Bug 992 – 16-bit sample images open as 8-bit

Bug 992 - 16-bit sample images open as 8-bit


Summary:	16-bit sample images open as 8-bit

Status:	RESOLVED WONTFIX

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2015-01-23 07:48 CST by norsimon
Modified:	2015-01-26 10:20 CST
CC List:	3 users (show)

See Also:

Description norsimon 2015-01-23 07:48:30 CST

File > open sample > M51 galaxy (16-bit)

Opens as an 8bit image, though it used to open as a 16-bit image (maybe 1 year ago)

Cheers,
Simon.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.10.1
  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-b14-466.1-11M4716
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-466.1
  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: CHECK_TURNED_OFF

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:20141109231443)
Fiji: http://fiji.sc/update/ (last check:20141119233103)

Files not up-to-date:
  c2c0efd7 (MODIFIED) 20150121175707 Contents/Info.plist
  d6d616c2 (LOCAL_ONLY) 20150121175430 plugins/Mosaic_ToolSuite.jar

Comment 1 Curtis Rueden 2015-01-23 08:08:13 CST

Can you please run Help > Update and test again with the latest version?

Comment 2 norsimon 2015-01-23 08:31:28 CST

Hi Curtis,

Thanks for rapid response!

I tried update (was hesitant on this since lately the newest versions simply haven't launched on my mac).
Same result: The built-in sample images open as 8bit (cached).

I checked /Applications/Fiji.app/samples/m51.zip.
This image is stored as 16bit and opens as such in Fiji after unzipping and drag&drop.


Simon.

Comment 3 Curtis Rueden 2015-01-23 11:08:19 CST

> was hesitant on this since lately the newest versions
> simply haven't launched on my mac

You can always make a copy of Fiji and try running & updating that; if it fails, then you'll still have the non-updated version, too.

> Same result: The built-in sample images open as 8bit (cached).

This was a known bug from a few months ago, which Mark Hiner fixed (we thought). Unfortunately, I cannot find any record of the problem or the fix in email archives, or Git commit histories. I also cannot reproduce this problem on my machine.

Please check whether "Use SCIFIO when opening files" option in Edit > Options > ImageJ2 is unchecked. Mark & I cannot recall the details of the bug-fix, so are not certain whether that is actually relevant (it might have been a bug somewhere else), but it's worth checking, just to be sure.

Comment 4 Mark Hiner 2015-01-24 05:49:04 CST

The only commit I could find on the matter is:
https://github.com/fiji/fiji-compat/commit/b3236a8c67edd9972f48731780935febdd46b49c

For debugging purposes, the relevant code in IJ 1.x is:
https://github.com/imagej/ImageJA/blob/0059c81b610ad184e85e612fc68614bc7f55cb94/src/main/java/ij/plugin/URLOpener.java

FWIW, I wasn't able to reproduce this problem - with and without SCIFIO enabled, whether the image is cached or not, M51 galaxy always opens as 16-bit for me.

Comment 5 norsimon 2015-01-26 08:19:02 CST

"Use SCIFIO when opening files" was turned off.
Turning it on opens the 16bit sample images as 8-bit - but shows them as empty (white) images.
This is true for "M51 Galaxy" and "CT" (both 16bit), but not "Gel" (8bit) which opens fine with SCIFIO.
"T1 Head" (16bit) doesn't open at all with SCIFIO.

Furthermore: 
Drag & drop of /Applications/Fiji.app/samples/m51.zip 
opens as correct 16bit image with SCIFIO turned off, 
and opens as all-white 8bit image with SCIFIO turned on.

So, obviously, Fiji can read and open a 16bit image correctly - only the File > Open Samples function seems to have some issues.
Not crucial, just disturbing, as this is (now, used to be)  part of our teaching examples for image processing using Fiji here at ETH.

Best,
Simon.

Comment 6 norsimon 2015-01-26 08:41:17 CST

In case it wasn't clear from the initial bug-report data: The problem was with a life-line version (Fiji Life-Line version, 2014 November 25).

The build from 2015-01-22 (765d87fca4) does not have this particular problem - so I switched to that, for now.

Comment 7 Mark Hiner 2015-01-26 10:20:39 CST

Thanks for following up, Simon.

>In case it wasn't clear from the initial bug-report data: The problem was with a
>life-line version (Fiji Life-Line version, 2014 November 25).

Unfortunately, though we can see the update timestamp, we currently have no way to tell it's a lifeline version automatically - and the usual appropriate instinct when seeing an "out-of-date" timestamp like that is just to suggest updating.

Updating definitely makes less sense for teaching environments. We can't "fix" the broken lifeline version but it's a good reason to cut a new lifeline version, and/or encourage development of features to help avoid these situations.