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Bug 1034 - Error when opening TIFF files
Error when opening TIFF files
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Windows
: P4 normal
Assigned To: Mark Hiner
Depends on:
Blocks:
 
Reported: 2015-03-23 10:21 CDT by johnnyh.2007
Modified: 2015-03-24 10:16 CDT
4 users (show)

See Also:
Description johnnyh.2007 2015-03-23 10:21:45 CDT 
With the most recent update of FIJI/ImageJ, I cannot open TIFF files either by drag and drop or by File>Open...
This is the error message I receive: 

(Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 38MB of 55000MB (<1%)
 
java.lang.NoClassDefFoundError: Could not initialize class loci.formats.gui.LegacyQTTools
	at loci.formats.in.PictReader.<init>(PictReader.java:103)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at loci.formats.ImageReader.<init>(ImageReader.java:126)
	at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:79)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at loci.formats.ImageReader.<init>(ImageReader.java:126)
	at io.scif.bf.BioFormatsFormat.createImageReader(BioFormatsFormat.java:137)
	at io.scif.bf.BioFormatsFormat.getCachedImageReader(BioFormatsFormat.java:147)
	at io.scif.bf.BioFormatsFormat.getCachedImageReader(BioFormatsFormat.java:524)
	at io.scif.bf.BioFormatsFormat.access$100(BioFormatsFormat.java:81)
	at io.scif.bf.BioFormatsFormat$Checker.isFormat(BioFormatsFormat.java:361)
	at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:331)
	at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:310)
	at io.scif.services.DefaultDatasetIOService.canOpen(DefaultDatasetIOService.java:81)
	at io.scif.io.DatasetIOPlugin.supportsOpen(DatasetIOPlugin.java:65)
	at org.scijava.io.DefaultIOService.getOpener(DefaultIOService.java:66)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:130)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:329)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:152)
	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:662)

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\HEDDLE~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\HEDDLE~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150319131059)
Fiji: http://fiji.sc/update/ (last check:20150319162456)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20141208025245)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141221100506)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150320212719)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214074119)

Files not up-to-date:
  b0038cbf (MODIFIED) 20150323111603 jars/ij-1.49p.jar
  1ad3be0d (LOCAL_ONLY) 20140627205826 jars/jpedalSTD.jar
  1c12f9db (LOCAL_ONLY) 20140825171504 macros/deskew.ijm
  4da741fc (LOCAL_ONLY) 20140502134400 plugins/ColorSegmentation_.jar
  55f1c5c5 (LOCAL_ONLY) 20140502134411 plugins/Hypervolume_Shuffler.class
  a75d3b5e (LOCAL_ONLY) 20140502134407 plugins/Shape_Descriptor1u.class
  c272aa4d (LOCAL_ONLY) 20140502134349 plugins/SpotTrackerX2D_.jar
  5f60d96e (LOCAL_ONLY) 20140502134342 plugins/Watershed_.jar
  f4dea927 (LOCAL_ONLY) 20150108101051 plugins/deskew.ijm
Comment 1 Mark Hiner 2015-03-23 11:21:25 CDT 
Hello,

 Unfortunately, the Bio-Formats update site contains Bio-Formats 5.1.x which is incompatible with SCIFIO.

You can work around the issue by either:

a) Disabling the Bio-Formats update site[1]
or
b) Disable SCIFIO[2]


[1] http://imagej.net/How_to_follow_a_3rd_party_update_site
[2] http://imagej.net/SCIFIO
Comment 2 Mark Hiner 2015-03-23 11:24:06 CDT 
Curtis - what's your preference for updating the Bio-Formats-Fiji job[1] to upload the 5.1-modified dependencies? Maybe just have jenkins manually replace them for now? Otherwise they're getting blown away when the update job runs.


[1] http://jenkins.imagej.net/job/Bio-Formats-Fiji/
Comment 3 Curtis Rueden 2015-03-23 15:37:04 CDT 
Mark - I maintain OME 5.1 forks of the affected projects on "ome-5.1" branches, which I build manually and upload the Bio-Formats update site:

* https://github.com/fiji/Stitching/compare/ome-5.1
* https://github.com/fiji/legacy-imglib1/compare/ome-5.1
* https://github.com/bigdataviewer/SPIM_Registration/compare/ome-5.1

So there is no need to update the Bio-Formats-Fiji job to do anything differently. We just need to do the same for scifio-ome-xml and scifio-bf-compat. I started it:

* https://github.com/scifio/scifio-ome-xml/compare/ome-5.1
* https://github.com/scifio/scifio-bf-compat/compare/ome-5.1

These branches fix all compilation issues against the latest develop branch of Bio-Formats. But they have not been tested at all. You can resolve this bug by building the snapshots locally, testing them, fixing any problems, and finally uploading them to the Bio-Formats update site.
Comment 4 Curtis Rueden 2015-03-23 15:42:08 CDT 
Mark - Thinking about this further, I guess I misunderstood you when you said that the modified 5.1 JARs are getting blown away? You mean that the upload-update-site.sh is not preserving the manually uploaded artifacts, I am guessing... and yeah, that's a problem. We can discuss and fix tomorrow -- my preference right now is to enhance upload-update-site.sh to turn on the update site in question first before downloading JARs and doing a full upload.

Johnny - Thanks for your patience; we'll get this sorted out soon, so that you use both features (Bio-Formats and SCIFIO) at the same time.
Comment 5 johnnyh.2007 2015-03-23 15:48:48 CDT 
Great! Thank you both for your help. For now, disabling Bio-formats has worked as a short term solution for the data analysis I need to do.
Comment 6 Mark Hiner 2015-03-24 08:18:31 CDT 
Curtis - correct. When the Bio-Formats update site is enabled I am no longer getting a modified Stitching, SPIM_Registration, etc...

What's especially crazy is that it looks like the updater knows to track these jars from the Bio-Formats update site, but it doesn't install them.
Comment 7 Mark Hiner 2015-03-24 08:19:42 CDT 
Also, even the core functionality (e.g. Bio-Formats Importer) doesn't work! [1]


[1] https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;aa0257c5.1503
Comment 8 Curtis Rueden 2015-03-24 10:16:20 CDT 
I have fixed all the problems with the Bio-Formats update site:
- You can now mix and match the Bio-Formats update site with SCIFIO.
- Bio-Formats itself works again, and as well.

Please update your Fiji, and let us know if you have any further difficulties.