sentinel_slc_renamer

#!/bin/bash
# Joaquín Escayo 2019 (j.escayo@csic.es)
# V 1.0 - Initial version, lot to re-do but works as intended. Not fool-proof, be careful with the inputs. (22/11/2017)
# V 1.1 - Some bugfixes. Added the option to remove VH polarization. (1/3/2018)
# V 1.2 - Big update: inteligent ZIP extraction keeping only selected polarizations. (27/10/2019)
# V 1.3 - Check for existing folders. (28/10/2019)
# V 1.4 - Fixed a bug that prevents to extract correctly the zip and saves the unzip log to the image folder (29/10/2019)


# TODO:
# A proper report file with details of every file decompressed extracted from manifest.safe (like geometry, relative orbit, etc).
# Check correct ZIP extraction (should be easy)

#########################
# SOME USEFUL FUNCTIONS #
#########################

containsElement () { for e in "${@:2}"; do [[ "$e" = "$1" ]] && return 0; done; return 1;} # Function to check if an element is part of an array
sentinel_unzip () {                                                                # Function to decompress Sentinel Image, uses 2 arguments (input file and output folder)
if [[ -z $1 ]] || [[ -z $2 ]]; then echo "You must specify file and output folder"; exit; fi
unzip -d $2 $1 &> $2/unzip.log                                                          
mv $2/*SAFE/* $2/
}
sentinel_unzip_pol () {                                                                # Function to decompress Sentinel Image, uses 3 arguments (input file, output folder and pol channel in that order)
if [[ -z $1 ]] || [[ -z $2 ]] || [[ -z $3 ]]; then echo "You must specify file, output folder and pol channel"; exit; fi
unzip -d $2 $1 S1*/support/* S1*/preview/* S1*/measurement/*$3* S1*/annotation/*$3* S1*/S1* S1*/manifest.safe &> $2/unzip.log
mv $2/*SAFE/* $2/
}
lowercase () {
echo $1 | tr '[:upper:]' '[:lower:]'
}


#########################
# DIRECTORIES CHECK     #
#########################
# Check of the input variable (directory)
if [ -z "$1" ]; then
	echo "############# ERROR ###################################"	
	echo "No SLC directory used as input"
	echo "Use slc_image_renamer.sh slc_directory"
	echo "If you want to use current directory as input:"
	echo "slc_image_renamer.sh ."
	echo "Do not use special characters in the route (as spaces)"
	echo "#######################################################"	
	exit
elif [ $1 == "." ]; then
    DIR=$(pwd)
#checkign for absolute or relative path
elif [[ $(expr substr $1 1 1) == "/" ]]; then # absolute path as input
    DIR=$1
else # relative path
    DIR=$(pwd)/$1
fi

############################
# Variables initialization #
############################
totalno=0
totalsi=0
REPORT=$DIR/files
rm $REPORT &> /dev/null
MSLICES=()                                                                        # Array to index multiple slices dates

touch $REPORT
echo "Generating list of files"
for i in $(find $DIR \( -name "S1A_*.zip" -or -name "S1B_*.zip" \)); do
SAT=$(basename $i | cut -d'_' -f1)
MODE=$(basename $i | cut -d'_' -f2)
TYPE=$(basename $i | cut -d'_' -f3)
POL=$(basename $i | cut -d'_' -f5)
DATE_TIME=$(basename $i | cut -d'_' -f6)
DATE=$(basename $i | cut -d'_' -f6 | cut -c1-8)
TIME=$(basename $i | cut -d'_' -f6 | cut -c10-15)
ID=$(basename $i | cut -d'_' -f10 | cut -d'.' -f1)
echo "$i,$(basename $i),$SAT,$MODE,$TYPE,$POL,$DATE_TIME,$DATE,$TIME,$ID" >> $REPORT
done
NIMAGES=$(cat $REPORT | wc -l)
if [ $(cat $REPORT | wc -l) == 0 ]; then                                         # Check that at least one image is found
    echo "No images found, please make sure that the"
    echo "directory contains at least one SLC image"
    exit
fi

sort --field-separator=',' --key=6 $REPORT -o $REPORT                             # sort file list by time and date and save in the same file
echo "The following files has been found:"
awk -F',' '{print $2}' $REPORT
#sed -i '1s/^/Full Path,File name,Satellite,Acquisition Mode,Processing level,Polarimetry,Date,Time,ID\n/' $REPORT
echo "Found $NIMAGES Sentinel-1 files in the input directory"

# Checking Polarisation on detected files
POL_TYPES=$(cut -d , -f6 $REPORT | sort | uniq)
POL_TYPES_NUM=$(cut -d , -f6 $REPORT | sort | uniq | wc -l)

# Different cases to address
if [ $POL_TYPES_NUM == "1" ]; then
	# Most common cases
	echo "One polarisation channel found in all images"
	case $POL_TYPES in
	1SSV)
		echo "All files has single VV polarisation"
	;;
	1SSH)
		echo "All files has single HH polarisation"
	;;
	1SDH)
		echo "All files has dual HH+HV polarisation"
                while [ true ]; do
                echo "Select if you want to extract both polarisation channels or specify which one"
                read -r -p "Enter HH, HV or both: " respuesta
                respuesta=$(lowercase $respuesta)
                case $respuesta in
                hh)
                echo "Extracting only HH channel"
                POLI=SINGLE
		CHANNEL=hh
                break
                ;;
                hv)
                echo "Extracting only HV channel"
                POLI=SINGLE
		CHANNEL=hv
                ;;
                both)
                echo "Extracting both channels"
                POLI=DUAL
		break
                ;;
                *)
                echo "Posible options are HH, HV or both"
                ;;
                esac
                done
	;;
	1SDV)
		echo "All files has dual VV+VH polarisation"
		while [ true ]; do
                echo "Select if you want to extract both polarisation channels or specify which one"
                read -r -p "Enter VV, VH or both: " respuesta
                respuesta=$(lowercase $respuesta)
                case $respuesta in
                vv)
                echo "Extracting only VV channel"
                POLI=SINGLE
		CHANNEL=vv
                break
                ;;
                vh)
                echo "Extracting only VH channel"
                POLI=SINGLE
		CHANNEL=vh
                ;;
                both)
                echo "Extracting both channels"
                POLI=DUAL
		break
                ;;
                *)
                echo "Posible options are HH, HV or both"
                ;;
                esac
                done
	;;
	*)
	echo "Something went wrong"
	;;
	esac
else
	echo "Multiple polarisation types detected"
	case $POL_TYPES_NUM in
	2)
	echo "Two different polarisations detected: $POL_TYPES"
	case $POL_TYPES in
		"1SDH 1SSH")
		echo "##############################################################"
		echo "#                       WARNING                              #"
		echo "##############################################################"
		echo "             Found files with HH and HH+HV."
		echo "      Only common polarisation will be extracted (HH)"
		echo "##############################################################"
		POLI=SINGLE
		CHANNEL=hh
		;;
		"1SDV 1SSV")
		echo "##############################################################"
		echo "#                       WARNING                              #"
		echo "##############################################################"
		echo "           Found files with VV and VV+VH."
		echo "      Only common polarisation will be extracted (VV)"
		echo "##############################################################"
		POLI=SINGLE
		CHANNEL=vv
		;;
		*)
		echo "Two different polarisations detected: $POL_TYPES with no common channel"
		echo "##############################################################"
		echo "#                       WARNING                              #"
		echo "##############################################################"
		echo "             MULTIPLE POLARISATION MODES DETECTED"
		echo "       ALL WILL BE EXTRACTED, THIS CAN CAUSE PROBLEMS"
		echo "                  IN INSAR PROCESSINGS"
		echo "          CHECK FILES AND REPORT WHEN FINISH"
		echo "##############################################################"
		;;
	esac	
	;;	
	3)
	echo "Four different polarisations detected: $POL_TYPES"
	echo "##############################################################"
	echo "#                       WARNING                              #"
	echo "##############################################################"
	echo "             MULTIPLE POLARISATION MODES DETECTED"
	echo "       ALL WILL BE EXTRACTED, THIS CAN CAUSE PROBLEMS"
	echo "                  IN INSAR PROCESSINGS"
	echo "          CHECK FILES AND REPORT WHEN FINISH"
	;;
	4)
	echo "Four different polarisations detected: $POL_TYPES"
	echo "##############################################################"
	echo "#                       WARNING                              #"
	echo "##############################################################"
	echo "             MULTIPLE POLARISATION MODES DETECTED"
	echo "       ALL WILL BE EXTRACTED, THIS CAN CAUSE PROBLEMS"
	echo "                  IN INSAR PROCESSINGS"
	echo "          CHECK FILES AND REPORT WHEN FINISH"
	esac
fi

read -n1 -r -p "Press any key to continue..." key

#############################
# Start to processing images#
#############################


for i in $(cat "files"); do
DATE=$(echo $i | awk -F',' '{print $8}')
DATE_TIME=$(echo $i | awk -F',' '{print $7}')
N_IMAGES=$(grep $DATE $REPORT | wc -l)

if [[ $(containsElement $DATE ${MSLICES[@]}; echo $?) == 1 ]];then                # Check if it is a multiple slice image if it is a multiple slice file, skip it
echo "Satellite image: $(basename $(echo $i | awk -F',' '{print $1}'))"

POL=$(echo $i | awk -F',' '{print $6}' | cut -c3-4)
if [ $POL == "SV" ] || [ $POL == "SH" ] || [ $POLI == "SINGLE" ]; then
            CPTDIR=$DIR/$DATE.sen1
elif [ $POLI == "DUAL" ]; then
            CPTDIR=$DIR/$DATE.sen1.dp
elif [ $POL = "DV" ] || [ $POL == "DH" ]; then
	    CPTDIR=$DIR/$DATE.sen1.dp
fi

########################
# SINGLE IMAGE FOUND   #
########################
if [ $N_IMAGES == 1 ]; then
    FILE=$(echo $i | awk -F',' '{print $1}')
	echo "Processing image $(echo $totalsi+1 | bc) of $NIMAGES"
    echo "One image found for $DATE"
    echo "Ouput folder: $CPTDIR"
    # check if directory exists
    if [ ! -d $CPTDIR ]; then
    	mkdir $CPTDIR
    	if [ $POL == "SV" ] || [ $POL == "SH" ] || [ $POLI = "DUAL" ]; then
    		sentinel_unzip $FILE $CPTDIR
    	elif [ $POLI == "SINGLE" ]; then
    		sentinel_unzip_pol $FILE $CPTDIR $CHANNEL
    	fi
    	totalsi=$((totalsi+1))
    else
	echo "Directory already exists, check that the image is already decompressed"
    fi
echo "-------------------------------------------------------------------------"

########################
#MULTIPLE IMAGES FOUND #
########################
else
    echo "Processing images $(echo $totalsi+1 | bc) to $(echo $totalsi+$N_IMAGES | bc) of the total $NIMAGES images"
    echo "$DATE appears to have more than one slices"
    MSLICES+=($DATE)
    counter=1
    if [ ! -d $CPTDIR ]; then
    	mkdir $CPTDIR
    	for i in $(grep $DATE $REPORT);do
        	FILE=$(echo $i | awk -F',' '{print $1}')
        	DATE_TIME=$(echo $i | awk -F',' '{print $7}')
        	echo "Processing $DATE_TIME slice #$counter"
        	echo "Output folder: $CPTDIR/slice$counter"
        	mkdir $CPTDIR/slice$counter
		if [ $POL == "SV" ] || [ $POL == "SH" ] || [ $POLI = "DUAL" ]; then
    			sentinel_unzip $FILE $CPTDIR/slice$counter
    		elif [ $POLI == "SINGLE" ]; then
    			sentinel_unzip_pol $FILE $CPTDIR/slice$counter $CHANNEL
    		fi   
        	counter=$((counter+1))
        	totalsi=$((totalsi+1))
    	done
    else
	echo "Directory already exists, check that the image is already decompressed"
    fi
    echo "-------------------------------------------------------------------------"

fi
fi
done

echo "A total of $totalsi SLC images has been processed"
if [ $totalsi == $(cat $REPORT | wc -l) ]; then
    echo "All images has been processed"
else
    echo "Some images has been not processed, please check"
fi

########################
#   Clean temp files   #
########################
#rm $REPORT