Addendum to SV-POW!’s “SO close”

Mike Taylor recently sent me an email asking for a larger version of a figure I once published in a book chapter. Naturally, I promised to send it to him. But, being away from my computer, with email available only via my phone, I couldn’t send it right away. And promptly forgot.

Thus, Mike had to go ahead and publish the planned blog post without my figure. Here’s the link.

Now, I finally remembered, and through sheer persistence managed to find my original submitted files in my sorry heap of data backup. Here goes – starting with a small part of a big figure, but a part that shows nearly all that needs to be shown to make Mike’s point:

so_close_01

This is a CAD model of Diplodocus I built long ago. It is rough, and takes air spaces within the body into account in a fairly rough way, but – and that’s a big issue with dinosaur models – there is enough soft tissue mass modelled onto the tail, especially its base.

I used a rather complex multibody dynamics program to do all kinds of shit with the model, but first of all I had it calculate the position of the center of mass (COM). I won’t bore you with the full story; suffice to say that I put a small white dot in the figure to show the result.

Yes, the COM is that close to the hind limbs.

Now, one model alone would be bad practice, so I ran a bunch of variations. As long as my assumptions about density and volume stayed reasonable, the COM stayed really close to the hind limbs.

The next thing I did is look at another sauropod, one with a quite different overall look: Giraffatitan. Unsurprisingly, a much shorter and thinner tail and much longer and stouter forelimbs meant the COM came to rest somewhere else entirely. You’ll see in a moment…..

Then, I went ahead with the work I had set out to do originally: look at the ability of the two sauropods to rear into an upright stance. Not just rear up and come back down with a thump! right away thanks to gravity, but the ability to adopt a bipedal pose that puts the head high up for feeding on large trees. A position that must thus be held for quite a while, which in turn requires that it is inherently stable, that you can get there easily, and that you can get back down speedily, too.

Why inherently stable? Well, think of a ladder and how you behave on it. When you are high up on a ladder you will either be careful and restrict your movements, or you will fall. If you’re positioned so that the tiniest motion unbalances you, there is no way you can do useful work for a prolonged time. For a sauropod poking its head into a mass of branches, grabbing them and pulling vigorously most certainly was an activity that required it to be posed so that it did not constantly worry about toppling over.

Why easy to reach? Because if it is really hard to reach, harder to reach than a similar pose is for an elephant, then the effort to get there makes it so difficult to use that it is no good for regular behaviour. Sure, you can do the weirdest stuff, like walking on your hands. But every day?

And why is getting back down so important? That is in fact the simplest point: if a big theropod ambles by, you do not want to spent several minutes carefully letting yourself back down into a pose in which you can deal with the threat.

So, I modelled on, and here are the figures as the appear in full in the article:

so_close_04

This is one way Diplodocus can easily get into an upright position. By pushing its butt backwards a bit, flexing the knees a tiny bit, the COM comes to rest right above the hind feet. Now, all it takes is a very slight rotation in the hip joints, easily achieved by the strong caudofemoral muscles of both sides acting together, and the entire animal minus the legs starts rotating. When the tail hits the ground (slowly and softly) it is time to stop. There you go – feeding height doubled, or tripled, depending on how mobile you believe the neck is in extension.

Back down is also easy: just a push forward with the forelimbs to get some momentum, and slowly relaxing the caudofemoralis muscles and the animal is back down in a few seconds, ready to fight or run away (well, amble away that is).

In between, all is well balanced, because the limbs that can counter a slight imbalance easily, the hind limbs, are attached to the body at roughly the height the center of mass is at. Motions of the COM can therefore be countered quickly, before the shit hits the fan. If there was a long lever arm between the point where the animal can influence the trunk’s position relative to the limbs and the COM, it would be a very difficult task to fiddle things into equilibrium.  Additionally, in lateral view the angle between the line connecting the edge of the support area and the COM and the vertical through the COM is larger the further down the COM is, meaning higher stability as well.

so_close_03

Giraffatitan left, Diplodocus right. Guess who’s standing stably, and who’s more like a drunk on a ladder?

so_close_02

Various poses I tried for Giraffatitan. The COM is shown by a tiny sphere in the middle of the body. High, high up, far away from the hip joints. This doesn’t look good for balance. Add to that the emaciated tail base and thus weak caudofemoralis muscles of Giraffatitan, and you get an animal that was really bad at rearing up and staying there. Diplodocus, on the other hand, was (I concluded) well capable of rearing up and staying there for an extended feast.

So, what does that mean for Mike’s bipedal Diplodocus? For one thing, the COM is in the right place. The other thing is that a bipedal pose would have required somewhat flexed hind limbs. Not something I guess the animal did for a long time. And there are lots of issues with walking bipedally, not least the issue of retaining steering. Obviously, one can use various tricks for keeping the body position stable, but why bother if there is an easier way? Even a paltry 10% of body weight supported by a forelimb placed well forward of the hind feet would help a  tremendous lot with going in the actual direction you want to go. So bipedal Diplodocus yes, but not regularly!

Oh, here’s the full citation for the paper; email me for a PDF.

Mallison, H. (2011). Rearing Giants – kinetic-dynamic modeling of sauropod bipedal and tripodal poses. Pp. 237-250 in Klein, N., Remes, K., Gee, C. & Sander M. (eds): Biology of the Sauropod Dinosaurs: Understanding the life of giants. Life of the Past (series ed. Farlow, J.) Indiana University Press.

 

 

Posted in 3D modeling, Biomechanics, classic CAD, Dinosaur models, Dinosauria, Diplodocus, Giraffatitan, Sauropoda, Sauropodomorpha | 11 Comments

PHOTOGRAMMETRY IN PALEONTOLOGY – A PRACTICAL GUIDE

While I was on holiday my latest paper finally went online. It is a joint effort with Oliver Wings that details some good approaches for photogrammetric 3D modelling specimens. You can find the PDF at this link. The web version at the Journal of Palaeontological Techniques is not up yet, but should be within the next few days, starting with this link.

The paper is by far not exhaustive; there are plenty of other approaches to getting good models, and I am sure we could have added 50 more tricks for getting better models. However, the basics are all covered. Basically, if you read this paper beforehand, or if you have it handy while doing photogrammetry, you should be able to consistently produce good-quality models of specimens either in your own collection or during travel.

JOPT_01

I have been toying with the idea of writing such a paper for quite a while, even got to the point where I started sorting my thoughts by pre-writing parts of the paper as a series of posts here (Part 1, part 2, part 3, part 4). Just then, Oliver Wings contacted me with the suggestion of writing a Photogrammetry How-to paper together. He sent along a list of dos and don’ts of his own, and we quickly set to work. Totally unusual for paper publishing: the review was the fastest part, the writing and revising was done nearly as quickly, with the figure creation barely longer. Proofing took much longer, and the wait for the paper to appear was the longest part – not because of a printing backlog, but because small journals run by volunteers are typically not too well staffed during the holiday/fieldwork season. Overall, despite the “summer hole” delay, things went very quickly.

We decided very early on that this paper would go to a no-cost open access journal, for the obvious reasons: we did not have much publishing money, and wanted the paper to be available to as many people as possible.

A really cool thing is that I was allowed to use images (and models made from them) taken during my 2013 American Museum of Natural History visit for the blog posts and paper. A huge THANK YOU to Carl Mehling and Mark Norrell for that!

JOPT_02

Many thanks also to the two reviewers, Matthew Wedel (svpow.com) and Stuart Pond (paleoillustrata.blogspot.com/)! Stu was the “expert reviewer”, the person who knows a lot about photogrammetry, whereas Matt was the “novice” – someone with little knowledge of photogrammetry, thus our target audience. The editors made an excellent choice :)

In the end, Stu suggested a re-structuring that we didn’t do because we wanted the paper to be less a scientific work, with words used as efficiently as possible, and more a how-to guide. The latter requires that some things get repeated in several sections, so that readers do not have to scroll back and forth between sections. Also, if you’re a photogrammetry novice, quite often you will not even realize that another section of the paper has some helpful info, and thus miss out on in when you consult the paper during your work.

We also received unofficial reviews from several people, for which we are very grateful. The more people read such a paper before publication, the better. It eliminates stupid errors that would later confuse lots of people.

A very special thank you goes to Emanuel Tschopp and Peter Falkingham, who handled our submission as editors. They did a very fine job! If you have a palaeo-technical paper to submit, consider JoPT or Palaeontologia Electronica’s Technical Article section. Two excellent choices :)

Oliver himself proved to be a very nice person to work with on this manuscript, as he was only interested in producing the best-possible result and dealt with the paper promptly, despite having a lot on his plate. That’s how it should be among co-authors :) I’ve published with him before, most notably a paper (Wings et al. 2007) on a tracksite in the Turfan Basin (PDF here), and I’ll happily do it again. Thank you, Oliver!

My biggest regret, now that the paper is out and immutable, is that my highly successful experiments with photogrammetry with a macro lens came too late. I would have loved adding an example.

So, check out the paper if you want some pointers on photogrammetry – or just come to the DigitalSpecimen 2014 conference! There is a special photogrammetry workshop by Brent Breithaupt and Neffra Matthews, and plenty of talks about it. :)

 

 

Posted in 3D modeling, AMNH, Conferences, DigitalSpecimen 2014, Digitizing, Dinopics, Dinosaur models, How to, Khaan, Maniraptora, Open Access publishing, Oviraptorosauridae, papers, photogrammetry, photography, Theropoda | 1 Comment

Photogrammetry with a macro lens

So far, most of my photogrammetry efforts have dealt with specimens in the several centimetre to meter range. Bones, skulls, entire skeletons. The smallest models I created were of ammonites – more on that currently on-hold project later – with diameters of several centimetres. “several” here meaning more than 4, i.e. 40 mm. That’s a range where my kit 18-135 mm lens is hard pressed at the lower end, because the specimens are so small on the image that the alignment in Photoscan often fails unless I let the program use the image background. And that causes further bother later on if I need to digitize a specimen in 720°, as I call it: 360° around horizontally, and also all around (another 360°) vertically – a specimen that I want to capture the “bottom” of, too. In contrast, a specimen embedded in rock would be only 360°, because I do not wish to digitize it from below.

If now a specimen makes up only a small part of each image, its surface isn’t well resolved in them, and Photoscan is hard pressed to find features to correlate with other images. That means that I can’t just mask the background out of all images and toss them all into one chunk for alignment, because the angle difference between many images will be too big for Photoscan to work it out based on few matching points.

Quite the obvious solution is the use of a macro lens. Which requires having a macro lens. And that’s as far as I got – until Wednesday! Here’s how I got by a macro lens and what I did with it:

Continue reading

Posted in 3D modeling, Conferences, DigitalSpecimen 2014, Digitizing, photogrammetry, photography, plants, raves | 2 Comments

How to easily de-conflict event timings for conferences

Today’s topic has nothing to do with dinosaurs, but it is something some of you may encounter every once in a while. Let’s say you’re planning a conference with many events – talk sessions, poster sessions, workshops, whatnot. Obviously, you’ll ideally time all events so that everybody can take part in all events they want to. However, it is usually not possible to have only one single session at any one time. As soon as you have dozens of people attending you’ll end up with more events than time.

So now, you’d ideally find out who wants to attend which events, then find the combination of timings that reduces collisions to a minimum. But how to do that? How do you find out which potential collisions occur least often?

I am facing this problem right now for the DigitalSpecimen 2014 conference, where up to 100 people may wish to attend up to 8 workshops each. Here’s how I solved the problem with a little very primitive EXCEL magic.

1. Polling the attendants
I asked people to register for the workshops they WANT to attend. I assume that they all answer truthfully. Thus, I know who wants to attend what combination of events, i.e. which events should not be at the same time for that person.

2. Hacking the data into EXCEL
I now made a table in EXCEL where each line is for one attendant. It has one column for each workshop. I enter a “1” if the person registered for the workshop, and a “0” if the person did not register. This is what things look like now:

Excel_01

Don’t mind the gap – I only use it to separate MfN employees from the rest. Sums and all work across gaps, too.

3. Computing collisions
I now added further column, one each for each possible conflict. Thus, I no have columns titles 1/2, 1/3, 1/4….. 2/3, 2/4, 2/5…. 3/4….. and so on. (Remember to format the cells as “text”, otherwise the program will turn these entries into dates or whatnot!)  Now, I enter formulas into the cell from the row with the first attendant: =PRODUCT(Cell1;Cell2), with Cell1 the cell that holds the info for that attendant on the first of the two possibly conflicting workshops, and Cell2 the info on the other one.
If the person registered for both workshops, the result obviously is 1*1=1. If she or he registered only for one or for none of the workshops, the result is 1*0=0 or 0*1=0 or 0*0=0. Thus, if there is a potential conflict, the result is 1, if there is none the result is 0.
Now, I know which collisions occur for the first person whose data I entered. By pulling down the bottom right corner of the field across all rows that hold names I can make EXCEL apply the same formula for all of them, and quickly have the info for all attendants.

4. Summing up collisions
To find out how often each collision occurs, I now add a row of sums at the bottom. Under each column of 0s and 1s (for no collision and collision) I enter =SUM(Cell3:Cell4), with Cell3 the top-most data cell in the column, and Cell4 the last one. And presto – I get a nice row of numbers that tell me how often each collision would occur for a given pair of workshops.
Here’s how that looks:
Excel_02

And now, I can see at a simply glance which events I can place at the same time without pissing off too many of my esteemed colleagues, and which pairings I better avoid! In this case, Workshops 1, 3, 5 and 7 should all be planned to not run in parallel, whereas a WS 2 – WS 8 collision would hurt only few people.

 

Posted in Conferences, DigitalSpecimen 2014, How to, non-palaeo | 1 Comment

A digital dino bone

This post is a re-blog, or more accurately the English translation re-blog (with minor alterations to adapt it to pre-existing content here on dinosaurpalaeo), of a post I wrote for the Museum für Naturkunde Berlin‘s blog Museumsdinge. The title roughly translates to “museum things/objects/topics” – as often, there is no one-on-one corresponding translation between German and English.

The bone in the image below is nothing extraordinary, really, at least not in a natural history museum. The left thighbone of a dinosaur – so what’s special so about it?Still, this is no ordinary dinosaur! And what is that red stuff on it?

Kentrosaurus femur digital model

You won’t find this dinosaur in a lot of museums. First of all, because the dinosaur in question, Kentrosaurus aethiopicus Hennig, 1915, isn’t present in many collections. Only in the Museum für Naturkunde Berlin and the Palaeontology department and museum, Institute for Geosciences, Eberhard-Karls-University Tuebingen (homepage) can you see a Kentrosaurus.

Continue reading

Posted in 3D modeling, Berlin, Conferences, DigitalSpecimen 2014, Digitizing, Dinosauria, Kentrosaurus, MfN Berlin, Ornithischa, photogrammetry, Stegosauria, SVP 2014 | 3 Comments

China 2014 part 1

My colleague Michael Pittman is a young, ambitious and smart researcher who has done some very nice work on tail stiffness in archosaurs. Now, Michael has a grant going for a project that expands on his previous work, and there are a lot of big names on the grant along with him – and I am on it as well! Not because I am one of the bigshots (most certainly not), nor because I know much about tail stiffness in archosaurs, but because I can build nice research 3D models in a variety of programs, including the necessary 3D digitizing. Previously, I collected data at the AMNH for this project. And in February it took me to China two weeks ago.

Michael and I wanted to check out some fossils in this place: the famous IVPP.

china_01
Pics taken from my hotel room; the XiYuan hotel is a very good place to stay and IVPP visitors get a very reasonable rate.

The IVPP is a research institute, and I’ll have some thing to say on that topic later, but it also has a museum part. For reasons that will become apparent in due course my visit to that museum was rather short and somewhat strenuous, and I have little to write and show. Let’s get this over with, and then advance from the holiday part of my trip to the work aspects.

In the center of the main room of the IVPP museum there is a big pit that houses a number of dinosaur mounts. Here’s a hapless Tuojiangosaurus multispinus having a very bad day at the hands… erh, teeth of Monolophosaurs jiangi (thanks, Dave Hone: I forgot to take a pic of the label of the latter dinosaur, but your photo of the two mounts includes it).

IVPP_02

Of more interest to me, given my history of involvement with plateosaurid dinosaurs, is this critter below: Lufengosaurus!

IVPP_03

OK, looks rather clumsy. The dinosaur below is much nicer:

IVPP_04

Sinornithosaurus millenii. Fluffy! :) It was really cool to see this really famous specimen.

Now, work. What took me to China this year was Michael’s rather cool project on oviraptor tails. But as I happened to be at the IVPP anyway, and as my esteemed colleague Jingmai O’Connor had suggested that I give a talk on photogrammetry there, and as there actually was a time window that allowed me to give that talk, and as my famous colleague Xu Xing at the IVPP actually managed to arrange things……

IVPP_01

… I did give a quick intro to a rapid and cheap 3D-digitizing technique. The announcement, above the one that hung in the elevator, suffered a bit from being copied from what I jotted down for Xu, who apparently had some trouble reading my admittedly horrible handwriting. But the presentation was a success, with the listeners (palaeontologists and archaeologists alike) becoming increasingly interested instead of nodding off to sleep – always a good sign!

Michael and I studied a number of specimens I can’t show you, because they are not on exhibit, but I can show you one that is on exhibit in the National Geological Museum (homepage if you read Chinese) in Beijing. The specimen is labelled Shenzhousaurus orientalis NGMC 97-4-002, and it is shown in a glass-covered steel-cornered box. Very safe, which is good. Although I hate when exhibits are behind glass because it makes seeing and especially photographing them so much harder, it is much better to have them behind glass than damaged or stolen. And too many museums, the NHM London and the MfN included, have had dinosaurs on exhibit pawed and fingered and broken by the unwashed masses. In this case, I would have done things a tiny bit different with regards to the lighting, but then, I always have photography and photogrammetry on my mind, whereas museum exhibit planners have other priorities, mainly the dramatic impact.

Shenzhou01

Shenzhousaurus orientalis type specimen with calipers for scale. Note the blueish light stemming from a neon tube mounted inside the glass cabinet.

So, I set to photographing this small precious raptor, which was a bit of a bother because of an unfortunate meeting of my left knee with the Beijing sidewalk asphalt the day before (the reason why my IVPP museum visit was not that much fun, and short). Suffice to say that I felt very House-ish limping through Beijing and through the Geological Museum (a place well worth an extensive visit!) on my crutch. I was, however, capable of handling my camera and tripod quite well. Here’s a glimpse at the results of ~5 minutes of photography.

geol inst

As you cannot see in this screenshot, the model came out quite nicely, although not quite perfect. I blame the dust on the inside of the glass for some imperfections – and I can’t get rid of that horrible colour!

 

 

 

Posted in "Prosauropoda", Dinopics, Dinosauria, Hadrosauridae, IVPP, Ornithischa, Sauropodomorpha, Theropoda, Travels | Leave a comment

A wonderful Plateosaurus drawing

Currently, I am horribly busy and thus not able to blog much. But here I have something that I must show you, now that I have finally managed to scan it.

PlateoDrawing
click for larger size

Last fall I received this wonderful drawing of a Plateosaurus stealing my birthday cake from none other than Himmapaan (Niroot Puttapitat), a exceptionally gifted (and extremely diligent and thorough!) artist – find more of his work here on his blog and here on deviantART, or here on Facebook. He is also a very modest and friendly person, as I found out when I had the pleasure for visiting the London Zoo with him.

As you can see, the Plateosaurus above is not only properly muscled and proportioned (and appropriately bipedal), but also meticulously drawn in tiny detail. Oh, and the dragonfly that tries to hide away on the top left is gorgeous, too! Every time I look at this wonderful picture I can’t pull away and study the minute details afresh.

What a wonderful present – thank you very much, Niroot! It gives me great joy every time I see it!

Posted in "Prosauropoda", Dinopics, Dinosauria, Plateosaurus, Sauropodomorpha | 4 Comments