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Message-ID:  <[log in to unmask]>
Date:         Sat, 23 Aug 2003 06:07:26 -0400
Reply-To:     ImageJ Interest Group <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Ralf Weger <[log in to unmask]>
Subject:      running macros from command line

Hi everybody,

I am pretty new to ImageJ and cant figure out how to use it from command
line.

I tried ImageJ from within Matlab. But I run into memory issues with large
images
(most of the images I process are ~4000x4000 picel RGB).
It would be better to independently use ImageJ from command line.

All I would need is to open an Image, do basic processing steps such as
math/threshold,
run a Particle analyzer, and write the results to an asci file.

I tried running Macros from command line using the example posted on
ImageJ News at http://rsbweb.nih.gov/ij/notes.html
it said that it can be done using

java -cp C:\ImageJ\ij.jar ij.ImageJ c:\ImageJ\plugins\macro.txt

but, I get

Exception in thread "main" java.lang.NullPointerException
        at java.io.File.<init>(Unknown Source)
        at ij.Menus.getPlugins(Menus.java:401)
        at ij.Menus.installPlugins(Menus.java:321)
        at ij.Menus.addMenuBar(Menus.java:183)
        at ij.ImageJ.<init>(ImageJ.java:62)
        at ij.ImageJ.main(ImageJ.java:373)

as an answer to the macro
run("MRI Scan (48K)");
run("Threshold");
run("Analyze Particles...", "minimum=1 maximum=999999 bins=20 show=Nothing
display clear");

the macro runs fine if executed from ImageJ by mouse, but fails if called
from command line

I also tried the analyze plugin programming example posted on ImageJ plugin
website.
It runs fine from within ImageJ, but command

java -Dplugins.dir=C:\ImageJ -cp C:\ImageJ\ij.jar;. analyze test.tif >
results.txt

produces

Exception in thread "main" java.lang.NullPointerException
        at java.io.File.<init>(Unknown Source)
        at ij.Menus.getPlugins(Menus.java:401)
        at ij.Menus.installPlugins(Menus.java:321)
        at ij.Menus.addMenuBar(Menus.java:183)
        at ij.IJ.init(IJ.java:285)
        at ij.IJ.run(IJ.java:264)
        at analyze.process(analyze.java:28)
        at analyze.main(analyze.java:52)

pls help

Ralf Weger
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
RSMAS / MGG
(305) 361-4811 office
University of Miami
(305) 361-4794 lab
4600 Rickenbacker Causeway
(305) 361-4732 fax
Miami, FL 33149 USA
[log in to unmask]
http://mgg.rsmas.miami.edu/students/ralf
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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