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Bug 625 - Differences in fill holes behavior under windows and mac
Differences in fill holes behavior under windows and mac
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-06-27 10:18 CDT by Antonio
Modified: 2013-06-28 12:38 CDT
2 users (show)

See Also:


Attachments
Example mask (2.71 KB, image/gif)
2013-06-27 10:22 CDT, Antonio

Description Antonio 2013-06-27 10:18:00 CDT
Using Fiji on a mac or windows (same version updated at the same time,  IJ 1.4tu) I get different results when I apply fill holes to a binary image.

The starting image is a binary mask with non-connected blobs (8 bit tif, value = 255) on 0 background.
Under mac/windows the image open as white blobs on black. The correct behavior after  Process-> Binary -> Fill Holes should be no changes in the image.

windows: Fill holes -> no changes, correct result
Mac: Fill holes -> all blobs in the middle of the image are filled. Only blobs at the boundary remain. However, if you invert the LUT then one obtain the same result as with windows.

May be you are aware of this problem

Thanks

Antonio

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.8.4
  java.version => 1.6.0_51
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_51-b11-457-11M4509
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.51-b01-457
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji.app

Information about the version of each plugin:

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Comment 1 Antonio 2013-06-27 10:22:32 CDT
Created attachment 105
Example mask
Comment 2 Curtis Rueden 2013-06-27 10:34:01 CDT
From Gabriel Landini on fiji-devel:
> I bet that you have set differently the background in the
> Process>Binary>Options
> 
> There is no way for a program to know what you think is foreground or
> background. The issue gets more confusing if you use an inverted look
> up table.
> 
> So, it is the user responsibility to know what kind of pixel value is
> being processed and set this in Process>Binary>Options.
> 
> Let us know if that is not the issue
Comment 3 Curtis Rueden 2013-06-28 12:38:09 CDT
And Antonio's reply:
> it was not a bug a the end and I now learned something more about
> Fiji. I was not aware of different settings of fresh installed fiji on
> a mac and windows.

I definitely agree that finding the solution in Process > Binary > Options is highly unintuitive. Perhaps in ImageJ2 we can incorporate that flag into the binary processing commands themselves, to make it more obvious. But for ImageJ1/Fiji, it is how it is...