Direct PDF download link for Mallison and Wings 2014

I keep getting emails requesting a PDF of the paper I wrote with Oliver Wings (link to blog post) on how to do photography for photogrammetry. That’s because the download link on the journal’s web page of the article is so well hidden that most people miss it.

Well, here it is!

Can you find it on the web page? It’s where it says “JPT No12” ;)

Posted in Open Access publishing, photogrammetry | 2 Comments

I thought I knew what ACAB means

Walking from the msueum to my car I recently happened upon a trashcan in a public park. It had some grafitti on it, and lots of stickers. One read ACAB, which normally means All Cops Are Bastards. Not a sentiment I agree with. But coming closer I could read the smaller-print full text…..

 

ACAB1

ACAB1

What the hell??????

All curators are bastards?

First of all, nearly all curators I ever met are really cool people. The rest may not be the nicest people in the world, and I may not want to be friends with some of them, but I have never met a curator whom I would call names. Not one.

Secondly, the generalization has me stumped: all? What insane idiot is so weirdly twisted that s/he believes that an entire group of people, and a large one at that, are all mean – and then curators?

Lastly, who in their semi-right minds would go to the bother of actually having stickers printed with this slogan?

 

Colour me totally confused…..

Posted in WTF? | 3 Comments

3D digitizing black, shiny bones

Obiwan

I know you all wait for news on Tristan, the Tyrannosaurus rex that will soon grace the exhibition spaces of the Museum für Naturkunde Berlin. I know, and I understand, and I feel with you. Really, I do. But…. see above: this post has nothing whatsoever to do with Tristan. Rather, it deals with a hypothetical. Let’s say that you need to digitize a large number of fossils, fossils that are of a very dark colour and very shiny, and that have a complex surface shape with many holes and deep depressions. Fossils like…. the skull bones of a very large theropod from a sediment that is rich in organic materials. If – and this is entirely hypothetical – if you wish to mount such a skull so that museum visitors can see it up close, and so that researchers can have good and easy access, then you can’t mount the real skull with the rest of the skeleton. It would end up several meters above the heads of visitors, laypeople and researchers alike. So what, then, do you mount in front of cervical 1 (atlas) of the skeleton? A cast? That means making moulds of all the oh-so-fragile skull bones, and if in any way possible the damage that may (and often does) associate with casting is something a curator will wish to avoid. Quite obviously, you can CT scan the bones, and have them rapid protyped. But if the bones are a bit bigger – say, like those of a megapredator of Late Cretaceous times – then 0.25 mm slices, the best really good large medical CTs can do, just do not cut it. One point per 0.25 mm translates to 4 dpmm (dots per millimeter), i.e. 10.16 dpi. Your screen on which you are reading this text has 72 dpi. So, we need a data capture method that has a much better resolution. Laser scanning – requires a really nice laser scanner. No money no laser scanner. Structured light scanning – requires a really nice structured light scanner. No money…. you get the drift.

Photogrammetry to the rescue!

Yeah, I know, this is getting kinda old. But then, photogrammetry offers really high resolution 3D digitizing at relatively low cost, with relatively little effort. Just perfect for Tristan the megapredator skull bones.

So, photogrammetry…. if you are using a regular lens, say an 18-135 mm Canon EF-S lens, you can easily get files with a resolution of 1/20th of a millimeter. That’s roughly 500 dpi. And once you have such files, bone for bone can be laser sintered. Those of you who talked to me at SVP 2014 in Berlin probably remember my poor imitation of a beach watch salesman, pulling some bone replicas out of my jacket pockets. Those were laser sintered, by the very helpful and capable 3D Lab of Technical University Berlin. The folks there, especially Joachim Weinhold and Ben Jastram, have been a joy to work with, and now we take our cooperation a step further, with the skull of Tristan a large dinosaur skull. The layer thickness if 0.1 mm, or ca. 260 dpi. THAT’s cool, because it means that at half of arm’s length you can’t see the difference between original and print, and if the prints are properly coloured you can’t even see the difference at a much shorter distance.

printed bones

3D laser sintered bones of the stegosaurian dinosaur absolute king bad-ass of the Jurassic of Africa, Kentrosaurus aethiopicus Hennig 1915, at various degrees of scaling. The big femur at the bottom with the hole in it is hollow, with a wall thickness of less than 1/2 mm (< 1/50th of an inch for my ex-British-colonial friends). The walls are so thin they actually flex when pressed, but the models are tough enough to toss (hard) at anything without taking damage!

But before any printing there is digitizing and data editing. And that’s where the problems begin with our entirely hypothetical large theropod skull….. black, shiny bones, is turns out, aren’t giving anything up easily!

In the field our hypothetical black bone often looks like fossil charcoal. I was only able to distinguish wood from bone in the field this summer because there is a layer of white matter around bones, but not around wood, and because a guy who excavated a dinosaur at that site actually told me which is which. Let me show you:

bone in the field

Fossil bone eroding out of a hillside at a dig site in Montana. Estwing hammer for scale – you ain’t no true geologist unless you own and use(!) a regular Estwing rock pick (pointed tip) – and no, rock picks with a chisel edge do not count, they are good only for archaeologists and other mud scrapers ;) Both leather covered and blue grips are acceptable, and the grey colouring or the naked metal looks are interchangable, too. Just don’t show up with an ACE-brand hammer. Just……. don’t……. EVER!

OK, so the bones are black, and they are shiny. For photogrammetry that normally means  that any light on the bones will cause strong reflections, and that I need to expose the photographs so that the black bone is not uniform black, but actually has colour variation in the images. Looooong exposures, as a consequence, because I can’t just use a strong flash (remember: reflections!), which again means using a tripod. With a good image stabiliser I can handhold a 20th of a second, but not hundreds of times in a row. Sometimes.
The next problem is that of lighting – if I shine enough light on the bone to get rid of the usual shadows on the underside of projections and the outside rim, and light up deep recesses sufficiently, I end up creating more highlight…… impasse!
There is obviously no way around putting a lot of light on the specimen. Necessarily lens-parallel, as anything else would lead to deep shadows in recesses. This means a ring light or ring flash. And lots of reflections. Therefore, I need to take so many photos that either there are enough images for each spot on the bone that happen to have no reflection, or that there are enough photos with the same brightness of reflection in it. In the former case, the software can build the model from the good bits, in the latter I’ll end up with a nearly white model – but I will get a model!
Here’s the set-up I am using:

set_up

The turntable is huge, and in fact that is a nice thing I should have realized long ago: if the turntable is much bigger than a specimen, the photos will show practically no background that doesn’t turn with the specimen. Also note how I am using styrofoam to make the background all-white. Photoscan is so incredibly good at finding points (real or fake) even on totally out-of-focus parts of an image that a structured background that doesn’t rotate with the specimen can really mess up the alignment.

So, with this setup I take a few photos from a steep angle (as in the photo above), then I bring the camera down ot a shallow angle and take many photos – one every 5° of rotation or so. And then I bring the camera down all the way, so that it looks perfectly sideways at the specimen, and again take very many photos. If necessary, I add more rings of images, so that the part of the specimen that is currently up is well-covered. Notice that there are scale bars on the turntable – obviously, I make sure that they can be seen in many images.

Then, I take the specimen off the turntable and completely exchange the cover. A blue trash bag that covers the cushioning material serves well. Or a different type of cushioning material. I also take the scale bars off. Now, I put the specimen down again, but upside down. And then I repeat the above photo sequence. Here’s how the alignment looks with one side done (blue rectangles represent photos), and the other side just started (red rectangles).

alignment example

In theory you can now toss all images into one chunk. There are no features on the two backgrounds for the two sets of images that connect them – after all I exchanged the entire background. That’s why I don’t use scale bars for the second round: they might give features that match between set 1 and set 2. So if all works out I get a very nice alignment of all images in one go.

In reality, this worked very well for many of the ca. 30 bones I have worked on during the last week. The more photos I took, however, the more problems surfaced. For one thing, Photoscan kept being unable to align the vast majority of images. In the example above, only 155 out of 828 photos were initially aligned. I was able to manually align the rest (i.e., select them in the image list and ask Photoscan to align them without running point detection and matching first), but I ended up with several groups of images aligned well within the groups, but not between the groups.

So now I decided to help Photoscan along. The obvious big issue was that the bone in question has a thin margin, it is essentially a flat piece. Thus, the overlap between the two image sets is a small area with a high curvature, and thus prone to produce photos with lots of reflections and few features. I therefore manually aligned all images of one side – 514 in all worked out, and some 12 or so didn’t. Now, I optimized that alignment by using Gradual Selection (setting 10 for Reconstruction Uncertainty and setting 1 for Reprojection error). This led to a very nice sparse point cloud, less than 10% of the initially calculated one, but already a lot of bone detail was recognizable. It also dumped a few photos due to lack of points, so I ended up with 495 still aligned.

Now I chose those images of the second set that were shot with the camera level with the edge of the bone, and manually aligned them one by one. This worked quite well (see photo above; it’s the red images that got aligned to the whole set of blue ones), because now Photoscan had an excellent tie point set with a nice bone rim available that it could match the points on the new photo to. And once the first circle of photos from the second set was aligned, I could align all the rest of the second set to the sparse cloud, as this now contained also all the tie points that connected the second set’s first circle between themselves, including features on the background (i.e. on the turntable and the cushioning material).

During this process, the tie point cloud went from a very nice recognizable bone to ape-shit. In order to be able to recognize if a newly aligned group was totally out of whack I intermittently ran Gradual Selection again – and the sparse cloud always popped back to a nice one. With only one or two images tossed out, this repetitive optimization kept new alignments tight and nice. After a while, I began to see not only the medial side of the bone, corresponding to the first set of images, but also the lateral side, corresponding to the second set of images.

I ended up with 769 photos aligned, nice and tight! Not too shabby, given the original number of 155, and the total chaos that erupted when I simply asked Photoscan to align all non-aligned images willy-nilly. The time I spent sorting which images to align at what time, and to optimize the point cloud in between, turned chaos into a solid alignment.

alignment example

This is the final result, with the last few aligned images in red. As you can see from the small peek you get at the tie point cloud, the bone is not all over, but concise. Now I look forward to the dense cloud, which will be computed in a day or two…. *sigh* The punishment for a large number of high-res images.

The take-home lesson

If you digitize dark, glossy stuff,

  • take very many photos
  • make sure that you use lens-parallel light
  • make sure that you take two circles of photos of the connecting area between the various specimen positions that are near-identical, to maximize your chance of the sets aligning
  • be willing to invest a lot of time into manually helping the alignment along
  • intermittently, use sparse point cloud optimization to keep the alignment on track
  • do not give up too early!

To end this post, here’s a view of the alignment from a different angle, which shows the tie point cloud a bit better.
alignment example
Oh, and please remember:

Obiwan

Posted in 3D modeling, Conferences, Digitizing, Dinosaur models, Dinosauria, Kentrosaurus, MfN Berlin, Ornithischa, Stegosauria, SVP 2014, Theropoda, Tristan, Tyrannosauridae, Tyrannosaurus | 8 Comments

Going to Tristan the T. rex’s dig site

I guess it was kinda hard to miss that the Museum für Naturkunde in Berlin is getting a real Tyrannosaurus rex. I’ll have much to say about the beast here on dinosaurpalaeo over the course of the next few years. For now, I can show you a few photos and report on the trip to the site it was dug out. The Tyrannosaurus skeleton was named Tristan by its owner, Danish businessman Niels Nielsen, after his son. I’ll add some of the press photos of it below, but I won’t rehash what you’ve read in the press already. There’s tons more of photos on my hard drive, but anything that hasn’t been approved already by the PR people I would have to run by them, and they are quite busy enough already at this time. Patience, thus – you’ll see plenty of Tristan soon. maxilla

Medial view of the right maxilla. Photo: Niels Nielsen

all bones

Bones of Tristan during preparation. Photo: Niels Nielsen

Continue reading

Posted in Aves, Botany, Dinosauria, historical buildings etc., insects, landscapes, Mammal pic, Maniraptora, non-palaeo, photography, Theropoda, Travels, Tristan, Tyrannosauridae, Tyrannosaurus | 7 Comments

Urgent: Please reply! Can you get a bad reputation from poor academic etiquette?

Heinrich Mallison:

Jacquelyn’s post for your contemplation in case I am late replying/reviewing/authoring :)

Originally posted on The Contemplative Mammoth:

Academics juggle a lot of balls. The absent-minded professor stereotype is, for some of us, an apt one. Because our jobs involve multiple independent demands on our time, we’re often tossed (or hold on to) more balls than we can handle. Balls get dropped, neglected, or stay in the air for far too long after they should have been safely placed on the shelf.

We forget deadlines, studiously ignore emails we should be answering, miss meetings, triage our to-do lists based on which thing that’s most overdue. In my first couple of years as a PI, I’ve seen (and committed) my share of academic courtesy faux pas: never-returned emails, late reviews, late manuscripts, that one person who holds up the special issue, forgetting to notify co-authors of a conference abstract submission*, leaving names off of manuscripts or talks. We may be new PIs still figuring out academic workloads, we may suck at saying no…

View original 556 more words

Posted in Uncategorized | Leave a comment

GSA’s single article access scam

Note: I am not using the word scam in a legal sense here, but as an everyday language term. Maybe a case could be made that GSA’s behavior is in fact fraudulent, but I believe such a case would fail on a technicality (see below). Still, personally I’d feel scammed, defrauded, swindled if I had fallen for GSA’s trick.

A few days ago work required me to look for various scientific papers on the Hell Creek Formation, including one on its palaeobotany.

screenshot of GSA website

There it is, but as you can see the article is not open access, and the Museum für Naturkunde does not have institutional access. That’s not uncommon. And GSA offers a bunch of options to access the article PDF:

screenshot of GSA website

So, I can:

  1. Sign in, if I have a user account with access.
  2. Purchase short term access – 1 day from the very computer I am on, for US$ 25.00
  3. Use some weird thing I have never heard of that sounds like a publisher’s bad version of LEGO
  4. Sign up…..

Well, obviously, 1, 3 and 4 are not really good for anything. Bloc of Docs is nothing but a credit thing that reduced the number of separate credit card purchases, but doesn’t give you a rebate. Signing uP is for

Member/Fellow and Affiliate Student/K-12 Teacher

I ain’t any of that, so no good. And Signing in if I haven’t signed up….. well, you get the idea. In the end, this means I need to fork over a whopping US$ 25.00 for a single article. Ain’t gonna do do for sure! Thus, I started writing an email to our library, asking them to but the article – and then I stopped. After all, this article is part of a special issue, and it is highly likely that we will need more articles from it soon. Thus, I thought it worth checking if maybe there would be a rebate on the entire special issue. And lookie: You can’t buy it in print, but you can buy it in one go as an ebook!
screenshot of GSA website

And incidentally, the price is quite reasonable all of a sudden:  mere US$ 20.00 for both GSA members and non-members!

Why didn’t you say so in the first place? Why was there no link on the article’s page (the page I get directed to by Google and other searches) saying “Purchase entire Special Issue containing this article for US$ 20.00”?

I guess I know why there is no such link. Quite obviously, nobody in their right mind would spent US$ 25.00 for one-day access to one single individual article if they can instead spend LESS MONEY, US$ 20.00, to get PERMANENT ACCESS to MORE ARTICLES!

So, I click the ebook link and get this:

 

screenshot of GSA website

Oh, so now it is not an ebook format, but a PDF? Suits me, but why can’t GSA get things straight on their own freakin’ website? And it costs even less now, a mere US$ 9.99!

I did buy this, out of my own pocket, and successfully downloaded the entire PDF.

So, to sum up:

If you search for an article of this Special Issue by title, you are directed to a page where you can buy it for one day for US$ 25.00. The page does not inform you that you can buy this article along with the rest of the Special Issue for less than 40% of the cost of one-day-one-article access.

I guess GSA is making a hell of a lot of money by not telling you!

Why is this not legally fraud? In order to be illegal, GSA would have to falsify or misrepresent facts, and gain a financial advantage for them or others while causing you a financial loss. That’s arguably the case if they pretend you need to fork over US$25.00 when in fact US$ 9.99 is enough. But those prices are for two different items, one of which simply happens to contain the other. Nowhere does GSA claim explicitly that the only way to access this one single article is via buying it outright. They just implicitly pretend it is. Thus, any court would throw out a lawsuit.

Morally, GSA’s behavior is clearly wrong. That’s undeniable, and I am looking forward to what GSA has to say when I email them about this.

 

Posted in Open Access, Open Access publishing, rants, WTF? | 4 Comments

Less than 4 minutes to 3D digitize a large bone! (digiS project)

It’s been quiet here recently, and as is usually the case my work load is to blame. It’s not just that there is way more work than time to do it, but that I am currently doing a bunch of very tedious and a bunch of very thrilling things in parallel. The latter are mostly super-secret (sorry!), but I can tell you that a non-secret one deals with how fat dinosaur tails really were, and how their musculature was arranged. Yes, that old can of worms again. More on that soon!

The boooooooring stuff is, well, boooooring, so let’s skip right ahead. Let’s check out what remains in between totally exciting and secret and yawn-worthy: the latest developments in my digiS project. What I am currently doing for it has its tedious moments, but also some excitement, and a lot of quietly satisfying moments.

Recently, I showed the method for photographing bones I developed for the project. Well, it’s a method that has been shown to work very well indeed, thank you. But does it work reliably? What’s the percentage of failures? And how does it adapt to smaller bones, ones that can be set on a table instead of having to stay on the floor?

I’ve been busy photogrammetrizing more stuff, and trying to find out why my method works so well some of the time, and why I am admittedly getting some abject failures with it. My colleague Matteo Belvedere and I suspected that the cause of some of the failures I experienced was the lack of a sufficient number of overview images. What we saw were slight but noticeable offsets between the point clouds stemming from one set of photos showing one side of the bone and the other set showing the other side. Usually, I had been diligently trying to take photos at angles as low as possible in each set, so that the positions of some images in each of the sets were in fact near-identical – and still there was this odd offset.

Well, I must admit that I have solved the problem but not explained it with my latest tests. I simply took a lot more photos per set, and voilà! no more offset! But because these sets do not only include more photos, but also more overview images and more images of the bones’ “corners”, where th problem was usually most manifest, I can’t really tell what the cause of the issue was. Doesn’t really matter, though :) It’s not as if the additional photos take serious time to take.

Here’s an example of the bones of which “many” images were taken and that worked out just fine:

bone example

Yes, 23 million polygons. 23 MILLION! That’s from 117 images, taken in 2 minutes and 50 seconds, with a break in between to flip the bone over. In this case I spent nearly three minutes to do this, which means I was in fact talking to someone or doing something else. Typical flipping times are in the order of 20 seconds to one minute.

Let me say this in bold: Photographing this bone took less than 3 minutes!

I’ve also tried more difficult shapes, including a dorsal vertebra of Giraffatitan brancai. That took a lot longer, but then the bone is huge and has a complex geometry.

spreadsheet

I really had to show this, just to get SV-POWer Mike Taylor salivating. As you can read on the mesh (no texture calculated) this is AR1, a posterior dorsal of G. brancai that was found isolated. I can’t access the collection database right now, so I can’t tell you the new collection number.

Let me give you a screenshot of part of the Excel sheet I use to document my work times:

spreadsheet

606 images of the posterior dorsal took nearly 12 minutes to take, and the model is excruciatingly beautiful. Longbones are typically done in less than 6 minutes overall, despite some chatting in between – hard pressed I could on average do one every 4 minutes, provided they are set out on a table for easy access. In fact, the average photography time of anything classified as a longbone of the entire spreadsheet (with some more bones than in the screenshot above) is 4:17 minutes, and the typical breaks without interruption are less than 30 seconds.

Yeeha! This photogrammetry thing is really cool :)

Posted in digiS, Digitizing, Dinosauria, Giraffatitan, Kentrosaurus, MfN Berlin, Ornithischa, photogrammetry, Sauropoda, Sauropodomorpha, Stegosauria | 13 Comments