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Bug 799 - SCIFIO does not allow .LIF file to be opened in ImageJ2
SCIFIO does not allow .LIF file to be opened in ImageJ2
Status: RESOLVED FIXED
Product: ImageJ
Classification: Unclassified
Component: SCIFIO
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-19 09:21 CDT by Keith Siew
Modified: 2015-04-06 15:49 CDT
5 users (show)

See Also:

Description Keith Siew 2014-06-19 09:21:01 CDT
The following exception window (below) opens when I try to load a .LIF file from "FILE---> OPEN", while the drag-&-drop feature just says "Computing min/max complete." and does nothing else. If I disable the SCIFIO feature I can open my file as normal.

(Fiji Is Just) ImageJ 2.0.0-rc-5/1.49b; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 34MB of 12221MB (<1%)
 
java.lang.IndexOutOfBoundsException: Index: 4, Size: 4
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at io.scif.AbstractImageMetadata.getAxis(AbstractImageMetadata.java:496)
	at net.imagej.legacy.translate.AbstractImagePlusCreator.fillImageInfo(AbstractImagePlusCreator.java:222)
	at net.imagej.legacy.translate.AbstractImagePlusCreator.fillInfo(AbstractImagePlusCreator.java:198)
	at net.imagej.legacy.translate.AbstractImagePlusCreator.makeImagePlus(AbstractImagePlusCreator.java:185)
	at net.imagej.legacy.translate.GrayImagePlusCreator.makeImagePlus(GrayImagePlusCreator.java:197)
	at net.imagej.legacy.translate.GrayImagePlusCreator.makeExactImagePlus(GrayImagePlusCreator.java:217)
	at net.imagej.legacy.translate.GrayImagePlusCreator.createLegacyImage(GrayImagePlusCreator.java:128)
	at net.imagej.legacy.translate.DefaultImageTranslator.createLegacyImage(DefaultImageTranslator.java:128)
	at net.imagej.legacy.translate.DefaultImageTranslator.createLegacyImage(DefaultImageTranslator.java:110)
	at net.imagej.legacy.LegacyImageMap.registerDisplay(LegacyImageMap.java:178)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:157)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:434)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:156)
	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 NT (unknown)
  os.version => 6.2
  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\Keith\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Keith\Desktop\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140618205931)
Fiji: http://fiji.sc/update/ (last check:20140618210039)

Files not up-to-date:
  c83c26ea (OBSOLETE_UNINSTALLED) 20140519014204 jars/forms-1.3.0.jar
  78314a5e (MODIFIED) 20140519014205 jars/ij-1.49a.jar
  18337fb7 (MODIFIED) 20140619150751 jars/ij-1.49b.jar
  e5852db5 (OBSOLETE_UNINSTALLED) 20140519014216 jars/jai_imageio-1.0.1.jar
  7ecaf631 (OBSOLETE_UNINSTALLED) 20140519014228 jars/jruby-complete-1.7.11.jar
  24d47d70 (OBSOLETE_UNINSTALLED) 20140519014229 jars/junit-4.8.1.jar
  6d88799a (OBSOLETE_UNINSTALLED) 20140519014130 plugins/Script_Editor-2.0.0-SNAPSHOT.jar
Comment 1 Mark Hiner 2014-06-19 09:24:31 CDT
Hi Keith,

 Would you be able to upload your image that caused this problem, via Help > Upload Sample Image in Fiji?

Thanks,
Mark
Comment 2 Keith Siew 2014-06-19 09:26:30 CDT
Hi Mark,

The file is 513MB. Is this okay?
Comment 3 Mark Hiner 2014-06-19 09:31:10 CDT
Hi Keith,

That should be fine. I can always delete it after downloading locally.
Comment 4 Keith Siew 2014-06-19 09:32:46 CDT
Cool. Uploading now
Comment 5 Keith Siew 2014-06-19 09:34:10 CDT
How will I know when it's completed uploading?
Comment 6 Mark Hiner 2014-06-19 10:20:05 CDT
Keith,

 There should have been a progress update, and an "Upload completed!" message at the end. There has been some confusion about using Upload Sample Image, so I filed a ticket to try and make it clearer what's going on: https://github.com/imagej/imagej-plugins-commands/issues/7

 Anyway, your image did upload successfully! It's on a private site for use by Fiji developers for testing. Thanks, we'll try to get this issue resolved quickly.
Comment 7 Mark Hiner 2014-06-19 10:53:39 CDT
This was a ridiculously stupid bug that is now fixed in this commit: https://github.com/imagej/imagej-legacy/commit/0c263f62d0aead6316b8c1c238555859b78f1cf1

It's not yet uploaded to Fiji but should be later today.

However, it exposed a new issue in the ImageJ2 layer, in that datasets with multiple images just open the first image in the series.

So I filed a new ticket for that: https://github.com/imagej/imagej-legacy/issues/61 which will allow all the images in your dataset to be opened.
Comment 8 Keith Siew 2014-06-19 11:11:09 CDT
Thanks for that I look forward to the fix.

I'll let you know if I stumble upon anything else.
Comment 9 Johannes Schindelin 2014-06-19 16:06:27 CDT
Mark had to leave for a well-deserved two week absence, so I uploaded his fix. Keith, it would be really nice if you could try with again with an updated Fiji and verify that it fixes your problem.
Comment 10 Keith Siew 2014-06-19 16:19:43 CDT
Hi Johannes,

I just updated and tried the drag and drop, as well as the File-->Open and it opens the .LIF file but only the first image and doesn't not ask about opening up other stacks within the file. 

If you look at Comment no.7 Mark has filed a separate ticket for this issue which he identified also.

Please let me know if there is anything else I can provide to help.

Regards,
Keith
Comment 11 Curtis Rueden 2014-06-19 16:39:16 CDT
Thanks for the feedback, Keith!
Comment 12 Keith Siew 2014-06-24 02:39:34 CDT
Dear Curtis/Johannes,

Is there any update on the other ticket for opening multiple images from a .LIF file format?


From this ticket:

https://github.com/imagej/imagej-legacy/issues/61


Kind Regards,
Keith
Comment 13 Curtis Rueden 2014-06-24 07:45:50 CDT
Hi Keith,

As Johannes said, Mark is on vacation now for the next couple of weeks. I _might_ be able to tackle the imagej-legacy issue 61 before he returns, but I don't want to promise anything -- there is a lot going on.

If you want to receive automatic updates via email, you can create a GitHub account (it's free) and make a comment on the issue at https://github.com/imagej/imagej-legacy/issues/61. Then you will receive a notification whenever the issue changes.

Until the problem is fixed, you can work around the issue by using the File>Import>Bio-Formats command!
Comment 14 Johannes Schindelin 2014-06-24 08:16:30 CDT
> If you want to receive automatic updates via email, you can create a GitHub account (it's free) and make a comment on the issue at https://github.com/imagej/imagej-legacy/issues/61.

It might be necessary to click the "Watch" button on the top, AFAIR GitHub switched off the automatic mail notification by default.