6. We can also change the color scheme and each color's range in the data. To do this, click the Edit button under Coloring.

7. Under the Information tab (on left side next to properties), we can get learn more about the data, including the size of the dataset, the data ranges, and data type. 

8. In the third row of the top section, there are various cube icons that help us alter and further analyze a volume, including contour (surface rendering), slicing (cutting a plane from the data set), and clipping (cutting a section of the dataset). Experiment with these functions!

• If these appear greyed out, try pressing the Apply button under Properties.

• Once you choose one of these cube icon option, press Apply again. Then, disable the view of the main data layer (i.e. by using the eye icon), and enable the view of the new layer you added

9. Choose a visualization to view in VR. Then connect your headset to your machine using Remote Desktop. 

10. Once connected, open the Tools dropdown of the upper left menu in Paraview from your desktop and select Manage Plugins.

10. Scroll down to the OpenVR plugin, click on it, and select load plugin.

11. Click the Send to OpenVR button in the left menu. If you get errors (about SteamVR / your headset not being connected), try to enter SteamVR home on your headset (or any other app in SteamVR), and then press "Send to OpenVR" from your desktop -- you should then automatically be re-routed to Paraview from whichever app you are in.

11. Put on your headset again. You should now see your visualization in VR. Take a screenshot of it and post it to the class board.

Controls

Hold both side triggers and push them towards/away from each other to move the visualization up/down. 

Some example visualizations from past years: 

Credit: Alejandro Romero (Spring 2021)

Ben's Volume Renderer

Estimated time: 40 minutes

Requirements:  Windows 10*, SteamVR, and Visual Studio Community 2019 (or later versions).

Overview

In this section of the tutorial, you'll be visualizing three different datasets: 

• The rat heart vessel 

• A 3D model of the Narragansett bay 

• A 3D model of microtissue cells captured from a confocal microscope 

You'll be visualizing these datasets with a partner, which will be given at the beginning of class. Note that the volume renderer implements controller-viewer collaboration, in which one user -- the controller -- performs actions while the other users -- the viewers -- spectate. Practically speaking, this means that you and your partner will have to take turns as the controller. 

Objectives

While working through this section of the tutorial, complete the following objectives:

• Recreate a similar rat heart vessel visualization to the one you created in the Paraview tutorial (this will require scaling and z-scaling; see the Volume Renderer Controls section for more information). Then, make a screenshot of your recreation and add it to the activity board doc. 

• Visualize the two other datasets, take screenshots, and add them to the activity board doc. Be sure to play around with the color curves mentioned in the Volume Renderer Controls section 

Installation

Steps:

• Download the Volume Renderer zip file.

  • If you are using paperspace:

    • copy the link above, open the paperspace console and open Google Chrome on your console

    • Click the circle icon menu in the top right, and click sync clipboard

    • Press the command to sync your local clipboard to Paperspace (Ctrl+V on Windows and Cmd+V on Mac)

    • Then press Ctrl+V to paste the download link into your browser on paperspace and download.

    • (Before downloading, delete any older versions of the VolumeViewer folder in your downloads)

• Click the downloaded file to open it and unzip it by clicking Extract Here / Extract All

• Next, run setup.bat by double clicking on the file. You'll be prompted with the following screen: 

• Enter your name. 

• Next, enter your appid, which will be given to you at the beginning of class. 

• At this point, the Volume Renderer should be ready to run!

Starting the Volume Renderer

• Close SteamVR if it's running on your machine and connect your headset to your machine using Virtual Desktop. 

• Launch Virtual Desktop and connect your headset to your remote machine. 

• Launch SteamVR IN YOUR HEADSET using the Virtual Desktop menu.

• Depending on what dataset you want to visualize and whether you're the controller or viewer, you'll need to run one of the files from the file explorer:

  • To visualize the rat heart vessel as the controller, select rat_heart_controller.bat

  • To visualize the rat heart vessel as an observer, select rat_heart_observer.bat

  • To visualize the Narragansett Bay dataset as the controller, select OSOM_HMD_controller.bat

  • To visualize the Narragansett Bay dataset as an observer, select OSOM_HMD_observer.bat

  • To visualize the microtissue dataset as the controller, select NRRD_HMD_controller.bat

  • To visualize the microtissue dataset as an observer, select NRRD_HMD_observer.bat

• To exit out of the current visualization, press the hamburger menu button on your left controller, then press the Desktop button in the bottom left and select a new file. 

Volume Renderer Controls

Ben's Volume Renderer supports a variety of controls that utilize both the Oculus Quest controllers and a menu. While working on the above objectives, you'll likely want to view these controls in your headset. This can be done launching the SteamVR menu (click the button with three bars on the left Oculus controller) and selecting Desktop from left panel of the SteamVR menu. 

Quest 2 Controller Controls

Menu Controls

The menu in the Volume Renderer allows you to customize the appearance of the rendered model. Here is a brief description of what each option does:

• alpha multiplier -> changes the opacity of the rendered model (less alpha = more transparent)

• threshold -> adjusts the minimum value required for a data point to be visualized (larger threshold = less details)

• scale -> changes the overall scale of the model (in all dimensions)

• z-scale -> adjusts scale of the z dimension of the model 

• slices -> adjusts the number of slices used to visualize the model (less slices = less detail)

• use transferfunction -> activate this to adjust the colors of the model; see the second image below demonstrates what your menu should look like once this feature is activated

Troubleshooting

AppId Errors:

• If you run the run_steam_vr.bat file and see errors in the terminal about appID -- you entered your appID wrong in the setup.bat file, or haven't set it up at all. If you already ran the setup.bat file once, you cannot run it again. You must open the HMD_controller.minvr or HMD_observer.minvr (depending on which role you choose) and enter your appID and name in the correct field manually, i.e.

  • • • <AppID>ENTERYOURAPPIDHERE</AppID>

      • <PlayerName>ENTERYOURPLAYERNAMEHERE</PlayerName>

• Your appid is case sensitive, so make sure it is entered exactly

• If you don't see that popup, click on the hamburger menu (☰) in the SteamVR popup on your Virtual Machine -- then navigate to Settings. 

• In the settings window, make sure Advanced Settings are enabled (Show Advanced Settings, at the bottom). From here, go to the Startup/Shutdown tab, and click on Manage Addons -- make sure the Virtual Desktop Streamer (Quest) addon is enabled. 

• Once done, make sure to restart SteamVR for these changes to take effect.