Bug 50 – can't open trakEM2 .xml files

Bug 50 - can't open trakEM2 .xml files


Summary:	can't open trakEM2 .xml files

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P4 normal
Assigned To:	Albert Cardona

URL:

Depends on:
Blocks:

Reported:	2009-04-24 10:49 CDT by german
Modified:	2009-05-01 10:00 CDT
CC List:	1 user (show)

See Also:

Attachments
screenshot (201.24 KB, image/jpeg) 2009-04-24 15:46 CDT, german

Description german 2009-04-24 10:49:27 CDT

Useful Java System Properties:
  os.arch => amd64
  os.name => Windows 2003
  os.version => 5.2
  java.version => 1.6.0_04
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_04-b12
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 10.0-b19
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

Bug Report Text:

hi albert

I just copied the latest jars from /edge into the plugins folder. now, if i do ->file ->open and select a .xml file, fiji opens only one window which displays the content of this .xml file as text.

Comment 1 Albert Cardona 2009-04-24 13:32:34 CDT

Does "File - Open" also have the same effect?

Comment 2 german 2009-04-24 14:19:21 CDT

i am not sure if I understood your question, but if I do "File - Open" (in fiji's menu bar) for a jpeg, it opens the image. and when i do the same for my trakEM2 project (which is a .xml), a single window opens with the content of this xml as TEXT.

Comment 3 Albert Cardona 2009-04-24 15:19:05 CDT

I cannot reproduce the problem, so my guess is that something is wrong with the HandleExtraFileTypes in your Fiji installation.

To provide a workaround, I've uploaded a TrakEM2_.jar to edge/ that includes a "File > Import > TrakEM2 XML..." menu option.

Please try it and let me know if this at least lets you open TrakEM2 files.

Also: do any error messages print to stdout?

Comment 4 german 2009-04-24 15:46:49 CDT

Created attachment 1
screenshot

Comment 5 german 2009-04-24 15:49:05 CDT

ok, i now did "File > Import > TrakEM2 XML..." and it gives the following error message: Plugin ini.trakem2.Open_Project did not find required class: loci/formats/FormatExeption

Comment 6 Albert Cardona 2009-04-24 15:52:26 CDT

Do you have the file plugins/loci_tools.jar ? It's also in edge/

Comment 7 german 2009-04-24 16:00:55 CDT

yes, it's there. i copied it today from /edge and placed it in the plugins folder

Comment 8 Albert Cardona 2009-04-24 16:21:47 CDT

There may then be a classloader problem in Windows. I have no idea otherwise what could possibly be wrong. Works fine in Linux.

As a temporary workaround, you could try adding the loci_tools.jar to the classpath when launching fiji. For windows, you would have to open a cmd window, then 'cd' to fiji folder and launch:

  fiji.exe -cp plugins/loci_tools.jar

... but that should be done by default anyway.

Comment 9 german 2009-04-24 17:01:19 CDT

ok. i'll try this next week.

Comment 10 Albert Cardona 2009-05-01 10:00:52 CDT

Was fixed with a new loci_tools.jar