Intarsis_02_allign

#!/bin/bash

# Start the IW allignement
# You must input as arguments the IW as F1, F2 or F3 and the master date as YYYYMMDD
# Also, a master_image file containing the date of MM is possible to use.
# TODO: check if MM is present in the SLC.

# Intarsis root folder check
if [ ! -f ".intarsis_folder" ]; then
        echo "You must run Intarsis_02a_allign inside a Intarsis root folder"
        echo "Run Intarsis_01_file_preparation and other routines first"
        exit
fi
INTARSIS_FOLDER=$(pwd)

# Intarsis previous step check
if [ ! -f ".intarsis_step01" ]; then
        echo "You must run Intarsis_02_allign first"
        exit
fi

if [ -f "intarsis.config" ]; then
echo "intarsis.config found, importing variables"
IW=$(grep swath_number intarsis.config | awk '{print $2}'| tr '[:lower:]' '[:upper:]')
MM=$(grep master_slc intarsis.config | awk '{print $2}')
ESD=$(grep use_esd intarsis.config | awk '{print $2}')
ESD_MODE=$(grep esd_mode intarsis.config | awk '{print $2}')
fi

if [[ "$1" == "F1" ]] || [[ "$1" == "F2" ]] || [[ "$1" == "F3" ]]; then
	IW=$1
	IWN=$(echo $IW | cut -c 2)
	IW_config=false
elif [[ "$IW" == "F1" ]] || [[ "$IW" == "F2" ]] || [[ "$IW" == "F3" ]]; then
	IWN=$(echo $IW | cut -c 2)
	IW_config=true
elif [ -z $1 ]; then
	echo "Must specify IW and MM date as parameters or configure it in intarsis.config"
	echo "Example: Intarsis_02_allign F[1,2,3] YYYYMMDD"
	exit
else
	echo "You must specify the IW as F1,F2 or F3"
	exit
fi

if [[ ! -z $MM ]] && [[ $(echo "$MM > 20140000" | bc -l) == 1 ]] && [[ $(echo "$MM < 20250000" | bc -l) == 1 ]]; then
	#echo "master SLC selected via intarsis.config: $MM"
	MM_config=true
elif [ -z $2 ]; then
	echo "Must specify IW and MM date as parameters or configure it in intarsis.config"
	echo "Example: Intarsis_02_allign F[1,2,3] YYYYMMDD"
	exit
elif [[ $(echo "$2 > 20140000" | bc -l) == 1 ]] && [[ $(echo "$2 < 20250000" | bc -l) == 1 ]]; then
	#echo "Master Master set to $2"
	MM=$2
	MM_config=false
else
	echo "Error in Master Master date"
	exit
fi

if [ -z $ESD ]; then
	echo "Disabling ESD mode (default)"
	ESD=false
fi

echo "###################################################################"
echo "Intarsis corregistration settings:"
if $MM_config; then
	echo "Master master date: $MM (imported from intarsis.config)"
else
	echo "Master master date: $MM (command line)"
fi
if $IW_config; then
	echo "Swath to process: $IW (imported from intarsis.config)"
else
	echo "Swath to process: $IW (command line)"
fi

if $ESD; then
	echo "ESD for fine corregistration is enabled"
	if [ -z $ESD_MODE ]; then
		echo "ESD mode is not defined. Configure it in intarsis.config or disable ESD"
		exit
	else 
		if [ $ESD_MODE == "0" ]; then
			echo "ESD mode is set to: 0 (average)"
		elif [ $ESD_MODE == "1" ]; then
			echo "ESD mode is set to: 1 (median)"
		elif [ $ESD_MODE == "2" ]; then
			echo "ESD mode is set to: 2 (interpolation)"
		else
			echo "Invalid ESD mode, please use 0, 1 or 2"
			exit
		fi
	fi 
else
	echo "ESD is disabled"
fi
echo "###################################################################"

echo "$(date "+%d/%m/%y %H:%M") - Run Allign $IW" >> intarsis.log

# Creating Directories
# TODO: ask before remove existing IW folder
rm -r $IW &> /dev/null # Cleaning from previous processings
mkdir $IW $IW/raw $IW/topo
ln -s $(pwd)/topo/dem.grd $IW/topo/

cd $IW/raw

ln -s ../../data/F*/*.SAFE/*/*iw$IWN*vv*xml .
ln -s ../../data/F*/*.SAFE/*/*iw$IWN*vv*tiff .
ln -s ../../data/*EOF .
ln -s ../topo/dem.grd .
ln -s ../../data/orbits.list .

prep_data_linux.csh

# RUN FIRST STEP OF PREPROC_BATCH (generates baseline_table.dat)
if $ESD; then
preproc_batch_tops_esd.csh data.in dem.grd 1 $ESD_MODE
else
preproc_batch_tops.csh data.in dem.grd 1
fi

# Modify data.in to put the MM on the top
grep '\-vv\-'$MM'' data.in > data.in_temp
grep -v '\-vv\-'$MM'' data.in >> data.in_temp
mv data.in data.in.old
mv data.in_temp data.in

# RUN SECOND STEP OF PREPROC_BATCH
if $ESD; then
preproc_batch_tops_esd.csh data.in dem.grd 2 $ESD_MODE
else
preproc_batch_tops.csh data.in dem.grd 2
fi

# Generation of baseline_table.dat (due to bug present in trunk)

rm baseline_table.dat &> /dev/null

MM_PRM='S1_'$MM'_ALL_'$IW'.PRM'
for i in $(ls *ALL*PRM); do
baseline_table.csh $MM_PRM $i >> baseline_table.dat
done

cp baseline_table.dat ..

# Update log & create control files
cd $INTARSIS_FOLDER
touch .intarsis_step02_$IW &> /dev/null	# Creates a file to identify step02 done
echo "$(date "+%d/%m/%y %H:%M") - Finished Allign $IW" >> intarsis.log