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Bug 878 - tif file does not open
tif file does not open
Status: ASSIGNED
Product: ImageJ
Classification: Unclassified
Component: SCIFIO
unspecified
PC Linux
: P4 normal
Assigned To: Mark Hiner
Depends on:
Blocks:
 
Reported: 2014-08-05 03:45 CDT by Benoit Aigouy
Modified: 2015-04-06 15:49 CDT
3 users (show)

See Also:
Description Benoit Aigouy 2014-08-05 03:45:34 CDT 
Dear IJ/Scifio (LOCI?) developpers,

I fail to open the image I called 4D_sample.tif (Image originating from a zeiss mdb confocal series and saved as tif using the current version of FIJI). The image opens just fine using the life line version of FIJI but does not on the current version of FIJI. FIJI seems to enter an infinite loop of some kind and I have to kill the process to quit it. The only message I get before the crash is:
10:41:11.238 [DrawAndDrop] DEBUG loci.common.NIOByteBufferProvider - Using mapped byte buffer? false. Hope this helps.

best,

benoit

ps: File>import>bio-formats opens the image just fine but the LUT is incorrect

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.13.0-32-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/benoit/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/benoit/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140802175300)
Fiji: http://fiji.sc/update/ (last check:20140730210634)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526164644)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140711200224)

Files not up-to-date:
  a5d02cb7 (LOCAL_ONLY) 20131005162326 plugins/Kymo_graph1001.jar
  740a32b3 (LOCAL_ONLY) 20140109112924 plugins/SplittedChannelsMerger_.class
  d31ed141 (LOCAL_ONLY) 20131016094131 plugins/Stack_Focuser_.class
  188c85ca (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/GraphThemes/BasicTheme.txt
  01085dcb (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/GraphThemes/theme3007994286031749119.txt
  67db385e (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/JournalStyles/Cell.txt
  cc7237c4 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/JournalStyles/Development.txt
  5584a6b9 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/JournalStyles/NATUREMETHODS.txt
  ba9a3bdc (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/JournalStyles/Nature.txt
  9f264c8c (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/JournalStyles/PLOSONE.txt
  5be60f41 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/JournalStyles/PowerPoint2010.txt
  4434b72a 20140804181524 plugins/Tissue_Analyzer/ScientiFigPrefs.txt
  967b726a (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/TA_additions/TA_plugins/Cortex.jar
  17d3b815 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/TA_additions/TA_plugins/FlowPlugin.jar
  e87dbc68 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/TA_additions/TA_plugins/OptimizedZProjectionPlugin.jar
  5a330876 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/TA_additions/TA_plugins/QiyanPlugin.jar
  035ccfcf (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/TA_additions/TA_plugins/TA_prefs/-5016441619325897676.txt
  50bc25c3 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/TA_additions/TA_plugins/additionalCloneTools.jar
  be4da579 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/TA_additions/TA_plugins/cloneRoughness.jar
  cae64ab2 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/Tissue_Analyzer.jar
  a3f77cd0 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/changes.txt
  7bf59685 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/compilationDate.txt
  0bf38115 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/lib/Icons.jar
  4164a351 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/lib/IconsPA.jar
  c3cdf2d0 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/lib/REngine.jar
  6ba3fcd5 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/lib/Rserve.jar
  269cc20e (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/lib/Rsession.jar
  694bbee3 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/lib/sqlite-jdbc-3.7.2.jar
  3887dab6 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/license.txt
  397bab67 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/otherLicenses/licenseIcons.txt
  0f96dbd0 (LOCAL_ONLY) 20140805085038 plugins/Tissue_Analyzer/otherLicenses/licenseRsession.txt
  5f60d96e (LOCAL_ONLY) 20140306085844 plugins/Watershed_.jar
Comment 1 Benoit Aigouy 2014-08-05 03:47:01 CDT 
4D_sample.tif was uploaded
Comment 2 Benoit Aigouy 2014-08-14 08:50:04 CDT 
bug is gone when SCIFIO is inactivated.

best,

benoit
Comment 3 Mark Hiner 2014-08-14 08:52:54 CDT 
Hi Benoit,

 I suspect you can work around this issue for now by disabling "Edit > Options > ImageJ2... > Use SCIFIO when opening files."

 Thank you for providing the sample data - that should make it very easy to reproduce! This issue is in my personal "must fix for SCIFIO" queue so I hope to look at it in depth soon.

Thank you for the report,
Mark