Intarsis_05_unwrap

#!/bin/bash

# This program unwrap the phase using snaphu.csh or snaphu_interp.csh
# It uses parallel to spawn the unwrapping across several threads.
# A script called unwrap_intf.csh is needed in order to run this program.

# TODO: include generation of unwrap_intf.csh, allow enable or disable interpolation

# Intarsis root folder check
if [ ! -f ".intarsis_folder" ]; then
        echo "You must run Intarsis_05_unwrap inside a Intarsis root folder"
        echo "Run Intarsis_01_file_preparation and other routines first"
        exit
fi

# Getting parameters from intarsis.config
if [ -f "intarsis.config" ]; then
MERGE=$(grep merge_swaths intarsis.config | awk '{print $2}')
if $MERGE; then IW=merged; else IW=$(grep swath_number intarsis.config | awk '{print $2}' | tr '[:lower:]' '[:upper:]'); fi
COHERENCE=$(grep unwrap_coherence intarsis.config | awk '{print $2}')
INTERPOLATION=$(grep unwrap_interpolation intarsis.config | awk '{print $2}')
PARALLEL=$(grep use_parallel intarsis.config | awk '{print $2}')
NUM_THREADS=$(grep num_cores 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 [[ $1 == "merged" ]] || [[ $1 == "MERGED" ]]; then
	IW=merged
	IW_config=false
elif [[ $IW == "merged" ]]; then
	IW=merged
	IW_config=true
elif [ -z $1 ]; then
	echo "Must specify IW as parameters or configure it in intarsis.config"
	echo "Example: Intarsis_05_unwrap F1"
	exit
else
	echo "You must specify the IW as F1,F2 or F3"
	exit
fi

# Intarsis previous step check
if [ $IW == "merged" ]; then
	if [ ! -f ".intarsis_step04a" ]; then
        	echo "You must run Intarsis_04a_merge first"
        	exit
	fi
else 
	if [ ! -f ".intarsis_step03_$IW" ]; then
        	echo "You must run Intarsis_03_interferograms first"
        	exit
	fi
fi

# Report of the selected parameters
echo "###################################################################"
echo "Intarsis Unwrap parameters:"
if $IW_config; then
	echo "Swath to process: $IW (imported from intarsis.config)"
else
	echo "Swath to process: $IW (command line)"
fi
# Check if B_P and B_T are configured as valid numbers
if [ $(echo "$COHERENCE > 0" | bc -l) ] && [ $(echo "$COHERENCE < 1" | bc -l) ] 2>/dev/null; then
	echo "Coherence threshold for unwrap: $COHERENCE (imported from intarsis.config)"
else
	COHERENCE=0.15	
	echo "Coherence threshold for unwrap: $COHERENCE (default value)"
fi
if $INTERPOLATION; then
	echo "Selected interpolation for low coherence pixels"
else
	echo "No interpolation in unwrapping"
fi

if $PARALLEL; then
	echo "Paralellization is on"
	if [ -n "$NUM_THREADS" ] && [ "$NUM_THREADS" -eq "$NUM_THREADS" ] 2>/dev/null; then
		echo "Number of CPU threads: $NUM_THREADS (imported from intarsis.config)"
	else
		NUM_THREADS=6
		echo "Number of CPU threads: $NUM_THREADS (default value)"
	fi
else
	echo "Paralelization is off"
fi

# Test for unwrap_intf.csh for parallelization
which unwrap_intf.csh &> /dev/null
if [ "$?" -eq 0 ]; then
	echo "unwrap_intf.csh is found"
else
	echo "unwrap_intf.csh not found, exiting"
	exit
fi
echo "###################################################################"

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

if [ $IW == "merged" ]; then
	cd merged
else
	cd $IW/intf_all
fi
rm intflist
ls -d 2*/ > intflist
sed -i 's/\///g' intflist

unwrap_parallel.csh intflist $NUM_THREADS

rm log_*.txt # clean log files

if [ $IW == "merged" ]; then
	cd ..
else
	cd ../..
fi

# Update log & create control files
touch .intarsis_step05_$IW &> /dev/null # Intarsis step control file
echo "$(date "+%d/%m/%y %H:%M") - Finished unwrap $IW" >> intarsis.log