SEN3R - Sentinel 3 Reflectance Retrieval over Rivers

SEN3R is a stand-alone command-line utility inspired by MOD3R and made to simplify the pipeline of image processing over ESA's Sentinel-3 mission.

⚠️ GDAL is a requirement for the installation, therefore, usage of a conda environment (Anaconda.org) is strongly recommended. Unless you know what you are doing (-:

Installation

Create a Conda environment (python versions above 3.7 were not tested but they should also be compatible):

conda create --name sen3r python=3.7

Activate your conda env:

conda activate sen3r

Install GDAL before installing requirements.txt to avoid dependecy error with pyshp:

conda install -c conda-forge gdal

Install the requirements:

python -m pip install -r requirements.txt

We recommend you to run the internal setup (more up-to-date) but you can also use PyPI pip install sen3r:

python setup.py install 

Do a quick test:

sen3r -h 

If all runs well, you should see:

(sen3r) D:\user_path\sen3r>sen3r -h
usage: sen3r [-h] [-i INPUT] [-o OUT] [-r ROI] [-p PRODUCT] [-c CAMS]
             [-k CLUSTER] [-s] [-v]

SEN3R (Sentinel-3 Reflectance Retrieval over Rivers) enables extraction of
reflectance time series from Sentinel-3 L2 WFR images over water bodies.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        The products input folder. Required.
  -o OUT, --out OUT     Output directory. Required.
  -r ROI, --roi ROI     Region of interest (SHP, KML or GeoJSON). Required
  -p PRODUCT, --product PRODUCT
                        Currently only WFR is available.
  -c CAMS, --cams CAMS  Path to search for auxiliary CAMS file. Optional.
  -min IRMIN, --irmin IRMIN
                        Default bottom dropping threshold for IR. Optional.
  -max IRMAX, --irmax IRMAX
                        Default upper dropping threshold for IR. Optional.
  -k CLUSTER, --cluster CLUSTER
                        Which method to use for clustering. Optional.
  -s, --single          Single mode: run SEN3R over only one image instead of
                        a whole directory. Optional.
  -v, --version         Displays current package version.

Windows users: For OS compatibility reasons the supported vector formats for -r are .json and .geojson. But if you are under Linux there are implementations in the code to also support .shp, .kml and .kmz. Just check for them inside commons.py > Utils > roi2vertex.

Usage

For a folder of WFR files:

sen3r -i "C:\PATH\TO\L2_WFR_FILES" -o "C:\sen3r_out" -r "C:\path\to\your_vector.json"

For a single WFR file:

sen3r -s -i "C:\PATH\TO\L2_WFR_IMG" -o "C:\sen3r_out" -r "C:\path\to\your_vector.json"

Citing

While the official paper is not published you can use the Zenodo citation:

Franca, David, Martinez, Jean-Michel, & Cordeiro, Mauricio. (2021). SEN3R - Sentinel 3 Reflectance Retrieval over Rivers (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.5710870

or the BibTex:

@software{franca_david_2021_5710870,
  author       = {Franca, David and Martinez, Jean-Michel and
                  Cordeiro, Mauricio},
  title        = {{SEN3R - Sentinel 3 Reflectance Retrieval over 
                   Rivers}},
  month        = nov,
  year         = 2021,
  publisher    = {Zenodo},
  version      = {v1.0.0},
  doi          = {10.5281/zenodo.5710870},
  url          = {https://doi.org/10.5281/zenodo.5710870}
}