FAQ

NOTEBOOKS

A notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. It is based on the Open Source Jupyter notebooks application, and tailored to the needs of remote sensing users. Each notebook has direct access to the Terrascope, PROBA-V, SPOT-VGT and Copernicus Global Land datasets.

Notebooks are only enabled for users on specific demand.

On https://notebooks.terrascope.be, you can login to the notebooks application with your Terrascope username and password, which is the same account as used on www.vito-eodata.be or PROBA-V MEP.

Notebook samples

By default, some sample notebooks are provided under folder Private/notebook-samples. You may want to run git pull inside this directory to get the latest version.

The samples are subdivided in two sections:

  • datasets: notebooks using either Sentinel or PROBA-V data
  • tools: notebooks using tools provided by the Terrascope platform (e.g. SNAP, R, catalogclient, etc ...)

Sharing a notebook with another user:

Notebooks can be shared with other Terrascope users by saving it in the Public folder. Your notebook then becomes accessible for other users under folder /data/users/Public/<your_username>/<path_to_notebook>.

Accessing a shared notebook:

Copy the notebook from the user's Public folder (/data/users/Public//) to your Public or Private folder. First, start a Terminal (via "New" dropdown box > "Terminal"). Then, use this command to copy the notebook:

cp /data/users/Public/<username>/<path_to_notebook> /data/users/Public/<your_username>/

Another option is to push your notebook sample to a public Git repository (e.g. GitHub). Other users can then clone this repository to get a copy of your notebook sample. This can also be done from a Terminal started in the Jupyter environment as a Git client is preinstalled.

Installing additional packages

You can install additional Python packages. For a Python 2.7 notebook, include a cell like this to install the mpld3 library:

import sys
! pip27 install --user mpld3

The notebook environment also supports opening a terminal, in which this command can be executed as well. Packages are installed in your home directory, which is persistent across notebook restarts.

 

SENTINEL-1

“The image that is shown in the terrascope viewer, is a color combination of backscatter images:

  • The red channel contains the VV backscatter
  • The green channel contains the VH backscatter
  • The blue channel contains the ratio of VV/VH

Most water surfaces (and other flat surfaces, such as airport runways) color blue, because booth VV and VH backscatter is low (either absorbed in water, or reflected away on flat surfaces). Built up areas show up in yellow, indicating that VV and VH are approximately the same. Forests are mostly grey, because the backscatter is very unstructured. Metal objects are good reflectors, hence, the wind power parks and ships in the North Sea show up very clearly.”

  • SENTINEL data products are distributed using a SENTINEL-specific variation of the Standard Archive Format for Europe (SAFE) format specification. The SAFE format has been designed to act as a common format for archiving and conveying data within ESA Earth Observation archiving facilities. SAFE was recommended for the harmonisation of the GMES missions by the GMES Product Harmonisation Study.

The SENTINEL-SAFE format wraps a folder containing image data in a binary data format and product metadata in XML. This flexibility allows the format to be scalable enough to represent all levels of SENTINEL products.

A SENTINEL product refers to a directory folder that contains a collection of information. It includes:

  • a 'manifest.safe' file which holds the general product information in XML
  • subfolders for measurement datasets containing image data in various binary formats
  • a preview folder containing 'quicklooks' in PNG format, Google Earth overlays in KML format and HTML preview files
  • an annotation folder containing the product metadata in XML as well as calibration data
  • a support folder containing the XML schemes describing the product XML.

(Referentie: https://sentinel.esa.int/web/sentinel/user-guides/sentinel-1-sar/data-formats/safe-specification)

 

SENTINEL-2

 

Initially, VITO generates the Sentinel-2 products covering Belgium. The following grids represent the area of Belgium:   31UET, 31UFT, 31UDS, 31UES, 31UFS, 31UGS, 31UER, 31UFR, 31UGR, 31UFQ. Only those tiles will be downloaded and processed in the initial phase of the VITO Sentinel-2 project. The figure below outlines in red the grids covering Belgium which  are downloaded and processed by VITO. The map is based on an OpenStreetMap layer.

Figure:  Sentinel-2 grids covering Belgium

 

The naming conventions for the Sentinel 2 products are:

 

<MISSION>_<DATE>T<UTCTIME>Z_<GRIDID>_<CONTENT>_<RESOLUTION>_V<VERSION>_<OP>

 

With:

<MISSION>                       Mission ID (S2A/S2B)

<DATE>                            Start date of the segment identifier (format: YYYYMMDD)

<TIME>                             Start time (UTC) of the segment (format: hhmmss)

<GRIDID>                          ID of the granule/tile in UTM/WGS84 projection

<CONTENT>                      Content of the file. For details see the table below.

<RESOLUTION>                               Resolution of the product/file (not always available).

<VERSION>                                      Version identifier, three digits starting from ‘101’ for the first operational version

<OP>                                                   Optional, only used for the QuickLook (QL).

 

Example: S2A_20160908T105416Z_31UFS_FAPAR_10M_V101

Content

Description

TOC

Top Of Canopy total product

TOC-B01

Top of Canopy B01

TOC-B02

Top of Canopy B02

TOC-B03

Top of Canopy B03

TOC-B04

Top of Canopy B04

TOC-B05

Top of Canopy B05

TOC-B06

Top of Canopy B06

TOC-B07

Top of Canopy B07

TOC-B08

Top of Canopy B08

TOC-B08A

Top of Canopy B08A

TOC-B11

Top of Canopy B11

AOT

Aerosol Optical Thickness

CLOUDMASK

Cloudmask file

SHADOWMASK

Shadowmask file

SCENECLASSIFICATION

Scene Classification file

FAPAR

Fraction of Absorbed Photosynthetically Active Radiation

FCOVER

Fraction of green Vegetation Cover

LAI

Leaf Area Index

NDVI

Normalized Difference Vegetation Index

 

Table: Possible values for the <CONTENT>

 

The naming conventions for the Sentinel 2 products are:

 

<MISSION>_<DATE>T<UTCTIME>Z_<GRIDID>_<CONTENT>_<RESOLUTION>_V<VERSION>_<OP>

 

With:

<MISSION>                       Mission ID (S2A/S2B)

<DATE>                            Start date of the segment identifier (format: YYYYMMDD)

<TIME>                             Start time (UTC) of the segment (format: hhmmss)

<GRIDID>                          ID of the granule/tile in UTM/WGS84 projection

<CONTENT>                      Content of the file. For details see the table below.

<RESOLUTION>                               Resolution of the product/file (not always available).

<VERSION>                                      Version identifier, three digits starting from ‘101’ for the first operational version

<OP>                                                   Optional, only used for the QuickLook (QL).

 

Example: S2A_20160908T105416Z_31UFS_FAPAR_10M_V101

Content

Description

TOC

Top Of Canopy total product

TOC-B01

Top of Canopy B01

TOC-B02

Top of Canopy B02

TOC-B03

Top of Canopy B03

TOC-B04

Top of Canopy B04

TOC-B05

Top of Canopy B05

TOC-B06

Top of Canopy B06

TOC-B07

Top of Canopy B07

TOC-B08

Top of Canopy B08

TOC-B08A

Top of Canopy B08A

TOC-B11

Top of Canopy B11

AOT

Aerosol Optical Thickness

CLOUDMASK

Cloudmask file

SHADOWMASK

Shadowmask file

SCENECLASSIFICATION

Scene Classification file

FAPAR

Fraction of Absorbed Photosynthetically Active Radiation

FCOVER

Fraction of green Vegetation Cover

LAI

Leaf Area Index

NDVI

Normalized Difference Vegetation Index

 

Table: Possible values for the <CONTENT>

 

All Sentinel-2 image files are delivered in the GeoTIFF format. The accompanied metadata file is in XML format following the INSPIRE metadata standard (ISO19115).

VITO offers 4 Sentinel-2 vegetation indices or biophysical parameters: fAPAR, fCover, LAI, CCC, CWC and NDVI. All the products of these vegetation indices contain 6 files. Four datafiles (including the CloudMask ShadowMask and the Scene Classification), a metadata file describing the data (INSPIRE format) and a Quicklook image.  All the files, except the Scene classification files (20meter resolution), have a spatial resolution of 10 meter.

The table below lists the technical information of the Sentinel-2 derived products providing information on how to calculate the physical values from the digital numbers available in the files. The physical number can be defined by using the following formula:

Physical Number= Scaling * Digital Number + offset.

 

 

FAPAR

FCOVER

LAI

NDVI

Physical min

0.0

0.0

0.0

-0.08

Physical max

1.0

1.0

10.0

0.92

Digital number min

0

0

0

0

Digital number max

200

200

250

250

Scaling

1/200

1/200

10/250

1/250

Offset

0.0

0.0

0.0

-0.08

No data

255

255

255

255

Data type

Byte

Byte

Byte

Byte

Saturation min*

/

/

/

-1.0

Saturation max**

/

/

/

1.0

Table: Sentinel-2 derived vegetation products technical information

*Values between saturation min and physical min will be set to physical min before quantization is applied.

** Values between saturation max and physical max will be set to physical max before quantization is applied.

 

FAPAR

The Fraction of Absorbed Photosynthetically Active Radiation quantifies the fraction of the solar radiation absorbed by live leaves for the photosynthesis activity. Then, it refers only to the green and alive elements of the canopy. The FAPAR depends on the canopy structure, vegetation element optical properties, atmospheric conditions, and angular configuration. To overcome this latter dependency, a daily integrated FAPAR value is assessed.

The figure below shows the files included in the S2 FAPAR product.

Figure: S2 FAPAR product file list

 

LAI

The Leaf Area Index is defined as half the total area of green elements of the canopy per unit horizontal ground area. The satellite-derived value corresponds to the total green LAI of all the canopy layers, including the understory which may represent a very significant contribution, particularly for forests. Practically, the LAI quantifies the thickness of the vegetation cover.

The figure below shows the files included in the S2 LAI product.

Figure: S2 LAI product file list

 

FCOVER

The Fraction of Vegetation Cover corresponds to the fraction of ground covered by green vegetation. Practically, it quantifies the spatial extent of the vegetation. Because it is independent from the illumination direction and it is sensitive to the vegetation amount, fCover is a very good candidate for the replacement of classical vegetation indices for the monitoring of ecosystems.

The figure below shows the files included in the S2 fCover product.

Figure: S2 FCOVER product file list

 

NDVI

The Normalized Difference Vegetation Index is an indicator of the greenness of the biomes. As such, it is closely linked to the FAPAR. More information on the NDVI can be found in section 2.6.

The figure below shows the files included in the S2 NDVI product.

Figure: S2 NDVI product file list

 

The figure below shows the high level diagram on the Sentinel-2 processing workflow performed in this context at VITO.

More information on the different processing steps can be found in the VITO Sentinel-2 Products User Manual.

 

All products are delivered together with the classification map which gives an indicating on the pixel quality of the delivered product. The different values and their meaning are given in the table below.

Label

Classification

0

NO_DATA

1

SATURATED_OR_DEFECTIVE

2

DARK_AREA_PIXELS

3

CLOUD_SHADOWS

4

VEGETATION

5

BARE_SOIL

6

WATER

7

CLOUD_LOW_PROBABILITY

8

CLOUD_MEDIUM_PROBABILITY

9

CLOUD_HIGH_PROBABILITY

10

THIN_CIRRUS

11

SNOW

Table: Pixel quality classification map

 

SENTINEL-3

 

Sentinel-3 synergy (SYN) products will be made available through the Terrascope platform as soon as they are officially released by ESA. According to the latest Sentinel-3 mission status reports, SYN products based on Sentinel-3A data are currently only available to expert users with an official release planned after upgrades of the processor baseline. Furthermore it should be noted that both Sentinel-3A and 3B acquisitions are required for fully operational SYN products comparable to the VGT and PROBA-V S1 and S10 products. Sentinel-3B is currently in the commissioning phase with routine operations expected to start in 2019. VITO is a member of the Sentinel-3 Mission Performance Center (MPC). As Expert Support Laboratory (ESL), VITO provides expert analyses with respect to the OLCI L1 radiometry and the SYN VGT products. Within the ESL Level 2 LAND VAL group, the objective is to validate the Sentinel-3 SYN VGT products and to verify the similarity of these products with the combined time series of SPOT-VGT and PROBA-V.

 

SERVICES

 

The Web Map Tile Service (WMTS) is a standard protocol for serving pre-rendered georeferenced map tiles over the internet. VITO applies to the OGC WMTS Implementation Standard (OGC 07-057r7). 

It is possible to access the WMTS directly by using a simple web browser or desktop tools such as QGIS.

VITO Sentinel WMTS URL:

http://sentineldata.vito.be/wmts?service=WMTS&request=GetCapabilities

The available layers are:

  • CGS_S2_NDVI
  • CGS_S2_FAPAR
  • CGS_S2_RADIOMETRY

Examples:

https://sentineldata.vito.be/mapcache/wmts?layer=CGS_S2_RADIOMETRY&style=default&tilematrixset=g3857&Service=WMTS&Request=GetTile&Version=1.0.0&Format=image%2Fpng&TileMatrix=9&TileCol=262&TileRow=171&TIME=2018-02-25T10%3A50%3A18.000Z

 https://sentineldata.vito.be/mapcache/wmts?layer=CGS_S2_NDVI&style=default&tilematrixset=g3857&Service=WMTS&Request=GetTile&Version=1.0.0&Format=image%2Fpng&TileMatrix=9&TileCol=262&TileRow=171&TIME=2018-02-25T10%3A50%3A18.000Z

 

The Web Map Service (WMS) is a standard protocol for serving pre-rendered georeferenced map images over the internet. VITO applies to the OGC WMTS Implementation Standard (OGC 06-042). 

It is possible to access the WMS directly by using a simple web browser or desktop tools such as QGIS.

VITO Sentinel WMS URL:

http://sentineldata.vito.be/ows?service=WMS&request=GetCapabilities

The available layers are:

  • CGS_S2_NDVI
  • CGS_S2_FAPAR
  • CGS_S2_RADIOMETRY_BROWSE

Example:

http://sentineldata.vito.be/ows?SERVICE=WMS&VERSION=1.1.1&REQUEST=GetMap&LAYERS=CGS_S2_RADIOMETRY_BROWSE&FORMAT=image/png&TIME=2017-05-19T09:05:30.000Z&SRS=EPSG:4326&WIDTH=1920&HEIGHT=800&BBOX=1.7630521849289855,50.91914684746945,1.9539396361008605,50.99861922054515