OS X 10.13 High Sierra, ImageJ Java 6 and text editing?

[Jeff Hardin]

Hi all,
I’m sorry if this has been mentioned already, but I can’t seem to be able to edit text in any ImageJ text field or in new text files under OS X 10.13/High Sierra with Java 6 versions of ImageJ. Is this a known bug? This error happens in Micro-Manager’s packaged version of ImageJ (1.48v) and 1.51p in the standalone ImageJ bundle for OS X, 32- or 64-bit versions, under JRE 6.

This does not occur with the Java 8 bundled version, but this is 64-bit only, and I”m afraid I’m wanting to use 32-bit ImageJ for legacy plugins…

Thanks in advance for your help!
Cheers,
Jeff
__________________________
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Integrative Biology
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: [phone]
fax: [phone]
email: [hidden email]<mailto:[hidden email]>
web page: http://worms.zoology.wisc.edu

On Nov 14, 2017, at 11:00 PM, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]>> wrote:

There are 2 messages totaling 74 lines in this issue.

Topics of the day:

 1. Alternative to Tif?
 2. Variable in filename

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Date:    Tue, 14 Nov 2017 16:46:32 -0500
From:    Wayne Rasband <[hidden email]<mailto:[hidden email]>>
Subject: Re: Alternative to Tif?

On Nov 13, 2017, at 8:08 AM, Adrian Daerr <[hidden email]<mailto:[hidden email]>> wrote:

When dealing with stacks of these sizes, I prefer to work with virtual stacks. [..] Even a raw file can be opened as a virtual stack if you know its data layout.

I concur on the convenience of virtual stacks. A small but annoying shortcoming of raw virtual stacks however is that when you do not know the exact number of images, and enter a higher number in the dialog, then your stack display will irreversibly freeze once you attempt to access a slice beyond the end of file instead of merely updating the size of the stack. Of course you can calculate the right size from the byte size of your file divided by the camera resolution, but this operation partly negates the convenience of being able to quasi-instantaneously view and browse through recordings on the disk via virtual stacks.

This bug is fixed in the latest ImageJ daily build (1.51s24). Now when you enter a higher number of images in the dialog ImageJ will calculate the correct number based on the offset, image size, gap between images and the file size.

-wayne

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Date:    Tue, 14 Nov 2017 18:56:04 -0700
From:    "lihong.zhan" <[hidden email]<mailto:[hidden email]>>
Subject: Re: Variable in filename

Hi,

Thanks for the post. I run into the same problem and was able to solve by
simply add "&" in front of my variable.

Lihong

Detailed explanation can be found in the following link.

https://imagej.nih.gov/ij/developer/macro/macros.html


With ImageJ 1.43 and later, there is an easier method that only requires
adding "&" to the variable name in the options string:
  noise = 50;
  output = "Point Selection";
  run("Find Maxima...", "noise=&noise output=&output light");
String variables passed using this method do not have to be enclosed in
brackets. For more examples, see the ArgumentPassingDemo macro.



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End of IMAGEJ Digest - 14 Nov 2017 (#2017-311)
**********************************************


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[Jeff Hardin]

P.S.- Sorry! I accidentally quoted the previous digest. My bad...

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[ctrueden]

Hi Jeff,

I am able to reproduce that bug on my High Sierra system running with Java
6 (in both 32-bit and 64-bit modes).

It does not happen with the ImageJ2 Script Editor -- only with the ImageJ1
text editor. (It might be a Swing vs. AWT thing, but that is pure
speculation.)

I also see an exception stack trace [1] every time I press a key,
regardless of which ImageJ window is currently active. This error may be
related to the keystrokes being eaten in some circumstances. It appears to
be a bug in Java -- or perhaps more likely, the legacy Apple Java 6
interacting with the newer High Sierra OS.

My advice would be to use an older version of MacOS if you continue to need
Java 6 functionality.

Regards,
Curtis

[1] The stack trace is as follows:

Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Non-Java
exception raised, not handled! (Original problem: Deprecated in 10_12... DO
NOT EVER USE CGSEventRecord directly. Bad things, man.... bad things.)
at apple.awt.ComponentModel._handleEvent(Native Method)
at apple.awt.ComponentModel.handleEvent(ComponentModel.java:273)
at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(Defaul
tKeyboardFocusManager.java:753)
at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(Def
aultKeyboardFocusManager.java:1000)
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Def
aultKeyboardFocusManager.java:865)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKe
yboardFocusManager.java:686)
at java.awt.Component.dispatchEventImpl(Component.java:4648)
at java.awt.Container.dispatchEventImpl(Container.java:2142)
at java.awt.Component.dispatchEvent(Component.java:4604)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege
(AccessControlContext.java:86)
at java.security.AccessControlContext$1.doIntersectionPrivilege
(AccessControlContext.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:690)
at java.awt.EventQueue$3.run(EventQueue.java:688)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege
(AccessControlContext.java:86)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis
patchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat
chThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis
patchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Nov 15, 2017 at 9:25 PM, Jeff Hardin <[hidden email]> wrote:

> P.S.- Sorry! I accidentally quoted the previous digest. My bad...
>
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>

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[Jeff Hardin]

Hi Curtis,
I should have checked the log myself. Thanks for doing that. My main need is to support legacy QuickTime plugins I wrote eons ago that are still in use for compressing large Nomarski 4d datasets in my lab. There are other options, but it would be nice to maintain legacy support. Ironically, everything still works fine in Windows 10…Apple makes it hard to stay with older OS revisions!

I’d found the same (normal) behavior with the ImageJ2/Fiji script editor, as well as the one in Micro-Manager…

Cheers,
Jeff
__________________________
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Integrative Biology
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: [phone]
fax: [phone]
email: [hidden email]<mailto:[hidden email]>
web page: http://worms.zoology.wisc.edu

On Nov 17, 2017, at 11:00 PM, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]>> wrote:

Date:    Fri, 17 Nov 2017 15:23:11 -0600
From:    Curtis Rueden <[hidden email]<mailto:[hidden email]>>
Subject: Re: OS X 10.13 High Sierra, ImageJ Java 6 and text editing?

Hi Jeff,

I am able to reproduce that bug on my High Sierra system running with Java
6 (in both 32-bit and 64-bit modes).

It does not happen with the ImageJ2 Script Editor -- only with the ImageJ1
text editor. (It might be a Swing vs. AWT thing, but that is pure
speculation.)

I also see an exception stack trace [1] every time I press a key,
regardless of which ImageJ window is currently active. This error may be
related to the keystrokes being eaten in some circumstances. It appears to
be a bug in Java -- or perhaps more likely, the legacy Apple Java 6
interacting with the newer High Sierra OS.


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