Paraview + Volume Rendering tutorial

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.

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.

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.

• Click the downloaded file to open it and unzip it by clicking 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