#!/bin/sh

# Shell script to stack the data from multiple EKOS sessions.
# It is intended to be used on data from a cooled camera,
# and uses a common set of darks and biases for all sessions.
#
# It assumes dithering and uses the drizzle algorithm.
#
# Required directory structure:
#
# [Working Directory]
#
#	\ Master		Master dark and bias frames, if they already exists, they take precedence over dark and bias frames.
#				If the masters are absent, they are created from the dark end bias frames.
#       	\ Dark		Dark calibration frames, used for all sessions
#       	\ Bias		Biases calibration frames, used for all sessions
#
#	\ Session[name]
#		\ Flat		Flat frames for this sessions
#		\ Light		Light frames for this session
#		\ Master	(optional) Master dark and bias frames for this session,
#				if found they take precendence over the global masters.
#
# Output:
#
#	\ Process		
#		\ Calibrated	Calibrated light frames created from all sessions
#		\ Session[name]	Per-session preprocessed files
#
#	result_xxx.fits		Stacked output

# ------------------------------------------------------------------
# CONFIGURATION

# Directory names
LIGHTDIR=Light
FLATDIR=Flat
DARKDIR=Dark
BIASDIR=Bias
MASTERDIR=Master
CALIBRATEDDIR=Calibrated
PROCESSDIR=Process

# Output file names
MASTERDARK=master_dark
MASTERBIAS=master_bias
MASTERFLAT=master_flat

# Framing style 
# --framing=[cog|max|min]
OPT_FRAMING=min

# ------------------------------------------------------------------
# COMMAND LINE OPTIONS

while [ ! -z "$1" ]; do

	case "$1" in
		-f | --framing)
			shift
			OPT_FRAMING=$1
			echo "Framing ${OPT_FRAMING}"
			shift
			;;
		*)
			echo "Invalid option $1"
			exit 1;
			;;
	esac
done

# ------------------------------------------------------------------
# SAFETY CHECK

if [ -d "${PROCESSDIR}" ]; then
	echo "${PROCESSDIR} directory already exists!"
	exit 1
fi

# ------------------------------------------------------------------
# CREATE MASTER DARK

masterdarkdir="${MASTERDIR}/${DARKDIR}"
masterdarkfile="${MASTERDIR}/${MASTERDARK}.fits"

echo "------------------------------------------------------------------"
if [ -r "${masterdarkfile}" ]; then
	echo "Using master dark ${masterdarkfile}"
else
	if [ ! -d "${masterdarkdir}" ]; then
		echo "Couldn't find ${masterdarkdir}";
		exit 1
	fi
	
	echo "Creating master dark ${masterdarkfile}"	
	#notify-send "${NOTIFICATIONTITLE}" "Creating master dark ${masterdarkfile}"
		
	siril-cli -d . -s - <<ENDSIRILDARK
requires 1.2.0

# Convert Dark Frames to .fit files
cd ${masterdarkdir}
convert dark -out=../../${PROCESSDIR}
cd ../../${PROCESSDIR}

# Stack Dark Frames to master_dark.fit
stack dark rej 3 3 -nonorm -out=../${MASTERDIR}/${MASTERDARK}
cd ..

close

ENDSIRILDARK

fi

# ------------------------------------------------------------------
# CREATE MASTER BIAS

masterbiasdir="${MASTERDIR}/${BIASDIR}"
masterbiasfile="${MASTERDIR}/${MASTERBIAS}.fits"

echo "------------------------------------------------------------------"
if [ -r "${masterbiasfile}" ]; then
	echo "Using master bias ${masterbiasfile}"
else
	if [ ! -d "${masterbiasdir}" ]; then
		echo "Couldn't find ${masterbiasdir}";
		exit 1
	fi
	
	echo "Creating master bias ${masterbiasfile}"
	#notify-send "${NOTIFICATIONTITLE}" "Creating master bias ${masterbiasfile}"
	
	siril-cli -d . -s - <<ENDSIRILBIAS
requires 1.2.0

# Convert Bias Frames to .fit files
cd ${masterbiasdir}
convert bias -out=../../${PROCESSDIR}
cd ../../${PROCESSDIR}

# Stack Bias Frames to master_bias.fit
stack bias rej 3 3 -nonorm -out=../${MASTERDIR}/${MASTERBIAS}
cd ..

close

ENDSIRILBIAS

fi

# ------------------------------------------------------------------
# CREATE OUTPUT DIRECTORY

mkdir -p "${PROCESSDIR}/${CALIBRATEDDIR}"

# ------------------------------------------------------------------
# CREATE SESSION FLAT
# CALIBRATE SESSIONS LIGHTS

# Create calibrated light frames for each session
for session in `find -maxdepth 1 -type d -iname "session*"`; do

	sessionname=`basename "${session}"`
	
	echo "------------------------------------------------------------------"
	echo "Preprocessing session ${sessionname}"
	#notify-send "${NOTIFICATIONTITLE}" "Preprocessing session ${sessionname}"

	sessionlightdir="${sessionname}/${LIGHTDIR}"
	sessionflatdir="${sessionname}/${LIGHTDIR}"
	
	if [ ! -d "${sessionlightdir}" ]; then
		echo "Couldn't find ${sessionlightdir}"
		exit 1;
	fi
		
	if [ ! -d "${sessionflatdir}" ]; then
		echo "Couldn't find ${sessionflatdir}"
		exit 1;
	fi
	
	cd "${sessionname}"
	
	SESSIONDARK="${MASTERDIR}/${MASTERDARK}"
	if [ -r "${SESSIONDARK}.fits" ]; then
		SESSIONDARK="../../${sessionname}/${SESSIONDARK}"
		echo "Using session master dark for ${sessionname}"
		
	else
		SESSIONDARK="../../${MASTERDIR}/${MASTERDARK}"
	fi
	
	SESSIONBIAS="${MASTERDIR}/${MASTERBIAS}"
	if [ -r "${SESSIONBIAS}.fits" ]; then
		SESSIONBIAS="../../${sessionname}/${SESSIONBIAS}"
		echo "Using session master bias for ${sessionname}"
	else
		SESSIONBIAS="../../${MASTERDIR}/${MASTERBIAS}"
	fi
	
	SESSIONFLAT="${MASTERDIR}/${MASTERFLAT}"
	if [ -r "${SESSIONFLAT}.fits" ]; then
		SESSIONFLAT="../../${sessionname}/${SESSIONFLAT}"
		echo "Using session master flat for ${sessionname}"
	else		
		echo "------------------------------------------------------------------"
		echo "Creating master flat for session ${sessionname}"
		
		siril-cli -d . -s - <<ENDSIRILFLAT

requires 1.2.0

# Convert Flat Frames to .fit files
cd ${FLATDIR}
convert flat -out=../../${PROCESSDIR}/${sessionname}
cd ../../${PROCESSDIR}/${sessionname}

# Pre-process Flat Frames
calibrate flat -bias=${SESSIONBIAS}

# Stack Flat Frames to session_flat.fits
stack pp_flat rej 3 3 -norm=mul -out=${MASTERFLAT}

cd ../../${sessionname}
close

ENDSIRILFLAT

		SESSIONFLAT="../../${sessionname}/${SESSIONFLAT}"

		if [ ! -d "${MASTERDIR}" ]; then
			mkdir "${MASTERDIR}"	
		fi

		cp -v "../${PROCESSDIR}/${sessionname}/${MASTERFLAT}.fits" "${MASTERDIR}"
	fi

	echo "------------------------------------------------------------------"
	echo "Calibrating lights for session ${sessionname}"

	siril-cli -d . -s - <<ENDSIRILLIGHT

requires 1.2.0

# Convert Light Frames to .fit files
cd ${LIGHTDIR}
convert light -out=../../${PROCESSDIR}/${sessionname}
cd ../../${PROCESSDIR}/${sessionname}

# Calibrate light frames
calibrate light -dark=${SESSIONDARK} -flat=${SESSIONFLAT} -cfa -cc=dark -equalize_cfa -prefix=${sessionname}_pp_

cd ../../${sessionname}
close

ENDSIRILLIGHT
	
	# move calibrated files
	
	echo "------------------------------------------------------------------"
	cd ..
	mv -v ${PROCESSDIR}/${sessionname}/${sessionname}_pp_*.fits ${PROCESSDIR}/${CALIBRATEDDIR}/
done

# ------------------------------------------------------------------
# REGISTER LIGHTS

echo "------------------------------------------------------------------"
echo "Registering calibrated lights"
#notify-send "${NOTIFICATIONTITLE}" "Registering calibrated lights"

siril-cli -d . -s - <<ENDSIRILREGISTER

requires 1.2.0

# Convert Light Frames to .fit files
cd ${PROCESSDIR}/${CALIBRATEDDIR}
convert preprocess -out=../
cd ../

# Register lights

# extra options: -2pass -nostarlist (find reference image)
register preprocess -drizzle -2pass -nostarlist
# extra options --framing=[cog|max|min]
seqapplyreg preprocess -drizzle -framing=${OPT_FRAMING}

cd ..
close

ENDSIRILREGISTER

# ------------------------------------------------------------------
# STACK LIGHTS

echo "------------------------------------------------------------------"
echo "Stacking calibrated lights"
#notify-send "${NOTIFICATIONTITLE}" "Stacking calibrated lights"

siril-cli -d . -s - <<ENDSIRILSTACK

requires 1.2.0

cd ${PROCESSDIR}

# Stack calibrated lights to result.fits
stack r_preprocess rej 3 3 -norm=addscale -output_norm -rgb_equal -out=result

# mirror the result
load result
mirrorx -bottomup
save ../result_drizzle_${OPT_FRAMING}_\$LIVETIME:%d\$s

cd ..
close

ENDSIRILSTACK

notify-send -a "Siril" "Stacking (Finished)"