Re: problem with using external jar-files with the "compile and run" command

Posted by Robert Dougherty on Jan 16, 2006; 7:50am
URL: http://imagej.273.s1.nabble.com/problem-with-using-external-jar-files-with-the-compile-and-run-command-tp3704060p3704062.html

In Windows, I think you are supposed to be able to add a .jar file to the
class path in the Target line of a shortcut that runs ImageJ.  It didn't
work for me; I still got "Package Jama not found in import."  Plan B was to
download the source for the Jama package to the Plugins folder.  This
produced an error I haven't seen before:

error: Invalid class file format in C:\ImageJFST\plugins\Jama\Matrix.class.
invalid constant type: 13

What I finally stumbled through is given below.  It obviously should not be
this difficult.  One thing that is probably still not right is that Matrix
has a print method that writes to System.out, and this does not seem to be
visible.

1. Download the source from http://math.nist.gov/javanumerics/jama/#Package
2. Expand and place the Jama folder in ImageJ\Plugins
3. Delete all the .class files in the top level of the Jama folder
4. Move Maths.java from Jama\util to Jama
5. Delete the Jama\util folder.
6. Edit Math.java and change "Package Jama.util;" to "Package Jama;"
7. Edit Matrix.java, EigenvalueDecomposition.java, QRDecomposition.java, and
SingularValueDecomposition.java to remove "import Jama.util.*;"
8. Create a test plugin, such as Test_Jama.java, below.
9. Start ImageJ and "compile and run" the test plugin.
   
Test_Jama.java:

import ij.*;
import ij.plugin.PlugIn;
import Jama.*;

public class Test_Jama implements PlugIn{
    public void run(String arg) {
                double[][] F = new double[3][3];
                for (int j = 0; j < 3; j++)
                        for (int i = 0; i < 3; i++)
                                F[i][j] = i+j;
                Matrix Fm = new Matrix(F);
                SingularValueDecomposition svd = Fm.svd();
                int rank = svd.rank();
                IJ.write("Rank = "+rank);
        }
}


Bob



Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 
 

> On Mac OSX (like my system) that's usually in ~/Library/Java/
> Extensions.  On a Windoze system it's in the lib\ext directory of
> your Java installation.  If you are using the JRE that comes with
> ImageJ, it's in the lib\ext directory of that installation.
>
> I use Jama in ImageJ plugins using the above locations without problem.
>
> Since you ARE on Windoze (from your post), if the above locations
> can't be found, perhaps someone else on the list more familiar with
> your operating system can chime in.
>
> >
> >
> > When using the ImageJ "Compile and run..." command for my plugin, I
> > get the following error:
> >
> > ----------------------------------------------------------------------
> > --
> > Note: sun.tools.javac.Main has been deprecated.
> > C:\Programme\ImageJ\plugins\Template_Matching_.java:25: Package
> > Jama not found in import.
> > import Jama.*;
> >        ^
> > What can I do to use the package "Jama-1.0.2.jar".
> > I copied this jar-File to my imagej-directory and to the plugins-
> > directory.