05_execute_sen2cor.sh

#!/usr/bin/env bash


#
#	script to run Sen2Cor (Sentinel-2 atmospheric correction)
#	on each L1C realization drawn from the radiometric uncertainty
#	modelling approach.
#	The resulting L2A data is stored in the same directory as the
#	input L1C datasets, i.e., in the single scenario folders.
#
#	NOTE: To speed things up, it might be useful to run several
#	instances of Sen2Cor in parallel. In this case, the variable
#	$unc_scenarios (L#28) might have when the scenarios are located
#	at different locations on the file system.
#
#	Requires Sen2Cor (atmospheric correction and scene classification software).
#	In our case, version 2.09.00 is used.
#   Make sure that the L2A_Bashrc file can be found and sourced! We placed it
#	in the ../bin directory but other locations (usually in your home directory) are
#	possible as well. In this case replace the path in line 29 of this script.
#

# USER INPUT
# define directory where Sen2Cor is installed to
sen2cor_install_dir="/home/graflu/Downloads/Sen2Cor-02.09.00-Linux64"
source "$sen2cor_install_dir"/L2A_Bashrc

# define directory where the L1C realizations are located
unc_scenarios="../../S2A_MSIL1C_RUT-Scenarios"

cd "$unc_scenarios" 

IFS=""
# find all sub-directories (each scene is a sub-directory without the .SAFE of the original dataset)
mapfile -t scenario_list < <( find ${unc_scenarios} -maxdepth 1 -mindepth 1 -type d -printf '%f\n' )

# loop over single scenes
for unc_dir in ${scenario_list[@]}; do
	# check if directory starts with S2
	if [[ "$unc_dir" == S2* ]]
	then

		# find the scenarios of each scene (each scenario run is a sub-directory labelled starting from
		# 1, 2, ..., n_scenarios)
		mapfile -t dirlist < <( find ${unc_scenarios}/${unc_dir} -maxdepth 2 -mindepth 2 -type d -printf '%f\n' )

		# loop over scenarios
		counter=1
		for dir in ${dirlist[@]}; do
			if [[ "$dir" == S2*_MSIL1C_* ]]
			then
			    scenario="${unc_dir}"/"${counter}"/"${dir}"
			    output_dir="${unc_dir}"/"${counter}"
			    counter=$((counter+1))
			    # call Sen2Cor (L2A_Process must be located in $PATH or provide full path to executable)
			    L2A_process --resolution 10 --output_dir "${output_dir}" "${scenario}"
			    echo Processed "${scenario}"
			fi
		done
	fi
done