jSNARK


A Programming System for the Reconstruction of 2D and 3D Images from Their Projections

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NetBeans

jSNARK has been developed using NetBeans and the NetBeans project files are present in the SVN repository.

Adding a new plug-in to jSNARK

It is not necessary to download the jSNARK source files in order to add a new plug-in to the system. Using NetBeans, the process is as follows:

  1. Create a new NetBeans project of the type "Java Class Library".
    Click "File"=>"New Project..." or the "New Project" icon. Choose "Java", then "Java Class Library". Click "Next". Enter the name of the new project. By default, the new project will be created in the "Project Location" folder with your project name. Click the "Browse" button if you want the project located somewhere else. Click "Finish" to complete creating the project.
  2. Add jSNARK.
    Right click on the project and select Properties at the bottom of the pop-up menu. In the Properties window, click Libraries, then "Add Jar/Folder". Navigate to where you unpacked the jSNARK zip file and then to the lib directory. Select the jSNARK.jar.
  3. Create the new plug-in.
    In the project, right click on the "Source Packages" folder and select New => Java Package. Give the package a name. Right click on the package and select New=>Java Class. Add the extends and implements jSNARK classes that are appropriate for the plug-in. NetBeans will offer to generate the necessary import statements and stub methods. Complete the implementation of those methods.
  4. Create a jar file containing the new plug-in.
    Click the "Clean and Build" icon or right click the project and then click "Clean and Build." If errors were reported, fix them and repeat this step.
  5. Create a jSNARK input file that uses the new plug-in.
    When the new plug-in compiles successfully, start the jSNARK_GUI. Click "Load Plug-in" and navigate to the "dist" directory of the NetBeans project and click the jar file contained in that directory. Either open an existing snark script or start a new one. If everything is correct, your new plug-in will appear in the appropriate drop-down list in the GUI. Modify the script to create a jSNARK experiment and run it.
Now you have all the pieces, but unless you were extremely lucky, your plug-in does not work. So, how do you debug it?

If you are comfortable using JUNIT, test your plug-in independently of the jSNARK program. This is the preferred testing method. NetBeans has tools to create a skeleton test file and allows the test file to be run in the debugger. Use the Properties->Run window to set the working directory.

-OR-

NetBeans does not allow you to run the jSNARK jar file from within your project. Instead, you will have to download the jSNARK sources following the instructions below. NetBeans should have found and opened the jSNARK project. Fix the references to the jdom, xercesImpl, and jsnark_plugins jar files. These are all located in the lib directory where you unzipped the jSNARK distribution. Also, add a reference to your jar file. Now select "Run". Change the "Working Directory" to where you created the jSNARK test script and put the name of the script in the "Arguments" field. Running jSNARK in debug mode from NetBeans will allow you to insert breakpoints in your code, examine variables, and perform other debugging operations.

SVN organization

jSNARK consists of a number of components. They are:
jSNARK_GUI
A graphical interface to create and edit jSNARK XML input files.
jSNARK
The jSNARK program.
lib
The external libraries used by jSNARK.
runJSNARK
A helper program used by the jSNARK.sh and runall.sh scripts.
jSNARK_plugins
Stubs for plug-ins that have not been written yet.
jSNARK_tools
A catchall for useful utilities. Currently this only contains the skeleton program to convert a user's real projection data file into the format needed by jSNARK.
netbeans
Instructions and files needed to set up jSNARK with the NetBeans IDE.
examples
The set of example files in the distribution.
manual
The LyX sources for the manual.
regression
Tools to preform regression testing of a new version against an old version.
compareCSVfiles
A tool used by regression testing.
ant
Ant scripts to create the distribution package.
Under each of these top level SVN directories are the usual "trunk", "branches", and "tags" directories.

SVN checkout

To checkout jSNARK using NetBeans, go to Team->SVN->checkout. Enter:

svn://svn.code.sf.net/p/jsnark/code/

in the Repository URL field. Leave the User name and password fields blank for anonymous access. Click "Next". Click browse in the next window. for each of the jSNARK components navigate to the trunk entry. Click the checkbox to skip "trunk" and checkout only its content. Set the directory where the checkout should occur. Click the checkbox for scan the directory for NetBeans Projects after Checkout. All the JAVA directories are NetBeans projects. The others are not. Click "Finish" to checkout the files.

Building and running jSNARK

The NetBeans project files reference libraries using paths on my system. This will result in reference problems on your system. Fix the reference problems for the jSNARK component. It references libraries from the lib component. Build jSNARK. Now one by one fix the reference problems with the rest of the components and build them. Some of these reference the jSNARK.jar file created by the first build.

To run jSNARK from within NetBeans, it is necessary to pass the full path name to the *.snark file you wish to execute on the arguments line. Set the working directory to where you want the outputs to be written.

To execute jSNARK_GUI from within NetBeans, it must be compiled with the "Compile on Save" option turned off.

Joining jSNARK

Join jSNARK if you wish to contribute to its development.