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Bug 779 - SCIFIO does not restore saved LUTs and display min/max metadata
SCIFIO does not restore saved LUTs and display min/max metadata
Status: ASSIGNED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: Mark Hiner
Depends on:
Blocks:
 
Reported: 2014-06-12 10:28 CDT by soyer.magali
Modified: 2014-06-23 16:50 CDT
3 users (show)

See Also:
Description soyer.magali 2014-06-12 10:28:52 CDT 
Hi,
I'm trying to save stacks composed of 2 channels (C1 grey, C2 green), 16-bit, in TIFF format.
It doesn't keep the LUTs or Brightness/Contrast infos.
I updated IJ2 today.
Thanks

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Magali\DOCUME~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Magali\DOCUME~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140611183802)
Fiji: http://fiji.sc/update/ (last check:20140610230938)

Files not up-to-date:
  b2afde18 (LOCAL_ONLY) 20140612154616 plugins/Analyze/3D_Blob_Segmentation-2.0.0-SNAPSHOT.jar
Comment 1 Curtis Rueden 2014-06-12 12:32:19 CDT 
I am guessing it *does* keep the LUTs and B/C values, but that when reopening they are ignored by SCIFIO. Can you please try Edit > Options > ImageJ2 and disable SCIFIO, then try opening your saved TIFF again? If that looks correct, then it is a bug in the SCIFIO opener. And if it is still incorrect, it is a bug with saving. Please let us know which. Thanks!
Comment 2 soyer.magali 2014-06-12 12:50:40 CDT 
Thanks Curtis, it was a bug in the SCIFIO openener.
Comment 3 Curtis Rueden 2014-06-12 12:52:39 CDT 
Thanks, I have changed the title of the bug to reflect the actual problem, and we'll pursue a fix. It might be a few days though, so in the meantime, I suggest keeping the SCIFIO opener disabled if you need to read back LUTs or min/max ranges, or ROIs for that matter.
Comment 4 Curtis Rueden 2014-06-23 16:50:37 CDT 
Just wanted to follow up saying that this one may be awhile longer before we can fix. Keeping SCIFIO disabled is still the workaround for now.

Assigning to Mark. But note that he is on vacation for the next couple of weeks, and has a lot on his plate to boot. However, this is important to get working, so I hope we can tackle it before the end of the summer.