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Bug 714 - after update ".czi" files do not open anymore
after update ".czi" files do not open anymore
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-03-08 16:02 CST by Arvydas Dapkunas
Modified: 2014-03-09 08:10 CDT
2 users (show)

See Also:
Description Arvydas Dapkunas 2014-03-08 16:02:40 CST 
I have update fiji today (8th March 2014) and after that the .czi file does not open anymore.
here's output from log file (Here I have edited the path by substituting real with "Path"):

There was a problem with the class org.joda.time.Instant which can be found here:
/C: "Path" /FIJI-W~1/Fiji.app/jars/jruby-1.6.7.2.jar
/C: "Path" /FIJI-W~1/Fiji.app/jars/joda-time-2.2.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: org.joda.time.Instant.parse(Ljava/lang/String;Lorg/joda/time/format/DateTimeFormatter;)Lorg/joda/time/Instant;
	at ome.xml.model.primitives.Timestamp.<init>(Timestamp.java:82)
	at ome.xml.model.primitives.Timestamp.valueOf(Timestamp.java:107)
	at loci.formats.in.ZeissCZIReader$SubBlock.parseMetadata(ZeissCZIReader.java:2583)
	at loci.formats.in.ZeissCZIReader$SubBlock.fillInData(ZeissCZIReader.java:2480)
	at loci.formats.in.ZeissCZIReader.readSegment(ZeissCZIReader.java:2189)
	at loci.formats.in.ZeissCZIReader.readSegments(ZeissCZIReader.java:822)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:437)
	at loci.formats.FormatReader.setId(FormatReader.java:1319)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:479)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:454)
	at ij.io.Opener.openImage(Opener.java:311)
	at ij.io.Opener.openImage(Opener.java:334)
	at ij.io.Opener.open(Opener.java:144)
	at ij.io.Opener.open(Opener.java:71)
	at ij.plugin.Commands.run(Commands.java:27)
	at ij.IJ.runPlugIn(IJ.java:169)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  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.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:\HY-Data\DAPKUNAS\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => C:\HY-Data\DAPKUNAS\FIJI-W~1\Fiji.app

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  95dc5b19 20131228172257 plugins/Simple_Neurite_Tracer-2.0.2-SNAPSHOT.jar
  0bd5f179 20131012120910 plugins/Siox_Segmentation-1.0.1-SNAPSHOT.jar
  52fecf09 20131012120910 plugins/Skeletonize3D_-1.0.1-SNAPSHOT.jar
  b0820703 20131012120910 plugins/Snakuscule_-2.0.0-SNAPSHOT.jar
  33b6af85 20131228172256 plugins/SplineDeformationGenerator_-2.0.0-SNAPSHOT.jar
  27de591e 20131012120910 plugins/StackReg_-2.0.0-SNAPSHOT.jar
  736bb192 20131012120910 plugins/Stack_Manipulation-2.0.0-SNAPSHOT.jar
  59f36299 20131012120910 plugins/Statistical_Region_Merging-2.0.0-SNAPSHOT.jar
  08a4daec 20140308133947 plugins/Stitching_-2.0.0-SNAPSHOT.jar
  30100de7 20131012120910 plugins/Sync_Win-1.7-fiji2-SNAPSHOT.jar
  685ca9dc 20131012120910 plugins/Thread_Killer-2.0.0-SNAPSHOT.jar
  2cee6c37 20131012120910 plugins/Threshold_Colour-2.0.1-SNAPSHOT.jar
  d822b123 20131012120910 plugins/Time_Stamper-2.0.0-SNAPSHOT.jar
  584cb5b9 20131012120910 plugins/ToAST_-25.0.1-SNAPSHOT.jar
  4cf59217 20131012120910 plugins/TopoJ_-2.0.0-SNAPSHOT.jar
  a2b2409b 20140206192307 plugins/TrackMate_-2.1.1-SNAPSHOT.jar
  279a86b1 20140212204655 plugins/Trainable_Segmentation-2.0.0-SNAPSHOT.jar
  59124982 20131012120910 plugins/TrakEM2_-1.0b-SNAPSHOT.jar
  8e7f3b79 20131012120910 plugins/TransformJ_-2.8.1-SNAPSHOT.jar
  c4e87a76 20131012120910 plugins/TurboReg_-2.0.0-SNAPSHOT.jar
  9558400d 20131012120910 plugins/UnwarpJ_.jar
  a32dfe46 20131012120911 plugins/Utilities/Close_All_Without_Saving.txt
  253c6df4 20131012120910 plugins/VIB_-2.0.0-SNAPSHOT.jar
  baa78901 20131012120910 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar
  81279d21 20131012120910 plugins/Video_Editing-2.0.0-SNAPSHOT.jar
  73396eef 20131012120910 plugins/View5D_-1.3.1-SNAPSHOT.jar
  980c0ed9 20131012120910 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar
  b9742297 20131012120910 plugins/Volume_Viewer-2.01.1-SNAPSHOT.jar
  2079ca32 20131012120910 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar
  5d479ffe 20140308134011 plugins/bio-formats_plugins-5.0.0.jar
  0307564a 20131012120910 plugins/blockmatching_-2.0.0-SNAPSHOT.jar
  659ad6a3 20131012120910 plugins/ij-ImageIO_.jar
  82f900ac 20131012120910 plugins/level_sets-1.0.1-SNAPSHOT.jar
  df2af815 20131012120910 plugins/mpicbg_-0.6.1-SNAPSHOT.jar
  5e32d936 20131012120910 plugins/panorama_.jar
  96b34801 20131012120910 plugins/readme.txt
  4bd07822 20140308133947 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar
  16012d5a 20131012120910 plugins/registration_3d-2.0.0-SNAPSHOT.jar
  34b7341d 20131012120919 retro/backport-util-concurrent-3.1.jar
  8759ba20 20131012120919 retro/retrotranslator-runtime-1.2.9.jar
  a6d5a3b2 20131012120919 retro/retrotranslator-transformer-1.2.9.jar
  d7160d38 20131012120917 scripts/InstallJava3D.m
  05a92a3c 20131012120917 scripts/IsJava3DInstalled.m
  ff34d026 20131012120917 scripts/Matlab3DViewerDemo_1.m
  25be149f 20131012120917 scripts/Matlab3DViewerDemo_2.m
  cb529b6c 20131012120917 scripts/Matlab3DViewerDemo_3.m
  53d2da73 20131012120917 scripts/Matlab3DViewerIntroduction.m
  4bb342fa 20131012120917 scripts/Miji.m
  868cd434 20131012120917 scripts/Miji_Test.m
  dc94c3a3 20131012120917 scripts/bfopen.m
  a77cab39 20131012120917 scripts/importTrackMateTracks.m
Comment 1 Curtis Rueden 2014-03-09 05:10:22 CDT 
I uploaded a fix. Please update your Fiji and try again!
Comment 2 Arvydas Dapkunas 2014-03-09 08:10:08 CDT 
Thank you so much! works like charm!