Photogrammetry tutorial 9: Quick and dirty!

Over the course of previous tutorials and in my paper with Oliver Wings I’ve given quite a bit of advice on how to photogrammetrize objects properly. Today, I’ll address the other end of the spectrum: how to approach photogrammetry unprepared and without proper equipment. Oliver and I mentioned a minimum kit in our paper, but what if you’re really stuck with just a digital camera? What can you do with everyday materials to improve your results, and how do you approach the entire thing?

First of all, you really need to know how to handle your camera. If you have a tripod and control over the lighting, it is easy to take in-focus and well-lit images. But if the light is low, comes from one direction, and you must hand-hold your camera, then it becomes important that you know with which lens at what zoom setting you can reliably take good photographs with what ISO settings. There’s one thing that will help you a lot that usually I’d strongly recommend against: use flash! Yes, you read that right: it is better to use a flash, even your camera’s internal flash, than take blurry photos. (If your camera doesn’t have an internal flash, then it is a top notch DSLR and I can’t believe you don’t have a whole shitload of equipment with you). There’s an important thing to do when you use your internal flash, but I’ll save that for later when I talk about the process of photographing a specimen.

One thing to remember is that your zoom lenses will allow shorter exposure times / lower ISO / smaller apertures if you use them at a low extension length. So do consider stepping closer to the specimen rather than zooming in. As long as you do not go into the ultra-wide angles or use a fisheye, your models should turn out just fine. And if your modelling software happens to be Agisoft Photoscan Pro, you can even use a fisheye lens, as the program has a feature that allows dealing with fisheye distortion.

Another issue with q&d photogrammetry is usually the inability to use a turntable or optimize the background. Normally, you’ll want to use a background that doesn’t offer any features for the software to detect. However, given the lower quality of images you are wont to achieve, using a feature-rich background can actually be a boon! Normally, you’ll always want to aim for one-chunk model creation, where you toss all images into one chunk, even if the specimen was moved versus the background in between. Instead, now try to use a highly structured background, such as a colour ad newspaper page! And once you’ve finished shooting the specimen from one side and move it by flipping it over, use a different feature-rich background! This way, the background can be included in model creation and thus help with alignment, but doesn’t cause images to align based on the background that were taken with different specimen positions.

Let me explain step by step:

  1. Put specimen on a double-wide newspaper page with colour adverts, or some other crazy stuff. Persian rug or whatever.
  2. Clean, as far as possible, the area around or use additional newspaper etc. to hide anything that would be in the picture.
  3. Shoot images from all around.
  4. Remove specimen and all stuff you used to cover the table.
  5. Place different newspaper – maybe even something totally different like a tablecloth.
  6. Return specimen in different position (flipped over).
  7. Shoot images from all around.

Now, you can use multi-chunk alignment with points-based chunk alignment, as nothing but the specimen is there to make the chunks match each other. Granted, it may not work, but you can always resort to manually placed markers.

OK, now is the time to say that bit about using the internal flash. Obviously, in an ideal world, you have brought a ring light (usually LED) or ring flash, but let’s assume that you haven’t. If you point your camera at the specimen you’ll usually hold it upside up, so that the flash is above the lens. And in normal conditions, whether outside or indoors, the majority of the light will come form above. This means that you naturally get a darker, less-lit underside of the specimen, and that you add to this effect by having the flash light slightly from above, too. So, fix this: flip your camera upside-down! It sounds stupid, and it can be cumbersome, but having the flash under the lens gives you an extra 10% or so of surface you capture well-lit, right where it matters: on the outward edge of the specimen, where you want to find many good points to match one chunk to another.

What else? For one thing, do try out unusual camera programmes! Many DSRLs and even cheap point&shooters offer HDR modes. These modes take several images at different ISOs (usually) or exposures (better but rarer), and combine them into one image that is more evenly lit than any normal photo. As this post direly needs a photo now, here’s one – a HDR mode photo I took with my Canon EOS 650D of the AMNH’s Tyrannosaurus mount.

AMNH T. rex

AMNH T. rex

Oh well, it’s a cool mount, so two photographs instead of one ;) Notice how there are no black shadows and no white-outs? That’s the power of automated HDR. Sadly, the 650D does this via ISO variation, and that includes high ISO values, leading to a lot of noise in the image. But still: these images align and produce dense point clouds much better in Photoscan than normal, hand-held ones would. So, no tripod? Try the HDR mode! If you run Magic Lantern on your camera, you can do better, varying the exposure, not the ISO, too.

Anything else? Consider making a makeshift turntable from a sandbox or so for small specimens, or just using a smooth board on a smooth table. Use white pieces of paper or white shirts to reflect light onto specimens. And so on – happy digitizing! :)

 

Posted in AMNH, Digitizing, Dinopics, Dinosauria, How to, photogrammetry, Theropoda, Tyrannosauridae, Tyrannosaurus | 1 Comment

Photogrammetry tutorial 8: scaling “with hindsight”

Recently, I mentioned in passing that I took some photographs of specimens at the AMNH in New York so that I could better scale models I had calculated from photographs taken during my previous visit. Here’s how that worked out, with a step-by-step explanation.

Here’s one of the models again, as calculated before, without a proper large scale bar.

oviporn

If your name is Jaime H., click for a larger version ;)

This is a model of the Khaan mckennai holotype IGM 100/1127. It has only some 17.5 million polygons. Still, a nice model! Obviously, given the advances in the photogrammetry software that happened since I previously calculated the models, I could simply have re-run them from scratch, just with the new images added. In fact, I am doing that also, to compare the results. But with a calculation time of 183 hours for the alignment and 75 hours for dense point cloud generation – and that is for ONE of the models – it is a major task. If I can avoid it, that’s an option nice to have. I just recalculated on of my models, and that has 279 million points in the dense point cloud. So, “only” 17.5 million here, but a model that I certainly do not wish to re-calculate, as it is good enough for the vast majority of purposes.

So, how to proceed?
First of all, I created a new chunk in the project file, and added my new photographs with the big scale bars into it. I ran alignment, obviously at ‘High’ accuracy. Then, I added markers on my scale bars in the photographs:

markers

Obviously, the surroundings have changed. And if you look closely you will note that the specimen itself has changed a bit, due to further preparation work. However, the by far largest part of the area photographed has stayed the same. Therefore, it is now possible to align the two chunks to each other via points. And then I merged the chunks, which retained the already-calculated model.

markers

This is the chunk with the old photos, showing the alignment. And here’s the two chunks aligned and merged:

markers

Note that I set the alignment photos to “inactive” so that they are shown in a different colour.

Now, I just updated the merged chunks using two scale bars created from the four markers – and done!

OK, that’s it! And now, to tease certain colleague a bit more, another view of the model. This time without colour, so that the high quality is more apparent:

oviporn2

 

 

 

 

Posted in AMNH, Digitizing, Dinopics, Dinosaur models, Dinosauria, Khaan, Maniraptora, Oviraptorosauridae, photogrammetry, Theropoda | 3 Comments

Attempts at macro photography of minerals

Software for photogrammetric 3D reconstructions pretty much doesn’t care what scale the photographs are that you feed it. As long as there are pixels and EXIF data, all is fine. Without EXIF it requires a bit of fiddling; see for example the wonderful Paluxy river trackway 3D model in this paper. Wish I’d done it! I had played with the idea, but Peter Falkingham was so much more obviously the guy to do it… well, anyways. Software doesn’t care about scale, so you can feed in satellite images or macro images – it will calculate ahead. I did some macro photogrammetry before (here and here), but in both cases I loaned the macro lens only for that specific purpose. However, I wanted to play around with the lens a bit for straightforward macro photography, too. Now, I finally got around to that.

macro_01

Markasite FeS2 and Lostlabelit (maybe Cerussite PbCO3 ?
I’m too lazy busy to check right now)

The lens in question is one of the coolest toys in this field you can imagine: a Canon MP-E 65 mm! What’s so cool about it is that, although it seems, from its name, to be  regular 65mm macro lens, it is in fact a 5:1 lens! Yes, you read that right: 5x magnification! You can go all the way from 1:1 to 5:1! Most macro lenses go from 0.5:1 to 2:1 or so.

macro_02

Vanadinite Pb5(VO4)3Cl

The huge magnification does have its drawbacks, though. For one thing, the lens does not have autofocus. When you see it in action, it becomes immediately clear, why an autofocus would not really be a good idea. The dinky 65 mm’s 98 mm total length turn into a whopping 300 or so mm (I didn’t measure) – this lens is longer when used at 5x magnification than many a good tele! And focusing via the focus ring and changing magnification is the same thing – therefore, I tend to set magnification first, then move the whole camera or the subject until it is in focus.

macro_05

Anapaite Ca2Fe2+(PO4)2·4H2O

macro_03

Bornite tarnish Cu5FeS4

macro_04

Calcite CaCO3

Overall, this lens quite clearly is not for the noobs and lazy out there! I count among the former, but I did have a lot of fun with it. It makes many of my at first glance boring minerals and crystals look really impressive, and the effort is tolerable. And it is surprisingly cheap (well, kinda) at currently slightly over 1000 €! As a colleague wrote on Facebook, he gets better results photographing microfossils with this lens than with the Senckenberg’s dedicated equipment that costs 40x as much.

Posted in macro, photography | Leave a comment

Absurd Addendum to Gut Check

Yesterday, I posted some pictures that I took with a fisheye lens. As mentioned, one has to be hellishly careful not to get into the picture by accident. Well, I mentioned lying down on the floor…….

hiding_01

hiding_02

Note the camera under Diplodocus‘ belly.

Also, I took an unintended selfie. My tripod head allows tilting the camera down to 90°, and up to 45°. If I want to tilt it any further, I need to reverse it: take it off, loosen the screw that fixes the holder plate to the camera, turn the plate around 180°, then fasten the screw again and set the camera back onto the tripod. I did this without turning the camera off, and because it was in liveview mode, where you can release the shutter by touching the liveview screen, and because I happened to brush against the screen when I set the camera back into the bracket….. well, the camera was, due to the rotation, pointing in the exact opposite direction of “upward at Giraffatitan;)

selfie

There you go, critical looking palaeontologist with Elaphrosaurus. Needs a shave ;)

Posted in FUN!!!, photography | 2 Comments

Sauropod gut check

In the past I have posted a few times on unusual perspectives of our MfN dinosaurs, especially the big sauropods Giraffatitan (ex Brachiosaurus), Diplodocus and Dicraeosaurus. There’s one view that I didn’t write much about before, and I won’t write much today – but I’ll show you a few pictures. Gut check pics. Can you tell which is which?

D_gut

D_gut2

G_gut

K_gut

These photographs were all taken with a Canon EF 8-15 mm Fisheye lens set to 15 mm. Obviously a fisheye, but there’s way more this lens allows! Below, a few more “gut check” and other views of the dinosaur hall I took today.

D_gut3

K_gut2

If you look closely, you can see the low railing that runs around the low platform under the dinosaurs. The lens allows depicting almost a hemisphere! My colleague Matteo Belvedere, who helped me with the pic taking, and I had to hide ourselves well so we wouldn’t be in the photos! In fact, I used the 10 second timer release on the shutter and laid myself flat on the ground next to the platform – which gave Matteo a good laugh ;)

By now, I suspect every last reader of this blog has found out what wonderful image these photographs remind us of. Julius Csontonyi’s wonderful fisheye view of a sauropod. One of the coolest bits I’ve seen in a loooong time. Here‘s one version on the web. Isn’t it great? My images were taken from under the animals, not just next to them, but the oddness of ther perspective is similar.

Now, to round this off, for two shots of the hall from a more conventional viewpoint.

hall_hdr

hall_hdr2

The latter shows off the huge size of Giraffatitan very well, as well as the hall’s overall classical proportions and architecture. And the great skylight. I makes for great lighting, but I must admit that it can be a challenge to photograph something big, as one invariably ends up photographing it against the light. In this case, shooting a series of different exposures and HDR-merging them helped ;)

 

 

 

 

 

Posted in Dicraeosaurus, Dinopics, Dinosauria, Diplodocus, Giraffatitan, MfN Berlin, photography, Sauropoda, Sauropodomorpha | 10 Comments

AMNH Feb 2015

A short while ago I paid a rather unexpected and sudden visit to the AMNH in New York. American Museum of Natural History – that name stands for one of the greatest museums in the world, and it has much more to offer than just absolutely cool dinosaur galleries. But hey, I’m a dino researcher, so guess where I was headed ;)

Aside from being the first ‘big’ natural history museum I remember visiting at age 10 (I do not count the back-then small and cramped SMNS in Stuttgart; mucho has changed there since, including an additional building much bigger than the old one), the AMNH has been a special place for my own research career. It has, therefore, popped up here and there on this blog a few times. Well, many times. Very many times.

This time, I happened to have a flight back to Germany on a Monday evening, but learned after booking it that I would run out of work in Pennsylvania on Thursday evening. So the question was: change the flight, or make use of the time in NY? As not staying for one Saturday night in the US makes the flights become some $220 more expensive, and as the rescheduling fee was another $210, the decision was simple: stay in NY and try to get into the AMNH collections! Luckily, I know collection manager Carl Mehling pretty well by now, and luckily Carl is a really great guy. I posted a fun photo of him a while ago, and he’s still a big, knowledgeable, kind and funny bear of a man. I emailed him about my predicament of being stuck in NY, and sent along the required official letter requesting access – and got back a rather short email: “Sounds good to me Heinrich. See you soon.” Typical Carl :)

entrance

The AMNH’s  Central Park entrance with Teddy Roosevelt on his horse.

Thus I found myself at the entrance punctually at 9:30 in the morning, ready to fill my camera’s memory card….. One of the things I hoped to achieve during this short visit was going back to the wonderful oviraptor specimens from Mongolia stored at the AMNH. I had photogrammetrized them during my last visit (see here and here), but because I was young an stupid I forgot to use a big scale bar. ‘big’ being important because when you scale the 3D model, the error of where you place your marker on the photo is pretty much the same, absolutely, however big or small your scale bar is. So a longer scale bar means that the error in each marker’s position becomes proportionally less! Thus, the accuracy overall goes up. So this time, I brought bigger scale bars, and was hoping to be able to take a few additional photos of each specimen, with the big scale bars draped around them.

scaloviraptor

scaloviraptor_2

Well, as those two samples show, I was able to access the specimens. Now I just had to find my old Photoscan project files, put the new photographs with the big scale bars into them, and re-scale. Here we go…… two scale bars of 50 cm each, and Photoscan calculates their errors as very slightly over 0.002 m (i.e., 2 mm!) each.

model

I also took photographs of the Edmontonia mount and the Protoceratops mount I digitized last time, for the same purpose. However, as they are encased in glass, I had to lean the scale bars against the glass on one side of the mount, then go around to the other side and take photographs from there. Any distance from the glass means there will be too many reflections. No idea if this will work out; I’ll let you know!

Obviously, I checked out a bunch of other things, too. Some of this I can’t write about right now, but you’ll be let in on the secret in a few months – promise! What I can say is that I spent a lot of time photogrammetrizing some of the many well preserved foot bones of Albertosaurus the AMNH keeps in the collection.

drawer_alberto

Bones like those in this drawer. I am always struck by a bit of institutional envy when I enter the AMNH main collections or the big bone room. Proper shelves and cabinets! A fairly flat and level floor! Our bone cellar has its own charm, with the wooden shelves and the brick floor, but for doing actual work in the room the AMNH is two leagues above us.

 

 

Posted in AMNH, Digitizing, Dinopics, Dinosauria, Khaan, Maniraptora, Oviraptorosauridae, photogrammetry, photography, Theropoda, Travels, Tyrannosauridae, Tyrannosaurus | 11 Comments

snaphots

“snapshot” – that word is usually used to describe an amateurish photograph (unless you are talking about a screen capture on your computer). But the term is not so much tied to the low level of professional knowledge as rather the haste/speed/lack of preparation that goes into taking the photograph. So the word has carried over into military use for a hastily taken shot – even for such a shot by an expert marksman. The same is true, obviously, for photography by experts: if there is no time, if you just yank up your camera and hit the trigger, it’s a snapshot, even if you’re Helmut Newton!

Now, obviously, an expert photographer will more often take snapshots that actually look like something, whereas us amateurs tend to produce, well….. erh…. let me just say that it’s a good thing that digital photography costs only the price of electrical power, and that I love the inventor of the “delete” button! And that better outcome quality is surely in part linked to the on average better equipment professional photographers and serious experienced amateurs lug around. It also correlates with knowledge of how to set up your camera so you’re ready for anything at short notice, and with practice.  And, to be perfectly honest, with not being lazy ;) Let me explain how and why on an example, one that’s putting this post within the range of the impending Theropod Thursday:

snapshot

A subadult ringbilled gull (Larus delawarensis) I photographed in New York, with the Peking and the Wavertree serving as the near-perfect frame. I caught the bird in flight and “froze” it perfectly – but only a half-second before I took the shot my camera had been dangling down by my leg. How did I do this? Am I a magician?

Certainly not – no magic involved at all! But two simple tricks and, admittedly, an OK camera. First of all, my camera is a fairly new DSLR, with a fairly new lens, which means it has a fast autofocus. And a smart one, too, that doesn’t get hung up on a tiny speck, but focusses quickly and reliably on whatever I ask it to focus on. If I handle the settings right, it’s point&shoot and the image will be in focus. A cell phone cam simply can’t do this, and even good compact cameras are usually hard pressed!

And secondly, I put it on settings that made the task easy. Here’s what you should do when you expect to be around birds, little children or other potential victims for snapshots:

–  set you camera to time variable mode (Tv for Canon). In this mode, you manually select the exposure time, and the camera tries to make aperture work for an OK exposure.
– select a short exposure time (here 1/1000 s). The shorter the less motion blur will you see, both from your moving the camera and from the subject you photograph moving versus the camera.
– check against the background you expect to photograph: can the camera come up with a well-exposed image with the settings you chose? If not, consider increasing the ISO value. I went to ISO 400 here, as I know this value gives OK images. For the shot above ISO 200 would have been possible (the image is F13!), but I was also expecting to shoot in the direction of the FDR Drive, which is a raised road, so that it’s kinda dark under it. And very low F-stops are not that great if your subject may be close to the camera. You may end up having part of it sharp, and parts already out of focus. If in doubt, let the camera take photos that are underexposed. You can always brighten them up on the computer. You can’t un-blur an image blurry from motion!
– depending on what you intend to photograph, decide between continuous, single-shot or some other autofocus mode.

So, now the camera is set up properly. I am a bit of a snob with regards to battery live, as I can always afford to carry enough spares. Therefore, I’ve set my camera not to switch off properly, but only “slumber” when there’s no action. This means that it comes back, ready to shoot, within a split-second if I press any button.

The second thing I do to make sure I am always ready for a snapshot is NOT dangling my camera from a long strap around my neck. I have a wrist strap, a short thing that serves as insurance only, and hand-carry my camera whenever I am in situations where I might be tempted to a snapshot. This means two things: I do not need to reach for my camera when an opportunity for a good photo comes around, and I do not have anything else in my right hand at that time!

So, when I see something, up comes the camera, and as I bring it up I lightly press the trigger. This turns the camera on, and by the time my eye is on the viewfinder it is ready to shoot. SNAP!

snapshot_2

Another ringbill. Rats of the Air, some call them. Whatever – they are pretty ;)

snapshot_3

Oh, a final hint: do not run out your zoom lens to the max length! With fast moving things close to you, a long lens means you spend a lot of time waving it around trying to find and focus on your subject. Rather, keep it short, and if there is time run out the zoom after acquiring your “prey”.

Oh, and if you want to read this advice again, but coming from someone who (as opposed to me) really knows what he’s talking about, go visit www.tornadoropa.eu/, the blog of my esteemed colleague Christian Neumann ;)

 

Posted in Aves, Dinopics, Dinosauria, How to, photography, Theropoda | 2 Comments