Digitizing the Em2

Some of you may be familiar with the Raspberry Pi minicomputer concept. Some of you might also be familiar with the Arduino digital interface/controller. My colleague Todd ordered a Raspberry Pi and it arrived this last week. I couldn't help but imagining how we could incorporate this tiny little computer into our Em2 hacks.

The Raspberry Pi has a few advantages over the Arduino board that makes the Pi a better base platform for digitizing the Em2.

Linux-based operating system, programming opportunities with Python

HDMI output for display on a large monitor

USB input/output for keyboard, mouse, hard drives, Kinect scanner, etc.

Ethernet (10/100) connectivity

SD card as boot/flash drive (download/mount data and images with regular computer)

General purpose Input/Output pins for connecting other devices

That last item - the I/O pins provide opportunities to connect to digital devices like the LRRD's digital flow controller, or other sensors that could collect data and then combine and sync all the output.

My first priority is to get the Raspberry Pi to talk to the Kinect and automate the 3D scanning process. Ideally, we'd have two Kinects to cover the entire stream table. These would then be linked to an overall timeline of a particular experiment run (with information on discharge, sediment supply, and base level). There is a digital camera in development (5 MP) that could form the basis of photogrammetry measurements. Being automated, one could lock the cameras into position to maintain consistency.

My dream setup includes a Raspberry Pi (or two) controlling:
•Discharge from digital flow controller (or monitoring via simple Ventury tube, pump voltage, etc)
•Kinect/3D data
•Sediment Supply system voltage (either the LEGO version I've got, or something more robust)
•Base Level elevation measurements
•Time lapse photography
•Optical sediment sensor consisting of a UV LED to record the presence of individual fluorescent plastic bits that make up a small fraction of the sediment (as an estimate of bedload transport)
•All synchronized to a single timeline

So, I'll keep on hacking and we'll see where we're at in a month, semester, or year, etc. Who knows - these kinds of things always end up changing as new opportunities arise, plans end up being overly ambitious, technology doesn't cooperate, or whatever. The thing to keep in mind is that (to rephrase John Lennon) "Research is what happens while you are busy making other plans."

Emriver color-coded sediment, un-mixing the media.

My soil mechanics students had their grain size analysis lab this week. It's fun - they get to analyze granular materials by playing with sand. Specifically, the plastic sand that comes standard with the Em2 stream table. Last year I ran the standard media through a stack of sieves. This year, I ran the color-coded plastic media through the sieves.

These gradation curves are a quick way of describing and comparing different sediments. The standard media (blue curve) is different by having a little bit less material between 2 and 1mm in size (but more material larger than 2.4mm), and quite a bit more fine material around 0.5mm. The horizontal axis is in microns (1 mm = 1,000 microns) and it's on a log scale, because there's such a huge range in diameter.

Here's a frequency curve showing the relative proportions of various size fractions. The "Phi Value" is another way sedimentologists scale the wide range of particles (Phi Value = -log₂diameter in mm). So the Phi Value of a sand grain 1 mm in diameter is zero. Notice the big bump in the standard media between 1.5 and 2 phi. My own speculation is that as the material moves around, the big particles grind themselves down into particles around this size (0.3mm).

What you can't see, and what is the true brilliance behind the color-coded material, is how moving water separates the color-coded particles into various color patterns. You can also see the colors in the sieve separates, too.

So let's look at the distribution of grain sizes in the color coded media a little more closely:

 I like the distribution graph (given a little bit of visual "boost" by arbitrarily smoothing the line graph in Excel) because it hints at the formula for the Emriver sediment. There are four "bumps" that correspond to the sizes of the four different colors (Yellow = 1.4mm, White = 1mm, Brown = 0.7mm, Red = 0.4mm).

Here's an overlay of the color fractions - the curves below represent approximate distributions of each individual fraction.

Here's a picture from Steve, the big guy at LRRD's blog (Riparian Rap), showing the Em4 being filled with unmixed coded media. Given that some of the smallest yellow particles are smaller than the largest white particles, un-mixing the coded media into perfect color fractions isn't possible by mechanical means alone.

My plan now: use the grain size distributions to create "color facies" for the plastic media - providing a way to do grain size analysis with time lapse photographs.

Update: talking with Steve over email, I realized that the color fraction "curves" as drawn above may imply more quantitative "knowledge" than I really have about the distribution of each color. Here's a histogram, with the color fractions approximated by visually estimating the proportion of different colors visible in each container (vertical scale is in grams):

Slow-Mo Sedimentation: When Stokes' Law Doesn't Apply

Thanks to the ever helpful folks at LRRD, the colored sediment for my lab's Em2 arrived last week. I shot some high speed video of a scoop falling through water. Based on the results, I tried again with the help of my colleague Todd Zimmerman. We tried a few different colored gels on the translucent backdrop, but the first one that I used, a nice deep blue, works the best. I think it's because of the red-orange hues in all of the sediment particle sizes contrast well with the blue.

Colored sediment: when Stokes Law does not apply from Matt Kuchta on Vimeo.

Contrast this video with the footage we captured a few years ago of ball bearings falling through corn syrup:
What a Drag! Falling Through Syrup from Matt Kuchta on Vimeo.

The single ball bearing is a good example of how Stokes' Law works. I blogged about it before, too. But the first video shows many particles. These particles are banging into each other, the combined mass of the particles is also pushing the water around in turbulent eddies. Stokes' Law does not apply because the settling of each particle is hindered by interactions with other particles and the surrounding fluid. In these cases, we're often without a simple, elegant equation to describe what's happening. Instead, we have to rely on empirical observations. Such as the bedforms left behind in the sediments after the particles are deposited. In the end, however, many of the smallest particles are left behind to drape over the entire pile of material. So even in these chaotic, turbulent systems, Stokes' observations can still help inform us of these processes.

Emriver Color-Coded sediment in action

A little test run with the new color-coded sediment that arrived last week. It's so pretty!

I seem to recall some fluvial stratigraphy diagrams tossing around facies patterns that look strikingly similar.

I'm rather excited about 3D facies mapping possibilities here. Too bad I have so many other irons in the fire. 

Thurs-Demo: The one with Terraces

Part of my research deals with the history of rivers. Well, a few rivers in particular, but they are an example of how the landforms associated with rivers and streams can tell us about past changes to the river system. Terraces are one of my favorite. Terraces reflect periods of transition for the river system. Periods when something happened - whether it be tectonics, climate, or changes in the base level (lowest point) terraces mark a change from a stream that is relatively "stable" to a stream that is able to erode down into its floodplain.

Callan, over at Mountain Beltway, had a post about terraces last year. The picture below shows some of the work I'm doing along the Red Cedar River - a tributary of the Chippewa River - which itself is a tributary of the Mississippi River.



Depending on how picky I feel like being, I count over six terrace levels - possibly as many as ten. One of the questions I'd really like to answer is "how did these terraces form?" Did they form as a result of changes in sediment supply? Cutting off sediment supply (or increasing water discharge) allows the stream to pick up sediment along the floodplain and erode downwards. Or base level drop? A drop in the main stream would lower the mouth of the tributary. This would increase the slope of the stream locally. Increased stream flow would increase erosion. I've sketched out the two most likely scenarios for the Red Cedar below (I'm ruling out tectonics for now, but isostatic readjustment as a result of glacial retreat may play a role).



It's important to note that these terraces may not be synchronous - depending on the rate of erosion, one part of the terrace may form much later than another. Also, the direction that the terrace develops is different. With sediment supply, the erosion starts upstream and progresses downstream. By contrast, a drop in base level occurs at the mouth first and erosion progresses upstream.

This is rather an abstract concept. It's hard to intuitively understand these processes. That's where the Emriver model comes in. By manipulating the system, it becomes easier to see what's going on. But how well does the Emriver replicate these terrace forming processes? Pretty good, actually. Here's a video where I managed to alter sediment supply (by limiting the sediment mobilized upstream) and dropping the standpipe to simulate a fall in base level. Pay close attention to the direction that the incision propagates.

Halloween Stream Table Run

Today's stream table run was an adventure in basin geometry. I've been wanting to find a way to keep the stream from getting hung up on the sides of the table.



I have a bunch of rubber sheeting left over from a roofing project. Yes, I saved several square feet of sheet rubber. Because I'm an experimentalist. And I used it to created coved corners at the base of the table. I built up curved sides with the plastic media and then draped the plastic over it.


The finished sub-base, prior to filling with additional media.


Here's about a 4-hour time lapse. You can see the stream pull away from the side of the table on a few occasions, but I think I may try and make the angle a little shallower.

Permeability and the Emriver Stream Table

Got the students to do some groundwater stuff in lab today. One of the steps was to estimate the permeability of a column of sand. I used the falling-head permeameter rig that I had videotaped and demo'd earlier.

But instead of a third column of sand, I tossed some of the plastic media that comes with the Emriver setup. If you've seen these stream tables in action, you know that groundwater flow is pretty important in determining bank stability and, ultimately, what the open channel is doing.

Here's the rig:


Here's a scatter plot of all the measurements made by me and the students. For the most part, my measurements are the series that don't vary too much, while the student measurements are all over the place (well, within about 20% anyway)


This ins't a really good way to display univariate data - it's hard to determine any kind of tendency or something like that. So if I collect all the calculated permeability values and display them in a box plot, you can see that the permeability of the plastic media is about 0.3 cm/sec.


So the permeability of this material is really pretty high. You could decrease permeability a little bit more by compacting the media, but there's typically a lot of water that's flowing through the media as "groundwater." So if you're sketching up a plan for Emriver experiments, accounting for groundwater flow is probably a helpful step - especially if you're trying to produce steep gradients in a stream bed. The extra groundwater flow will tend to encourage movement of the plastic media in directions you may not expect at first.

Transformative works at the intersection of art and science

Sometimes there comes a product or concept that completely transforms the way you see things. This has happened to me recently when my lab got its Emriver stream table.



Why am I so jazzed about this thing? Well for one, it's a stream table. There's no easier way to teach and learn about stream processes than by watching a stream move sediment around. Secondly, it's the way in which Steve has chosen to implement the concept. By using ground-up melamine plastic, he has managed to address (if not completely solve) the problem of scale. And by using plastic, there isn't nearly the wear and tear on the recirculation pump, hardware, hands, floor, countertops, etc. that mineral sand would have.

In fact, by working with the plastic media, I have a whole set of plans for teaching soil mechanics with this stuff. I've shied away from some lab activities and demonstrations in the past because of the mess that real soil would cause. I've also stopped doing a few of them because the students inevitably scratch up the table tops as they drag sand around. But the ground plastic is easier to clean up, doesn't cause problems for the other folks who will use the lab room later, and by being less dense than mineral sand scales to other activities more readily as well.

This is what I mean by a transformative work. It is something that is immediately recognizable, useable, and the tools/ideas that underly its use are transferable to a wide variety of other activities. It may be a stream table, but it has already given me ideas that I can use in other courses beyond introductory geology. In fact, there is a great deal of potential simply in the aesthetics.



I brought a handheld UV flashlight to the GSA meeting (like you do) and discovered that the standard plastic media fluoresces bright blue under long wave ultraviolet light. So I set up a whole bank of 18" fluorescent UV bulbs (5 of them to start with) and started filming the stream table. Then, of course, I realized that I could place some of the fluorescent plastic BBs that I had been experimenting with earlier into the stream and watch them move down the channel. The long exposure then traces their path. Of course, I had to shoot some video:



And here we have the nub of my gist, as it were. To me, this is art. And it is also science. As an undergraduate, I majored in both Art and Geology. Part of it was my strong interest in Natural History Reconstruction (aka drawing dinosaurs). But part of it was that as a geologist, I spent as much time representing the natural world via abstraction. Most of these abstractions were intended to represent the real world, but they were themselves not the real world. Much of the work I did as an artist was informed by my interest in science. Techniques for making complex color palettes relied as much on color theory and the physics of light as they did on the aesthetics/emotional connotations of what colors I used. Photography is dependent on the optics of the light moving through lenses and the chemistry of the film (this was before cheap digital, of course) as well as the choices of subject matter, position in the frame, object of focus, etc.

To me, art and science are inextricably linked. They aren't so much two sides of the same coin, because you can deal with them at the same time. In my mind, science and art are part of the same lens. You can't use one without the other, but you can emphasize one or both. It's kind of like the whole process of learning. You can learn by having the information formally presented to you in some fashion, or you can learn by discovery. You can do both at the same time, or have one emphasized over the other.

This brings me back to the stream table. You can teach formally with this thing. You can allow people to discover and learn completely on their own. It may seem like I'm just "playing" with the Emriver system right now. But what I am doing is more complex than that. I am testing the setup. How do I need to adjust stream flow in order to achieve the best (quickest and most obvious) meandering behavior? How big an impact does a small or large adjustment in the standpipe (base level) have on the stream? How easy would it be for a small group of undergraduates to manipulate the variables or make observations about a stream system? What other activities can I do with my students using the Em2?

This isn't just "play," but joyful discovery: seeing new possibilities and creating new syntheses where none existed. Ideally, students who don't have the background I do will make their own discoveries - learning what I want but also something new. Generating a sense of excitement and accomplishment through discovery is one of my favorite parts of teaching.

Oh, and the stream table can be more than just a teaching tool. I've already got some ideas for research. Particularly as regards fossils in river deposits. For example, snail shells have a much larger hydrodynamic cross section than the sediments in the stream. These BBs are similar in that they are much easier to move despite being bigger. Where do the BBs tend to "pile up?" Are there relationships between the "facies" of plastic media (fine/course/mixed, etc) and where the BBs pile up - is this related to the fluid dynamics of the stream alone, or is it a combination of stream power and the surrounding sediment? In the field, there is a distinct connection between sedimentary facies and where we find particular fossils (or how well-preserved these fossils are). We can infer a fluvial process, but with the stream table, we can see it happen. I'm very excited about where this can go.

Do I recommend you get one? Well, if you have the funds and the space I absolutely do. But these things aren't cheap. And they do take up some space (although their storage footprint fits on a standard 4'x4' shipping pallet). But if you're limited in funds, or already have a stream table, you can still learn from the research and design done by the Emriver folks. In fact, you might be able to get parts and supplies to outfit your own system. If nothing else, go and play in a sandbox - you never know what you'll discover by playing around.

A longer run, with a little funk

I let the stream table run for over 2 hours straight yesterday. I would have an even longer video, but the flash card on my camera filled up. I really like how you can see small perturbations cancel each other out in some places and become amplified in others. In the words of Spock, "Fascinating."

Thurs-Demo:The first one with the stream table

There's a new addition to the Dirt Lab's inventory. We're the proud owners of a shiny Em2 stream table, manufactured by the folks at Little River Research & Design. Overall, I'm more than thrilled with the design and performance. I've spent the past week putting it through its paces and testing out some ideas for labs/demos for teaching and some research possibilities. I'll be adding more to this over time - the other bloggers who also have stream tables are invited to share ideas and perhaps we can have some kind of "users group" dedicated to extracting the most from these things. Maybe that's something that Google+ may actually be good for? Or perhaps with their redesigned site, perhaps the LRRD folks can provide a type of forum for these discussions.



Without much description, here are a few time lapse movies I shot over the last week. Each "run" was probably 1-2 hrs. The less "jumpy" ones were shot at 15 sec/frame while the others were made at 30 sec/frame. I shared a few previews on G+ last night and Steve Gough (LRRD's Prime Kahuna) mentioned a top-bottom view works better. Fortunately, iMovie lets me rotate the movie. So here's the adjusted film.

Cutting off the meanders

I ended up experimenting with making meanders today. I found that if you add just a little bit of extra "sand" to the lateral accretion areas (e.g. point bars) you end up producing very strong meanders. Particularly if you reduce the slope of the table.


Here's a shot of a few oxbow lakes being formed mid-run.


Here's a quick time-lapse video that demonstrates how adding extra material to the point bars rapidly increases the sinuosity of the stream. Keep in mind that the only thing I did here was to add sediment to areas of accretion. I didn't dig any channels or remove any material. I did have to add sediment along the floodplain in a few places to compensate for the change in gradient as the sinuosity increased.

Emriver setup

Before and after shots of the new stream table that arrived this week. If you look at the clock in the background, you can see that it only took me about an hour to set up. I'll have to provide more detail about setup and running the stream table.