How to get Cytoscape scaled on high DPI monitor?

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Matthias König

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Jan 27, 2017, 5:42:36 AM1/27/17
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Hi all,

does anybody know how to scale Cytoscape/Swing programs on high DPI monitors?
Especially the font size of the menus?

After updating to high-DPI 4k monitors the Cytoscape menu is unusable small, same for all displayed text.
I googled a lot but did not find any solution which simply scales Java Swing applications.

Some info here

http://kynosarges.org/GuiDpiScaling.html
http://stackoverflow.com/questions/28673127/how-can-i-scale-fonts-on-a-high-resolution-screen
http://askubuntu.com/questions/526484/fix-scaling-of-java-based-applications-for-a-high-dpi-screen
-> not really working because I am using other non-Java programs which scale nicely

I am on Ubuntu Linux, but apparently the same issues exist for Swing on Windows.

If anybody found a solution for this please let me know.

Just a note, idea provides for instance a setting for the font size of the menus, which than scales very nicely, perhaps Cytoscape could provide
a similar option to scale the fonts.

Thanks for any help
Matthias

Barry Demchak

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Jan 30, 2017, 11:37:07 AM1/30/17
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Fair enough, Matthias …

 

Does this RedMine report capture what you’re seeing, or is there more to this??

 

http://code.cytoscape.org/redmine/issues/3262

 

Thanks!

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Matthias König

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Jan 30, 2017, 12:36:42 PM1/30/17
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Hi Barry,
thanks a lot. This is the same issue.
Unfortunately, on Linux not even the menus are scaled making the situation even worse than in the screenshots of the issue (see my screenshot attached).
Personally, I can't believe that there is no way to make Java Swing Applications scale on high DPI monitors via some system setting.
This makes many java swing applications very difficult to use on Linux with high DPI.

M

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Barry Demchak

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Jan 30, 2017, 2:07:59 PM1/30/17
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Interesting … yes, from my perspective, I see a properly scaled picture … where everything appears as I would expect.

 

The 4K part, though, probably means that your eye would be much happier with certain sections larger, as Windows would do with its font scaling.  Even so, the real experience on Windows is pretty far from perfect, too. Upscaling menu items is one thing. Trouble starts with upscaling fonts in tabs in tabbed displays and in dialog boxes where positioning of controls relative to each other is complex.  In general, font scaling is not solvable.

 

As relates to Cytoscape, though, would you enumerate the areas you’d like to see scaled?? It’s not a frivolous question, though, because as I try to enumerate them, I run into a lot of questions.

 

Good problem …

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Matthias König

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Jan 31, 2017, 3:04:53 AM1/31/17
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Hi Barry,
yes everything is scaled correctly, but the fonts are just too small.
The screenshot I send did not show the full effect of the problem, see attached a fullscreen view on how Cytoscape (most Swing applications) looks now for me. This is barely unusable.

M

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Barry Demchak

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Jan 31, 2017, 9:55:45 AM1/31/17
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(Cytostaff: Definitely worth a read … Matthias and Dimitry have brought this to us … question is “what to do about it”)

 

Hi, Matthias –

 

Thanks … I pretty much expected that this is the situation, and appreciate the full picture … very helpful.

 

The question on the table, though, is what would be a proper alternative?

 

For example, as you say, the Menu items are too small to read. The tab names and *all* of the icons on the control panel are also too small. I think the toolbar icons are barely usable, as are the contents of the Results panel. If the node table was filled in, I’d probably say the same thing about that, too.

 

If I had to net this out, I’d say that *all* controls, text, and buttons should be scaled up. The only thing that should not be scaled up would be the network view windows … that is where the real capacity benefit of the 4K monitor has value.

 

Would you agree?? Please feel free to argue  my position. We need a goal if we’re to move in a direction.

 

(I’m including cytostaff on this thread, and re-attaching your picture … this is something that everyone should see.)

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Matthias König

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Jan 31, 2017, 11:29:03 AM1/31/17
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If I had to net this out, I’d say that *all* controls, text, and buttons should be scaled up. The only thing that should not be scaled up would be the network view windows … that is where the real capacity benefit of the 4K monitor has value.
Yes this. Especially because I can set the font sizes of nodes and edges via visual mappings if I want.
Just a thought: I could imagine that there are issues with the layout-algorithms, i.e. spaces between nodes, but did not try this so far (but for me everything in the network view windows works fine).

By the way, I have the same problems with the display of text in my apps (cy3sbml on the right side of the screenshot).
Luckily this is all javafx & Webview and I can easily scale them up compared to the Swing components (if I find a way to get the resolution & DPI in Java).

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Barry Demchak

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Jan 31, 2017, 11:38:38 AM1/31/17
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Thanks, Matthias –

 

As for the size of nodes, I’m pretty sure this can easily be handled using the Zoom In and Zoom Out controls, right?? And zooming to fit the whole network should also work.

 

True??

 

From: 'Matthias König' via cytoscape-helpdesk [mailto:cytoscape...@googlegroups.com]
Sent: Tuesday, January 31, 2017 8:29 AM
To: cytoscape...@googlegroups.com
Subject: Re: [cytoscape-helpdesk] How to get Cytoscape scaled on high DPI monitor?

 

If I had to net this out, I’d say that *all* controls, text, and buttons should be scaled up. The only thing that should not be scaled up would be the network view windows … that is where the real capacity benefit of the 4K monitor has value.

Yes this. Especially because I can set the font sizes of nodes and edges via visual mappings if I want.
Just a thought: I could imagine that there are issues with the layout-algorithms, i.e. spaces between nodes, but did not try this so far (but for me everything in the network view windows works fine).

By the way, I have the same problems with the display of text in my apps (cy3sbml on the right side of the screenshot).
Luckily this is all javafx & Webview and I can easily scale them up compared to the Swing components (if I find a way to get the resolution & DPI in Java).

On Tue, Jan 31, 2017 at 3:54 PM, Barry Demchak <idekerlab...@gmail.com> wrote:

(Cytostaff: Definitely worth a read … Matthias and Dimitry have brought this to us … question is “what to do about it”)

 

Hi, Matthias –

 

Thanks … I pretty much expected that this is the situation, and appreciate the full picture … very helpful.

 

The question on the table, though, is what would be a proper alternative?

 

For example, as you say, the Menu items are too small to read. The tab names and *all* of the icons on the control panel are also too small. I think the toolbar icons are barely usable, as are the contents of the Results panel. If the node table was filled in, I’d probably say the same thing about that, too.

 

If I had to net this out, I’d say that *all* controls, text, and buttons should be scaled up. The only thing that should not be scaled up would be the network view windows … that is where the real capacity benefit of the 4K monitor has value.

 

Would you agree?? Please feel free to argue  my position. We need a goal if we’re to move in a direction.

 

(I’m including cytostaff on this thread, and re-attaching your picture … this is something that everyone should see.)

 

Thanks!

 

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Matthias König

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Jan 31, 2017, 11:47:37 AM1/31/17
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Yes, zooming & everything related to the new NetworkViewer is working great.
I am using Cy3.5-SNAPSHOT.

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Barry Demchak

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Feb 6, 2017, 11:25:19 AM2/6/17
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Hi, Matthias …

 

We have been kicking this around a little bit. It seems that on Mac and Windows, this doesn’t seem to be as much of a problem, as the menus and other text seems to respond to system settings. Would you be in a position to give an opinion on either Mac or Windows? I think your perspective would be pretty valuable.

 

Thanks.

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Matthias König

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Mar 27, 2017, 1:36:26 PM3/27/17
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Hi Barry,
I finally managed to test it in a virtual machine on Win 7 with the same monitors.
I can scale Cytoscape on Windows by just using the system settings (150%)
Screen Resolution -> Make text and other items larger and smaller -> Larger 150%

But than everything looks extremely blurry in Cytoscape, especially the text. The native windows windows scale nicely and are sharp, but it looks like Java swing is just up-interpolated resulting in very blurry fonts. Cy3.4 looks like a png on too large zoom setting for the pixel content.
You should have a look if you mean this by "respond to system setting", because if it is what you mean this is also not working on Win and Mac.

On Linux still the same issues, but in the meanwhile I got used to very small fonts :/

M


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tim.kacprowski

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Sep 17, 2018, 9:14:37 AM9/17/18
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hi all,

i'm having the same issue and it's very annoying.
also adding java-specific scaling to the vm options or fiddling around with cytoscape.sh and /framework/bin/karaf to get 
java -Dsun.java2d.uiScale=2 -jar some_application.jar
to work as suggest by https://wiki.archlinux.org/index.php/HiDPI#Java_applications
has no effect.
as you can maybe appreciate from the screenshot cytoscape is unusable like this. it's a pain to change all resolutions each time i want to use cytoscape.
as more and more displays will become highres, please fix this to make cytoscape usable again!

cheers
tim

Screenshot from 2018-09-17 15-11-52.png

Matthias König

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Sep 18, 2018, 4:55:21 AM9/18/18
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Yes, I could not find any solution for this so far.
It basically makes Cytoscape unusable on Linux with high DPI monitors which is very unfortunate, because all my systems are like that.

Would be great to have a solution for this.
Best M

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Joan Gibert Fernandez

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Jan 31, 2020, 4:29:45 AM1/31/20
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Hi,

I am facing exactly the same issue. Using now Cytoscape 3.7.2 with high DPI laptop. 
Is there any update on this issue?

Thanks
Joan


El martes, 18 de septiembre de 2018, 10:55:21 (UTC+2), Matthias König escribió:
Yes, I could not find any solution for this so far.
It basically makes Cytoscape unusable on Linux with high DPI monitors which is very unfortunate, because all my systems are like that.

Would be great to have a solution for this.
Best M

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Joan Gibert Fernandez

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Jan 31, 2020, 5:06:06 AM1/31/20
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Hi again,


Briefly, you should identify the name of your screen using `xrandr` and then running this python script as its mentioned. Something like:

./resolution_script.py --output eDP-1-1 --resolution 2048x1152 cytoscape.sh

I did it some test and seems to work nice. When cytoscape is closed, you go back to your default resolution. Browser seems to downscale correctly but I found some programs that do not.

Hope it helps,
Cheers,
J

Matthias König

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Jan 31, 2020, 12:38:53 PM1/31/20
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I did not find any solution so far.
Thanks for the input, I will give it a try. But it seems to me that this will just rescale my monitor when starting the program which is not a good solution.
Basically I have cytoscape running but have to switch a lot to other programs where I need the full resolution.

I got used over the years to just sit super close to my monitor when working with Cytoscape to be able to read anything.
Somehow oracle managed to make 20 java releases but was not able to bring swing on high-dpi monitors on linux.
I dropped all Java applications I was using (e.g., Jabref is a great tool, but if you can't read anything so far), but did not find any non-Java Cytoscape replacement for me so far.

Probably only have to only wait a few month more until Cytoscape supports openjdk 11, where the issue should be fixed since 2017/02/23

M





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Scooter Morris

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Feb 6, 2020, 10:43:02 AM2/6/20
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Hi Matthias,
   The Cytoscape 3.8 release candidate is out and uses OpenJDK 11.  Can you give that a try?

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Matthias König

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Feb 6, 2020, 11:51:53 AM2/6/20
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Hi Scooter,
I just tried Cy3.8.0 but get the same look and feel of the fonts then in Cy3.7.2.
See screenshot attached on how the two versions look on my monitor.

On the upside, all my javafx code seems somehow to work with openjdk 11 and Cy3.8.0 (?!) which seems to be some magic going on.
Also the new version looks super nice (especially love the update in how the tabs look) This is a major improvement.
I am basically doing the switch to Cy3.8.0 right now to get rid off all the oracle-8 trouble.

Not sure what is going on with the dpi-scaling. I will investigate some more in the next few days. As I understood it this should work on openjdk-11, but probably some additional settings required somewhere.

Best Matthias
high_dpi_cy3.7.2_cy3.8.0.png

Scooter Morris

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Feb 6, 2020, 12:55:38 PM2/6/20
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Hi Matthias,
   Yes, Cytoscape 3.8 now includes OpenJFX 13 as a dependency, which seems to work really well.  I don't have a high-dpi monitor on my linux machines, so I can't do any testing, right now, but I know that things do work on a Mac.  I'll try to source a 4K display and see what I can figure out.

-- scooter

C S

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Nov 4, 2020, 4:20:06 PM11/4/20
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This is an old thread but the problem is still there with Cytoscape 3.8 in nov 2020. However, the solution that works for jalview also seems to work for Cytoscape (http://www.jalview.org/faq/linuxhidpi). One needs to add at the top of the cytoscape.sh file the scaling option:
export GDK_SCALE=2
This works on Ubuntu 18.04 with GNOME/Cinnamon. However, scaling is not respected if one starts the application via the Cytoscape.desktop application shortcut, only if launched from the terminal.

Matthias König

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Nov 5, 2020, 3:41:29 AM11/5/20
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Hi all,

thanks for the information. Unfortunately, this solves part of the issue, but creates new problems.
The Cytoscape menus are now scaled correctly, but the network view is completely blurred. It seems the scaling is not working for the network view probably due to how this is rendered.
For the scaling to work the networks must be rendered with 4x the pixels to get a sharp scaling of 2.

So in summary: yes menus are scaling nice. Network view does not scale and is very blurry.
I prefer unreadable menus to blurry/difficult to read network views ;)
See screenshot attached


Best Matthias
cytoscape_scaling.png

C S

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Nov 5, 2020, 12:26:47 PM11/5/20
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I'm sorry to hear that the network view is blurred. For unknown reasons, I don't have this problem - scaling affected in the same way all the graphical elements for Cytoscape. For what it's worth, I'm using Cinnamon 4.2.4 on a Ubuntu 18.04 with openjdk 11.0.9 2020-10-20, OpenJDK Runtime Environment (build 11.0.9+11-Ubuntu-0ubuntu1.18.04.1) and, from the About menu: Cytoscape Version: 3.8.2 Java: 11.0.9 by Ubuntu Java Home: /usr/lib/jvm/java-11-openjdk-amd64 OS: Linux 5.0.0-1070-oem-osp1 - amd64. Best regards,
Cosmin

Matthias König

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Aug 8, 2023, 5:03:04 PM8/8/23
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Finally working after 6.5 years of not being able to read anything in the cytoscape interface ;)

The
export GDK_SCALE=2
now works with openjdk-17, Cytoscape 3.10, and ubuntu 20.04 and 22.04.

Best Matthias

Scooter Morris

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Aug 9, 2023, 8:19:38 PM8/9/23
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Cool!  Thanks, Matthias!

-- scooter

Valentina Cappelletti

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Feb 28, 2024, 11:01:42 PM2/28/24
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Works for me too! thanks a lot!!
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