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Bug 797 - File->Open Samples->Cache Sample Images fails in Fiji
File->Open Samples->Cache Sample Images fails in Fiji
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-18 12:00 CDT by Graeme Ball
Modified: 2014-06-24 08:07 CDT
3 users (show)

See Also:

Description Graeme Ball 2014-06-18 12:00:50 CDT
File->Open Samples->Cache Sample Images fails in Fiji, but works in ImageJ. This happens whether or not Edit->Options->ImageJ2 "Use SCIFIO when opening files" is ticked. I didn't manage to figure out how Fiji & ImageJ differ here, or whether perhaps something like Bio-Formats intercepts the request to open the images from a URL and screws it up, but anyhow, for each sample image the following sort of error appears in the log window:-
  "java.io.FileNotFoundException: http://imagej.nih.gov/ij/images/http://imagej.nih.gov/ij/images/AuPbSn40.jpg http://imagej.nih.gov/ij/images/http://imagej.nih.gov/ij/images/AuPbSn40.jpg"

i.e. looks like the URL string ends up with the URL repeated twice separated by a space?

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.3
  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:20140618043041)
Fiji: http://fiji.sc/update/ (last check:20140617231732)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20140604070506)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140519192603)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20131220231857)

Files not up-to-date:
  5d5835b0 (MODIFIED) 20140609102817 Contents/Info.plist
  7ecaf631 (OBSOLETE_UNINSTALLED) 20140401203606 jars/jruby-complete-1.7.11.jar
  24d47d70 (OBSOLETE_UNINSTALLED) 20140401203606 jars/junit-4.8.1.jar
  f96af9c5 (LOCAL_ONLY) 20140528155339 macros/BatchMacro.ijm
  8de72b0a (LOCAL_ONLY) 20140519122352 macros/DisplayRangeMacros.txt
  0d6e4e4a (LOCAL_ONLY) 20140519123218 macros/Gamma.txt
  c6a2a812 (LOCAL_ONLY) 20140528012911 macros/StartupMacros.txt
  0a5c1981 (LOCAL_ONLY) 20140509155303 plugins/Color_Profiler.jar
  37955112 (LOCAL_ONLY) 20140529103845 plugins/FRAP_Analysis.class
  2099d7a7 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/LoG3D.class
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  1fe5cd25 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/Access.class
  7cdd61d3 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/Buffer.class
  f1da288c (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/Builder.class
  9052d070 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/ByteAccess.class
  d122c864 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/ByteBuffer.class
  dd47fc25 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/BytePointwise.class
  140ed17c (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/ByteProcess.class
  31c0d21f (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/ByteSet.class
  11d4a88b (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/Convolver.class
  03cca71a (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/Display.class
  4d942e3d (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/DoubleAccess.class
  ff3fd92c (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/DoubleBuffer.class
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  b75069ca (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/DoubleSet.class
  60c4dbb3 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/FMath.class
  856f718c (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/FloatAccess.class
  1a374b16 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/FloatBuffer.class
  95dce0f9 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/FloatPointwise.class
  9b8a6a1c (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/FloatProcess.class
  bbdd7dd7 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/FloatSet.class
  159fd13f (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/ImageAccess.class
  bb737658 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/ImageWare.class
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  42737fb1 (LOCAL_ONLY) 20060217161502 plugins/LoG3D/imageware/ShortPointwise.class
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  0af1624e (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/backport-util-concurrent.jar
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  189f61fa (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/bufr.jar
  19c30fe9 (LOCAL_ONLY) 20140224162650 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/common.jar
  940245e0 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-codec.jar
  64d8a654 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-collections.jar
  86ab9004 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-digester.jar
  9e9eb622 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-discovery.jar
  c62bea1b (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-httpclient.jar
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  1911c9e1 (LOCAL_ONLY) 20131120130114 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ice-glacier2.jar
  b1d709fb (LOCAL_ONLY) 20131120130114 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ice-grid.jar
  c49b8fa2 (LOCAL_ONLY) 20131120130114 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ice-storm.jar
  53aa5393 (LOCAL_ONLY) 20131120130114 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ice.jar
  6e7614ee (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ij.jar
  6ce638fb (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ini4j.jar
  f1b65457 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/java-getopt.jar
  c827227f (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/java-image-scaling.jar
  e72f9b2b (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/jaxrpc.jar
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  f4d01930 (LOCAL_ONLY) 20140224162610 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/specification.jar
  ba32bfdf (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/swingx.jar
  7c4005e7 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/wsdl4j.jar
  c8694e76 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/xalan.jar
  56a05ff0 (LOCAL_ONLY) 20140224163050 plugins/OMERO.insight-ij-5.0.0-ice35-b19/omero_ij.jar
  b7319cc1 (LOCAL_ONLY) 20140606170132 plugins/SIMcheck_.jar
  71331805 (LOCAL_ONLY) 20140501010801 plugins/jacop_.jar
Comment 1 Mark Hiner 2014-06-18 12:14:00 CDT
Hi Graeme,

 Note that there are two "Cache Sample Images" commands - an ImageJ and a Fiji version.

 If you look for Cache Sample Images in the command finder, you'll see one points to "fiji.SampleImageLoader" and the other "ij.plugin.URLOpener".

We will remove or change the behavior of the ImageJ entry with the resolution of this ticket: https://github.com/imagej/imagej-legacy/issues/41

In the mean time, the Fiji version should work. It is also present in the Fiji > Open Samples menu, at the bottom of the list.


Thanks,
Mark
Comment 2 Graeme Ball 2014-06-18 12:45:00 CDT
Oh, I see, you're right, the second "Cache Sample Images" command does work
... and you're also right that it's a bit confusing there are 2 versions of the command ;-) I didn't spot the one at the bottom.

Thanks Mark.
Comment 3 Johannes Schindelin 2014-06-18 14:22:43 CDT
Yes, it is very, very unfortunate.

Wayne implemented the same function as we already had implemented. Instead of using Fiji's code -- which would have been exactly what we were working for -- ImageJ 1.x unfortunately chose to use an incompatible, much more limited version.

Which is too bad.

There is code in ImageJ 1.x that tries to determine whether it is running inside Fiji (to trigger different behavior; the opposite of what is intended with Fiji, which is supposed to really just be ImageJ). This code is very fragile and consequently broke recently: when ImageJ is instantiated, the window title does not start with "Fiji".

We will fix that directly after a couple "slightly" more pressing issues.
Comment 4 Johannes Schindelin 2014-06-24 08:07:53 CDT
Fixed in https://github.com/fiji/fiji-compat/commit/6eb34e6d29b5c1cfd7bd0d04c0096d4cd54eb613. Deployed and uploaded!