Craig Ulmer

Pattern-of-Life Activity Recognition in Seismic Data

2022-04-15 pub data seismic

A collaborator in one of my research projects included me on a clustering paper that he had accepted in Applied Artificial Intelligence. Erick was interested in developing new algorithms that could help characterize different activities taking place in seismic data. As a data engineer in the project, I gathered data and did a lot of tedious, manual inspection to extract ground truth the team could use to train their algorithms. You can tell I had a hand in making labels, given the descriptive category "workers unroll white thing".


Abstract

Pattern-of-life analysis models the observable activities associated with a particular entity or location over time. Automatically finding and separating these activities from noise and other background activity presents a technical challenge for a variety of data types and sources. This paper investigates a framework for finding and separating a variety of vehicle activities recorded using seismic sensors situated around a construction site. Our approach breaks the seismic waveform into segments, preprocesses them, and extracts features from each. We then apply feature scaling and dimensionality reduction algorithms before clustering and visualizing the data. Results suggest that the approach effectively separates the use of certain vehicle types and reveals interesting distributions in the data. Our reliance on unsupervised machine learning algorithms suggests that the approach can generalize to other data sources and monitoring contexts. We conclude by discussing limitations and future work.

Publication


SmartNICs for Data Management in HPC

2021-10-12 smartnic faodel hpc

Carlos Maltzahn invited me to give a talk about SmartNICs at the annual UCSC CROSS Research Symposium. I put the below talk togethers to cover some of our work in moving data with the BlueField SmartNICs. One of the things we have found recently is that while the current SmartNIC ARM processors are slower than x86_64 host processors, they can perform some data management tasks just as fast as other alternative processors being used in HPC (eg, KNL or ThunderX2 ARM). Here are the slides (UUR SAND2021-12527 PE).


Presentation


FAODEL 1.2108.1 Released

2021-10-08 faodel code

I am happy to report that we (finally) shipped the "Fluid" release of FAODEL on Github this week. Looking back now, it's been over two years since our last external release. We had intended to make the updates available last year after our big milestone project with SPARC completed, but we ran into a number of chicken-and-the-egg problems with other software libraries (eg, we can't test our release until you release updates that use our release). It also didn't help that we added a few new featured while waiting on the release logistics to work themselves out. Continually adding "just one more thing" winds up resetting the release process a lot, which is lengthy when you have to test against multiple platforms, multiple nics, and multiple software stacks. Todd Kordenbrock did an excellent job of working out all the painful details and finalizing everything. Thanks, Todd!


Highlights of New Features

I'm really pleased with some of the new features in this release:

  • Tracing/Playback: We added some tracing and playback tools to FAODEL that allow you to capture the list of operations a user is performing with a pool so that you can play them back at a later point in time. We found this to be very useful in our SPARC milestone because it lets you capture an application's behavior and then re-run it with different conditions, without having to use to the application. Given that sims are always bulky and difficult to tweak, this feature is really handy for architecture studies. We found the playback option was also really useful for scenarios where we needed to setup pools in a specific way.
  • Kelpie Blast: There's a new option in the faodel command that blasts data at a pool in a way that's similar to simulations. This tools is handy for seeing what the impact of different pool configurations will be on write-focused operations.
  • faodel-stress: Taking inspiration from stress-ng we created a new tool called faodel-stress that measures how quickly a local compute node can perform non-network tasks that are relevant to data management services (eg, key sorting, hash maps, serialization). We've used these tests to compare the processors in different platforms and have found several deficiencies that we'll be reporting on soon.
  • RoCE: We've added support to work with RDMA over Converged Ethernet (RoCE). While we've typically focused on HPC platforms, we're seeing a number of HPDA systems with Ethernet start to use RoCE to overcome TCP overheads. Adding support for RoCE allows us to run on our own Carnac platform and do experiments on some BlueField platforms in the clouds.
  • User-Defined Functions: We added a new, experimental API for performing user-defined functions in pool nodes. Functions are static and must be registered when the pool nodes start, but the interface provides a simple way for users to query a row and generate a single reply. This capability has been on our todo list since the beginning. This API will almost certainly change in the future, but I'm excited to think about how we can use this to make the pool nodes more active.

The following are the more terse release notes from NEWS.md:

Release Improvements

  • Kelpie: Added Drop and RowInfo operations for remote use
  • Kelpie: Added ResultCollector to simplify async requests
  • Kelpie: New trace pool for client-side pool activities
  • Lunasa: Added DataObjectPacker for easier packing
  • Lunasa: Added StringObject for easier packing of text
  • NNTI: Added support for RoCE
  • faodel-cli: config-info dumps out configuration options
  • faodel-cli: New playback option that can use traces
  • faodel-cli: New kblast option generates parallel kelpie traffic
  • faodel-stress: New tool for benchmarking CPU for non-net activities
  • OpBox: Ability to capture timing traces for ops
  • Backburner: New notification methods to decrease CPU usage

Significant User-Visible Changes:

  • Kelpie: kv_row/col_info_t replaced by object_info_t (smaller, simpler)
  • config: "ioms" are now "kelpie.ioms" config: backburner.notification_method for pipe, polling, sleep_polling
  • Examples can now be built inside the build via BUILD_EXAMPLES
  • OpBoxStandard is now OpBoxDeprecatedStandard

Experimental Features

  • kelpie 'Compute' allows server to perform computations on objects via UDFs

A Few Photogrammetry Experiments with Max

2021-09-04 3d viz

While 3D printing bones from CT scans was fun, what I'd really like to do is scan in ordinary objects that I could manipulate and print. Professionals that do this kind of scanning use expensive LiDAR scanners or setup special rooms with calibrated camera arrays. Intel's RealSense L515 camera looked like it would be a promising, lower-cost LiDAR camera, but Intel just announced that they're killing off all the RealSense products (yet another failed intel product line). Apple's phones and tablets with LiDAR sound like what I need, but I just can't force myself to buy anything from Apple (not even that laptop that thieves just ordered with my credit card and shipped to my house by mistake!). That leaves me with plain old photogrammetry from images.

Qlone

Previous experiments with Meshroom left me feeling like I could get some good results, but only if I put a lot of effort into doing the photography right. In hopes of finding something that was more integrated with a phone, I skimmed websites and found some positive reviews of an Android app named Qlone that could scan simple objects using just a phone. The clever part about their approach is that they use a specially formatted mat that you print out to help orient the camera. I downloaded the free version of the app, printed the map, and set off to scan in an old Max Headroom candy container I bought from a gas station back in the eighties (interestingly, someone else has already scanned this in and posted it to thingiverse).


One of the nice things about Qlone's approach is that the mat makes it possible for the camera to figure out its orientation in real time. It renders a dome over your camera view while you're scanning so you can see what angles need to be done. While I initially tried moving the phone around the object to get all the pictures, it was a lot easier to hold the camera at one orientation and then just rotate the mat. Once the app had pictures from all angles, it went through the math to chip out a 3D model. While the model did look like Max Headroom, the quality was pretty low. This might have been because the subject was plastic (photogrammetry has trouble with glossy surfaces), but I'd also suspect its difficult to get good results out of a phone app.


The free version didn't have a way to export the model in a useful way, so the only result I have is this gif. The app baited me with a "buy in the next 20 minutes and get a discount" option. I declined though, figuring anything with a time-limited sale like this probably isn't worth it. While I really liked the user interface for this tool, it didn't produce results that would be good enough for printing.

Back to Meshroom

I decided to hunker down and spend some time experimenting with how to take pictures that would be better for meshroom. People online suggested using a prime lens and constant camera settings, so I impaled Max on a pvc pipe, set him up in my garage, and the did a sweep of pictures using my Canon D77 with a 50mm EF prime lens. I (wrongly!) guessed that I should use a low f-stop (ie, F/1.8) to maximize the blur in the background, hoping that this would make it easier for Meshroom to pick out the foreground. About midway through the pictures I realized that the lighting wasn't very even in the garage and that several of my photos were out of whack due to me having to step around junk sitting around my garage. As I feared, Meshroom was only able to infer about half of Max's head. I moved Max's pipe outside and did another round of pictures in the sunlight.


Meshroom did a much better job reconstructing Max with the second round of pictures. The results are bumpy, but the general shape is there with a decent amount of detail. I was impressed at how well it found the lines in the glasses and the creases in his forehead.


Scan Problems

While the scan looks pretty good visually, you begin to see more of the flaws when you take away the texture map and just look at the durface mesh. If you look at the arms of Max's glasses below, you'll notice that the mesh doesn't know there's a space between the glasses and his face. The texture map adds some color shading to the triangles that makes it look like the glasses are floating and casting a shadow on his skin. Unfortunately, I need the mesh to look good by itself if I want to make a good 3D print.


It's difficult for photogrammetry software to recognize separations like this without a lot of supplemental pictures that aim through the gap. If I wanted to scan Max in the right way, I'd probably pull the Max figure apart and scan each item separately. I'd probably also spray him with something to make the plastic less reflective. This is more work than I want to put into it right now.

Reading through some other web pages, I've realized that I got my camera settings backwards: primes are good for consistency, but the background should not be blurry. A presentation at the Slade School of Fine Art on Photogrammetry recommended an f-stop of F/8.0 as a starting point. Given the number of pictures that Meshroom threw away, I suspect it's useful to have some background detail to help figure out what's going on in the foreground. In any case, these are all good ideas to try out another day.

Files

Here's a copy of the mesh and textures: maxmesh.tar.xz


3D Printing My Pelvis from a CT Scan

2021-06-06 viz print

A few months ago I bought my son a Creality LD-002H Resin 3D Printer so we could play around with printing some simple objects. Like most people, we watched a lot of videos to get a better handle on how to (safely) work with resin, printed a bunch of example objects from Thingiverse, and then watched more videos to figure out how to make better prints. While printing models has been fun, I'd really like the kids to get a better handle on how to create their own objects through photogrammetry tools like Meshroom or editors like Blender.


The last few weeks I've been working through the details of how I could convert and CT scan of me into something I could print. Through a combination of open-source tools I was able to generate a mesh model of my pelvis and print a small version of it. I seem to forget how to use all these tools after a few days, so this post is just some notes for me to be able to recreate the process in the future.


Viewing CT Data in 3D Slicer

Back in 2013 I had to go to the hospital because I had a bad infection that needed surgery. The doctors ran me through a CT machine to get a better view of what was happening inside me. After my surgery I learned that Kaiser will burn a CD with your data on it for only $20 if you ask them. Being curious, I ordered a copy and poked around with it for a bit. While the data isn't in a format that I recognized, a viz friend pointed me at a tool called 3D Slicer (based on VTK) that's designed to look at medical data. It's a little confusing to get started, but you basically:

  • Start Slicer
  • Use 'Add Data' to point it at your CD
  • Use DICOM to see the available entries in the data
  • Select the entry with scan data (eg SAG 3MM) and Load
  • Change to volume rendering and open the eye icon
  • Adjust the Shift value to change the threshold level

I always stumble around with the default view settings. Usually the problem is that I haven't loaded a DICOM entry with anything in it (eg, a patient record) or I forgot to tell Slicer to view the data by turning the volume's closed eye into an open eye. Once the 3D data shows up, I switch to a 3D-only view by selecting View and Layout.


Extracting and Smoothing Contours

While the volume rendering tool is a nice way to poke through the data, what you really need to do is extract the contour for the bone so you can extract it as a mesh (ie, isosurfacing). To do this you need to run the Segmentation tool to build a mesh and then smooth it to make it more printable.

  • Turn off the volume rendering
  • Switch to the Segment Editor
  • Select the Master volume to segment (note: default may not be right)
  • Add a new segment and click Edit
  • Click Show 3D to view
  • Select Threshold, pick a value, and then apply
  • Use Islands to remove background noise
  • Use Smoothing to fix some bumps

It took some trial and error to find a threshold value that produced a good view of my pelvis (too low and you get tissue, too high and the bone starts disappearing). The two main issues I saw with segmentation were that some regions had small holes and some curving regions were bumpy like corduroy. Selecting the Smoothing option from the Segmentation options helped fix some of these problems. I'm sure you could do a lot more here to fix things- some of the videos I watched showed how to get precise segmentation by hand labeling points. I'm not printing an actual hip replacement so I didn't go into to much detail. Once I was done I clicked on the Segmentations button and exported to STL.


Cleanup in Meshlab

I pulled the STL file into MeshLab to verify it looked ok in another meshing tool and do some additional cleanup. While I think Slicer can do this cleanup, MeshLab seemed like an easier way to make some hand edits. I looked around in the mesh and manually removed some leftover polygons.


Adding Supports in Chitubox

The final step for me was to load the model into Chitubox to turn it into printable object. Chitubox is pretty amazing- it'll analyze an object and figure out what supports would be added to make it printable on a 3D printer. My neighbor does a lot of 3D printing and gave me a lot of tips on making good prints with Chitubox. eg, Make the back side of the model face the build plate so the supports don't leave bumps in important places, angle the structure to make it easier to build, use the skate support platform shape to make it easier to remove, etc.


I manually placed the pelvis model and rotated it slightly, but pretty much used the default settings everywhere else. Even with a ton of supports, Chitubox still wasn't too happy with the printing risk. Once it was done I adjusted the print's first layer exposure time to 60s and the remaining layers to 6s. Based on previous prints, if you don't expose the first layer for long enough it doesn't stick to the build plate and your print fails.


Printing, Cleaning, and Curing

The final step was to take the model to the printer and print it out. Resin printing is a pretty messy and dangerous process. You align the print head (crucial!), pour resin into the vat, load the vat into the printer, and then print the model. This print took about four hours, but I didn't have to babysit it after I verified the first few layers had stuck. When it finished, I chiseled the part off the build plate and dropped it in a pickle jar (w/ strainer) filled with isopropyl to clean off the uncured resin. After a lot of shaking, I took it out and clipped off all the supports (which is unusually satisfying). From there I did another quick rinse in isopropyl, patted it down with paper towels, and put it under a UV light to cure it.

I'm still new to 3D printing but I think it looks pretty decent. The main problem with this print is that I scratched it up quite a bit when I was cleaning it up with paper towels (the print is still pretty soft at this point). In the future I'll probably buy a curing station which simplifies a lot of the cleaning and curing problems. The other problem with the print is that there are some extra holes in the back because I set the contouring threshold value too high. At least that's what I hope- maybe I just have really thin bones.

Safety and Cleanup

I should point out that the resin I'm using is toxic when uncured and it's important to follow safety procedures when doing this kind of printing. I wear disposable nitrile gloves and safety classes whenever I work with uncured resin, and crack the garage door to help vent the area. When it comes time to handling wet prints my neighbor suggested a practice of having one clean hand and one dirty hand, since there's always something you need to grab and you want to minimize what gets dirty. I use an excessive amount of isopropyl to clean up the build plate, vat, and tools when I'm done. Fortunately, you can just leave all the dirty towels and gloves in the sun for 30mins to cure them and make them safe for disposal.