Gap Filling of Biophysical Parameter Time Series with Multi-Output Gaussian Processes

In this work we evaluate multi-output (MO) Gaussian Process (GP) models based on the linear model of coregionalization (LMC) for estimation of biophysical parameter variables under a gap filling setup. In particular, we focus on LAI and fAPAR over rice areas. We show how this problem cannot be solved with standard single-output (SO) GP models, and how the proposed MO-GP models are able to successfully predict these variables even in high missing data regimes, by implicitly performing an across-domain information transfer.CICYT TIN2015-64210-RIn this work we evaluate multi-output (MO) Gaussian Process (GP) models based on the linear model of coregionalization (LMC) for estimation of biophysical parameter variables under a gap filling setup. In particular, we focus on LAI and fAPAR over rice areas. We show how this problem cannot be solved with standard single-output (SO) GP models, and how the proposed MO-GP models are able to successfully predict these variables even in high missing data regimes, by implicitly performing an across-domain information transfer

Statistical uncertainty of eddy flux–based estimates of gross ecosystem carbon exchange at Howland Forest, Maine

We present an uncertainty analysis of gross ecosystem carbon exchange (GEE) estimates derived from 7 years of continuous eddy covariance measurements of forest-atmosphere CO2fluxes at Howland Forest, Maine, USA. These data, which have high temporal resolution, can be used to validate process modeling analyses, remote sensing assessments, and field surveys. However, separation of tower-based net ecosystem exchange (NEE) into its components (respiration losses and photosynthetic uptake) requires at least one application of a model, which is usually a regression model fitted to nighttime data and extrapolated for all daytime intervals. In addition, the existence of a significant amount of missing data in eddy flux time series requires a model for daytime NEE as well. Statistical approaches for analytically specifying prediction intervals associated with a regression require, among other things, constant variance of the data, normally distributed residuals, and linearizable regression models. Because the NEE data do not conform to these criteria, we used a Monte Carlo approach (bootstrapping) to quantify the statistical uncertainty of GEE estimates and present this uncertainty in the form of 90% prediction limits. We explore two examples of regression models for modeling respiration and daytime NEE: (1) a simple, physiologically based model from the literature and (2) a nonlinear regression model based on an artificial neural network. We find that uncertainty at the half-hourly timescale is generally on the order of the observations themselves (i.e., ∼100%) but is much less at annual timescales (∼10%). On the other hand, this small absolute uncertainty is commensurate with the interannual variability in estimated GEE. The largest uncertainty is associated with choice of model type, which raises basic questions about the relative roles of models and data

Fusing optical and SAR time series for LAI gap filling with multioutput Gaussian processes

The availability of satellite optical information is often hampered by the natural presence of clouds, which can be problematic for many applications. Persistent clouds over agricultural fields can mask key stages of crop growth, leading to unreliable yield predictions. Synthetic Aperture Radar (SAR) provides all-weather imagery which can potentially overcome this limitation, but given its high and distinct sensitivity to different surface properties, the fusion of SAR and optical data still remains an open challenge. In this work, we propose the use of Multi-Output Gaussian Process (MOGP) regression, a machine learning technique that learns automatically the statistical relationships among multisensor time series, to detect vegetated areas over which the synergy between SAR-optical imageries is profitable. For this purpose, we use the Sentinel-1 Radar Vegetation Index (RVI) and Sentinel-2 Leaf Area Index (LAI) time series over a study area in north west of the Iberian peninsula. Through a physical interpretation of MOGP trained models, we show its ability to provide estimations of LAI even over cloudy periods using the information shared with RVI, which guarantees the solution keeps always tied to real measurements. Results demonstrate the advantage of MOGP especially for long data gaps, where optical-based methods notoriously fail. The leave-one-image-out assessment technique applied to the whole vegetation cover shows MOGP predictions improve standard GP estimations over short-time gaps (R 2 of 74% vs 68%, RMSE of 0.4 vs 0.44 [m 2 m −2 ]) and especially over long-time gaps (R 2 of 33% vs 12%, RMSE of 0.5 vs 1.09 [m 2 m −2 ])

Multi-Season Phenology Mapping of Nile Delta Croplands Using Time Series of Sentinel-2 and Landsat 8 Green LAI

Space-based cropland phenology monitoring substantially assists agricultural managing practices and plays an important role in crop yield predictions. Multitemporal satellite observations allow analyzing vegetation seasonal dynamics over large areas by using vegetation indices or by deriving biophysical variables. The Nile Delta represents about half of all agricultural lands of Egypt. In this region, intensifying farming systems are predominant and multi-cropping rotations schemes are increasing, requiring a high temporal and spatial resolution monitoring for capturing successive crop growth cycles. This study presents a workflow for cropland phenology characterization and mapping based on time series of green Leaf Area Index (LAI) generated from NASA’s Harmonized Landsat 8 (L8) and Sentinel-2 (S2) surface reflectance dataset from 2016 to 2019. LAI time series were processed for each satellite dataset, which were used separately and combined to identify seasonal dynamics for a selection of crop types (wheat, clover, maize and rice). For the combination of L8 with S2 LAI products, we proposed two time series smoothing and fitting methods: (1) the Savitzky–Golay (SG) filter and (2) the Gaussian Processes Regression (GPR) fitting function. Single-sensor and L8-S2 combined LAI time series were used for the calculation of key crop Land Surface Phenology (LSP) metrics (start of season, end of season, length of season), whereby the detection of cropland growing seasons was based on two established threshold methods, i.e., a seasonal or a relative amplitude value. Overall, the developed phenology extraction scheme enabled identifying up to two successive crop cycles within a year, with a superior performance observed for the seasonal than for the relative threshold method, in terms of consistency and cropland season detection capability. Differences between the time series collections were analyzed by comparing the phenology metrics per crop type and year. Results suggest that L8-S2 combined LAI data streams with GPR led to a more precise detection of the start and end of growing seasons for most crop types, reaching an overall detection of 74% over the total planted crops versus 69% with S2 and 63% with L8 alone. Finally, the phenology mapping allowed us to evaluate the spatial and temporal evolution of the croplands over the agroecosystem in the Nile Delta.E.A. was supported by the predoctoral scholarship, grant number ACIF/2019/187, funded by the Generalitat Valenciana and co-funded by the European Social Fund. J.V. and S.B. were supported by the European Research Council (ERC) under the ERC-2017-STG SENTIFLEX project, grant number 755617. J.V. was additionally supported by a Ramón y Cajal Contract (Spanish Ministry of Science, Innovation and Universities). S.B. was additionally supported by the Generalitat Valenciana SEJIGENT program (SEJIGENT/2021/001) and European Union—NextGenerationEU (ZAMBRANO 21-04)

Quantifying Fundamental Vegetation Traits over Europe Using the Sentinel-3 OLCI Catalogue in Google Earth Engine

Thanks to the emergence of cloud-computing platforms and the ability of machine learning methods to solve prediction problems efficiently, this work presents a workflow to automate spatiotemporal mapping of essential vegetation traits from Sentinel-3 (S3) imagery. The traits included leaf chlorophyll content (LCC), leaf area index (LAI), fraction of absorbed photosynthetically active radiation (FAPAR), and fractional vegetation cover (FVC), being fundamental for assessing photosynthetic activity on Earth. The workflow involved Gaussian process regression (GPR) algorithms trained on top-of-atmosphere (TOA) radiance simulations generated by the coupled canopy radiative transfer model (RTM) SCOPE and the atmospheric RTM 6SV. The retrieval models, named to S3-TOA-GPR-1.0, were directly implemented in Google Earth Engine (GEE) to enable the quantification of the traits from TOA data as acquired from the S3 Ocean and Land Colour Instrument (OLCI) sensor. Following good to high theoretical validation results with normalized root mean square error (NRMSE) ranging from 5% (FAPAR) to 19% (LAI), a three fold evaluation approach over diverse sites and land cover types was pursued: (1) temporal comparison against LAI and FAPAR products obtained from Moderate Resolution Imaging Spectroradiometer (MODIS) for the time window 2016–2020, (2) spatial difference mapping with Copernicus Global Land Service (CGLS) estimates, and (3) direct validation using interpolated in situ data from the VALERI network. For all three approaches, promising results were achieved. Selected sites demonstrated coherent seasonal patterns compared to LAI and FAPAR MODIS products, with differences between spatially averaged temporal patterns of only 6.59%. In respect of the spatial mapping comparison, estimates provided by the S3-TOA-GPR-1.0 models indicated highest consistency with FVC and FAPAR CGLS products. Moreover, the direct validation of our S3-TOA-GPR-1.0 models against VALERI estimates indicated good retrieval performance for LAI, FAPAR and FVC. We conclude that our retrieval workflow of spatiotemporal S3 TOA data processing into GEE opens the path towards global monitoring of fundamental vegetation traits, accessible to the whole research community.We gratefully acknowledge the financial support by the European Space Agency (ESA) for airborne data acquisition and data analysis in the frame of the FLEXSense campaign (ESA Contract No. 4000125402/18/NL/NA). The research was also supported by the Action CA17134 SENSECO (Optical synergies for spatiotemporal sensing of scalable ecophysiological traits) funded by COST (European Cooperation in Science and Technology, www.cost.eu, accessed on: 8 January 2022). This publication is also the result of the project implementation: “Scientific support of climate change adaptation in agriculture and mitigation of soil degradation” (ITMS2014+313011W580) supported by the Integrated Infrastructure Operational Programme funded by the ERDF

LINKING MULTIVARIATE OBSERVATIONS OF THE LAND SURFACE TO VEGETATION PROPERTIES AND ECOSYSTEM PROCESSES

Remotely sensed images from satellites and aircrafts, as well as regional networks and monitoring stations such as eddy flux towers, are collecting large volumes of multivariate data that contain information about the land surface and ecosystem processes. To derive from these systems information and knowledge relevant to how the Earth system functions and how it is changing, we need tools that to filter and mine the large data streams currently being acquired at different spatial and temporal scales. A challenge for Earth System Science lies in accurately identifying and portraying the relationships between the measurements at the sensor and quantity o f interest (i.e. ecosystem process or land surface property)

Exploitation of SAR and optical Sentinel data to detect rice crop and estimate seasonal dynamics of leaf area index

This paper presents and evaluates multitemporal LAI estimates derived from Sentinel-2A data on rice cultivated area identified using time series of Sentinel-1A images over the main European rice districts for the 2016 crop season. This study combines the information conveyed by Sentinel-1A and Sentinel-2A into a high-resolution LAI retrieval chain. Rice crop was detected using an operational multi-temporal rule-based algorithm, and LAI estimates were obtained by inverting the PROSAIL radiative transfer model with Gaussian process regression. Direct validation was performed with in situ LAI measurements acquired in coordinated field campaigns in three countries (Italy, Spain and Greece). Results showed high consistency between estimates and ground measurements, revealing high correlations (R^2>0.93) and good accuracies (RMSE<0.83, rRMSE_m<23.6% and rRMSE_r<16.6%) in all cases. Sentinel-2A estimates were compared with Landsat-8 showing high spatial consistency between estimates over the three areas. The possibility to exploit seasonally-updated crop mask exploiting Sentinel-1A data and the temporal consistency between Sentinel-2A and Landsat-7/8 LAI time series demonstrates the feasibility of deriving operationally high spatial-temporal decametric multi-sensor LAI time series useful for crop monitoring

Improving Satellite Leaf Area Index Estimation Based On Various Integration Methods

Leaf Area Index (LAI) is an important land surface biophysical variable that is used to characterize vegetation amount and activity. Current satellite LAI products, however, do not satisfy the requirements of the modeling community due to their large uncertainties and frequent missing values. Each LAI product is currently generated from only one satellite sensor data. There is an urgent need for advanced methods to integrate multiple LAI products to improve the product's accuracy and integrality for various applications. To meet this need, this study proposes four methods, including the Optimal Interpolation (OI), Bayesian Maximum Entropy (BME), Multi-Resolution Tree (MRT) and Empirical Orthogonal Function (EOF), to integrate multiple LAI products. Three LAI products have been considered in this study: Moderate Resolution Imaging Spectroradiometer (MODIS), Multi-angle Imaging SpectroRadiometer (MISR) and Carbon cYcle and Change in Land Observational Products from an Ensemble of Satellites (CYCLOPES) LAI. As the basis of data integration, this dissertation first validates and intercompares MODIS and CYCLOPES LAI products and also evaluates their geometric accuracies. The CYCLOPES LAI product has smoother temporal profiles and fewer spatial variations, but tends to produce spurious large errors in winter. The Locally Adjusted Cubic-spline Capping algorithm is revised to smooth multiple years' average and variance. Although OI, BME and MRT based methods have been used in other fields, this is the first research to employ them in integrating multiple LAI products. This dissertation also presents a new integration method based on EOF to solve the problem of large data volume and inconsistent temporal resolution of different datasets. High resolution LAI reference maps generated with ground measurements are used to validate these algorithms. Validation results show that all of these four methods can fill data gaps and reduce the errors of the existing LAI products. The data gaps are filled with information from adjacent pixels and background. These algorithms remove the spurious large temporal and spatial variation of the original LAI products. The combination of multiple satellite products significantly reduces bias. OI and BME can reduce the RMSE from 1.0 (MODIS) to 0.7 and reduce the bias from +0.3 (MODIS) and -0.2 (CYCLOPES) to -0.1. MRT can produce similar results with OI but with significantly improved efficiency. EOF also generates the results with the RMSE of 0.7 but zero bias. Limited ground measurement data hardly prove which methods outperform the others. OI and BME theoretically produce statistically optimal results. BME relaxes OI's linear and Gaussian assumption and explicitly considers data error, but bears a much higher computational burden. MRT has improved efficiency but needs strict assumptions on the scale transfer function. EOF requires simpler model identification, while it is more "empirical" than "statistical". The original contributions of this study mainly include: 1) a new application of several different integration methods to incorporate multiple satellite LAI products to reduce uncertainties and improve integrality, 2) an enhancement of the Locally Adjusted Cubic-spline Capping by revising the end condition, 3) a novel comprehensive comparison of MODIS C5 LAI product with other satellite products, 4) the development of a new LAI normalization scheme by assuming the linear relationship between measurement error and LAI natural variance to account for the inconsistency between products, and finally, 5) the creation of a new data integration method based on EOF

Leaf Area Index (LAI) monitoring at global scale (improved definition, continuity and consistency of LAI estimates from kilometric satellite observations)

Le suivi des variables biophysiques à l échelle globale sur de longues périodes de temps est essentiellepour répondre aux nouveaux enjeux que constituent le changement climatique et la sécurité alimentaire. L indice foliaire (LAI) est une variable de structure définissant la surface d interception du rayonnement incident et d échanges gazeux avec l atmosphère. Le LAI est donc une variable importante des modèles d écosystèmes et a d ailleurs été reconnue comme variable climatique essentielle (ECV). Cette thèse a pour objectif de fournir des estimations globales et continues de LAI à partir d observations satellitaires en temps quasi-réel en réponse aux besoins des utilisateurs pour fournir des diagnostiques et pronostiques de l état et du fonctionnement de la végétation. Quelques produits LAI sont déjà disponibles mais montrent des désaccords et des limitations en termes de cohérence et de continuité. Cette thèse a pour objectif de lever ces limitations. Dans un premier temps, on essaiera de mieux définir la nature des estimations de LAI à partir d observations satellitaires. Puis, différentes méthodes de lissage te bouchage des séries temporelles ont été analysées pour réduire le bruit et les discontinuités principalement liées à la couverture nuageuse. Finalement quelques méthodes d estimation temps quasi réel ont été évaluées en considérant le niveau de bruit et les données manquantes.Les résultats obtenus dans la première partie de cette thèse montrent que la LAI effectif et bien mieux estimé que la valeur réelle de LAI du fait de l agrégation des feuilles observée au niveau du couvert. L utilisation d observations multidirectionnelles n améliore que marginalement les performances d estimation. L étude montre également que les performances d estimation optimales sont obtenues quand les solutions sont recherchées à l intérieur d une enveloppe définie par l incertitude associée aux mesures radiométriques. Dans la deuxième partie consacrée à l amélioration de la continuité et la cohérence des séries temporelles, les méthodes basées sur une fenêtre temporelle locale mais de largeur dépendant du nombre d observations présentes, et utilisant la climatologie comme information a priori s avèrent les plus intéressantes autorisant également l estimation en temps quasi réel.Monitoring biophysical variables at a global scale over long time periods is vital to address the climatechange and food security challenges. Leaf Area Index (LAI) is a structure variable giving a measure of the canopysurface for radiation interception and canopy-atmosphere interactions. LAI is an important variable in manyecosystem models and it has been recognized as an Essential Climate Variable. This thesis aims to provide globaland continuous estimates of LAI from satellite observations in near-real time according to user requirements to beused for diagnostic and prognostic evaluations of vegetation state and functioning. There are already someavailable LAI products which show however some important discrepancies in terms of magnitude and somelimitations in terms of continuity and consistency. This thesis addresses these important issues. First, the nature ofthe LAI estimated from these satellite observations was investigated to address the existing differences in thedefinition of products. Then, different temporal smoothing and gap filling methods were analyzed to reduce noiseand discontinuities in the time series mainly due to cloud cover. Finally, different methods for near real timeestimation of LAI were evaluated. Such comparison assessment as a function of the level of noise and gaps werelacking for LAI.Results achieved within the first part of the thesis show that the effective LAI is more accurately retrievedfrom satellite data than the actual LAI due to leaf clumping in the canopies. Further, the study has demonstratedthat multi-view observations provide only marginal improvements on LAI retrieval. The study also found that foroptimal retrievals the size of the uncertainty envelope over a set of possible solutions to be approximately equal tothat in the reflectance measurements. The results achieved in the second part of the thesis found the method withlocally adaptive temporal window, depending on amount of available observations and Climatology as backgroundestimation to be more robust to noise and missing data for smoothing, gap-filling and near real time estimationswith satellite time series.AVIGNON-Bib. numérique (840079901) / SudocSudocFranceF

Seamless Upscaling of the Field-Measured Grassland Aboveground Biomass Based on Gaussian Process Regression and Gap-Filled Landsat 8 OLI Reflectance

The spatially explicit aboveground biomass (AGB) generated through upscaling field measurements is critical for carbon cycle simulation and optimized management of grasslands. However, the spatial gaps that exist in the optical remote sensing data, underutilization of the multispectral data cube and unavailability of uncertainty information hinder the generation of seamless and accurate AGB maps. This study proposes a novel framework to address the above challenges. The proposed framework filled the spatial gaps in the remote sensing data via the consistent adjustment of the climatology to actual observations (CACAO) method. Gaussian process regression (GPR) was used to fully exploit the multispectral data cube and generated the pixelwise uncertainty concurrent with the AGB estimation. A case study in a 100 km × 100 km area located in the Zoige Plateau, China was used to evaluate this framework. The results show that the CACAO method can fill almost all of the gaps, accounting for 93.1% of the study area, with satisfactory accuracy. The generated AGB map from the GPR was characterized by a relatively high accuracy (R2 = 0.64, RMSE = 48.13 g/m2) compared to vegetation index-derived ones, and was accompanied by a corresponding uncertainty map that provides a new source of information on the credibility of each pixel. This study demonstrates the potential of the joint use of gap-filling and machine-learning methods to generate spatially explicit AG