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embl-cba / imagej-utils

BSD 2-Clause "Simplified" License
2 stars 4 forks source link

Source list #9

Closed martinschorb closed 4 years ago

martinschorb commented 4 years ago

Hi I open multiple sources and end up with a massive error log.

bdv_clem2

also I see that the sources show up multiple times in the list as "SPIMData" and in all sources. Is this connected?

Martin


    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.apply(SpimDataImporterXML.java:40)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.get(SpimDataImporterXML.java:33)
    at sc.fiji.bdvpg.scijava.command.spimdata.MultipleSpimDataImporterCommand.run(MultipleSpimDataImporterCommand.java:32)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
    at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
    at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
    at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
    ... 12 more
mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.apply(SpimDataImporterXML.java:40)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.get(SpimDataImporterXML.java:33)
    at sc.fiji.bdvpg.scijava.command.spimdata.MultipleSpimDataImporterCommand.run(MultipleSpimDataImporterCommand.java:32)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
    at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
    at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
    at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
    ... 12 more
mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.apply(SpimDataImporterXML.java:40)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.get(SpimDataImporterXML.java:33)
    at sc.fiji.bdvpg.scijava.command.spimdata.MultipleSpimDataImporterCommand.run(MultipleSpimDataImporterCommand.java:32)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
    at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
    at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
    at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
    ... 12 more
mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.apply(SpimDataImporterXML.java:40)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.get(SpimDataImporterXML.java:33)
    at sc.fiji.bdvpg.scijava.command.spimdata.MultipleSpimDataImporterCommand.run(MultipleSpimDataImporterCommand.java:32)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
    at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
    at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
    at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
    ... 12 more
mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.apply(SpimDataImporterXML.java:40)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.get(SpimDataImporterXML.java:33)
    at sc.fiji.bdvpg.scijava.command.spimdata.MultipleSpimDataImporterCommand.run(MultipleSpimDataImporterCommand.java:32)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
    at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
    at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
    at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
    ... 12 more
mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.apply(SpimDataImporterXML.java:40)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.get(SpimDataImporterXML.java:33)
    at sc.fiji.bdvpg.scijava.command.spimdata.MultipleSpimDataImporterCommand.run(MultipleSpimDataImporterCommand.java:32)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
    at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
    at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
    at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
    ... 12 more
mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.apply(SpimDataImporterXML.java:40)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.get(SpimDataImporterXML.java:33)
    at sc.fiji.bdvpg.scijava.command.spimdata.MultipleSpimDataImporterCommand.run(MultipleSpimDataImporterCommand.java:32)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
    at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
    at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
    at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
    ... 12 more
mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.apply(SpimDataImporterXML.java:40)
    at sc.fiji.bdvpg.spimdata.importer.SpimDataImporterXML.get(SpimDataImporterXML.java:33)
    at sc.fiji.bdvpg.scijava.command.spimdata.MultipleSpimDataImporterCommand.run(MultipleSpimDataImporterCommand.java:32)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
    at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
    at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
    at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
    at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
    at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
    at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
    at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
    ... 12 more
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