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Bug 502 - Exception opening a tif image
Exception opening a tif image
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Linux
: P3 blocker
Assigned To: Melissa Linkert
Depends on:
Blocks:
 
Reported: 2012-09-26 16:52 CDT by Jean-Marc Verbavatz
Modified: 2013-07-07 09:25 CDT
2 users (show)

See Also:
Description Jean-Marc Verbavatz 2012-09-26 16:52:45 CDT 
I get the following exception when trying to open a 160MB 16-bit tif file, originally produced by Amira:

java.lang.NegativeArraySizeException
	at ij.io.ByteVector.doubleCapacity(ImageReader.java:1022)
	at ij.io.ByteVector.add(ImageReader.java:1015)
	at ij.io.ImageReader.lzwUncompress(ImageReader.java:917)
	at ij.io.ImageReader.uncompress(ImageReader.java:855)
	at ij.io.ImageReader.readCompressed16bitImage(ImageReader.java:170)
	at ij.io.ImageReader.read16bitImage(ImageReader.java:103)
	at ij.io.ImageReader.readPixels(ImageReader.java:758)
	at ij.io.FileOpener.readPixels(FileOpener.java:532)
	at ij.io.FileOpener.open(FileOpener.java:77)
	at ij.io.Opener.openTiff2(Opener.java:894)
	at ij.io.Opener.openTiff(Opener.java:728)
	at ij.io.Opener.openImage(Opener.java:245)
	at ij.io.Opener.openImage(Opener.java:309)
	at ij.io.Opener.open(Opener.java:138)
	at ij.io.Opener.openAndAddToRecent(Opener.java:224)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:662)

If necessary i can provide the tif file in question. But given the size of the file i'll wait for you to ask for it.

Any idea ?

Thanks,

Jean-Marc Verbavatz

Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => amd64
  os.name => Linux
  os.version => 2.6.32-43-generic
  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.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: You wanted never to be reminded.

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /usr/local/Fiji.app/java/linux-amd64/jdk1.6.0_24/jre/
  ij.dir => /usr/local/Fiji.app

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Comment 1 Melissa Linkert 2012-09-26 17:43:28 CDT 
That error is coming from ImageJ's internal TIFF reader, not Bio-Formats.

Could you please try opening the file using "Plugins > LOCI > Bio-Formats Importer" and see if that works?
Comment 2 Jean-Marc Verbavatz 2012-09-26 17:57:22 CDT 
Yes, it works with the bioformats importer ("Plugins > LOCI > Bio-Formats Importer").

So you're right, the error is coming from ImageJ's internal TIFF reader, not Bio-Formats.

I can live with that, but isn't that something that would need to be addressed anyway ?
Comment 3 Johannes Schindelin 2013-07-07 09:25:09 CDT 
Apparently, IJ1 will stay unchanged. Please use Bio-Formats or SCIFIO.