Overlapping Adaptive Mesh Refinement (AMR) in ParaView

First year of grad school done, second one about to start! It’s been an absolutely amazing experience so far – more to come about the bioinformatics aspect of it in future posts.

For this post, I wanted to discuss one of the plugins I developed during my scientific visualization class, and my newfound (at that time) love for the VTK framework and ParaView.

Visualize Everything!

If you haven’t encountered it before, VTK (Visualization Tool Kit) is a framework developed by Kitware for handling the entire pipeline process from consuming organized data, processing, filtering, visualizing, and/or exporting. They’ve also developed an accompanying GUI application for easily manipulating VTK, called ParaView. Both of these packages have been around for many years, but I had (unfortunately) not been exposed to them until my class – however, after using the software for a short time, I quickly realized how ridiculously powerful the framework is, and I really wanted to do more work with it.

The UNH Granite Scientific Database System

Being an open source pipeline, one of the places VTK shines is in its modularity and expandability – almost every part of the pipeline can call a custom plugin. I decided to take advantage of this – UNH has a custom Java library named The Granite Scientific Database System (Granite SDB), which provides a comprehensive set of classes for accessing multidimensional scientific data. It was originally developed, and continues to be maintained by, UNH Professor Daniel Bergeron, and has been expanded over the years by a number of students. While it is very powerful in its capabilities, it is designed strictly as a processing and storage library – it leaves the actual visualization routines to the developer. With this in mind, I thought it would be a perfect match to write a Granite plugin for ParaView.

Single Resolution Data

Before diving head first into the full capabilities of VTK, I decided to start with a simple read plugin for working with single resolution data. Since there are such a large number of medical images/datasets available in on the net (CT and MRI scans), especially in DICOM format, I decided to start with loading this data into Granite, and then seeing if I could visualize this with ParaView via the plugin. After only a few days, I was able to get perfect results! Here are some examples of sets loaded through the plugin:

Mummy (CT)

Head Slice (MRI)
Head (MRI)

Beetle Micro CT
Beetle (Micro CT)

Cool stuff! With that working, I wanted to tackle more…

Multi and Adaptive Resolution

One of the challenges when visualizing data, especially large amounts of data, are the limitations of the underlying hardware. By necessity, different methods must be employed to only visualize the relevant portions, whether it be the amount rendered, areas rendered, streaming portions at a time, etc. Along these lines, VTK offers a newer portion of the pipeline that allows for streaming blocks of overlapping data at different resolutions. In this way, only specific areas (dependent on the viewport focus – direction and zoom) will be rendered, and done so in a streaming manner, so the user can continue to manipulate the program while searching for areas of interest in the render.

Long story short, the following video is the end result of the plugin supporting overlapping AMR. In this demo, the plugin resets the visualization every time the camera is rotated to demonstrate clearly how it operates. As can be seen, the data starts out at a very low resolution for quick rendering, then continues to resolve to higher and higher resolutions, centered around the area being viewed, as data is streamed from the Granite, through the plugin, into VTK. I used the same mummy CT scan as shown above.

For the plugin and documentation, check out the GitHub repository.

For the extended documentation, including theory, results, structure diagrams, citations, etc, see the plugin final report.

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