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Bug 408 - Manual Tracking on 3D image doesn't increase Z
Manual Tracking on 3D image doesn't increase Z
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2012-02-29 09:59 CST by Tom Kazimiers
Modified: 2012-05-03 22:54 CDT
1 user (show)

See Also:
Description Tom Kazimiers 2012-02-29 09:59:15 CST 
Hi,

it seems some changes have been made to the Manual Tracking plugin in recent time (possibly due to this bug: http://fiji.sc/cgi-bin/bugzilla/﷒0﷓). Since a recent update the Manual Tracking plugin doesn't work for me anymore like I was expecting it:

What it should do: When opening a 3D image and the Manual Tracking plugin, I click on "Add track". When clicking in the image, Z should automatically be increased when entering new points.

What the problem is: When clicking "Add track" I can add a point, but Z doesn't increase. In fact, when I change it manually, I can't continue tha track -- I have to click on "Add track" again on the new slice.

How to reproduce: With an up-to-date Fiji version run this macro to start the plugin on a Z stack:
---------------------------
run("Bat Cochlea Volume (19K)");
run("Manual Tracking");
---------------------------
Next click "Add track" and add different points.

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

  os.arch => amd64
  os.name => Linux
  os.version => 3.2.5-1-ARCH
  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: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/tom/dev/fiji/java/linux-amd64/jdk1.6.0_24/jre
  ij.dir => null

Information about the version of each plugin:

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Comment 1 Jan Eglinger 2012-02-29 15:00:33 CST 
The recent fix by Johannes ( http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=commitdiff;h=1ec64fb ) made the plugin work with Hyperstacks, but lets it fail with z-stacks that don't contain multiple t frames.

You can work around this by converting your stack to a hyperstack with your z slices moved to the t dimension:

(In reply to comment #0)
> ---------------------------
> run("Bat Cochlea Volume (19K)");

// Convert to t-stack
run("Stack to Hyperstack...", "order=xyczt(default) channels=1 slices=1 frames=114");

> run("Manual Tracking");
> ---------------------------

Maybe there should be an option in the plugin to choose if you want to track t or z dimension.

Jan
Comment 2 Johannes Schindelin 2012-04-20 23:14:32 CDT 
Tom, since you are quite able to program yourself and since you already have a clone of fiji.git, why don't you just add the code that tests whether image.getNSlices() > 1 && image.getNFrames() == 1 and adjusts that automatically?

This would be a nice contribution in the Open Source spirit!
Comment 3 Tom Kazimiers 2012-04-21 10:56:56 CDT 
Alright, I'll have a look at it in the upcoming week.
Comment 4 Tom Kazimiers 2012-05-03 14:06:14 CDT 
I just pushed a change to contrib (32e07d3d):

    Manual Tracking: re-add support for tracking in Z
    
    By default, the tracking is done in the time dimenension. However,
    if the image has only a single frame and more than one z slice, the
    plugin will do the tracking in the z dimension. To reduce the
    introduction of complexity, the access to information about the
    tracking dimension (current position, maximum) is factored out in
    separate methods.

For now I did not add a choice for the user, but let the plugin decide (condition like suggested by Johannes). If wanted I can add the choice for the user as well. I just didn't add it because the user interface is already full of options and I didn't know if it was needed.
Comment 5 Johannes Schindelin 2012-05-03 22:54:09 CDT 
I reviewed your change, pushed and uploaded it. In the future, please wait with marking an issue as resolved when it has been resolved only on the developers' side but not on the users' side.

Thanks!