Friday 30 March 2012

Confuciusornis - gathering 3D data from a museum exhibit

A couple of weeks ago I took a trip up to Manchester Museum to peruse the excellent fossil gallery and test out my new camera (a Fuji x10). Whilst there my eye was caught by a rather fine fossil of the Lower Cretaceous bird Confuciusornis sanctus, from the Jianshangou Bed of the Yixian Formation (the label in the cabinet gives the location as the Chaomidianzi Formation but according to Wikipedia[!] this is a synonym for the Jianshangou Bed and has fallen out of use; the ref citied in the wiki is behind a paywall and so I can't access it to check), West Laioning Province, China. I thought it might be worth trying to gather 3D data from the fossil using the technique of photogrammetry. Although the specimen is behind glass I got good data, and here are the results.

The first image is a conventional photograph taken from directly in front of the fossil. I've adjusted the levels in the image to bring out the detail. Note the rather wonderful feather impressions of the wings and the fuzz on the neck.

This is the 3D data generated from the photographs taken for reconstruction using photogrammetry. There were 38 images in all, and these were combined to generate the above mesh. The bones are clearly visible, and the feathers of the left (our right, we're looking at the front of the bird) wing are also visible. The rectilinear features visible on this mesh are possibly artefacts of the alignment of the photos, perhaps due to subtle changes in the way each photo was lit or having the glass in-between the camera and the subject. However, I'd have to check this - oh for the luxury of on-site processing!

Above is an unadjusted render of the final textured mesh. Below is a close-up of the final mesh, with the camera positioned at a jaunty angle which shows off the quality of the model. This is lit with a single omni light with ambient occlusion active.

The quality of the mesh is well displayed in this image, and enables us to examine the fossil from all angles and also by loading the model into a viewer we can take a high-quality 3D model of this fossil anywhere we can take our laptops, iPads or smartphones. This is an effective way of accessing fossils, gathering usable data which is readily available at any time, and creating a record of the specimen which is useful for research.

Sunday 18 March 2012

Science, art and the wonder of it all.

Sun and rain in the Wessex Formation.
© Stu Pond 2012.
It’s a cold, windy day in mid-February, and I have stowed by trusty Donegal tweed flat cap in the pocket of my jacket and I am tightening the hood against the coming rain, the first spots of which are falling around me now. As I look to the north I watch as the chalk cliffs become enveloped by a translucent wall of grey; the full force of the weather will be upon me within minutes. Hopefully it’s just a squall, but it looks bigger than that.

I have waded across a shallow, narrow channel, startling several loitering Oystercatchers in the process to what is presently a small islet off the coast of the island. Too impatient to wait for the tide to fall I crossed the gap carefully, trying to avoid a boot full of the murky, freezing English Channel by short-stepping through the water and hopping across seaweed-coated rocks. Plenty of places to look for bone here, but that’s not why I’m drawn to this place once again.

The rain starts in earnest and I look down at the rock I am standing on. The deep red clays erode quickly on this part of the coast, a reminder of the transient nature even of the very geology under our feet, the turning of the wheel of deep time. A yard or so from where I stand is the impression of large tridactyl footprint sunken into the rock surface, and I can see two more striding away towards the south-east. A dinosaur walked here. I’m not noticing the wind and rain for the moment, although as the afternoon wears on it’s presence will become ever more immediate. In my mind’s eye I am standing on a broad mud bank on the edge of a streams which itself is part of a large braided river system. To the west there is the hint of highlands on the far horizon, but that might be the cloud, or possibly the smoke from the wildfires that occur here and in the hinterland during the dry season. It’s hot and humid and though the streams still flow at present as the season wears on some will dry up, as will the ponds and oxbows in the surrounding land. However, for now the streams are for the most part shallow enough to wade; if you’re a dinosaur that is.

Something makes me turn back, a noise perhaps, or that six sense the ecology of fear seems to awake within possible prey, and suddenly she is there. A 4.5 metre theropod dinosaur is walking towards me, head bobbing from side to side and eyes glittering with awareness and a birdlike intelligence. Her three-toed feet are sinking into the soft mud but she is moving with purpose, and as she passes close to me I can hear her steady breathing, see the landscape reflected in her eyes, a landscape she feels completely at one with. Her walk is the walk of predator, relaxed and self-assured, fully alive to her surroundings. She passes close enough for me to touch, and I see her scarred snout, the tuft of feathers on the crown of her head, the hide of her flanks scaly but fantastically patterned, and I notice her colouration which match the scale patterning in may places. She halts a few strides on, sniffs the air and walks on into a future long passed. I am back in the present; the rain stings my face, and I get my camera and field notebook out and get to work.

Rewind five months and I’m standing in the Warner Valley, Utah. It’s still only mid-morning but the sun is getting hot, and as I stare out across the sagebrush and creosote I can’t discern the presence of man in the landscape. Behind me spectacular red cliffs rise and march away to the north-west, but here at their feet lies a treasure beyond price. Here too are the tracks of a large theropod dinosaur, as well as the tracks of many smaller bipedal dinosaurs and a lone four-toed ornithischian. These criss-cross trackways indicate a busy spot for dinosaurs, probably a river system that stretched across several states and was bordered in the north-east by a mighty erg, a sand sea that also contains evidence of dinosaur activity. On a warm, dry, bright morning like this it isn’t too hard to imagine small theropod dinosaurs skittering around your feet as they hunt for insects and small animals, their birdlike chattering filling the air as they speed off into the distance. We’ll be heading off in a few minutes to another site, to another time.

This is why I love science. For myself, like so many others it evokes wonder and awe and confers a continuing sense of amazement, and the more you learn the more you understand when you look; the world we live in becomes a palimpsest that with the right tools can be read, deciphered and comprehended. Standing in the cold wind with horizontal rain driving into your face might not be everybody’s idea of fun, but for me the footprints I stand next to fill me with emotion; they are a tangible connection between me and the animal that made them, a meeting of two distinct species across the vastness of time, walking on the same surface as each other. It’s a fleeting moment of oneness in the universe, the unimaginable infinity of time and space. Here is actual behavior, an animal caught in the act of doing something definite, with intent and with awareness. And here I am too, and that dinosaur is as close as the back of a shadow.

I am convinced science and art are the soulmates of human endeavor, the two things that are the best qualities of us as a species. Like science, art is the pursuit of fundamental truth, and one complements the other. We need to send artists to the moon, poets to the ISS, musicians to the deeps of the oceans.  Science and art are explorers of both the outer and inner worlds; they are the interface between the two in so many ways. We can reveal the incredible complexity of science through the beauty only seeing can convey, through the verses poets fashion that stir something within us, to the intuitive, emotional understanding only music can communicate. This is why I love art.

Science, like art, is also capable of revealing things about ourselves and the universe we are part of in ways that both delight and inform. Often in the pursuit of science I am filled with wonder, a profound and deep sense of being part of something bigger than being me, of being connected to some vastness, intangible to me perhaps, but ultimately explicable. Of course that something is the fact we are the universe made conscious, curious about itself and filled with awe and questions as it contemplate its own existence. Art is the only other endeavor that creates this condition within humans.  From the birth of young stars in distant nebulae to the chiton clinging onto a fossil bone fragment plucked from a rockpool, this sense of wonder is enhanced by the fact the universe observable and we can formulate and test hypotheses, hopefully understanding the processes which enable our existence, the universe and all it contains existence, its processes. Like art, it illuminates our inner selves, and makes the abstract tangible.

I pack up my camera and field notebook and look around. It’s raining hard now, and the falling tide has made the trip back a tad easier as I don’t have to negotiate the shallows and risk a booty. I take a last glance at the tracks, knowing that next time I’m on the island I will be drawn here once more to see the prints, feel the presence of the animal. To make the connection. I’ve a few hours left before the tide comes in, and I head off southwards with the storm lashing at my back, and lightness in my heart. I’ve been walking in the company of dinosaurs, and it feels really, really good.

Monday 12 March 2012

iPalaeontology — the iPad as a research tool.

As an aspiring researcher, I have found that my iPad has become an invaluable piece of kit in my paleontological toolset, enabling me to gather, organise and review information as well as enable me to write, draw and disseminate my own work from one mobile platform. Following on from my post on the art apps on my iPad, here I have a look at some of the apps I use to complement other research tools, plus one or other apps that have found a home on my iPad. I have taken my iPad on planes for work and entertainment (it's currently loaded with all episodes of the BBC's Live From Dinosaur Island), carried it around meetings and flung it into my rucksack and headed out into the field with it.

One of the reasons I purchased an iPad was so I could have access to all the papers I wanted to read, and have on hand at all times. The application iBooks (free) enables you to organise and store PDFs and books purchased from the iTunes Store, and is very useful. Instead of printing papers out and having reams of paper lying about everything is on one place and readily accessible. At the SVP meeting in Las Vegas it was possible to carry around the abstracts book and other documents (such as maps etc) on the iPad, and they are of course searchable which is very useful. Open a pdf online in Safari, and you can save it to iBooks and file as you wish in custom folders.

Kindle books are also available on the iPad and you simply download a Kindle reader and off you go; I downloaded Brian Switek's excellent book Written in Stone for Kindle and is a great way to have the book handy at all time. Combined with iBooks, both these apps make for a powerful library facility on your iPad. Out of copyright publications are often free and many texts which would be difficult to find are more readily available, for instance I have a copy of Gideon Mantell's journals which I have never seen available in print. Of course for an old bibliophile like myself the very nature of books mean they are irreplaceable and electronic readers will never take their place, but there is a lot to be said for the convenience of the iPad.

I'm typing this post in Apple's own word procession app, Pages (£6.99). This is a very capable word-processor and although it's not packed with features it's more than adequate for my writing needs. You could quite easily create some relatively sophisticated documents with Pages as you can import images and format the text easily, and it supports multi-page documents. I have used it for taking notes in lectures and it works a treat.

One problem with Pages as a note-taking app is the inability to draw within a document. To scribble down charts and diagrams I use a notebook app called Penultimate (This cost me 69p in an online sale). This wonderful little program enables users to create individual notebooks, individual pages of which can be saved out and imported into other apps, or emailed to a desktop. With a stylus Penultimate really comes into its own and sketching is very quick and simple. During a lecture it's possible to switch between the two apps with ease, and is a lot less clumsy than it sounds.

Despite the apparent world domination of PowerPoint, arguably the worst application ever to (dis)grace the hard drives of the world's computers, Apple's presentation building program Keynote (£6.99) is vastly superior. With genuinely useful, well-designed templates and a simple workflow it produces far superior results to it's lumbering, slug-like rival and movies actually work with it too. It is certainly an improvement on Microsoft's maddening monstrosity.

Other apps are available according to your interests. As I become more interested in 3D data gathering of fossils and ichnofossils, I find myself using 3D viewer MeshLab (free) as it’s a great tool for importing .obj or .ply files and examining the models; especially usefully for photogrammetrists is the ability to alter the lighting angle, and this reveals all sort of details previously unseen. There are desktop versions available too, and these are fuller featured.

Dropbox (free up to 2.5gb) is massively useful for transferring files. You can invite people to a public folder to view files, but fellow Dropbox users can also be invited to share folders, which makes collaborations much easier.

Similar is iCloud, Apples own cloud computing service, free to Apple users. This excellent service allows you to share pictures, files and music between all your Apple devices. For instance, I take a picture on my iPhone and within an hour it’s also available on my iPad. However, it's not quite as useful as Dropbox as you can't share folders with third parties.

Other apps are equally useful and entertaining. As a palaeontologist it’s pretty difficult to resist anything to do with animal skulls, and Skulls (£10.99) is no exception. It is an app featuring a collection of 300-plus animal skulls (plus the odd ornament or whatnot), all in high definition, with 360 degree rotation. You may never have the urge to study a Warty Frogfish skull, but you’ll be stunned by it’s beauty. The Gila Monster? Wow.

iGeology (free) has detailed drift and solid maps of UK geology, and is fully zoomable. If you have an iPhone it also works with the GPS on your phone. Exoplanet (free) features information on every extrasolar planet discovered, and is updated every time a new one if found, which is more often than I ever imagined. Fractal Plus (free) lets you explore Mandelbrot and Julia Set fractals down to the nth degree, and shows off the iPads power in spectacular fashion. As for the games . . .

Finally, iTunes U offers university courses through your iPad. This app is a game-changer for educators and students alike, making university-quality courses online, many of them totally free in a wide range of subjects. Also, materials of interest are included free of charge too. Darwin’s Library? It’s here. Astronomy, statistics, chemistry . . . the list goes on. From the OU to Stanford, many of the world’s leading education institutions have course on offer here.

One last thing. It’s worth having a look at Apple’s app store frequently not just for new apps, but because they frequently have unadvertised sales and single-app discounts, and you might just pick up a bargain.

Monday 5 March 2012

iPad art and the making of the mark

Technology is a wonderful thing, and occasionally a gadget comes on the market which is a real game-changer, and the latest of these to arrive at Paleo Illustrata is the iPad.  I've had it for around six months now and it's become a vital tool that makes doing art, work and science productive when away from the desktop. I'm typing this post on it now.

As an old-school graphic designer I've never really been that taken with the input devices available for drawing and painting on computers. I like pen and paper (see this post on sketch books for more). The mouse is fine for pointing and clicking, works great with bezier curves but makes a poor drawing tool. Tablets are better but still seem to make the drawing or painting process feel slightly detached from the artist. The iPad changes all this however. Combined with a stylus the iPad makes for an excellent painting and drawing too. Painting directly on the screen makes the experience seem very immediate, and it's positively pleasurable to be able to punish paint around on the screen. One of the device's leading advocates is the English painter David Hockney, who paints on his iPad and then prints the results out in large format.

Valley of Fire, Nevada. Painted by the author on an iPad2 using Procreate.

There are several painting and drawing apps on the market that are worth looking at. Brushes (£5.49) is Hockney's app of choice and indeed it is a very capable application, featuring layers and blending modes. Inspire pro (£5.49) is popular, again featuring layers and a wide range of brushes. My personal favourite is Procreate (69p at the moment - grab it now!), which allows HD size painting, includes layers and a wide range of brushes. However, Procreate is given a run for its money by the excellent Sketchbook Pro (£2.99) made by Autodesk. This app has a superb range of drawing and painting tools and is capable of high-quality results. Giant graphic sauropod Adobe have also weighed in recently with their tablet version of Photoshop, Adobe Photoshop Touch (£6.99). I havent tried this yet so cant comment but hopefully the app avoids the bloatware behemoth syndrome of its desktop cousins.

3D modelling application 123d Sculpt (free) takes the iPad's tactile approach to interaction and allows the user to pull geometry around as if was clay. This approach works very well and whilst it's not in the same league as professional desktop 3D apps it is ideal as a sort of 3D doodler, and what's more is it's free.

There are many photography apps available from the AppStore, and in truth I tend to process images on my desktop in Photoshop. I mentioned earlier that Adobe has Photoshop Touch available, but I use Snapseed (£2.99) which has a range of effects and enhancement options, and is more than enough for tablet use, although I suspect that will change as the iPad develops.

Art is about making a mark. The marks an artist makes are how they define themselves, how they communicate. The iPad makes you feel like you are making a mark because of the immediacy of it's feedback; as you paint the colour appears under your stylus or finger. You can organize colour palettes quickly, get down big daubs of paint to block out composition and tonal range. Its far from perfect, but for the first time a piece of technology has come along that complements the other tools I use in my research, art and day job.