Problems loading TrakEM XML files

[Jörg Hammel]

Hi,

 

We have recently had problems with the very nice TrakEM plugin in Fiji.
Since a very short time we have difficulties opening saved TrakEM projects
on two Win7 x64 machines. The projects have been set up on the same machine.
However, even downgrading to an earlier version of Fiji, e.g. one of the
Heidelberg releases doesn’t fix the problem.

The error logs we keep getting are basically the following ones:

 

Restarted mipmap Executor Service for all projects with 4 threads.

Fatal error: column=12 line=313

==================

ERROR:

org.xml.sax.SAXParseException: An invalid XML character (Unicode: 0x{2}) was
found in the value of attribute "{1}" and element is "0".

 

                at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractS
AXParser.java:1231)

 

                at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SA
XParserImpl.java:522)

 

                at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)

 

                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 ini.trakem2.Open_Project.run(Open_Project.java:34)

 

                at ij.IJ.runUserPlugIn(IJ.java:184)

 

                at ij.IJ.runPlugIn(IJ.java:151)

 

                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 ij.Command.runPlugIn(Command.java:148)

 

                at ij.Command.runCommand(Command.java:97)

 

                at ij.Executer.run(Executer.java:64)

 

                at java.lang.Thread.run(Thread.java:662)

 

==================

 

And from the TrakEM SystemLog:

 

MAX_MEMORY: 6188294144

cache size: 2475317760

project file path 1: E:/Henry/Master/2006a_usb02/TrakEM/test/untitled.xml

Loader.openFSProject: path is null

storage folder is E:/Henry/Master/2006a_usb02/TrakEM/test/

Restarted mipmap Executor Service for all projects with 4 threads.

mipmaps folder is
E:/Henry/Master/2006a_usb02/TrakEM/test/trakem2.1358868921994.42186459.21116
42674/trakem2.mipmaps/

Set mipmap format to 4

parsed: layer_mipmaps=true

parsed: n_mipmap_threads=4

parsed: n_undo_steps=32

parsed: look_ahead_cache=0

WARNING: could not delete crash detector file .open.t2 from trakem2.mipmaps
folder at
E:/Henry/Master/2006a_usb02/TrakEM/test/trakem2.1358868921994.42186459.21116
42674/trakem2.mipmaps/

MAX_MEMORY: 6188294144

cache size: 2475317760

project file path 1: E:/Henry/Master/2006a_usb02/TrakEM/test/untitled.xml

Loader.openFSProject: path is null

storage folder is E:/Henry/Master/2006a_usb02/TrakEM/test/

Restarted mipmap Executor Service for all projects with 4 threads.

mipmaps folder is
E:/Henry/Master/2006a_usb02/TrakEM/test/trakem2.1358868921994.42186459.21116
42674/trakem2.mipmaps/

Set mipmap format to 4

parsed: layer_mipmaps=true

parsed: n_mipmap_threads=4

parsed: n_undo_steps=32

parsed: look_ahead_cache=0

WARNING: could not delete crash detector file .open.t2 from trakem2.mipmaps
folder at
E:/Henry/Master/2006a_usb02/TrakEM/test/trakem2.1358868921994.42186459.21116
42674/trakem2.mipmaps/

 

 

Any help and suggestions are highly appreciated. I assume it is somehow
related to a configuration problem, not really a bug in the software.
However, we have no idea in what we should have a look any further.

 

 

Best

 

                 Jörg

 

_________________________________________________

Dr. Jörg U. Hammel

Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem
Museum

Erbertstr. 1

07743 Jena

 

T:  [phone]

M:  <mailto:[hidden email]> [hidden email]

 

 <http://www.porifera.net/> www.porifera.net

 <http://www.uni-jena.de/szeb.html> www.uni-jena.de/szeb.html

 


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[Albert Cardona-2]

On Jan 23, 2013, at 3:39 AM, Jörg Hammel <[hidden email]> wrote:

> Hi,
>
>
>
> We have recently had problems with the very nice TrakEM plugin in Fiji.
> Since a very short time we have difficulties opening saved TrakEM projects
> on two Win7 x64 machines. The projects have been set up on the same machine.
> However, even downgrading to an earlier version of Fiji, e.g. one of the
> Heidelberg releases doesn’t fix the problem.
>
> The error logs we keep getting are basically the following ones:
>
>
>
> Restarted mipmap Executor Service for all projects with 4 threads.
>
> Fatal error: column=12 line=313

Jorg,

Open the XML file with a text editor, go to line 313, and check the character at position 12. It is an invalid character gor XML. Perhaps you named something using quotes or symbols, and TrakEM2 didn't prevent you from doing do (it should have).

Albert

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[jgbr20]

Hello,

I am a final year undergraduate student working on a project that involves using TrackEM2. For some reason, my file came up as an error when I opened it via Fiji. I think this is a similar problem to you Jorg. I'm just wondering if you found a solution to this? The error came up as follows.

StdOut
WARNING: could not delete crash detector file .open.t2 from trakem2.mipmaps folder at C:/Users/JovenGerardBenesa/Fiji.app/trakem2.1476899785442.2053776621.1560497569/trakem2.mipmaps/
MAX_MEMORY: 8251891712
cache size: 3300756736
project file path 2: C:/Users/JovenGerardBenesa/Fiji.app/FYProject.xml.gz
Loader.openFSProject: path is C:/Users/JovenGerardBenesa/Fiji.app/FYProject.xml.gz
storage folder is C:/Users/JovenGerardBenesa/Fiji.app/
mipmaps folder is C:/Users/JovenGerardBenesa/Fiji.app/trakem2.1476899785442.2053776621.1560497569/trakem2.mipmaps/
Set mipmap format to 4
WARNING: could not delete crash detector file .open.t2 from trakem2.mipmaps folder at C:/Users/JovenGerardBenesa/Fiji.app/trakem2.1476899785442.2053776621.1560497569/trakem2.mipmaps/


Fatal error: column=829 line=17436
==================
ERROR:
org.xml.sax.SAXParseException: Premature end of file.
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:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
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.io.Opener.openAndAddToRecent(Opener.java:292)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
at java.lang.Thread.run(Thread.java:662)
==================

I would appreciate any kind of help. Thank you.

Best,

Joven

P.S. I've tried using Albert's suggestion below about using a text editor, but those lines/columns in my case (17436, 829) don't even exist in the file?