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Bug 762 - .png open fails with exception IJ 2 RC 2 Win 8.1 64bit
.png open fails with exception IJ 2 RC 2 Win 8.1 64bit
Status: RESOLVED REMIND
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-08 11:39 CDT by Rob Baer
Modified: 2014-06-09 09:10 CDT
3 users (show)

See Also:

Description Rob Baer 2014-06-08 11:39:25 CDT
(Fiji Is Just) ImageJ 2.0.0-rc-2/1.49b; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 44MB of 24475MB (<1%)
 
java.lang.ArrayIndexOutOfBoundsException: -1
	at java.util.Vector.elementAt(Vector.java:430)
	at java.awt.Menu.getItemImpl(Menu.java:230)
	at java.awt.Menu.getItem(Menu.java:222)
	at java.awt.Menu.remove(Menu.java:385)
	at net.imagej.legacy.IJ1Helper.updateRecentMenu(IJ1Helper.java:323)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:154)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:428)
	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: E:\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => E:\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140607141124)
Fiji: http://fiji.sc/update/ (last check:20140607203306)
Comment 1 Rob Baer 2014-06-08 12:07:17 CDT
Apparently, I get excetiond opening .jpg files as well.

(Fiji Is Just) ImageJ 2.0.0-rc-2/1.49b; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 74MB of 24475MB (<1%)
 
java.lang.ArrayIndexOutOfBoundsException: -1
	at java.util.Vector.elementAt(Vector.java:430)
	at java.awt.Menu.getItemImpl(Menu.java:230)
	at java.awt.Menu.getItem(Menu.java:222)
	at java.awt.Menu.remove(Menu.java:385)
	at net.imagej.legacy.IJ1Helper.updateRecentMenu(IJ1Helper.java:323)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:154)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:428)
	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)
Comment 2 Johannes Schindelin 2014-06-08 12:22:53 CDT
It actually looks as if the problem is not the file format but that your File>Open Recent menu is empty.

I would like to ask you to replace your Fiji.app/jars/imagej-legacy-0.5.6.jar with the version in http://jenkins.imagej.net/job/ImageJ-legacy/lastSuccessfulBuild/artifact/target/imagej-legacy-0.5.7-SNAPSHOT.jar and then test again. If you could do that, you would help me greatly!
Comment 3 Rob Baer 2014-06-08 15:41:59 CDT
Making the replacement DID allow the images to open without an exception. 

replacenment:
http://jenkins.imagej.net/job/ImageJ-legacy/lastSuccessfulBuild/artifact/target/imagej-legacy-0.5.7-SNAPSHOT.jar
 

Additional notes:
I note that the progress bar never gets past about ~10% even with imagej-legacy-0.5.7-SNAPSHOT.jar.  The image does open, though.  File opening is extremely slow, given that these are single frame images.  3264x1840 .jpg takes about 6 seconds.  Much of the time the status reads initializing.

BTW, the non-FIJI ImageJ-2 .zip version appears to suffer from the same opening problem, but you likely knew that.
Comment 4 Johannes Schindelin 2014-06-08 16:02:14 CDT
Thank you for testing. I uploaded the new release; you will have to mark the file as "update it" manually in your updater because it is "locally modified" for the moment.

As to the performance issues: we will be working on those soon. First we have to make it work, then we can make it work fast.
Comment 5 Rob Baer 2014-06-08 18:28:10 CDT
Update went fine and exceptions are gone.  Understand about performance being secondary.



Update on open dysfunction:
.avi files are treated like they succeed with no exception, but no window becomes visible.  

The progress bar still seems flaky as indicating load progress.

I tried opening a GIMP .xcf and although these may not be supported, the result is to simply display a different file chooser with no clear information about what has happened.
Comment 6 Mark Hiner 2014-06-09 07:21:45 CDT
Rob - thanks for the observation about multiple file chooser dialogs popping. If SCIFIO doesn't support the selected file we fall back to IJ1, but we were doing so naively (without remembering which file was chosen in the IJ2 dialog).

So we need to be smarter about that... I opened a new issue for it:

https://github.com/imagej/imagej-legacy/issues/43
Comment 7 Johannes Schindelin 2014-06-09 09:10:35 CDT
Robert, I appreciate your input, but I will have to ask for a little help here. The subject of this ticket says ".png open fails with exception  IJ 2 RC 2   Win 8.1 64bit" and that issue has been addressed.

You raised a couple more issues, which I really think will help us make Fiji/ImageJ better, but it would be so much easier if we had one ticket per issue, and also if we could show the world how fast and well we address issues by having them closed. I mean, if you add more wishes to the same ticket, and the ticket is still open ("REMIND" is still kind open...), it looks as if we did not address your issue at all...

So may I ask you to open a separate ticket for the remaining issues? Mark already did that for the "multiple file choosers" ticket. It would be really nice if you raised the two remaining issues as separate tickets: .avi are not opened without a message, and the progress bar is flakey.

Thank you so much for all your help!