Geospatial environmental data modelling applications using remote sensing, GIS and spatial statistics

This thesis presents novel modelling applications for environmental geospatial data using remote sensing, GIS and statistical modelling techniques. The studied themes can be classified into four main themes: (i) to develop advanced geospatial databases. Paper (I) demonstrates the creation of a geospatial database for the Glanville fritillary butterfly (Melitaea cinxia) in the Åland Islands, south-western Finland; (ii) to analyse species diversity and distribution using GIS techniques. Paper (II) presents a diversity and geographical distribution analysis for Scopulini moths at a world-wide scale; (iii) to study spatiotemporal forest cover change. Paper (III) presents a study of exotic and indigenous tree cover change detection in Taita Hills Kenya using airborne imagery and GIS analysis techniques; (iv) to explore predictive modelling techniques using geospatial data. In Paper (IV) human population occurrence and abundance in the Taita Hills highlands was predicted using the generalized additive modelling (GAM) technique. Paper (V) presents techniques to enhance fire prediction and burned area estimation at a regional scale in East Caprivi Namibia. Paper (VI) compares eight state-of-the-art predictive modelling methods to improve fire prediction, burned area estimation and fire risk mapping in East Caprivi Namibia. The results in Paper (I) showed that geospatial data can be managed effectively using advanced relational database management systems. Metapopulation data for Melitaea cinxia butterfly was successfully combined with GPS-delimited habitat patch information and climatic data. Using the geospatial database, spatial analyses were successfully conducted at habitat patch level or at more coarse analysis scales. Moreover, this study showed it appears evident that at a large-scale spatially correlated weather conditions are one of the primary causes of spatially correlated changes in Melitaea cinxia population sizes. In Paper (II) spatiotemporal characteristics of Socupulini moths description, diversity and distribution were analysed at a world-wide scale and for the first time GIS techniques were used for Scopulini moth geographical distribution analysis. This study revealed that Scopulini moths have a cosmopolitan distribution. The majority of the species have been described from the low latitudes, sub-Saharan Africa being the hot spot of species diversity. However, the taxonomical effort has been uneven among biogeographical regions. Paper III showed that forest cover change can be analysed in great detail using modern airborne imagery techniques and historical aerial photographs. However, when spatiotemporal forest cover change is studied care has to be taken in co-registration and image interpretation when historical black and white aerial photography is used. In Paper (IV) human population distribution and abundance could be modelled with fairly good results using geospatial predictors and non-Gaussian predictive modelling techniques. Moreover, land cover layer is not necessary needed as a predictor because first and second-order image texture measurements derived from satellite imagery had more power to explain the variation in dwelling unit occurrence and abundance. Paper V showed that generalized linear model (GLM) is a suitable technique for fire occurrence prediction and for burned area estimation. GLM based burned area estimations were found to be more superior than the existing MODIS burned area product (MCD45A1). However, spatial autocorrelation of fires has to be taken into account when using the GLM technique for fire occurrence prediction. Paper VI showed that novel statistical predictive modelling techniques can be used to improve fire prediction, burned area estimation and fire risk mapping at a regional scale. However, some noticeable variation between different predictive modelling techniques for fire occurrence prediction and burned area estimation existed.

Open source computer-vision based guidance system for UAVs on-board decision making

The use of UAVs for remote sensing tasks; e.g. agriculture, search and rescue is increasing. The ability for UAVs to autonomously find a target and perform on-board decision making, such as descending to a new altitude or landing next to a target is a desired capability. Computer-vision functionality allows the Unmanned Aerial Vehicle (UAV) to follow a designated flight plan, detect an object of interest, and change its planned path. In this paper we describe a low cost and an open source system where all image processing is achieved on-board the UAV using a Raspberry Pi 2 microprocessor interfaced with a camera. The Raspberry Pi and the autopilot are physically connected through serial and communicate via MAVProxy. The Raspberry Pi continuously monitors the flight path in real time through USB camera module. The algorithm checks whether the target is captured or not. If the target is detected, the position of the object in frame is represented in Cartesian coordinates and converted into estimate GPS coordinates. In parallel, the autopilot receives the target location approximate GPS and makes a decision to guide the UAV to a new location. This system also has potential uses in the field of Precision Agriculture, plant pest detection and disease outbreaks which cause detrimental financial damage to crop yields if not detected early on. Results show the algorithm is accurate to detect 99% of object of interest and the UAV is capable of navigation and doing on-board decision making.

Automatic Path Planning and Control Design for Autonomous Landing of UAVs using Dynamic Inversion

In this paper a nonlinear control has been designed using the dynamic inversion approach for automatic landing of unmanned aerial vehicles (UAVs), along with associated path planning. This is a difficult problem because of light weight of UAVs and strong coupling between longitudinal and lateral modes. The landing maneuver of the UAV is divided into approach, glideslope and flare. In the approach UAV aligns with the centerline of the runway by heading angle correction. In glideslope and flare the UAV follows straight line and exponential curves respectively in the pitch plane with no lateral deviations. The glideslope and flare path are scheduled as a function of approach distance from runway. The trajectory parameters are calculated such that the sink rate at touchdown remains within specified bounds. It is also ensured that the transition from the glideslope to flare path is smooth by ensuring C-1 continuity at the transition. In the outer loop, the roll rate command is generated by assuring a coordinated turn in the alignment segment and by assuring zero bank angle in the glideslope and flare segments. The pitch rate command is generated from the error in altitude to control the deviations from the landing trajectory. The yaw rate command is generated from the required heading correction. In the inner loop, the aileron, elevator and rudder deflections are computed together to track the required body rate commands. Moreover, it is also ensured that the forward velocity of the UAV at the touch down remains close to a desired value by manipulating the thrust of the vehicle. A nonlinear six-DOF model, which has been developed from extensive wind-tunnel testing, is used both for control design as well as to validate it.

Development of a robust framework for an outdoor mobile manipulation UAV

There is a growing interest to autonomously collect or manipulate objects in remote or unknown environments, such as mountains, gullies, bush-land, or rough terrain. There are several limitations of conventional methods using manned or remotely controlled aircraft. The capability of small Unmanned Aerial Vehicles (UAV) used in parallel with robotic manipulators could overcome some of these limitations. By enabling the autonomous exploration of both naturally hazardous environments, or areas which are biologically, chemically, or radioactively contaminated, it is possible to collect samples and data from such environments without directly exposing personnel to such risks. This paper covers the design, integration, and initial testing of a framework for outdoor mobile manipulation UAV. The framework is designed to allow further integration and testing of complex control theories, with the capability to operate outdoors in unknown environments. The results obtained act as a reference for the effectiveness of the integrated sensors and low-level control methods used for the preliminary testing, as well as identifying the key technologies needed for the development of an outdoor capable system.

Uncertainty based online planning for UAV target finding in cluttered and GPS-denied environments

There are some scenarios in which Unmmaned Aerial Vehicle (UAV) navigation becomes a challenge due to the occlusion of GPS systems signal, the presence of obstacles and constraints in the space in which a UAV operates. An additional challenge is presented when a target whose location is unknown must be found within a confined space. In this paper we present a UAV navigation and target finding mission, modelled as a Partially Observable Markov Decision Process (POMDP) using a state-of-the-art online solver in a real scenario using a low cost commercial multi rotor UAV and a modular system architecture running under the Robotic Operative System (ROS). Using POMDP has several advantages to conventional approaches as they take into account uncertainties in sensor information. We present a framework for testing the mission with simulation tests and real flight tests in which we model the system dynamics and motion and perception uncertainties. The system uses a quad-copter aircraft with an board downwards looking camera without the need of GPS systems while avoiding obstacles within a confined area. Results indicate that the system has 100% success rate in simulation and 80% rate during flight test for finding targets located at different locations.

Investigating limitations of SURF approach for thermal imaging analysis and mapping

Wildlife conservation involves an understanding of a specific animal, its environment and the interaction within a local ecosystem. Unmanned Aerial Vehicles (UAVs) present cost effective, non-intrusive solution for detecting animals over large areas and the use thermal imaging cameras offer the ability detect animals that would otherwise be concealed to visible light cameras. This report examines some of limitations on using SURF for the development of large maps using multiple stills images extracted from the thermal imaging video camera which contain wildlife (eg. Koala in them).

Expression of hyoscyamine 6 beta-hydroxylase in the root pericycle cells and accumulation of its product scopolamine in leaf and stem tissues of Datura metel L.

Hyoscyamine 60-hydroxylase (H6H: EC 1.14.11.11), a key enzyme at the terminal step of tropane alkaloid biosynthesis, converts hyoscyamine to scopolamine. The accumulation of scopolamine in different organs, in particular the aerial parts for storage, is subject to the expression of hyoscyamine 6-phydroxylase as well as its transport from the site of synthesis. To understand the molecular basis of this regulation, we have analyzed, in parallel, the relative levels of hyoscyamine and scopolamine, and the accumulation of H6H (both protein and transcript) in leaves, stems and roots of D. metel. The root, stem and leaf tissues all contain about 0.51-0.65 mg g(-1) dry weight of scopolamine. Hyoscyamine content was extremely low in leaf and stem tissues and was about 0.28 mg g(-1) dry weight in the root tissue. H6H protein and its transcript were found only in roots but not in the aerial parts viz. stems and leaves. The immunolocalization studies performed on leaf, stem, root as well as hairy root tissues showed that H6H was present only in the pericycle cells of young lateral and hairy roots. These studies suggest that the conversion of hyoscyamine to scopolamine takes place in the root pericycle cells, and the alkaloid biosynthesized in the roots gets translocated to the aerial parts in D. metel. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

Characterization of hydrophobin proteins at interfaces and in solutions using x rays

Hydrophobins are a group of particularly surface active proteins. The surface activity is demonstrated in the ready adsorption of hydrophobins to hydrophobic/hydrophilic interfaces such as the air/water interface. Adsorbed hydrophobins self-assemble into ordered films, lower the surface tension of water, and stabilize air bubbles and foams. Hydrophobin proteins originate from filamentous fungi. In the fungi the adsorbed hydrophobin films enable the growth of fungal aerial structures, form protective coatings and mediate the attachment of fungi to solid surfaces. This thesis focuses on hydrophobins HFBI, HFBII, and HFBIII from a rot fungus Trichoderma reesei. The self-assembled hydrophobin films were studied both at the air/water interface and on a solid substrate. In particular, using grazing-incidence x-ray diffraction and reflectivity, it was possible to characterize the hydrophobin films directly at the air/water interface. The in situ experiments yielded information on the arrangement of the protein molecules in the films. All the T. reesei hydrophobins were shown to self-assemble into highly crystalline, hexagonally ordered rafts. The thicknesses of these two-dimensional protein crystals were below 30 Å. Similar films were also obtained on silicon substrates. The adsorption of the proteins is likely to be driven by the hydrophobic effect, but the self-assembly into ordered films involves also specific protein-protein interactions. The protein-protein interactions lead to differences in the arrangement of the molecules in the HFBI, HFBII, and HFBIII protein films, as seen in the grazing-incidence x-ray diffraction data. The protein-protein interactions were further probed in solution using small-angle x-ray scattering. Both HFBI and HFBII were shown to form mainly tetramers in aqueous solution. By modifying the solution conditions and thereby the interactions, it was shown that the association was due to the hydrophobic effect. The stable tetrameric assemblies could tolerate heating and changes in pH. The stability of the structure facilitates the persistence of these secreted proteins in the soil.

Two-agent cooperative search using game models with endurance-time constraints

In this article, the problem of two Unmanned Aerial Vehicles (UAVs) cooperatively searching an unknown region is addressed. The search region is discretized into hexagonal cells and each cell is assumed to possess an uncertainty value. The UAVs have to cooperatively search these cells taking limited endurance, sensor and communication range constraints into account. Due to limited endurance, the UAVs need to return to the base station for refuelling and also need to select a base station when multiple base stations are present. This article proposes a route planning algorithm that takes endurance time constraints into account and uses game theoretical strategies to reduce the uncertainty. The route planning algorithm selects only those cells that ensure the agent will return to any one of the available bases. A set of paths are formed using these cells which the game theoretical strategies use to select a path that yields maximum uncertainty reduction. We explore non-cooperative Nash, cooperative and security strategies from game theory to enhance the search effectiveness. Monte-Carlo simulations are carried out which show the superiority of the game theoretical strategies over greedy strategy for different look ahead step length paths. Within the game theoretical strategies, non-cooperative Nash and cooperative strategy perform similarly in an ideal case, but Nash strategy performs better than the cooperative strategy when the perceived information is different. We also propose a heuristic based on partitioning of the search space into sectors to reduce computational overhead without performance degradation.

Robust fixed order lateral H-2 controller for micro air vehicle

This paper presents a robust fixed order H-2 controller design using Strengthened discrete optimal projection equations, which approximate the first order necessary optimality condition. The novelty of this work is the application of the robust H-2 controller to a micro aerial vehicle named Sarika2 developed in house. The controller is designed in discrete domain for the lateral dynamics of Sarika2 in the presence of low frequency atmospheric turbulence (gust) and high frequency sensor noise. The design specification includes simultaneous stabilization, disturbance rejection and noise attenuation over the entire flight envelope of the vehicle. The resulting controller performance is comprehensively analyzed by means of simulation.

Hila- ja kuviotason laskennan vaikutus kuvion kokonaistilavuuteen, tallennustilaan ja laskentaaikaan teoreettista läpimittajakaumaa ja runkolukusarjaa käyttämällä

Metsäsuunnittelussa tarvittavan metsävaratiedon keräämisessä ollaan Suomessa siirtymässä kuvioittaisesta arvioinnista laserkeilaus- ja ilmakuvapohjaiseen kaukokartoitukseen. Tämän tutkimuksen tarkoitus oli selvittää kuvion kokonaistilavuuden ja läpimittajakauman ennustamisen tarkkuus koealan metsikkö- ja puustotunnuksista MSN-, PRM-, ML- ja FMM-menetelmiä sekä Weibull-jakaumaa hyödyntäen seuraavilla tavoilla: 1. PRM-menetelmällä hilatasolla, 2. PRMmenetelmällä kuviotasolla, 3. ML-menetelmällä hilatasolla ja 4. ML-menetelmällä kuviotasolla. Lisäksi kuvion kokonaistilavuuden ennustamisen tarkkuus selvitettiin hyödyntäen kuviolle tuotettua runkolukusarjaa. Tulokset laskettiin puulajikohtaisesti männylle, kuuselle, koivulle ja muille puulajeille. Puulajien tulokset laskettiin kuviotasolla yhteen. Lisäksi selvitettiin menetelmien laskenta-ajan ja tallennustilan tarve. Tutkimuksen aineistona käytettiin Hämeen ammattikorkeakoulun Evon toimipisteen metsistä mitattuja kiinteäsäteisiä ympyräkoealoja, joita oli 249 kappaletta. Hakkuukoneella mitattiin 12kuvion, joiden pinta-alat vaihtelivat välillä 0,2 – 1,94 hehtaaria, puustotiedot. Aluepohjaisen laserkeilausaineiston pulssin tiheys oli 1,8/m2 ja ilmakuvien pikselikoko 0,5 metriä. Kuvion kokonaistilavuus ennustettiin tai estimoitiin laserkeilaus- ja ilmakuva-aineiston piirteiden avulla koealojen puustotunnuksista. Tulokset laskettiin erikseen kaikille kuvioille ja kuvioille, joiden pinta-ala oli yli 0,5 hehtaaria. Yli 0,5 hehtaarin kuvioita oli 8 kappaletta. Kuvion hilojen naapureina käytettiin 1 - 10 koealaa. Menetelmästä ja naapurien määrästä riippuen kokonaistilavuuden suhteellinen RMSE ja harha vaihtelivat välillä 20,76 – 52,86 prosenttia ja -12,04 – 46,54 prosenttia. Vastaavat luvut yli 0,5 hehtaarin kuvioilla olivat 6,74 – 59,41 prosenttia ja -8,04 – 49,59 prosenttia. Laskenta-aika vaihteli menetelmien ja käytettyjen naapurien määrän mukaan voimakkaasti. Kehittyneemmällä ohjelmoinnilla ja ohjelmistolla laskenta-ajat voivat laskea merkittävästi. Tallennustila ei testatuilla menetelmillä ole rajoittava tekijä laajassakaan mittakaavassa. Läpimittajakauman perusteella PRM-menetelmä ennustaa puulajille erittäin kapean läpimittajakauman, jos koeala koostuu vain muutamasta lähes samankokoisesta puusta. Tämä vaikutti tuloksiin erityisesti menetelmällä PRM2.

Social networks for volunteered geographic information - A case study of OpenStreetMap

The world of mapping has changed. Earlier, only professional experts were responsible for map production, but today ordinary people without any training or experience can become map-makers. The number of online mapping sites, and the number of volunteer mappers has increased significantly. The development of the technology, such as satellite navigation systems, Web 2.0, broadband Internet connections, and smartphones, have had one of the key roles in enabling the rise of volunteered geographic information (VGI). As opening governmental data to public is a current topic in many countries, the opening of high quality geographical data has a central role in this study. The aim of this study is to investigate how is the quality of spatial data produced by volunteers by comparing it with the map data produced by public authorities, to follow what occurs when spatial data are opened for users, and to get acquainted with the user profile of these volunteer mappers. A central part of this study is OpenStreetMap project (OSM), which aim is to create a map of the entire world by volunteers. Anyone can become an OpenStreetMap contributor, and the data created by the volunteers are free to use for anyone without restricting copyrights or license charges. In this study OpenStreetMap is investigated from two viewpoints. In the first part of the study, the aim was to investigate the quality of volunteered geographic information. A pilot project was implemented by following what occurs when a high-resolution aerial imagery is released freely to the OpenStreetMap contributors. The quality of VGI was investigated by comparing the OSM datasets with the map data of The National Land Survey of Finland (NLS). The quality of OpenStreetMap data was investigated by inspecting the positional accuracy and the completeness of the road datasets, as well as the differences in the attribute datasets between the studied datasets. Also the OSM community was under analysis and the development of the map data of OpenStreetMap was investigated by visual analysis. The aim of the second part of the study was to analyse the user profile of OpenStreetMap contributors, and to investigate how the contributors act when collecting data and editing OpenStreetMap. The aim was also to investigate what motivates users to map and how is the quality of volunteered geographic information envisaged. The second part of the study was implemented by conducting a web inquiry to the OpenStreetMap contributors. The results of the study show that the quality of OpenStreetMap data compared with the data of National Land Survey of Finland can be defined as good. OpenStreetMap differs from the map of National Land Survey especially because of the amount of uncertainty, for example because of the completeness and uniformity of the map are not known. The results of the study reveal that opening spatial data increased notably the amount of the data in the study area, and both the positional accuracy and completeness improved significantly. The study confirms the earlier arguments that only few contributors have created the majority of the data in OpenStreetMap. The inquiry made for the OpenStreetMap users revealed that the data are most often collected by foot or by bicycle using GPS device, or by editing the map with the help of aerial imageries. According to the responses, the users take part to the OpenStreetMap project because they want to make maps better, and want to produce maps, which have information that is up-to-date and cannot be found from any other maps. Almost all of the users exploit the maps by themselves, most popular methods being downloading the map into a navigator or into a mobile device. The users regard the quality of OpenStreetMap as good, especially because of the up-to-dateness and the accuracy of the map.

Diterpenoids of Roylea calycina(Roxb.) Briq.

The structures of three new diterpenes, calyone, calyenone, and precalyone, isolated from the aerial portion of Roylea calycina have been shown to be 3-acetoxy-15,16-epoxy-9-hydroxylabda-1 3(16),14-dien-7-one (2), 3-acetoxy-15,16-epoxylabda-8,13(16),14-trien-7-one (5), and 3-acetoxy-9,13;15,16-diepoxylabda-14-en-7-one (7), respectively, by chemical and spectroscopic studies. Precalyone showed antitumor activity against P-388 lymphocytic leukaemia.

Monitoring Indigenous Tropical Montane Forests in the Taita Hills Using Airborne Digital Camera Imagery

The loss and degradation of forest cover is currently a globally recognised problem. The fragmentation of forests is further affecting the biodiversity and well-being of the ecosystems also in Kenya. This study focuses on two indigenous tropical montane forests in the Taita Hills in southeastern Kenya. The study is a part of the TAITA-project within the Department of Geography in the University of Helsinki. The study forests, Ngangao and Chawia, are studied by remote sensing and GIS methods. The main data includes black and white aerial photography from 1955 and true colour digital camera data from 2004. This data is used to produce aerial mosaics from the study areas. The land cover of these study areas is studied by visual interpretation, pixel-based supervised classification and object-oriented supervised classification. The change of the forest cover is studied with GIS methods using the visual interpretations from 1955 and 2004. Furthermore, the present state of the study forests is assessed with leaf area index and canopy closure parameters retrieved from hemispherical photographs as well as with additional, previously collected forest health monitoring data. The canopy parameters are also compared with textural parameters from digital aerial mosaics. This study concludes that the classification of forest areas by using true colour data is not an easy task although the digital aerial mosaics are proved to be very accurate. The best classifications are still achieved with visual interpretation methods as the accuracies of the pixel-based and object-oriented supervised classification methods are not satisfying. According to the change detection of the land cover in the study areas, the area of indigenous woodland in both forests has decreased in 1955 2004. However in Ngangao, the overall woodland area has grown mainly because of plantations of exotic species. In general, the land cover of both study areas is more fragmented in 2004 than in 1955. Although the forest area has decreased, forests seem to have a more optimistic future than before. This is due to the increasing appreciation of the forest areas.

Suomussalmen varhaisproterotsooisten diabaasien mineralogia tektonisessa tulkinnassa

The object of this research is to study the mineralogy of the diabase dykes in Suomussalmi and the relevance of the mineralogy to tectonic events, specifically large block movements in the Archaean crust. Sharp tectonic lines separate two anomalies in the dyke swarms, shown on a geomagnetic map as positive anomalies. In one of these areas, the Toravaara anomaly, the diabases seem to contain pyroxenes as a main component. Outside the Toravaara anomaly hornblende is the main ferromagnesian mineral in diabases. The aim of this paper is to research the differences in the diabases inside and outside the anomalies and interpret the processes that formed the anomalies. The data for this sudy consist of field observations, 120 thin sections, 334 electron microprobe analyses, 19 whole-rock chemical analyses, a U-Pb age analysis and geomagnetic low-altitude aerial survey maps. The methods are interpretation of field observations, chemical analyses, microprobe analyses of single minerals and radiometric age determination, microscopic studies of the thin sections, geothermometers and geobarometers. On the basis of field observations and petrographic studies the diabases in the area are divided into pyroxene diabases, hornblende diabases and the Lohisärkkä porphyritic dyke swarm. Hornblende diabases are found in the entire study area, while the pyroxene diabases concentrate on the area of the Toravaara geomagnetic anomaly. The Lohisärkkä swarm transects the whole area as a thin line from east to west. The diabases are fairly homogenous both chemically and by mineral composition. The few exceptions are part of rarer older swarms or are significantly altered. The Lohisärkkä dyke swarm was dated as 2,21 Ga old, significantly older than the most common 1,98 Ga swarm in the area. The geothermometers applied showed that the diabases on the Toravaara anomaly were stabilized at a much higher temperature than the dykes outside the anomaly. The geobarometers showed the pyroxenes to have crystallized at varying depths. The research showed the Toravaara anomaly to have formed by a vertical block movement, and the fault on its west side to have a total lateral transfer of only a few kilometers. The formation of the second anomaly was also interpreted to be tectonic in nature. In addition, the results of the geothermobarometry uncovered necessary conditions for the study of diabase emplacement depth: the minerals for the study must be chosen by minimum crystallization depth, and a geobarometer capable of determining the magmatic temperature must be used. In addition, it would be more suitable to conduct this kind of study in an area where the dykes are more exposed.