Intarsis_04a_merge

#!/bin/bash
################################################
# Intarsis_04a_merge:                          #
# This program merges several swaths from the  #
# same track together. This is a optional step #
# Joaquin Escayo jescayo@ucm.es November 2019  #
################################################

if [ -f "intarsis.config" ]; then
MERGE=$(grep merge_swaths intarsis.config | awk '{print $2}')
SWATHS=$(grep swaths_to_merge intarsis.config | awk '{print $2}' | tr '[:lower:]' '[:upper:]')
MM=$(grep master_slc intarsis.config | awk '{print $2}')
fi

if ! $MERGE; then
	echo "Merge swaths is disabled in intarsis.config, exitting"
	exit
fi

if [[ ! -z $1 ]]; then
	SWATHS=($(echo $1 | sed 's/,/\ /g')) # Converting into an array the SWATHS variable
	SWATHS_config=false
else
	SWATHS=($(echo $SWATHS | sed 's/,/\ /g')) # Converting into an array the SWATHS variable
	SWATHS_config=true
fi

# Sorting the SWATHS array
IFS=$'\n' MERGE_SWATHS=($(sort <<<"${SWATHS[*]}"))
unset IFS

if [[ ${SWATHS[*]} == "F1 F2 F3" ]] || [[ ${SWATHS[*]} == "F1 F2" ]] || [[ ${SWATHS[*]} == "F2 F3" ]]; then
	VALID=true
else
	echo "Invalid Swaths detected or bad formating, only consecutive arrays are posible to merge"
	exit
fi

if [ ${#MERGE_SWATHS[@]} -lt 2 ]; then
	echo "There is not enough swaths to merge. Please check configuration"
	exit
fi

if [ -z $MM ]; then
	echo "Error on Master Master image, please check intarsis.config"
	exit
fi

# Intarsis root folder check
if [ ! -f ".intarsis_folder" ]; then
	echo "You must run Intarsis_04a_merge inside a Intarsis root folder"
	echo "Run Intarsis_01_file_preparation and other routines first"
	exit
fi

# Intarsis step 02 check
for i in $SWATHS; do
if [ ! -f ".intarsis_step03_$i" ]; then
	echo "Interferograms from swath $i are not present"        
	echo "You must run Intarsis_03_interferograms $i first"
        exit
fi
done

echo "###################################################################"
echo "Intarsis swath merging parameters:"
echo "Merging ${#MERGE_SWATHS[@]} swaths: ${MERGE_SWATHS[*]}"
if $SWATHS_config; then
echo "Imported from intarsis.config"
else
echo "Configured via command-line"
fi
echo "Master-Master SLC date: $MM (Imported from intarsis.config)"
echo "###################################################################"

echo "$(date "+%d/%m/%y %H:%M") - Starting Swath Merging ${MERGE_SWATHS[*]}" >> intarsis.log

##############################################
#  Data check (folder,swaths, intf, etc)     #
##############################################
# Check that the interograms are ready for all swaths
for i in ${MERGE_SWATHS[@]}; do
	if [ ! -d $i/intf_all ]; then
	echo "Missing interferogram folder for swath $i"
	exit
	else
	echo "Found interferogram folder for $i"
	fi
done

# Check there are the same interferograms in every swath
for i in $(ls -d ${MERGE_SWATHS[0]}/intf_all/2*); do
	INTF=${i##*/}
	for i in ${MERGE_SWATHS[@]}; do
		if [ ! -d "$i/intf_all/$INTF" ]; then
		echo "The interferograms are not the same across all the swaths. Please check $INTF"
		exit
		fi
	done
done

#############################################
# Creation of merge_list file               #
#############################################

if [ -d "merged" ]; then
	echo "Directory merged is present"
	read -p "Do you want to overwrite it? Yes/No" -n 1 -r
	echo    # (optional) move to a new line
	if [[ $REPLY =~ ^[Yy]$ ]]; then
	    	rm -rf merged &> /dev/null
		mkdir merged
	else
		echo "Check merged directory and try again"
		exit
	fi
else
	mkdir merged
fi

for i in $(ls -d ${MERGE_SWATHS[0]}/intf_all/2*); do
        INTF=${i##*/}
	MASTER=$(echo $INTF | cut -c1-7)
	SLAVE=$(echo $INTF | cut -c9- )
	MASTER_FILE=$(cat ${MERGE_SWATHS[0]}/baseline_table.dat | grep -F $MASTER"." | awk '{print $1}' | cut -c1-16)
	SLAVE_FILE=$(cat ${MERGE_SWATHS[0]}/baseline_table.dat | grep -F $SLAVE"." | awk '{print $1}' | cut -c1-16)
	counter=0
	unset line # clean line var
	for swath in ${MERGE_SWATHS[@]}; do
		line[$counter]=$(echo "../"$swath"/intf_all/"$INTF"/:"$MASTER_FILE"$swath".PRM":"$SLAVE_FILE$swath".PRM")
		counter=$((counter+1))
	done
	# Generating the list
	echo ${line[*]} | sed 's/\ ../,../g' >> merged/merge_tmp
done

# Copy baseline_line.dat of the first Swath to merge
cp ${MERGE_SWATHS[0]}/baseline_table.dat merged/ &> /dev/null

# Put first lines that contain the MM SLC
grep $MM merged/merge_tmp | sed -n '1!G;h;$p' > merged/merge_MM 	# Getting lines with the MM and reverse the list
grep -v $MM merged/merge_tmp > merged/merge_rest 			# getting lines without MM
cat merged/merge_MM > merged/merge_list
cat merged/merge_rest >> merged/merge_list
rm merged/merge_MM merged/merge_rest merged_tmp 			# cleanup of temporal files

# Copying batch_tops.config from first swath
cp ${MERGE_SWATHS[0]}/batch_tops.config merged/

# Linking dem to this
ln -s ../topo/dem.grd merged/

# Starting the merge procedure
cd merged
merge_batch.csh merge_list batch_tops.config

# Update log & create control files
cd ..
touch .intarsis_step04a &> /dev/null		# Intarsis step control file
echo "$(date "+%d/%m/%y %H:%M") - Finished Merge Swaths ${MERGE_SWATHS[*]}" >> intarsis.log