1. Setup instructions

1.1. Requirements

This toolset is written for use in Linux.

You will need access to a PC or server with at least:

1.2. Installing Anaconda Python

These tools are written in Python. We recommend the Anaconda distribution of Python, which contains all the modules necessary to run these scripts.

To install Anaconda Python, open a terminal window, change directory to the location you’d like to install Anaconda Python, and run the following commands:

wget https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh
chmod +x Anaconda3-2019.03-Linux-x86_64.sh

If this has functioned, on executing python in a terminal window, you should ssee the following:

Python 2.7.14 |Anaconda, Inc.| (default, Dec  7 2017, 17:05:42)
[GCC 7.2.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.

1.3. Setting up your Anaconda environment


The Anaconda environment required for sen1mosaic and sen2mosaic is identical. If you already have a sen1mosaic environment set up, it can be used in place of a new environment.

To ensure you are working with the appropriate version of Python as well as the correct modules, we recommend that you create an Anaconda virtual environment set up for running sen2mosaic. This is done by running the following commands in your terminal or the Anaconda prompt (recommended procedure):

conda create -n sen2mosaic -c conda-forge python=3.7 scipy pandas psutil scikit-image gdal opencv pyshp

Activate the sen2mosaic environment whenever opening a new terminal window by running this command:

conda activate sen2mosaic

1.4. Installing sen2cor

sen2cor is an ESA program to perform atmospheric correction and cloud masking of Sentinel-2 level 1C images. It generates a new file containing bottom of atmosphere reflectance values and a cloud mask.

For further details and up-to-date installation instructions, see the sen2cor website.

At the time of writing, sen2cor can be installed using the following commands. sen2cor must be installed after Anaconda Python. Open a terminal window, change directory to the location you’d like sen2cor to be installed, and run the following commands:

wget http://step.esa.int/thirdparties/sen2cor/2.8.0/Sen2Cor-02.08.00-Linux64.run
chmod +x Sen2Cor-02.08.00-Linux64.run

Once complete, you need to reference this software in your .bashrc file as follows:

echo "source ~/Sen2Cor-02.08.00-Linux64/L2A_Bashrc" >> ~/.bashrc
exec -l $SHELL

To test the installation, type L2A_Process --help in a terminal window to show running instructions. You should see something that looks like the following:

usage: L2A_Process.py [-h] [--mode MODE] [--resolution {10,20,60}]
                    [--datastrip DATASTRIP] [--tile TILE]
                    [--output_dir OUTPUT_DIR] [--work_dir WORK_DIR]
                    [--img_database_dir IMG_DATABASE_DIR]
                    [--res_database_dir RES_DATABASE_DIR]
                    [--processing_centre PROCESSING_CENTRE]
                    [--archiving_centre ARCHIVING_CENTRE]
                    [--processing_baseline PROCESSING_BASELINE] [--raw]
                    [--tif] [--sc_only] [--cr_only] [--debug]
                    [--GIP_L2A GIP_L2A] [--GIP_L2A_SC GIP_L2A_SC]
                    [--GIP_L2A_AC GIP_L2A_AC] [--GIP_L2A_PB GIP_L2A_PB]

Sentinel-2 Level 2A Processor (Sen2Cor). Version: 2.8.0, created: 2019.02.20,
supporting Level-1C product version 14.2 - 14.5.

positional arguments:
input_dir             Directory of Level-1C input

optional arguments:
-h, --help            show this help message and exit
--mode MODE           Mode: generate_datastrip, process_tile
--resolution {10,20,60}
                        Target resolution, can be 10, 20 or 60m. If omitted,
                        only 20 and 10m resolutions will be processed
--datastrip DATASTRIP
                        Datastrip folder
--tile TILE           Tile folder
--output_dir OUTPUT_DIR
                        Output directory
--work_dir WORK_DIR   Work directory
--img_database_dir IMG_DATABASE_DIR
                        Database directory for L1C input images
--res_database_dir RES_DATABASE_DIR
                        Database directory for results and temporary products
--processing_centre PROCESSING_CENTRE
                        Processing centre as regex: ^[A-Z_]{4}$, e.g "SGS_"
--archiving_centre ARCHIVING_CENTRE
                        Archiving centre as regex: ^[A-Z_]{4}$, e.g. "SGS_"
--processing_baseline PROCESSING_BASELINE
                        Processing baseline in the format: "dd.dd", where
--raw                 Export raw images in rawl format with ENVI hdr
--tif                 Export raw images in TIFF format instead of JPEG-2000
--sc_only             Performs only the scene classification at 60 or 20m
--cr_only             Performs only the creation of the L2A product tree, no
--debug               Performs in debug mode
--GIP_L2A GIP_L2A     Select the user GIPP
                        Select the scene classification GIPP
                        Select the atmospheric correction GIPP
                        Select the processing baseline GIPP

1.5. Installing sentinelsat

Sentinelsat is the toolset used to access data from the Sentinel-2 archive at the Copernicus Open Access Data Hub.

Up-to-date installation instructions can be found here.

At the time of writing, the installation process is as follows:

pip install sentinelsat

1.6. Installing sen2mosaic

sen2mosaic can be downloaded to a machine from its repository . To do this, open a terminal window and input:

git clone https://github.com/smfm-project/sen2mosaic.git

To install sen2mosaic, navigate to the sen2mosaic directory and run the following within your sen2mosaic environment.

python setup.py install

To avoid having to reference the full path of the Python scripts in sen2mosaic, it’s a good idea add the following line to your .bashrc file:

echo "alias s2m='_s2m() { python ~/sen2mosaic/cli/\"\$1\".py \$(shift; echo \"\$@\") ;}; _s2m'" >> ~/.bashrc

1.7. Is there a Dockerfile?

Coming soon!

1.8. Where do I get help?

For help installing sen2cor, it’s best to refer to the ESA STEP forum. For assistance in setting up and using sen2mosaic, email sam.bowers@ed.ac.uk.