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Bug 406 - Manual Tracking when using 4D data increments z not t when you pick a point
Manual Tracking when using 4D data increments z not t when you pick a point
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2012-02-22 14:59 CST by Sherry Clendenon
Modified: 2012-02-23 19:34 CST
1 user (show)

See Also:
Description Sherry Clendenon 2012-02-22 14:59:42 CST 
[Enter details of the problem or bug and how to reproduce it here.]

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

  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: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Jeff\Desktop\Fiji.app/java/win64/jdk1.6.0_24/jre
  ij.dir => C:\Users\Jeff\Desktop\Fiji.app

Information about the version of each plugin:

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Comment 1 Sherry Clendenon 2012-02-22 15:07:48 CST 
The result of this is that instead of just picking my next point, I have to manually go back one step in z and increment t, then from there choose my next point in x,y,z. This makes tracking in 4D take much more concentration and much more time and makes the whole process much more error prone.
Comment 2 Johannes Schindelin 2012-02-22 19:05:33 CST 
I understand your frustration at this bug.

But please understand my frustration at having to guess how to reproduce the bug. And understand the frustration when I fail to reproduce the issue, wasting precious hours of my time and and not exactly helping my motivation to help resolve the issue at all.

So: please replace this line in your report:

[Enter details of the problem or bug and how to reproduce it here.]

by a detailed explanation how to encounter the bug.
Comment 3 Sherry Clendenon 2012-02-22 22:31:53 CST 
My workflow. 

File, Import, Image Sequence
	Image sequence has this naming convention: prefixC###Z###T###.tif
		Images are 3D time lapse in one color from Olympus FV1000
		Generally have 5000 to 7500  images, 512x512 pixels, 12 bit. 
File, Save As, Tif
Plugins, Image 5D, Stack to Image 5D
	Choose z and t as 3rd and 4th dimensions
	When 5D window opens, z-slider is above t-slider
	Scroll through z then t to see that images have sorted correctly
Plugins, Tracking, Manual Tracking
	In tracking window, set parameters, Time Interval 15 min, x/y 1.24 micron, z 1.24 micron
	In tracking window
		Add Track
	Move z slider at bottom of 5D image to appropriate plane.
	Click on image to pick point
	After that click to pick point, Z-slider INCREMENTS ONE STEP, t-slider DOES NOT

What it should do after picking a point:
Z-slider should NOT increment
 t-slider SHOULD increment one step.

Plugin works correctly for 2D time lapse. When working with 2D time lapse data, t- increments after each point is picked. 
Plugin increments incorrectly when working with 3D time lapse data.
Comment 4 Johannes Schindelin 2012-02-23 12:22:51 CST 
The crucial tidbit of information was that the data were converted to Image5D.

Since I do not have access to any of your data, I used the Mitosis sample from the File>Open Samples menu, and happily, I could reproduce the problem now, without spending another hour.

Since I needed to have a quick way to reproduce, I recorded this macro (tip for the future: such a recorded macro saves me even more time, making it much more likely that I can squeeze a bug fix into my work schedule):

-- snip --
run("Mitosis (26MB, 5D stack)");
run("Stack to Image5D", "3rd=ch 4th=z 3rd_dimension_size=2 4th_dimension_size=5 assign");
run("Manual Tracking");
-- snap --

After that, I had to spend another hour fighting with the incompatibilities in ImageJ1 with regards to Image5D, but I think I managed to beat it into submission.

I uploaded a new version, please call Help>Update Fiji, restart, and test.

Thank you.
Comment 5 Curtis Rueden 2012-02-23 18:42:22 CST 
Dscho, if there are any changes that would be helpful in Image5D to address these sorts of issues, let me know, since we are maintaining that plugin as well now.
Comment 6 Johannes Schindelin 2012-02-23 19:34:03 CST 
The problem is the incompatible API ImageJ added after Image5D. Image5D's getCurrentSlice() *predates* ImagePlus'. And its meaning is more in line with the getCurrentChannel() and getCurrentFrame(). But then in ImageJ it was decided to use getChannel() and getSlice() and getFrame() instead and let getCurrentSlice() return the *stack index*.

So: no matter what, if we change something in Image5D, we break it, if we leave it, we leave it broken. Catch 666.