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Bug 1187 - ND2 file error
ND2 file error
Status: RESOLVED MOVED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-11-11 13:51 CST by Behzad
Modified: 2015-11-11 15:00 CST
2 users (show)

See Also:
Description Behzad 2015-11-11 13:51:21 CST 
When trying to open ND2 file through drag and drop and have the options hyperstack, display metadata and open all series checked, I get the following error.

(Fiji Is Just) ImageJ 2.0.0-rc-41/1.50d; Java 1.7.0_45 [64-bit]; Mac OS X 10.9.5; 64MB of 3179MB (2%)
 
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.rangeCheck(ArrayList.java:635)
	at java.util.ArrayList.get(ArrayList.java:411)
	at loci.formats.FormatReader.getSizeC(FormatReader.java:719)
	at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1342)
	at loci.formats.FormatReader.setId(FormatReader.java:1426)
	at loci.formats.DelegateReader.setId(DelegateReader.java:290)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
	at loci.plugins.in.Importer.showDialogs(Importer.java:140)
	at loci.plugins.in.Importer.run(Importer.java:76)
	at loci.plugins.LociImporter.run(LociImporter.java:78)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.IJ.runPlugIn(IJ.java:165)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:503)
	at ij.io.Opener.openImage(Opener.java:369)
	at ij.io.Opener.openImage(Opener.java:243)
	at ij.io.Opener.open(Opener.java:110)
	at ij.io.Opener.openAndAddToRecent(Opener.java:292)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:181)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:744)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.5
  java.version => 1.7.0_45
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.7.0_45-b18
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 24.45-b08
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.7
  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: /Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home//jre
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20151026195651)
Fiji: http://update.fiji.sc/ (last check:20151111150059)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20151107022641)
OMERO 5.1: http://sites.imagej.net/OMERO-5.1/ (last check:20151008173318)

Files not up-to-date:
  dcea879b (LOCAL_ONLY) 20050509104822 plugins/Deconvolution/Diffraction_PSF_3D.class
  2eb14160 (LOCAL_ONLY) 20050509104814 plugins/Deconvolution/Iterative_Deconvolve_3D.class
  307b18a4 (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/ParallelSpectralDeconvolution_2D.txt
  d7212d28 (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/ParallelSpectralDeconvolution_3D.txt
  0f36d33a (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/blas.jar
  6c215965 (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/f2jutil.jar
  aa4768eb (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/lapack.jar
  ce8d21de (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/optimization.LICENSE.txt
  f5348be4 (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/parallel_spectral_deconvolution-1.7.jar
  21693cce (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/parallel_spectral_deconvolution.LICENSE.txt
  0b42dba4 (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/parallelcolt-0.5.jar
  ba9e4c71 (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/parallelcolt.LICENSE.txt
  a26f0a2d (LOCAL_ONLY) 20080826162008 plugins/Deconvolution/xerbla.jar
  ec17890b (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/JHotDraw.jar
  91ece67d (LOCAL_ONLY) 20131203182004 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/JWlz.jar
  36cb5c0a (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/TableLayout.jar
  7c4005e7 (LOCAL_ONLY) 20050801102630 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/axis-wsdl4j.jar
  364315a9 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/axis.jar
  3370a633 (LOCAL_ONLY) 20070427143948 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/axis2-saaj.jar
  0af1624e (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/backport-util-concurrent.jar
  43dc5c59 (LOCAL_ONLY) 20150729114720 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/blitz-javadoc.jar
  f2b8b783 (LOCAL_ONLY) 20150729114640 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/blitz-sources.jar
  82891217 (LOCAL_ONLY) 20150729114730 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/blitz.jar
  189f61fa (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/bufr.jar
  f2f356c2 (LOCAL_ONLY) 20150729114218 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/common-javadoc.jar
  3646964f (LOCAL_ONLY) 20150729114214 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/common-sources.jar
  46ae381d (LOCAL_ONLY) 20150729114218 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/common.jar
  940245e0 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/commons-codec.jar
  64d8a654 (LOCAL_ONLY) 20060622214518 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/commons-collections.jar
  86ab9004 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/commons-digester.jar
  9e9eb622 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/commons-discovery.jar
  d59d3e4c (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/commons-io.jar
  f6139801 (LOCAL_ONLY) 20100225002342 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/commons-lang.jar
  fa9b8239 (LOCAL_ONLY) 20130516210522 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/commons-logging.jar
  60a83b54 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/commons-validator.jar
  abf211c5 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/ehcache-core.jar
  e33cecc2 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/grib.jar
  2cd0d04c (LOCAL_ONLY) 20140422214746 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/guava.jar
  85c28658 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/hibernate-jpa-2.0-api.jar
  0c6e277e (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/httpclient.jar
  9f61e37d (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/httpcore.jar
  d216e98a (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/httpmime.jar
  1911c9e1 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/ice-glacier2.jar
  b1d709fb (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/ice-grid.jar
  c49b8fa2 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/ice-storm.jar
  53aa5393 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/ice.jar
  84b54b46 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/ij.jar
  6ce638fb (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/ini4j.jar
  f1b65457 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/java-getopt.jar
  c827227f (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/java-image-scaling.jar
  e72f9b2b (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/jaxrpc.jar
  07f15e96 (LOCAL_ONLY) 20140724163642 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/jcommon.jar
  c4eeeb8f (LOCAL_ONLY) 20140731133446 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/jfreechart.jar
  5defc8da (LOCAL_ONLY) 20150209145000 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/jhdf5.jar
  df7a0b63 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/jna.jar
  4c09d41c (LOCAL_ONLY) 20130308132342 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/joda-time.jar
  4a754817 (LOCAL_ONLY) 20140504140434 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/kryo.jar
  fb9a1e44 (LOCAL_ONLY) 20150717175952 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/lwf-stubs.jar
  ab8ff4ee (LOCAL_ONLY) 20120719212102 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/metadata-extractor.jar
  16b765c2 (LOCAL_ONLY) 20120531132650 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/minlog.jar
  e345904c (LOCAL_ONLY) 20150729114210 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/model-psql-javadoc.jar
  01a47b35 (LOCAL_ONLY) 20150729114158 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/model-psql-sources.jar
  26031f35 (LOCAL_ONLY) 20150729114210 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/model-psql.jar
  66de339f (LOCAL_ONLY) 20140821153824 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/native-lib-loader.jar
  a51a31db (LOCAL_ONLY) 20140612124526 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/netcdf.jar
  aff28c0e (LOCAL_ONLY) 20131010222536 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/objenesis.jar
  18382f06 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/ome-java.jar
  7af6ddeb (LOCAL_ONLY) 20100312195702 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/perf4j.jar
  b3056152 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/platform.jar
  4ef2cfd3 (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/poi.jar
  eedc0cd9 (LOCAL_ONLY) 20080930090254 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/serializer.jar
  5085d943 (LOCAL_ONLY) 20140205213714 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/slf4j-api.jar
  dfe60310 (LOCAL_ONLY) 20150717175920 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/specification.jar
  ba32bfdf (LOCAL_ONLY) 20150721211426 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/swingx.jar
  36cdef55 (LOCAL_ONLY) 20080930090254 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/xalan.jar
  93f166fd (LOCAL_ONLY) 20061007130232 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/xercesImpl.jar
  a5c15945 (LOCAL_ONLY) 20120703111340 plugins/OMERO.insight-ij-5.1.3-ice35-b52/libs/xmpcore.jar
  26a14fee (LOCAL_ONLY) 20150729115200 plugins/OMERO.insight-ij-5.1.3-ice35-b52/omero_ij.jar
  0e8ddb6d (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/arpack-combo.jar
  1a08e201 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/csparsej.jar
  924b8d62 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/jplasma.jar
  fca468e8 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/jtransforms.jar
  dd8c3801 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/licenses/parallelcolt.LICENSE.txt
  de89ab4e (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/licenses/paralleliterativedeconvolution.LICENSE.txt
  60508fb7 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/macros/ParallelIterativeDeconvolution2D.txt
  20e21511 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/macros/ParallelIterativeDeconvolution3D.txt
  89cb5823 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/netlib-java.jar
  25802519 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/optimization.jar
  33f69ff8 (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/parallel_iterative_deconvolution-1.12.jar
  87fc836e (LOCAL_ONLY) 20130919191546 plugins/ParallelIterativeDeconvolution/parallelcolt-0.9.4.jar
Comment 1 Curtis Rueden 2015-11-11 15:00:22 CST 
Please report this bug to the OME Bio-Formats team, using the procedure described here:

http://openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html

Or on GitHub at:

https://github.com/openmicroscopy/bioformats/issues/new