Error when reading project .xml files from TrakEM2 into FIJI

Hi everyone,

I’m having a bit of an unexpected issue in FIJI. I am using the plugin TrakEM2 to trace structures in serial section SEM slices of brain tissue. TrakEM2 likes .xml files,which is what I have been using in FIJI/TrakEM2 for the past year.

However, this morning I came in and, for no apparent reason, FIJI can’t open the .xml file I’ve been working on. I closed the program yesterday as usual with no apparent problems. Our most recent backup is about 2 weeks ago and it would be really helpful to recover the lost data. Any help on this would be greatly appreciated.

Here is the error code I am getting:


Fatal error: column=5 line=373
==================
ERROR:
org.xml.sax.SAXParseException: Attribute name "rue" associated with an element type "t2_layer_set" must be followed by the ' = ' character.
	at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
	at ini.trakem2.persistence.FSLoader.openFSProject(FSLoader.java:298)
	at ini.trakem2.Project.openFSProject(Project.java:554)
	at ini.trakem2.Project.openFSProject(Project.java:544)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at HandleExtraFileTypes.tryOpen(HandleExtraFileTypes.java:298)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:485)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:503)
	at ij.io.Opener.openImage(Opener.java:369)
	at ij.io.Opener.openImage(Opener.java:243)
	at ij.io.Opener.open(Opener.java:110)
	at ij.RecentOpener.run(RecentOpener.java:19)
	at java.lang.Thread.run(Thread.java:662)

This looks like your XML file is broken. Please check line 373 in your XML file. May be you can fix it by manually editing? Related, are you saving the XML on a network file system? I have experienced TrakEM2 to not deal with network filesystems well (and have no idea why that should be an issue).

Indeed the error signals that your XML file is corrupted. Reach back to a backup.