S3_wrapper.sh

#!/usr/bin/env bash

# Wrapper for running SICE pipeline

set -o errexit
set -o nounset
set -o pipefail
set -x

red='\033[0;31m'
orange='\033[0;33m'
green='\033[0;32m'
nc='\033[0m' # No Color
log_info() { echo -e "${green}[$(date --iso-8601=seconds)] [INFO] ${*}${nc}"; }
log_warn() { echo -e "${orange}[$(date --iso-8601=seconds)] [WARN] ${*}${nc}"; }
log_err() { echo -e "${red}[$(date --iso-8601=seconds)] [ERR] ${*}${nc}" 1>&2; }

# CREODIAS
SEN3_local=/eodata/Sentinel-3
SEN3_source=/sice-data/SICE/S3
proc_root=/sice-data/SICE/proc
mosaic_root=/sice-data/SICE/mosaic

# Scihub credentials (from local auth.txt in SICE folder)
username=$(sed -n '1p' auth.txt)
password=$(sed -n '2p' auth.txt)

# Geographic area
area=Greenland

# Slope correction
slopey=false

# Fast processing
fast=true

# Error reporting
error=false

if [ "$fast" = true ]; then
	# so far the only speed up done is to not extract all bands
	xml_file=S3_fast.xml
else
	xml_file=S3.xml
fi

LD_LIBRARY_PATH=. # SNAP requirement

for year in 2020; do
	for doy in $(seq -w 91 276); do

		### DEBUG
		# for year in 2018; do
		#   for doy in 227; do  # 2017-08-15=227

		date=$(date -d "${year}-01-01 +$((10#${doy} - 1)) days" "+%Y-%m-%d")

		if [[ -d "${mosaic_root}/${date}" ]] && [[ -e "${mosaic_root}/${date}/conc.tif" ]]; then
			log_warn "${mosaic_root}/${date} already exists, date skipped"
			continue
		fi

		### Fetch one day of OLCI & SLSTR scenes over Greenland
		## Use local files (PTEP, DIAS, etc.)
		./dsget_wrapper.sh -d "${date}" -l ${SEN3_local} -o ${SEN3_source}/${year}/"${date}" \
			-f ${area} -u "${username}" -p "${password}" || error=true
		## Download files
		# ./dsget_wrapper.sh -d ${date} -o ${SEN3_source}/${year}/${date} \
		# 			 -f Svalbard -u "${username}" -p "${password}"

		# SNAP: Reproject, calculate reflectance, extract bands, etc.
		./S3_proc.sh -i ${SEN3_source}/${year}/"${date}" -o ${proc_root}/"${date}" -X ${xml_file} -t || error=true

		# Run the Simple Cloud Detection Algorithm (SCDA)
		python ./SCDA.py ${proc_root}/"${date}" || error=true

		# Mosaic
		./dm.sh "${date}" ${proc_root}/"${date}" ${mosaic_root} || error=true

		if [ "${slopey}" = true ]; then
			# Run the slopey correction
			python ./get_ITOAR.py ${mosaic_root}/"${date}"/ "$(pwd)"/ArcticDEM/ || error=true
		fi

		# SICE
		python ./sice.py ${mosaic_root}/"${date}" || error=true

		if [ "${error}" = true ]; then
			echo "Processing of ${date} failed, please check logs."
		fi
	done
done