Enhancing the usability of Satellite Earth Observations through Data Driven Models. An application to Sea Water Quality

Earth Observation from satellites has the potential to provide comprehensive, rapid and inexpensive information about land and water bodies. Marine monitoring could gain in effectiveness if integrated with approaches that are able to collect data from wide geographic areas, such as satellite observation. Integrated with in situ measurements, satellite observations enable to extend the punctual information of sampling campaigns to a synoptic view, increase the spatial and temporal coverage, and thus increase the representativeness of the natural diversity of the monitored water bodies, their inter-annual variability and water quality trends, providing information to support EU Member States’ action plans. Turbidity is one of the optically active water quality parameters that can be derived from satellite data, and is one of the environmental indicator considered by EU directives monitoring programmes. Turbidity is a visual property of water, related to the amount of light scattered by particles in water, and it can act as simple and convenient indirect measure of the concentration of suspended solids and other particulate material. A review of the state-of-the-art shows that most traditional methods to estimate turbidity from optical satellite images are based on semi-empirical models relying on few spectral bands. The choice of the most suitable bands to be used is often site and season specific, as it is related to the type and concentration of suspended particles. When investigating wide areas or long time series that include different optical water types, the application of machine learning algorithms seems to be promising due to their flexibility, responding to the need of a model that can adapt to varying water conditions with smooth transition, and their ability to exploit the wealth of spectral information. Moreover, machine learning models have shown to be less affected by atmospheric and other background factors. Atmospheric correction for water leaving reflectance, in fact, still remains one of the major challenges in aquatic remote sensing. The use of machine learning for remotely sensed water quality estimation has spread in recent years thanks to the advances in algorithm development, computing power, and availability of higher spatial resolution data. Among all existing algorithms, the choice of the complexity of the model derives from the nature and number of available data. The present study explores the use of Sentinel-2 MultiSpectral Instrument (MSI) Level-1C Top of Atmosphere spectral radiance to derive water turbidity, through application of a Polynomial Kernel Regularized Least Squares regression. This algorithms is characterized by a simple model structure, good generalization, global optimal solution, especially suitable for non-linear and high dimension problems. The study area is located in the North Tyrrhenian Sea (Italy), covering a coastline of about 100 km, characterized by a varied shoreline, embracing environments worthy of protection and valuable biodiversity, but also relevant ports, and three main river flow and sediment discharge. The coastal environment in this area has been monitored since 2001, according to the 2000/60/EC Water Framework Directive, and in 2008 EU Marine Strategy Framework Directive 2008/56/EC further strengthened the investigation in the area. A dataset of combination of turbidity measurements, expressed in nephelometric turbidity units (NTU), and values of the 13 spectral bands in the pixel corresponding to the sample location was used to calibrate and validate the model. The developed turbidity model shows good agreement of the estimated satellite-derived surface turbidity with the measured one, confirming that the use of ML techniques allows to reach a good accuracy in turbidity estimation from satellite Top of Atmosphere reflectance. Comparison between turbidity estimates obtained from the model with turbidity data from Copernicus CMEMS dataset named ’Mediterranean Sea, Bio-Geo-Chemical, L3, daily observation’, which was used as benchmark, produced consistent results. A band importance analysis revealed the contribution of the different spectral bands and the main role of the red-edge range. Finally, turbidity maps from satellite imagery were produced for the study area, showing the ability of the model to catch extreme events and, overall, how it represents an important tool to improve our understanding of the complex factors that influence water quality in our oceans

Uncertainties in Digital Elevation Models: Evaluation and Effects on Landform and Soil Type Classification

Digital elevation models (DEMs) are a widely used source for the digital representation of the Earth's surface in a wide range of scientific, industrial and military applications. Since many processes on Earth are influenced by the shape of the relief, a variety of different applications rely on accurate information about the topography. For instance, DEMs are used for the prediction of geohazards, climate modelling, or planning-relevant issues, such as the identification of suitable locations for renewable energies. Nowadays, DEMs can be acquired with a high geometric resolution and over large areas using various remote sensing techniques, such as photogrammetry, RADAR, or laser scanning (LiDAR). However, they are subject to uncertainties and may contain erroneous representations of the terrain. The quality and accuracy of the topographic representation in the DEM is crucial, as the use of an inaccurate dataset can negatively affect further results, such as the underestimation of landslide hazards due to a too flat representation of relief in the elevation model. Therefore, it is important for users to gain more knowledge about the accuracy of a terrain model to better assess the negative consequences of DEM uncertainties on further analysis results of a certain research application. A proper assessment of whether the purchase or acquisition of a highly accurate DEM is necessary or the use of an already existing and freely available DEM is sufficient to achieve accurate results is of great qualitative and economic importance. In this context, the first part of this thesis focuses on extending knowledge about the behaviour and presence of uncertainties in DEMs concerning terrain and land cover. Thus, the first two studies of this dissertation provide a comprehensive vertical accuracy analysis of twelve DEMs acquired from space with spatial resolutions ranging from 5 m to 90 m. The accuracy of these DEMs was investigated in two different regions of the world that are substantially different in terms of relief and land cover. The first study was conducted in the hyperarid Chilean Atacama Desert in northern Chile, with very sparse land cover and high elevation differences. The second case study was conducted in a mid-latitude region, the Rur catchment in the western part of Germany. This area has a predominantly flat to hilly terrain with relatively diverse and dense vegetation and land cover. The DEMs in both studies were evaluated with particular attention to the influence of relief and land cover on vertical accuracy. The change of error due to changing slope and land cover was quantified to determine an average loss of accuracy as a function of slope for each DEM. Additionally, these values were used to derive relief-adjusted error values for different land cover classes. The second part of this dissertation addresses the consequences that different spatial resolutions and accuracies in DEMs have on specific applications. These implications were examined in two exemplary case studies. In a geomorphometric case study, several DEMs were used to classify landforms by different approaches. The results were subsequently compared and the accuracy of the classification results with different DEMs was analysed. The second case study is settled within the field of digital soil mapping. Various soil types were predicted with machine learning algorithms (random forest and artificial neural networks) using numerous relief parameters derived from DEMs of different spatial resolutions. Subsequently, the influence of high and low resolution DEMs with the respectively derived land surface parameters on the prediction results was evaluated. The results on the vertical accuracy show that uncertainties in DEMs can have diverse reasons. Besides the spatial resolution, the acquisition technique and the degree of improvements made to the dataset significantly impact the occurrence of errors in a DEM. Furthermore, the relief and physical objects on the surface play a major role for uncertainties in DEMs. Overall, the results in steeper areas show that the loss of vertical accuracy is two to three times higher for a 90 m DEM than for DEMs of higher spatial resolutions. While very high resolution DEMs of 12 m spatial resolution or higher only lose about 1 m accuracy per 10° increase in slope steepness, 30 m DEMs lose about 2 m on average, and 90 m DEMs lose more than 3 m up to 6 m accuracy. However, the results also show significant differences for DEMs of identical spatial resolution depending on relief and land cover. With regard to different land cover classes, it can be stated that mid-latitude forested and water areas cause uncertainties in DEMs of about 6 m on average. Other tested land cover classes produced minor errors of about 1 – 2 m on average. The results of the second part of this contribution prove that a careful selection of an appropriate DEM is more crucial for certain applications than for others. The choice of different DEMs greatly impacted the landform classification results. Results from medium resolution DEMs (30 m) achieved up to 30 % lower overall accuracies than results from high resolution DEMs with a spatial resolution of 5 m. In contrast to the landform classification results, the predicted soil types in the second case study showed only minor accuracy differences of less than 2 % between the usage of a spatial high resolution DEM (15 m) and a low resolution 90 m DEM. Finally, the results of these two case studies were compared and discussed with other results from the literature in other application areas. A summary and assessment of the current state of knowledge about the impact of a particular chosen terrain model on the results of different applications was made. In summary, the vertical accuracy measures obtained for each DEM are a first attempt to determine individual error values for each DEM that can be interpreted independently of relief and land cover and can be better applied to other regions. This may help users in the future to better estimate the accuracy of a tested DEM in a particular landscape. The consequences of elevation model selection on further results are highly dependent on the topic of the study and the study area's level of detail. The current state of knowledge on the impact of uncertainties in DEMs on various applications could be established. However, the results of this work can be seen as a first step and more work is needed in the future to extend the knowledge of the effects of DEM uncertainties on further topics that have not been investigated to date

Google Earth Engine cloud computing platform for remote sensing big data applications: a comprehensive review

Remote sensing (RS) systems have been collecting massive volumes of datasets for decades, managing and analyzing of which are not practical using common software packages and desktop computing resources. In this regard, Google has developed a cloud computing platform, called Google Earth Engine (GEE), to effectively address the challenges of big data analysis. In particular, this platformfacilitates processing big geo data over large areas and monitoring the environment for long periods of time. Although this platformwas launched in 2010 and has proved its high potential for different applications, it has not been fully investigated and utilized for RS applications until recent years. Therefore, this study aims to comprehensively explore different aspects of the GEE platform, including its datasets, functions, advantages/limitations, and various applications. For this purpose, 450 journal articles published in 150 journals between January 2010 andMay 2020 were studied. It was observed that Landsat and Sentinel datasets were extensively utilized by GEE users. Moreover, supervised machine learning algorithms, such as Random Forest, were more widely applied to image classification tasks. GEE has also been employed in a broad range of applications, such as Land Cover/land Use classification, hydrology, urban planning, natural disaster, climate analyses, and image processing. It was generally observed that the number of GEE publications have significantly increased during the past few years, and it is expected that GEE will be utilized by more users from different fields to resolve their big data processing challenges.Peer ReviewedPostprint (published version

TerraSenseTK: a toolkit for remote soil nutrient estimation

Intensive farming endangers soil quality in various ways. Researchers show that if these practices continue, humanity will be faced with food production issues. For this matter, Earth Observation, more concretely Soil Sensing, along with Machine Learning, can be employed to monitor several indicators of soil degradation, such as soil salinity, soil heavy metal contamination and soil nutrients estimation. More concretely, Soil Nutrients are of great importance. For instance, to understand which crop better suits the land, the soil nutrients must be identified. However, sampling soil is a laborous and expensive task, which can be leveraged by Remote Sensing and Machine Learning. Several studies have already been developed in this matter, although many gaps still exist. Among them, the lack of cross-dataset evaluations of existing algorithms, and also the steep learning curve to the Earth Observation domain that prevents many researchers from embracing this field. In this sense, we propose TerraSense ToolKit (TSTK), a python toolkit that addresses these challenges. In this work, the possibility to use Remote sensing along with Machine Learning algorithms to per form Soil Nutrient Estimation is explored, additionally, a nutrient estimation toolkit is proposed, and the effectivity of it is tested in a soil nutrient estimation case study. This toolkit is capable of simplifying Remote Sensing experiments and aims at reducing the barrier to entry to the field of Earth Observation. It comes with a preconfigured case study which implements a soil sensing pipeline. To evaluate the usability of the toolkit, experiments with five different crops were executed, namely with Wheat, Barley, Maize, Sunflower and Vineyards. This case study gave visibility to an underlying unbalanced data problem, which is not well addressed in the current State of the Art.A agricultura intensiva poe em perigo a qualidade do solo de v ˜ arias formas. Os investigadores ´ mostram que, se continuarmos com estas praticas, a humanidade ser ´ a confrontada com quest ´ oes de ˜ produc¸ao alimentar. Para este efeito, a Observac¸ ˜ ao da Terra, mais concretamente o Sensoriamento ˜ do Solo, juntamente com a aprendizagem automatica, podem ser utilizadas para monitorizar v ´ arios ´ indicadores da degradac¸ao do solo, tais como a salinidade do solo, a contaminac¸ ˜ ao do solo por metais ˜ pesados e a quantificac¸ao dos nutrientes do solo. Mais concretamente, os Nutrientes do Solo s ˜ ao de ˜ grande importancia. Por exemplo para compreender qual a cultura que melhor se adapta ao solo, os ˆ nutrientes do solo devem ser identificados. No entanto, a amostragem do solo e uma tarefa trabalhosa ´ e dispendiosa, que pode ser impulsionada pela percepc¸ao remota e pela aprendizagem autom ˜ atica. ´ Ja foram desenvolvidos v ´ arios estudos sobre este assunto, embora ainda existam muitas lacunas. ´ Entre eles, a falta de avaliac¸oes cruzadas dos algoritmos existentes, e tamb ˜ em a curva de aprendiza- ´ gem acentuada para o campo de Observac¸ao da Terra que impede muitos investigadores de enveredar ˜ por este campo. Neste sentido, propomos TSTK, um toolkit em python que aborda estes desafios. Neste trabalho, e explorada a possibilidade de usar a Percepc¸ ´ ao Remota juntamente com os algo- ˜ ritmos de Aprendizagem Automatica para realizar a Estimativa de Nutrientes do Solo. Al ´ em disso, ´ e´ proposto um toolkit de estimativa de nutrientes e tambem um pipeline para o devido efeito, a efetividade ´ do toolkit e testada num caso de estudo de Estimac¸ ´ ao de Nutrientes no Solo. ˜ Este toolkit e capaz de simplificar as experi ´ encias de Percepc¸ ˆ ao Remota e visa reduzir a barreira ˜ de entrada no campo da Observac¸ao da Terra. Para avaliar a usabilidade do toolkit, foram executadas ˜ experiencias com cinco culturas diferentes, nomeadamente Trigo, Cevada, Milho, Girassol e Vinha. Este ˆ caso de estudo deu visibilidade a um problema subjacente de dados desiquilibrados, o qual nao˜ e bem ´ identificado no Estado da Arte atual

Data Acquisition and Processing for GeoAI Models to Support Sustainable Agricultural Practices

There are growing opportunities to leverage new technologies and data sources to address global problems related to sustainability, climate change, and biodiversity loss. The emerging discipline of GeoAI resulting from the convergence of AI and Geospatial science (Geo-AI) is enabling the possibility to harness the increasingly available open Earth Observation data collected from different constellations of satellites and sensors with high spatial, spectral and temporal resolutions. However, transforming these raw data into high-quality datasets that could be used for training AI and specifically deep learning models are technically challenging. This paper describes the process and results of synthesizing labelled-datasets that could be used for training AI (specifically Convolutional Neural Networks) models for determining agricultural land use pattern to support decisions for sustainable farming. In our opinion, this work is a significant step forward in addressing the paucity of usable datasets for developing scalable GeoAI models for sustainable agriculture

Quantitative Mapping of Soil Property Based on Laboratory and Airborne Hyperspectral Data Using Machine Learning

Soil visible and near-infrared spectroscopy provides a non-destructive, rapid and low-cost approach to quantify various soil physical and chemical properties based on their reflectance in the spectral range of 400–2500 nm. With an increasing number of large-scale soil spectral libraries established across the world and new space-borne hyperspectral sensors, there is a need to explore methods to extract informative features from reflectance spectra and produce accurate soil spectroscopic models using machine learning. Features generated from regional or large-scale soil spectral data play a key role in the quantitative spectroscopic model for soil properties. The Land Use/Land Cover Area Frame Survey (LUCAS) soil library was used to explore PLS-derived components and fractal features generated from soil spectra in this study. The gradient-boosting method performed well when coupled with extracted features on the estimation of several soil properties. Transfer learning based on convolutional neural networks (CNNs) was proposed to make the model developed from laboratory data transferable for airborne hyperspectral data. The soil clay map was successfully derived using HyMap imagery and the fine-tuned CNN model developed from LUCAS mineral soils, as deep learning has the potential to learn transferable features that generalise from the source domain to target domain. The external environmental factors like the presence of vegetation restrain the application of imaging spectroscopy. The reflectance data can be transformed into a vegetation suppressed domain with a force invariance approach, the performance of which was evaluated in an agricultural area using CASI airborne hyperspectral data. However, the relationship between vegetation and acquired spectra is complicated, and more efforts should put on removing the effects of external factors to make the model transferable from one sensor to another.:Abstract I Kurzfassung III Table of Contents V List of Figures IX List of Tables XIII List of Abbreviations XV 1 Introduction 1 1.1 Motivation 1 1.2 Soil spectra from different platforms 2 1.3 Soil property quantification using spectral data 4 1.4 Feature representation of soil spectra 5 1.5 Objectives 6 1.6 Thesis structure 7 2 Combining Partial Least Squares and the Gradient-Boosting Method for Soil Property Retrieval Using Visible Near-Infrared Shortwave Infrared Spectra 9 2.1 Abstract 10 2.2 Introduction 10 2.3 Materials and methods 13 2.3.1 The LUCAS soil spectral library 13 2.3.2 Partial least squares algorithm 15 2.3.3 Gradient-Boosted Decision Trees 15 2.3.4 Calculation of relative variable importance 16 2.3.5 Assessment 17 2.4 Results 17 2.4.1 Overview of the spectral measurement 17 2.4.2 Results of PLS regression for the estimation of soil properties 19 2.4.3 Results of PLS-GBDT for the estimation of soil properties 21 2.4.4 Relative important variables derived from PLS regression and the gradient-boosting method 24 2.5 Discussion 28 2.5.1 Dimension reduction for high-dimensional soil spectra 28 2.5.2 GBDT for quantitative soil spectroscopic modelling 29 2.6 Conclusions 30 3 Quantitative Retrieval of Organic Soil Properties from Visible Near-Infrared Shortwave Infrared Spectroscopy Using Fractal-Based Feature Extraction 31 3.1 Abstract 32 3.2 Introduction 32 3.3 Materials and Methods 35 3.3.1 The LUCAS topsoil dataset 35 3.3.2 Fractal feature extraction method 37 3.3.3 Gradient-boosting regression model 37 3.3.4 Evaluation 41 3.4 Results 42 3.4.1 Fractal features for soil spectroscopy 42 3.4.2 Effects of different step and window size on extracted fractal features 45 3.4.3 Modelling soil properties with fractal features 47 3.4.3 Comparison with PLS regression 49 3.5 Discussion 51 3.5.1 The importance of fractal dimension for soil spectra 51 3.5.2 Modelling soil properties with fractal features 52 3.6 Conclusions 53 4 Transfer Learning for Soil Spectroscopy Based on Convolutional Neural Networks and Its Application in Soil Clay Content Mapping Using Hyperspectral Imagery 55 4.1 Abstract 55 4.2 Introduction 56 4.3 Materials and Methods 59 4.3.1 Datasets 59 4.3.2 Methods 62 4.3.3 Assessment 67 4.4 Results and Discussion 67 4.4.1 Interpretation of mineral and organic soils from LUCAS dataset 67 4.4.2 1D-CNN and spectral index for LUCAS soil clay content estimation 69 4.4.3 Application of transfer learning for soil clay content mapping using the pre-trained 1D-CNN model 72 4.4.4 Comparison between spectral index and transfer learning 74 4.4.5 Large-scale soil spectral library for digital soil mapping at the local scale using hyperspectral imagery 75 4.5 Conclusions 75 5 A Case Study of Forced Invariance Approach for Soil Salinity Estimation in Vegetation-Covered Terrain Using Airborne Hyperspectral Imagery 77 5.1 Abstract 78 5.2 Introduction 78 5.3 Materials and Methods 81 5.3.1 Study area of Zhangye Oasis 81 5.3.2 Data description 82 5.3.3 Methods 83 5.3.3 Model performance assessment 85 5.4 Results and Discussion 86 5.4.1 The correlation between NDVI and soil salinity 86 5.4.2 Vegetation suppression performance using the Forced Invariance Approach 86 5.4.3 Estimation of soil properties using airborne hyperspectral data 88 5.5 Conclusions 90 6 Conclusions and Outlook 93 Bibliography 97 Acknowledgements 11

Multi-temporal, multi-sensor land use/land cover mapping: Google Earth Engine and Random Forest for the classification of the Scottish flow country

Long-term monitoring of Land Use/Land Cover (LULC) dynamics is fundamental for implementing effective policy and mitigating the effects of climate change. In the UK, the Scottish Flow Country represents an area of ~4000km2 spanning Caithness and Sutherland, encompassing 25% of global blanket bogs. There is a need to understand these peatland ecosystems in a broader context, appreciating their importance within evolving landscapes. Frequent advances in remote sensing (RS) have provided a means for large-scale LULC mapping to be executed with increasing temporal and spatial resolutions. In addition, cloud-computing services such as Google Earth Engine (GEE) have enabled the processing and analysis of geospatial data, allowing various stakeholders to address challenges with the assistance of “Geo Big Data”. This study looks to assess how the LULC mapping can take advantage of geospatial data, cloud-computing and machine learning for the monitoring of peatland ecosystems within a broader economic and environmental policy-driven context. The following objectives were defined: (1) determine the optimal combination of optical, radar and topographic data for LULC mapping of the Scottish Land Use Strategy; (2) assess their application in GEE; and (3) evaluate Random Forest for classification of LULC classes. Results suggest a combination of optical, radar and topographic features is necessary for comprehensive LULC mapping (LUSTOR OA=0.823 and KA=0.792), particularly when delineating ecologically, hydrologically and geomorphologically heterogenous landscapes. Finally, RF performance was evaluated, future improvements were outlined and the effectiveness of LULC mapping for policy assessments is discussed