Re: Roi Manager headless mode

Posted by Rasband, Wayne (NIH/NIMH) [E] on Feb 24, 2015; 3:04pm
URL: http://imagej.273.s1.nabble.com/Roi-Manager-headless-mode-tp5011750p5011751.html

On Feb 24, 2015, at 9:28 AM, Greg <[hidden email]> wrote:
>
> Hi,
>
> also if I think "headlessmode" is a troublesome issue for the brave
> developers/supporters here,
> I also got the impression people are trying to fix this intermingled GUI
> java.awt issues inherited from imageJ 1.x .

Consider using an Overlay instead of the RoiManager. An Overlay is like an RoiManager without a GUI. Here is a JavaScript example that creates an Overlay and lists all of its ROIs:

  img = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif");
  IJ.setAutoThreshold(img, "Default");
  IJ.run(img, "Analyze Particles...", "  show=[Overlay Outlines] exclude");
  overlay = img.getOverlay();
  for (i=0; i<overlay.size(); i++)
     IJ.log(i+" "+overlay.get(i));

-wayne

> So I read this post
>
> http://imagej.1557.x6.nabble.com/Headless-execution-of-RoiManager-true-gives-exception-td5008274.html 
>
> where it states that the ROI Manager is not available in headless mode.
> I want to ask how the situation concerning(!) the ROI manager is nowadays ?
> It is a really useful tool, and I would like to use it for some cluster
> headlessmode image analysis.
>
> I thought about implementing some of its functionality on my own, but I
> think this can get tedious ?!
>
> Greets,
> Greg
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Roi-Manager-headless-mode-tp5011750.html
> Sent from the ImageJ mailing list archive at Nabble.com.

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