NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 111 - Not able to save virtual stack as *.img file
Not able to save virtual stack as *.img file
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: ImageJ1
unspecified
PC Linux
: P2 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2009-11-30 23:07 CST by Kannan U V
Modified: 2009-12-07 17:36 CST
1 user (show)

See Also:

Description Kannan U V 2009-11-30 23:07:10 CST
ImageWriter: fi.pixels==null. I use plugins->registration->register virtual stack slices and create a virtual stack. When I try saving it, I get a error dialog. FileSaver. An error occured writing the file.
Comment 1 Johannes Schindelin 2009-12-01 09:50:35 CST
Please specify what menu entry (or what plugin) you used to try to save a .img file.
Comment 2 Stephan Saalfeld 2009-12-01 10:04:18 CST
It's easy to reproduce:

Open an arbitrary sequence of images as a virtual stack, then `Save As->Analyze'.

Bang!

It seems that the Analyze_Writer tries to directly access the pixels array which, in a virtual stack, is empty.

I do not know how trivial it is to fix that.  For now, the only possible workaround to get a .img saved is from a non-virtual stack.
Comment 3 Wayne Rasband 2009-12-07 17:36:09 CST
The bugs that prevented saving virtual stacks in Analyze (.img) format are are fixed in the updated Analyze Reader/Writer plugin at

   http://rsb.info.nih.gov/ij/plugins/analyze.html

and in ImageJ 1.43m. ImageJ 1.43m also allows virtual stack to be saved as TIFF stacks, as "Raw Data", and to be saved using the FileSaver.saveAsRawStack() method.