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Bug 895 - Importing of Image Sequences VERY slow
Importing of Image Sequences VERY slow
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-12 00:40 CDT by Simon Carr
Modified: 2015-04-06 14:27 CDT
3 users (show)

See Also:
Description Simon Carr 2014-08-12 00:40:42 CDT 
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
Comment 1 Mark Hiner 2014-08-18 14:26:18 CDT 
Hi Simon,

There are known performance issues when SCIFIO is used to open datasets right now.. could you see if "Edit > Options > ImageJ2 > Use SCIFIO when opening files" is checked and, if so, disable it?

That should work around the problem until we resolve these performance problems.

Thanks for the report!