Open Microscopy Environment

Hi
I read a BigTIFF file using the standard loci.formats.ImageReader

Code: Select all

ImageReader tr = new ImageReader();
tr.setId("BigTIFF.tif");

The file reads fine, I can access the content, but I get this exception at tr.setId("BigTIFF.tif"):

Code: Select all

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.LeicaSCNReader.isThisType(LeicaSCNReader.java:111) ~[bioformats_package.jar:na]
   at loci.formats.ImageReader.getReader(ImageReader.java:181) [bioformats_package.jar:na]
   at loci.formats.ImageReader.setId(ImageReader.java:832) [bioformats_package.jar:na]
   at TestReader.main(TestReader.java:24) [bin/:na]
Caused by: org.xml.sax.SAXParseException: Premature end of file.
   at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:441) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:368) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1436) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:1019) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649) ~[na:1.8.0_45]
   at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:333) ~[na:1.8.0_45]
   at javax.xml.parsers.SAXParser.parse(SAXParser.java:195) ~[na:1.8.0_45]
   at loci.common.xml.XMLTools.parseXML(XMLTools.java:428) ~[bioformats_package.jar:na]
   ... 6 common frames omitted

Bio-formats 5.2.2
All this isn't critical, but it would be better to avoid the exception.

Hi,

If you would like to upload the file to us using http://qa.openmicroscopy.org.uk/qa/upload/ we can take a look into the error in more detail.


Regards,
Roger

The file is 23GB. I guess I'll see if I can reproduce the issue with a smaller file.