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Bug 848 - cannot open TIF files with or without updates
cannot open TIF files with or without updates
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: Mark Hiner
Depends on:
Blocks:
 
Reported: 2014-07-09 16:04 CDT by jcoleman
Modified: 2014-09-04 14:41 CDT
4 users (show)

See Also:

Attachments
tif file stack (77 bytes, text/plain)
2014-07-29 15:01 CDT, jcoleman

Description jcoleman 2014-07-09 16:04:10 CDT 
With or without updates on July 9 2014 on MacOS Mevericks or Win 7 Enterprise, I get this exception when importing TIF files or trying to open them.  JPG and PNG works.  I tried re-installing appropriate up to date versions of Fiji to no avail. will try emergency back versions.

(Fiji Is Just) ImageJ 2.0.0-rc-8/1.49c; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.4; 21MB of 3991MB (<1%)
 
java.lang.IllegalArgumentException: Not a linear axis: null
	at io.scif.util.FormatTools.calibrate(FormatTools.java:257)
	at io.scif.ome.formats.OMETIFFFormat$Metadata.populateImageMetadata(OMETIFFFormat.java:385)
	at io.scif.AbstractParser.parse(AbstractParser.java:254)
	at io.scif.ome.formats.OMETIFFFormat$Parser.parse(OMETIFFFormat.java:603)
	at io.scif.ome.formats.OMETIFFFormat$Parser.parse(OMETIFFFormat.java:546)
	at io.scif.AbstractParser.parse(AbstractParser.java:335)
	at io.scif.AbstractParser.parse(AbstractParser.java:52)
	at io.scif.AbstractReader.setSource(AbstractReader.java:270)
	at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
	at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
	at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
	at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:420)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:153)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  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-b14-462-11M4609
  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.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140702194308)
Fiji: http://fiji.sc/update/ (last check:20140702124334)

Files not up-to-date:
  d015a2f7 (MODIFIED) 20140706222639 Contents/Info.plist
  5646e99c (LOCAL_ONLY) 20140221060934 plugins/Alpha_Channel.class
Comment 1 jcoleman 2014-07-09 16:20:51 CDT 
Older "life-line" version of FIJI does open TIF files (and imports tif stacks) on Windows 7.  So not sure what happened with the updates on 7-9-14.
Comment 2 Mark Hiner 2014-07-14 13:54:04 CDT 
Thanks for reporting this issue!

Could you please upload your .tif dataset that's not opening via Help>Upload Sample Image? All of the sample .tif datasets I have access to are opening correctly.

This is probably related to the ImageJ2/SCIFIO update.. you can temporarily disable this by running the Edit>Options>ImageJ2 plugin and unchecking the SCIFIO option.

Let us know if that doesn't help. Once I have the sample image I can work on a fix on the SCIFIO side as well.
Comment 3 jcoleman 2014-07-29 15:01:35 CDT 
Created attachment 187
tif file stack

this is an example file that would not open on windows or mac under bug 848.
Comment 4 jcoleman 2014-09-04 12:26:10 CDT 
I think the problem has been solved by the suggestion from Mark Hiner:

"This is probably related to the ImageJ2/SCIFIO update.. you can temporarily disable this by running the Edit>Options>ImageJ2 plugin and unchecking the SCIFIO option."

I use several machines that have generated this error, and the last couple (windows or mac)  of times I ran into this issue with subsequent updates, I just turned the ImageJ2 plugin off and all worked fine (although still throws up an results-with-error window sometimes).  So I think it's ImageJ2-related and good to go until that gets fixed.
Comment 5 Mark Hiner 2014-09-04 14:41:21 CDT 
thanks for the feedback, glad you were able to use the work-around.

Tracking for the SCIFIO side of this issue can be found at: https://github.com/scifio/scifio/issues/221