EMODnet Chemistry Map viewer uses OceanBrowser as a web-service that allows the on-line visualisation of GIS layers and gridded fields. It is used in the frame of SeaDataCloud (http://sdn.oceanbrowser.net/web-vis/) and in EMODnet Chemistry (https://ec.oceanbrowser.net/emodnet).
Within the SeaDataNet, SeaDataCloud and EMODnet (Chemical lot) projects, several national ocean data centers have created gridded climatologies of different ocean properties using the data analysis software tools DIVA or DIVAnd. In order to give a common viewing service to those interpolated products, the GHER has developed OceanBrowser which is based on open standards from the Open Geospatial Consortium (OGC), in particular Web Map Service (WMS) and Web Feature Service (WFS). These standards define a protocol for describing, requesting and querying two-dimensional maps at a given depth and time.
EMODnet Chemistry Map viewer displays:
- Eutrophication – spatially interpolated maps of different parameters concentration
- Ocean acidification and Eutrophication – Spatial distribution maps and dynamic plots
- Marine litter – maps of spatial distribution, composition and abundance
- Contaminants – maps of spatial distribution and MSFD focused data evaluation
DIVAnd maps features
EMODnet Chemistry Map viewer currently supports the following operations for DIVA maps:
- Horizontal sections of the 4-dimensional fields (longitude, latitude, depth and time) can be visualized at a selected depth and time. The climatological fields can also be interpolated and visualized on arbitrary vertical sections.
- The maps displayed in the browser are created dynamically and therefore several options are made available to the user to customize the graphical rending of those layers. Layers can be displayed either using interpolated shading, filled contours or simple contours and several options controlling the color-map are also available.
- The horizontal and vertical sections can be animated in order to study the evolution in time.
- Image can be saved in raster format (PNG) and vector image formats (SVG, EPS, PDF). It can also be saved as a KML file so that the current layer can be visualized in programs like Google Earth and it can be combined with other information imported in such programs.
- The underlying 4-dimensional NetCDF file can be either downloaded as a whole from the interface or only as a subset using the linked OPeNDAP server.
- The web interface can also import third-party layers by using standard WMS requests. The user needs only to specify the URL of the WMS server and its supported version.
For the Plots
Different plot types are available for data concerning ocean acidification and eutrophication through the section EMODnet Chemistry Plots. Click on a group of parameters (e.g. Acidity), then on a specific parameter (e.g., number of observation of water body pH). After setting min-max depth and time on the right, click on a marker to customize your plot.
The number of observations for different components can be overlaid on the map. When clicking on the marker, additional information is provided in the form of a pop-up window. The image below illustrates this feature with the Mercury observations.
- Select a domain, season and variable in the “EMODNET CHEMISTRY – EUTROPHICATION BY SEA REGION » dialog. Under the variable name, the variable with 0.5 error thresholds can be chosen. In “additional fields” the full field with 0.3 and without error thresholds are available as well as data distribution (Logarithm10 of number of data in bins), outliers distribution (Logarithm10 of number of outliers data in bins), relative error and the near bottom value (deepest value). A “data bin” is a grid cell of the interpolated grid.
- To remove a field from the map, click on the “remove” button.
- After changing the depth and/or time dimension, the map can be refreshed with the “update” button.
- Several data sets can be visualized at the same time. For example, ocean temperature from the North Sea, Atlantic Ocean and Mediterranean Sea can be visualized at the same time. The consistency of the several ocean products in adjacent regions can be easily assessed and potential problems can be highlighted (Figure 1). This feature is available for horizontal as well for as for vertical sections. By choosing simple contours of one field in combination with filled contours of other field one visually sees the correspondence or location of frontal structures.
The appearance of the field can be customized by clicking on the style button
where you can range color map, color range, plot style (flat shading, contours and filled contours).
Per default the surface layer and the first time slice is shown. This can be changed in the depth and time select boxes next to the color bar (on the right). After the choice is confirmed by clicking on ‘Update’, the map is redrawn.
The location of the observations are shown with a marker on the map. The marker is semi-transparent so that stronger colors give an indication of density of the observations at the particular location.
- Vertical sections can be extracted by selecting the corresponding tab on the upper left.
- The overview map shows the same time instance and depth levels as the horizontal view (which is the the first time instance of the surface layer per default).
- With a mouse a section can be draw in the overview map. A simple click starts a section or adds a point and double-click finishes it.
- After a section is finished it will appear, the field will be interpolated onto the requested section and drawn in the central part (labeled “vertical section” in the figure below). The coordinates of this plots are distance in arc degrees from the starting point (1 arc degree is always equal to 1 degree in the North-South direction and approximately 111 km) and depth (0 is the surface and value are negative in water).
Instead of drawing a section by the mouse, one can generate a section based on a fixed distance from coast or depth. The corresponding option has be chosen in “Interaction mode”. The work-flow is illustrated in the following figure. As multiple disconnected line segments are at a fixed distance form coast (or constant ocean depth). One has the select by the mouse in the overview map the desired section.
Adding external layers
The map viewer allows users to add other layers, for instance layers showing the data locations. After clicking on the corresponding button in the left-side menu.
A new dialog box will open, where you can select a WMS server from a drop-down list or add manually the server URL.
Downloading data products
You can open the download dialog by clicking on the download icon next to the color bar.
You can either download the data (netCDF or OPeNDAP) or download images for the current layer.
Data products can be downloaded as netCDF files by using the button labeled “Download NetCDF”. A NetCDF file will contain the DIVA analysis for a single parameter as well as meta data as netCDF attributes. User can also download subset of the data products by using the button “OPeNDAP Service”. By click this button, a new window will open with the attributes of the NetCDF file. The URL of this window need to be copied into your OPeNDAP application.
- ncBrowse: A Graphical netCDF File Browser
Panoply: netCDF, HDF and GRIB Data Viewer
Ncview: a netCDF visual browser
If you want to download all NetCDF files for a specific zone you can use the command wget. For example to download the all analyses from EMODNET Chemistry from the Baltic Sea you can use:
wget -nH --cut-dirs=2 -np -r -A '*nc' 'http://ec.oceanbrowser.net/data/emodnet-domains/Baltic Sea/'
Replace “Baltic Sea”, to download the data for a different region. The names of the regions can be seen here for EMODNET Chemistry and here for SeaDataNet. This command will preserve the directory structure.
It is also possible to download the current view as an image file by specifying the width and height of the image and the longitude and latitude range.
- For partners of the SeaDataNet and EMODNET Chemistry, description about importing data has been written.
- OceanBrowser WMS Server
Question and comments can be addressed to Alexander Barth (a dot barth at ulg dot ac dot be)
OceanBrowser is combined with a software called “Diva on web”. Both can be installed following the instruction detailed here.
Funding was provided by SeaDataNet (FP7), SeaDataCloud and EMODnet Chemistry (DG-MARE).
GEBCO project is acknowledged for providing the GEBCO world map, http://www.gebco.net/