User Tools

Site Tools


Sidebar

Top
Seminar
Courses -2016
Courses 2018-
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
Weblog
RSS aggregates
Discussions
Archives


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

... so don't think that you need to submit a full text.
About 3 days, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

The deadline next week for NEUBAIS Gateway article is just for the **PROPOSAL.** you just need to fill and submit… https://t.co/2aTmNDxtvz
About 3 days, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

I really like the article refers to the MoU of NEUBIAS. We made pretty much of efforts in polishing our initial "Ma… https://t.co/E1417kBAAF
About 3 days, 5 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

recommendation to read https://t.co/3BAl3lzcMc
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @florianjug: If you missed the webinar but are interested to have a look, a recording is now available: https://t.co/qVuhexTz3c Thanks a…
About 1 week, 3 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @SuperResoluSian: We've collated all the links from our @NEUBIAS_COST webinar on SMLM analysis into a post!⬇️ From here you can navigate…
About 2 weeks ago by: Kota Miura (@cmci_)
blogtng:2011-03-07:testing_groovy_-_imagej

testing Groovy - ImageJ

There is a new ImageJ plugin that allows you to fo scripting with Groovy.

ij-Groovy
http://ij-plugins.sourceforge.net/plugins/groovy/tutorials.html#RecordingScripts

so I became interested in how it would be like using it. GroovyConsole seems to be an handy Editor, so instead of installing the plugin to ImageJ, I made a trial to use ImageJ as a libray, accessing directly from Groovy. It was pretty simple to do this task, but I note down how I installed mainly because I will forget what I did.

1. Go to the groovy site, and download the zipped binary.
http://groovy.codehaus.org/Download

I downloaded Groovy 1.7.8 and unzipped the folder groovy-1.7.8 under C:\dev.

2. Add path C:\dev\groovy-1.7.8 as a new environmental variable “GROOVY_HOME” .

3. Add path %GROOVY_HOME%\bin to the system path.

4. Launch the console by clicking %GROOVY_HOME%\bin\GroovyConsole.bat

5. set path to ij.jar by [Script > Add Jar to Classpath]

Following is the code I tested, which worked fine without opening ImageJ main menu.

import ij.*

imp = IJ.openImage("http://rsb.info.nih.gov/ij/images/gel.gif");
IJ.log(imp.getDimensions()[0].toString());
imp.show();

Running this code, an image window pops sup and also the width of the image is printed in the output field of the console. IJ.log command which normally should print out the string argument in log window seems to be diverted to the console output.
Interpreter runs with a speed comparable to Javascript and Jython running with ImageJ jar.

Good point about this console is that referencing to a jar file could be easily be done, by [scripts > add jar to classpath] This affords a good simple interface for test assembling several Java libraries.

Comments



69 -4 =
blogtng/2011-03-07/testing_groovy_-_imagej.txt · Last modified: 2016/05/24 05:46 (external edit)