ImageJ
Login  Register

TrakEM problem writing XML after elastic alignment

Posted by tmacrina on Apr 29, 2015; 12:51am
URL: http://imagej.273.s1.nabble.com/TrakEM-problem-writing-XML-after-elastic-alignment-tp5012641.html

Hey guys, I have a project with a few layers of montaged images. I align the layers using the elastic mode. After the alignment process finishes (spring mesh optimization is completed, and the log reads "Done"), the patches are submitted for mipmap regeneration, but I encounter the first error below repeatedly for a large number of patches. If I "save as" the project, close it, and reopen it, I get a message "Error reading the project .xml file" and the second error below. (I can still open the original project - the one before elastic alignment - without an issue.) If I open the offending XML file in a text editor and look near the row listed in that second error, I do find content in a trailing section - see below for the few lines from the file. Any thoughts on how to prevent this from happening? Thanks for the help! Tommy Error 1 
*** ERROR: Can't generate mipmaps for patch Tile_r2-c1_S2-W001_sec2.tif z=2.0 #1779
==================
ERROR:
java.lang.RuntimeException: org.xml.sax.SAXParseException: Content is not allowed in trailing section.
	at ini.trakem2.display.Patch.getCT(Patch.java:2282)
	at ini.trakem2.display.Patch.getCoordinateTransform(Patch.java:1373)
	at ini.trakem2.display.Patch.createCoordinateTransformedImage(Patch.java:1416)
	at ini.trakem2.display.Patch.createTransformedImage(Patch.java:1513)
	at ini.trakem2.persistence.FSLoader.generateMipMaps(FSLoader.java:1580)
	at ini.trakem2.persistence.FSLoader$6.call(FSLoader.java:2441)
	at ini.trakem2.persistence.FSLoader$6.call(FSLoader.java:2434)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:662)
Caused by: org.xml.sax.SAXParseException: Content is not allowed in trailing section.
	at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
	at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
	at ini.trakem2.io.CoordinateTransformXML.parse(CoordinateTransformXML.java:33)
	at ini.trakem2.display.Patch.fetchCoordinateTransform(Patch.java:2294)
	at ini.trakem2.display.Patch.getCT(Patch.java:2279)
	... 11 more
==> Caused by:
org.xml.sax.SAXParseException: Content is not allowed in trailing section.
	at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
	at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
	at ini.trakem2.io.CoordinateTransformXML.parse(CoordinateTransformXML.java:33)
	at ini.trakem2.display.Patch.fetchCoordinateTransform(Patch.java:2294)
	at ini.trakem2.display.Patch.getCT(Patch.java:2279)
	at ini.trakem2.display.Patch.getCoordinateTransform(Patch.java:1373)
	at ini.trakem2.display.Patch.createCoordinateTransformedImage(Patch.java:1416)
	at ini.trakem2.display.Patch.createTransformedImage(Patch.java:1513)
	at ini.trakem2.persistence.FSLoader.generateMipMaps(FSLoader.java:1580)
	at ini.trakem2.persistence.FSLoader$6.call(FSLoader.java:2441)
	at ini.trakem2.persistence.FSLoader$6.call(FSLoader.java:2434)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:662)
==================
Error 2 
Fatal error: column=7 line=503
==================
ERROR:
org.xml.sax.SAXParseException: The element type "t2_patch" must be terminated by the matching end-tag "</t2_patch>".
	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:291)
	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:268)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:439)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:66)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:486)
	at ij.io.Opener.openImage(Opener.java:360)
	at ij.io.Opener.openImage(Opener.java:239)
	at ij.io.Opener.open(Opener.java:106)
	at ij.io.Opener.open(Opener.java:73)
	at ij.plugin.Commands.run(Commands.java:27)
	at ij.IJ.runPlugIn(IJ.java:169)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)
==================
Excerpt from XML file 
501				</ict_transform_list>1961.43 57528.0 23380.182 39164.0 [numbers removed] 23380.182"/>
502					<iict_transform class="mpicbg.trakem2.transform.AffineModel2D" data="1.0096908374866078 [numbers removed] -27593.40685207644" />
503				</ict_transform_list>
504				<t2_filter class="ini.trakem2.imaging.filters.CLAHE" fast="true" blockradius="63" bins="255" slope="3.0" />
505			</t2_patch>
Free forum by Nabble Disable Popup Ads | Edit this page