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Extraction of reflectance from Sentinel-2 data

The vector file created in the previous step is used to extract reflectance from Sentinel-2 data.

Running this step using a script

Add the following instructions to your script to extract reflectance corresponding to datapoints saved in preprocessed_obs_path from Sentinel-2 time series. First make sure that the directory defined in the export_path variable exists.

from fordead.validation.extract_reflectance import extract_reflectance

extracted_reflectance_path = output_dir / "extracted_reflectance.csv"

    obs_path = preprocessed_obs_path,
    sentinel_dir = sentinel_dir, 
    export_path = extracted_reflectance_path,
    name_column = "id")
Running this step from the command invite

This step can also be ran from the command prompt.

fordead extract_reflectance --obs_path <MyWorkingDirectory>/vector/preprocessed_obs_tuto.shp --sentinel_dir <MyWorkingDirectory>/sentinel_data/validation_tutorial/sentinel_data/ --export_path <MyWorkingDirectory>/extracted_reflectance.csv --name_column id

The command fordead extract_reflectance -h will print the help information of this step. For example, to use it with the same parameters, the following command can be used:

The csv written in export_path includes the following attributes corresponding to the different pixels :

  • epsg:
  • area_name: Sentinel-2 tile ID when available
  • id:
  • id_pixel:
  • Date: date of acquisition
  • B2-B11: reflectance extracted from Sentinel-2 data for the corresponding pixel [sort by increasing wavelength: B2-B11, not B11-B8A]
  • Mask:


The file will not be overwritten if the process is re-run with the same data. New Sentinel-2 acquisitions or ground observations will be appended to the file if added to the input data.

The update procedure can be tested with additional Sentinel-2 data located in /validation_tutorial/sentinel_data_update: copy and paste this additional data to the sentinel_data directory and run this step again.