Data Interpolating Empirical Orthogonal Functions (DINEOF): a tool for geophysical data analyses

in Mediterranean Marine Science (in press)

An overview of the technique called DINEOF (Data Interpolating Empirical Orthog- onal Functions) is presented. DINEOF reconstructs missing information in geophys- ical data sets, such as satellite imagery ... [more ▼]

An overview of the technique called DINEOF (Data Interpolating Empirical Orthog- onal Functions) is presented. DINEOF reconstructs missing information in geophys- ical data sets, such as satellite imagery or time series. A summary of the technique is given, with its main characteristics, recent developments and future research di- rections. DINEOF has been applied to a large variety of oceanographic variables in various domains of different sizes. This technique can be applied to a single variable (monovariate approach), or to several variables together (multivariate approach), with no complexity increase in the application of the technique. Error fields can be computed to establish the accuracy of the reconstruction. Examples are given to illustrate the capabilities of the technique. DINEOF is freely offered to download, and help is provided to users in the form of a wiki and through a discussion email list. [less ▲]

Outlier detection in satellite data using spatial coherence

in Remote Sensing of Environment (2012), 119

Satellite data sets often contain outliers (i.e., anomalous values with respect to the surrounding pixels), mostly due to undetected clouds and rain or to atmospheric and land contamination. A methodology ... [more ▼]

Satellite data sets often contain outliers (i.e., anomalous values with respect to the surrounding pixels), mostly due to undetected clouds and rain or to atmospheric and land contamination. A methodology to detect outliers in satellite data sets is presented. The approach uses a truncated Empirical Orthogonal Function (EOF) basis. The information rejected by this EOF basis is used to identify suspect data. A proximity test and a local median test are also performed, and a weighted sum of these three tests is used to accurately detect outliers in a data set. Most satellite data undergo automated quality-check analyses. The approach presented exploits the spatial coherence of the geophysical fields, therefore detecting outliers that would otherwise pass such checks. The methodology is applied to infrared sea surface temperature (SST), microwave SST and chlorophyll-a concentration data over different domains, to show the applicability of the technique to a range of variables and temporal and spatial scales. A series of sensitivity tests and validation with independent data are also conducted. [less ▲]

Cloud filling of ocean colour and sea surface temperature remote sensing products over the Southern North Sea by the Data Interpolating Empirical Orthogonal Functions methodology.

in Journal of Sea Research (2011), 65(1), 114-130

Optical remote sensing data is now being used systematically for marine ecosystem applications, such as the forcing of biological models and the operational detection of harmful algae blooms. However ... [more ▼]

Optical remote sensing data is now being used systematically for marine ecosystem applications, such as the forcing of biological models and the operational detection of harmful algae blooms. However, applications are hampered by the incompleteness of imagery and by some quality problems. The Data Interpolating Empirical Orthogonal Functions methodology (DINEOF) allows calculation of missing data in geophysical datasets without requiring a priori knowledge about statistics of the full data set and has previously been applied to SST reconstructions. This study demonstrates the reconstruction of complete space-time information for 4 years of surface chlorophyll a (CHL), total suspended matter (TSM) and sea surface temperature (SST) over the Southern North Sea (SNS) and English Channel (EC). Optimal reconstructions were obtained when synthesising the original signal into 8 modes for MERIS CHL and into 18 modes for MERIS TSM. Despite the very high proportion of missing data (70%), the variability of original signals explained by the EOF synthesis reached 93.5 % for CHL and 97.2 % for TSM. For the MODIS TSM dataset, 97.5 % of the original variability of the signal was synthesised into 14 modes. The MODIS SST dataset could be synthesised into 13 modes explaining 98 % of the input signal variability. Validation of the method is achieved for 3 dates below 2 artificial clouds, by comparing reconstructed data with excluded input information. Complete weekly and monthly averaged climatologies, suitable for use with ecosystem models, were derived from regular daily reconstructions. Error maps associated with every reconstruction were produced according to Beckers et al. (2006) [6]. Embedded in this error calculation scheme, a methodology was implemented to produce maps of outliers, allowing identification of unusual or suspicious data points compared to the global dynamics of the dataset. Various algorithms artefacts were associated with high values in the outlier maps (undetected cloud edges, haze areas, contrails, cloud shadows). With the production of outlier maps, the data reconstruction technique becomes also a very efficient tool for quality control of optical remote sensing data and for change detection within large databases. [less ▲]

Reconstruction of sea surface temperature by means of DINEOF: a case study during the fishing season in the Bay of Biscay

in International Journal of Remote Sensing (2011), 32(4), 933-950

The Spanish surface fishery operates mainly during the summer season in the waters of the Bay of Biscay. Sea surface temperature (SST) data recovered from satellite images are being used to improve the ... [more ▼]

The Spanish surface fishery operates mainly during the summer season in the waters of the Bay of Biscay. Sea surface temperature (SST) data recovered from satellite images are being used to improve the operational efficiency of fishing vessels (e.g. reduce search time and increase catch rate) and to improve the understanding of the variations in catch distribution and rate needed to properly manage fisheries. The images used for retrieval of SST often present gaps due to the existence of clouds or satellite malfunction periods. The data gaps can totally or partially affect the area of interest. Within this study, an application of a technique for the reconstruction of missing data called DINEOF (data interpolating empirical orthogonal functions) is analysed, with the aim of testing its applicability in operational SST retrieval during summer months. In this case study, the Bay of Biscay is used as the target area. Three months of SST Moderate Resolution Imaging Spectroradiometer (MODIS) images, ranging from 1 May 2006 to 31 July 2006, were used. The main objective of this work is to test the overall performance of this technique, under potential operational use for the support of the fleet during the summer fishing season. The study is designed to analyse the sensitivity of the results of this technique to several details of the methodology used in the reconstruction of SST, such as the number of empirical orthogonal functions (EOFs) retained, the handling of the seasonal cycle or the length (number of images) of the SST database used. The results are tested against independent SST data from International Comprehensive Ocean–Atmosphere Data Set (ICOADS) ship reports and standing buoys and estimations of the error of the reconstructed SST fields are given. Conclusions show that over this area three months of data are enough for efficient SST reconstruction, which yields four EOFs as the optimal number needed for this case study. An extended EOF experiment with SST and SST with a lag of one day was carried out to analyse whether the autocorrelation of the SST data allows better performance in the SST reconstruction, although theexperiment did not improve the results. The validation studies show that the reconstructed SSTs can be trusted, even when the amount of missing data is very high. The mean absolute deviation maps show that the error is greatest near to the coast and mainly in the upwelling areas close to the French and north-western Spanish coasts. [less ▲]

Correcting surface winds by assimilating High-Frequency Radar surface currents in the German Bight

in Ocean Dynamics (2011), 61(5), 599-610

Surface winds are crucial for accurately modeling the surface circulation in the coastal ocean. In the present work, high-frequency (HF) radar surface currents are assimilated using an ensemble scheme ... [more ▼]

Surface winds are crucial for accurately modeling the surface circulation in the coastal ocean. In the present work, high-frequency (HF) radar surface currents are assimilated using an ensemble scheme which aims to obtain improved surface winds taking into account ECMWF (European Centre for Medium-Range Weather Forecasts) winds as a first guess and surface current measurements. The objective of this study is to show that wind forcing can be improved using an approach similar to parameter estimation in ensemble data assimilation. Like variational assimilation schemes, the method provides an improved wind field based on surface current measurements. However, the technique does not require an adjoint and it is thus easier to implement. In addition, it does not rely on a linearization of the model dynamics. The method is validated directly by comparing the analyzed wind speed to independent in situ measurements and indirectly by assessing the impact of the corrected winds on model sea surface temperature (SST) relative to satellite SST. [less ▲]

Ensemble perturbation smoother for optimizing tidal boundary conditions by assimilation of High-Frequency radar surface currents - application to the German Bight

in Ocean Science (2010), 6(1), 161-178

High-Frequency (HF) radars measure the ocean surface currents at various spatial and temporal scales. These include tidal currents, wind-driven circulation, density-driven circulation and Stokes drift ... [more ▼]

High-Frequency (HF) radars measure the ocean surface currents at various spatial and temporal scales. These include tidal currents, wind-driven circulation, density-driven circulation and Stokes drift. Sequential assimilation methods updating the model state have been proven successful to correct the density-driven currents by assimilation of observations such as sea surface height, sea surface temperature and in-situ profiles. However, the situation is different for tides in coastal models since these are not generated within the domain, but are rather propagated inside the domain through the boundary conditions. For improving the modeled tidal variability it is therefore not sufficient to update the model state via data assimilation without updating the boundary conditions. The optimization of boundary conditions to match observations inside the domain is traditionally achieved through variational assimilation methods. In this work we present an ensemble smoother to improve the tidal boundary values so that the model represents more closely the observed currents. To create an ensemble of dynamically realistic boundary conditions, a cost function is formulated which is directly related to the probability of each boundary condition perturbation. This cost function ensures that the boundary condition perturbations are spatially smooth and that the structure of the perturbations satisfies approximately the harmonic linearized shallow water equations. Based on those perturbations an ensemble simulation is carried out using the full three-dimensional General Estuarine Ocean Model (GETM). Optimized boundary values are obtained by assimilating all observations using the covariances of the ensemble simulation. [less ▲]

A nested model of the Cariaco Basin (Venezuela): description of the basin’s interior hydrography and interactions with the open ocean

in Ocean Dynamics (2009), 59(1), 97-120

A high-resolution (1/60°), three-dimensional numerical circulation model of the Cariaco Basin (Venezuela) is constructed by nesting the Regional Ocean Modeling System (ROMS) in the 1/12° global Hybrid ... [more ▼]

A high-resolution (1/60°), three-dimensional numerical circulation model of the Cariaco Basin (Venezuela) is constructed by nesting the Regional Ocean Modeling System (ROMS) in the 1/12° global Hybrid Coordinate Ocean Model (HYCOM). A new bathymetry, computed by merging DBDB2 data and in situ depth measurements using optimal interpolation, is described. This new bathymetry corrects the depth of the channels that connect the Cariaco Basin with the open ocean and which play a very important role in the basin circulation. Results from a 2004 ROMS hindcast are presented. Observations (temperature, salinity, and currents) are used to validate the model results before using the model to describe the annual cycle of the Cariaco Basin and the interactions between the basin and the open ocean. Two modes of interaction are described, the first being the meanders and eddies that travel westward with the Caribbean Current, and the second being a subsurface eastward current that flows along the north coast of South America. The circulation path within the basin is directly related to the intensity of this current. Both mechanisms described play a role in the ventilation of the basin. The present study is also an example of the feasibility of one of the objectives of GODAE (Global Ocean Data Assimilation Experiment): downscaling from a large-scale model to a regional model. In particular, the nesting ratio of 5 used in this work demonstrates that a high-resolution model can be successfully nested in HYCOM. [less ▲]

A coordinated coastal ocean observing and modeling system for the West Florida Continental Shelf

in Harmful Algae (2009), 8(4), 585-597

The evolution of harmful algal blooms, while dependent upon complex biological interactions, is equally dependent upon the ocean circulation since the circulation provides the basis for the biological ... [more ▼]

The evolution of harmful algal blooms, while dependent upon complex biological interactions, is equally dependent upon the ocean circulation since the circulation provides the basis for the biological interactions by uniting nutrients with light and distributing water properties. For the coastal ocean, the circulation and the resultant water properties, in turn, depend on interactions between both the continental shelf and the deep-ocean and the continental shelf and the estuaries since the deep-ocean and the estuaries are primary nutrient sources. Here we consider a coordinated program of observations and models for the West Florida Continental Shelf (WFS) intended to provide a supportive framework for K. brevis red-tide prediction as well as for other coastal ocean matters of societal concern. Predicated on lessons learned, the goal is to achieve a system complete enough to support data assimilative modeling and prediction. Examples of the observations and models are presented and application is made to aspects of the 2005 red-tide. From an observational perspective, no single set of measurements is adequate. Required are a broad mix of sensors and sensor delivery systems capable of describing the three-dimensional structure of the velocity and density fields. Similarly, models must be complete enough to include the relevant physical processes, and data assimilation provides the integrative framework for maximizing the joint utility of the observations and models. While we are still in the exploratory stages of development, the lessons learned and application examples may be useful to similar programs under development elsewhere. One scientific finding is that the key to understanding K. brevis red-tide on the WFS lies not at the surface, but at depth [less ▲]

Assimilation of high-frequency radar currents in a nested model of the West Florida Shelf

in Journal of Geophysical Research. Oceans (2008), 113(C8),

High-frequency radar currents are assimilated in a West Florida Shelf (WFS) model based on the Regional Ocean Model System (ROMS), which is nested in the Atlantic Hybrid Coordinate Ocean Model (HYCOM) for ... [more ▼]

High-frequency radar currents are assimilated in a West Florida Shelf (WFS) model based on the Regional Ocean Model System (ROMS), which is nested in the Atlantic Hybrid Coordinate Ocean Model (HYCOM) for the purpose of including both local and deep-ocean forcing, particularly the Gulf of Mexico Loop Current. Tides are not included in this model. An ensemble simulation of the WFS model is carried out under different wind-forcings in order to estimate the error covariance of the model state vector and the covariance between ocean currents and winds. Radial currents measured by high-frequency radar antennas near Saint Petersburg and Venice, Florida, USA, are assimilated using this ensemble-based error covariance. Different assimilation techniques using a time-average ensemble, a filter to reduce surface-gravity waves and an extended state vector including wind stress were tested. Results of the WFS model assimilating surface currents show an improvement of the model currents not only at the surface but also at depth. [less ▲]

Benefit of nesting a regional model into a large-scale ocean model instead of climatology. Application to the West Florida Shelf

in Continental Shelf Research (2008), 28(4-5), 561-573

The impact of open boundary conditions on the dynamics and accuracy of a regional West Florida Shelf model is addressed. A ROMS-based model nested in monthly climatological temperature and salinity and in ... [more ▼]

The impact of open boundary conditions on the dynamics and accuracy of a regional West Florida Shelf model is addressed. A ROMS-based model nested in monthly climatological temperature and salinity and in the North Atlantic HYCOM model is implemented. The model results of these nesting implementations are compared to altimetry, in situ temperature time series, and ADCP and high-frequency (HF) radar currents. A significant improvement of the model results is found using the boundary conditions of the HYCOM model over the climatology. The ageostrophic nature of the LC is studied and the benefit using the velocity and surface elevation boundary conditions is shown. (C) 2007 Elsevier Ltd. All rights reserved. [less ▲]