Software I wrote to complement ImageJ

Here are the Java applications I wrote to extend ImageJ to SEP data and applications. Some of this is very preliminary but could easily be improved. The source code is and API documentation is at:

 
http:/sepwww.stanford.edu/sep/matt/join/ijDoc/plugs
http:/sepwww.stanford.edu/sep/matt/jest/jdocs/api/Package-ijDoc.plugs.html

• SepCubeHandler implements a Java Contenthandler for SEP data cubes. Given a URL connection to a SEP data cube the SepCubeHandler reads the dimensions of the header information and loads the corresponding floats into a Java array.
• SepCubeHandlerFactory implements a Java ContentHandlerFactory for SEP data cubes. It creates a SepCubeHandler when it encounters a URL with file suffix .H or Mime type application/x-sepcube. It is currently not used since the security manager does not allow applets to execute ContentHandlerFactories.
• SepCube2FloatArray converts a two-dimensional Java array to a one-dimensional array. The conversion is necessary since my SEP applications expect multi-dimensional Java arrays while ImageJ expects a one-dimensional array.
• Nmo applies hyperbolic move out to a two dimensional Java array.
• Sep downloads an SEP data file (using SepCubeHandler), applies hyperbolic move out to the loaded data (using NMO), and displays the result using ImageJ. This class implements a Plug-in.