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Bug 441 - ROI Manager Option Change
ROI Manager Option Change
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: Wayne Rasband
Depends on:
Blocks:
 
Reported: 2012-06-23 11:48 CDT by Davide
Modified: 2013-07-07 09:50 CDT
2 users (show)

See Also:
Description Davide 2012-06-23 11:48:00 CDT 
Dear Fiji-Developers,
     I am not sure whether this classifies as bug but in my view it does create un unwanted behaviour by FIJI. I recently discovered a change in the behaviour of the ROI manager of Fiji, namely that ROI events are by default not any more registered with the slice information. By investigating the cause I discovered that the ROI Manager>Option panel was changed significantly. While in previous versions it stated as option: 
associate "Show All" ROIs with the stack slices (as also discribed by the help section (http://imagej.nih.gov/ij/docs/menus/analyze.html#manager)
now it was changed to: Associate ROIs with Stack positions

The change has so far caused quite some trouble to me, first  wasting working time not realizing that the stacks were not registered  anymore and second I could not find an option that would allow to overlay of all the point marks regardless of the stack slice property.

I hope the old option can be restored or at least an alternative option to have the same viewing as in the old editions.

With best regards,
Davide

P.s. I am quite sure that the change came with the new update of Fiji, I apologise for not being able to give the specific detail. Currently I am running the latest version which does have the changed option.

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: You wanted never to be reminded.

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\DAVIDH~1\DOCUME~1\Uni\2012-S~3\programs\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24/jre/
  ij.dir => C:\Users\DAVIDH~1\DOCUME~1\Uni\2012-S~3\programs\FIJI-W~1\Fiji.app

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Comment 1 Johannes Schindelin 2012-06-23 16:00:58 CDT 
Indeed, the information Fiji assembled includes:

e1dd0fb41b87b6021cad9af473593f3009e9e051 20120623111436 jars/ij.jar

which means that you have ImageJ 1.46q now.

Wayne?
Comment 2 Wayne Rasband 2012-06-23 16:52:07 CDT 
This regression should be fixed in the ImageJ 1.46r3 daily build. You can upgrade by using the Help>Update ImageJ command and selecting "daily build" from the drop down menu.

-wayne
Comment 3 Davide 2012-06-25 10:12:38 CDT 
Dear Wayne and Johannes, 
  thanks a lot for the fast help. The daily build fixed my problem. I'll be back on the stable version when 1.46r is released right?

Thanks,
Davide
Comment 4 Wayne Rasband 2012-06-25 14:59:24 CDT 
This fix will be back in the stable version when 1.46r is released in a few days.

-wayne
Comment 5 Davide 2012-07-04 18:50:24 CDT 
Dear Wayne,
  while the option "Associate 'Show All' ROIs with Slices" returned as mentioned in 1.46r, I just noticed that by default Fiji/ImageJ does still not register the stack information. Is this behaviour a desired feature? Moreover it seems not possible to register the slice information while maintaining the upper option off. On the contrary ImageJ 1.46a on my Ubuntu 12.04 machine works as I would expect: slice registration by default both with and without the option in question.

Many thanks,
Davide
Comment 6 Wayne Rasband 2012-07-05 04:04:35 CDT 
This regression should be fixed in the ImageJ 1.47c daily build. The RoiManager.getLabel() method was incorrectly setting the first part of the ROI label to "0000-" if "Associate 'Show All' ROIs with Slices" was not enabled.

-wayne