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Bug 1040 - Metadata collection interfering with opening virtual stack
Metadata collection interfering with opening virtual stack
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-03-30 12:04 CDT by Erin Cram
Modified: 2015-03-30 13:18 CDT
2 users (show)

See Also:

Attachments
Screen grab of the error messages (39.29 KB, image/png)
2015-03-30 12:06 CDT, Erin Cram
Another screen grab of error messages (74.21 KB, image/png)
2015-03-30 12:06 CDT, Erin Cram

Description Erin Cram 2015-03-30 12:04:47 CDT 
Mac 0S 10.9.5 - newest update of Fiji -now I can't make virtual stacks.  
I attempt to a open folder of tifs as a virtual stack by dragging the folder to the >> symbol, or by using File>Import>Image Sequence. 
An error is generated for EACH tif as Fiji attempts to extract metadata. 
Fiji Warning "Expected positive value...; got 0.0" generated on each frame. See uploaded screen grabs.
This is preventing me from making the stack in a finite amount of time. 
I have uploaded two screen grabs of the console windows.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.5
  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:20150328005348)
Fiji: http://fiji.sc/update/ (last check:20150324232333)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20140504174929 jars/jpedalSTD.jar
Comment 1 Erin Cram 2015-03-30 12:06:03 CDT 
Created attachment 246
Screen grab of the error messages
Comment 2 Erin Cram 2015-03-30 12:06:37 CDT 
Created attachment 247
Another screen grab of error messages
Comment 3 Mark Hiner 2015-03-30 13:12:26 CDT 
Hi Erin,

 Can you take a look at "Edit > Options > ImageJ2"?

 If "Use SCIFIO when opening files" is checked, uncheck it and try opening your files again.

 Do you remember ever setting this option in the past?

Sorry for any inconvenience. Thanks for the helpful report and screenshots.
Comment 4 Erin Cram 2015-03-30 13:18:51 CDT 
The SCIFIO box was checked!  When I unchecked it, the virtual stack opened and displayed without generating any error messages!  Yay!