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References: <[log in to unmask]>
Message-ID:  <007001c202ac$9692f8c0$05a8a8c0@lazarus>
Date:         Thu, 23 May 2002 15:53:00 -0700
Reply-To:     ImageJ Interest Group <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         cjtaylor <[log in to unmask]>
Organization: nbresearch.com
Subject:      ImageJ: Is there a clean way to write a command line tool that
              uses ImageJ

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?

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?

Thanks for any feedback,

CJ

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