Add Clara Viz operator.

[AndreasHeumann]

Signed-off-by: Andreas Heumann aheumann@nvidia.com

[vikashg]

Hey @AndreasHeumann, I tried to read a simple MR image (MNI template) using the monai transform and I wanted to display it on the jupyter notebooks but nothing happens. I followed the documentation here.

[AndreasHeumann]

Hi @vikashg. I tried the jupyter notebook you provided and indeed the Python kernel crashes for me as well. But it works if i remove the line print(Renderer(image)). I'm not sure why it crashes when doing the print in that way but print(renderer) for example works. I'll open an issue in Clara Viz on this.

[vikashg]

Hi @AndreasHeumann, So I removed the line print(renderer) line but still there is no display on my notebook. Can you share maybe your environment details. I wish I could give more info other than the terminal output

Opening in existing browser session.
[651765:651765:0100/000000.850456:ERROR:angle_platform_impl.cc(44)] Display.cpp:894 (initialize): ANGLE Display::initialize error 12289: Unsupported GLX version (requires at least 1.3).
[651765:651765:0100/000000.850557:ERROR:gl_surface_egl.cc(782)] EGL Driver message (Critical) eglInitialize: Unsupported GLX version (requires at least 1.3).
[651765:651765:0100/000000.850576:ERROR:gl_surface_egl.cc(1382)] eglInitialize OpenGL failed with error EGL_NOT_INITIALIZED, trying next display type
[651765:651765:0100/000000.856389:ERROR:angle_platform_impl.cc(44)] Display.cpp:894 (initialize): ANGLE Display::initialize error 12289: Unsupported GLX version (requires at least 1.3).
[651765:651765:0100/000000.856459:ERROR:gl_surface_egl.cc(782)] EGL Driver message (Critical) eglInitialize: Unsupported GLX version (requires at least 1.3).
[651765:651765:0100/000000.856484:ERROR:gl_surface_egl.cc(1382)] eglInitialize OpenGLES failed with error EGL_NOT_INITIALIZED
[651765:651765:0100/000000.856504:ERROR:gl_ozone_egl.cc(20)] GLSurfaceEGL::InitializeOneOff failed.
[W 19:12:37.813 NotebookApp] Notebook 06_integrating_clara_viz.ipynb is not trusted
[W 19:12:37.841 NotebookApp] 404 GET /nbextensions/clara-viz-widgets/extension.js?v=20220114191109 (127.0.0.1) 20.650000ms referer=http://localhost:8888/notebooks/06_integrating_clara_viz.ipynb
[I 19:12:38.067 NotebookApp] Kernel started: ee55c289-ab1f-42ab-ac14-fb5b2d44256f, name: python3
[W 19:12:38.077 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20220114191109 (127.0.0.1) 2.080000ms referer=http://localhost:8888/notebooks/06_integrating_clara_viz.ipynb
[W 19:13:21.845 NotebookApp] 404 GET /static/clara-viz-widgets.js?v=20220114191109 (127.0.0.1) 6.400000ms referer=http://localhost:8888/notebooks/06_integrating_clara_viz.ipynb
[I 19:14:38.734 NotebookApp] Saving file at /06_integrating_clara_viz.ipynb

[AndreasHeumann]

The first few lines come from the browser not being able to initialize OpenGL. Did you run the Jupyter Lab command from a ssh connection? Usually I run it on ssh with jupyter lab --no-browser --ip=* on my LInux desktop and then open the browser on my Windows Laptop and navigate to the IP address of the desktop, e.g. http://192.168.178.44:8888/.
On my desktop I'm using Ubuntu 20.04, I'm using a conda environment with Monai Deploy App SDK, Jupyter Lab and Clara Viz installed.

[vikashg]

Hi @AndreasHeumann, So yes it works with jupyter-lab but not with jupyter-notebook

[AndreasHeumann]

jupyter-lab and jupyter-notebook are using different interfaces for the widgets. Clara Viz should support both, but we had issues with that in the past. I'll check why it does not work with jupyter-notebook.

[AndreasHeumann]

I filed NVIDIA/clara-viz#9 for the bug that the Clara Viz widget is not working in Jupyter Notebook (only in Lab).

[AndreasHeumann]

@vikashg I just released Clara Viz 0.1.2. That version fixes the crash you were seeing with print(Renderer(data)) and now the widget also works in Jupyter Notebook (not just Jupyter Lab).

[vikashg]

Thanks @AndreasHeumann I will check it out today/tomorrow.

[MMelQin]

Look good to me, and I tested out this operator in the Spleen Seg App.

[dbericat]

Is it fair to say we already have a good Clara Viz operator? @MMelQin what are the plans to update the Jupyter notebooks with it?

[MMelQin]

In the upcoming v0.3 release, yes.

[vikashg]

We have to prepare a jupyter notebook for tutorials and maybe update demos 4 and 5 with some clara-viz operators. to fully integrate it. i was making a tutorial. I will update it with spleen segmentation