molet_driver.in

#!/bin/bash


myprocess () {
    msg=$1
    cmd_list=$2
    log_file=$3

    
    echo "COMMAND: $cmd_list" >> $log_file
    dum="=========================================="
    echo $dum$dum$dum$dum$dum >> $log_file

    printf "%-100s" "$msg"

    error_file=$(mktemp)
    out=$($cmd_list 2>$error_file)
    exit_code=$?
    err=$(< $error_file)
    rm $error_file
    
    if [ ! -z "$err" ]
    then
        printf "\n===> Failed with error: \n%s" "$err"
	printf "\n===> Use the following command on its own to debug:\n"
	printf "$cmd_list\n"
	exit
    fi

    if [ "$exit_code" -ne "0" ]
    then
	printf "\n===> Failed with unspecified error\n===> Use the following command on its own to debug:\n"
	printf "$cmd_list\n"
    fi
           
    if [ ! -z "$out" ]
    then
       echo "$out" >> $log_file
    fi
       
    printf "%-10s\n" "...done"
}




infile=$1
infile=`realpath $infile`
injson=`grep -o '^[^//]*' $infile`
in_path=`dirname $infile`"/"
molet_home=@MOLET_HOME@"/"
map_path=`${molet_home}"bin/check_get_map_path"`



# Step -1:
# Convert input file from coolest standard if necessary and change execution paths
####################################################################################
if grep -q "COOLEST" $infile
then
    # Make run directories first (needed for the log.txt)
    @MKDIR_P@ ${in_path}MOLET_RUN/
    @MKDIR_P@ ${in_path}MOLET_RUN/input_files
    @MKDIR_P@ ${in_path}MOLET_RUN/output
    log_file=${in_path}MOLET_RUN/output/log.txt

    # Copy the input files
    cp ${in_path}*.dat ${in_path}*.txt ${in_path}psf.fits ${in_path}MOLET_RUN/input_files 2>/dev/null

    # Run the conversion
    msg="Check: conversion from coolest..."
    cmd=$molet_home"bin/check_coolest_conversion "$molet_home" "$in_path" "$infile
    myprocess "$msg" "$cmd" "$log_file"

    # Move newly created MOLET input file
    mv ${in_path}molet_input.json ${in_path}MOLET_RUN/molet_input.json
    mv ${in_path}*_molet_units.fits ${in_path}MOLET_RUN/input_files/

    # Change the input file name, the input path, and the json string for the rest of the script and codes
    in_path=${in_path}MOLET_RUN/
    infile=${in_path}/molet_input.json
    injson=`grep -o '^[^//]*' $infile`
else
    # A directory named 'input_files' must exist at the same path as the 'molet_input.json' file, even if it is empty!
    if [ ! -d ${in_path}"input_files" ]
    then
	@MKDIR_P@ ${in_path}"input_files"
    fi
    if [ ! -d ${in_path}"output" ]
    then
	@MKDIR_P@ ${in_path}"output"
    fi
    log_file=${in_path}"output/log.txt"
fi
out_path=$in_path



# Step 0:
# Perform initialization checks
####################################################################################
msg="Check: perform initialization checks..."
cmd=$molet_home"bin/check_initialization "$molet_home" "$in_path" "$infile
myprocess "$msg" "$cmd" "$log_file"


    
# Step 1:
# Get angular diameter distances
####################################################################################
msg="Getting angular diameter distances..."
cmd=$molet_home"bin/angular_diameter_distances "$infile" "$out_path
myprocess "$msg" "$cmd" "$log_file"



# Step 2:
# Get extended lensed images of the source
####################################################################################
msg="Getting extended source lensed features..."
cmd=$molet_home"bin/vkl_fproject "$infile" "$in_path" "$out_path
myprocess "$msg" "$cmd" "$log_file"



# Intermediate step:
# Get point source images, their locations are needed for the following
####################################################################################
check=`echo $injson | @AM_JQ@ '. | select(.point_source)'`
if [ ! -z "${check}" ]
then
    msg="Getting point-like source lensed images..."
    cmd=$molet_home"bin/vkl_point_source "$infile" "$in_path" "$out_path
    myprocess "$msg" "$cmd" "$log_file"
fi



# Step 3:
# Get light profile of the lens (and compact matter if required)
####################################################################################
msg="Getting light profile of the lens..."
cmd=$molet_home"bin/vkl_lens "$infile" "$in_path" "$out_path
myprocess "$msg" "$cmd" "$log_file"


    
# Intermediate step:
# Get variability
####################################################################################
check=`echo $injson | @AM_JQ@ '. | select(.point_source.variability)'`
if [ ! -z "${check}" ]
then
    # Intrinsic
    in_type=`echo $injson | @AM_JQ@ '.point_source.variability.intrinsic.type' | @SED@ -e 's/^"//' -e 's/"$//'`
    if [ $in_type != "custom" ]
    then
	if [ $in_type = drw ]
	then
	    msg="Generating Damped Random Walk intrinsic light curves..."
	    cmd=$molet_home"bin/var_drw "$infile" "$out_path
	    myprocess "$msg" "$cmd" "$log_file"
	elif [ $in_type = dum ]
	then
	    msg="DUM..."
	fi
    fi

    # Perform check of light curve lengths: needs intrinsic, unmicro (if needed), tobs, and the time delays.
    # If intrinsic and unmicro light curves are generated from Molet, then no need to check them, they will conform by construction
    msg="Check: compatibility of light curve lengths and observing time + time delay length..."
    cmd=$molet_home"bin/check_time_vector "$infile" "$in_path" "$out_path
    myprocess "$msg" "$cmd" "$log_file"
    
    # Extrinsic
    ex_type=`echo $injson | @AM_JQ@ '.point_source.variability.extrinsic.type' | @SED@ -e 's/^"//' -e 's/"$//'`
    if [ $ex_type != "custom" ]
    then
	msg="Matching macro-images to GERLUMPH maps..."
	cmd=$molet_home"bin/var_match_to_gerlumph "$molet_home"data/gerlumph.db "$out_path
	myprocess "$msg" "$cmd" "$log_file"

	msg="Check: if GERLUMPH maps exist locally..."
	cmd=$molet_home"checks/check_map_files.sh "$map_path" "$out_path
	myprocess "$msg" "$cmd" "$log_file"

	if [ $ex_type = moving_fixed_source ] || [ $ex_type = moving_fixed_source_custom ]
	then
	    msg="Getting 'moving_fixed_source' microlensing variability for each image..."
	    cmd=$molet_home"bin/var_moving_fixed_source "$infile" "$in_path" "$out_path
	    myprocess "$msg" "$cmd" "$log_file"
	elif [ $ex_type = moving_variable_source ]
	then
	    cmd=$molet_home"bin/check_confirm_convolutions_vs "$infile" "$out_path
	    eval "$cmd"
	    exit_code=$?
	    
	    if [ "$exit_code" -ne "0" ]
	    then
	    	echo "Quitting MOLET..."
	    	exit
	    else
		msg="Getting 'moving_variable_source' microlensing variability for each image..."
		cmd=$molet_home"bin/var_moving_variable_source "$infile" "$in_path" "$out_path
		myprocess "$msg" "$cmd" "$log_file"	    
	    fi	    

	elif [ $ex_type = expanding_source ]
	then
	    cmd=$molet_home"bin/check_confirm_convolutions "$infile" "$out_path
	    eval "$cmd"
	    exit_code=$?
	    
	    if [ "$exit_code" -ne "0" ]
	    then
		echo "Quitting MOLET..."
		exit
	    else
		msg="Getting 'expanding_source' microlensing variability for each image..."
		cmd=$molet_home"bin/var_expanding_source "$infile" "$out_path
		myprocess "$msg" "$cmd" "$log_file"
	    fi
	fi  
    fi    
fi


# Step 4:
# Combine different light components
####################################################################################
# Create output directories if necessary
check=`echo $injson | @AM_JQ@ '. | select(.point_source.variability)'`
if [ ! -z "${check}" ]
then
   msg="Mock output directories created..."
   cmd=$molet_home"combine_variability/setup_dirs.sh "$infile" "$in_path" "$out_path
   myprocess "$msg" "$cmd" "$log_file"

   # Combine variability
   msg="Combining variability..."
   cmd=$molet_home"bin/final_combine_variability "$infile" "$in_path" "$out_path
   myprocess "$msg" "$cmd" "$log_file"
fi


# Combine light
msg="Combining light components and including instrumental effects..."
cmd=$molet_home"bin/final_combine_light "$infile" "$in_path" "$out_path
myprocess "$msg" "$cmd" "$log_file"
    

printf "\nCompleted successfully!\n\n"
printf "Output in: %s\n" $out_path