Posted by
ctrueden on
Jul 07, 2015; 9:18pm
URL: http://imagej.273.s1.nabble.com/WindowManager-finds-no-windows-tp5013317p5013460.html
Hi Jeff,
> I am not providing the --headless option, so my assumption is that
> even on the cluster, Fiji thinks it has a monitor and is displaying a
> GUI.
Yes, that is important. If you pass --headless then GUI-based classes like
WindowManager behave differently.
> However, the macro essentially opens four images, and then polls
> WindowManager for a list of image titles (I have included the macro at
> the bottom, as well as the xvfb command used to run it). On my
> computer, this reports (as expected) four open windows. However, on
> the cluster, it reports 0 open windows.
That is strange, and sounds more like something that might happen if
--headless is passed.
Unfortunately, I am no expert on xvfb. But it looks like your invocation is
substantially different (simpler, actually) than the way currently
recommended on the wiki:
http://imagej.net/Headless#XvfbHave you tried doing it the way described at that link?
Anyone else here have success with the xvfb-based approach?
Regards,
Curtis
On Fri, Jun 26, 2015 at 10:20 AM, Jeff Farrell <
[hidden email]>
wrote:
> Hi all,
>
> I am having a problem using WindowManager in a BeanShell macro in Fiji.
> Namely, the macro behaves differently when I run it on my Mac, or when I
> run
> it through X11 virtual frame buffer (xvfb) on our university's linux
> cluster. I am not providing the --headless option, so my assumption is that
> even on the cluster, Fiji thinks it has a monitor and is displaying a GUI.
>
> However, the macro essentially opens four images, and then polls
> WindowManager for a list of image titles (I have included the macro at the
> bottom, as well as the xvfb command used to run it). On my computer, this
> reports (as expected) four open windows. However, on the cluster, it
> reports
> 0 open windows. I can give the command saveAs("Tiff", "/path/to/tiff.tif")
> and save one of the images, though, so they must actually be open! But, I
> cannot select windows using commands (e.g. IJ.selectWindow() will report
> they are not open) or get a list of them. It is as if WindowManager does
> not
> know they exist.
>
> I am not sure what is the root — Mac vs. Linux, something weird about
> running in xvfb, etc, but I was wondering if anyone had any additional
> information that might help me with my problem.
>
> Thank you so very much.
> Cheers,
> Jeff
>
> ---------------------------------
> THE BEANSHELL MACRO IN QUESTION:
>
> import ij.IJ;
> import ij.WindowManager;
> import java.lang.Runtime;
> import java.lang.String;
> import java.io;
>
> pathbase="/path/on/my/server";
>
> // Open a few images.
> IJ.open(pathbase+"spim_TL1_Angle1.tif");
> IJ.open(pathbase+"spim_TL1_Angle2.tif");
> IJ.open(pathbase+"spim_TL1_Angle3.tif");
> IJ.open(pathbase+"spim_TL1_Angle4.tif");
> System.out.println("Opened some windows!");
>
> // Get a list of the windows
> allWindows = ij.WindowManager.getImageTitles();
> System.out.println("WindowManager thinks there are " + allWindows.length +
> "
> open windows.");
>
> ------------------------------------------------
>
> THE XVFB CALL TO RUN THE MACRO ON THE CLUSTER
> xvfb-run -a /path/to/fiji-1.49/ImageJ-linux64 -Xms200m -Xmx200m --
> --no-splash WindowTest.bsh
>
>
>
> --
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>
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