Stockholm

In June I visited sunny Stockholm for the Intelligent Systems for Molecular Biology (ISMB) conference, a scientific meeting on the subjects of bioinformatics and computational biology that has been held annually since 1993, and has grown to the largest and most prestigious meetings in these fields. The conference and special interest groups went on for a week so I had quite a bit of free time to shoot some little planets. About 10 minutes walk from my hotel was this church which I think is called the Church of Riddarholmen – seems to be a pretty good match with this model that someone has created – which would make it one of the oldest buildings in Stockholm. I was a bit optimistic shooting this as stitching a nadir composed of cobblestones is usually a bit of a nightmare. I got lucky this time though and Hugin stitched it perfectly first time.

Close by is an area know as Gamla stan which means ‘Old City’. Gamla stan consists primarily of the island Stadsholmen and is home to Stockholm Cathedral, the Nobel Museum and Sweden’s baroque Royal Palace. Here are two of my partners in crime for the trip, Daniel and Tracey, who assisted me in conducting a thorough analysis of Stockholm’s nightlife.

One of the conference receptions was held in Stockholm City Hall. It stands on the eastern tip of Kungsholmen island, next to Riddarfjärden’s northern shore and facing the islands of Riddarholmen and Södermalm. It houses offices and conference rooms as well as ceremonial blue and golden halls. It is the venue of the Nobel Prize banquet and one of Stockholm’s major tourist attractions.

One of the strangest things about Stockholm in summer is that night seems to last only a few hours. It was dark by about midnight, but then light again by about 2.30am. If you’re out drinking until this sort of time then you face an inevitable walk of shame home without the cover of darkness. Not particulaly fair, but in winter I imagine the situation is reversed so things probably even out. This was taken using ISO 1600 at just before 3am.

I didn’t have my tripod with me for this trip so all these planets were handheld, so no bracketing, enfusing or HDR. I’ve recently reinstalled Windows XP and am having lots of fun with CS4 and a plugin called Topaz Adjust, which produces HDR/enfuse-like effects via adaptive exposure adjustments – perfect for handheld panoramas. There’s a free trial but it’s quite cheap anyway.

Wimbledon

The weather in London over the last few days has been pretty awful, and it made me realise that some parts of our recently departed summer were actually pretty nice. June for example was fantastic – living in Wimbledon, where the All England Club host the annual tennis grand slam, we had two weeks of glorious weather, almost certainly a jinx due to the construction of the new sliding roof on centre court. As much as I like to complain about the traffic restrictions they impose during the tournament and the influx of slow moving tourists, I love watching the tennis and you feel quite privileged getting your local weather forecast on the national news.

On the Wednesday of the first week I got in line and queued for a good three hours to get it. Armed to the teeth with booze, crisps and some roasting sunshine, that wasn’t as tough as it sounds so seemed to pass quite quickly. But when we got in the afternoon drinking had gone to my head a little so we went and had a sit down on the hill adjacent to court number one.

A couple of year back it was Henman hill, now I think they call it Murray mountain. Either way, it’s a great place to sit back, have a drink and soak up the atmosphere. There’s also a big TV screen where you can watch what’s going on in centre or court number one. I wasn’t the only one who was feeling the effects of afternoon drinkies as there were more than a few casualties having a siesta, surrounded by a plethora of empty beer cans and wine bottles.

At the top of the hill they have a white picket fence which encloses a little water feature complete with lilies and a fountain. Here my friend Sarah gazes out (eyes closed obviously) over the 19 tournament courts that make up the club.

In the heart of the complex they have some pretty fancy architecture like this spiral staircase that leads up to what I think is the press area. Lots of glass and steel, obviously very high budget.

And a very heavy media presence too. This is Wimbledon park golf club, just across the road. When else are you going to be allowed to park a van like this on the 18th hole? There was no one inside so I was very tempted to jump in and start pressing some buttons.

And more to the point, when else am I going to be able to take a load of photos from inside a sand bunker, without getting chased off by some angry guy wielding a golf club?

Wimbledon park golf club

Stations

Time for a few stereographic shots from some of London’s many train stations. First up is Paddington station, from where you can catch trains to the west country (I used to  travel from here to Bristol when I was a undergraduate). This was taken at about two in the morning so it was completely deserted apart from us lot. The huge 200 meter long roof is supported by wrought iron arches in three spans – this shot only shows one of those so you get some idea of the scale.  Lots of detail and not too much noise at ISO 3200.

Next up is Waterloo station, the main London terminus for trains to the south west of England and the suburbs of London. What works nicely here in a stereographic projection is the roof. It was a bit of pain to stitch and retouch the beams and girders but I think it was worth it. Most planetoids have relatively little going on in the ’sky’ region but here the situation is reversed.

Waterloo is a big station – apparently it has more platforms than any other station in the UK – this is a little further along. It was unusually busy for this time of day due to tube strikes so I had to remove quite a few duplicate people from this one.

Flip it 180 degrees and you get a better view of the roof. This is right underneath the central clock.

MathMap

A few weeks back, Yuv posted a how-to on MathMap, a Gimp plugin that allows distortion of images specified in a simple programming language. Yuv’s instruction on compiling from source work fine but you can also grab .deb and .rpm binaries from the MathMap homepage. What made me want to try MathMap was this image I found on FlickR, generated using the Pierce Quincuncial projection – a conformal map projection that presents a sphere as a square. It also has the mind bending recursive Droste effect for maximum weirdness. If you want to play with this projection, copy and paste the script from here. I used fpsurgeon’s version, though I had to comment out two lines at the end to get it to wrap properly (starting imagex= and imagey=).

To get started, load up an equirectangular panorama (aspect ratio must be 2:1) then go to Filters -> Generic -> MathMap and paste in the Quincuncial script. By setting imageH to 1, adjusting the number of tiles and equator level, I quickly came up with this (click for a bigger version).

This one works quite well with multiple tiles as they seem to be interconnected by the Millennium bridge.

Click ‘Drostify’ to apply the Escher-esque effect to the tiles. ‘DrosteP1′ is the number of  strands spiraling in, and ‘DrosteP2′ is the number of repetitions of the basic element per cycle. The effect of the Quincuncial projection is lost a little in this image of Brighton Pier but the Droste effect is fairly insane.

And by playing around with some of the other options you can really go to town. These effects are all so abstract that the problem is knowing when to stop tweaking – it really is quite addictive. Here’s St. Paul’s Cathedral disappearing into a vortex.

Diving

One of my photographic passions other than creating planets and panoramas is underwater photography. Unfortunately it’s a pricey game – underwater camera gear is very expensive, as are flights and dive trips to tropical destinations where all the good fish hang out. At the moment I use my trusty Canon G7 in an Ikelite housing, with Inon wide angle and macros lenses, and an Inon z240 strobe. This kit has served me very well so far and I’ve been pleased enough with the results to get a few shots printed on canvas. The setup does have its limitations though. The Ikelite housing is robust but it’s certainly not particularly ergonomic – it is essentially an expensive perspex box. And while the G7 is a great camera in bright conditions, like most compacts with small sensors, noise becomes a problem in the depths where light struggles to reach. Shutter delay is a problem too, as it is for all types of nature photography. Compacts do have their advantages underwater though – in particular, wet lenses that you can swap on or off mid-dive. The G7 also has a great macro capability which you can enhance further with an Inon macro lens. In the future I hope to purchase a housing for my Nikon D90, with an Aquatica or Hugyfot looking like good (although eye-wateringly expensive) options. Here are a few of my favourite shots from my recent trip to the Similan islands. You can see the rest of them on Flickr.

Unfortunately the conditions in the Similan islands weren’t great for taking panoramics or planets. Above land, photographers always talk of the need to rotate the camera around the nodal point in order to minimise parallax errors. Underwater in a strong current this can be a real challenge! Ok true, parallax errors are less of a problem here where there are rarely straight lines about, but if you end up 5 or 6 meters away from where you took the first shot of a pano, the end result might not be so good. That’s what happened here but luckily a bit of clone tool on the coral saved the day (click for a bigger version).

In addition to light currents, to make a good pano underwater you need a combination of a shallow dive with attractive topology, and good natural light. Unfortunately this combination was somewhat elusive so the colours in the pano above weren’t great, even though I shot RAW and fixed the white balance afterwards. The colours in these panos from Sipadan off the coast of Malaysian Borneo I took a few years ago came out much better (click for big).

The one above is taken as Barracuda point, the one below was on the West ridge. Both are about 6 photos. With an SLR and fisheye with a dome port I could probably have done them in 3.

Last year I went on a liveaboard trip around the southern Red sea. We were mostly diving around offshore reefs, looking for sharks, so we were quite deep in strong currents and there wasn’t much coral. So again, not great conditions for panos. One of the islands we dived around looking for hammerheads, Big Brother island, did have a lighthouse which provided a great backdrop for this rather desolate planet.

Thailand

I’ve just returned from a fantastic two week trip to Thailand. The highlight was eight days diving from a liveaboard around the Similan Island (I’ll write a separate post about this later), but I spent some time before and afterwards relaxing in Phuket and Bangkok. The day after I arrived we headed to Pantip Plaza, a huge 5-storey IT shopping mall in the Ratchathewi district of Bangkok. I spent a few hours checking out prices and tapping on all the different netbooks. I was considering buying a new lens for my D90 but prices were much higher than I expected; I think you could get better deal from UK suppliers over the internet. The same could be said for netbooks, though to be honest I’m going to wait until specs are a little higher before buying one. So I came away with a 100 baht (£2) torch containing 16 super bright LEDs, and this planet.

A few days later we caught an Air Asia flight down to Phuket and headed out for the dive trip. This was great fun, but exhausting, so on our return we spent a few days exploring Phuket’s beaches. I’m not sure what this one’s called, but it was just south of Kata Noi on the west coast, and there’s a wind turbine on the hill at the south end. The sun was hot and the sand was nice, but for snorkelling give this one a miss.

The next day we headed to Patong beach. Patong is the main tourist beach in Phuket and has everything that you probably want to avoid when you’re on holiday – 24 hour McDonalds, Subway, Starbucks etc.. you get the picture. Just as we parked up it started raining so we didn’t stay long, which was no bad thing. If you visit Phuket I’d recommend giving this one a miss. The planet came out pretty well though, I do like a nice thick atmosphere.

Later that evening I flew back to Bangkok for a night of partying in the RCA district. I got to the airport pretty bleary eyed the following morning and managed to take a few more shots before I caught my flight home. The new Suvarnabhumi airport in Bangkok is impressive; a mixture of glass, steel and and lots of curves make it well suited to a fisheye lens. I grabbed one more planet before getting on my plane; this one probably took longest to stitch and it’s not quite perfect but I’m glad I put the effort in as I think it came out pretty well. The abstract swirls do however bring memories of my hangover flooding back!

Stadia

A few stadiums from my travels over the last year. First up, the vast Camp Nou, home of Barcelona FC. I went to Barcelona last February and was lucky enough to get tickets for the derby game against Espanyol.. and these don’t come cheap. Our seats were right at the back of the 2nd tier so the view was nothing like the one below. And the final score was a pretty disappointing 0-0. Still, this is an incredible stadium and well worth a visit. This pano has had some HDR treatment via qtpfsgui and the Fattal tone mapping operator (click for a larger image, I’ve had to squash it a bit to fit it in).

Next is Stamford Bridge, home of Chelsea FC. I went to a Premiership game a few weeks ago against Middlesbrough; this time our seats were pretty good  – great view of the whole pitch from the 3rd tier of the west stand. And being Chelsea, they weren’t cheap either! At least we got a couple of goals in a 2-0 win. And the pie I had at half time was pretty good too.

Last but not least – the Emirates Stadium, home to the mighty Arsenal FC. This was a Champion’s League game on a cold Wednesday night against Dynamo Kiev, where the Gunners eventually prevailed 1-0. We were sat behind the goal so not the best view in the house, but it’s still an awesome stadium. I  made a planetoid here but unfortunately it didn’t come out very well; next time I’ll have both hands on the camera rather than just the one with a (not so nice) Emirates hot dog in the other.

Timelapse photography on Linux

Over Christmas I had a bit of spare time on my hands so I decided to get to grips with a few new c++ libraries. I already had some experience with wxWidgets, a cross-platform widgets toolkit, from my Hugin/GSOC endeavours but I wanted to write my own GUI from scratch. Similarly, I’ve played with libgphoto/gPhoto2 a little using Perl scripts to make timelapse movies (of my dog) using my Canon G7. These tools and libraries allow you to control a wide range of cameras via USB from UNIX-like operating systems.

When a quick trawl for Linux software to create timelapse movies came up with nothing, I decide to use these two libraries to write my own. This is what I’ve come up with so far.

I based this project on the notebook example that comes with the wxWidgets source code. It’s fairly easy to add tabs (or pages); at the moment the main one (above) shows the timelapse settings – interval, max time/frames, start, stop and preview capture. There’s also an option to change the number of frames that are taken at each interval – useful if you want to make an HDR timelapse film. The second tab (below)  shows the camera settings – ISO, shutter speed, aperture etc. The options that are available here depend on your camera – an SLR will have lots to choose from wheras a point and shoot might have very little if anything.

To start capturing images, you just have to set a few values on the timelapse page (e.g. max frames/run time – though leaving these on zero will make it run until your camera/laptop run out of batteries) – then hit start. You can set the camera up using the second tab or just use the camera’s current values (which are the values that get loaded on initialisation). Hit stop when you’re done and your working directory should be full of images. I then use mencoder or ffmpeg to create the video, though I’m thinking of incorporating this stage into another tab. Other things I may add include some HDR creation/tone mapping functions, a preview tab showing a grid made up of captured images, and some re-size/scaling functions. When I’ve ironed out a few minor bugs and added some new functions I’ll probably start a project at Sourceforge.

The weekend before last my friend Sarah threw a big party in a Chapel she’d hired close to Glastonbury in the west of England. At about 2am I decided it would be a good idea to get my laptop, camera and new Gorillapod out and give the program a test drive. After 5 more hours of partying, here’s what I came up with. With hindsight though, the real success is that none of my gear got trashed!

(Btw that’s me in the rabbit ears)

EDIT:

You can download the code via subversion from here:

https://sourceforge.net/projects/gtimelapse/

Compile with ./configure then make then make install. Good luck!

Research images as art

Every year at UCL, the graduate school holds the Research Images as Art competition. I’m happy to announce that, out of about 250 entries, my mosaic of Charles Darwin was runner-up in this year’s competition!

My image is based on a photograph of Charles Darwin by Julia Margaret. I’ve turned it into a 1.2 gigapixel mosaic using images of protein structures from the Protein Data Bank (PDB), generated from X-ray crystallography and nuclear magnetic resonance data. The mosaic is composed of image tiles from a pool of about 19000 non-identical PDB structures and so represents the current content of the entire PDB. To produce the image I used a mosaic generator called Metapixel.

At the moment I’m struggling to embed the flash applet into (free) WordPress, so to explore the image using the flash applet click here. If you zoom in using the flash controls (the triangular slider works best), you should be able to make out one or two crystal structures. If you can’t view the flash applet, you can see the various levels of zoom here.

As Darwin’s 200th birthday is rapidly approaching, I’ve had some very enthusiastic feedback from my department who are keen to display a large print of this image in the entrance hall as part of a celebratory Darwin exhibit.  This is pretty exciting for me – I just hope they can afford to do it justice and print it at a scale where you can make the proteins out. At 300DPI you could print it at 9×11 feet though I dread to think how much that would cost. For more large scale science images you may want to check out some of Ben Fry’s projects. His image of chromosome 13 is very big.

My other entry in the competition is an image of a potassium channel. Due to the use of detergents in protein crystallography, transmembrane proteins are rarely visualised in their natural state – embedded in a lipid bilayer. However, computational approaches now allow us to predict the position of such proteins within the membrane and reconstruct the ensemble. This image shows a bacterial inward rectifying potassium channel [pdb code 1p7b] embedded in the inner membrane, with potassium ions flowing through it into the cell. It was generated using Pymol, taking about 4 hours to render due to the huge number of atoms that make up the membrane. The potassium ions were added afterwards using Gimp.

Unfortunately I didn’t win anything for this one, which actually took a lot longer to produce than the Darwin one. However, I’ve got some ideas to expand it into a more panoramic view of the plasma membrane, with a large number of membrane proteins embedded inside it. Roll on the 2009 competition..

The Natural History Museum

On sunday I went to see the BBC Wildlife Photographer of the Year exhibition at the Natural History Museum. It’s an exhibition I’ve been to for about the last four years and really showcases the best in wildlife photography. I’m particularly keen on underwater photography and again the standard here was exceptional. One of my favourite shots was a black and white image of a whale shark by Fergus Kennedy entitled ‘Little big mouth’. This is the real reason I bought my fisheye lens – to take pictures of huge critters like this. Now I’ve just got to start saving for a trip to Djibouti. Oh and a housing for my D90..

The museum is particularly famous for its dinosaur skeletons and ornate architecture, both exemplified by the large Diplodocus cast which dominates the vaulted central hall. I stopped to take a quick planet or two before diving in to the gift shop, which has always been my favourite part of visiting museums! The toys in there are pretty high tech these days – the remote control tarantulas and humming birds looked like great fun. They still do those little bugs on a ribbon with googly eyes too.

Speaking of bones, a quick get-well-soon to Alexandra (below, next to the diplodocus) who today had to undergo the surgeon’s knife in order to get her snowboarding career back on track. Go easy on the Oramorph…