Comparison of Methods for Modeling Fractional Cover Using Simulated Satellite Hyperspectral Imager Spectra

Remotely sensed data can be used to model the fractional cover of green vegetation (GV), non-photosynthetic vegetation (NPV), and soil in natural and agricultural ecosystems. NPV and soil cover are difficult to estimate accurately since absorption by lignin, cellulose, and other organic molecules cannot be resolved by broadband multispectral data. A new generation of satellite hyperspectral imagers will provide contiguous narrowband coverage, enabling new, more accurate, and potentially global fractional cover products. We used six field spectroscopy datasets collected in prior experiments from sites with partial crop, grass, shrub, and low-stature resprouting tree cover to simulate satellite hyperspectral data, including sensor noise and atmospheric correction artifacts. The combined dataset was used to compare hyperspectral index-based and spectroscopic methods for estimating GV, NPV, and soil fractional cover. GV fractional cover was estimated most accurately. NPV and soil fractions were more difficult to estimate, with spectroscopic methods like partial least squares (PLS) regression, spectral feature analysis (SFA), and multiple endmember spectral mixture analysis (MESMA) typically outperforming hyperspectral indices. Using an independent validation dataset, the lowest root mean squared error (RMSE) values were 0.115 for GV using either normalized difference vegetation index (NDVI) or SFA, 0.164 for NPV using PLS, and 0.126 for soil using PLS. PLS also had the lowest RMSE averaged across all three cover types. This work highlights the need for more extensive and diverse fine spatial scale measurements of fractional cover, to improve methodologies for estimating cover in preparation for future hyperspectral global monitoring missions

CLASSIFYING SOIL MOISTURE CONTENT USING REFLECTANCE-BASED REMOTE SENSING

The ability to quantify soil moisture spatial variability and its temporal dynamics over entire fields through direct soil observations using remote sensing will improve early detection of water stress before crop physiological or economic damage has occurred, and it will contribute to the identification of zones within a field in which soil water is depleted faster than in other zones of a field. The overarching objective of this research is to develop tools and methods for remotely estimating soil moisture variability in agricultural crop production. Index-based and machine learning methods were deployed for processing hyperspectral data collected from moisture-controlled samples. In the first of five studies described in this dissertation, the feasibility of using “low-cost” index-based multispectral reflectance sensing for remotely delineating soil moisture content from direct soil and crop residue measurements using down-sampled spectral data were determined. The relative reflectance from soil and wheat stalk residue were measured using visible and near-infrared spectrometers. The optimal pair of wavelengths was chosen using a script to create an index for estimating soil and wheat stalk residue moisture levels. Wavelengths were selected to maximize the slope of the linear index function (i.e., sensitivity to moisture) and either maximize the coefficient of determination (R2) or minimize the root mean squared error (RMSE) of the index. Results showed that wavelengths centered near 1300 nm and 1500 nm, within the range of 400 to 1700 nm, produced the best index for individual samples; however, this index worked poorly on estimating stalk residue moisture. In the second of five studies, 20 machine learning algorithms were applied to full spectral datasets for moisture prediction and comparing them to the index-based method from the previous objective. Cubic support vector machine (SVM) and ensemble bagged trees methods produced the highest composite prediction accuracies of 96% and 93% for silt-loam soil samples, and 86% and 93% for wheat stalk residue samples, respectively. Prediction accuracy using the index-based method was 86% for silt-loam soil and 30% for wheat stalk residue. In the third study, a spectral measurement platform capable of being deployed on a UAS was developed for future use in quantifying and delineating moisture zones within agricultural landscapes. A series of portable spectrometers covering ultraviolet (UV), visible (VIS), and near-infrared (NIR) wavelengths were instrumented using a Raspberry Pi embedded computer that was programmed to interface with the UAS autopilot for autonomous reflectance data acquisition. A similar ground-based system was developed to keep track of ambient light during reflectance target measurement. The systems were tested under varying ambient light conditions during the 2017 Great American Eclipse. In the fourth study, the data acquisition system from the third study was deployed for recognizing different targets in the grayscale range using machine learning methods and under ambient light conditions. In this study, a dynamic method was applied to update integration time on spectrometers to optimize sensitivity of the instruments. It was found that by adjusting the integration time on each spectrometer such that a maximum intensity across all wavelengths was reached, the targets could be recognized simply based on the reflectance measurements with no need of a separate ambient light measurement. Finally, in the fifth study, the same data acquisition system and variable integration time method were used for estimating soil moisture under ambient light condition. Among 22 machine learning algorithms, linear and quadratic discriminant analysis achieved the maximum prediction accuracy. A UAS-deployable hyperspectral data acquisition system containing three portable spectrometers and an embedded computer was developed to classify moisture content from spectral data. Partial least squares regression and machine learning algorithms were shown to be effective to generate predictive models for classifying soil moisture

Density Estimates as Representations of Agricultural Fields for Remote Sensing-Based Monitoring of Tillage and Vegetation Cover

We consider the use of remote sensing for large-scale monitoring of agricultural land use, focusing on classification of tillage and vegetation cover for individual field parcels across large spatial areas. From the perspective of remote sensing and modelling, field parcels are challenging as objects of interest due to highly varying shape and size but relatively uniform pixel content and texture. To model such areas we need representations that can be reliably estimated already for small parcels and that are invariant to the size of the parcel. We propose representing the parcels using density estimates of remote imaging pixels and provide a computational pipeline that combines the representation with arbitrary supervised learning algorithms, while allowing easy integration of multiple imaging sources. We demonstrate the method in the task of the automatic monitoring of autumn tillage method and vegetation cover of Finnish crop fields, based on the integrated analysis of intensity of Synthetic Aperture Radar (SAR) polarity bands of the Sentinel-1 satellite and spectral indices calculated from Sentinel-2 multispectral image data. We use a collection of 127,757 field parcels monitored in April 2018 and annotated to six tillage method and vegetation cover classes, reaching 70% classification accuracy for test parcels when using both SAR and multispectral data. Besides this task, the method could also directly be applied for other agricultural monitoring tasks, such as crop yield prediction

Density Estimates as Representations of Agricultural Fields for Remote Sensing-Based Monitoring of Tillage and Vegetation Cover

We consider the use of remote sensing for large-scale monitoring of agricultural land use, focusing on classification of tillage and vegetation cover for individual field parcels across large spatial areas. From the perspective of remote sensing and modelling, field parcels are challenging as objects of interest due to highly varying shape and size but relatively uniform pixel content and texture. To model such areas we need representations that can be reliably estimated already for small parcels and that are invariant to the size of the parcel. We propose representing the parcels using density estimates of remote imaging pixels and provide a computational pipeline that combines the representation with arbitrary supervised learning algorithms, while allowing easy integration of multiple imaging sources. We demonstrate the method in the task of the automatic monitoring of autumn tillage method and vegetation cover of Finnish crop fields, based on the integrated analysis of intensity of Synthetic Aperture Radar (SAR) polarity bands of the Sentinel-1 satellite and spectral indices calculated from Sentinel-2 multispectral image data. We use a collection of 127,757 field parcels monitored in April 2018 and annotated to six tillage method and vegetation cover classes, reaching 70% classification accuracy for test parcels when using both SAR and multispectral data. Besides this task, the method could also directly be applied for other agricultural monitoring tasks, such as crop yield prediction.Peer reviewe

Manifold learning based spectral unmixing of hyperspectral remote sensing data

Nonlinear mixing effects inherent in hyperspectral data are not properly represented in linear spectral unmixing models. Although direct nonlinear unmixing models provide capability to capture nonlinear phenomena, they are difficult to formulate and the results are not always generalizable. Manifold learning based spectral unmixing accommodates nonlinearity in the data in the feature extraction stage followed by linear mixing, thereby incorporating some characteristics of nonlinearity while retaining advantages of linear unmixing approaches. Since endmember selection is critical to successful spectral unmixing, it is important to select proper endmembers from the manifold space. However, excessive computational burden hinders development of manifolds for large-scale remote sensing datasets. This dissertation addresses issues related to high computational overhead requirements of manifold learning for developing representative manifolds for the spectral unmixing task. Manifold approximations using landmarks are popular for mitigating the computational complexity of manifold learning. A new computationally effective landmark selection method that exploits spatial redundancy in the imagery is proposed. A robust, less costly landmark set with low spectral and spatial redundancy is successfully incorporated with a hybrid manifold which shares properties of both global and local manifolds. While landmark methods reduce computational demand, the resulting manifolds may not represent subtle features of the manifold adequately. Active learning heuristics are introduced to increase the number of landmarks, with the goal of developing more representative manifolds for spectral unmixing. By communicating between the landmark set and the query criteria relative to spectral unmixing, more representative and stable manifolds with less spectrally and spatially redundant landmarks are developed. A new ranking method based on the pixels with locally high spectral variability within image subsets and convex-geometry finds a solution more quickly and precisely. Experiments were conducted to evaluate the proposed methods using the AVIRIS Cuprite hyperspectral reference dataset. A case study of manifold learning based spectral unmixing in agricultural areas is included in the dissertation.Remotely sensed data collected by airborne or spaceborne sensors are utilized to quantify crop residue cover over an extensive area. Although remote sensing indices are popular for characterizing residue amounts, they are not effective with noisy Hyperion data because the effect of residual striping artifacts is amplified in ratios involving band differences. In this case study, spectral unmixing techniques are investigated for estimating crop residue as an alternative approach to empirical models developed using band based indices. The spectral unmixing techniques, and especially the manifold learning approaches, provide more robust, lower RMSE estimates for crop residue cover than the hyperspectral index based method for Hyperion data