Friday, 21 November 2014

Kim's paper out in MEE

Kim's paper on testing the TLS-derived biomass estimates against destructive harvests was published today in Methods in Ecology and Evolution. For a local PDF go here. Wageningen University and UCL did press releases on it. It's a good paper - Kim should be proud of it. It's the real hard evidence that the TLS plus QSM really can do volume ok, particularly once you consider the uncertainty in the QSM reconstruction methods more systematically, which is what we've been able to contribute. A key result in my mind is that it really shows how the uncertainty in the TLS-derived values are independent of tree size, unlike the allometry-derived values which tend to grow with tree size, mainly due to the smaller and smaller numbers of larger trees. Now to do the same across the tropical trees we have, and we'll hopefully start seeing how this affects things across the tropics!
TLS point cloud and reconstructed model, from Calders et al. (2014).
And here's a really nice animation of the Brisbane field plot from WU.

Monday, 10 November 2014

Trees in their eyes

Here's a shot of our Wytham tree, scanned, reconstructed and looped, projected onto a screen and then reflected in my eye from close-up. Got it? Lovely.

Saturday, 8 November 2014

Shipping out

So we've reached our last day in Brazil, for now. We took the overnight boat from Brevez to Belem, which was an adventure in itself. 14 hours up river, with decks of colourful hammocks slung from every available piece of metal. We had small cabins - comfortable enough despite the tiny bunks and freezing a/c. Better than a hammock though!

Hammocks on the boat from Brevez to Belem.
I watched the sun rise over the river and we made our way off the docks to the hotel, with all our cargo still in tact. Minus the target poles, which we left behind for Alex to use to mark the plots in the forest. We managed to lose/break only about 5 or 6 poles out of 70-odd, which is pretty good going and a testament to Lucy's organisation with the pole layout. That's been a very valuable experience in terms of the registration - we now know how to do this much more effectively than we did before, and how more poles isn't necessarily better. Systematic is the way to go.
Sunrise heading towards to Belem.
We've had a couple of days in Belem, doing some sightseeing - the old colonial parts of the city remain, slightly run down, but with some spectacular architecture including the old cathedral, the Theatre of Peace and the fort. We lucked out with the Theatre - after taking a tour we were given free tickets for a Richard Strauss concert that night. It was really beautiful, and a very strange contrast after getting off the boat from the remote jungle that morning, to sitting in a 19th C concert hall listening to Viennese waltzes.

Fresco on the ceiling of the Theatre de Paz, Belem.

Cathedral in Belem.
Our last thing to do was go to the Institute of Geoscience at UFPA, the University Federal do Para, to see Prof. Lola Da Costa, the driving force behind the Caxiuana experiment. Lola has been working at Caxiuana for more than 20 years, and is the reason the experiment exists, and has survived various funding threats over the years. We showed Lola some of early results from the scanning, and he was excited about the prospects of what we can do with data to elucidate links between structure and physiology. We're all extremely grateful for Lola's help in organising our trip and I'm sure we'll be back.
Pro. Da Costa with Lucy, outside the best fried fish place in town.
Lola took us for dinner on our last night at a small fish place - only thing on the menu was fried fish and prawns, and it was amazing. Some great local Para musicians were playing, (many) beers were drunk and it was a fitting finale for our trip to Brazil. Andy and I chatted about the tasks ahead for processing the lidar data - we worked out that we think we can do the registration much more efficiently, which would be hugely time-saving. Our idea needs needs testing but I don't know why we didn't think of it before - better late than never though eh?

Tuesday, 4 November 2014

Scanning done

So we finished the two towers today, although I don't know which one was Orthanc. I'm quite happy not to have to lug the scanner up, down, across or under anything for a while, other than on and off the odd boat or plane. The view from the towers is pretty special though, even if it is a little harder to appreciate when you're pouring with sweat and cursing gravity.
Looking down on the drought plot. Andy top centre, next to the runnel, looking up slightly nervously before making his way up (in harness of course) to help me bring stuff down.

Looking out into the treetops, seeing what the scanner is seeing.
The scanner is picking up the upper part of the canopy beautifully from on the tower platforms. If (and it's a bit of an unknown right now) we can hand-register the scans together from bottom to top, we'll have an amazing profile of wood and foliage all the way up. Another first I reckon.
A first view of a single scan, from the tower (which is the little red dot in the centre). Colours are height (0 to 43m in red).

Another view of the same scan.
These images are just single scans, and of course the platform and scaffolding obscure significant chunks of the view. But we're still seeing trees from out towards the edges of the plot, as well as the upper crowns, which is really encouraging. These were taken from platform 12 of about 20, so the upper views will be even better.

Meanwhile, the guys working on the panels in the drought plot are slowly but surely putting them back on, repairing some, replacing rotten ones. The scale of the experiment is much more obvious with the panels on - it's really something to see. And feel - the temperature underneath is pretty steamy, unsurprisingly, given it's effectively a 10,000 sq m greenhouse.
I bet you could grow some serious courgettes in here.
The team spent the afternoon trying to ID trees from the census data in the scanner data, to make our lives easier later. So far so good on that too. Tomorrow, we'll finish off a few loose ends, and hopefuylly try out the drone if it's calm. We also want to scan the station so we can give them a nice laminated print to remember us by ;-) We'll then pack up our stuff and load it on the boat before supper, as we're heading out downriver in the pitch dark at 4am, to catch the 8am catamaran from Brevez to Belem. Lucy has had her mind very much on a waterfront ice cream in Belem for about a week. I wouldn't say no either. I will miss this though.
Not many of these in North London.

Monday, 3 November 2014

First cuts of data

So today I was dragging the Riegl from level to level up the tall tower in the control plot. 18 levels, the heat, and it's pretty heavy. I was pretty much sopping after about 2 hours of it, and by the end, practically on my knees. Whose stupid idea was that? Oh.

Meanwhile, Andy's been furiously registering, slicing, dicing and generally working like a demon to pull out stem maps from the data so we can try and match them off the field data before we leave on weds night. He's produced a hugely downsampled pointcloud just to make life manageable until we can get our big machines in the lab on it. The examples below are from roughly 15 million points, which is < 1% of the data, and only from the upright scans. When we include the tilt scans, we'll obviously sample preferentially in the upper part of the canopy, and double the number of points.
An overview of the drought plot, coloured by height.

A zoom in of the largest tree in the plot - towards the centre back above.
 Amazingly, even in this (relatively) extremely sparse point cloud, the tops of some of the largest canopy trees are clearly visible. Also, the registration looks better than we could have hoped for. We've really been able to put what we've learned over the last 12 months into practice here, and I think it's really paid off. I may have even indulged in a very dignified whoop of delight on seeing this, slightly frightening Andy in the process.

A slice through the drought plot from 1.3 to 2.3 m above the ground. Lines running right to left are the wooden railings and runnels carrying the panels that keep the rainfall off the plot.
The slice through the data also shows up the wooden runnels that carry the panels very clearly. It's amazing to see them all laid out like this in such detail (the images above are rather low quality just because of the bandwidth) - and the trenches around the edges, clear of any vegetation. Even Lucy and Alex, who are extremely familiar with the plot, and essentially know every tree in there, are seeing it in a new way. It's funny - you can get buried in the details of measurements and kit, and data and logistics, but when you see the results stand out so clearly, it really brings home why we do these things.

Sunday, 2 November 2014

Day of rest

We took a well-earned rest day today, had a lazy breakfast, drank a lot of coffee. Ed managed to buy 24 litres of beer in Brevez "by accident" - he says he definitely asked for 24 330ml cans. Riiiight Ed. But he's trying his best to put it right and hence rolled out of bed a little later than usual this morning. We took the smaller boat to a beach about 30 mins up river - really beautiful little spit of sand. Saw river dolphin, as you do. I must admit I didn't entirely believe Lucy's claim to have spotted one until I saw it, but it was definitely a dolphin. Oh, and it was very, very hot. Equator hot. Nothing that a quality hat can't deal with though.
Mat in a hat. Looking like a

Not too shabby for a morning sunbathe.
The local station staff and workers laugh at us for drinking black coffee with no sugar - particularly after lunch - totally unheard of here. They think it's hilarious and now make me two flasks of coffee in the morning, 1 for lunch and then there's often one waiting for me when we get back in from the field. It's tough but I'm getting through it.

Saturday, 1 November 2014

Plots 1 and 2 complete

So after 7 days continuous work, with 10 hour days of scanning, we finished the main plots we came for - the 1ha drought and control plots. The weather has been nigh on perfect - calm, almost no rain. We'll all be grateful for a day off tomorrow, and maybe some beach action, cleaning clothes, and really just relief at not lugging stuff around the forest. We're all seeing reflectance targets wherever we look and I'm hearing the Riegl's bleeping scan noise in my sleep. Here's what we came for.
Literally the first cut - a tiny slice through only 6 upright scans, representing about 40m along and 20m across.
The scanner data look really, really good. The systematic target layout seems to have worked better than we could have hoped, with a team of 3 marshalled by Lucy keeping track of 60+ poles in 2 duplicate sets of 6 colours - a triumph of organisation! Andy cracks a big grin when the scans match up to within a few mm; when he frowns I know it means more work. But this is the first time anyone has seen this forest like this, and there is so much to come.
Done and done. Happy team after the 144th and final scan of the two plots.
On the way out of the plot, we saw this little fella.
Climbing snake - no ID as yet.
And so what's next after the rest day? Well, right on cue the heavens opened this evening, so looks like we got our core work done just in time. But I've thought that scanning up through the canopy would be great *if* we could do it - the two 45m towers give us a really good shot, and the detailed profiles would be very interesting - and never been done. We discussed how we might go about it and we've got a plan. Monday, we put it into action.
An old jedi mind trick.