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TrakEM problem writing XML after elastic alignment

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tmacrina
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TrakEM problem writing XML after elastic alignment

tmacrina
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>
Saalfeld, Stephan
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Re: TrakEM problem writing XML after elastic alignment

Saalfeld, Stephan
Hi Tommy,

does this happen with the latest Fiji update?

Does the error happen after you have deleted the directory

trakem2.cts

in your project directory before opening and aligning?  It's possible
that some leftovers there from a previous failure make problems.

Stephan



On Tue, 2015-04-28 at 17:51 -0700, tmacrina wrote:

> 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 2**Excerpt from XML file*
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/TrakEM-problem-writing-XML-after-elastic-alignment-tp5012641.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
tmacrina
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Re: TrakEM problem writing XML after elastic alignment

tmacrina
Hey Stephan,

Yeah - I updated FIJI this morning at 11:00AM EST and was still able to recreate the error.

But removing the trakem2.cts directory worked! I created a new project, ran the elastic aligner successfully, then saved it under a different name. I removed the trakem2.cts folder, then opened the initial project file and was able to rerun the elastic aligner without a problem.

Thanks for all the help!

Tommy
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