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Delivered-To: [log in to unmask]@fixme
References: <[log in to unmask]>
Content-Type: multipart/mixed;
Message-ID:  <[log in to unmask]>
Date:         Wed, 22 May 2002 22:32:49 -0700
Reply-To:     [log in to unmask]
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Bob Dougherty <[log in to unmask]>
Organization: OptiNav, Inc.
Subject:      Re: batch processing of stacks and saving results

Rachel,

Yes,  I assumed that the files are just images.  Here is a version that is intended to work for stacks or images.  I
adapted engineered Wayne's FolderOpener.java.

There are probably ways to do this with scripts, but they would be OS dependent.

Bob

Rachel Bearon wrote:

> Thanks for your help Bob! However the plugin you attatched acts in some
> rather strange ways. Reading through it, I realised that perhaps I didn't
> make myself clear. The plugin I have written opens up a file (which is a
> movie so itself is a stack), analyzes the stack, and writes the results of
> the whole stack to a specfied file. What I am hoping to do is analyze a
> collection of such files using some kind of for loop in the plugin. The
> specific problem I came across was how to specify the filename path
> outside the IJ.run command. Eg. you can write
>  IJ.run("Measurements...", "path=/home/rachelb/R14002R.txt");
>
> but I couldn't work out how to do something like
>
> path= "/home/rachelb/R14002R.txt"
> IJ.run("Measurements...", path);
>
> which would be a necessary step in the loop.
>

--
Robert Dougherty
President, OptiNav, Inc.
(425) 467-1118
[log in to unmask]
http://www.optinav.com


import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import java.io.*;
import ij.plugin.*;
import ij.io.*;

public class Macro_ implements PlugIn {

        public void run(String arg) {
                IJ.run("Set Measurements...", "area centroid decimal=3");
                OpenDialog od = new OpenDialog("Choose a file in the directory... ", arg);
                String directory = od.getDirectory();
                String name = od.getFileName();
                if (name==null)
                        return;

                String[] list = new File(directory).list();
                if (list==null)
                        return;
                //IJ.register(Macro_.class);
                //ij.util.StringSorter.sort(list);
                try {
                        for (int i=0; i<list.length; i++) {
                                if (list[i].endsWith(".txt"))
                                        continue;
                                ImagePlus imp = new Opener().openImage(directory, list[i]);
                                if (imp==null)
                                        IJ.write(list[i] + ": unable to open");
                                else {
                                        imp.show();
                                        ImageWindow iw = imp.getWindow();
                                        IJ.showStatus((i+1)+"/"+list.length);
                                        IJ.showProgress((double)(i+1)/list.length);
                                int dot = list[i].lastIndexOf('.');
                                String outFile = list[i] + ".txt";
                                if (dot > 0){
                                        outFile = list[i].substring(0,dot) + ".txt";
                                }

                        IJ.run("Processbugs ");
                                        IJ.run("Custom Particle Analyzer", "minimum=4 maximum=20 bins=20 show=Nothing display clear stack");
                        IJ.run("Measurements...", directory+outFile);
                        //System.out.println(directory+outFile);

                        iw.close();
                                }
                                //System.gc();
                        }
                } catch(OutOfMemoryError e) {
                        IJ.outOfMemory("Macro_");
                }
        }
}

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