Working with ImageJ plugins on the HPCC

Blog post edited by Anonymous - "Migration of unmigrated content due to installation of a new plugin"

Post written by Dan Perez (iCER Intern)

Errors

One of the iCER users has had problems getting ImageJ - ImageViewer scripts and plugins working on the HPCC. The ImageViewer classes, plugins, and scripts are in a directory called MyMacro. When I execute RunJavaOnly.sh I get:

cd MyMacro
module load Java
./RunJavaOnly.sh

File > Open > 30_1_DE2_C2crop/temp/mask0001.tif (this is an 8-bit image)

Plugins > Analyze > Particle Analyser

Error:
Plugin org.double.bonej.ParticleCounter did not find required class: javax/media/j3d/Shape3D

And when I execute ./runmacro.sh I get:

./runmacro.sh

Error:
Unrecognized command: 3D Fast Filters

Fixes

RunJavaOnly.sh

I've had some success getting this to work by installing the latest version of ImageJ (v1.46r) and adding class paths and a shared object path:

1. Download the latest version of ImageJ. This will create a directory called ImageJ in you home directory.

cd ~
wget http://rsb.info.nih.gov/ij/download/linux/ij146-linux64.tar.gz
tar -zxf ij146-linux64.tar.gz

2. Delete the old version of ImageJ and copy the new version to your MyMacro directory. Assuming that MyMacro is also in your home directory:

rm MyMacro/ij-1.45q.jar
cp ImageJ/ij.jar MyMacro/ij.jar

3. Edit the RunJavaOnly.sh script. Java needs to know where to find the libj3dcore-ogl.so shared object file (it's in the /opt/software/Java3D/lib/amd64 directory). You'll also need to update the script to use the new version of ImageJ you just installed. The script should look like:

Post created by Daniel Perez (ICER Student Intern):

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#!/bin/bash
java -Xmx8000m -Dplugins.dir=./plugins/ -Djava.library.path=/opt/software/Java3D/lib/amd64 -jar ./ij.jar &

4. Edit the MyMacro/ij.jar/META-INF/MANIFEST.MF file. Java needs to know where to find Java3D classes. Add the following line to the end of the file:

Class-Path: /opt/software/Java3D/lib/ext/j3dcore.jar /opt/software/Java3D/lib/ext/j3dutils.jar

If this continues to create problems, you can also try adding /opt/software/Java3D/lib/ext/vecmath.jar to the Class-Path. At this point I think RunJavaOnly.sh works. However, I don't know what this program is supposed to do, so Dirk should test this.

runmacro.sh

Works better using the plugins directory (instead of plugins2):

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#!/bin/bash -login
java -Xmx8000m -Dplugins.dir=./plugins/ -jar ./ij.jar -macro ./SplitLargePiece.txt

Runs for awhile. Don't get the 3D Fast Filters error. Get the following errors instead:

No window with the title "particleID_parts" found.
This command requires a stack.

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Blogpost migrated from ICER Wiki using custom python script. Comment on errors below.