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Bug 699 - Kendall Tau Coloc 2 Error
Kendall Tau Coloc 2 Error
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-01-28 19:17 CST by Ginger Pocock
Modified: 2014-06-17 15:34 CDT
3 users (show)

See Also:

Attachments
Temporary version of Coloc 2 (hopefully fixing the reported issue) (125.00 KB, application/octet-stream)
2014-01-29 13:56 CST, Johannes Schindelin

Description Ginger Pocock 2014-01-28 19:17:09 CST 
(Fiji Is Just) ImageJ 1.48p; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 79MB of 5903MB (1%)
 
java.lang.ArrayIndexOutOfBoundsException: -256
	at net.imglib2.img.basictypeaccess.array.LongArray.getValue(LongArray.java:66)
	at net.imglib2.type.numeric.integer.LongType.get(LongType.java:107)
	at net.imglib2.type.numeric.integer.LongType.getIntegerLong(LongType.java:113)
	at algorithms.Histogram2D.generateHistogramData(Histogram2D.java:207)
	at algorithms.Histogram2D.execute(Histogram2D.java:169)
	at Coloc_2.colocalise(Coloc_2.java:439)
	at Coloc_2.run(Coloc_2.java:156)
	at ij.IJ.runUserPlugIn(IJ.java:196)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)

Information about your version of Java:

  os.arch => amd64
  os.name => Windows NT (unknown)
  os.version => 6.2
  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: C:\PROGRA~2\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => C:\PROGRA~2\Fiji.app

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2014-01-29 13:56:47 CST 
Created attachment 130
Temporary version of Coloc 2 (hopefully fixing the reported issue)
Comment 2 Johannes Schindelin 2014-01-29 13:57:37 CST 
Hi Ginger,

thank you for providing the example images and the stack trace. It was important to provide the stack trace, too, so I could verify that the problem I encountered was actually exactly the same as you reported.

It turns out that the bug is not in the Kendall Tau calculation but in the 2d histogram code. Which is really bad: it is a core part of Coloc 2 and has not been reported yet, which makes me wonder how many people *actually* use Coloc 2.

In any case, I fixed this issue in the version I attached (at least for me, it does not encounter the problem any longer).

Could you please test? Thank you!
Comment 3 Johannes Schindelin 2014-01-29 14:43:05 CST 
On Wed, 29 Jan 2014, Pocock, Ginger wrote:

> Hi Johannes,
> 
> Thank you for looking at this. I will test this later on this afternoon first chance I get.
> 
> Ginger
Comment 4 Curtis Rueden 2014-06-16 15:22:51 CDT 
Johannes, has this fix been uploaded? If so, can we close this bug?
Comment 5 Johannes Schindelin 2014-06-17 15:34:38 CDT 
It was uploaded, but just to make certain, I just uploaded yet another version (including a bug fix by Tom Kazimiers who was not completely swallowed by a certain black hole yet).