Fiji on OSX with latest Java

[lechristophe]

Hi,

I got the new OSX launcher and Fiji is now using Java 1.8 under Yosemite.
I have problems with the 3D viewer (crashes) and the Interactive Stack
Rotation (isn't very interactive, in fact nothing happens, not even an
error or console log).

Is it possible to switch back to Fiji with Java 1.6 without removing 1.8
from my system? Something like an option in Fiji to choose which Java to
use (or make it use the Java chooser preference panel)?

Thanks,

Christophe

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[Mark Hiner]

Hi Christophe,

> Is it possible to switch back to Fiji with Java 1.6 without removing 1.8
from my system?

Definitely![1] Unless your Java 1.6 is an Apple Java, in which case you
would need to remove the non-Apple java installations. Java 1.7 should be
easy to switch to, though.

>I have problems with the 3D viewer (crashes)

Were there any error messages from the crash? The simplest thing would be
to try manually installing the Java3D extension[2] into the Java
installation you want to use, and removing the Java3D from
/Fiji.app/java/macosx-java3d/ (if present). If you can't get this working
and want to help us debug the problem further, just let Curtis and me know,
and we can discuss the process of identifying your Java3D installations and
determining which is being used, and which should be used.

>Something like an option in Fiji to choose which Java to use (or make it
use the Java chooser preference panel)?

This and the Java3D issues are ones we want to address as part of our
summer overhaul[3]. A Java selection panel is something we've been
discussing for a while - it's just a matter of foundation work to make it
possible.

Best,
Mark

[1] http://imagej.net/Frequently_Asked_Questions#On_OS_X
[2] https://java3d.java.net/binary-builds.html
[3] http://imagej.net/2015-06-15_-_Major_updates_in_the_works

On Thu, Jun 18, 2015 at 7:54 AM, Christophe Leterrier <
[hidden email]> wrote:

> Hi,
>
> I got the new OSX launcher and Fiji is now using Java 1.8 under Yosemite.
> I have problems with the 3D viewer (crashes) and the Interactive Stack
> Rotation (isn't very interactive, in fact nothing happens, not even an
> error or console log).
>
> Is it possible to switch back to Fiji with Java 1.6 without removing 1.8
> from my system? Something like an option in Fiji to choose which Java to
> use (or make it use the Java chooser preference panel)?
>
> Thanks,
>
> Christophe
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[lechristophe]

Hi Mark,

On Thu, Jun 18, 2015 at 4:59 PM, Mark Hiner <[hidden email]> wrote:

> Hi Christophe,
>
> > Is it possible to switch back to Fiji with Java 1.6 without removing 1.8
> from my system?
>
> Definitely![1] Unless your Java 1.6 is an Apple Java, in which case you
> would need to remove the non-Apple java installations. Java 1.7 should be
> easy to switch to, though.
>
> >I have problems with the 3D viewer (crashes)
>
> Were there any error messages from the crash? The simplest thing would be
> to try manually installing the Java3D extension[2] into the Java
> installation you want to use, and removing the Java3D from
> /Fiji.app/java/macosx-java3d/ (if present). If you can't get this working
> and want to help us debug the problem further, just let Curtis and me know,
> and we can discuss the process of identifying your Java3D installations and
> determining which is being used, and which should be used
>

I found two java3D (j3dcore.jar, j3dutils.jar and vecmath.jar) on my system:
one at
/Library/Java/Extensions
and one at
Fiji.app/java/macosx-java3d/Home/lib/ext

I removed both a placed the three files freshly downloaded from the link
you provided (https://java3d.java.net/binary-builds.html) either at one
place or another, but to no avail.

Is this considered still a work in progress (I can wait, I don't have an
urgent need of the 3D viewer), or is is supposed to be working right now
with Java 1.8.?

Thanks,

Christophel <http://imagej.nih.gov/ij/list.html>

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[Mark Hiner]

Hi Christophe,

> Is this considered still a work in progress (I can wait, I don't have an
urgent need of the 3D viewer), or is is supposed to be working right now
with Java 1.8.?

Definitely a work in progress. Apologies for giving you directions that
didn't work - it was second-hand information and not solidified yet. Now
that I'm more familiar with Curtis's updates to the 3D Viewer and
investigations in the future of Java 3D/JOGL, I would recommend using the
jogl-java3d branch of the 3D Viewer[1] - as it uses Maven to provide the
latest Java3D and JOGL, and updates the 3D viewer for the new API.

If you clone that project, the README has brief installation instructions.
They are unfortunately a bit redundant right now, forcing you to manually
copy dependencies due to the way the native JOGL libraries are deployed.
But I can confirm that this did get the 3D viewer working on OSX 10.10 with
both Java 7 and 8.

If any of this is unclear or you get stuck, please let me know right away
and we can troubleshoot.

Best,
Mark

[1] https://github.com/fiji/3D_Viewer/tree/jogl-java3d

On Wed, Jun 24, 2015 at 8:47 AM, Christophe Leterrier <
[hidden email]> wrote:

> Hi Mark,
>
> On Thu, Jun 18, 2015 at 4:59 PM, Mark Hiner <[hidden email]> wrote:
>
>> Hi Christophe,
>>
>> > Is it possible to switch back to Fiji with Java 1.6 without removing 1.8
>> from my system?
>>
>> Definitely![1] Unless your Java 1.6 is an Apple Java, in which case you
>> would need to remove the non-Apple java installations. Java 1.7 should be
>> easy to switch to, though.
>>
>> >I have problems with the 3D viewer (crashes)
>>
>> Were there any error messages from the crash? The simplest thing would be
>> to try manually installing the Java3D extension[2] into the Java
>> installation you want to use, and removing the Java3D from
>> /Fiji.app/java/macosx-java3d/ (if present). If you can't get this working
>> and want to help us debug the problem further, just let Curtis and me
>> know,
>> and we can discuss the process of identifying your Java3D installations
>> and
>> determining which is being used, and which should be used
>>
>
> I found two java3D (j3dcore.jar, j3dutils.jar and vecmath.jar) on my
> system:
> one at
> /Library/Java/Extensions
> and one at
> Fiji.app/java/macosx-java3d/Home/lib/ext
>
> I removed both a placed the three files freshly downloaded from the link
> you provided (https://java3d.java.net/binary-builds.html) either at one
> place or another, but to no avail.
>
> Is this considered still a work in progress (I can wait, I don't have an
> urgent need of the 3D viewer), or is is supposed to be working right now
> with Java 1.8.?
>
> Thanks,
>
> Christophel <http://imagej.nih.gov/ij/list.html>
>
>

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