Bug 783 – Does not open some TIF images

Bug 783 - Does not open some TIF images


Summary:	Does not open some TIF images

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-06-12 12:21 CDT by Giorgio G.
Modified:	2014-06-16 08:31 CDT
CC List:	2 users (show)

See Also:

Attachments
Incriminated image (100 bytes, text/plain) 2014-06-12 13:58 CDT, Giorgio G.
Image working correctly (63 bytes, text/plain) 2014-06-12 14:00 CDT, Giorgio G.

Description Giorgio G. 2014-06-12 12:21:15 CDT

Sometimes it does not open images from a hard drive, that are correctly open in ImageJ 1.49b (Java 1.6.0_12 64bit; outside the Fiji package). It does not work either with drag and drop or with the open menu. It works with some images in the same durectory, though: traces produced by the NeuronJ plugin. These are bigger that the images that cannot be opened (4.12MB vs 1.37MB) and are RGB instead of 8bit. Both are TIF, same resolution (1388x1040px).
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\GG\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\GG\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140611123802)
Fiji: http://fiji.sc/update/ (last check:20140610170938)

Files not up-to-date:
  a866249a (LOCAL_ONLY) 20140205115208 plugins/Concentric_Circles.class
  f07dd15c (LOCAL_ONLY) 20140131170814 plugins/NeuronJ_.jar
  6d88799a (OBSOLETE_UNINSTALLED) 20140130082026 plugins/Script_Editor-2.0.0-SNAPSHOT.jar
  0dfa5070 (LOCAL_ONLY) 20140131170827 plugins/imagescience.jar

Comment 1 Giorgio G. 2014-06-12 12:27:00 CDT

The updater had already run and updated the program. Despite what the information attached here say, the updates is not installing any other update.

Comment 2 Mark Hiner 2014-06-12 13:47:38 CDT

Hi Giorgio,

Could you upload some of the offending images that do not open correctly, using Help > Upload Sample Image? Without a failing image to test with, we can't really investigate the problem.

>Despite what the information attached here say, the updates is not installing 
>any other update

The "Files not up-to-date" dialog is perhaps slightly misleading. What it is saying is "these are the files whose integrity I can not verify." The explanation for why they can't be verified is in the parentheses, and is important to understand.

The majority of "not up-to-date" files in your report are "LOCAL_ONLY", which means that they exist on your local machine but not on any of the update sites you have enabled (ImageJ and Fiji in this case). And because they are unknown, there would be no way for them to be updated.

LOCAL_ONLY files would only be a problem if they were interfering somehow with the classes that are distributed with Fiji/ImageJ... you don't actually have any "outdated" files in need of updating. As you do not have a lot of local changes, I think it is worth trying to reproduce the TIFF failures on our end.

Let me know when you upload your sample data, and I'll take a look. Thanks!
- Mark

Comment 3 Giorgio G. 2014-06-12 13:58:36 CDT

Created attachment 159
Incriminated image

Comment 4 Giorgio G. 2014-06-12 14:00:11 CDT

Created attachment 160
Image working correctly

Comment 5 Mark Hiner 2014-06-12 14:07:20 CDT

Hi Giorgio,

 Did you upload these from Fiji with Help > Upload Sample Image? Was the failing image "WT1_PC1_1 10x.tif"? Your attachments are just coming through as the text descriptions of the images.

Thanks,
Mark

Comment 6 Giorgio G. 2014-06-12 14:14:49 CDT

Correct the failing image is "WT1_PC1_1 10x.tif". It fails also if copied on the desktop.
I don't manage to upload it with that function: once I select the image on that menu it does not do anything specific.
If it is ok for you, I can send by email.

Comment 7 Mark Hiner 2014-06-12 14:17:39 CDT

Actually I received WT1_PC1_1 10x.tif! I guess there's no confirmation message.. but it gets sent to a private page on the fiji.sc wiki, only accessible by those with the appropriate permissions.

So no worries, I have the image and can test it.

Comment 8 Mark Hiner 2014-06-13 14:36:57 CDT

This is a problem with false color images being translated to IJ 1.x data structures improperly. It is fixed on our development branches and should be uploaded to Fiji soon.

See:
https://github.com/scifio/scifio/commit/46ab7cb2a8796f3b35ba31cbc101f9c370083e58

and
https://github.com/imagej/imagej-legacy/commit/f9935f867f41a110206f63d09999d93b221090cf

Comment 9 Giorgio G. 2014-06-13 14:49:08 CDT

Great, thanks a lot!

Comment 10 Mark Hiner 2014-06-16 08:31:46 CDT

These fixes are now uploaded to Fiji, and the test dataset I received is opening and looking good.

Thanks for the report Giorgio. Please let us know if you have any more problems!