Food Security TEP Tutorial

The following pages provide the tutorial for the FS TEP platform.

You may also find it useful to refer to

  • The list of frequently_asked_questions.

  • The list of known_issues.

If none of these pages answer your question, then please contact FS TEP support at support@foodsecurity.net.

1. S2_BIOPAR: Calculating bio-physical parameters for Sentinel2 imagery

1.1. Description

This processor calculates bio-physical parameter products (i.e. NDVI, FAPAR, FCOVER or LAI) starting from Sentinel2 L1C products.

First, this processor applies an atmospheric correction which leads to a corresponding L2A product. The atmospherically corrected data are used as input to calculate the appropriate bio-physical parameters.

1.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “S2_BIOPAR” from the available list of FS-TEP services. The “S2_BIOPAR” panel is displayed with parameter values to be filled in.

_images/image3.png

1.3. Fill the parameters

1.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Input Sentinel2 products” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate bio-physical parameters images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

1.3.2. Input Sentinel2 products

  • Drag and drop a data basket filled with the appropriate Sentinel-2 L1C files into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L1C files and how to add these files to a data basket.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

1.3.3. Type of bio-physical parameter to be processed

String identifying the type of bio-physical parameter that needs to be processed. Can be one of following values:

  • NDVI (Normalized Difference Vegetation Index)

  • FAPAR (Fractional Absorbed Photosynthetic Active Radiation)

  • FCOVER (Fractional Vegetation Cover)

  • LAI (Leaf Area Index)

1.3.4. Collection ingestion specification

The collection specification. Once processed, the generated products are added to the “Analyst” view of the FS-TEP portal. Refer to the FS-TEP User Manual for further details.

The specified collection specification is a string of following syntax:

{

“<key>” : “<collection_id>”

}

Where:

  • <key>: identifier for the type of data to be added. Can be one of following values:

    • For the image data:

      • fapar

      • fcover

      • lai

      • ndvi

    • For the image meta-data:

      • fapar-metadata

      • fcover-metadata

      • lai-metadata

      • ndvi-metadata

  • <collection_id>: identifier for the FS-TEP collection, which can be found in the “Collections” panel of the “Manage/Share” window.

An example is given below:

{

“fapar”:”fstep3c52898984f44b0b962cefb489673ffa”,

“fcover”:”fstep83099f871c9b417ab632a6b2f559f9a7”,

“lai”:”fstep237fb985bd014205a815efed45f5ceb8”,

“ndvi”:”fstep22f0ff303b4349a68c51a193d4c76a19”,

“fapar-metadata”:”fstep3c52898984f44b0b962cefb489673ffa”,

“fcover-metadata”:”fstep83099f871c9b417ab632a6b2f559f9a7”,

“lai-metadata”:”fstep237fb985bd014205a815efed45f5ceb8”,

“ndvi-metadata”:”fstep22f0ff303b4349a68c51a193d4c76a19”

}

1.3.5. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

1.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image1 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

1.5. Results download and visualization

The generated results can be accessed from the “OUTPUT” tab of the executed job. An example is given below:

_images/image5.png

Refer to the FS-TEP User Manual for further details on how to access the data and how to visualize the data on the geo browser and the “Analyst” view.

2. S2_BI: Calculating brightness index for Sentinel2 imagery

2.1. Description

This processor calculates the brightness index for Sentinel2 imagery. The brightness index is sensitive to the brightness of soils which is highly correlated with the humidity and the presence of salts in the surface.

2.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “S2_BI” from the available list of FS-TEP services. The “S2_BI” panel is displayed with parameter values to be filled in.

_images/image6.png

2.3. Fill the parameters

2.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Input Sentinel2 tile” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate brightness index images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

2.3.2. Input Sentinel2 tile

  • Drag and drop a Sentinel-2 L1C file into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L1C files.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

2.3.3. Collection ID inputs

The collection specification. Once processed, the generated product is added to the “Analyst” view of the FS-TEP portal. Refer to the FS-TEP User Manual for further details.

The specified collection specification is a string of following syntax:

{

“<key>” : “<collection_id>”

}

Where:

  • <key>: identifier for the type of data to be added.

  • <collection_id>: identifier for the FS-TEP collection, which can be found in the “Collections” panel of the “Manage/Share” window.

2.3.4. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

2.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image2 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

3. S2_BANDRATIO: Band combination for Sentinel2 imagery

3.1. Description

This processor calculates the index results from the following equation:

Index = (Band_A) / (Band_B)

The default is to use Sentinel-2 Band 8 (Near Infrared) as Band_A and Band 4 (Red) as Band_B.

The default band values belong to the Ratio Vegetation Index (RVI). The RVI is a widely used vegetation index that indicates the amount of vegetation. The higher the value, the more vegetation. Low values show soil, ice, water etc. The user can choose every available band combination.

Kriegler, F.J. et al., Proceedings of the Sixth International Symposium on Remote Sensing of Environment, p.97(1969)

The spectral bands of the Sentinel-2 MSI sensor are defined in the table below:

Sentinel-2A Multispectral Imager Bands

3.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “S2_BANDRATIO” from the available list of FS-TEP services. The “S2_ BANDRATIO” panel is displayed with parameter values to be filled in.

_images/image10.png

3.3. Fill the parameters

3.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Input Sentinel2 tile” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate output images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

3.3.2. Input Sentinel2 tile

  • Drag and drop a Sentinel-2 L1C file into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L1C files.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

3.3.3. Band_A

Band index of “Band_A” in the formula “Band_A / Band_B”. Defaults to 8.

3.3.4. Band_B

Band index of “Band_B” in the formula “Band_A / Band_B”. Defaults to 4.

3.3.5. Collection ID inputs

The collection specification. Once processed, the generated product is added to the “Analyst” view of the FS-TEP portal. Refer to the FS-TEP User Manual for further details.

The specified collection specification is a string of following syntax:

{

“<key>” : “<collection_id>”

}

Where:

  • <key>: identifier for the type of data to be added.

  • <collection_id>: identifier for the FS-TEP collection, which can be found in the “Collections” panel of the “Manage/Share” window.

3.3.6. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

3.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image5 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

4. S2_NDWI: Calculating NDWI for Sentinel2 imagery

4.1. Description

This processor calculates the NDWI (Normalized Difference Water Index) for Sentinel2 imagery. The Normalized Difference Vegetation Index (NDWI) is sensitive to changes in liquid water content of vegetation canopies.

4.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “S2_NDWI” from the available list of FS-TEP services. The “S2_NDWI” panel is displayed with parameter values to be filled in.

_images/image7.png

4.3. Fill the parameters

4.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Input Sentinel2 tile” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate NDWI images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

4.3.2. Input Sentinel2 tile

  • Drag and drop a Sentinel-2 L1C file into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L1C files.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

4.3.3. Collection ID inputs

The collection specification. Once processed, the generated product is added to the “Analyst” view of the FS-TEP portal. Refer to the FS-TEP User Manual for further details.

The specified collection specification is a string of following syntax:

{

“<key>” : “<collection_id>”

}

Where:

  • <key>: identifier for the type of data to be added.

  • <collection_id>: identifier for the FS-TEP collection, which can be found in the “Collections” panel of the “Manage/Share” window.

4.3.4. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

4.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image3 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

5. S2_REP: Calculating REP for Sentinel2 imagery

5.1. Description

This processor calculates the REP (red-edge position) for Sentinel2 imagery.

Red edge, as the infliction point of the strong red absorption to near infrared reflectance, includes the information of both crop (chlorophyll content) N and growth status.

5.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “S2_REP” from the available list of FS-TEP services. The “S2_REP” panel is displayed with parameter values to be filled in.

_images/image8.png

5.3. Fill the parameters

5.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Input Sentinel2 tile” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate output images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

5.3.2. Input Sentinel2 tile

  • Drag and drop a Sentinel-2 L1C file into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L1C files.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

5.3.3. Collection ID inputs

The collection specification. Once processed, the generated product is added to the “Analyst” view of the FS-TEP portal. Refer to the FS-TEP User Manual for further details.

The specified collection specification is a string of following syntax:

{

“<key>” : “<collection_id>”

}

Where:

  • <key>: identifier for the type of data to be added.

  • <collection_id>: identifier for the FS-TEP collection, which can be found in the “Collections” panel of the “Manage/Share” window.

5.3.4. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

5.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image4 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

6. JUPYTER: Launching a Jupyter notebook application

6.1. Description

The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.

Refer to https://jupyter.org/ for further details.

6.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “JUPYTER” from the available list of FS-TEP services. The “JUPYTER” panel is displayed with parameter values to be filled in.

_images/image11.png

6.3. Fill the parameters

6.3.1. Input

  • Drag and drop a data basket filled with the appropriate Satellite products (e.g. Sentinel-1, Sentinel-2) into the field. Refer to the FS-TEP User Manual for further details on how to search and select satellite products and how to add these files to a data basket.

6.3.2. Timeout in minutes before the application automatically shuts down

The timeout (in minutes) before the application automatically shuts down. Defaults to 60 minutes. This parameter is used to make sure that the Jupyter notebook application is prevented from running forever.

Note that for every hour for which the Jupyter notebook application is kept running, 1 FS-TEP coin is charged.

6.3.3. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

6.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image6 and see the running job in the “JOBS” tab of the data panel. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

  • A confirmation dialog is shown to the user. Press “confirm” to continue.

_images/image12.png
  • Open the “JOBS” tab of the data panel and click the image7 button to launch the Jupyter notebook application. Note that, depending on the available hardware resources, it might take some time before this icon becomes visible.

  • The Jupyter Notebook application is launched in a new tab of your browser, as shown in the figure below.

    The input data (see “Input” parameter of the job) is available in the “workDir/inDir” folder. Output data can be stored in the “workDir/outDir”.

    Note that any data stored in the Jupyter Notebook application will be lost when the application is closed, except if the data are stored in the “workDir/persistentDir” folder. The “workDir/persistenDir” folder can be used to store any data (e.g. *.ipynb project files) that should be kept persistent between multiple Jupyter Notebook applications that are launched (by the same user).

_images/image14.png
  • Terminating the Jupyter Notebook application can be done using the “Quit” button at the top-right of the panel. Note that closing the browser panel in which the Jupyter Notebook application is running does not terminate the application, and thus allows to restart it by clicking the image8 button on the “JOBS” tab of the data panel.

6.5. References

Refer to here for the Jupyter Notebook user guide.

7. SNAP: Launching a SNAP application

7.1. Description

The ESA SNAP (Sentinel Application Platform) toolbox is a GUI combined with a set of tools intended for Earth Observation processing and analysis. It reunites all Sentinel toolboxes in order to offer the most complex platform for this mission.

Refer to here for further details.

7.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “SNAP” from the available list of FS-TEP services. The “SNAP” panel is displayed with parameter values to be filled in.

_images/image19.png

7.3. Fill the parameters

7.3.1. Input

  • Drag and drop a data basket filled with the appropriate Satellite products (e.g. Sentinel-1, Sentinel-2) into the field. Refer to the FS-TEP User Manual for further details on how to search and select satellite products and how to add these files to a data basket.

7.3.2. Timeout in minutes before the application automatically shuts down

The timeout (in minutes) before the application automatically shuts down. Defaults to 60 minutes. This parameter is used to make sure that the SNAP application is prevented from running forever.

Note that for every hour for which the SNAP application is kept running, 1 FS-TEP coin is charged.

7.3.3. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

7.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image11 and see the running job in the “JOBS” tab of the data panel. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

  • A confirmation dialog is shown to the user. Press “confirm” to continue.

_images/image20.png
  • Open the “JOBS” tab of the data panel and click the image12 button to launch the SNAP application. Note that, depending on the available hardware resources, it might take some time before this icon becomes visible.

  • First, the user is asked to login (see login panel below) and create a new session. Click the “OK” button to continue.

_images/image21.png
  • The SNAP is launched in a new tab of your browser.

The input data (see “Input” parameter of the job) is available in the “inDir” folder. Output data can be stored in the “outDir”.

Note that any data stored in the SNAP application will be lost when the application is closed, except if the data are stored in the “workDir/persistentDir” folder. The “workDir/persistenDir” folder can be used to store any data (e.g. SNAP project files) that should be kept persistent between multiple SNAP applications that are launched (by the same user).

_images/image22.png
  • Terminating the SNAP application can be done using “File - Exit” menu item from the application.

7.5. References

Some useful links w.r.t. SNAP:

Video tutorials

https://step.esa.int/main/doc/tutorials/snap-tutorials/

User manual

http://step.esa.int/main/doc/tutorials/

8. MONTEVERDI: Launching a Monteverdi application

8.1. Description

Monteverdi is a satellite image viewer application as part of the Orfeo Toolbox (OTB). Its main features are:

  • Performance: Navigate instantly in full size satellite images thanks to its hardware accelerated rendering engine. Compose tiles or compare multiple images in a stack with rapid cycling and shader effects.

  • Sensor geometry support: View raw images directly in sensor geometry! Resampling is handled by the GPU through texture mapping. OTB automagically handles coordinates mapping between actors and viewport geometries.

  • Powerful: Access to all processing application from OTB. Orthorectification, optical calibration, classification, SAR processing, and much more.

Refer to here for further details.

8.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “MONTEVERDI” from the available list of FS-TEP services. The “MONTEVERDI” panel is displayed with parameter values to be filled in.

_images/image23.png

8.3. Fill the parameters

8.3.1. Input

  • Drag and drop a data basket filled with the appropriate Satellite products (e.g. Sentinel-1, Sentinel-2) into the field. Refer to the FS-TEP User Manual for further details on how to search and select satellite products and how to add these files to a data basket.

8.3.2. Timeout in minutes before the application automatically shuts down

The timeout (in minutes) before the application automatically shuts down. Defaults to 60 minutes. This parameter is used to make sure that the MONTEVERDI application is prevented from running forever.

Note that for every hour for which the MONTEVERDI application is kept running, 1 FS-TEP coin is charged.

8.3.3. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

8.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image13 and see the running job in the “JOBS” tab of the data panel. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

  • A confirmation dialog is shown to the user. Press “confirm” to continue.

_images/image24.png
  • Open the “JOBS” tab of the data panel and click the image14 button to launch the MONTEVERDI application. Note that, depending on the available hardware resources, it might take some time before this icon becomes visible.

  • First, the user is asked to login (see login panel below) and create a new session. Click the “OK” button to continue.

_images/image25.png
  • The MONTEVERDI application is launched in a new tab of your browser.

The input data (see “Input” parameter of the job) is available in the “inDir” folder. Output data can be stored in the “outDir”.

Note that any data stored in the MONTEVERDI application will be lost when the application is closed, except if the data are stored in the “workDir/persistentDir” folder. The “workDir/persistenDir” folder can be used to store any data (e.g. MONTEVERDI project files) that should be kept persistent between multiple MONTEVERDI applications that are launched (by the same user).

_images/image26.png
  • Terminating the MONTEVERDI application can be done using “File - Quit” menu item from the application.

9. QGIS: Launching a QGIS application

9.1. Description

QGIS is a free and open-source Geographic Information System (GIS) application. Refer to https://qgis.org/en/site/ for further details.

9.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “QGIS” from the available list of FS-TEP services. The “QGIS” panel is displayed with parameter values to be filled in.

_images/image15.png

9.3. Fill the parameters

9.3.1. Input

  • Drag and drop a data basket filled with the appropriate Satellite products (e.g. Sentinel-1, Sentinel-2) into the field. Refer to the FS-TEP User Manual for further details on how to search and select satellite products and how to add these files to a data basket.

9.3.2. Timeout in minutes before the application automatically shuts down

The timeout (in minutes) before the application automatically shuts down. Defaults to 60 minutes. This parameter is used to make sure that the QGIS application is prevented from running forever.

Note that for every hour for which the QGIS application is kept running, 1 FS-TEP coin is charged.

9.3.3. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

9.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image9 and see the running job in the “JOBS” tab of the data panel. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

  • A confirmation dialog is shown to the user. Press “confirm” to continue.

_images/image16.png
  • Open the “JOBS” tab of the data panel and click the image10 button to launch the QGIS application. Note that, depending on the available hardware resources, it might take some time before this icon becomes visible.

  • First, the user is asked to login (see login panel below) and create a new session. Click the “OK” button to continue.

_images/image17.png
  • The QGIS is launched in a new tab of your browser.

The input data (see “Input” parameter of the job) is available in the “inDir” folder. Output data can be stored in the “outDir”.

Note that any data stored in the QGIS application will be lost when the application is closed, except if the data are stored in the “workDir/persistentDir” folder. The “workDir/persistenDir” folder can be used to store any data (e.g. QGIS project files) that should be kept persistent between multiple QGIS applications that are launched (by the same user).

_images/image18.png
  • Terminating the QGIS application can be done using “Project – Exit QGIS” menu item from the application.

9.5. References

Refer to here for the QGIS software user manual.

10. SEN2AGRIL2A: Atmospheric Correction service for Sentinel2 imagery

10.1. Description

The Sen2AGRI Level2A processor applies atmospheric correction to input Sentinel-2 L1C images to create a bottom of the atmosphere reflectance L2A image. This is an important step to enable the image to be subsequently used to generate more advanced scientific measurements. used to derive quantitate measures.

The atmospheric correction algorithm applies is the MACCS-ATCOR Joint Algorithm (MAJA), which has been developed by CESBIO, CNES and DLR. MAJA is an evolution of the MACCS algorithm which has been updated to include some methods inspired by the Atmospheric correction (ATCOR) software. MACCS (Multi-sensor Atmospheric Correction and Cloud Screening) is a Level2A processor, which detects the clouds and their shadows, and estimates aerosol optical thickness (AOT), water vapour and corrects for the atmospheric effects. MACCS was jointly developed by CESBIO and CNES.

This service allows the creation of L2A data that is the required input for the other Sen2Agri services.

As such it is a necessary precursor service for all other Sen2Agri services.

Note this service and product specification has been developed within the ESA-sponsored Sentinel-2 for Agriculture (Sen2Agri) project. Further details of this project and its products can be found here: http://www.esa-sen2agri.org/.

10.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “Sen2AgriL2A” from the available list of FS-TEP services. The “Sen2AgriL2A” panel is displayed with parameter values to be filled in.

_images/image27.png

10.3. Fill the parameters

10.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Sentinel-2 Data” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate monthly cloud-free composite images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

10.3.2. Sentinel-2 Data

The input Sentinel-2 Level1C data to be processed.

  • Drag and drop a data basket filled with the appropriate Sentinel-2 L1C files into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L1C files and how to add these files to a data basket.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

10.3.3. Previous L2A file

An OPTIONAL field for the users to provide details of previously generated L2A products. The MACCS/MAJA processor may be run in 2 modes: L2INIT and L2NOMINAL.

The former will be used if there aren’t any previously processed tiles by MACCS/MAJA. The latter will be used if there are already previously processed tiles and can be used by MACCS/MAJA to enhance the final result.

The tiles should be inserted as a list separated by spaces.

10.3.4. ID of target collection

If you want to store the processing results in a collection that you have write access to, add the following in this field:

{“l2a”:”[collectionID]”}

You can discover the IDs of collections in the Manage/Share section. Typically, [collectionID] consists of “fstep” followed by 32-digit hexadecimal code.

10.3.5. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

10.3.6. Product start date

The date at which the systematic processing should start.

  • Select the desired date from the date widget that pops up when clicking the field. Note that the date can also filled in manually by entering the values in the format DD-MM-YYYY.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

10.3.7. Product end date

The date at which the systematic processing should end.

Note that the “Product end date” is optional and is only available in case the “Processor running mode” field is set to “Systematic”. If not provided, the systematic processing will continue generating cloud-free mosaic products forever (i.e. until all user TEP-coins have been consumed).

10.3.8. Collection

The collection identifier identifying the type of data for which a cloud-free mosaic should be generated. Its value should be set to “Sentinel-2”.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

10.3.9. Processing level

The processing level identifying the type of input Sentinel-2 data. Should be set to L1C.

  • Select the appropriate processing level from the dropdown list.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic” and in case the “Collection” field is set to “Sentinel-2”.

10.3.10. AOI

The AOI defining the area for which a cloud-free composite should be generated. As detailed in the FS-TEP User Manual, the AOI can be specified in two ways:

  1. By manually entering a polygon in the OGC WKT (Well-Known Text) format in the “AOI” text field. For example, the WKT polygon “POLYGON((1 2,1 4,3 4,3 2,1 2))” indicates a rectangle whose four corners are indicated by (1,2), (1,4), (3,4), and (3,2). Note that a polygon must be closed, so the first and last points in the provided WKT must match. Refer to here for further details on the WKT format.

  2. By drawing or importing an AOI using one of the activated AOI buttons, as shown in the figure below. Refer to the FS-TEP User Manual for further details.

_images/image28.png

For example, the figure below shows a rectangular AOI covering the Belgium and Luxemburg area.

_images/image29.png

10.3.11. Cloud coverage

The maximum allowed cloud cover percentage. The default value is 10 meaning that only images with max. 10% cover will be used in this processor.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

10.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image15 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

10.5. Service outputs

The Sen2Agri MAJA Atmospheric Correction service will generate numerous outputs:

  • A zip file containing the generated Sentinel-2 L2A image along with ancillary information.

The resulting outputs files can be visualised and analyzed in one of the GUI applications, such as QGIS, SNAP or MONTEVERDI.

11. SEN2AGRIL3A: Generating cloud-free mosaic from Sentinel2 imagery

11.1. Description

The Sen2AGRI Level3A processor provides a cloud-free composite of surface reflectance values in the 10 S2 bands designed for land observation and keeping their native spatial resolution (10 or 20 meters). The product is delivered on a monthly basis.

_images/image30.png

Complete specifications are detailed in the table below.

_images/image31.png

The product is delivered with several masks that will help appraising its quality:

  • the number of valid observations over the period used to generate the composite;

  • the status of the pixel over the period: no-data (pixel never observed during the compositing period), cloud (pixel always cloudy during the compositing period), snow (pixel always covered by snow for the available cloud-free observations), water (pixel always covered by water for the available cloud-free observations), land (pixel free from cloud / cloud shadow, snow and water at least once during the compositing period);

  • the weighted average of dates used in the synthesis (which informs about the date within the compositing period from which the synthesis is representative).

Further details can be found in the Sen2AGRI Software User Manual.

Note this service and product specification has been developed within the ESA-sponsored Sentinel-2 for Agriculture (Sen2Agri) project. Further details of this project and its products can be found here: http://www.esa-sen2agri.org/.

11.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “Sen2AgriL3A” from the available list of FS-TEP services. The “Sen2AgriL3A” panel is displayed with parameter values to be filled in.

_images/image32.png

11.3. Fill the parameters

11.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Sentinel-2 L2A” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate monthly cloud-free composite images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

11.3.2. Sentinel-2 L2A

  • Drag and drop a data basket filled with the appropriate Sentinel-2 L2A files into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L2A files and how to add these files to a data basket.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

11.3.3. Date of synthesis

The date of the synthesis, which must be defined as the central date of the synthesis time window. The format of the date should be YYYYMMDD.

For example, if set to “20201015” (i.e. October 15th 2020) and in case the “Half synthesis period” is set to 15 days, the processor will generate a cloud-free composite product containing data between 20201001 (i.e. October 1st 2020) and 20201030 (i.e. October 30th 2020).

11.3.4. Half synthesis period

The half synthesis period (in days). Valid values are within the range between 15 and 25 days. For example, setting this value to 15 indicates that 2x15=30 days should be used as moving time window using “Date of synthesis” as the central date of the synthesis time window.

This parameter defaults to 25 days which is advised in case of very cloudy observations.

11.3.5. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

11.3.6. Product start date

The date at which the systematic processing should start.

  • Select the desired date from the date widget that pops up when clicking the field. Note that the date can also filled in manually by entering the values in the format DD-MM-YYYY.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

11.3.7. Product end date

The date at which the systematic processing should end. Note that the “Product end date” is optional and is only available in case the “Processor running mode” field is set to “Systematic”. If not provided, the systematic processing will continue generating cloud-free mosaic products forever (i.e. until all user TEP-coins have been consumed).

11.3.8. Collection

The collection identifier identifying the type of data for which a cloud-free mosaic should be generated. Its value should be set to “Sentinel-2”.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

11.3.9. Processing level

The processing level identifying the type of input Sentinel-2 data. Can be either L1C or L2A. If set to L1C, the Sen2COR tool is applied first to generate a corresponding Sentinel-2 L2A (i.e. atmospherically corrected) image. To gain computation time, it is advised to set this parameter to L2A.

  • Select the appropriate processing level from the dropdown list.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic” and in case the “Collection” field is set to “Sentinel-2”.

11.3.10. AOI

The AOI defining the area for which a cloud-free composite should be generated. As detailed in the FS-TEP User Manual, the AOI can be specified in two ways:

  1. By manually entering a polygon in the OGC WKT (Well-Known Text) format in the “AOI” text field. For example, the WKT polygon “POLYGON((1 2,1 4,3 4,3 2,1 2))” indicates a rectangle whose four corners are indicated by (1,2), (1,4), (3,4), and (3,2). Note that a polygon must be closed, so the first and last points in the provided WKT must match. Refer to here for further details on the WKT format.

  2. By drawing or importing an AOI using one of the activated AOI buttons, as shown in the figure below. Refer to the FS-TEP User Manual for further details.

_images/image28.png

For example, the figure below shows a rectangular AOI covering the Belgium and Luxemburg area.

_images/image29.png

11.3.11. Cloud coverage

The maximum allowed cloud cover percentage. The default value is 10 meaning that only images with max. 10% cover will be used in this processor.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

11.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image16 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

11.5. Service outputs

The primary output is the cloud-free temporal composite in a GeoTIFF format. This is provided within the product formation as defined by the Sen2Agri service. This contains a zipped folder with various subfolders containing additional data and information such as auxiliary files and legacy data. Further details are available on the Sen2Agri website.

Additionally, the input images are provided as multi-band RGB images which can be visualised on the GeoBrowser. The resulting outputs GeoTIFF files can be downloaded, re-used or visualised in the FS-TEP GeoBrowser. The screenshot below shows the one of the input displayed in the FS-TEP GeoBrowser.

_images/image33.png

Further analysis can be undertaken in one of the GUI applications, such as QGIS, SNAP or MONTEVERDI.

12. SEN2AGRIL3B: Bio-physical parameters generation from Sentinel2 imagery

12.1. Description

The biophysical vegetation processor provides three types of products informing about the evolution of the green vegetation:

  • The NDVI, the most popular indicator operationally used for vegetation monitoring,

provided to ensure continuity with existing long-term time series and thus, allowing

anomalies detection;

  • The LAI, an intrinsic canopy primary variable that should not depend on observation

conditions, which determines the size of leaf interface for exchange of energy and mass

between the canopy and the atmosphere;

  • Phenology indices, also referred to as NDVI metrics, which inform about specific key

parameters of the growing season (starting date, season length and date of maximum

growth rate).

With regard to the LAI product, the system proposes three processing options (not mutually exclusive). First, LAI time series can be produced in near-real time based on a mono-date approach. For the second and third options, the LAI time series are built on a multi-temporal approach, i.e. each LAI value is estimated using more than one date as input. In the second option, the LAI value is also produced in near-real time based on “n” last acquisitions. The third option consists in a re-processing at the end of the season by fitting a phenological model, which should allow having a higher quality time series.

Complete specifications of all products generated by this processor are detailed in the table below:

_images/image34.png

The products are delivered with several masks that will help appraising its quality:

  • For the NDVI maps:

    • The number of valid observations (i.e. cloud-free and land) over the period used the generate the NDVI;

    • The number of observations associated with the other statuses (“water”, “snow”, “cloud”, “cloud shadow”, “no data”) over the same period;

  • For the mono-date LAI maps:

    • The number of valid observations (i.e. cloud-free and land) over the period used the generate the LAI;

    • The number of observations associated with the other statuses (“water”, “snow”, “cloud”, “cloud shadow”, “no data”’) over the same period;

    • The uncertainty, which will represent Root Mean Square Error (RMSE) as a function of the estimated value.

  • For the multi-date LAI based on “n” last acquisitions: the number of valid observations (i.e. cloud-free and land) over the search window; knowing that the multi-date LAI will not be computed if this number is lower than 2);

  • For the LAI re-processed at the end of the season and for the NDVI metrics:

    • The number of valid observations (i.e. cloud-free and land) over the season, knowing that the re-processed LAI and the NDVI metrics will not be computed if this number is lower than 4);

    • The number of observations associated with the other statuses (“water”, “snow”, “cloud”, “cloud shadow”, “no data”’) over the same period.

Further details can be found in the Sen2AGRI Software User Manual.

12.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “Sen2AgriL3B” from the available list of FS-TEP services. The “Sen2AgriL3B” panel is displayed with parameter values to be filled in.

_images/image35.png

12.3. Fill the parameters

12.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Sentinel-2 L2A” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate bio-physical parameter images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

12.3.2. Sentinel-2 L2A

  • Drag and drop a data basket filled with the appropriate Sentinel-2 L2A files into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L2A files and how to add these files to a data basket.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

12.3.3. Resolution

The desired spatial resolution (in meter) of the generated output products. Defaults to 10 (meter).

12.3.4. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

12.3.5. Product start date

The date at which the systematic processing should start.

  • Select the desired date from the date widget that pops up when clicking the field. Note that the date can also filled in manually by entering the values in the format DD-MM-YYYY.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

12.3.6. Product end date

The date at which the systematic processing should end. Note that the “Product end date” is optional and is only available in case the “Processor running mode” field is set to “Systematic”. If not provided, the systematic processing will continue generating output products forever (i.e. until all user TEP-coins have been consumed).

12.3.7. Collection

The collection identifier identifying the type of data for which a product should be generated. Its value should be set to “Sentinel-2”.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

12.3.8. Processing level

The processing level identifying the type of input Sentinel-2 data.

  • Select the appropriate processing level from the dropdown list. Its value should be set to “L2A”.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic” and in case the “Collection” field is set to “Sentinel-2”.

12.3.9. AOI

The AOI defining the area for which a cloud-free composite should be generated. As detailed in the FS-TEP User Manual, the AOI can be specified in two ways:

  1. By manually entering a polygon in the OGC WKT (Well-Known Text) format in the “AOI” text field. For example, the WKT polygon “POLYGON((1 2,1 4,3 4,3 2,1 2))” indicates a rectangle whose four corners are indicated by (1,2), (1,4), (3,4), and (3,2). Note that a polygon must be closed, so the first and last points in the provided WKT must match. Refer to here for further details on the WKT format.

  2. By drawing or importing an AOI using one of the activated AOI buttons, as shown in the figure below. Refer to the FS-TEP User Manual for further details.

_images/image28.png

For example, the figure below shows a rectangular AOI covering the Belgium and Luxemburg area.

_images/image29.png

12.3.10. Cloud coverage

The maximum allowed cloud cover percentage. The default value is 10 meaning that only images with max. 10% cover will be used in this processor.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

12.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image17 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

12.5. Service outputs

The primary output is the cropland mask which is a binary map separating annual cropland areas and other areas at 10 meters spatial resolution. This mask is produced along the agricultural season, on a monthly basis to serve for instance as a mask to monitor crop growing conditions. Its accuracy is expected to increase along the season as long as new images are integrated.

The product is delivered with several masks that will inform about the number of dates (i.e. L2A products) which are associated with the different classes resulting from the cloud detection (land, water, snow, cloud, cloud shadow and no data) during the period used to generate the mask. The metadata file contains the thematic accuracy figures (overall accuracy and contingency matrix).

The resulting outputs GeoTIFF files can be downloaded, re-used or visualised in the FS-TEP GeoBrowser.

_images/image36.png

Further analysis can be undertaken in one of the GUI applications, such as QGIS, SNAP or MONTEVERDI.

13. SEN2AGRIL4A: Generating crop land mask from Sentinel2 imagery

13.1. Description

The cropland mask consists in a binary map separating annual cropland areas and other areas at 10 meters spatial resolution. This mask is produced along the agricultural season, on a monthly basis to serve for instance as a mask to monitor crop growing conditions. Its accuracy is expected to increase along the season as long as new images are integrated.

_images/image37.png

Complete specifications are provided in the table below.

_images/image38.png

The product is delivered with several masks that will inform about the number of dates (i.e. L2A products) which are associated with the different classes resulting from the cloud detection (land, water, snow, cloud, cloud shadow and no data) during the period used to generate the mask. The metadata file contains the thematic accuracy figures (overall accuracy and contingency matrix).

Further details can be found in the Sen2AGRI Software User Manual.

Note this service and product specification has been developed within the ESA-sponsored Sentinel-2 for Agriculture (Sen2Agri) project. Further details of this project and its products can be found here: http://www.esa-sen2agri.org/.

13.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

\_images/FS-TEP_overview.jpg

Select the processing service “Sen2AgriL4A” from the available list of FS-TEP services. The “Sen2AgriL4A” panel is displayed with parameter values to be filled in.

_images/image39.png

13.3. Fill the parameters

13.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Sentinel-2 L2A” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate monthly cropland mask images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

13.3.2. Sentinel-2 L2A

  • Drag and drop a data basket filled with the appropriate Sentinel-2 L2A files into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L2A files and how to add these files to a data basket.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

13.3.3. In-situ data shapefile

The shapefile containing the cropland information. It contains samples of the main crops as well as non-crop areas spread throughout the considered site. The in-situ data should be gathered in a single zipped shapefile, projected in the WGS 84/UTM grid system, containing both cropland and no-cropland information. If not provided, the default 2015 ESA-CCI landcover map is used.

The shapefile should be a zip-file containing all shapefile components (.shp, .shx, .prj, .dbf). The format of the shapefile attribute table is presented in:

Variable Name

Des cription

Var. Type

Var. Length

Var. values / comments

Null accepted

ID

Feature ID

Numeric

6

000000 - 999999

N

CROP

Binary Class

Numeric

1

0 if non- cropland

1 if cropland

N

LC

Land Cover

Text

70

Name of the crop type or the non-crop type class

N

CODE

Code of the class

Numeric (Long integer)

8

Cfr. JECAM Gu idelines

N

IR RIGATION

Inf ormation about ir rigation of the field

Numeric

1

Only if known:

0 = not c oncerned or inf ormation not a vailable

1 = i rrigated

2 = not i rrigated

Y

Refer to Sen2AGRI Software User Manual for further details on the specifications of the in-situ data shapefile.

13.3.4. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

13.3.5. Product start date

The date at which the systematic processing should start.

  • Select the desired date from the date widget that pops up when clicking the field. Note that the date can also filled in manually by entering the values in the format DD-MM-YYYY.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

13.3.6. Product end date

The date at which the systematic processing should end. Note that the “Product end date” is optional and is only available in case the “Processor running mode” field is set to “Systematic”. If not provided, the systematic processing will continue generating cropland mask products forever (i.e. until all user TEP-coins have been consumed).

13.3.7. Collection

The collection identifier identifying the type of data for which a cropland mask should be generated. Its value should be set to “Sentinel-2”.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

13.3.8. Processing level

The processing level identifying the type of input Sentinel-2 data. Should be set to “L2A”.

  • Select the appropriate “L2A” processing level from the dropdown list.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic” and in case the “Collection” field is set to “Sentinel-2”.

13.3.9. AOI

The AOI defining the area for which a cloud-free composite should be generated. As detailed in the FS-TEP User Manual, the AOI can be specified in two ways:

  1. By manually entering a polygon in the OGC WKT (Well-Known Text) format in the “AOI” text field. For example, the WKT polygon “POLYGON((1 2,1 4,3 4,3 2,1 2))” indicates a rectangle whose four corners are indicated by (1,2), (1,4), (3,4), and (3,2). Note that a polygon must be closed, so the first and last points in the provided WKT must match. Refer to here for further details on the WKT format.

  2. By drawing or importing (from a shapefile) an AOI using one of the activated AOI buttons, as shown in the figure below. Refer to the FS-TEP User Manual for further details.

_images/image28.png

For example, the figure below shows a rectangular AOI covering the Belgium and Luxemburg area.

_images/image29.png

13.3.10. Cloud coverage

The maximum allowed cloud cover percentage. The default value is 10 meaning that only images with max. 10% cover will be used in this processor.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

13.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image18 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

13.5. Service outputs

The primary output is a GeoTIFF of the cropland mask which is a binary mask at 10 meters’ spatial resolution. The cropland mask is provided in two versions:

  • A single-band GeoTIFF for use and visualisation on the Analyst viewer

  • The crop type map within the product format as defined by the Sen2Agri service. This contains a zipped folder with various subfolders containing additional data and information such as auxiliary files and legacy data. Further details are available on the Sen2Agri website

The details of the primary output (the L4A file is provided below).

Correspondent file

Dynamic Cropland Mask

Information type

Classified images of cropland extent

Raster format

GeoTIFF

Resolution

10m

Projection Type

WGS84 Transverse Mercator

Bit depth

16-bit signed integer (single band)

Processing level

Classified Image (L4B)

Naming convention

S2Agri_L4B_[Input_Sentinel-2_L2A].tif

The image below shows a Crop Type map of central Netherlands from April 2020, displayed in the Analyst viewer.

_images/image40.png

Further analysis can be undertaken in one of the GUI applications, such as QGIS, SNAP or MONTEVERDI.

14. SEN2AGRIL4B: Generating crop type map from Sentinel2 imagery

14.1. Description

The cropland type product is a map of the main crop types or groups at 10 meters spatial resolution. Crop types are classified only over the crop area identified in the crop mask. The map is generated twice over the season, with a first delivery at the middle of the season and the second one at the end. The accuracy expected to increase along the season as long as new images are integrated and crops are growing.

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Complete specifications are provided in the table below:

Properties

Value

Spatial resolution

10 meter

Temporal resolution

Twice over the growing season: first product delivered after an initialization

period (up to 6 months); second delivery at the end

Legend

Same as in-situ data provided by users

Geometric accuracy

Same than L1C input data

Thematic accuracy

Progressively increasing along the season

Overall accuracy of 50% at the middle of the season and of F1-Score higher than 65% for the main classes

Format

GEOTIFF raster images

Projection

UTM / WGS84

Metadata

XML file

The product is delivered with several masks that will inform about the number of dates (i.e. L2A products) which are associated with the different classes resulting from the cloud detection (land, water, snow, cloud, cloud shadow and no data) during the period used to generate the mask. The metadata file contains the thematic accuracy figures (overall accuracy and contingency matrix).

Further details can be found in the Sen2AGRI Software User Manual.

Note this service and product specification has been developed within the ESA-sponsored Sentinel-2 for Agriculture (Sen2Agri) project. Further details of this project and its products can be found here: http://www.esa-sen2agri.org/.

14.2. Select the processing

  • Login to the platform as detailed in the FS-TEP User Manual

  • Down the left hand side is a menu containing amongst others the “ServicesServices button: clicking on it brings up a panel allowing user to search for available services that can be run on the data.

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Select the processing service “Sen2AgriL4B” from the available list of FS-TEP services. The “Sen2AgriL4B” panel is displayed with parameter values to be filled in.

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14.3. Fill the parameters

14.3.1. Processor running mode

Set the “Processor running mode” to one of following values:

  • Standard: indicates that this processor should be executed as a single-shot process containing the input data as indicated in the “Sentinel-2 L2A” parameter.

  • Systematic: indicates that this processor should be executed in systematic mode, meaning that the processor will generate monthly crop type map images between a given time period. In case the user selects “Systematic”, this processor enables some additional parameters identifying the input data to be processed which are detailed below.

14.3.2. Sentinel-2 L2A

  • Drag and drop a data basket filled with the appropriate Sentinel-2 L2A files into the field. Refer to the FS-TEP User Manual for further details on how to search and select Sentinel-2 L2A files and how to add these files to a data basket.

Note that this parameter is only applicable in case the “Processor running mode” field is set to “Standard”.

14.3.3. In-situ data

The shapefile containing the in-situ crop information. If not provided, the default 2015 ESA-CCI landcover map is used. The shapefile should be a zip-file containing all shapefile components (.shp, .shx, .prj, .dbf).

The shapefile contains samples of the main crops as well as non-crop areas spread throughout the considered site. The in-situ data should be gathered in a single zipped shapefile, projected in the WGS 84/UTM grid system, containing both cropland and no-cropland information.

The format of the shapefile attribute table is presented in:

Variable Name

Des cription

Var. Type

Var. Length

Var. values / comments

Null accepted

ID

Feature ID

Numeric

6

000000 - 999999

N

CROP

Binary Class

Numeric

1

0 if non- cropland

1 if cropland

N

LC

Land Cover

Text

70

Name of the crop type or the non-crop type class

N

CODE

Code of the class

Numeric (Long integer)

8

Cfr. JECAM Gu idelines

N

IR RIGATION

Inf ormation about ir rigation of the field

Numeric

1

Only if known:

0 = not c oncerned or inf ormation not a vailable

1 = i rrigated

2 = not i rrigated

Y

Refer to Sen2AGRI Software User Manual for further details on the specifications of the in-situ data shapefile.

14.3.4. Label

A freeform text to be used as job description for identification of this job. Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs).

14.3.5. Product start date

The date at which the systematic processing should start.

  • Select the desired date from the date widget that pops up when clicking the field. Note that the date can also filled in manually by entering the values in the format DD-MM-YYYY.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

14.3.6. Product end date

The date at which the systematic processing should end. Note that the “Product end date” is optional and is only available in case the “Processor running mode” field is set to “Systematic”. If not provided, the systematic processing will continue generating crop type maps forever (i.e. until all user TEP-coins have been consumed).

14.3.7. Collection

The collection identifier identifying the type of data for which a crop type map should be generated. Should be set to “Sentinel-2”.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

14.3.8. Processing level

The processing level identifying the type of input Sentinel-2 data. Should be set to “L2A”.

  • Select the appropriate “L2A” processing level from the dropdown list.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic” and in case the “Collection” field is set to “Sentinel-2”.

14.3.9. AOI

The AOI defining the area for which a cloud-free composite should be generated. As detailed in the FS-TEP User Manual, the AOI can be specified in two ways:

  1. By manually entering a polygon in the OGC WKT (Well-Known Text) format in the “AOI” text field. For example, the WKT polygon “POLYGON((1 2,1 4,3 4,3 2,1 2))” indicates a rectangle whose four corners are indicated by (1,2), (1,4), (3,4), and (3,2). Note that a polygon must be closed, so the first and last points in the provided WKT must match. Refer to here for further details on the WKT format.

  2. By drawing or importing (from a shapefile) an AOI using one of the activated AOI buttons, as shown in the figure below. Refer to the FS-TEP User Manual for further details.

_images/image28.png

For example, the figure below shows a rectangular AOI covering the Belgium and Luxemburg area.

_images/image29.png

14.3.10. Cloud coverage

The maximum allowed cloud cover percentage. The default value is 10 meaning that only images with max. 10% cover will be used in this processor.

Note that this field is only available in case the “Processor running mode” field is set to “Systematic”.

14.4. Run the job

  • Once all parameters have been properly filled in, click on the button “Run Job” image19 and see the running job in the “JOBS” tab of the data panel.

  • Refer to the FS-TEP User Manual for further details on how to access the job details (i.e. input, output and logs)

14.5. Service outputs

The primary output is a GeoTIFF of the crop type map which is a map the main crop type groups at 10 meters’ spatial resolution. The crop type map is provided in three versions:

  • A single-band GeoTIFF for use and visualisation on the Analyst viewer

  • The crop type map within the product format as defined by the Sen2Agri service. This contains a zipped folder with various subfolders containing additional data and information such as auxiliary files and legacy data. Further details are available on the Sen2Agri website

  • A multiband RGB image which has an applied colour scheme for easier interpretation on the Analyst viewer.

The details of the primary output (the L4B file is provided below).

Correspondent file

Crop Type Map

Information type

Classified images of crop type

Raster format

GeoTIFF

Resolution

10m

Projection Type

WGS84 Transverse Mercator

Bit depth

16-bit signed integer (single band)

Processing level

Classified Image (L4B)

Naming convention

S2Agri_L4B_[Input_Sentinel-2_L2A].tif

The image below shows a Crop Type map of central Netherlands from April 2020, displayed in the Analyst viewer.

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Further analysis can be undertaken in one of the GUI applications, such as QGIS, SNAP or MONTEVERDI.

15. Exploring the FS-TEP data catalog

Down the left hand side is a menu containing amongst others the “SearchSearch button. Clicking on it brings up a panel allowing users to search for data. This can be satellite data, reference data or products already processed on the FS-TEP.

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As shown in the figure above, this is divided into four groups:

  • Satellite data, containing the various satellite data available

    to all users

  • Reference data, containing reference and in situ data uploaded by

    users of the platform

  • FS-TEP products, containing outputs of services already run on

    the FS-TEP platform.

  • Copernicus Land Monitoring Service, containing all the

    collections available in the Copernicus Land Monitoring Service, to which the FS-TEP is connected.

15.1. Searching for satellite data products

15.1.1. Select the satellite data catalog

  • Click the “Satellite” icon at the left hand side of the panel.

    This brings up a “Search” panel allowing users to search for data allowing to fill in the parameters.

15.1.2. Fill the parameters

15.1.2.1. Collection

The collection identifier identifying the type of data to search for. Can be one of following values:

  • Sentinel-1

  • Sentinel-2

  • Sentinel-3

  • Sentinel-5P

  • Landsat

  • Envisat MERIS L1B

  • SMOS

15.1.2.2. Processing level

The processing level identifying the type of Sentinel-2 data to search for. Can be either L1C or L2A. Note that this parameter is only available in case the “Collection” parameter has been set to “Sentinel-2”.

15.1.2.3. Product date

Clicking the “Product date” checkbox allows to specify a time period (i.e. begin and end acquisition time) to search for. Selecting the checkbox allows the user to specify a begin and end acquisition time to search for. By default a three month time interval (i.e. current day minus 3 months) is set.

_images/image45.png
  • Select the desired date from the date widgets that pops up when clicking the field. Note that the dates can also filled in manually by entering the values in the format DD-MM-YYYY.

15.1.2.4. AOI

The AOI defining the area to search for. As detailed in the FS-TEP User Manual, the AOI can be specified in two ways:

  1. By manually entering a polygon in the OGC WKT (Well-Known Text) format in the “AOI” text field. For example, the WKT polygon “POLYGON((1 2,1 4,3 4,3 2,1 2))” indicates a rectangle whose four corners are indicated by (1,2), (1,4), (3,4), and (3,2). Note that a polygon must be closed, so the first and last points in the provided WKT must match. Refer to here for further details on the WKT format.

  2. By drawing or importing an AOI using one of the activated AOI buttons, as shown in the figure below. Refer to the FS-TEP User Manual for further details.

_images/image28.png

For example, the figure below shows a rectangular AOI covering the Belgium and Luxemburg area.

_images/image29.png
15.1.2.5. Cloud coverage

The maximum allowed cloud cover percentage. The default value is 10 meaning that only images with max. 10% cover will be searched for.

15.1.2.6. Polarization

The polarization mode. Only available in case the “Collection” has been set to “Sentinel-1”.

Refer to here for further details on the polarimetry of Sentinel-1.

15.1.2.7. Sensor mode

The acquisition mode. Only available in case the “Collection” has been set to “Sentinel-1”.

Refer to here for further details on the acquisition modes of Sentinel-1.

15.1.2.8. Product type

The product type. Only available in case the “Collection” has been set to “Sentinel-1”.

Refer to here for further details on the acquisition modes of Sentinel-1.

15.1.2.9. Orbit direction

The orbit direction, can be “ASCENDING” or “DESCENDING”. Only available in case the “Collection” has been set to “Sentinel-1”.

15.1.2.10. Identifier

A string identifying the product. This parameter is optional.

15.1.3. Discover and visualize the data

An example search for Sentinel-2 data is shown in the figure below:

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Once the criteria have been set, clicking on the Search-Icon symbol will start the search. The results will be shown in the data panel as shown below. Selecting a product in the list will highlight its footprint in the geo-browser.

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The outputs of a search can be used directly as inputs to a service, or else they can be added to a data basket.

Refer to the FS-TEP User Manual for further details.

15.2. Searching for Copernicus Land Monitoring Service

15.2.1. Select the satellite data catalog

  • Click the “Copernicus Land Monitoring Service” icon at the left

    hand side of the panel. This brings up a “Search” panel allowing users to search for data allowing to fill in the parameters.

15.2.2. Fill the parameters

15.2.2.1. Collection

The collection identifier identifying the type of data to search for. Refer to here for a list of available products of the Copernicus Global Land Monitoring service.

15.2.2.2. Product date

Clicking the “Product date” checkbox allows to specify a time period (i.e. begin and end acquisition time) to search for. Selecting the checkbox allows the user to specify a begin and end acquisition time to search for. By default a three month time interval (i.e. current day minus 3 months) is set.

_images/image45.png
  • Select the desired date from the date widgets that pops up when clicking the field. Note that the dates can also filled in manually by entering the values in the format DD-MM-YYYY.

15.2.2.3. AOI

The AOI defining the area to search for. As detailed in the FS-TEP User Manual, the AOI can be specified in two ways:

  1. By manually entering a polygon in the OGC WKT (Well-Known Text) format in the “AOI” text field. For example, the WKT polygon “POLYGON((1 2,1 4,3 4,3 2,1 2))” indicates a rectangle whose four corners are indicated by (1,2), (1,4), (3,4), and (3,2). Note that a polygon must be closed, so the first and last points in the provided WKT must match. Refer to here for further details on the WKT format.

  2. By drawing or importing an AOI using one of the activated AOI buttons, as shown in the figure below. Refer to the FS-TEP User Manual for further details.

_images/image28.png

For example, the figure below shows a rectangular AOI covering the Belgium and Luxemburg area.

_images/image29.png
15.2.2.4. Identifier

A string identifying the product. This parameter is optional.

15.2.3. Discover and visualize the data

Once the criteria have been set, clicking on the Search-Icon symbol will start the search. The results will be shown in the data panel as shown below. Selecting a product in the list will highlight its footprint in the geo-browser.

_images/image49.png

The outputs of a search can be used directly as inputs to a service, or else they can be added to a data basket.

Refer to the FS-TEP User Manual for further details.

15.3. Searching for reference and in-situ data

15.3.1. Select the reference and in-situ data catalog

  • Click the “Reference” icon at the left hand side of the panel.

    This brings up a “Search” panel allowing users to search for data allowing to fill in the parameters.

15.3.2. Fill the parameters

15.3.2.1. Collection

The collection identifier identifying the type of data to search for.

15.3.2.2. Product date

Clicking the “Product date” checkbox allows to specify a time period (i.e. begin and end acquisition time) to search for. Selecting the checkbox allows the user to specify a begin and end acquisition time to search for. By default a three month time interval (i.e. current day minus 3 months) is set.

_images/image45.png
  • Select the desired date from the date widgets that pops up when clicking the field. Note that the dates can also filled in manually by entering the values in the format DD-MM-YYYY.

15.3.2.3. Publication date

Indicates the the date when this data was uploaded to the FS-TEP platform.

Clicking the “Publication date” checkbox allows to specify a time period (i.e. begin and end acquisition time) to search for. Selecting the checkbox allows the user to specify a begin and end acquisition time to search for. By default a three month time interval (i.e. current day minus 3 months) is set.

_images/image50.png

Select the desired date from the date widgets that pops up when clicking the field. Note that the dates can also filled in manually by entering the values in the format DD-MM-YYYY.

15.3.2.4. Owner

The owner of the reference data. Note that this parameter is optional.

15.3.2.5. AOI

The AOI defining the area to search for. As detailed in the FS-TEP User Manual, the AOI can be specified in two ways:

  1. By manually entering a polygon in the OGC WKT (Well-Known Text) format in the “AOI” text field. For example, the WKT polygon “POLYGON((1 2,1 4,3 4,3 2,1 2))” indicates a rectangle whose four corners are indicated by (1,2), (1,4), (3,4), and (3,2). Note that a polygon must be closed, so the first and last points in the provided WKT must match. Refer to here for further details on the WKT format.

  2. By drawing or importing an AOI using one of the activated AOI buttons, as shown in the figure below. Refer to the FS-TEP User Manual for further details.

_images/image28.png

For example, the figure below shows a rectangular AOI covering the Belgium and Luxemburg area.

_images/image29.png
15.3.2.6. Identifier

A string identifying the product. This parameter is optional.

15.3.3. Adding new in-situ and reference data

Refer to the FS-TEP User Manual for further details how to add new in-situ and reference data to the FS-TEP platform.

15.3.4. Discover and visualize the data

Once the criteria have been set, clicking on the Search-Icon symbol will start the search. The results will be shown in the data panel as shown below. Selecting a product in the list will highlight its footprint in the geo-browser.

_images/image51.png

The outputs of a search can be used directly as inputs to a service, or else they can be added to a data basket.

Refer to the FS-TEP User Manual for further details.