[ImageJ-bugs] [Bug 895] New: Importing of Image Sequences VERY slow

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=895

            Bug ID: 895
           Summary: Importing of Image Sequences VERY slow
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: s.j.carr at qmul.ac.uk
                CC: s.j.carr at qmul.ac.uk

I'm not sure this is a bug, but it is certainly something that has really
compromised my work recently!

Having recently updated FIJI/ImageJ, I have noticed that the process of
importing image sequences has become really, really slow. Previously, it would
take around 15 seconds to import a 2GB image sequence of 1024 tiff files, but
now, it takes many minutes.

I notice that when ImageJ is importing the stack, there is an additional
reporting in the menu bar that the software is initializinfg the volume from
which the sequence is being imported for each tiff file, which was certainly
not evident in the previous versions of FIJI/ImageJ. I note that importing a
RAW version of the same volume is as quick as usual. I have uninstalled and
re-installed a fresh build of FIJI, but the problem is still there, and I have
experienced the same problem on two different iMacs.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140810132118)
Fiji: http://fiji.sc/update/ (last check:20140808190226)

Files not up-to-date:
  71f2da38 (LOCAL_ONLY) 20140812062714 plugins/BoneJ_.jar
  a1e32b23 (LOCAL_ONLY) 20140812062841
plugins/Compute_Curvatures$FloatArray.class
  3ccf02f5 (LOCAL_ONLY) 20140812062853
plugins/Compute_Curvatures$FloatArray2D.class
  81183bf9 (LOCAL_ONLY) 20140812062901
plugins/Compute_Curvatures$FloatArray3D.class
  f8c3160f (LOCAL_ONLY) 20140812062832 plugins/Compute_Curvatures.class
  d546883b (LOCAL_ONLY) 20140812062814 plugins/jars/Jama-1.0.1.jar
  0dfa5070 (LOCAL_ONLY) 20140812062741 plugins/jars/imagescience.jar
  199fcd64 (LOCAL_ONLY) 20140812062802 plugins/jars/mcib3d-core.jar
  3b5f97ef (LOCAL_ONLY) 20140812062749 plugins/mcib3d_plugins.jar

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