<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 2.0cm 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="DE-CH" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US">Dear list,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am using bioformats in the openBIS Importer Toolset (http://www.scs2.net/next/index.php?id=150) to extract metadata information from microscopy files and I am facing an issue that puzzles me. Consider the following
code snippet (I only leave what is important):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><code><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ...<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> // Create the reader<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> reader = new ImageProcessorReader(<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> new ChannelSeparator(<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> LociPrefs.makeImageReader()));<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ...<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> try {<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> factory = new ServiceFactory();<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> service = factory.getInstance(OMEXMLService.class);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> } catch (DependencyException e) {<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ...<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> }<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> try {<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> omexmlMeta = service.createOMEXMLMetadata();<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> } catch (ServiceException e) {<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ...<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> }<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> reader.setMetadataStore(omexmlMeta);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> // Try to open the image file<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> try {<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> reader.setId(filename.getCanonicalPath());<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> } catch (FormatException e) {<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ...<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> }<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"></code><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Now, if I add loci_tools.jar (5.0.4) to the build path, everything works without any problem; if I add bioformats_package.jar (5.0.4, both downloaded from http://downloads.openmicroscopy.org/bio-formats/5.0.4/) I get
the following when<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> reader.setId(filename.getCanonicalPath());<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">is reached:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><log><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.ImageReader - ND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.768 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - ND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.768 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - loci.formats.in.ND2Reader.initFile(D:\user\pontia\Experiment_2\Captured for 4.nd2)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.768 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - NativeND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.768 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - loci.formats.in.NativeND2Reader.initFile(D:\user\pontia\Experiment_2\Captured for 4.nd2)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Searching for blocks<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ND2 FILE SIG' 0%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.774 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageCalibra' 0%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.782 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">java.lang.NegativeArraySizeException: null<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.795 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">java.lang.NegativeArraySizeException: null<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">...<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:53.990 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">java.lang.NegativeArraySizeException: null<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.005 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageMetadat' 0%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.008 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageDataSeq' 2%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.008 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageTextInf' 94%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 95%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|P' 96%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|P' 97%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|X' 97%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Y' 97%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 97%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.012 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.012 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageAttribu' 99%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ND2 FILEMAP ' 99%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.015 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - Could not parse XML<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">java.io.IOException: null<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.common.xml.XMLTools.parseXML(XMLTools.java:436) ~[bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.common.xml.XMLTools.parseXML(XMLTools.java:414) ~[bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.common.xml.XMLTools.parseXML(XMLTools.java:393) ~[bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.parseText(NativeND2Reader.java:2054) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:726) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at javax.xml.parsers.SAXParser.parse(Unknown Source) ~[na:1.7.0_51]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> at loci.common.xml.XMLTools.parseXML(XMLTools.java:428) ~[bioformats_package.jar:na]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ... 21 common frames omitted<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.029 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatTools - Expected positive value for PhysicalSizeZ; got 0.0<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.029 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatTools - Expected positive value for EmissionWavelength; got 0<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">14:22:54.037 [SwingWorker-pool-2-thread-5] DEBUG loci.common.Location - Location.mapFile: embedded-stream.raw -> null<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"></log><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">There is absolutely no issue (logged at least) when loci_tools.jar is used. Interestingly, the metadata seems to be read even when bioformats_package.jar is used, despite all exceptions. The problem is that openBIS monitors
the execution of dropboxes and if it catches exceptions it stops the registration of data. This is the case when bioformats_package.jar is used, and is not when loci_tools.jar is used.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I attached the full log and the ND2 file from the example (other ND2 files behave the same; LSM files, for instance, don't). Can anyone give me a hint what might be happening here? Nothing seems to be missing from the
bioformats_package.jar that would be in loci_tools.jar.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks a lot,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">a2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">----<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">Dr. Aaron Ponti<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">Software and Data Management Engineer<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">Single Cell Unit<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">Department of Biosystems Science and Engineering (D-BSSE)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">ETH Zürich<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">Office 2.24<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">Mattenstrasse 26<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">4058 Basel, Switzerland<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">aaron.ponti@bsse.ethz.ch<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">+41 61 387 33 74<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>