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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 14:23:57 -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

Sorry, worng file.  I meant to attach this one.

Rachel Bearon wrote:

> I would like to process all files in a directory and record the results. I
> wrote the following plugin to process one file at a time, but I would like
> to be able to automatically loop through all files in the directory. In
> the archives I found reference to a method for opening and processing all
> files in a directory, but it didn't seem to allow one to automatically
> save the results to a specified file.
>
> import ij.*;
> import ij.process.*;
> import ij.gui.*;
> import java.awt.*;
> import ij.plugin.*;
>
> public class Macro_ implements PlugIn {
>
>         public void run(String arg) {
>                 IJ.run("Set Measurements...", "area centroid decimal=3");
>                 IJ.run("Open...", "path=/home/rachelb/R14002R.tif");
>                 IJ.run("Processbugs ");
>                 IJ.run("Custom Particle Analyzer", "minimum=4 maximum=20 bins=20 show=Nothing display clear stack");
>                 IJ.run("Measurements...", "path=/home/rachelb/R14002R.txt");
>         }
>
> }
>
> (Processbugs is just a little plugin I wrote which does some image
> calculations and thresholding.)
>
> Thanks in advance for any help!
>
> Rachel

--
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 ij.plugin.*;

public class Macro_ implements PlugIn {

        public void run(String arg) {
                        String outputFolder = "/home/rachelb/";
                IJ.run("Set Measurements...", "area centroid decimal=3");
                IJ.run("Image Sequence...");
                processBugStack();
         }
        public void processBugStack(){
                ImagePlus imp = WindowManager.getCurrentImage();
                ImageStack stack = imp.getStack();
                int numSlices = imp.getStackSize();
                for (int i = 1; i <= numSlices; i++){
                        imp.setSlice(i);
                        String file = stack.getSliceLabel(i);
                        int dot = file.lastIndexOf('.');
                        String outFile = file + ".txt";
                        if (dot > 0){
                                outFile = file.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...", outputFolder+outFile);                }
        }
}

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