Two months in Switzerland

Research visits are an important part of my term as Academy of Finland Research Fellow. This year, my bodyguard and I spent February and March visiting the University of Zurich in Switzerland. My original plan for the visit had been to learn about the various activities going on at the Remote Sensing Laboratories and to see if there would be opportunities for future collaboration.

After a couple of days in Zurich the visit took new course -- active collaboration started immediately! The spectroscopy laboratories (especially the goniometerlab) were something we can only dream of in Helsinki, and my host, Michael, kindly offered us the opportunity to use the labs and to have help from a skilled technician. The offer was very tempting, and in a few days, a plan for an experiment was drawn together. We decided to develop a method for measuring the spectral albedo of coniferous shoots -- something that has not been reported in scientific literature prior to this. In collaboration with RSL's needle optics team, we were also able to measure needle spectral albedo for our study shoots. In addition, we did a detailed structural analysis of the shoots.

This all sounds very simple in a blog. But it wasn't! Just setting up the lab for measuring shoot albedo took us three weeks of intensive planning in a dark laboratory room. The measurements were another story -- we ended up working close to 10 hours per day in the lab and spending a couple of more hours per day preanalyzing the data. Didn't see much sunlight during those days...

The intensive period did pay off: we are now proud to present results from a unique study on the spectral properties of Scots pine shoots. We now have an idea of how needle spectral albedo scales up to shoot spectral albedo, what the scattering phase function of coniferous shoots looks like and how it affects canopy reflectance (and remote sensing of forests!).

Two papers presenting the results from our experiment have been accepted for publication during the past week. You can all enjoy them (soon online):

Rautiainen, M., Mõttus, M., Yáñez-Rausell, L., Homolová, L., Malenovský, Z. & Schaepman, M. 2011. A note on upscaling coniferous needle spectra to shoot spectral albedo. Remote Sensing of Environment, in press.

Mõttus, M., Rautiainen, M. & Schaepman, M. 2011. Shoot scattering phase function for
Scots pine and its effect on canopy reflectance. Agricultural and Forest Meteorology, in press.

(And this is what Switzerland looked like when we were not in the lab. )

New challenges

My thesis project was finally finished a month ago and now it is time to think of something new. May was really busy, because I had three projects going on simultaneously: preparing for final exams needed for PhD, planning the field campaign scheduled to start in June, and the seedling stand inventory project, for which I mainly work at the moment.

The seedling-laser project is aimed at predicting the seedling stand management need directly from laser data and aerial images. An expert forester determined management need categories (urgent / five years / no need) for each of 238 sample plots in our data. The problem is to make the supervised classification work so that this training data could be used to predict the management need for new stands. Basically, we need to determine which remotely sensed features provide the best class separability, and which analysis methods or models work the best. This is quite difficult, as the classes are defined subjectively and overlap heavily. Nevertheless, it seems to be possible to detect at least the recently managed stands, as well as the stands where conifer seedlings are heavily shadowed by rapidly growing deciduous species.

From the LAI Detectives' viewpoint, the Toplaser-project field measurements are more interesting, as they are a direct continuation for my earlier work with canopy measurements. Two students are working at Hyytiälä for two months - apparently I've become too well educated to work in the field for longer periods... First, they rephotograph the 2008 hemispherical image plots that has already been used in two papers by me and Janne. They also make tree level crown shape and transparency measurements. This data should be very useful for studying the canopy structure with full-waveform LiDAR data. There will be plenty of calculations and analysis next winter!

Juha measures crown shape

In addition, during the week I spent supervising the workers at Hyytiälä, I helped Ilkka to establish a special close-range photogrammetry experiment in the forest. We placed some calibration targets high into the canopy, measured their coordinates with a tacheometer, and took photos of them from carefully located image points. This should enable us to visualize the LiDAR waveforms in the images, like in this experimental photo where you can see the waveforms of some LiDAR pulses from the building and ground. Extremely interesting!

Intensity peaks at ground and roof edge

Calibration targets in up in the trees

Before my vacation starts in the middle of June, there's also some teaching in sight. I'll work as an assistant teacher in the field course for the UEF first-year forestry students at Mekrijärvi research station. The course is quite the same as it was back in 2002 when I passed it myself: students learn to use relascopes, calipers, hypsometers etc. It is interesting to see how the students are able to apply the theory taught in the winter in a real forest.

Have a nice summer!

Aftermath

My thesis defence went quite well. I think that everyone is quite nervous before such an event, and I was not an exception. Of course I tried to prepare myself by reading the book through once more, but as the April 15th got closer I found that the best thing to be done was not to think about it too much. It also helped that my opponent, Dr. Varjo kindly told me in advance that anything nasty would not be coming up, and pointed out some technical details that I should be aware of.

The actual defence started with my (short) speech and the following two-hour discussion was most of the time quite general. At least I thought that it was quite interesting also for the audience. More than 40 people were present, which was actually one of the largest audiences I've seen in these events. The feedback that I got was mostly positive although there were of course some things that I could have done better. Dr. Varjo had one particularly interesting "academic" question - if the top of the tree is broken so that there are leaves around the stem but not above it, does the stem create a gap in the canopy? Now that I've had time to think of it, I'd say that the stem should be considered as a within-crown gap, i.e. it doesn't belong to the canopy, but as it is inside the "crown envelope", it should still be included in the measured canopy cover.





After the actual ceremony and congratulations, coffee and cake were offered to everyone who had patience to stay there until the end. The post-doctoral party with all the speeches and acknowledgements followed later in the evening, and next day there was another party to friends and relatives. Thanks to everyone that participated!

On Monday, I returned to my office and started to prepare for the final exams that I should pass before getting the diploma. Somehow the exams felt insignificant compared to everything that I had to do during the previous weeks. But now after a short holiday staying focused is hopefully easier...

Arrangements

My thesis project is getting close to its culmination. The date of the public defence was agreed already in January with my opponent, Dr. Jari Varjo from the Finnish Forest Research Institute. Since the (positive) pre-examiner comments arrived three weeks ago and the faculty board granted me a permission to print the thesis, there have been plenty of things to arrange. Before the editor of Dissertationes Forestales could accept the manuscript, the style had to be exactly as the instructions said. The book had to be printed ten days before the defence, and I was very happy when Kopijyvä could arrange the printing very quickly, and I could send the books forward eight days after the first contact with printers. Electronic version is also now online. In addition, I have this far prepared the post-doctoral party, written a press release and visited a photographer. A few things still remain, such as delivering the book to the Rector, writing the "lectio praecursoria", and finally, renting a dress coat for the big day. The preceding week will be devoted to going through everything once more in order to be ready for the examination.

I welcome everyone to follow the debate in the auditorium BOR100 of the University of Eastern Finland, Yliopistokatu 7, Joensuu, on 15th April 2011, at 12 o’clock noon!

Laser work

The last sub-study of my thesis project, dealing with canopy cover estimation using airborne laser scanning, was finally published in RSE. This one was by far the most laborious of the five papers that belong to my dissertation. The first four were nice and compact studies concerned with clearly defined problems. But the last one became a mammoth with four variables of interest, seven different data sets, and several techniques that were tested. This is a story of how it evolved.

From the very beginning it was obvious that laser scanning had potential to provide very detailed canopy cover measurements. Laser-based cover indices had been shown to have a high correlation with cover estimates derived from hemispherical images, but how would it perform when compared with Cajanus tube measurements? Both methods provide a large number of binary canopy/open samples from the area of interest, with the difference that laser pulses are not usually exactly vertical.

The field work for this study started already in the spring of 2006 at the Koli national park, which had been scanned previous summer. Looking back now, this one was one of the best field campaigns I’ve had – sunny days, no mosquitoes, beautiful lake views from the hills and good company made the time there enjoyable, despite the rather primitive accommodation...

When the Koli campaign was finished, it actually took me more than two years until I finally got the first results out! There were just so many other research papers to be written. In addition, 30 plots from Koli were not quite enough. Summer 2008 saw the continuation measurements take place at the Hyytiälä research station. I came to contact with Dr. Ilkka Korpela, who already had several laser data sets with basic field measurements from Hyytiälä. I measured canopy cover at 22 plots, and an additional LAI data set by hemispherical photography. Plenty of work, but I was quite happy with the resultant data set, even though it was not without problems…

The next fall was mostly spent analyzing the various field data. Spring 2009 I finally started the actual work with laser data. I had written one LiDAR paper before, but then the laser calculations were made by the others, and I focused on modeling and writing. An unwritten rule in the Joensuu forest inventory research group is that every PhD student writes his/her own software for analyzing LiDAR point data, just to learn how it is done. Of course the results would come more quickly if we just used one of the existing implementations, but sometimes the process is more important than the result.

The simultaneous programming/writing part took more than a year. The contents of the study evolved a lot during the process. The original idea of publishing also the aerial image results in the same paper was abandoned early on. Still, there were seven separate laser data sets and several methods of deriving the canopy cover from them (even after the LiDAR intensity variables were omitted). That would have been enough for a research paper, but I decided to also publish the results from hemispherical images in the same study. In my view some of the existing research papers had confusion with the field data: different field measurements were used but the results were still considered comparable. Often it seemed that the quality of field data was much inferior to the quality of the laser data. Now I had a chance to show that different field measurements are best modeled using different LiDAR metrics and models, so I decided to put it all into a single paper to give a clear view of my opinion.

The manuscript became quite long, which could be the reason why two out of five reviewers gave up reviewing it. The completed reviews were mostly positive. Of course there were plenty of corrections and we had to decrease the length of the paper considerably (which of course made it better). But most importantly, I got my point through, and the final version has practically everything that I (currently) have to say about this issue. The paper came out in January, so the process took nearly five years! Hopefully it will find its audience.

Busy times

I finally left my thesis for inspection yesterday – and today starts my long awaited Christmas holiday. So wrapping up the thesis summary really took the whole autumn. It is rumored that PhD thesis summaries have been written in a couple of days, and even in reality some of us manage to make it a couple of weeks. I started the summary already in June, so I had plans to finish the summary at latest in October. Then there would have been some time for free research. The free time diminished to just two days, but at least the work was finished before my 4-year GSForest scholarship ends at 31 December.

How was the time spent then? Reading the literature. Recalculating some results that were presented differently in the sub-studies. Compiling the yet unpublished results. Writing – I decided not to copy-paste very much from the sub-studies, so most of the text is new. And finally, corrections. I was quite satisfied with the first draft, but the supervisor comments helped to make it much better. Still, there is at least one error in the submitted summary, and probably more that I’m not aware of. It is interesting to see what the pre-examiners find!

Some time was also spent on other things, including the Silvilaser conference trip, teaching, seedling inventory project, and the last sub-study, which was happily accepted right before I returned the summary. So although the autumn was busy and the deadlines moved ahead several times, looking back now I think that it went quite well. But the next year will be even more interesting…

Happy holidays!

Dreams about cables

Last week was a week full of cables that needed to be untangled in Hyytiälä. We spent so much time untangling hundreds of meters of cables that I started to have dreams where I was in the middle of a huge cable mess...

What we were doing was setting up the PASTiS57 experiment together with INRA to monitor changes in boreal LAI from August to October (or November). The new instrument, PASTiS57, is an autonomous ground system with photodiodes facing 57° towards North in the blue spectral domain. The data will be used for phenology modeling and validation of biophysical satellite products. It is a pilot study, at least in the cold and wet conditions of the boreal zone, but we do hope to get an idea of how useful the system could be at our study sites.

Field work ....

... and 'office work'