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+#!/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)"
+