Problems While Using Command Line

Posted by Alphonso Magri on Mar 20, 2008; 3:48pm
URL: http://imagej.273.s1.nabble.com/Loosing-Particles-when-Rotating-Image-tp3696797p3696799.html

I am attempting to run a custom made plugin on many different image  
sets and tried making  a macro to do this. I found that after the  
second image set ImageJ crashes. The image sets are very large so this  
crash usually occurs after 1.5 days of running. I then looked for an  
automated way to open ImageJ, run the plugin twice, then close imageJ  
and repeat the process. I found that I can use a terminal on my Mac  
and call ImageJ and a macro. I do so by typing something like...

"cd /Applications/ImageJ_1_37; java -jar ij.jar -batch Trial_run_1".

I found that this can work for macros that do not call custom made  
plugins, and when I try to call my plugin from the macro which I call  
from the command line I get an error like...

"Unrecognized command: Fitting algo", where Fitting algo is the name  
of my custom plugin.

Why is it incapable of recognizing the plugin?

The plugin is already complied and has a class file. To add to my  
confusion when I double click on the ij.jar file I get ImageJ with a  
plugins tab pull down menu full of plugins, however when I call ImageJ  
from the command line I find that the pull down menu for the plugins  
tab empty of plugins.

Is there a way to call ImageJ from the Command line and being able to  
recognize custom plugins? Does anyone have another suggestion to solve  
my problem?

Alphonso