[ImageJ-bugs] [Bug 1114] New: severe performance and memory issues

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1114

            Bug ID: 1114
           Summary: severe performance and memory issues
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: andreas.w.ettinger at gmail.com
                CC: andreas.w.ettinger at gmail.com

Hi, I experience severe performance issues after a recent update. Fiji slows to
a crawl and eventually freezes, even with no data-heavy analysis. 

Specifically, I experienced this when doing the following analysis:
- I am loading microscopy data of typically 80-200 MB stacks, one image stack
at a time. 
- I draw ROIs and run a macro to measure fluorescence intensity values in all
ROIs to save to a text file.
- I close the image and open the next one for the same analysis. 
- After a few images, Fiji slows significantly.
- Memory used by Fiji (assessed via Mac OS activity monitor) increases quickly
with use and was as high as 2.7 GB, even with no image open (Memory allocated
to Fiji at the time was 3.5 GB). 
- When adding ROIs, the ROIs appears in the manager with delay or only when I
click on the manager.
- When I close Fiji and restart, performance is ok at the beginning, but after
a few images it slows down again, concomittant with the described increase in
memory use. I wonder if this is caused by an issue with Java heap. 

Additionaly, though not sure if this is a bug:
- Brightness and contrast windows and the channels tool move together with the
menu panel. Not a problem, but somewhat annoying.

In general, the current version seems to run slower and image adjustments take
more time. 

Thank you for looking into these issues.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.10.4
  java.version => 1.8.0_31
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_31-b13
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.31-b07
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to:
/Library/Java/JavaVirtualMachines/jdk1.8.0_31.jdk/Contents/Home//jre
  imagej.dir => /Users/ucsf/Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150715140840)
Fiji: http://fiji.sc/update/ (last check:20150714092641)

Files not up-to-date:
  ccc2be91 (MODIFIED) 20150716185745 Contents/Info.plist
  ca5a7064 (LOCAL_ONLY) 20150530191602
plugins/Mosaic_ToolSuite/Mosaic_ToolSuite.jar
  e1e481c6 (LOCAL_ONLY) 20150711194120 plugins/multiFitBend2_.py
  62fc0557 (LOCAL_ONLY) 20150712172717 plugins/multiFitBend3_.py
  df703eb4 (LOCAL_ONLY) 20150712172940 plugins/multiFitBend4.txt
  19200071 (LOCAL_ONLY) 20150712210517 plugins/multiFitBend4_.py
  c5a40692 (LOCAL_ONLY) 20150713172914 plugins/multiFitBend5_.py
  9e42853a (LOCAL_ONLY) 20150709183919 plugins/multiFitBend_.py

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