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Bug 976 - Some large actions result in ImageJ (Fiji) freeze, sometimes
Some large actions result in ImageJ (Fiji) freeze, sometimes
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-12-16 09:50 CST by Vassilis Kehayas
Modified: 2014-12-19 22:08 CST
3 users (show)

See Also:
Description Vassilis Kehayas 2014-12-16 09:50:22 CST 
For example, when I try to get the histogram of a 512x128x3427 stack (428MB), by using the shortcut Cntrl + H,
the application freezes.
I am not limited by processing power or memory (~20GB are allocated to Fiji).
This issue started happening today. Only one plugin was updated, I think (SPIM Registration, that I don't use).
However, it's not happening every time and I am unable to locate the reason.
Let me know if I can provide any other relevant information.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.13.0-43-generic
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/vassilis/Apps/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/vassilis/Apps/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141211185341)
Fiji: http://fiji.sc/update/ (last check:20141216104440)

Files not up-to-date:
  e8d11864 (LOCAL_ONLY) 20141104141133 macros/CalciumAnalysis_VK.ijm
  e4cb5a42 (LOCAL_ONLY) 20141203135405 macros/StartupMacros.txt
  bddf2b19 (LOCAL_ONLY) 20141203142626 plugins/CalciumAnalysis_VK.ijm
  b0398adb (LOCAL_ONLY) 20140212174320 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  adeb04d4 (LOCAL_ONLY) 20130627155627 plugins/Stack_Aligner.jar
Comment 1 Vassilis Kehayas 2014-12-16 09:53:48 CST 
OK, maybe it has nothing to do with what image it is.
I am using Gnome Ubuntu 14.04 and I now noticed that the whole application is freezing when I try to maximize an image window by dragging it on the edge of the scree, so it might be an Ubuntu bug.
Comment 2 Curtis Rueden 2014-12-16 11:35:49 CST 
Debugging crashes is not the easiest thing, but here is a guide:
   http://imagej.net/Debugging#Debugging_hard_JVM_crashes

Or if the application hangs without crashing, see:
    http://imagej.net/Debugging#Debugging_JVM_hangs
Comment 3 Vassilis Kehayas 2014-12-19 04:22:27 CST 
OK, it's silly but this is what happens: Whenever there is a pop-up dialog window from Fiji, it is displayed in another workspace, that's why I was missing it and thought Fiji was freezing.
My setup if the following: I have two screens connected and setup workspaces to be active on only one of those screens through Gnome Tweak Tool.
This is reproducible: I open a stack image and select to apply Gaussian blur. If the main Fiji panel is on the screen that doesn't have workspaces enabled then the pop-up dialog will go to another workspace that doesn't have focus.
I don't expect this to be supported necessarily but I am putting it out there anyway.
Comment 4 Wayne Rasband 2014-12-19 08:47:35 CST 
What are the values of the "Screen size" and "Max window bounds" properties displayed by the Plugins>Utilities>ImageJ Properties command?
Comment 5 Vassilis Kehayas 2014-12-19 09:13:05 CST 
Screen size: 1920x1080
Max window bounds: x=0,y=0,width=1920,height=1080
Union of bounds: x=0,y=0,width=3840,height=1080
Monitor1: x=0,y=0,width=1920,height=1080
Monitor2: x=1920,y=0,width=1920,height=1080
Comment 6 Wayne Rasband 2014-12-19 22:08:44 CST 
It appears you have two displays, both with a resolution of 1920x1080. ImageJ will show dialogs on the display on the left ("Monitor1") because it has an origin of (0,0). You might be able to work around this problem by swapping the two displays so that the primary display is the one on the left. ImageJ cannot use the display on the right ("Monitor2") because it's origin is not at (0,0), which is normally the case on Linux. There is a lot of code in ImageJ, and in plugins and macros, that assume that the primary display has its origin at (0,0).