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Bug 767 - zvi files open corrupted
zvi files open corrupted
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-09 20:56 CDT by SuzeH
Modified: 2014-06-12 16:08 CDT
3 users (show)

See Also:
Description SuzeH 2014-06-09 20:56:59 CDT 
Opened z-stack zvi files in multichannels are corrupt.  I'm getting huge black lines running across part of the image, but also instead of one image am getting a checkerboard of four images (all the same) in the one window.  Switching channels isn't changing anything but the colour, and running through the z-stack appears in a random order, the picture focus jumps around, not smooth like a properly assembled z-stack.  I've tried multiple different files and this happens to all.
I updated FIJI last week and when I tried to open it this morning it failed everytime.  I removed it and reinstalled and everything is up to date but now this is happening.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  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-b14-462-10M4609
  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/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140610070633)
Fiji: http://fiji.sc/update/ (last check:20140608110306)

Files not up-to-date:
  18337fb7 (MODIFIED) 20140610112002 jars/ij-1.49b.jar
  a866249a (LOCAL_ONLY) 20140610105735 plugins/Concentric_Circles.class
Comment 1 Mark Hiner 2014-06-11 14:29:27 CDT 
Hi SuzeH,

 I just wanted to let you know that I'm in the middle of debugging this problem. We've been reworking how color images are translated between ImageJ2 and ImageJ 1.x data structures, so there are still a few bugs to work out.

First of all, the pixel type was erroneously always set to byte type... so any non-8bit dataset with 2-7 channels would open incorrectly. That's fixed but not uploaded yet (https://github.com/imagej/imagej-legacy/commit/35dd86034673b556bcf54d3cd10d54850e010e0e).

Then it looks like color lookup tables are not being preserved properly up to the final ImagePlus that's displayed. That's about 75% fixed.

The last piece will be determining why all the channels are compressed to a horizontal strip.. which I'm looking into right now.

Thank you very much for taking the time to report this issue, as it touches on many fundamental areas beyond just ZVI support.
Comment 2 Mark Hiner 2014-06-12 07:53:11 CDT 
I think this was closed by mistake.. this issue is not quite fixed for me.
Comment 3 Mark Hiner 2014-06-12 16:08:58 CDT 
This should be fixed if you update your Fiji. We should have significantly improved handling of:

* non-8-bit composite images
* composite/RGB images in general
* >5D images and images with non-traditional (XYZCT) axes

All my test datasets that were broken similarly to yours are now opening correctly. If your data still has issues, please re-open this issue (or open a new one, if the problem is significantly different) and upload your data with Help > Upload Sample Image.

Thank you again for reporting this problem! Its resolution has made ImageJ2 and its components significantly improved.
- Mark