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Message-ID:  <[log in to unmask]>
Date:         Fri, 24 May 2002 15:24:57 -0400
Reply-To:     ImageJ Interest Group <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Wayne Rasband <[log in to unmask]>
Subject:      Re: ImageJ: Is there a clean way to write a command line tool
              that uses ImageJ
In-Reply-To:  <[log in to unmask]>

> Hi. I'm using ImageJ both on the Windows side and on a Linux box. On the
> Linux box,
> I'm trying create a set of command-line tools that I can call and use
> for
> batch processing of images from
> shell scripts (on 3D Analyze format images using Guy William's
> Plugins). The
> following
> class example appears to do the job:
>
> import ij.*;
> import ij.measure.*;
> import java.io.*;
>
> public class CommandLineMaskImage{
>     public static void main(String argv[]){
>        if (argv.length!=3){
>             System.out.println("MaskImage usage:"+
>              "MaskImage [mask image] [input image] [outputimage]");
>             return;
>        }
>        else{
>             ImageJ mainFrame=null;
>             if (IJ.getInstance()==null){
>                 mainFrame= new ImageJ();
>             }
>
>             IJ.run("Analyze Reader", "path='"+argv[0]+".hdr'");
>             IJ.run("Rename...", "title=mask");
>             IJ.run("Analyze Reader", "path='"+argv[1]+".hdr'");
>             IJ.run("Rename...", "title=image");
>             ImagePlus imp=WindowManager.getCurrentImage();
>             Calibration c = imp.getCalibration();
>             IJ.run("Image Calculator...", "image1=mask operation=AND
> image2=mask create");
>
>             IJ.selectWindow("Result");
>             ImagePlus rimp =WindowManager.getCurrentImage();
>             rimp.setCalibration(c);
>
>             IJ.run("Analyze Writer", "path='"+argv[2]+".hdr'");
>
>             mainFrame.quit();
>        }
>    }
> }
>
> It can be executed from the command line with something like:
>
> java CommandLineMaskImage /home/cjtaylor/javaf/maskimage
> /home/cjtaylor/javaf/actualimage  /home/cjtaylor/javaf/outputImage
>
> Two Questions:
>
> 1) When I run this, I need to have the plugins folder directly
> underneath
> the folder containing CommandLineMaskImage.class. Is there someway to
> set
> this folder  by calling an ImageJ instance or through an IJ static
> method
> when not running the standard ImageJ GUI?

You can specify the path to the plugins directory by setting the
"plugins.dir" property. This can be done from the command line using the
-D option, for example:

     java -Dplugins.dir=path-to-plugins-dir -cp ij.jar:.
ClassThatUsesImageJ

You can also set this property from within a program:

        Properties p = System.getProperties();
        p.setProperty("plugins.dir", "path-to-plugins-dir");
       System.setProperties(p);

Set the "plugins-dir" property to "user.home" and ImageJ will look for
the plugins directory in the users home directory.

> 2) Since each of the IJ.run() commands are supposed to run on separate
> threads, I would have throught that this code might not work properly
> due to
> synchronization issues, but it appears to be working. Is this simply a
> machine timing fluke and, in truth, I'm playing with fire or is there
> something that guarantees that each command waits for the previous
> command
> to complete?

The IJ.run() commands do not run on a separate thread.

-wayne

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