[ImageJ-bugs] [Bug 913] New: Fiji cannot open .jp2 (nikon microscope files)

bugzilla at fiji.sc bugzilla at fiji.sc
Tue Aug 26 03:43:12 CDT 2014 

http://fiji.sc/bugzilla/show_bug.cgi?id=913

            Bug ID: 913
           Summary: Fiji cannot open .jp2 (nikon microscope files)
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: tobias.buschmann at hhu.de
                CC: tobias.buschmann at hhu.de

Fiji cannot open .jp2 (nikon microscope files)
Not via drag and drop and not via open command.
Tried with SCIFIO and without, both gave me this bug report:



(Fiji Is Just) ImageJ 2.0.0-rc-8/1.49c; Java 1.6.0_65 [64-bit]; Mac OS X
10.9.4; 26MB of 2611MB (1%)

java.lang.StringIndexOutOfBoundsException: String index out of range: -9011
    at
java.lang.AbstractStringBuilder.substring(AbstractStringBuilder.java:881)
    at java.lang.StringBuffer.substring(StringBuffer.java:416)
    at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1385)
    at loci.formats.FormatReader.setId(FormatReader.java:1315)
    at loci.formats.DelegateReader.setId(DelegateReader.java:253)
    at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
    at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
    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:202)
    at ij.IJ.runPlugIn(IJ.java:166)
    at ij.IJ.runPlugIn(IJ.java:155)
    at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
    at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
    at ij.IJ.runUserPlugIn(IJ.java:202)
    at ij.IJ.runPlugIn(IJ.java:166)
    at ij.IJ.runPlugIn(IJ.java:155)
    at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:460)
    at ij.io.Opener.openImage(Opener.java:315)
    at ij.io.Opener.openImage(Opener.java:338)
    at ij.io.Opener.open(Opener.java:145)
    at ij.io.Opener.openAndAddToRecent(Opener.java:248)
    at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
    at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
    at java.lang.Thread.run(Thread.java:695)

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: CHECK_TURNED_OFF

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:20140709212330)
Fiji: http://fiji.sc/update/ (last check:20140709223742)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140710145338)
IBMP: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526164644)
Jan's cool update site:
http://www-public.rz.uni-duesseldorf.de/~eglinger/plugins/ (last
check:20140424102012)

Files not up-to-date:
  7ecaf631 (OBSOLETE_UNINSTALLED) 20140604114338 jars/jruby-complete-1.7.11.jar
  24d47d70 (OBSOLETE_UNINSTALLED) 20130521235059 jars/junit-4.8.1.jar
  3ace1851 (LOCAL_ONLY) 20140331145334 plugins/Dot_Blot.txt
  0fb65ed4 (OBSOLETE_UNINSTALLED) 20140604114415
plugins/Filters/Adaptive_Filter.class
  7f2acd01 (OBSOLETE_UNINSTALLED) 20140604114416
plugins/Filters/Enhance_True_Color_Contrast.class
  448b2287 (OBSOLETE_UNINSTALLED) 20140604114415
plugins/Filters/Gaussian_Weighted_Median.class
  2c9ade75 (OBSOLETE_UNINSTALLED) 20140604114415
plugins/Filters/Limited_Mean.class
  1656d24d (OBSOLETE_UNINSTALLED) 20140604114415
plugins/Filters/Pseudo_flat_field_correction.class
  4c13cc04 (LOCAL_ONLY) 20121012113314
plugins/Liver_Analaysis/Analyze_pH3_Liver.ijm
  5026ebc3 (LOCAL_ONLY) 20120426114912
plugins/Liver_Analaysis/Area_AFP_Lyve1.ijm
  e5217bc7 (LOCAL_ONLY) 20120827140920
plugins/Liver_Analaysis/LiverLumenQuant.js
  8ddf00ed (LOCAL_ONLY) 20121012112539 plugins/Liver_Analaysis/Liver_pH3.js
  6d112716 (LOCAL_ONLY) 20120306141215
plugins/Liver_Analaysis/MacroGamma0.5JANImprovedAktuell.ijm
  1fe4769a (LOCAL_ONLY) 20121012095037
plugins/Liver_Analaysis/MacroGamma0.5JANImprovedmitZProject121012.ijm
  8f8b1049 (LOCAL_ONLY) 20120813154556
plugins/Liver_Analaysis/MeasureMaxPerParticle.js
  7ba658b6 (LOCAL_ONLY) 20120427114357
plugins/Liver_Analaysis/Quant_Beta1_in_EC.ijm
  065b6ff5 (LOCAL_ONLY) 20120813155153
plugins/Liver_Analaysis/Second_MaxPerParticle.js
  ca06e85f (LOCAL_ONLY) 20120503142710 plugins/Liver_Analaysis/Tiff.ijm
  3a3a000d (LOCAL_ONLY) 20120621093421 plugins/Liver_Analaysis/image.ijm
  9b53ff8e (LOCAL_ONLY) 20140331144658 plugins/MicroArray_Profile.jar
  d84cc2bb (LOCAL_ONLY) 20100922214634 plugins/Morphology/Add_Borders.class
  5cccefae (LOCAL_ONLY) 20100913095428 plugins/Morphology/AnnularClosing.txt
  763870ef (LOCAL_ONLY) 20100913095434 plugins/Morphology/AnnularDilation.txt
  5d777e5e (LOCAL_ONLY) 20100928170030
plugins/Morphology/BinaryConditionalDilate_.class
  6cfae168 (LOCAL_ONLY) 20060525192652
plugins/Morphology/BinaryConditionalErode_.class
  877be8e6 (LOCAL_ONLY) 20060525192958
plugins/Morphology/BinaryConnectivity_.class
  ebe4d9b0 (LOCAL_ONLY) 20111110085448
plugins/Morphology/BinaryDilateNoMerge4_.class
  65b35fcd (LOCAL_ONLY) 20111109155612
plugins/Morphology/BinaryDilateNoMerge8_.class
  da5dc033 (LOCAL_ONLY) 20081019152450 plugins/Morphology/BinaryDilateTest.txt
  fe9208a2 (LOCAL_ONLY) 20060525193012 plugins/Morphology/BinaryDilate_.class
  9f2b4ef9 (LOCAL_ONLY) 20081019152918 plugins/Morphology/BinaryErodeTest.txt
  b38e2aa0 (LOCAL_ONLY) 20060525193102 plugins/Morphology/BinaryErode_.class
  3f39caaf (LOCAL_ONLY) 20060525101716
plugins/Morphology/BinaryFilterReconstruct.txt
  76eb6799 (LOCAL_ONLY) 20090525193222
plugins/Morphology/BinaryFilterReconstruct_.class
  6a2c8b7a (LOCAL_ONLY) 20111109154430
plugins/Morphology/BinaryGeodesicDilateNoMerge8_.class
  14c67860 (LOCAL_ONLY) 20080602091844
plugins/Morphology/BinaryHitOrMiss_.class
  33b507c2 (LOCAL_ONLY) 20100418152848
plugins/Morphology/BinaryKillBorders_.class
  4204c1c6 (LOCAL_ONLY) 20101206082940 plugins/Morphology/BinaryLabel8_.class
  d3c84f8c (LOCAL_ONLY) 20070712112240 plugins/Morphology/BinaryLabelMacro.txt
  59e1afe9 (LOCAL_ONLY) 20100508085308 plugins/Morphology/BinaryLabel_.class
  36e4a042 (LOCAL_ONLY) 20060525101718 plugins/Morphology/BinaryPrune.txt
  c8c66f92 (LOCAL_ONLY) 20090526165400
plugins/Morphology/BinaryReconstruct_.class
  3ff298c7 (LOCAL_ONLY) 20060525193502 plugins/Morphology/BinaryThick2_.class
  b73f68f4 (LOCAL_ONLY) 20060525193450 plugins/Morphology/BinaryThick_.class
  2c4c813e (LOCAL_ONLY) 20060525193520 plugins/Morphology/BinaryThin2_.class
  d8a5d664 (LOCAL_ONLY) 20060525193512 plugins/Morphology/BinaryThin_.class
  3e83cc61 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Boundary4.txt
  9d64440e (LOCAL_ONLY) 20060525101718 plugins/Morphology/Boundary8_.txt
  e9fc745d (LOCAL_ONLY) 20090602153322
plugins/Morphology/Catalogue_Particles.txt
  4d0095a2 (LOCAL_ONLY) 20070607090848
plugins/Morphology/Classify_Particles.class
  f53a898e (LOCAL_ONLY) 20090511083446
plugins/Morphology/CloseByReconstructionTopHat.txt
  2c7f38f5 (LOCAL_ONLY) 20101005103840
plugins/Morphology/CloseByReconstruction_.txt
  1c33105a (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull1.txt
  7cb69fdf (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull2.txt
  b19cb415 (LOCAL_ONLY) 20060525101718 plugins/Morphology/ConvexHull3.txt
  bd22187f (LOCAL_ONLY) 20060525101718 plugins/Morphology/Corners.txt
  55c709bf (LOCAL_ONLY) 20061116092256
plugins/Morphology/Correlate_Results.class
  d463ee86 (LOCAL_ONLY) 20081019163010 plugins/Morphology/Delete_ZeroArea.txt
  8df2eb76 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Diagonal8to4.txt
  61193e21 (LOCAL_ONLY) 20100929125932 plugins/Morphology/Domes_.class
  e428a0f5 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Domes_stack.txt
  1be944ae (LOCAL_ONLY) 20090506082436 plugins/Morphology/DoubleWaterfall.txt
  925d3d8c (LOCAL_ONLY) 20111208091210 plugins/Morphology/DrawBoundingBox.txt
  63c4cd27 (LOCAL_ONLY) 20111208091158
plugins/Morphology/DrawBoundingCircle.txt
  b97f945a (LOCAL_ONLY) 20111208091142 plugins/Morphology/DrawConvexHulls.txt
  2adcfe94 (LOCAL_ONLY) 20111208091226 plugins/Morphology/DrawFeret&Breadth.txt
  b60f4365 (LOCAL_ONLY) 20111208091236 plugins/Morphology/DrawMinR&MaxR.txt
  288ace7a (LOCAL_ONLY) 20100805124116 plugins/Morphology/EDM_16bits.txt
  71d10273 (LOCAL_ONLY) 20081019170232 plugins/Morphology/Euler.txt
  63757672 (LOCAL_ONLY) 20090511083446 plugins/Morphology/Extended_Maxima.txt
  285e4c16 (LOCAL_ONLY) 20090511083446 plugins/Morphology/Extended_Minima.txt
  2b80b381 (LOCAL_ONLY) 20100418175426
plugins/Morphology/FillHolesReconstruct.txt
  205b6052 (LOCAL_ONLY) 20060525130102 plugins/Morphology/Fill_Border_Holes.txt
  54d7ef21 (LOCAL_ONLY) 20090506082436
plugins/Morphology/Fill_Greyscale_Holes.txt
  75041650 (LOCAL_ONLY) 20101001143722
plugins/Morphology/GreyBlackTopHatByReconstruction_.txt
  6f716dcc (LOCAL_ONLY) 20101001143322
plugins/Morphology/GreyWhiteTopHatByReconstruction_.txt
  579b5383 (LOCAL_ONLY) 20090504142458
plugins/Morphology/GreyscaleCentreFilter.txt
  c4267b67 (LOCAL_ONLY) 20060525193602
plugins/Morphology/GreyscaleDilate_.class
  965f297a (LOCAL_ONLY) 20060525193612 plugins/Morphology/GreyscaleErode_.class
  0a50379d (LOCAL_ONLY) 20100920132950
plugins/Morphology/GreyscaleKillBorders.txt
  d3047959 (LOCAL_ONLY) 20090503182436
plugins/Morphology/GreyscaleProperAutomedian.txt
  b4d94111 (LOCAL_ONLY) 20090504122820
plugins/Morphology/GreyscaleProperClose.txt
  44d81a95 (LOCAL_ONLY) 20090504123000
plugins/Morphology/GreyscaleProperOpen.txt
  9aadbae0 (LOCAL_ONLY) 20090526165732
plugins/Morphology/GreyscaleReconstruct_.class
  4d7e6035 (LOCAL_ONLY) 20100908144402 plugins/Morphology/GreyscaleTopHat.txt
  cb2dc22a (LOCAL_ONLY) 20100908144826 plugins/Morphology/GreyscaleWell.txt
  282495a6 (LOCAL_ONLY) 20060525101718 plugins/Morphology/H-break.txt
  a73d2279 (LOCAL_ONLY) 20090511130552 plugins/Morphology/HMaxima_Transform.txt
  f1c1b630 (LOCAL_ONLY) 20090527092132 plugins/Morphology/HMinima_Transform.txt
  af3183b2 (LOCAL_ONLY) 20080605122624 plugins/Morphology/Hole_Counter.txt
  930ee9e1 (LOCAL_ONLY) 20090527171616 plugins/Morphology/HomotopicMarking.txt
  3429c4f3 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Hysteresis.txt
  2511df4c (LOCAL_ONLY) 20090513103656 plugins/Morphology/Impose_Minimum.txt
  6be72748 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Influence_Zones.txt
  5859277c (LOCAL_ONLY) 20060525101718
plugins/Morphology/KeepLargestParticle.txt
  559e475f (LOCAL_ONLY) 20080521222500
plugins/Morphology/KeepLargestParticlePixels_.txt
  4605ad0a (LOCAL_ONLY) 20080605144602
plugins/Morphology/KeepParticlesInRange.txt
  b46b2695 (LOCAL_ONLY) 20110415151004 plugins/Morphology/Lines8_.class
  43259a0b (LOCAL_ONLY) 20090519121520 plugins/Morphology/LocalMaxima.txt
  c0207001 (LOCAL_ONLY) 20090519122406 plugins/Morphology/LocalMinMax.txt
  b2139bd8 (LOCAL_ONLY) 20090519121444 plugins/Morphology/LocalMinima.txt
  05f0502d (LOCAL_ONLY) 20060525101718 plugins/Morphology/MCentroids.txt
  b3ea5e05 (LOCAL_ONLY) 20101007145910 plugins/Morphology/MinimaDynamic.txt
  57e4bbaa (LOCAL_ONLY) 20060525101718
plugins/Morphology/Morphological2Derivative1.txt
  35b51e7e (LOCAL_ONLY) 20060525101718
plugins/Morphology/Morphological2Derivative2.txt
  ef809632 (LOCAL_ONLY) 20060525101718
plugins/Morphology/Morphological2Derivative3.txt
  73902be6 (LOCAL_ONLY) 20100908144214
plugins/Morphology/MorphologicalContrastTopHat.txt
  86d43a13 (LOCAL_ONLY) 20100906132436
plugins/Morphology/MorphologicalExternalGradient.txt
  66d657f2 (LOCAL_ONLY) 20100908173708
plugins/Morphology/MorphologicalGradient3.txt
  2cd67873 (LOCAL_ONLY) 20100906132436
plugins/Morphology/MorphologicalGradientBeucher.txt
  b141cc35 (LOCAL_ONLY) 20100906132436
plugins/Morphology/MorphologicalInternalGradient.txt
  babf8d91 (LOCAL_ONLY) 20060525101718
plugins/Morphology/MorphologicalSharpGradient.txt
  7e05ec43 (LOCAL_ONLY) 20060525101718
plugins/Morphology/MorphologicalSmoothing1.txt
  df30c851 (LOCAL_ONLY) 20060525101718
plugins/Morphology/MorphologicalSmoothing2.txt
  b4232d82 (LOCAL_ONLY) 20100913095526
plugins/Morphology/Morphological_Clustering.txt
  c4024220 (LOCAL_ONLY) 20100922234422 plugins/Morphology/Morphological_PCA.txt
  44b58573 (LOCAL_ONLY) 20101005101848
plugins/Morphology/Morphological_SelfDualCentre.txt
  d20caeeb (LOCAL_ONLY) 20101005163722
plugins/Morphology/Morphological_contrast.txt
  c40dcb5d (LOCAL_ONLY) 20100908144252
plugins/Morphology/MultiscaleGradient.txt
  7fa60ae6 (LOCAL_ONLY) 20110425171914 plugins/Morphology/NumberParticles8_.txt
  cd6cf4de (LOCAL_ONLY) 20090511083446
plugins/Morphology/OpenByReconstructionTopHat.txt
  5f844fa9 (LOCAL_ONLY) 20101005103856
plugins/Morphology/OpenByReconstruction_.txt
  8fdf1b15 (LOCAL_ONLY) 20080521221818 plugins/Morphology/Parameter_Matrix.txt
  65c22a1e (LOCAL_ONLY) 20080529224340 plugins/Morphology/ParticleHoleArea.txt
  9a713d79 (LOCAL_ONLY) 20080529224456
plugins/Morphology/ParticleHoleNumber.txt
  9c0a7763 (LOCAL_ONLY) 20080529224152 plugins/Morphology/Particle_Data_Map.txt
  85b99ff0 (LOCAL_ONLY) 20100914150816 plugins/Morphology/Particles4_.class
  583118b2 (LOCAL_ONLY) 20100914150808 plugins/Morphology/Particles8_.class
  ac25812c (LOCAL_ONLY) 20080521215826
plugins/Morphology/Plot_BivariateGraphs.txt
  e8ea53cb (LOCAL_ONLY) 20080606114752 plugins/Morphology/Plot_Histograms.txt
  ce077644 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Prune1.txt
  c4126534 (LOCAL_ONLY) 20060525101718 plugins/Morphology/PruneAll.txt
  916ac5a4 (LOCAL_ONLY) 20090511083446 plugins/Morphology/RegionalMinMax.txt
  3dcf6fa2 (LOCAL_ONLY) 20090511083446 plugins/Morphology/Regional_Maxima.txt
  bc61499e (LOCAL_ONLY) 20101001113926 plugins/Morphology/Regional_Minima.txt
  358d5270 (LOCAL_ONLY) 20100922235812
plugins/Morphology/SelfComplementaryTopHat.txt
  36e7e0b4 (LOCAL_ONLY) 20101005094120
plugins/Morphology/SelfDualReconstruction_.txt
  64886ac9 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Skeleton1.txt
  64fa451e (LOCAL_ONLY) 20060525101718 plugins/Morphology/Skeleton2.txt
  809a6770 (LOCAL_ONLY) 20060525101718 plugins/Morphology/Skeleton3.txt
  16447730 (LOCAL_ONLY) 20090511121302 plugins/Morphology/Skeleton4.txt
  b2242712 (LOCAL_ONLY) 20100922212400 plugins/Morphology/SkeletonFiltering.txt
  5d0400a0 (LOCAL_ONLY) 20080521215352 plugins/Morphology/Summarize_Results.txt
  ab0b29c3 (LOCAL_ONLY) 20080603111018
plugins/Morphology/Thin_Results_Table.txt
  090f96c1 (LOCAL_ONLY) 20100621090218 plugins/Morphology/UnbiasedCounting.txt
  fecf6a46 (LOCAL_ONLY) 20080605121016
plugins/Morphology/UnbiasedParticleArea.txt
  19a9433c (LOCAL_ONLY) 20090330080642
plugins/Morphology/Viscous_Geodesic_Reconstruction.txt
  6d88799a (OBSOLETE_UNINSTALLED) 20140604114410
plugins/Script_Editor-2.0.0-SNAPSHOT.jar
  5e73d56b (MODIFIED) 20130912114206 plugins/TrackMate_-2.1.0.jar

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