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Bug 897 - Process Stack Option inverted for Custom FFT filter
Process Stack Option inverted for Custom FFT filter
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-12 10:40 CDT by Kris Sheets
Modified: 2015-04-06 14:27 CDT
3 users (show)

See Also:
Description Kris Sheets 2014-08-12 10:40:28 CDT 
When performing custom FFT filter with the process stack option checked, only the active slice is filtered. When the option is unchecked, the entire stack is processed.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140810052118)
Fiji: http://fiji.sc/update/ (last check:20140808110226)

Files not up-to-date:
  86979d76 (MODIFIED) 20140811140918 Contents/Info.plist
  e5852db5 (OBSOLETE_UNINSTALLED) 20140602022601 jars/jai_imageio-1.0.1.jar
  7ecaf631 (OBSOLETE_UNINSTALLED) 20140602022601 jars/jruby-complete-1.7.11.jar
  24d47d70 (OBSOLETE_UNINSTALLED) 20140602022601 jars/junit-4.8.1.jar
  94ff9125 (LOCAL_ONLY) 20131118013440 plugins/Mosaic_ToolSuite_old.jar
  6d88799a (OBSOLETE_UNINSTALLED) 20140602022601 plugins/Script_Editor-2.0.0-SNAPSHOT.jar
  8f3eef77 (LOCAL_ONLY) 20100126022120 plugins/droplet_finder.jar
Comment 1 Kris Sheets 2014-08-12 10:45:11 CDT 
On first run of Custom FFT filter, process entire stack is unchecked and performs only on active slice. Repeating command with process entire stack checked still only affects active slice. A third repeat of the custom fft filter with the process entire stack unchecked performs the filter operation on the entire stack.
Comment 2 Mark Hiner 2014-08-18 14:27:41 CDT 
Hi Kris,

 Is "Edit > Options > ImageJ2 > Use SCIFIO when opening files" checked? If so, try unchecking it. There is a known bug where image stacks are not fully processed with SCIFIO.

Let us know if that doesn't work around the issue.

Thanks for the report!