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documents:100922imagej_cluster [2010/11/16 01:00]
kota
documents:100922imagej_cluster [2016/05/24 05:46] (current)
Line 61: Line 61:
 Using plugin is a bit tricky. In case of desktop ImageJ, what you need to install plugin is simply drug and drop .class or .jar files to plugins folder within imageJ folder. With headless mode, you need to do the following: Using plugin is a bit tricky. In case of desktop ImageJ, what you need to install plugin is simply drug and drop .class or .jar files to plugins folder within imageJ folder. With headless mode, you need to do the following:
   * explicitly state where the plugins folder resides by setting -ijpath. ​   * explicitly state where the plugins folder resides by setting -ijpath. ​
-  * all plugins must not be in jar. They all have to be class files.  +  * <del>all plugins must not be in jar. They all have to be class files.</​del> ​ 
-    * if you only have jar file, then you should open it by zip archiver and extract all class files. File hierarchy should be maintained within the plugin folder.  +    * <del>if you only have jar file, then you should open it by zip archiver and extract all class files. File hierarchy should be maintained within the plugin folder.</​del> ​ 
-... so the java command would look like this:+... so the java command would look like this: Macro file "​headlesstest2.ijm"​ is supposed to be at $HOME and images to be processed are under ~/test, and headlesstest2.ijm takes this path as an argument.  
 <​code>​ <​code>​
-/​usr/​struct/​bin/​java -cp /home/miura/test/​headless.jar:/​home/miura/test/​ij-1.44h.jar -Djava.awt.headless=true ij.ImageJ -ijpath /home/miura/test -batch headlesstest2.ijm /​home/​miura/​test+cd ~ 
 + 
 +/​usr/​struct/​bin/​java -cp /g/almf/software/ij/​headless.jar:/​g/almf/software/ij/​ij-1.44h.jar -Djava.awt.headless=true ij.ImageJ -ijpath /g/almf/software/​ij ​-batch headlesstest2.ijm /​home/​miura/​test
 </​code>​ </​code>​
-and the plugins folder resides within /home/miura/test.+and the plugins folder resides within /g/almf/software/​ij/​ in the above case. If you need to add a plugin, please ask Kota 
 ===== Spreading Jobs with qsub ===== ===== Spreading Jobs with qsub =====
  
documents/100922imagej_cluster.txt · Last modified: 2016/05/24 05:46 (external edit)