Task #13322 (new)
Opened 7 years ago
Last modified 7 years ago
Bug: ND2 Bfconvert issues
Reported by: | bramalingam | Owned by: | |
---|---|---|---|
Priority: | minor | Milestone: | Unscheduled |
Component: | Bio-Formats | Version: | Bio-Formats-5.1.8 |
Keywords: | n.a. | Cc: | |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
ref: https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8217
Testing summary:
Tested with Bio-Formats 5.3.3 command line tools and the error was reproducible.
Command:
ls29010:bftools533 bramalingam$ ./bfconvert /Users/bramalingam/Desktop/17541/supernd2.nd2 -debug -series 0 /Users/bramalingam/Desktop/17541/test/testseries_new.tiff
Stack trace:
Exception in thread "main" java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 72; Character reference "�" is an invalid XML character. at ome.xml.model.XMLAnnotation.asXMLElement(XMLAnnotation.java:265) at ome.xml.model.XMLAnnotation.asXMLElement(XMLAnnotation.java:234) at ome.xml.model.StructuredAnnotations.asXMLElement(StructuredAnnotations.java:679) at ome.xml.model.StructuredAnnotations.asXMLElement(StructuredAnnotations.java:660) at ome.xml.model.OME.asXMLElement(OME.java:896) at ome.xml.model.OME.asXMLElement(OME.java:773) at ome.xml.meta.AbstractOMEXMLMetadata.dumpXML(AbstractOMEXMLMetadata.java:110) at ome.xml.meta.OMEXMLMetadataImpl.dumpXML(OMEXMLMetadataImpl.java:105) at loci.formats.services.OMEXMLServiceImpl.getOMEXML(OMEXMLServiceImpl.java:465) at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:414) at loci.formats.tools.ImageConverter.main(ImageConverter.java:880) Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 72; Character reference "�" is an invalid XML character. at org.apache.xerces.parsers.DOMParser.parse(Unknown Source) at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source) at ome.xml.model.XMLAnnotation.asXMLElement(XMLAnnotation.java:261) ... 10 more
Change History (2)
comment:1 Changed 7 years ago by dgault
comment:2 Changed 7 years ago by mlinkert
Associated Trello card: https://trello.com/c/USjkdBVa/98-bug-bfconvert-on-nd2-files
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An update from forum thread https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8217