[ome-users] Errors importing MSR files
Nick Petersen
EPeterse at scripps.edu
Mon Jan 8 16:03:09 GMT 2018
I am using the most updated version of the Abberior STED microscope software and I'm getting the following errors when I try and import the files:
[WARN] Could not parse description as XML
org.xml.sax.SAXParseException: Content is not allowed in prolog.
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
at loci.common.xml.XMLTools.parseDOM(XMLTools.java:215)
at loci.common.xml.XMLTools.parseDOM(XMLTools.java:196)
at loci.formats.in.OBFReader.initStack(OBFReader.java:379)
at loci.formats.in.OBFReader.initFile(OBFReader.java:184)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:174)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:174)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:242)
at ij.io.Opener.open(Opener.java:109)
at ij.io.Opener.openAndAddToRecent(Opener.java:291)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
at java.lang.Thread.run(Thread.java:745)
Warning: org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Feature 'http://javax.xml.XMLConstants/feature/secure-processing' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd
Validating OME-XML
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
Error validating document: 3 errors found
Reading header
Finding image offsets
[WARN] Unknown Immersion value 'null' will be stored as "Other"
[WARN] Unknown Correction value 'null' will be stored as "Other"
[WARN] Unknown Immersion value 'null' will be stored as "Other"
[WARN] Unknown Correction value 'null' will be stored as "Other"
[WARN] Unknown Immersion value 'null' will be stored as "Other"
[WARN] Unknown Correction value 'null' will be stored as "Other"
[WARN] Unknown Immersion value 'null' will be stored as "Other"
[WARN] Unknown Correction value 'null' will be stored as "Other"
[WARN] Could not parse description as XML
org.xml.sax.SAXParseException: Content is not allowed in prolog.
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
at loci.common.xml.XMLTools.parseDOM(XMLTools.java:215)
at loci.common.xml.XMLTools.parseDOM(XMLTools.java:196)
at loci.formats.in.OBFReader.initStack(OBFReader.java:379)
at loci.formats.in.OBFReader.initFile(OBFReader.java:184)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:174)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:174)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:242)
at ij.io.Opener.open(Opener.java:109)
at ij.io.Opener.openAndAddToRecent(Opener.java:291)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
at java.lang.Thread.run(Thread.java:745)
Warning: org.apache.xerces.parsers.SAXParser: Feature 'http://javax.xml.XMLConstants/feature/secure-processing' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd
Validating OME-XML
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
Error validating document: 3 errors found
[WARN] Could not parse description as XML
org.xml.sax.SAXParseException: Content is not allowed in prolog.
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
at loci.common.xml.XMLTools.parseDOM(XMLTools.java:215)
at loci.common.xml.XMLTools.parseDOM(XMLTools.java:196)
at loci.formats.in.OBFReader.initStack(OBFReader.java:379)
at loci.formats.in.OBFReader.initFile(OBFReader.java:184)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:174)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:174)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:242)
at ij.io.Opener.open(Opener.java:109)
at ij.io.Opener.openAndAddToRecent(Opener.java:291)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
at java.lang.Thread.run(Thread.java:745)
Warning: org.apache.xerces.parsers.SAXParser: Feature 'http://javax.xml.XMLConstants/feature/secure-processing' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd
Validating OME-XML
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
Error validating document: 3 errors found
[WARN] Could not parse description as XML
org.xml.sax.SAXParseException: Content is not allowed in prolog.
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
at loci.common.xml.XMLTools.parseDOM(XMLTools.java:215)
at loci.common.xml.XMLTools.parseDOM(XMLTools.java:196)
at loci.formats.in.OBFReader.initStack(OBFReader.java:379)
at loci.formats.in.OBFReader.initFile(OBFReader.java:184)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:174)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:174)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:242)
at ij.io.Opener.open(Opener.java:109)
at ij.io.Opener.openAndAddToRecent(Opener.java:291)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
at java.lang.Thread.run(Thread.java:745)
Warning: org.apache.xerces.parsers.SAXParser: Feature 'http://javax.xml.XMLConstants/feature/secure-processing' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd
Validating OME-XML
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
[ERROR] cvc-identity-constraint.4.2.2: Duplicate key value [Channel:1] declared for identity constraint "ChannelIDKey" of element "OME".
Error validating document: 3 errors found
I have updated Bio-Formats to the most recent version (5.7.2) and still get this error. The images still open but I'm not sure if I'm losing more than metadata from the errors above. I have also updated Java to ensure the problem wasn't there. I have attached 2 example files to replicate the issue
Thanks for the help!
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