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Bug 747 - Can't open the second file of a series of CZI files (Carl Zeiss)
Can't open the second file of a series of CZI files (Carl Zeiss)
Status: RESOLVED DUPLICATE of bug 744
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-05-13 09:54 CDT by hfang7
Modified: 2014-05-13 15:00 CDT
2 users (show)

See Also:
Description hfang7 2014-05-13 09:54:20 CDT 
When I want open the second file of a series (muiti-location) of CZI files, there is "exception", the first one and the others are fine.

here is exception
===============
(Fiji Is Just) ImageJ 1.48v; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 40MB of 12229MB (<1%)
 
java.lang.IllegalArgumentException: Invalid T index: 1/1
	at loci.formats.FormatTools.getIndex(FormatTools.java:372)
	at loci.formats.FormatTools.getIndex(FormatTools.java:317)
	at loci.formats.FormatReader.getIndex(FormatReader.java:1051)
	at loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:1020)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:615)
	at loci.formats.FormatReader.setId(FormatReader.java:1315)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	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:454)
	at ij.io.Opener.openImage(Opener.java:311)
	at ij.io.Opener.openImage(Opener.java:334)
	at ij.io.Opener.open(Opener.java:144)
	at ij.io.Opener.openAndAddToRecent(Opener.java:247)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:662)

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

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  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 => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: F:\IMAGEP~1\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => F:\IMAGEP~1\FIJI-W~1\Fiji.app

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Comment 1 Curtis Rueden 2014-05-13 10:59:35 CDT 
This is a duplicate of bug #744:
http://fiji.sc/bugzilla/﷒0﷓

Can you please try the patched version of formats-gpl.jar available from:

   http://curtis.imagej.net/fiji-bug-744/formats-gpl.jar

and let us how it goes?

*** This bug has been marked as a duplicate of bug 744 ***
Comment 2 hfang7 2014-05-13 11:55:20 CDT 
I tried "formats-gpl.jar'', But I still can't open the file. BTW, I can open the same file in ImageJ (1.47 or 1.48v), I should mention this earlier.
Comment 3 Curtis Rueden 2014-05-13 12:33:41 CDT 
What does it mean that you can "open the same file in ImageJ"? I must assume you are talking about the vanilla distribution of ImageJ 1.x, as opposed to the Fiji distribution, but the vanilla distribution of ImageJ 1.x does not come bundled with support for CZI files. So I am confused.

When you say you "tried formats-gpl.jar" do you mean that you replaced the existing formats-gpl.jar that you found in your Fiji.app/jars/bio-formats folder with that one, then restarted Fiji and tried again?
Comment 4 hfang7 2014-05-13 13:38:59 CDT 
I think your patched version of formats-gpl.jar works, but I need change file name to exactly same with the old file. In this case "formats-gpl" doesn't work, "formats-gpl-5.0.1" works. Thank you very much!
Comment 5 Curtis Rueden 2014-05-13 15:00:13 CDT 
Great, glad to hear it is working for you! We will push a fix to Fiji as soon as it is merged into the main Bio-Formats codebase. (Probably within 1-2 weeks.)