screen click "Add JARs".
- Navigate to the root of the JIST project folder, and find the lib directory.
- Select all the jars in this "jist/lib" folder, and click "OK" to add them to the Build Path.

Figure L-8: Add JARs from JIST/lib

Click "OK" in the Build Path Screen to apply changes to the Build Path.

Figure L-9: Apply Build Path Settings

FOR WINDOWS/LINUX:
- First highlight the JRE System Library in the build path list. Click Edit.
- This brings up a new window. Select Alternate JRE. Click Installed JREs to add the MIPAV JRE to the list of JRE's that Eclipse will use.
- A new window appears with a list of the JREs Eclipse can use. Click Add.
- Next, type in a name for this JRE (ex. "mipav") and type in or browse to the JRE home directory in mipav. (this is usually ../mipav/jre). Click Finish.
- Click "Ok" to get back to the JRE window. Check the box next to the new MIPAV JRE. Click Ok to get back to the JRE System Library window. Change the Alternate JRE to be "mipav" instead of "jre6".
- Click "Finish".
- In Preferences, ensure that compiler under "Java Compiler" has the "Compliance Level" value set to 6.0.
FOR MAC:
- On Mac, the Java Runtime Environment is controlled by Apple and does not need to be adjusted
- In Preferences, ensure that compiler under "Java Compiler" has the "Compliance Level" value set to 6.0.

The second level of the hierarchy deals with "/cvsroot/jhumipavplugins". It's Build Path must be configured as follows:

Set a Source Folder for the Project.
- Expand the project until you see JIST folders.
- Right click on "src" and select Build Path -> Use as Source Folder.

Figure L-10: Use as Source Folder