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Sentinel-3 Toolbox - Quickstart

Sentinel-3 Toolbox - Quickstart

Owned by Tonio Fincke

Purpose of this document

This document is a guideline to present some features of the Sentinel Toolboxes. A special emphasis is on the features which are new. 

This guide makes use of the optical TDSs which have been handed out to the developers by ESA.

Installing the toolbox

In case you haven't already done so, please click/double-click the installer and follow the on-screen instructions.

Opening a Sentinel-3 product

Sentinel-3 products are provided not as single files but as a collection of files contained within a folder. The folder name is the actual product name, ending on .SEN3. Each folder contains a metadata file named xfdumanifest.xml and at least one netcdf-file. Each netcdf-file contains a subset of a Sentinel-3 product's content.

To open a Sentinel-3 product you can

  • Drag and drop the whole folder into the "Products View"
  • Drag and drop the xfdumanifest.xml-file into the "Products View"
  • Choose "File->Open Product", navigate to the xfdumanifest.xml file and click "Open Product"
  • Choose "File->Import Raster Data->Multispectral Data->SENTINEL-3", navigate to the xfdumanifest.xml file and click "Open Product"

 You can also open single netcdf-files. Just keep in mind that these will only show a part of the Sentinel-3 product and, in most cases, lack a geocoding.

Planned for Future Release 

In upcoming versions of the Sentinel-3 Toolbox, we will enable users to select the Sentinel-3 product folders from the file opening menu. We furthermore plan to open packed/zipped folder files and consider the integration of the folder opening functionality into the supported operating systems, so that the Sentinel-3 Toolbox can be started by clicking on the product folder.

Displaying flags

The Sentinel-3 Toolbox allows to display flags which contain both flag masks and flag values. This functionality comes to use for SLSTR L2 LST, SLSTR L2 WST and Synergy Vegetation products. The image below shows an example for this usage of flags:

In this image, six values ("no retrieval", "N2 retrieval", "N3R retrieval", "N3 retrieval", "D2 retrieval" and "D3 retrieval") are encoded through three bits. In the flags table view, both the combined total value of the bits (448) and the flag-depending check value is given. The "Mask Manager" derives masks directly from the flags. Note that flags encoded in this manner are mutually exclusive, so when they are all displayed at the same time they do not overlap in the Image View.

Displaying Uncertainty and Error Bands

Several of the Sentinel-3 products contain bands with assigned error or uncertainty bands (OLCI L2 L, OLCI L2 W, SLSTR L2 WST). Each uncertainty band is assigned to one non-uncertainty band from the product. Also, a color ramp ranging from purple for low values to red for high values is assigned to each uncertainty band. The Sentinel-3 Toolbox allows to simultaneously display image data along with its uncertainty through use of the "Uncertainty Visualisation" tool, which is by default located in the lower left panel. 

To use the tool, you need to select a band which has an uncertainty band assigned to it. The tool shows the distribution of colors within the uncertainty band. Clicking "More options" will bring up a menu where you can choose from several visualisation modes:

  • None: The Image View displays the selected band and nothing else.
  • Transparancy blending: Will alter the transparency to display the uncertainty: The higher the uncertainty, the more transparent the image will be. The two sliders set transparancy values of 0 and 1, respectively. All values left of (i.e., more certain than) the left slider will be completely opaque, all values right of (i.e., more uncertain than) the right slider will be completely transparent. 
  • Monochromatic blending: Encodes uncertainty as a color: The higher the uncertainty, the higher the saturation. All values left of (i.e., more certain than) the left slider will not obtain a color change, all values right of (i.e., more uncertain than) the right slider will be painted in the chosen color.
  • Polychromatic blending: Basically the same functionality as monochromatic blending with the main difference that uncertainty is not only encoded by the saturation but also by a hue.
  • Polychromatic overlay: Encodes uncertainty through the use of a color ramp: Each pixel is blended with the hue assigned by the histogram. By default, red stands for most uncertain and purple for most certain values.

The image below shows the uncertainty visualisation of a OLCI L2 W reflectance band using polychromatic overlay.

 Displaying spectra

The Sentinel-3 Toolbox contains the Spectrum Toolview which has been redesigned for BEAM 5. It allows to display multiple spectra at once. Sentinel-3 products containing spectra are OLCI L1, OLCI L2 W, SLSTR L1 B and SYN L2 products. The Spectrum Toolview is opened via the tool bar or the menu bar (View->Tool Windows->Spectrum). To use the Spectrum Toolview, an image needs to be opened. Spectra are defined by groups within the products. Groups can be set by richt-clicking on a product's name in the Products View and choosing Properties. In the Band grouping field, groups can be added and removed.

When you move the cursor over the image, the Spectrum Toolview will display the spectra as graphs in the diagram. When you click on the funnel symbol at the top right, the Spectrum Chooser will open. Here you can change line styles, symbols, and symbol sizes. Additionally, you can choose of which bands of the spectra the graph shall consist. 

The Spectrum Toolview also displays the spectra of pins. When you open the pin manager and alter a pin's name or color, this change will immediately be considered in the Spectrum Toolview. The image below shows a screenshot of the Synergy L2 test product where two spectra are shown for two pins.

Planned for Future Release

Currently, uncertainty bands assigned to spectral bands are displayed as separate spectra. Though it is not exactly wrong to do so, it would be preferable to show the relation of the band groups in the diagram, e.g., by displaying the uncertainty as range around the geophysical data. This approach could then be extended to other toolviews which display graphs.

Bands of different spatial extents and resolutions (multisized bands)

Some of the Sentinel products contain bands with different spatial extents and resolutions. For the Sentinel-3 products, this holds for the SLSTR L1B products. Here, we have bands with a 500m*500m (indicated by letters a, b, or c) and bands with a 1000m*1000m resolution (indicated by letter i). Also, the extend is different for bands with nadir (letter n) and oblique view (letter o). In the current release, this challenge is tackled by creating one grid in the finest resolution which covers the whole extent. Each image is mapped onto this grid. Images in the coarser resolution are "blown up", such that four pixels á 500*500m share the value of one pixel which represented a space o 1000*1000m (see image below).

Context help 

Parts of an image which are not covered by the original image are assigned no-data values. See the image below for nadir (above) and oblique view (below).

Planned for future release

This approach is only preliminary. We plan to keep differently sized bands in their native formats and allow them to use their own geocoding.

Context Help

The context help is designed to enable users to get additional information about product contents such as data nodes or metadata entries. When a product feature is selected, clicking Ctrl + F1 will open your web browser and bring up an internet search engine with search results. For Sentinel products, results from the ESA homepage are preferred, such that entries from the Sentinel handbook are found easily.