Intarsis_01_file_preparation

#!/bin/bash

# FILES IN TOP FOLDER: SAFE_filelist pins.ll 
# MAKE SURE THAT YOUR $HOME/.cshrc contains the following aliases:
# alias wgetasf 'wget --http-user=username --http-password=pass'


DEM=$(grep dem_filename intarsis.config | awk '{print $2}')

if grep -q wgetasf $HOME/.cshrc ; then
	echo "Found wgetasf alias in your $HOME/.cshrc file, should be able to download ASF data" 
else
	echo "Not found wgetasf alias in your $HOME/.cshrc file, please read Intarsis documentation"
	exit
fi

#check for DEM in folder
if [ ! -f $DEM ]; then
	echo "DEM is missing, please set up intarsis.config and try again"
	exit
fi

#Check for pins.ll file
if [ ! -f pins.ll ]; then
	echo "pins.ll file is missing. Create in the program's folder and try again"
	exit
fi

# Check for SAFE_filelist
if [ ! -f SAFE_filelist ]; then
	echo "SAFE_filelist file is missing. Create a SAFE_filelist containing full path to all SLC folers and try again"
	exit
else
	sed -i 's/SAFE\//SAFE/g' SAFE_filelist 	# To remove trail / from each line.
fi


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



mkdir data topo
cp $DEM topo/dem.grd

cp pins.ll data/
cp SAFE_filelist data/

if [ -f orbits.list ]; then
	ln -s orbits.list data/orbits.list
fi

cd data
organize_files_tops_linux.csh SAFE_filelist pins.ll 1
organize_files_tops_linux.csh SAFE_filelist pins.ll 2

# Update log & create control files
touch .intarsis_folder		
touch .intarsis_step01
echo "$(date "+%d/%m/%y %H:%M") - Finished directory preparation" > intarsis.log