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Re: batch measurements to single data file

Posted by Wayne Rasband on Nov 19, 2007; 5:55pm
URL: http://imagej.273.s1.nabble.com/batch-measurements-to-single-data-file-tp3697980p3697981.html

Remove 'clear' from

   run("Analyze Particles...", "size=0.15-Infinity circularity=0.00-1.00
show=Nothing display exclude clear");

It is equivalent to checking "Clear Results" in the Analyze Particles
dialog box.

-wayne


On Nov 19, 2007, at 12:27 PM, Justin Walker wrote:

> I have put together a simple macro to (batch) perform various
> manipulations and then measure particle diameters for a series of
> several hundred images of liquid droplets.  Everything works fine,
> except for each image that runs, the results window discards the data
> from the previous image.
>
> I'm sure there is a simple way to change that, but I've been searching
> the documentation and mailing list archives all morning and haven't
> been able to find anything useful.  Is there a simple way to have the
> data from previous measurements preserved when a new image is opened
> and processed?  Alternatively, is there a way I can have the results
> dumped to a data file (but a single data file for all the data with
> each measurement on a new line?).  I tried having a save as command as
> part of my macro, but it kept trying to over-write the data file on
> each iteration.
>
> I have attached my macro.
>
> Thanks;
>
> - Justin Walker, Ph. D. Student
> University of Maryland
> College Park, MD, USA
> [hidden email]
> 301-405-1920
> macro "Batch Particle Size" {
>     dir = getDirectory("Choose a Directory ");
>     list = getFileList(dir);
>     setBatchMode(true);
>     for (i=0; i<list.length; i++) {
>         path = dir+list[i];
>         showProgress(i, list.length);
>         if (!endsWith(path,"/")) open(path);
>         if (nImages>=1) {
>             run("Deinterlace ");
>    run("8-bit");
>    setAutoThreshold();
>    //run("Threshold...");
>    setAutoThreshold();
>    setThreshold(0, 164);
>    run("Convert to Mask");
>    run("Fill Holes");
>    run("Watershed");
>    run("Analyze Particles...", "size=0.15-Infinity
> circularity=0.00-1.00 show=Nothing display exclude clear");
>             close();
>         }
>     }
> }