Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Views area in the interface becomes transparent. #4

Open
umgpy opened this issue Jun 26, 2023 · 9 comments
Open

Views area in the interface becomes transparent. #4

umgpy opened this issue Jun 26, 2023 · 9 comments
Assignees
@RafaelPalomar

Comments

@umgpy
Copy link

umgpy commented Jun 26, 2023

Description
The Views area in the interface becomes transparent when the system window buttons are interacted with.

Steps to reproduce

  1. Run Slicer Flatpak.
  2. Navigate to the system window buttons with the cursor.
  3. The View area becomes transparent briefly until the cursor is moved.

System Information
Fedora 38 Linux 6.3.7-200.fc38.x86_64 GNU/Linux
Desktop env - Gnome 44

Additional information

Please see the screengrab for reference.

Screenshot from 2023-06-26 18-30-19
@RafaelPalomar
Copy link
Owner

RafaelPalomar commented Jun 27, 2023 •
edited
Loading

Thanks for the report, @umgpy.

Does it happen also with the regular binary distribution of slicer at https://download.slicer.org/?

Are you using Wayland?

@umgpy
Copy link
Author

umgpy commented Jun 27, 2023

Sorry, I forgot to mention it. It does not happen on the regular binary for both the stable and latest nightly install.

@RafaelPalomar
Copy link
Owner

RafaelPalomar commented Jun 28, 2023 •
edited
Loading

Thanks for the update. I have updated the flatpak to support wayland and x11 on fallback. @umgpy, could you give it a try and let me know? Also if you run the application from the terminal as flatpak run org.slicer.Slicer you probably get more information about anything going wrong. Thanks for checking.

@RafaelPalomar RafaelPalomar self-assigned this Jun 28, 2023
@umgpy
Copy link
Author

umgpy commented Jun 29, 2023

Hi, it's not running anymore after updating the flatpak repo.

 flatpak run org.slicer.Slicer  
Slicer: cannot connect to X server 
[user@user ~]$ QT_QPA_PLATFORM=wayland  flatpak run org.slicer.Slicer 
Slicer: cannot connect to X server

Let me know if I should try something else.

@RafaelPalomar
Copy link
Owner

Thanks for the info. At this point I think the best is that I try to get a VM with Fedora and try it myself. I'll get back with more info

@RafaelPalomar RafaelPalomar reopened this Jun 30, 2023
@RafaelPalomar
Copy link
Owner

@umgpy, I have done some changes and tested this again in a Fedora 38 fresh install (virtual machine) and it seems to work fine. Would you mind to give it a try? You may have to re-add the repository as the signing key has changed.

@umgpy
Copy link
Author

umgpy commented Jul 17, 2023

I removed the repository and did a clean install but the problem persists.

Below are the steps I followed to remove the application and then adding the repository again.

[user@user user]$ flatpak remote-delete Slicer 
The following refs are installed from remote 'Slicer':

   1) runtime/org.slicer.Slicer.Locale/x86_64/master
   2) app/org.slicer.Slicer/x86_64/master

Remove them? [y/n]: y
Uninstalling app/org.slicer.Slicer/x86_64/master
Uninstalling runtime/org.slicer.Slicer.Locale/x86_64/master
[user@user user]$ flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
[user@user user]$ flatpak remote-add --if-not-exists Slicer https://github.com/RafaelPalomar/org.slicer.Slicer-flatpak-repository/raw/main/slicer.flatpakrepo
[user@user user]$ flatpak install Slicer org.slicer.Slicer
Looking for matches…

org.slicer.Slicer permissions:
    ipc     network    wayland    x11    dri    file access [1]    dbus access [2]

    [1] xdg-config/kdeglobals:ro, xdg-data
    [2] com.canonical.AppMenu.Registrar, org.kde.KGlobalSettings, org.kde.kconfig.notify


        ID                                Branch          Op          Remote          Download
 1. [✓] org.slicer.Slicer.Locale          master          i           Slicer            5.0 kB / 55.3 MB
 2. [✓] org.slicer.Slicer                 master          i           Slicer          314.9 MB / 334.7 MB

Installation complete.

Upon running flatpak run org.slicer.Slicer I get the following terminal output slicer_err.log

Additionally, I manually deleted the ~/.var/app in case the previous configuration and cached data was causing issues, followed by a clean install. However, the problem of transparency still persists.

Checking the version gives this which seems to be the correct current build

[user@user user]$ flatpak run org.slicer.Slicer --version
QSocketNotifier: Can only be used with threads started with QThread
Slicer 5.3.0-2023-07-15

Let me know if I can provide more information about my system in case this is an isolated issue.

@RafaelPalomar
Copy link
Owner

Thanks for checking out, @umgpy!

The errors reported in the log seem to point to problems derived from #5: in short, SimpleITK support is not yet enabled in the SlicerFlatpak and exensions using it won't work (we are working on it). We can follow this up on #5.

As for the problem starting this issue:

(1) Do you continue experiencing the transparent interface?

(2) Do you continue experiencing the following error?

 flatpak run org.slicer.Slicer  
Slicer: cannot connect to X server 
[user@user ~]$ QT_QPA_PLATFORM=wayland  flatpak run org.slicer.Slicer 
Slicer: cannot connect to X server

I cannot reproduce either (1) or (2) anymore with the latest changes.

@umgpy
Copy link
Author

umgpy commented Jul 20, 2023

Hello @RafaelPalomar I am still experiencing (1) but not (2).

I am adding the error log from within Slicer for additional reference.

[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Session start time .......: 2023-07-20 15:26:07
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Slicer version ...........: 5.3.0-2023-07-15 (revision 31810 / d467797) linux-amd64 - installed release
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Operating system .........: Linux / 6.3.11-200.fc38.x86_64 / #1 SMP PREEMPT_DYNAMIC Sun Jul  2 13:17:31 UTC 2023 / UTF-8 - 64-bit
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Memory ...................: 15389 MB physical, 8191 MB virtual
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - CPU ......................: AuthenticAMD AMD Ryzen 7 xx, xx, 
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - VTK configuration ........: OpenGL2 rendering, Sequential threading
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Qt configuration .........: version 5.15.10, with SSL, requested OpenGL 3.2 (core profile)
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Internationalization .....: disabled, language=
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Developer mode ...........: disabled
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Application path .........: /app/Slicer/bin
[DEBUG][Qt] 20.07.2023 15:26:07 [] (unknown:0) - Additional module paths ..: (none)
[DEBUG][Python] 20.07.2023 15:26:08 [Python] (/app/Slicer/lib/Slicer-5.3/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 20.07.2023 15:26:08 [Python] (/app/Slicer/lib/Slicer-5.3/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 20.07.2023 15:26:08 [] (unknown:0) - Switch to module:  "Welcome"
[WARNING][Qt] 20.07.2023 15:26:08 [] (unknown:0) - Wayland does not support QWindow::requestActivate()
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b32b2b0)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b32b2b0)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b6aba20)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b6aba20)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8ba49200)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8ba49200)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b32b2b0)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b6aba20)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[WARNING][Qt] 20.07.2023 15:26:09 [] (unknown:0) - Could not find color scheme  ""
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8ba49200)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b6aba20)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b32b2b0)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b6aba20)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8bd08fa0)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8bd08fa0)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b32b2b0)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b6aba20)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8ba49200)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b32b2b0)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8b6aba20)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error
[ERROR][VTK] 20.07.2023 15:26:09 [vtkGenericOpenGLRenderWindow (0x560d8ba49200)] (vtkOpenGLRenderWindow.cxx:716) - GLEW could not be initialized: Unknown error

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@RafaelPalomar RafaelPalomar

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@RafaelPalomar @umgpy