3D Web App Next Steps

[davramov]

After discussing with Elizabeth, Dula, and Dylan, we came up with a few next steps about visualizing reconstructions both at the beamline, and when users return home.

When the new 8.3.2 Viz Computer arrives:

• Reinstall Jupyter/ITK visualization
• NFS mount the new viz computer's drive to data832 and use that globus endpoint for transfers
• Host reconstructions via Tiled server running on the new BL computer
• Build ITK widget into a web app
  • Link from SciCat to the web app (no code) and a Jupyter environment (deep dive)

Short term:

• Downsample raw data by a factor of 2 (bilinear) on data832 before processing reconstruction (for more immediate results)
  • Run a Prefect worker on data832 for downsampling
  • Register a downsampling flow on flow-prd
  • Call the downsampling flow after new_file_832 (once the raw data is on data832) and before sending to an HPC facility (NERSC or ALCF)
  • Create queues for "downsampled" (high priority, fast throughput) and "full-scale" (slow, can sit in the queue) reconstructions
• Start building ITK widget into a web app

[davramov]

Last week I tried getting the standalone web version of itkwidgets running locally, but couldn't, so I opened a git issue on their repository: InsightSoftwareConsortium/itkwidgets#765

Paul responded, and their instructions worked for me. I was able to start an HTTP file server (with CORS enabled) serving an NGFF-ZARR directory, and then appended that path to the viewer URL as described:
https://kitware.github.io/itk-vtk-viewer/app/?rotate=false&image=http://localhost:8000/rec20230606_152011_jong-seto_fungal-mycelia_flat-AQ_fungi2_fast.zarr

Using this approach, if we host the zarr reconstructions on Tiled, we could dynamically generate the URL to visualize each dataset, and add the link in SciCat.

[davramov]

Update on the standalone viewer. I attempted to sort out why the cli version of itkwidgets was not working properly via pip, but I still hit roadblocks there. Interestingly, on the kitware site documentation, they listed a npm package for cli access to the viewer that can be installed globally on a machine, rather than python. Using this method, I got the viewer to run locally in fullscreen mode in the browser!

Reproduction instructions:

1. Install npm. I downloaded the MacOS Installer .pkg version and installed it.
2. Run npm install itk-vtk-viewer -g in the terminal
3. Run itk-vtk-viewer in the terminal. This will open a new browser window at localhost:3000
4. In another terminal, start scripts/serve_zarr_cors.py rec20230606_152011_jong-seto_fungal-mycelia_flat-AQ_fungi2_fast.zarr
5. Update the url in the browser: http://localhost:3000/?fileToLoad=http://localhost:8001/rec20230606_152011_jong-seto_fungal-mycelia_flat-AQ_fungi2_fast.zarr

Now that I have the viewer running locally, I am trying to serve the zarr folder using Tiled rather than my python cors server.