S3_proc.sh

#!/usr/bin/env bash

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

function print_usage() {
	echo ""
	echo "./S3_proc.sh -i inpath -o outpath -X file.xml [-h -v -t]"
	echo "  -i: Path to folder containing S3?_*_EFR_*_002.SEN3 (unzipped S3 EFR) files"
	echo "  -o: Path where to store ouput"
	echo "  -X: Specify XML file"
	echo "  -v: Print verbose messages during processing"
	echo "  -t: Print timing messages during processing"
	echo "  -h: print this help"
	echo ""
}

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; }

trap ctrl_c INT # trap ctrl-c and call ctrl_c()
ctrl_c() {
	log_err "CTRL-C caught"
	log_err "Removing gpt progress..."
	[[ -d ${dest} ]] && (
		cd ${dest}
		rm *_x.tif
	)
}

debug() { if [[ ${debug:-} == 1 ]]; then
	log_warn "debug:"
	echo $@
fi; }

readonly t_0=$(date +%s)
declare t_last=$(date +%s)
timing() {
	if [[ ${timing:-} ]]; then
		log_info "Timing..."
		local t_now=$(date +%s)
		echo "    Time since start:" $((${t_now} - ${t_0}))"s"
		echo "    Time since last:" $((${t_now} - ${t_last}))"s"
		t_last=$(date +%s)
	fi
}

while [[ $# -gt 0 ]]; do
	key="$1"
	case $key in
	-h | --help)
		print_usage
		exit 1
		;;
	-i)
		inpath="$2"
		shift # past argument
		shift # past value
		;;
	-o)
		outpath="$2"
		shift
		shift
		;;
	-X)
		xml="$2"
		shift
		shift
		;;
	-v | --verbose)
		verbose=1
		set -o xtrace
		shift
		;;
	-t)
		timing=1
		shift
		;;
	*)                  # unknown option
		positional+=("$1") # save it in an array for later. Pass on to dsget.sh
		shift
		;;
	esac
done

if [[ -z ${inpath:-} ]]; then
	log_err "-i not set"
	print_usage
	exit 1
fi
if [[ -z ${outpath:-} ]]; then
	log_err "-o not set"
	print_usage
	exit 1
fi
if [[ -z ${xml:-} ]]; then
	log_err "-X not set"
	print_usage
	exit 1
fi

for folder in $(ls ${inpath} | grep S3._OL_1_EFR); do
	olci_folder=$(basename "${folder}")
	olci_dts=$(echo "${olci_folder}" | rev | cut -d_ -f11 | rev)
	dest=${outpath}/${olci_dts}

	# skipping if scene already processed
	if [[ -d "${dest}" ]]; then
		if [[ -f "${dest}/r_TOA_01.tif" ]]; then
			log_warn "${dest} already exists, scene skipped"
			continue
		fi
	fi

	# find nearest SLSTR folder. Timestamp is same or next minute.
	olci_date=${olci_dts:0:8}
	olci_time=${olci_dts:9:4}
	olci_time1=$(date -d "${olci_date} ${olci_time} + 1 minute" "+%H%M")
	olci_time2=$(date -d "${olci_date} ${olci_time} - 1 minute" "+%H%M")
	fileroot="S3._SL_1_RBT____........T" # grep for acquisition not ingest time
	# pick first nearby slstr
	slstr_folder=$(ls ${inpath} | grep -E "${fileroot}${olci_time}|${fileroot}${olci_time1}|${fileroot}${olci_time2}" | head -n1 || true)
	if [[ -z ${slstr_folder} ]]; then
		log_err "No nearby SLSTR scene found"
		continue
	fi
	log_info "${olci_folder}"
	log_info "${slstr_folder}"

	log_info "Generating ${dest}"
	mkdir -p "${dest}"

	log_info "gpt: Start"
	timing
	[[ $(which gpt) ]] || (
		log_err "gpt not found"
		exit 1
	)
	LD_LIBRARY_PATH=. gpt ${xml} \
		-POLCIsource="${inpath}/${olci_folder}" \
		-PSLSTRsource="${inpath}/${slstr_folder}" \
		-PtargetFolder="${dest}" \
		-Dsnap.log.level=ERROR \
		-e || (
		log_err "gpt error"
		exit 1
	)
	# -Ds3tbx.reader.olci.pixelGeoCoding=true \
	# -Ds3tbx.reader.slstrl1b.pixelGeoCodings=true \

	log_info "gpt: Finished"

	# # Discard out bad folders (defined as size > 10 GB)
	# (cd ${dest}/../; du -sm * | awk '$1 > 10000 {print $2}' | xargs rm -fr)
	if [[ ! -d "${dest}" ]]; then continue; fi # if we removed the directory, break out of the loop

	resize=1000
	log_info "Resampling to ${resize} m resolution..."
	log_info "Aligning SLSTR to OLCI..."
	grass -c ./mask.tif ${dest}/G_align --exec ./G_align.sh ${dest} ./mask.tif ${resize}
	(cd ${dest} && rm *_x.tif)
	(cd ${dest} && rm -fR G_align)
done

log_info "Finished: ${outpath}"
timing