WCS and other information not being displayed in Pop_OS!

[cduston]

Some critical information is not always displayed when using Pop_OS! - see the images. The WCS / image stack info is being blocked. I have previously seen this behavior when using my laptop (also running Pop_OS!), but I figured it was a screen size issue. Now that I've installed Pop_OS! to my desktop, I'm seeing it again. System info (Pop_OS! is Ubuntu-based):

$ lsb_release -a
No LSB modules are available.
Distributor ID: Pop
Description: Pop!_OS 20.04 LTS
Release: 20.04
Codename: focal
$ uname -a
Linux CygnusX1 5.4.0-7634-generic #38~1592497129~20.04~9a1ea2e-Ubuntu SMP Fri Jun 19 22:43:37 UTC  x86_64 x86_64 x86_64 GNU/Linux

Seems likely this is because of some strange setting in Pop_OS! graphics interface, so advice tracking that down would be helpful.

(and although when I took this screenshot AIJ was showing both behaviors, I've reopened these files ~5 times now and each time the WCS info has been hidden. And turning virtual stack on and off does not seem to help)

[karenacollins]

Hi AIJ community,

I don't know anything about Pop_OS, so if there are any users out there that could help out, please chime in!

Karen

On 6/29/2020 1:59 PM, cduston [via AstroImageJ] wrote:

Some critical information is not always displayed when using Pop_OS! - see the images. The WCS / image stack info is being blocked. I have previously seen this behavior when using my laptop (also running Pop_OS!), but I figured it was a screen size issue. Now that I've installed Pop_OS! to my desktop, I'm seeing it again. System info (Pop_OS! is Ubuntu-based):

$ lsb_release -a
No LSB modules are available.
Distributor ID: Pop
Description: Pop!_OS 20.04 LTS
Release: 20.04
Codename: focal
$ uname -a
Linux CygnusX1 5.4.0-7634-generic #38~1592497129~20.04~9a1ea2e-Ubuntu SMP Fri Jun 19 22:43:37 UTC  x86_64 x86_64 x86_64 GNU/Linux

Seems likely this is because of some strange setting in Pop_OS! graphics interface, so advice tracking that down would be helpful.

(and although when I took this screenshot AIJ was showing both behaviors, I've reopened these files ~5 times now and each time the WCS info has been hidden. And turning virtual stack on and off does not seem to help)

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[johnk]

Could you say what display manager you're using in POP_OS?  We know that AIJ displays properly in XFCE, KDE, and Gnome but I'm unfamiliar with POP_OS and its options.  This appears to be a problem with the interaction of the Java window and the display manager.

When the fields are missing, what happens if you grab the corner of the AIJ window and make it larger?  This may reset the the display  and fill in the missing fields.  

[cduston]

According to the developers: https://support.system76.com/articles/desktop-environment/

"While Pop and Ubuntu contain GNOME by default, both include a number of customizations to GNOME. "

So my guess it's one of those customizations - I use XFCE on other distros and AIJ works very well on them.

Resizing the windows (either with click-drag or double click on top bar to maximize) does not reveal the missing info.

[johnk]

I have not heard of a problem with Ubuntu .  It is specific to a Pop_OS! customization then there may not be an easy solution unless you run Pop_OS! with xfce (which is an option on this distribution).  But , maybe it is in Java.  There's no change in the AIJ image window with or without WCS header information, only in how those fields are updated.  I can't see on the images you posted what is being shown there when the image has WCS.  Is it empty?  If not, could you post a screenshot of that shows detail?

Do you start aij with a script such as this one?


#!/bin/sh
cd /usr/local/AstroImageJ/
java -Xmx32768m -jar /usr/local/AstroImageJ/ij.jar $1

which would be using the system "java".  In the OpenSuse Tumbelweed distribution I use this "java" would be a version of openjdk, and point to  

/usr/lib64/jvm/jre-1.8.0-openjdk/bin/java


What does Pop_OS! use for the default java?  

[cduston]

Thanks for the help here.

I can confirm that running XFCE on Pop_OS! fixes this problem. So, whatever the issue, it seems related to whatever customizations are happening in GNOME.

I run AIJ with the default script, which looks like the following:

$ which astroimagej
/usr/local/bin/astroimagej
$ more /usr/local/bin/astroimagej
#!/bin/sh
cd /usr/local/AstroImageJ/
java -Xmx8192m -jar /usr/local/AstroImageJ/ij.jar
exit
$ which java
/usr/bin/java
$ java --version
openjdk 11.0.7 2020-04-14
OpenJDK Runtime Environment (build 11.0.7+10-post-Ubuntu-3ubuntu1)
OpenJDK 64-Bit Server VM (build 11.0.7+10-post-Ubuntu-3ubuntu1, mixed mode, sharing)

I can try oracle java maybe? I don't strongly object to using XFCE (I actually really like XFCE generally), but I was hoping to get some vanilla Pop_OS! experience, given the approach taken by the creators.

[johnk]

That's really helpful to know that it works with xfce -- my reliable favorite.  OpenJDK should be fine. I confirmed that AIJ with the most recent updates works with the latest openJDK version 13, and I've used versions 8 and 11 as well.  I'd stay with that.  Let me also confirm that there are no similar issues with Gnome and its window manager and that will isolate the problem to how the customizations and Java are handling the cursor interrupts.

The WCS window stays empty, does not update when you move the cursor over the image?

On Thu, Jul 2, 2020 at 10:17 AM cduston [via AstroImageJ] <[hidden email]> wrote:

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Thanks for the help here.

I can confirm that running XFCE on Pop_OS! fixes this problem. So, whatever the issue, it seems related to whatever customizations are happening in GNOME.

I run AIJ with the default script, which looks like the following:

$ which astroimagej
/usr/local/bin/astroimagej
$ more /usr/local/bin/astroimagej
#!/bin/sh
cd /usr/local/AstroImageJ/
java -Xmx8192m -jar /usr/local/AstroImageJ/ij.jar
exit
$ which java
/usr/bin/java
$ java --version
openjdk 11.0.7 2020-04-14
OpenJDK Runtime Environment (build 11.0.7+10-post-Ubuntu-3ubuntu1)
OpenJDK 64-Bit Server VM (build 11.0.7+10-post-Ubuntu-3ubuntu1, mixed mode, sharing)

I can try oracle java maybe? I don't strongly object to using XFCE (I actually really like XFCE generally), but I was hoping to get some vanilla Pop_OS! experience, given the approach taken by the creators.

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--

[cduston]

Sorry, I missed in the earlier message that you were having trouble seeing the issue. I've attached an image which zooms in to the problem - the WCS/stack number information is being covered by the cursor location information. Passing the cursor over this section has no effect.

Since this seems to be focused on Pop_OS! rather then AIJ, I'll start cross-posting over there.  

Any other ideas? I appreciate the attention!