<html>
<head>
<base href="http://fiji.sc/bugzilla/" />
</head>
<body><table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - ND2 file error"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1187">1187</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>ND2 file error
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>Macintosh
</td>
</tr>
<tr>
<th>OS</th>
<td>Mac OS
</td>
</tr>
<tr>
<th>Status</th>
<td>NEW
</td>
</tr>
<tr>
<th>Severity</th>
<td>normal
</td>
</tr>
<tr>
<th>Priority</th>
<td>P4
</td>
</tr>
<tr>
<th>Component</th>
<td>Plugins
</td>
</tr>
<tr>
<th>Assignee</th>
<td>imagej-bugs@imagej.net
</td>
</tr>
<tr>
<th>Reporter</th>
<td>behr87@hotmail.com
</td>
</tr>
<tr>
<th>CC</th>
<td>behr87@hotmail.com
</td>
</tr></table>
<p>
<div>
<pre>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: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20151026195651)
Fiji: <a href="http://update.fiji.sc/">http://update.fiji.sc/</a> (last check:20151111150059)
Bio-Formats: <a href="http://sites.imagej.net/Bio-Formats/">http://sites.imagej.net/Bio-Formats/</a> (last check:20151107022641)
OMERO 5.1: <a href="http://sites.imagej.net/OMERO-5.1/">http://sites.imagej.net/OMERO-5.1/</a> (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</pre>
</div>
</p>
<hr>
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