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Bug 674 - TransformJ rotate uses incorrect voxel size
TransformJ rotate uses incorrect voxel size
Status: RESOLVED MOVED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-11-07 07:08 CST by laurent.holtzer
Modified: 2014-11-21 12:06 CST
2 users (show)

See Also:
Description laurent.holtzer 2013-11-07 07:08:00 CST 
This is a follow-up on my post to the imagej mailinglist, since I believe it is a real bug in FIJI. 

When using TransformJ rotate on a stack which has non-cubical voxels (in my case the distance between planes in z is more than 5x the pixel length in x or y) the plugin assumes that voxels are cubical, so x, y, and z size are the same.

This can be reproduced using for example the 'first-instar-brain.tif' sample shipped with FIJI. When I run TransformJ rotate on this file and set a rotation around y of 90 degrees, the voxel size remains unchanged and FIJI reports a width of 29.96 microns for the images in the stack. Since the original stack is composed of 56 planes with 2 micron inbetween them, this can not be true. TransformJ Turn does it correctly, and after turning the stack 90 degrees in y FIJI reports a width of 112 microns, and also a correct voxel size.

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: PROTECTED_LOCATION

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\PROGRA~1\Fiji.app\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => C:\PROGRA~1\Fiji.app\Fiji.app

Information about the version of each plugin:

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Comment 1 Curtis Rueden 2014-06-16 15:11:57 CDT 
This is a bug in TransformJ, which is maintained by its author, Erik Meijering. Your best bet might be to email him directly:

 http://www.imagescience.org/meijering/address/

In the meantime, I am migrating this issue to Fiji's TransformJ issue tracker at:

 https://github.com/fiji/TransformJ/issues/1

But the Fiji team probably won't have time to address the issue any time soon, unfortunately. If you have programming experience, you are more than welcome to look at the source and submit a pull request (https://help.github.com/articles/using-pull-requests) to attempt to fix the problem yourself.
Comment 2 Curtis Rueden 2014-11-21 12:06:18 CST 
For any who stumble across this issue: Erik wrote a nice reply on the GitHub issue thread, which I reproduce here:

> This is not a bug but a "feature" (although perhaps an inconvenient
> one). The TransformJ Rotate plugin simply assumes that voxels are
> isotropic. If they are not, one can use the TransformJ Affine plugin,
> which also allows scaling at the same time, to get a correctly rotated
> volume with isotropic voxels. In a future release I will try to deal
> with nonisotropic voxels in the TransformJ Rotate plugin.