MacOS 10.8 Java problems?

[Mike Holloway]

Forced to try using a Macbook running 10.8 in order to look at a new neuron
tracing plugin, Tubular Geodesics.  Windows version not available.  Supposed
to work with the Simple Neuron Tracer plugin in Fiji.  Running the first
plugin in the package, "Multi-Scale Oriented Flux Tubularity Measure",
crashes Imagej.  Not image specific.  The archive gives me the impression
that there may be some Java stability issues in the newer MacOS.  Does
anyone know what my best option is?  There's a Linux version available.
Would that be more stable?  Would an older Macbook be worth trying?

 

Thanks,

Mike Holloway


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[dscho]

Hi Mike,

On Fri, 28 Mar 2014, Mike Holloway wrote:

> Running the first plugin in the package, "Multi-Scale Oriented Flux
> Tubularity Measure", crashes Imagej.

The first thing to do if Fiji crashes is to follow the steps in
fiji.sc/Command_Line_Debugging to get ahold of any error messages, then
reproduce them in a reply to this mail.

It has quite likely to do with the rather dramatic changes Java underwent
in MacOSX: it used to be a fork of Sun's Java, made into a framework,
integrated into the Carbon way to do things, but now it is maintained by
Oracle (with just enough help of the Apple developers to make sure that it
requires at least MacOSX Lion to work), is a stand-alone application and
standard Mach-O library, and integrates with Carbon in a much different
way.

Given these circumstances, I hope that the console output is sufficient to
diagnose the problem; the output is certainly necessary to do so.

Ciao,
Johannes

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenneth Sloan]

I haven’t (yet) had any issues with FIJI, but I have seen serious problems with
showOpenDialog() in stand-along java programs (10.9.2, Java 7).

--
Kenneth Sloan
[hidden email]


On Mar 28, 2014, at 11:15 , Johannes Schindelin <[hidden email]> wrote:

> Hi Mike,
>
> On Fri, 28 Mar 2014, Mike Holloway wrote:
>
>> Running the first plugin in the package, "Multi-Scale Oriented Flux
>> Tubularity Measure", crashes Imagej.
>
> The first thing to do if Fiji crashes is to follow the steps in
> fiji.sc/Command_Line_Debugging to get ahold of any error messages, then
> reproduce them in a reply to this mail.
>
> It has quite likely to do with the rather dramatic changes Java underwent
> in MacOSX: it used to be a fork of Sun's Java, made into a framework,
> integrated into the Carbon way to do things, but now it is maintained by
> Oracle (with just enough help of the Apple developers to make sure that it
> requires at least MacOSX Lion to work), is a stand-alone application and
> standard Mach-O library, and integrates with Carbon in a much different
> way.
>
> Given these circumstances, I hope that the console output is sufficient to
> diagnose the problem; the output is certainly necessary to do so.
>
> Ciao,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[dscho]

Hi Kenneth,

On Fri, 28 Mar 2014, Kenneth Sloan wrote:

> I haven’t (yet) had any issues with FIJI,

obviously due to Fiji still relying on Java 6 on MacOSX ;-)

> but I have seen serious problems with showOpenDialog() in stand-along
> java programs (10.9.2, Java 7).

Care to share anything in the way of details?

Ciao,
Johannes

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenneth Sloan]

Here’s a minimal program that tickles the error.  It works on everyone’s machine except mine (so..you might not want to spend any time on this).  My last (wrong) theory was that it had to do with an interaction between Sophos version 8 and Mac OS/X 10.9. But, fixing *that* did not fix *this*.  Current status is that the program worked correctly ONCE after a reboot, and then failed; I suspect this is repeatable, but have not had time to test (I re-worked the program that needed this, so it’s no longer on my critical path).

Failure mode is that the OpenDialog box is invisible. The program behaves as if the dialog box has been displayed and is waiting for input.  The program displays “calling showOpenDialog” and sits quietly, waiting for showOpenDialog to return.

Note that this might be an improper use of Swing code without actually firing up Swing - but the docs say it’s legal, and it has worked for a long time.

MacOS/X 10.9.2, Java 7 - both installed at the same time.  Again - it works on other machines.  
==============
// File: OpenDialogTest.java
// Author: K R Sloan
// Last Modified: 24 March 2014
// Purpose: minimal program demonstrating bug

import java.util.*;
import java.io.*;
import javax.swing.*;
import javax.swing.filechooser.*;
import java.lang.*;

public class OpenDialogTest
{
   public static void main(String[] args) throws FileNotFoundException, Exception
    {
        JFileChooser chooser = new JFileChooser(".");
        FileNameExtensionFilter javaFilter
            = new FileNameExtensionFilter("Java Source Code","java");
        chooser.setFileFilter(javaFilter);
        chooser.setDialogTitle("Java Files");


        System.out.printf("calling showOpenDialog\n");
        int returnVal = chooser.showOpenDialog(null);
        System.out.printf("showOpenDialog returned %d\n", returnVal);


        if (returnVal != JFileChooser.APPROVE_OPTION)
            throw new Exception("no file chosen");
    }
}
==============
--
Kenneth Sloan
[hidden email]


On Mar 28, 2014, at 16:24 , Johannes Schindelin <[hidden email]> wrote:

> Hi Kenneth,
>
> On Fri, 28 Mar 2014, Kenneth Sloan wrote:
>
>> I haven’t (yet) had any issues with FIJI,
>
> obviously due to Fiji still relying on Java 6 on MacOSX ;-)
>
>> but I have seen serious problems with showOpenDialog() in stand-along
>> java programs (10.9.2, Java 7).
>
> Care to share anything in the way of details?
>
> Ciao,
> Johannes

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