Towards a Generalized Machine Learning Approach for Estimating Chlorophyll Values in Inland Waters with Spectral Data

Wasser ist ein wesentliches Element des Lebens. Seine Qualität ist jedoch bedroht, zum Beispiel durch schädliche Algenblüten oder anthropogene Verschmutzungen. Regelmäßige Kontrollen ermöglichen das Erkennen von Veränderungen der Wasserqualität von Binnengewässern. Konventionelle Wasserqualitätskontrollen werden hauptsächlich mittels In-situ-Probenahmen durchgeführt, eine teure und arbeitsintensive Vorgehensweise. Spektrale Fernerkundung kann eine Alternative zu In-situ-Beprobungen sein. Die sichtbare und nahinfrarote Strahlung, die von einem Sensor aufgenommen wird, hat mit dem Wasserkörper und dessen Inhaltsstoffen interagiert. Dadurch enthält die Strahlung Informationen über Absorptions- und Streuprozesse in der Wassersäule. Ein Parameter, der stark mit der Strahlung wechselwirkt, ist das pflanzliche Pigment Chlorophyll a. Chlorophyll a ist ein Proxy für die Phytoplanktonabundanz und kann daher mit der Wasserqualität in Verbindung gebracht werden. Die spektrale Überlappung mit anderen Wasserinhaltsstoffen erschwert die Bestimmung des Chlorophyll a-Gehalts mit spektralen Daten in der Wassersäule. Daher ist ein zuverlässiger Modellierungsansatz erforderlich, um diese nicht-lineare Regressionsaufgabe zu lösen und damit kontinuierliche Chlorophyll a-Werte aus Spektraldaten zu gewinnen. Eine zusätzliche Anforderung an einen solchen Ansatz ist die Anwendbarkeit auf die meisten der weltweiten Binnengewässer, da der Mangel an Referenzdaten nicht erlaubt, spezialisierte Modelle für jeden einzelnen See zu generieren. Diese Generalisierungsanforderung passt perfekt zu Ansätzen des überwachten maschinellen Lernens. Ein Hauptziel dieser Arbeit ist daher das Trainieren und Evaluieren von überwachten maschinellen Lernverfahren zum Schätzen kontinuierlicher Chlorophyll a-Werte von mehreren Binnengewässern. Die untersuchten Studien stützen sich dabei vollständig auf spektrale In-situ-Messungen. Dieser Aufbau erlaubt eine detailliertere Analyse der Beziehungen zwischen spektralen Daten und Wasserparametern. Außerdem wird der Einfluss der Atmosphäre verringert. Drei verschiedene Datensätze wurden im Rahmen dieser Arbeit aufgenommen, um den Generalisierungsprozess der generierten Modelle zu untersuchen. Die Variabilität der Datensätze nimmt dabei sukzessive zu. Daher wurden für diese Datensätze drei Studienkonfigurationen entworfen, die sukzessive die Anforderung zur Generalisierung der Modelle erhöhen. In der ersten Konfiguration werden lediglich Modelle untersucht, die sich auf ein einzelnes Gewässer beziehen. Im Gegensatz dazu stützt sich die letzte Konfiguration auf einen vollständig simulierten Datensatz für den Trainingsprozess der Modelle, während deren Evaluierung auf einem völlig unabhängigen Datensatz mit elf verschiedenen Binnengewässern erfolgt. Die Idee hinter diesem Konzept ist, wenn die Modelle die Chlorophyll a-Werte der elf völlig unbekannten Binnengewässer schätzen können, werden sie vermutlich auch weltweit, die Werte ähnlicher Binnengewässer schätzen können. Ein eindimensionales CNN als Vertreter der Deep-Learning-Verfahren hat sich dabei als das Modell mit den besten Generaliserungseigenschaften bei zufriedenstellender Schätzgenauigkeit erwiesen. Ein weiteres Augenmerk wird auf die spektrale Auflösung gelegt. Eine Verringerung der spektralen Auflösung von hyperspektral auf multispektral ist mit einem Informationsverlust verbunden. Die Schätzungsergebnisse aus dem eindimensionalen CNN zeigen, dass eine hyperspektrale Auflösung für ein vollständig generalisierendes Modell notwendig ist. Eine multispektrale Auflösung ist jedoch ausreichend für weniger generalisierende Modelle. Diese Erkenntnisse sind wichtig um im Hinblick auf ein zukünftiges Forschungsvorhaben den Upscaling-Ansatz auf reale Satellitendaten zu realisieren und damit eine flächendeckende Überwachung der Wasserqualität zu verwirklichen

Estimating Chlorophyll a Concentrations of Several Inland Waters with Hyperspectral Data and Machine Learning Models

Water is a key component of life, the natural environment and human health. For monitoring the conditions of a water body, the chlorophyll a concentration can serve as a proxy for nutrients and oxygen supply. In situ measurements of water quality parameters are often time-consuming, expensive and limited in areal validity. Therefore, we apply remote sensing techniques. During field campaigns, we collected hyperspectral data with a spectrometer and in situ measured chlorophyll a concentrations of 13 inland water bodies with different spectral characteristics. One objective of this study is to estimate chlorophyll a concentrations of these inland waters by applying three machine learning regression models: Random Forest, Support Vector Machine and an Artificial Neural Network. Additionally, we simulate four different hyperspectral resolutions of the spectrometer data to investigate the effects on the estimation performance. Furthermore, the application of first order derivatives of the spectra is evaluated in turn to the regression performance. This study reveals the potential of combining machine learning approaches and remote sensing data for inland waters. Each machine learning model achieves an R2-score between 80 % to 90 % for the regression on chlorophyll a concentrations. The random forest model benefits clearly from the applied derivatives of the spectra. In further studies, we will focus on the application of machine learning models on spectral satellite data to enhance the area-wide estimation of chlorophyll a concentration for inland waters.Comment: Accepted at ISPRS Geospatial Week 2019 in Ensched

Development of soft computing and applications in agricultural and biological engineering

Soft computing is a set of “inexact” computing techniques, which are able to model and analyze very complex problems. For these complex problems, more conventional methods have not been able to produce cost-effective, analytical, or complete solutions. Soft computing has been extensively studied and applied in the last three decades for scientific research and engineering computing. In agricultural and biological engineering, researchers and engineers have developed methods of fuzzy logic, artificial neural networks, genetic algorithms, decision trees, and support vector machines to study soil and water regimes related to crop growth, analyze the operation of food processing, and support decision-making in precision farming. This paper reviews the development of soft computing techniques. With the concepts and methods, applications of soft computing in the field of agricultural and biological engineering are presented, especially in the soil and water context for crop management and decision support in precision agriculture. The future of development and application of soft computing in agricultural and biological engineering is discussed

Development and Applications of Machine Learning Methods for Hyperspectral Data

Die hyperspektrale Fernerkundung der Erde stützt sich auf Daten passiver optischer Sensoren, die auf Plattformen wie Satelliten und unbemannten Luftfahrzeugen montiert sind. Hyperspektrale Daten umfassen Informationen zur Identifizierung von Materialien und zur Überwachung von Umweltvariablen wie Bodentextur, Bodenfeuchte, Chlorophyll a und Landbedeckung. Methoden zur Datenanalyse sind erforderlich, um Informationen aus hyperspektralen Daten zu erhalten. Ein leistungsstarkes Werkzeug bei der Analyse von Hyperspektraldaten ist das Maschinelle Lernen, eine Untergruppe von Künstlicher Intelligenz. Maschinelle Lernverfahren können nichtlineare Korrelationen lösen und sind bei steigenden Datenmengen skalierbar. Jeder Datensatz und jedes maschinelle Lernverfahren bringt neue Herausforderungen mit sich, die innovative Lösungen erfordern. Das Ziel dieser Arbeit ist die Entwicklung und Anwendung von maschinellen Lernverfahren auf hyperspektrale Fernerkundungsdaten. Im Rahmen dieser Arbeit werden Studien vorgestellt, die sich mit drei wesentlichen Herausforderungen befassen: (I) Datensätze, welche nur wenige Datenpunkte mit dazugehörigen Ausgabedaten enthalten, (II) das begrenzte Potential von nicht-tiefen maschinellen Lernverfahren auf hyperspektralen Daten und (III) Unterschiede zwischen den Verteilungen der Trainings- und Testdatensätzen. Die Studien zur Herausforderung (I) führen zur Entwicklung und Veröffentlichung eines Frameworks von Selbstorganisierten Karten (SOMs) für unüberwachtes, überwachtes und teilüberwachtes Lernen. Die SOM wird auf einen hyperspektralen Datensatz in der (teil-)überwachten Regression der Bodenfeuchte angewendet und übertrifft ein Standardverfahren des maschinellen Lernens. Das SOM-Framework zeigt eine angemessene Leistung in der (teil-)überwachten Klassifikation der Landbedeckung. Es bietet zusätzliche Visualisierungsmöglichkeiten, um das Verständnis des zugrunde liegenden Datensatzes zu verbessern. In den Studien, die sich mit Herausforderung (II) befassen, werden drei innovative eindimensionale Convolutional Neural Network (CNN) Architekturen entwickelt. Die CNNs werden für eine Bodentexturklassifikation auf einen frei verfügbaren hyperspektralen Datensatz angewendet. Ihre Leistung wird mit zwei bestehenden CNN-Ansätzen und einem Random Forest verglichen. Die beiden wichtigsten Erkenntnisse lassen sich wie folgt zusammenfassen: Erstens zeigen die CNN-Ansätze eine deutlich bessere Leistung als der angewandte nicht-tiefe Random Forest-Ansatz. Zweitens verbessert das Hinzufügen von Informationen über hyperspektrale Bandnummern zur Eingabeschicht eines CNNs die Leistung im Bezug auf die einzelnen Klassen. Die Studien über die Herausforderung (III) basieren auf einem Datensatz, der auf fünf verschiedenen Messgebieten in Peru im Jahr 2019 erfasst wurde. Die Unterschiede zwischen den Messgebieten werden mit qualitativen Methoden und mit unüberwachten maschinellen Lernverfahren, wie zum Beispiel Principal Component Analysis und Autoencoder, analysiert. Basierend auf den Ergebnissen wird eine überwachte Regression der Bodenfeuchte bei verschiedenen Kombinationen von Messgebieten durchgeführt. Zusätzlich wird der Datensatz mit Monte-Carlo-Methoden ergänzt, um die Auswirkungen der Verschiebung der Verteilungen des Datensatzes auf die Regression zu untersuchen. Der angewandte SOM-Regressor ist relativ robust gegenüber dem Rauschen des Bodenfeuchtesensors und zeigt eine gute Leistung bei kleinen Datensätzen, während der angewandte Random Forest auf dem gesamten Datensatz am besten funktioniert. Die Verschiebung der Verteilungen macht diese Regressionsaufgabe schwierig; einige Kombinationen von Messgebieten bilden einen deutlich sinnvolleren Trainingsdatensatz als andere. Insgesamt zeigen die vorgestellten Studien, die sich mit den drei größten Herausforderungen befassen, vielversprechende Ergebnisse. Die Arbeit gibt schließlich Hinweise darauf, wie die entwickelten maschinellen Lernverfahren in der zukünftigen Forschung weiter verbessert werden können

Sustainable Agriculture and Advances of Remote Sensing (Volume 1)

Agriculture, as the main source of alimentation and the most important economic activity globally, is being affected by the impacts of climate change. To maintain and increase our global food system production, to reduce biodiversity loss and preserve our natural ecosystem, new practices and technologies are required. This book focuses on the latest advances in remote sensing technology and agricultural engineering leading to the sustainable agriculture practices. Earth observation data, in situ and proxy-remote sensing data are the main source of information for monitoring and analyzing agriculture activities. Particular attention is given to earth observation satellites and the Internet of Things for data collection, to multispectral and hyperspectral data analysis using machine learning and deep learning, to WebGIS and the Internet of Things for sharing and publishing the results, among others

Hyperspectral Imaging for Fine to Medium Scale Applications in Environmental Sciences

The aim of the Special Issue “Hyperspectral Imaging for Fine to Medium Scale Applications in Environmental Sciences” was to present a selection of innovative studies using hyperspectral imaging (HSI) in different thematic fields. This intention reflects the technical developments in the last three decades, which have brought the capacity of HSI to provide spectrally, spatially and temporally detailed data, favoured by e.g., hyperspectral snapshot technologies, miniaturized hyperspectral sensors and hyperspectral microscopy imaging. The present book comprises a suite of papers in various fields of environmental sciences—geology/mineral exploration, digital soil mapping, mapping and characterization of vegetation, and sensing of water bodies (including under-ice and underwater applications). In addition, there are two rather methodically/technically-oriented contributions dealing with the optimized processing of UAV data and on the design and test of a multi-channel optical receiver for ground-based applications. All in all, this compilation documents that HSI is a multi-faceted research topic and will remain so in the future

Hyperspectral sensing for turbid water quality monitoring in freshwater rivers: Empirical relationship between reflectance and turbidity and total solids

Total suspended solid (TSS) is an important water quality parameter. This study was conducted to test the feasibility of the band combination of hyperspectral sensing for inland turbid water monitoring in Taiwan. The field spectral reflectance in the Wu river basin of Taiwan was measured with a spectroradiometer; the water samples were collected from the different sites of the Wu river basin and some water quality parameters were analyzed on the sites (in situ) as well as brought to the laboratory for further analysis. To obtain the data set for this study, 160 in situ sample observations were carried out during campaigns from August to December, 2005. The water quality results were correlated with the reflectivity to determine the spectral characteristics and their relationship with turbidity and TSS. Furthermore, multiple-regression (MR) and artificial neural network (ANN) were used to model the transformation function between TSS concentration and turbidity levels of stream water, and the radiance measured by the spectroradiometer. The value of the turbidity and TSS correlation coefficient was 0.766, which implies that turbidity is significantly related to TSS in the Wu river basin. The results indicated that TSS and turbidity are positively correlated in a significant way across the entire spectrum, when TSS concentration and turbidity levels were under 800 mg·L(-1) and 600 NTU, respectively. Optimal wavelengths for the measurements of TSS and turbidity are found in the 700 and 900 nm range, respectively. Based on the results, better accuracy was obtained only when the ranges of turbidity and TSS concentration were less than 800 mg·L(-1) and less than 600 NTU, respectively and used rather than using whole dataset (R(2) = 0.93 versus 0.88 for turbidity and R(2) = 0.83 versus 0.58 for TSS). On the other hand, the ANN approach can improve the TSS retrieval using MR. The accuracy of TSS estimation applying ANN (R(2) = 0.66) was better than with the MR approach (R(2) = 0.58), as expected due to the nonlinear nature of the transformation model

ESTIMATING CHLOROPHYLL A CONCENTRATIONS OF SEVERAL INLAND WATERS WITH HYPERSPECTRAL DATA AND MACHINE LEARNING MODELS

Water is a key component of life, the natural environment and human health. For monitoring the conditions of a water body, the chlorophyll a concentration can serve as a proxy for nutrients and oxygen supply. In situ measurements of water quality parameters are often time-consuming, expensive and limited in areal validity. Therefore, we apply remote sensing techniques. During field campaigns, we collected hyperspectral data with a spectrometer and in situ measured chlorophyll a concentrations of 13 inland water bodies with different spectral characteristics. One objective of this study is to estimate chlorophyll a concentrations of these inland waters by applying three machine learning regression models: Random Forest, Support Vector Machine and an Artificial Neural Network. Additionally, we simulate four different hyperspectral resolutions of the spectrometer data to investigate the effects on the estimation performance. Furthermore, the application of first order derivatives of the spectra is evaluated in turn to the regression performance. This study reveals the potential of combining machine learning approaches and remote sensing data for inland waters. Each machine learning model achieves an R2-score between 80% to 90% for the regression on chlorophyll a concentrations. The random forest model benefits clearly from the applied derivatives of the spectra. In further studies, we will focus on the application of machine learning models on spectral satellite data to enhance the area-wide estimation of chlorophyll a concentration for inland waters

Remote sensing and machine learning for prediction of wheat growth in precision agriculture applications

This thesis focuses on remote sensing and machine learning for prediction of wheat growth in precision agriculture applications. Agriculture is the primary productive force, which plays an important role in human activities. Wheat, as one of the essential sources of food, is also a widely planted crop. The impact of weather and climate and some other uncertain factors on wheat production is crucial. Therefore, it is necessary to use reliable and statistically reasonable models for crop growth and yield prediction based on vegetation index variables and other factors, so as to obtain reliable prediction for efficient production. Applying certain artificial intelligence algorithms to the precision agriculture can significantly improve the efficiency of traditional agriculture in crop planting and reduce the consumption of human and natural resources. Remote sensing can objectively, accurately and timely provide a large amount of information for ecological environment and crop growth in agriculture applications. By combining the image and spectral data obtained by remote sensing technology with machine learning, information about wheat growth, yield and insect pests can be learned in time. This thesis focuses on its applications in agriculture, particularly using effective prediction models such as the back propagation neural network and some optimisation algorithms for predicting wheat growth, yield and aphid. The work presented in this thesis address the issues of wheat growth prediction, yield assessment and aphid validation by model building and machine learning algorithm optimisation by means of remote sensing data. Specifically, the following objectives are defined: 1. Analyse multiple vegetation indexes based on the TM 1-4 band data of Landsat satellite and use regression algorithms to train the models and predict wheat growth; 2. Analyse and compare multiple vegetation indexes models by means of spectral data and use regression algorithms to predict wheat yield; 3. Combine spectral vegetation indexes and multiple regression algorithms to predict wheat aphid; 4. Use accurate evaluation criteria for validating the efficacy of the various algorithms. In this thesis, the remote sensing data from the satellite has been applied instead of the airborne-based remote sensing data. Based on the TM 1-4 band image data of Landsat satellite, multiple vegetation indexes were used as the input of regression algorithms. After that, four kinds of regression algorithms such as the multiple linear regression (MR) algorithm, back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm were used to train the model and predict the LAI and SPAD. The prediction results of each algorithm were compared with the ground truth information collected by hand held instruments on the ground. The relationship between wheat yield and spectral data has been studied. Based on the BPNN algorithm, four kinds of models such as visible hyperspectral index (VHI) model, hyperspectral vegetation index (HVI) model, difference hyperspectral index (DHI) model and normalized hyperspectral index (NHI) model have been utilized to predict wheat yield. For the optimal NHI model, three regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm, were compared to predict wheat yield, and RMSE and R-square of the three algorithms were compared and analysed. Finally, the relationship between wheat aphid and spectral data has been investigated. Nine vegetation indexes related to aphid have been estimated from spectral data as the input of regression algorithms. Five kinds of regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm, particle swarm optimisation (PSO) optimised BPNN algorithm, ant colony (ACO) optimisation algorithm optimised BPNN algorithm and cuckoo search (CS) optimised BPNN algorithm have been implemented to predict wheat aphid, which was validated with the ground truth information measured by hand-held instruments on the ground. The prediction results of each algorithm have been analysed. The major original contributions of this thesis are as follows: 1. A variety of optimisation algorithms are used to improve the regression analysis of the BPNN algorithm, so that the prediction results of each model for wheat growth, yield and aphid are more accurate. 2. The spectral characteristics of winter wheat canopy have been analysed. The correlation between the absorption band and the associated physical and chemical properties of crops, specially the red edge slope, with the crop yield and wheat aphid damage is established. 3. Adjusted MSE and un-centered R-square, as accurate evaluation criteria for practical applications, are used to compare the prediction results of the models under different dimensions of the observed data. 4. Improve algorithm training by using the cross-validation method to obtain reliable and stable models for the prediction of wheat growth, yield, and aphid. Through repeated cross-validation, a better model can be obtained in the last. Key word：Precision agriculture; BP network, wheat growth assessment; wheat yield prediction, wheat aphid validationThis thesis focuses on remote sensing and machine learning for prediction of wheat growth in precision agriculture applications. Agriculture is the primary productive force, which plays an important role in human activities. Wheat, as one of the essential sources of food, is also a widely planted crop. The impact of weather and climate and some other uncertain factors on wheat production is crucial. Therefore, it is necessary to use reliable and statistically reasonable models for crop growth and yield prediction based on vegetation index variables and other factors, so as to obtain reliable prediction for efficient production. Applying certain artificial intelligence algorithms to the precision agriculture can significantly improve the efficiency of traditional agriculture in crop planting and reduce the consumption of human and natural resources. Remote sensing can objectively, accurately and timely provide a large amount of information for ecological environment and crop growth in agriculture applications. By combining the image and spectral data obtained by remote sensing technology with machine learning, information about wheat growth, yield and insect pests can be learned in time. This thesis focuses on its applications in agriculture, particularly using effective prediction models such as the back propagation neural network and some optimisation algorithms for predicting wheat growth, yield and aphid. The work presented in this thesis address the issues of wheat growth prediction, yield assessment and aphid validation by model building and machine learning algorithm optimisation by means of remote sensing data. Specifically, the following objectives are defined: 1. Analyse multiple vegetation indexes based on the TM 1-4 band data of Landsat satellite and use regression algorithms to train the models and predict wheat growth; 2. Analyse and compare multiple vegetation indexes models by means of spectral data and use regression algorithms to predict wheat yield; 3. Combine spectral vegetation indexes and multiple regression algorithms to predict wheat aphid; 4. Use accurate evaluation criteria for validating the efficacy of the various algorithms. In this thesis, the remote sensing data from the satellite has been applied instead of the airborne-based remote sensing data. Based on the TM 1-4 band image data of Landsat satellite, multiple vegetation indexes were used as the input of regression algorithms. After that, four kinds of regression algorithms such as the multiple linear regression (MR) algorithm, back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm were used to train the model and predict the LAI and SPAD. The prediction results of each algorithm were compared with the ground truth information collected by hand held instruments on the ground. The relationship between wheat yield and spectral data has been studied. Based on the BPNN algorithm, four kinds of models such as visible hyperspectral index (VHI) model, hyperspectral vegetation index (HVI) model, difference hyperspectral index (DHI) model and normalized hyperspectral index (NHI) model have been utilized to predict wheat yield. For the optimal NHI model, three regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm, were compared to predict wheat yield, and RMSE and R-square of the three algorithms were compared and analysed. Finally, the relationship between wheat aphid and spectral data has been investigated. Nine vegetation indexes related to aphid have been estimated from spectral data as the input of regression algorithms. Five kinds of regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm, particle swarm optimisation (PSO) optimised BPNN algorithm, ant colony (ACO) optimisation algorithm optimised BPNN algorithm and cuckoo search (CS) optimised BPNN algorithm have been implemented to predict wheat aphid, which was validated with the ground truth information measured by hand-held instruments on the ground. The prediction results of each algorithm have been analysed. The major original contributions of this thesis are as follows: 1. A variety of optimisation algorithms are used to improve the regression analysis of the BPNN algorithm, so that the prediction results of each model for wheat growth, yield and aphid are more accurate. 2. The spectral characteristics of winter wheat canopy have been analysed. The correlation between the absorption band and the associated physical and chemical properties of crops, specially the red edge slope, with the crop yield and wheat aphid damage is established. 3. Adjusted MSE and un-centered R-square, as accurate evaluation criteria for practical applications, are used to compare the prediction results of the models under different dimensions of the observed data. 4. Improve algorithm training by using the cross-validation method to obtain reliable and stable models for the prediction of wheat growth, yield, and aphid. Through repeated cross-validation, a better model can be obtained in the last. Key word：Precision agriculture; BP network, wheat growth assessment; wheat yield prediction, wheat aphid validatio