Previous Message | Next Message Previous in Topic | Next in Topic Previous by Same Author | Next by Same Author Previous Page (May 2002) | Back to Main IMAGEJ Page
	Reply | Post a New Message | Join or Leave IMAGEJ, or Change Options | Search
	Chronologically | Most Recent First | Wrap Text (Proportional Font) | Don't Wrap Text (Non-proportional Font)

Content-Type: TEXT/PLAIN; charset=US-ASCII
Message-ID:  <[log in to unmask]>
Date:         Wed, 22 May 2002 15:36:48 -0700
Reply-To:     ImageJ Interest Group <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Rachel Bearon <[log in to unmask]>
Subject:      Re: batch processing of stacks and saving results
In-Reply-To:  <[log in to unmask]>

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.


On Wed, 22 May 2002, Bob Dougherty wrote:

> 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
>
>

Center for Information Technology National Institutes of Health Bethesda, Maryland 20892 301 594 6248 (v) 301 496 8294 (TDD) Comments and Assistance Accessibility