Re: batch process question

Posted by dpoburko on Jun 08, 2009; 4:01pm
URL: http://imagej.273.s1.nabble.com/batch-process-question-tp3692237p3692238.html

Hi Fabrice,
 
  Have you had a look at the BatchProcessFolders.txt or
BatchProcessFolders_onlyTifIn Subfolder.txt  macros in the ImageJ macro
examples? They layout the basic outline of how to set up a macro to step
through the files in a given directory or a set of subdirectories. These
examples should be pretty easy to merge into your current code.

Cheers,
Damon


Senger Fabrice wrote:

> Dear all,
>
> hereafter I send you a peace of code.
> I have an image with nuclei.
> I roughly segment them (this is not a problem)
> Next I convert the generated ROI's to new images and save them into a
> specified directory.
> To keep track of all the images (using the name of the image without
> the "." and the extension), i used this nice code I got from the list
> some time ago.
> But now I would like to batch process whole folders of such images.
> Usually I simply use the macro "BatchProcess" where I insert a
> function, but here due to the fact that I call the name of the image
> this doesn't work.
>
> Has someone suggestions about this ?
>
> Thank you very much,
>
> Fabrice.
>
>
> name = getTitle;
>           dotIndex = indexOf(name, ".");
>           title = substring(name, 0, dotIndex);
>
>
> // Get path to aurelien directory
> aurelien = getDirectory("aurelien");
> if (aurelien=="")
>     exit("No aurelien directory available");
>
> // Create a directory in temp
> myDir = aurelien+title+File.separator;
> File.makeDirectory(myDir);
> if (!File.exists(myDir))
>     exit("Unable to create directory");
>
> setBatchMode(true);
>
> // Segmentation process
>
> run("Duplicate...", "title=one.tif");
> run("Gaussian Blur...", "sigma=2");
> run("Make Binary");
> run("Watershed");
> run("Analyze Particles...", "size=8000-Infinity circularity=0.00-1.00
> show=Nothing exclude clear add");
> close();
>
> // Convert ROI's to new images and save to corresponding folder
>
> myID = getImageID();
> n = roiManager("count");
> for (i=0; i<n; i++) {
>    selectImage(myID);
>    roiManager("select", i);
>    run("Copy");
> newImage(title+"_"+i+1, "8-bit Black", 400, 400, 1);
> run("Paste");
> saveAs("tiff", myDir+getTitle);
> close();
> run("Select None");
>
> }
>

--

Damon Poburko, PhD
Postdoctoral Research Fellow
Stanford University School of Medicine
Dept. of Molecular & Cellular Physiology
279 Campus Dr., Beckman B103, Stanford, CA 94305
Ph: 650 725 7564, fax: [phone]