[ome-devel] Strange issue when bioformats_package.jar is used instead of loci_tools.jar
Melissa Linkert
melissa at glencoesoftware.com
Thu Sep 11 16:39:48 BST 2014
Hi Aaron,
> thanks for your reply: I'll try that. Still, this kind of scares me (a short excerpt from the log):
>
> ...
> 14:22:53.774 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageCalibra' 0%
> 14:22:53.782 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> java.lang.NegativeArraySizeException: null
> ...
> 14:22:54.015 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - Could not parse XML
> java.io.IOException: null
> at loci.common.xml.XMLTools.parseXML(XMLTools.java:436) ~[bioformats_package.jar:na]
> at loci.common.xml.XMLTools.parseXML(XMLTools.java:414) ~[bioformats_package.jar:na]
> ...
> Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
> ...
>
> I am confused: what are all those exceptions? Why are they logged but do not seem to disrupt the flow of the program?
The issue is that there are various blocks of metadata throughout an
.nd2 file that can be either XML or a plain text value. We don't
necessarily know ahead of time which format a particular block will be
in - the only way to find out for sure is to attempt to parse it as XML.
So what you're seeing is the XML parsing being attempted, failing, and
then the reader falling back to treating that metadata block as a plain
text value. It's not fatal as you've noticed, but it's occasionally
useful to see the these exceptions when debugging initialization failures.
Regards,
-Melissa
On Thu, Sep 11, 2014 at 02:28:50PM +0000, Ponti Aaron wrote:
> Hi,
>
> thanks for your reply: I'll try that. Still, this kind of scares me (a short excerpt from the log):
>
> ...
> 14:22:53.774 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageCalibra' 0%
> 14:22:53.782 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> java.lang.NegativeArraySizeException: null
> ...
> 14:22:54.015 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - Could not parse XML
> java.io.IOException: null
> at loci.common.xml.XMLTools.parseXML(XMLTools.java:436) ~[bioformats_package.jar:na]
> at loci.common.xml.XMLTools.parseXML(XMLTools.java:414) ~[bioformats_package.jar:na]
> ...
> Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
> ...
>
> I am confused: what are all those exceptions? Why are they logged but do not seem to disrupt the flow of the program?
>
> Thanks,
> a2
>
>
> -----Original Message-----
> From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf Of Melissa Linkert
> Sent: Donnerstag, 11. September 2014 16:23
> To: Ponti Aaron
> Cc: ome-devel at lists.openmicroscopy.org.uk
> Subject: Re: [ome-devel] Strange issue when bioformats_package.jar is used instead of loci_tools.jar
>
> Hi Aaron,
>
> > 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
> *snip*
> > 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.
> >
> > 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.
>
> The primary difference between bioformats_package.jar and loci_tools.jar
> is that the former includes the logback bindings for slf4j, and the
> latter includes the log4j bindings. The logback bindings default to
> displaying all messages at the "DEBUG" level or above; the log4j
> bindings do not. You should be able to change the log level by either
> placing this file on your classpath:
>
> https://github.com/openmicroscopy/bioformats/blob/v5.0.4/tools/logback.xml
>
> or by adding a call to:
>
> DebugTools.enableLogging("INFO");
>
> before calling setId on the reader. In both cases, that sets the
> logging level to "INFO"; using "WARN" or "ERROR" instead would give you
> even fewer messages.
>
> If neither of those approaches solves the problem, please let us know.
>
> Regards,
> -Melissa
>
> On Wed, Sep 10, 2014 at 01:02:15PM +0000, Ponti Aaron wrote:
> > Dear list,
> >
> > 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):
> >
> > <code>
> > ...
> >
> > // Create the reader
> > reader = new ImageProcessorReader(
> > new ChannelSeparator(
> > LociPrefs.makeImageReader()));
> >
> > ...
> >
> > try {
> > factory = new ServiceFactory();
> > service = factory.getInstance(OMEXMLService.class);
> > } catch (DependencyException e) {
> > ...
> > }
> >
> > try {
> > omexmlMeta = service.createOMEXMLMetadata();
> > } catch (ServiceException e) {
> > ...
> > }
> > reader.setMetadataStore(omexmlMeta);
> >
> > // Try to open the image file
> > try {
> > reader.setId(filename.getCanonicalPath());
> > } catch (FormatException e) {
> > ...
> > }
> >
> >
> > </code>
> >
> > 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
> >
> > reader.setId(filename.getCanonicalPath());
> >
> > is reached:
> >
> > <log>
> >
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.ImageReader - ND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - ND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2
> > 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)
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - NativeND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2
> > 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)
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Searching for blocks
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ND2 FILE SIG' 0%
> > 14:22:53.774 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageCalibra' 0%
> > 14:22:53.782 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.795 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> >
> > ...
> >
> > 14:22:53.990 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:54.005 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageMetadat' 0%
> > 14:22:54.008 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageDataSeq' 2%
> > 14:22:54.008 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageTextInf' 94%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 95%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|P' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|P' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|X' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Y' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%
> > 14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 97%
> > 14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%
> > 14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%
> > 14:22:54.012 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%
> > 14:22:54.012 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageAttribu' 99%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ND2 FILEMAP ' 99%
> > 14:22:54.015 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - Could not parse XML
> > java.io.IOException: null
> > at loci.common.xml.XMLTools.parseXML(XMLTools.java:436) ~[bioformats_package.jar:na]
> > at loci.common.xml.XMLTools.parseXML(XMLTools.java:414) ~[bioformats_package.jar:na]
> > at loci.common.xml.XMLTools.parseXML(XMLTools.java:393) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.parseText(NativeND2Reader.java:2054) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:726) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
> > at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(Unknown Source) ~[na:1.7.0_51]
> > at javax.xml.parsers.SAXParser.parse(Unknown Source) ~[na:1.7.0_51]
> > at loci.common.xml.XMLTools.parseXML(XMLTools.java:428) ~[bioformats_package.jar:na]
> > ... 21 common frames omitted
> > 14:22:54.029 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatTools - Expected positive value for PhysicalSizeZ; got 0.0
> > 14:22:54.029 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatTools - Expected positive value for EmissionWavelength; got 0
> > 14:22:54.037 [SwingWorker-pool-2-thread-5] DEBUG loci.common.Location - Location.mapFile: embedded-stream.raw -> null
> >
> > </log>
> >
> > 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.
> >
> > 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.
> >
> > Thanks a lot,
> > a2
> >
> > ----
> > Dr. Aaron Ponti
> > Software and Data Management Engineer
> > Single Cell Unit
> > Department of Biosystems Science and Engineering (D-BSSE)
> > ETH Zürich
> > Office 2.24
> > Mattenstrasse 26
> > 4058 Basel, Switzerland
> > aaron.ponti at bsse.ethz.ch
> > +41 61 387 33 74
> >
>
>
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.ImageReader - ND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - ND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2
> > 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)
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - NativeND2Reader initializing D:\user\pontia\Experiment_2\Captured for 4.nd2
> > 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)
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Searching for blocks
> > 14:22:53.768 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ND2 FILE SIG' 0%
> > 14:22:53.774 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageCalibra' 0%
> > 14:22:53.782 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.795 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.804 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.814 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.823 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.833 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.840 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.847 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.854 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.861 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:53.990 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler -
> > java.lang.NegativeArraySizeException: null
> > at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:406) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1570) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1644) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:420) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > 14:22:54.005 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageMetadat' 0%
> > 14:22:54.008 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageDataSeq' 2%
> > 14:22:54.008 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageTextInf' 94%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 95%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 95%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.009 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|C' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|P' 96%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|P' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|X' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Y' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%
> > 14:22:54.010 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|Z' 97%
> > 14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 97%
> > 14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%
> > 14:22:54.011 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%
> > 14:22:54.012 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%
> > 14:22:54.012 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomDataVa' 98%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'CustomData|A' 99%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ImageAttribu' 99%
> > 14:22:54.013 [SwingWorker-pool-2-thread-5] INFO loci.formats.FormatHandler - Parsing block 'ND2 FILEMAP ' 99%
> > 14:22:54.015 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatHandler - Could not parse XML
> > java.io.IOException: null
> > at loci.common.xml.XMLTools.parseXML(XMLTools.java:436) ~[bioformats_package.jar:na]
> > at loci.common.xml.XMLTools.parseXML(XMLTools.java:414) ~[bioformats_package.jar:na]
> > at loci.common.xml.XMLTools.parseXML(XMLTools.java:393) ~[bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.parseText(NativeND2Reader.java:2054) [bioformats_package.jar:na]
> > at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:726) [bioformats_package.jar:na]
> > at loci.formats.FormatReader.setId(FormatReader.java:1317) [bioformats_package.jar:na]
> > at loci.formats.DelegateReader.setId(DelegateReader.java:253) [bioformats_package.jar:na]
> > at loci.formats.ImageReader.setId(ImageReader.java:753) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) [bioformats_package.jar:na]
> > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) [bioformats_package.jar:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.init(MicroscopyReader.java:106) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.readers.MicroscopyReader.<init>(MicroscopyReader.java:66) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.processors.data.MicroscopyProcessor$MicroscopyFile.scanForSeries(MicroscopyProcessor.java:524) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:371) [bin/:na]
> > at ch.ethz.scu.obit.microscopy.gui.viewers.data.MicroscopyViewer$1Worker.doInBackground(MicroscopyViewer.java:1) [bin/:na]
> > at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_51]
> > at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_51]
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_51]
> > at java.lang.Thread.run(Unknown Source) [na:1.7.0_51]
> > Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
> > at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) ~[na:1.7.0_51]
> > at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(Unknown Source) ~[na:1.7.0_51]
> > at javax.xml.parsers.SAXParser.parse(Unknown Source) ~[na:1.7.0_51]
> > at loci.common.xml.XMLTools.parseXML(XMLTools.java:428) ~[bioformats_package.jar:na]
> > ... 21 common frames omitted
> > 14:22:54.029 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatTools - Expected positive value for PhysicalSizeZ; got 0.0
> > 14:22:54.029 [SwingWorker-pool-2-thread-5] DEBUG loci.formats.FormatTools - Expected positive value for EmissionWavelength; got 0
> > 14:22:54.037 [SwingWorker-pool-2-thread-5] DEBUG loci.common.Location - Location.mapFile: embedded-stream.raw -> null
>
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
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