Efficient Emulation of Radiative Transfer Codes Using Gaussian Processes and Application to Land Surface Parameter Inferences

There is an increasing need to consistently combine observations from different sensors to monitor the state of the land surface. In order to achieve this, robust methods based on the inversion of radiative transfer (RT) models can be used to interpret the satellite observations. This typically results in an inverse problem, but a major drawback of these methods is the computational complexity. We introduce the concept of Gaussian Process (GP) emulators: surrogate functions that accurately approximate RT models using a small set of input (e.g., leaf area index, leaf chlorophyll, etc.) and output (e.g., top-of-canopy reflectances or at sensor radiances) pairs. The emulators quantify the uncertainty of their approximation, and provide a fast and easy route to estimating the Jacobian of the original model, enabling the use of e.g., efficient gradient descent methods. We demonstrate the emulation of widely used RT models (PROSAIL and SEMIDISCRETE) and the coupling of vegetation and atmospheric (6S) RT models targetting particular sensor bands. A comparison with the full original model outputs shows that the emulators are a viable option to replace the original model, with negligible bias and discrepancies which are much smaller than the typical uncertainty in the observations. We also extend the theory of GP to cope with models with multivariate outputs (e.g., over the full solar reflective domain), and apply this to the emulation of PROSAIL, coupled 6S and PROSAIL and to the emulation of individual spectral components of 6S. In all cases, emulators successfully predict the full model output as well as accurately predict the gradient of the model calculated by finite differences, and produce speed ups between 10,000 and 50,000 times that of the original model. Finally, we use emulators to invert leaf area index ( L A I ), leaf chlorophyll content ( C a b ) and equivalent leaf water thickness ( C w ) from a time series of observations from Sentinel-2/MSI, Sentinel-3/SLSTR and Proba-V observations. We use sophisticated Hamiltonian Markov Chain Monte Carlo (MCMC) methods that exploit the speed of the emulators as well as the gradient estimation, a variational data assimilation (DA) method that extends the problem with temporal regularisation, and a particle filter using a regularisation model. The variational and particle filter approach appear more successful (meaning parameters closer to the truth, and smaller uncertainties) than the MCMC approach as a result of using the temporal regularisation mode. These work therefore suggests that GP emulators are a practical way to implement sophisticated parameter retrieval schemes in an era of increasing data volumes

Global sensitivity analysis of leaf-canopy-atmosphere RTMs: Implications for biophysical variables retrieval from top-of-atmosphere radiance data

Knowledge of key variables driving the top of the atmosphere (TOA) radiance over a vegetated surface is an important step to derive biophysical variables from TOA radiance data, e.g., as observed by an optical satellite. Coupled leaf-canopy-atmosphere Radiative Transfer Models (RTMs) allow linking vegetation variables directly to the at-sensor TOA radiance measured. Global Sensitivity Analysis (GSA) of RTMs enables the computation of the total contribution of each input variable to the output variance. We determined the impacts of the leaf-canopy-atmosphere variables into TOA radiance using the GSA to gain insights into retrievable variables. The leaf and canopy RTM PROSAIL was coupled with the atmospheric RTM MODTRAN5. Because of MODTRAN's computational burden and GSA's demand for many simulations, we first developed a surrogate statistical learning model, i.e., an emulator, that allows approximating RTM outputs through a machine learning algorithm with low computation time. A Gaussian process regression (GPR) emulator was used to reproduce lookup tables of TOA radiance as a function of 12 input variables with relative errors of 2.4%. GSA total sensitivity results quantified the driving variables of emulated TOA radiance along the 400-2500 nm spectral range at 15 cm-1 (between 0.3-9 nm); overall, the vegetation variables play a more dominant role than atmospheric variables. This suggests the possibility to retrieve biophysical variables directly from at-sensor TOA radiance data. Particularly promising are leaf chlorophyll content, leaf water thickness and leaf area index, as these variables are the most important drivers in governing TOA radiance outside the water absorption regions. A software framework was developed to facilitate the development of retrieval models from at-sensor TOA radiance data. As a proof of concept, maps of these biophysical variables have been generated for both TOA (L1C) and bottom-of-atmosphere (L2A) Sentinel-2 data by means of a hybrid retrieval scheme, i.e., training GPR retrieval algorithms using the RTM simulations. Obtained maps from L1C vs L2A data are consistent, suggesting that vegetation properties can be directly retrieved from TOA radiance data given a cloud-free sky, thus without the need of an atmospheric correction

Land Surface Processes Analysis Using Sentinel-3 OLCI and Modis Data

This communication describes the optical processing chain to use Sentinel-3 OLCI and MODIS data as part of the ESA funded Synergy project of the Scientific Exploitation of Sentinel Missions (SEOM) component of the EO Envelope programme. One of the goals of the project is to use Data Assimilation techniques to produce land surface products combining the data from Sentinels-2 and 3. Some of the derived products are the OLCI atmospherically corrected data that can be used to generate a spectral BRDF product from OLCI and MODIS, broadband albedo and different vegetation parameters. The project also implements a series of efficiency improvements to the algorithms to speed up the processing. The demonstrator product uses one year of OLCI and MODIS data (2017)

Radiative Transfer Speed-Up Combining Optimal Spectral Sampling With a Machine Learning Approach

The Orbiting Carbon Observatories-2 and -3 make space-based measurements in the oxygen A-band and the weak and strong carbon dioxide (CO2) bands using the Atmospheric Carbon Observations from Space (ACOS) retrieval. Within ACOS, a Bayesian optimal estimation approach is employed to retrieve the column-averaged CO2 dry air mole fraction from these measurements. This retrieval requires a large number of polarized, multiple-scattering radiative transfer calculations for each iteration. These calculations take up the majority of the processing time for each retrieval and slow down the algorithm to the point that reprocessing data from the mission over multiple years becomes especially time consuming. To accelerate the radiative transfer model and, thereby, ease this bottleneck, we have developed a novel approach that enables modeling of the full spectra for the three OCO-2/3 instrument bands from radiances calculated at a small subset of monochromatic wavelengths. This allows for a reduction of the number of monochromatic calculations by a factor of 10, which can be achieved with radiance errors of less than 0.01% with respect to the existing algorithm and is easily tunable to a desired accuracy-speed trade-off. For the ACOS retrieval, this speeds up the over-retrievals by about a factor of two. The technique may be applicable to similar retrieval algorithms for other greenhouse gas sensors with large data volumes, such as GeoCarb, GOSAT-3, and CO2M

Simulating arbitrary hyperspectral bandsets from multispectral observations via a generic Earth Observation-Land Data Assimilation System (EO-LDAS)

This paper presents results of using multi-sensor and multi-angular constraints in the generic Earth Observation-Land Data Assimilation System (EO-LDAS) for reproducing arbitrary bandsets of hyperspectral reflectance at the top-of-canopy (TOC) level by merging observations from multispectral sensors with different spectral characteristics. This is demonstrated by combining Multi-angle Imaging Spectroradiometer (MISR) and Landsat Enhanced Thematic Mapper Plus (ETM+) data to simulate the Compact High Resolution Imaging Spectrometer CHRIS/PROBA hyperspectral signal over an agricultural test site, in Barrax, Spain. However, the method can be more generally applied to any combination of spectral data, providing a tool for merging EO data to any arbitrary hyperspectral bandset. Comparisons are presented using both synthetic and observed MISR and Landsat data, and retrieving surface biophysical properties. We find that when using simulated MISR and Landsat data, the CHRIS/PROBA hyperspectral signal is reproduced with RMSE 0.0001– 0.04. LAI is retrieved with r2 from 0.97 to 0.99 and RMSE of from 0.21 to 0.38. The results based on observed MISR and Landsat data have lower performances, with RMSE for the reproduced CHRIS/PROBA hyperspectral signal varying from 0.007 to 0.2. LAI is retrievedwith r2 from 0.7 to 0.9 and RMSE from 0.7 to 1.4. We found that for the data considered here the main spectral variations in the visible and near infrared regions can be described by a limited number of parameters (3–4) that can be estimated from multispectral information. Results show that the method can be used to simulate arbitrary bandsets, which will be of importance to any application which requires combining new and existing streams of new EO data in the optical domain, particularly intercalibration of EO satellites in order to get continuous time series of surface reflectance, across programmes and sensors of different designs

Quantifying Vegetation Biophysical Variables from Imaging Spectroscopy Data: A Review on Retrieval Methods

An unprecedented spectroscopic data stream will soon become available with forthcoming Earth-observing satellite missions equipped with imaging spectroradiometers. This data stream will open up a vast array of opportunities to quantify a diversity of biochemical and structural vegetation properties. The processing requirements for such large data streams require reliable retrieval techniques enabling the spatiotemporally explicit quantification of biophysical variables. With the aim of preparing for this new era of Earth observation, this review summarizes the state-of-the-art retrieval methods that have been applied in experimental imaging spectroscopy studies inferring all kinds of vegetation biophysical variables. Identified retrieval methods are categorized into: (1) parametric regression, including vegetation indices, shape indices and spectral transformations; (2) nonparametric regression, including linear and nonlinear machine learning regression algorithms; (3) physically based, including inversion of radiative transfer models (RTMs) using numerical optimization and look-up table approaches; and (4) hybrid regression methods, which combine RTM simulations with machine learning regression methods. For each of these categories, an overview of widely applied methods with application to mapping vegetation properties is given. In view of processing imaging spectroscopy data, a critical aspect involves the challenge of dealing with spectral multicollinearity. The ability to provide robust estimates, retrieval uncertainties and acceptable retrieval processing speed are other important aspects in view of operational processing. Recommendations towards new-generation spectroscopy-based processing chains for operational production of biophysical variables are given

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

Evaluation of the PROSAIL Model Capabilities for Future Hyperspectral Model Environments: A Review Study

Upcoming satellite hyperspectral sensors require powerful and robust methodologies for making optimum use of the rich spectral data. This paper reviews the widely applied coupled PROSPECT and SAIL radiative transfer models (PROSAIL), regarding their suitability for the retrieval of biophysical and biochemical variables in the context of agricultural crop monitoring. Evaluation was carried out using a systematic literature review of 281 scientific publications with regard to their (i) spectral exploitation, (ii) vegetation type analyzed, (iii) variables retrieved, and (iv) choice of retrieval methods. From the analysis, current trends were derived, and problems identified and discussed. Our analysis clearly shows that the PROSAIL model is well suited for the analysis of imaging spectrometer data from future satellite missions and that the model should be integrated in appropriate software tools that are being developed in this context for agricultural applications. The review supports the decision of potential users to employ PROSAIL for their specific data analysis and provides guidelines for choosing between the diverse retrieval techniques

Quantifying Vegetation Biophysical Variables from Imaging Spectroscopy Data: A Review on Retrieval Methods

An unprecedented spectroscopic data stream will soon become available with forthcoming Earth-observing satellite missions equipped with imaging spectroradiometers. This data stream will open up a vast array of opportunities to quantify a diversity of biochemical and structural vegetation properties. The processing requirements for such large data streams require reliable retrieval techniques enabling the spatiotemporally explicit quantification of biophysical variables. With the aim of preparing for this new era of Earth observation, this review summarizes the state-of-the-art retrieval methods that have been applied in experimental imaging spectroscopy studies inferring all kinds of vegetation biophysical variables. Identified retrieval methods are categorized into: (1) parametric regression, including vegetation indices, shape indices and spectral transformations; (2) nonparametric regression, including linear and nonlinear machine learning regression algorithms; (3) physically based, including inversion of radiative transfer models (RTMs) using numerical optimization and look-up table approaches; and (4) hybrid regression methods, which combine RTM simulations with machine learning regression methods. For each of these categories, an overview of widely applied methods with application to mapping vegetation properties is given. In view of processing imaging spectroscopy data, a critical aspect involves the challenge of dealing with spectral multicollinearity. The ability to provide robust estimates, retrieval uncertainties and acceptable retrieval processing speed are other important aspects in view of operational processing. Recommendations towards new-generation spectroscopy-based processing chains for operational production of biophysical variables are given

Integration of satellite remote sensing data in ecosystem modelling at local scales: Practices and trends

1. Spatiotemporal ecological modelling of terrestrial ecosystems relies on climatological and biophysical Earth observations. Due to their increasing availability, global coverage, frequent acquisition and high spatial resolution, satellite remote sensing (SRS) products are frequently integrated to in situ data in the development of ecosystem models (EMs) quantifying the interaction among the vegetation component and the hydrological, energy and nutrient cycles. This review highlights the main advances achieved in the last decade in combining SRS data with EMs, with particular attention to the challenges modellers face for applications at local scales (e.g. small watersheds). 2. We critically review the literature on progress made towards integration of SRS data into terrestrial EMs: (1) as input to define model drivers; (2) as reference to validate model results; and (3) as a tool to sequentially update the state variables, and to quantify and reduce model uncertainty. 3. The number of applications provided in the literature shows that EMs may profit greatly from the inclusion of spatial parameters and forcings provided by vegetation and climatic‐related SRS products. Limiting factors for the application of such models to local scales are: (1) mismatch between the resolution of SRS products and model grid; (2) unavailability of specific products in free and public online repositories; (3) temporal gaps in SRS data; and (4) quantification of model and measurement uncertainties. This review provides examples of possible solutions adopted in recent literature, with particular reference to the spatiotemporal scales of analysis and data accuracy. We propose that analysis methods such as stochastic downscaling techniques and multi‐sensor/multi‐platform fusion approaches are necessary to improve the quality of SRS data for local applications. Moreover, we suggest coupling models with data assimilation techniques to improve their forecast abilities. 4. This review encourages the use of SRS data in EMs for local applications, and underlines the necessity for a closer collaboration among EM developers and remote sensing scientists. With more upcoming satellite missions, especially the Sentinel platforms, concerted efforts to further integrate SRS into modelling are in great demand and these types of applications will certainly proliferate