[ImageJ-bugs] [Bug 863] New: Very slow opening images and Memory leak

Tue Jul 22 01:29:49 CDT 2014

http://fiji.sc/bugzilla/show_bug.cgi?id=863

            Bug ID: 863
           Summary: Very slow opening images and Memory leak
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: jgburchfield.au at gmail.com
                CC: jgburchfield.au at gmail.com

Relative to imageJ and older Fiji incarnations, opening images has become very
very slow.
Secondly, there appears to be something strange occuring with memory
usage/allocation.
When  fiji is opened it appears to be using ~450MB memory (Windows task
manager).
Open a 280MB image and memory usage jumps to 1.4GB.  Shut it down and memory
usage remains at 1.4GB open another ~200MB image and usage jumps again to 2.2GB
Fiji itself thinks it is using 1269MB
This behaviour appears to continue with each image opened and closed.
The memory usage FIJI reports also continues to increase.  After opening and
closing 4 images it reports 2.2GB of memory used.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_20
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_20-b02
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 16.3-b01
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\PROGRA~4\Fiji.app/java/win64/jdk1.6.0_20//jre
  imagej.dir => C:\PROGRA~4\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140712080647)
Fiji: http://pacific.mpi-cbg.de/update/ (last check:20140715100940)

Files not up-to-date:
  ff27659f (LOCAL_ONLY) 20110719184843 jars/Fiji.jar
  efd0b4a7 (OBSOLETE_UNINSTALLED) 20100614001000 jars/clibwrapper_jiio.jar
  d760adf7 (OBSOLETE_UNINSTALLED) 20101214182806 jars/commons-math.jar
  9654e601 (MODIFIED) 20140722104931 jars/imagej-updater-0.5.0.jar
  85af6645 (OBSOLETE_UNINSTALLED) 20110119134549 jars/imglib-algorithms.jar
  2727a642 (OBSOLETE_UNINSTALLED) 20110119134548 jars/imglib-ij.jar
  3913aead (OBSOLETE_UNINSTALLED) 20110119134549 jars/imglib-io.jar
  4053be28 (OBSOLETE_UNINSTALLED) 20110119134551 jars/imglib-scripting.jar
  785fd9ee (OBSOLETE_UNINSTALLED) 20110119134537 jars/imglib.jar
  b9040757 (OBSOLETE_UNINSTALLED) 20110119134352 jars/jruby.jar
  8e9a4bd8 (OBSOLETE_UNINSTALLED) 20110119134353 jars/junit-4.5.jar
  62509daf (OBSOLETE_UNINSTALLED) 20100614001000 jars/weka.jar
  290be785 (LOCAL_ONLY) 20101217124405 macros/Unwarp_redchannel image.txt
  ec9f9e6e 20100614001000 macros/grey-squares.ijm
  bc1d6c6e 20100614001000 macros/spirals.txt
  c4583991 (LOCAL_ONLY) 20140408102236 macros/testscript_temp_deleteME.ijm
  f7efa1b3 (LOCAL_ONLY) 20110314142721 misc/headless.jar
  8f675b7b (LOCAL_ONLY) 20140722105836 plugins/Align_RGB_planes.class
  5b9f64df (LOCAL_ONLY) 20140214104952 plugins/Convert_LIF_to_TIFF.class
  1a992dbc (OBSOLETE_UNINSTALLED) 20100614001000 plugins/Daltonize_.jar
  3e7c14cf (LOCAL_ONLY) 20140605204040
plugins/Filters/Anisotropic_Diffusion_2D.class
  a8c14ae3 (LOCAL_ONLY) 20140409165641 plugins/HDF5_.jar
  9cdfe434 20101214182818 plugins/Jython_Scripts.jar
  306c9af0 20101214182807 plugins/Macro_Examples.jar
  3589dfdf (LOCAL_ONLY) 20100408181022 plugins/MultiStackReg1_45.jar
  c32c3597 (LOCAL_ONLY) 20080521101406 plugins/MultiStackReg_.jar
  970c7851 (LOCAL_ONLY) 20130815113254
plugins/ROI/BG_Subtraction_from_ROI.class
  6f058434 (LOCAL_ONLY) 20140212100504 plugins/Radial
Profiling/Radial_Profile_Angle_Ext.jar
  0ab9e3b0 (OBSOLETE_UNINSTALLED) 20100614001000 plugins/Record_Screen.jar
  424444d4 (LOCAL_ONLY) 20140428122029 plugins/Region_Growing_Segmentation.jar
  b8e50a7b (OBSOLETE_UNINSTALLED) 20110215125328 plugins/Script_Editor.jar
  4c3e4aee (NOT_INSTALLED) 20110119134407 plugins/Stack_Manipulation.jar
  2f7c1fb1 (LOCAL_ONLY) 20140310193004 plugins/Stack_Sorter.class
  e0122cde (LOCAL_ONLY) 20040909131042 plugins/Stacks - Reducing/Binner_.class
  ab872ecd (LOCAL_ONLY) 20040601145326 plugins/Stacks -
Reducing/Delete_slices_after_here.class
  5e51feb8 (LOCAL_ONLY) 20040601145318 plugins/Stacks -
Reducing/Delete_slices_before_here.class
  794c108d (LOCAL_ONLY) 20010207115620 plugins/Stacks -
Reducing/Slice_Remover.class
  ff504eff (LOCAL_ONLY) 20060627090428 plugins/Stacks -
Reducing/Stack_Splitter.class
  25874f3e (LOCAL_ONLY) 20030627131048 plugins/Stacks -
Reducing/Substack_Maker.class
  b7a74d8a (LOCAL_ONLY) 20080526103622 plugins/Stacks -
Reducing/Substack_Select.jar
  08564324 (LOCAL_ONLY) 20090921122950 plugins/Stacks -
T-functions/Grouped_Stack_Projector.class
  3ae569df (LOCAL_ONLY) 20050202153014 plugins/Stacks -
T-functions/Intensity_v_Time_Monitor.class
  03bba501 (LOCAL_ONLY) 20050202153404 plugins/Stacks -
T-functions/Running_Stack_Projector.class
  1c657c8d (LOCAL_ONLY) 20140305190818 plugins/TIRF_Analysis.class
  5796a251 (LOCAL_ONLY) 20140303144901 plugins/X_Shifter.class
  8c0467d1 (LOCAL_ONLY) 20140120115836 plugins/adaptiveThreshold_win64.jar
  460fd731 (LOCAL_ONLY) 20140303144910 plugins/correctXshift_.jar
  30e408c8 (OBSOLETE_UNINSTALLED) 20110215125326 plugins/loci_tools.jar
  d3260180 (LOCAL_ONLY) 20100614001000 scripts/Record_Desktop.py
  0ea7f8fc (LOCAL_ONLY) 20100614001000 scripts/Record_Window.py

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