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

A sensor invariant atmospheric correction method for satellite images

Land surface reflectance is the fundamental variable for the most of earth observation (EO) missions, and corrections of the atmospheric disturbs from the cloud, gaseous, aerosol help to get accurate spectral description of earth surface. Unlike the previous empirical ways of atmospheric correction, we propose a data fusion method for atmospheric correction of satellite images, with an initial attempt to include the uncertainty information from different data source. It takes advantage of the high temporal resolution of MODIS observations to get BRDF description of the earth surface as the prior information of the earth surface property, uses the ECMWF CAMS Near-real-time as the prior information of the atmospheric sates, to get optimal estimations of the atmospheric parameters. It guarantees the correction is consistent cross different satellites image tiles and even cross different sensors. The validations against the AERONET sites are also show high correlation at around 0.9, with a RMSE of about 0.02

Combining multitemporal optical and SAR data for LAI imputation with BiLSTM network

The Leaf Area Index (LAI) is vital for predicting winter wheat yield. Acquisition of crop conditions via Sentinel-2 remote sensing images can be hindered by persistent clouds, affecting yield predictions. Synthetic Aperture Radar (SAR) provides all-weather imagery, and the ratio between its cross- and co-polarized channels (C-band) shows a high correlation with time series LAI over winter wheat regions. This study evaluates the use of time series Sentinel-1 VH/VV for LAI imputation, aiming to increase spatial-temporal density. We utilize a bidirectional LSTM (BiLSTM) network to impute time series LAI and use half mean squared error for each time step as the loss function. We trained models on data from southern Germany and the North China Plain using only LAI data generated by Sentinel-1 VH/VV and Sentinel-2. Experimental results show BiLSTM outperforms traditional regression methods, capturing nonlinear dynamics between multiple time series. It proves robust in various growing conditions and is effective even with limited Sentinel-2 images. BiLSTM's performance surpasses that of LSTM, particularly over the senescence period. Therefore, BiLSTM can be used to impute LAI with time-series Sentinel-1 VH/VV and Sentinel-2 data, and this method could be applied to other time-series imputation issues

Analysing the PMIP4-CMIP6 collection: a workflow and tool (pmip_p2fvar_analyzer v1)

Experiment outputs are now available from the Coupled Model Intercomparison Project's sixth phase (CMIP6) and the past climate experiments defined in the Palaeoclimate Modelling Intercomparison Project's fourth phase (PMIP4). All of this output is freely available from the Earth System Grid Federation (ESGF). Yet there is overhead in analysing this resource that may prove complicated or prohibitive. Here we document the steps taken by ourselves to produce ensemble analyses covering past and future simulations. We outline the strategy used to curate, adjust the monthly calendar aggregation and process the information downloaded from the ESGF. The results of these steps were used to perform analysis for several of the initial publications arising from PMIP4. We provide post-processed fields for each simulation, such as climatologies and common measures of variability. Example scripts used to visualise and analyse these fields are provided for several important case studies

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

The structural impact of DNA mismatches

© 2015 © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We found that the presence of mismatches produced significant local structural alterations, especially in the case of purine transversions. Mismatched pairs often show promiscuous hydrogen bonding patterns, which interchange among each other in the nanosecond time scale. This therefore defines flexible base pairs, where breathing is frequent, and where distortions in helical parameters are strong, resulting in significant alterations in groove dimension. Even if the DNA structure is plastic enough to absorb the structural impact of the mismatch, local structural changes can be propagated far from the mismatch site, following the expected through-backbone and a previously unknown through-space mechanism. The structural changes related to the presence of mismatches help to understand the different susceptibility of mismatches to the action of repairing proteins.Peer Reviewe

Modeling vegetation fires and fire emissions

Fire is the most important ecological and forest disturbance agent worldwide, is a major way by which carbon is transferred from the land to the atmosphere, and is globally a significant source of greenhouse gases and aerosols. Wildfires across all major biome types globally consume about 5% of net annual terrestrial primary production per annum, and release about 2-4 Pg C per annum, of which approximately 0.6 Pg C comes from tropical deforestation and below-ground peat fires. The global figure is equivalent to about 20-30% of global emissions from fossil fuels. Tropical savannas comprise the largest areas burned and greatest emissions sources from vegetation wildfires. Fires in Mediterranean forests and shrublands, tropical forests and boreal forests are also significant sources of emissions because they are generally characterised by much higher fuel loads per unit area compared with grasslands. Improved satellite data and sophisticated biogeochemical modeling enables emis-sions assessments on a global scale with fine spatial and temporal resolution. Emissions estimates are still comparable to those based on older inventory-based techniques, but uncertainties remain large. Fires increase during El Niño periods because parts of the tropics where humans use fire as a tool for deforestation experience drought conditions. These spikes contribute to the inter-annual variability of CO2 and CH4 observed in the atmosphere. Recently developed dynamic fire-vegetation models are capable of simulating the extent of wildfires as well as their emissions of CO2 and other greenhouse gases for ambient as well as for projected climatic conditions. The performance of fire-vegetation models however needs to be strongly improved and validated

Uncertainty characterization & validation within ESA Fire-CCI

Uncertainty characterisation and validation are critical phases to generate any Essential Climate Variable (ECV), and therefore both have been included as key deliverables of the ESA CCI programme [1]. All products generated by the CCI are required to have an associated per pixel uncertainty characterisation. This paper describes both the uncertainty characterisation framework and the related uncertainty validation exercise of the Fire-CCI projectinfo:eu-repo/semantics/publishedVersio

Separability Analysis of Sentinel-2A Multi-Spectral Instrument (MSI) Data for Burned Area Discrimination

: Biomass burning is a global phenomenon and systematic burned area mapping is of increasing importance for science and applications. With high spatial resolution and novelty in band design, the recently launched Sentinel-2A satellite provides a new opportunity for moderate spatial resolution burned area mapping. This study examines the performance of the Sentinel-2A Multi Spectral Instrument (MSI) bands and derived spectral indices to differentiate between unburned and burned areas. For this purpose, five pairs of pre-fire and post-fire top of atmosphere (TOA reflectance) and atmospherically corrected (surface reflectance) images were studied. The pixel values of locations that were unburned in the first image and burned in the second image, as well as the values of locations that were unburned in both images which served as a control, were compared and the discrimination of individual bands and spectral indices were evaluated using parametric (transformed divergence) and non-parametric (decision tree) approaches. Based on the results, the most suitable MSI bands to detect burned areas are the 20 m near-infrared, short wave infrared and red-edge bands, while the performance of the spectral indices varied with location. The atmospheric correction only significantly influenced the separability of the visible wavelength bands. The results provide insights that are useful for developing Sentinel-2 burned area mapping algorithms